Title of Invention

A PY-RICH IMMUNOSTIMULATORY NUCLEIC ACID .

Abstract Immunostimulatory nucleic acids having a T nucleotide content greater than 60% and having a CpG dinucleotide or a TG motif and being free of CpG dinucleotides are provided. The invention also relates in part to compositions or nutritional supplements that include a sustained delivery device or other delivery device having an immunostimulatory nucleic acid of the invention. Compositions having an immunostimulatory nucleic acid of the invention that include an antigen, an anti-microbial agent, an anti-cancer therapy, or an asthma/allergy medicament are also provided.
Full Text A PY -RICH IMMUNOSTIMULATORY NUCLEIC ACID
BACKGROUND OF THE INVENTION
Bacterial DNA, but not vertebrate DNA, has direct immunostimulatory effects on
peripheral blood mononuclear cells (PBMC) in vitro (Krieg et al, 1995). Bacterial DNA has
immune stimulatory effects to activate B cells and natural killer cells, but vertebrate DNA
does not (Tokunaga, T., et al., 1988. Jpn. J. Cancer Res. 79:682-686; Tokunaga, T., et al.,
1984, JNCI 72:955-962; Messina, J.P., et al., 1991, J. Immunol. 147:1759-1764; and reviewed
in Krieg, 1998, In: Applied Oligonucleotide Technology, C.A. Stein and A.M. Krieg, (Eds.),
John Wiley and Sons, Inc., New York, NY, pp. 431-448). It is now understood that these
immune stimulatory effects of bacterial DNA are a result of the presence of unmethylated
CpG dinucleotides in particular base contexts (CpG motifs), which are common in bacterial
DNA, but methylated and underrepresented (CpG suppression, 1/50 to 1/60) in vertebrate
DNA (Krieg et al, 1995 Nature 374:546-549; Krieg, 1999 Biochim. Biophys. Acta 93321:1-
10). The immune stimulatory effects of bacterial DNA can be mimicked with synthetic
oligodeoxynucleotides (ODN) containing these CpG motifs. It appears likely that the rapid
immune activation in response to CpG DNA may have evolved as one component of the
innate immune defense mechanisms that recognize structural patterns specific to microbial
molecules.
CpG ODN have highly stimulatory effects on human and murine leukocytes, inducing
proliferation of almost all (>95%) B cells and increases immunoglobulin (Ig) secretion;
cytokine secretion; natural killer (NK) cell lytic activity and IFN-γ secretion; and activation of
dendritic cells (DCs) and other antigen presenting cells to express costimulatory molecules
and secrete cytokines, especially the Thl-like cytokines that are important in promoting the
development of Thl-like T cell responses. B cell activation by CpG DNA is T cell
independent and antigen non-specific. However, B cell activation by low concentrations of
CpG DNA has strong synergy with signals delivered through the B cell antigen receptor for
both B cell proliferation and Ig secretion (Krieg et al, 1995). This strong synergy between
the B cell signaling pathways triggered through the B cell antigen receptor and by CpG DNA
promotes antigen specific immune responses. In addition to its direct effects on B cells, CpG

DNA also directly activates monocytes, macrophages, and dendritic cells to secrete a variety
of cytokines, including high levels of IL-12 (Klinman et al, 1996; Halpem et al, 1996;
Cowdery et al, 1996). These cytokines stimulate natural killer (NK) cells to secrete g-
interferon (IFN-y) and have increased lytic activity (Klinman et al, 1996, supra; Cowdery et
al, 1996, supra; Yamamoto et al, 1992; Ballas et al, 1996). Overall, CpG DNA induces a
Thl like pattern of cytokine production dominated by IL-12 and IFN-y with little secretion of
Th2 cytokines (Klinman et al, 1996). The strong direct effects (T cell independent) of CpG
DNA on B cells, as well as the induction of cytokines which could have indirect effects on B-
cells via T-help pathways, suggests utility of CpG DNA in the form of ODN as a vaccine
adjuvant. (See PCT Patent Application Publication No.: WO98/40100.)
These immune stimulatory effects of native phosphodiester backbone CpG ODN are
highly CpG specific in that the effects are essentially abolished if the CpG motif is
methylated, changed to a GpC, or otherwise eliminated or altered (Krieg et al, 1995 Nature
374:546-549; Hartmann et al, 1999 Proc. Natl. Acad. Sci USA 96:9305-10). Phosphodiester
CpG ODN can be formulated in lipids, alum, or other types of vehicles with depot properties
or improved cell uptake in order to enhance the immune stimulatory effects (Yamamoto et al,
1994 Microbiol. Immunol. 38:831-836; Gramzinski et al, 1998 Mol. Med. 4:109-118).
In early studies, it was thought that the immune stimulatory CpG motif followed the
formula purine-purine-CpG-pyrimidine-pyrimidine (Krieg et al, 1995 Nature 374:546-549;
Pisetsky, 1996 J. Immunol. 156:421-423; Hacker et al., 1998 EMBO J. 17:6230-6240;
Lipford et al, 1998 Trends in Microbiol. 6:496-500). However, it is now clear that mouse
lymphocytes respond quite well to phosphodiester CpG motifs that do not follow this
"formula" (Yi et al., 1998 J. Immunol. 160:5898-5906) and the same is true of human B cells
and dendritic cells (Hartmann et al, 1999 Proc. Natl. Acad. Sci USA 96:9305-10; Liang, 1996
J. Clin. Invest. 98:1119-1129).
Several past investigators have looked at whether the nucleotide content of ODN may
have effects independently of the sequence of the ODN. Interestingly, antisense ODN have
been found to be generally enriched in the content of GG, CCC, CC, CAC, and CG
sequences, while having reduced frequency of TT or TCC nucleotide sequences compared to
what would be expected if base usage were random (Smetsers et al., 1996 Antisense Nucleic

Acid Drug Develop. 6:63-67). This raised the possibility that the over-represented sequences
may comprise preferred targeting elements for antisense oligonucleotides or visa versa. One
reason to avoid the use of thymidine-rich ODN for antisense experiments is that degradation
of the ODN by nucleases present in cells releases free thymidine which competes with 3H-
thymidine which is frequently used in experiments to assess cell proliferation (Matson et al.,
1992 Antisense Research and Development 2:325-330).
SUMMARY OF THE INVENTION
The present invention relates in part to pyrimidine rich (Py-rich) and in some
embodiments thymidine (T) rich imrnunostimulatory nucleic acids which do not require the
presence of a CpG motif. The present invention also relates in part to the discovery that
nucleic acids which contain a TG dinucleotide motif are also immunostimulatory. The
invention is based in part on the unexpected finding that nucleic acid sequences which do not
contain CpG motifs are immunostimulatory. It was discovered upon analysis of the immune
stimulation properties of many nucleic acid sequences that these sequences may be Py-rich
e.g., T-rich or that they may contain TG motifs. It was also discovered that these sequences
preferentially activate non-rodent immune cells. The Py-rich and TG sequences are only
minimally immunostimulatory with respect to rodent immune cells, compared to non-rodent
immune cells. Thus, it is possible according to the methods of the invention to induce an
immune response in a non-rodent subject by administering Py-rich or TG immunostimulatory
nucleic acids. The Py-rich and TG immunostimulatory nucleic acids of the invention may
optionally include CpG motifs. These findings have important implications for the clinical
development of immunostimulatory CpG containing and non-CpG containing nucleic acids.

In one aspect the invention is a pharmaceutical composition comprising an
effective amount for stimulating aft immune response of isolated Py-rich or TG
immunostimulatory nucleic acids, and a pharmaceutically acceptable carrier. In other
aspects the invention is a composition of matter, comprising an isolated Py-rich or TG
immunostimulatory nucleic acid. In other embodiments, the immunostimulatory nucleic
acid may be T-rich. In still other embodiments, the immunostimulatory nucleic acid may
be T-rich and also have at least one TG motif.
Preferably the Py-rich nucleic acid is a T-rich nucleic acid. In some
embodiments the T-rich immunostimulatory nucleic acid is a poly T nucleic acid
comprising 5' TTTT 3'. In yet other embodiments the poly T nucleic acid comprises 5'
X1 X2TTTTX3 X4 3' wherein X1, X2, X3 and X4 are nucleotides. In some embodiments
X1X2 is TT and/or X3X4 is TT. In other embodiments X1X2 is selected from the group
consisting of TA, TG, TC, AT, AA, AG, AC, CT, CC, CA, CG, GT, GG, GA, and GC;
and/or X3X4 is selected from the group consisting of TA, TG, TC, AT, AA, AG, AC,
CT, CC, CA, CG, GT, GG, GA, and GC.
The T-rich immunostimulatory nucleic acid may have only a single poly T motif
or it may have a plurality of poly T nucleic acid motifs. In some embodiments the T-rich
immunostimulatory nucleic acid comprises at least 2, at least 3, at least 4, at least 5, at
least 6, at least 7, or at least 8 T motifs. In other embodiments it comprises at least 2, at
least 3, at least 4, at least 5, at least 6, at least 7, or at least 8 CpG motifs. In preferred
embodiments the plurality of CpG motifs and poly T motifs are interspersed.
In yet other embodiments at least one of the plurality of poly T motifs comprises
at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, or at least 9 contiguous T
nucleotide residues. In other embodiments the plurality of poly T motifs is at least 3
motifs and wherein at least 3 motifs each comprises at least 3 contiguous T nucleotide
residues or the plurality of poly T motifs is at least 4 motifs and wherein the at least 4
motifs each comprises at least 3 contiguous T nucleotide residues.
In some cases the T-rich immunostimulatory nucleic acid may be free of poly T
motifs but may rather comprise a nucleotide composition of greater than 25% T. In other
embodiments the T-rich immunostimulatory nucleic acids have poly T motifs and also
comprise a nucleotide composition of greater than 25% T. In preferred embodiments the
T-rich immunostimulatory nucleic acid comprises a nucleotide composition of greater

than 35% T, greater than 40% T, greater than 50% T, greater than 60% T, greater than
80% T, or greater than 90% T nucleotide residues. In important embodiments, the
nucleic acid is at least 50% T.
The T-rich and TG immunostimulatory nucleic acids can have any length greater
than 7 nucleotides, but in some embodiments can be between 8 and 100 nucleotide
residues in length. In preferred embodiments the T-rich immunostimulatory nucleic acid
comprises at least 20 nucleotides, at least 24 nucleotides, at least 27, nucleotides, or at
least 30 nucleotides. In preferred embodiments, the TG immunostimulatory nucleic acid
is between 15 and 25 nucleotides in length. The T-rich and TG immunostimulatory
nucleic acids may be single stranded or double stranded.
In one preferred embodiment, the immunostimulatory nucleic acid has a T-rich
region located in the middle of its length (i.e., an approximately equal number of
nucleotides flank the T-rich region on the 5' and 3' ends).
The T rich nucleic acid in some embodiments is selected from the group
consisting of SEQ ID NO: 59-63, 73-75, 142, 215, 226, 241,267-269, 282, 301, 304,
330, 342, 358, 370-372, 393, 433,471,479, 486, 491,497, 503, 556-558, 567, 694, 793-
794, 797, 833, 852, 861, 867, 868, 882, 886, 905, 907, 908, and 910-913. In other
embodiments the T rich nucleic acids are sequence selected from the group consisting of
SEQ ID NO: 64, 98,112, 146, 185, 204, 208, 214, 224, 233,244, 246,247, 258, 262,
263, 265, 270-273, 300, 305, 316, 317, 343, 344, 350, 352,354, 374, 376, 392, 407, 411-
413,429-432, 434,435, 443, 474, 475,498-501, 518, 687, 692, 693, 804, 862, 883, 884,
888, 890, and 891.
In other embodiments the Py-rich immunostimulatory nucleic acid is a C-rich
nucleic acid. An immunostimulatory C-rich nucleic acid is a nucleic acid including at
least one and preferably at least 2 poly-C regions or which includes 50% or greater C
nucleotides.-
The Py-rich and TG immunostimulatory nucleic acids may include one or more
CpG motifs. The motifs may be methylated or unmethylated. In other embodiments the
Py-rich and TG immunostimulatory nucleic acids are free of one or more CpG
dinucleotides.
In other embodiments the Py-rich and TG immunostimulatory nucleic acids also
include poly-A, poly G, and/or poly C motifs. In yet other embodiments the Py-rich or

TG immunostimulatory nucleic acid is free of two poly C sequences of at least 3
contiguous C nucleotide residues or is free of two poly A sequences of at least 3
contiguous A nucleotide residues. In other embodiments the Py-rich or TG
immunostimulatory nucleic acid comprises a nucleotide composition of greater than 25%
C or greater than 25% A. In yet other embodiments the Py-rich or TG
immunostimulatory nucleic acid is free of poly-C sequences, poly-G sequences or poly-
A sequences.
A poly G nucleic acid in some embodiments is selected from the group consisting
of SEQ ID NO: 5, 6, 73,215,267-269,276, 282, 288, 297-299, 355, 359, 386, 387, 444,
476, 531, 557-559, 733, 768, 795, 796, 914-925, 928-931, 933-936, and 938. In other
embodiments the poly G nucleic acid includes a sequence selected from the group
consisting of SEQ ID NO: 67, 80-82,141,147,148,173,178,183,185,214,224,264,
265, 315, 329, 434, 435, 475, 519, 521-524, 526, 527, 535, 554, 565, 609, 628, 660, 661,
662, 725, 767, 825, 856, 857, 876, 892, 909, 926, 927, 932, and 937.
According to another aspect of the invention, the immunostimulatory nucleic
acids may be defined as those which possess a TG motif, herein referred to as TG
immunostimulatory nucleic acids. The TG nucleic acid in one embodiment contains at
least one TG dinucleotide having a sequence including at least the following formula:
5'N1X1TGX2N23'. In related embodiments, N1 is a nucleic acid sequence composed of a
number of nucleotides ranging from (11-N2) to (21-N2) and N2 is a nucleic acid sequence
composed of a number of nucleotides ranging from (11-N1) to (21-N1). In a preferred
embodiment, X2 is thymidine.
In other embodiments, the TG nucleic acid has at least the following formula: 5'
X1 X2TGX3 X4 3'. In yet another embodiment, the TG nucleic acid comprises the
following sequence: 5'N1X1X2TGX3X4N23'. In a related embodiment, N| is a nucleic
acid sequence composed of a number of nucleotides ranging from (9-N2) to (19-N2) and
N2 is a nucleic acid sequence composed of a number of nucleotides ranging from (9-N1)
to (19-N1). In one preferred embodiment, X3 is thymidine. X1X2 are nucleotides which
may be selected from the group consisting of GT, GG, GA, AA, AT, AG, CT, CA, CG,
TA and TT, and X3X4 are nucleotides which may be selected from the group consisting
of TT, CT, AT, AG, CG, TC, AC, CC, TA, AA, and CA. In some preferred
embodiments, X3 is a thymidine. In important embodiments, X3X4 are nucleotides

selected from the group consisting of TT, TC, TA and TG. In other embodiments X1X2
are GA or GT and X3X4 are TT. In yet other embodiments X1 or X2 or both are purines
and X3 or X4 or both are pyrimidines or X1X2 are GpA and X3 or X4 or both are
pyrimidines. In one embodiment X2 is a T and X3 is a pyrimidine.
In one embodiment the 5' X1 X2TGX3 X4 3' sequence of the TG nucleic acid or
the entire length or some fragment thereof of the TG nucleic acid is a non-palindromic
sequence, and in other embodiments it is a palindromic sequence.
In some preferred embodiments, the TG nucleic acid is also T-rich.
The Py-rich and TG immunostimulatory nucleic acids in some embodiments have
a nucleotide backbone which includes at least one backbone modification, such as a
phosphorothioate modification. The nucleotide backbone may be chimeric, or preferably
the nucleotide backbone is entirely modified. In one preferred embodiment, the
immunostimulatory nucleic acid has a poly T motif and a phosphorothioate backbone.
In another aspect the invention is a composition of an immunostimulatory
nucleic acid, in the form of a Py-rich or a TG nucleic acid, and an antigen, wherein the
nucleic acid is free of unmethylated CpG motifs.
Another composition of the invention is a Py-rich or TG immunostimulatory
nucleic acid and an anti-microbial agent, wherein the Py-rich or TG nucleic acid is free
of unmethylated CpG motifs. Preferably the anti-microbial agent is selected from the
group consisting of an anti-viral agent, an anti-parasitic agent, an anti-bacterial agent
and an anti-fungal agent.
A composition of a sustained release device including a Py-rich and/or TG
immunostimulatory nucleic acid, wherein the Py-rich and/or TG nucleic acid is free of
unmethylated CpG motifs, is provided according to another aspect of the invention.
The invention also includes nutritional supplements of a Py-rich or TG
immunostimulatory nucleic acid in a delivery device selected from the group consisting
of a capsule, a pill, and a sublingual tablet, wherein the Py-rich or TG nucleic acid is free
of unmethylated CpG motifs.
It should be understood that when it is useful to administer a Py-rich e.g., poly T,
T-rich, C-rich, or TG oligonucleotide and a CpG oligonucleotide, it may also be
desirable to co-administer a Py-rich or a TG oligonucleotide together with a physically
separate CpG, Py-rich or TG oligonucleotide. Alternatively, the CpG, Py-rich or TG

motif may be present on the same contiguous nucleic acid as the Py-rich or TG
oligonucleotide. In yet a further embodiment, all or some combination of Py-rich, TG
and CpG nucleic acids may be co-administered either on separate nucleic acids or in the
same nucleic acid molecule. By co-administer it is intended that the nucleic acids be
administered close enough in time to one another to achieve a combined benefit of both
oligonucleotides, preferably more than the benefit achieved by administering each of the
oligonucleotides alone at the same dose.
CpG oligonucleotides have, in general, the formula 5'X1X2CGX3X43', wherein
X1, X2, X3 and X4 are nucleotides and wherein at least the C of CpG is unmethylated.
Preferred CpG oligonucleotides are 8-100 nucleotides in length and have modified back
bones. Particular structures are detailed in the published PCT applications, U.S.
applications and references cited herein, the disclosures of which are incorporated herein
in their entirety. In one embodiment, the CpG oligonucleotide is free of poly T and TG
motifs and is not T-rich.
In other embodiments, the CpG oligonucleotide has a sequence selected from the
group consisting of SEQ ID NO: 1, 3, 4, 14-16, 18-24,28,29, 33-46,49, 50, 52-56, 58,
64-67, 69, 71, 72, 76-87, 90, 91, 93, 94, 96, 98, 102-124, 126-128, 131-133, 136-141,
146-150,152-153, 155-171, 173-178, 180-186,188-198,201,203-214,216-220,223,
224, 227-240,242-256, 258, 260-265,270-273,275, 277-281, 286-287, 292, 295-296,
300, 302, 305-307,309-312, 314-317, 320-327,329, 335, 337-341, 343-352, 354, 357,
361-365, 367-369, 373-376, 378-385, 388-392, 394, 395, 399, 401-404, 406-426,429-
433, 434-437, 439,441-443, 445, 447,448,450, 453-456,460-464, 466-469, 472-475,
477, 478, 480, 483-485, 488, 489, 492,493,495-502, 504-505, 507-509, 511, 513-529,
532-541, 543-555, 564-566, 568-576, 578, 580, 599, 601-605, 607-611, 613-615, 617,
619-622, 625-646, 648-650, 653-664, 666-697, 699-706, 708, 709, 711-716, 718-732,
736, 737, 739-744,746, 747, 749-761, 763, 766-767, 769,772-779, 781-783, 785-786,
7900792, 798-799, 804-808, 810, 815, 817, 818, 820-832, 835-846, 849-850, 855-859,
862, 865, 872, 874-877, 879-881, 883-885, 888-904, and 909-913.
In another embodiment, the Py-rich or TG oligonucleotide is free of a CpG
motifs. This embodiment of the invention also involves pharmaceutical compositions
and kits which contain both a CpG oligonucleotide (which can be free of poly T and TG
motifs and not be T-rich) and a Py-rich and/or TG oligonucleotide physically separate

from the CpG oligonucleotide. The pharmaceutical preparations are in effective amounts
and typically include pharmaceutically acceptable carriers, all as set forth in detail herein
with respect to Py-rich and TG oligonucleotides. The kits include at least one container
containing an oligonucleotide which is a Py-rich or TG oligonucleotide (or some
combination thereof). The same container, or in other embodiments, a second container,
may contain an oligonucleotide with a CpG motif, which may be tree of Py-rich and/or
TG motifs. The kit also contains instructions for administering the oligonucleotides to a
subject. The kits also may include a container containing a solvent or a diluent.
In summary, as if fully recited herein, a CpG oligonucleotide physically separate
from the Py-rich or TG oligonucleotide can be used together with the Py-rich or TG
oligonucleotides in the methods, compositions and products described above.
The invention relates in other aspects to immunostimulatory oligonucleotides
which have chimeric backbones and which do not require the presence of a CpG motif.
The invention is based in part on the discovery that nucleic acid sequences which did not
contain CpG motifs were immunostimulatory, and that those which have chimeric
backbones have unexpectedly enhanced immune stimulating properties. Thus the
invention in one aspect relates to a composition of an oligonucleotide having a formula:
5' Y1N1ZN2Y2 3', wherein Y1 and Y2 are, independent of one another, nucleic acid
molecules having between 1 and 10 nucleotides, wherein Y1 includes at least one
modified internucleotide linkage and Y2 includes at least one modified internucleotide
linkage and wherein N1 and N2 are nucleic acid molecules, each independent of one
another, having between 0 and 5 nucleotides, but wherein N1ZN2 has at least 6
nucleotides in total and wherein the nucleotides of N1ZN2 have a phosphodiester
backbone, and wherein Z is an immunostimulatory nucleic acid motif but does not
include a CG. In one embodiment Z is a nucleic acid sequence selected from the group
consisting of TTTT, TG, and a sequence wherein at least 50% of the bases of the
sequence are Ts.
In some embodiments Y1 and/or Y2 have between 3 and 8 nucleotides. In other
embodiments Y1 and/or Y2 are comprised of at least three Gs, at least four Gs, least
seven Gs, or all Gs. In other embodiments Y1 and/or Y2 are selected from the group
consisting of TCGTCG, TCGTCGT, and TCGTCGTT (SEQ ID NO: 1145). In yet other

embodiments Y1 and/or Y2 include at least one, two, three, four, or five poly-A, poly-T,
or poly-C sequences.
The center nucleotides (N1ZN2) of the formula Y1N1ZN2Y2 have phosphodiester
internucleotide linkages and Y1 and Y2 have at least one modified intemucleotide
linkage. In some embodiments Y1 and/or Y2 have at least two modified internucleotide
linkages. In other embodiments Y1 and/or Y2 have between two and five modified
internucleotide linkages. In yet other embodiments Y| has two modified internucleotide
linkages and Y2 has five modified internucleotide linkages or Y1 has five modified
internucleotide linkages and Y2 has two modified internucleotide linkages. The modified
internucleotide linkage, in some embodiments is a phosphorothioate modified linkage, a
phosphorodithioate modified linkage or a p-ethoxy modified linkage.
Portions of the formula Y1N1ZN2Y2 may optionally form a palindrome. Thus, in
some embodiments the nucleotides of N1ZN2 form a palindrome. In some embodiments
the palindrome is not a direct repeat. In yet other embodiments the nucleotides of N1ZN2
do not form a palindrome.
According to other embodiments N1ZN2 has a sequence of nucleotides selected
from the group consisting of GATTTTATCGTC (SEQ ID NO: 1098),
TCGATTTTTCGA (SEQ ID NO: 1099); TCATTTTTATGA (SEQ ID NO: 1100);
GTTTTTTACGAC (SEQ ID NO: 1101); TCAATTTTTTGA (SEQ ID NO: 1102);
ACGTTTTTACGT (SEQ ID NO: 1103); TCGTTTTTACGA (SEQ ID NO: 1104);
TCGATTTTTACGTCGA (SEQ ID NO: 1105); AATTTTTTAACGTT (SEQ ID NO:
1106); TCGTTTTTTAACGA (SEQ ID NO: 1107); ACGTTTTTTAACGT (SEQ ID
NO: 1108); GATTTTTATCGTC (SEQ ID NO: 1109); GACGATTTTTCGTC (SEQ ID
NO: 1110); GATTTTAGCTCGTC (SEQ ID NO: 1111); GATTTTTACGTC (SEQ ID
NO: 1112); ATTTTATCGT (SEQ ID NO: 1113); AACGATTTTTCGTT (SEQ ID NO:
1114); TCACTTTTGTGA (SEQ ID NO: 1115); TCGTATTTTA (SEQ ID NO: 1116);
ACTTTTGTACCGGT (SEQ ID NO: 1117); TCGATTTTTCGACGTCGA (SEQ ID
NO: 1118); ACGATTTTTCGT (SEQ ID NO: 1119); GATGATCGTC (SEQ ID NO:
1120); TCGATGTCGA (SEQ ID NO: 1121); TCATGTATGA (SEQ ID NO: 1122);
GTGTTACGAC (SEQ ID NO: 1123); TCAATGTTGA (SEQ ID NO: 1124);
ACGTGTACGT (SEQ ID NO: 1125); TCGTGTACGA (SEQ ID NO: 1126);
TCGATGTACGTCGA (SEQ ID NO: 1127); AATGTTAACGTT (SEQ ID NO: 1128);

TCGTGTTAACGA (SEQ ID NO: 1129); ACGTGTTAACGT (SEQ ID NO: 1130);
GATGTATCGTC (SEQ ID NO: 1131); GACGATGTCGTC (SEQ ID NO: 1132);
GATGAGCTCGTC (SEQ ID NO: 1133); GATGTACGTC (SEQ ID NO: 1134);
ATGATCGT (SEQ ID NO: 1135); AACGATGTCGTT (SEQ ID NO: 1136);
TCACTGGTGA (SEQ ID NO: 1137); TCGTATGA (SEQ ID NO: 1138);
ACTGGTACCGGT (SEQ ID NO: 1139); TCGATGTCGACGTCGA (SEQ ID NO:
1140); and ACGATGTCGT (SEQ ID NO: 1141).
The composition may optionally include a pharmaceutical carrier and/or be
formulated in a delivery device. In some embodiments the delivery device is selected
from the group consisting of cationic lipids, cell permeating proteins, and sustained
release devices. In one preferred embodiment the sustained release device is a
biodegradable polymer. In another embodiment the sustained release device is a
microparticle.
In another aspect the invention is a composition of an immunostimulatory
oligonucleotide having the formula Y1N1ZN2Y2, and an antigen.
Another composition of the invention is an immunostimulatory oligucleotide
having the formula Y1N1ZN2Y2, and an anti-microbial therapeutic agent. Halferably the
anti-microbial therapeutic agent is selected from the group consisting of an anti-viral
agent, an anti-parasitic agent, an anti-bacterial agent, or an anti-fungal agent.
A composition of a sustained release device including an immunostimulatory
oligonucleotide having the formula Y1N1ZN2Y2, is provided according to another aspect
of the invention.
The invention also includes nutritional supplements of an immunostimulatory
oligonucleotide having the formula Y1N1ZN2Y2, in a delivery device selected from the
group consisting of a capsule, a sublingual tablet, and a pill.
In another aspect the compositions described above also include an
immunostimulatory nucleic acid having an unmethylated CG dinucleotide, a TG
dinucleotide or a Py-rich sequence wherein the immunostimulatory nucleic acid having
an unmethylated CG dinucleotide, a TG dinucleotide or a Py-rich sequence has a
different sequence than the oligonucleotide comprising 5' Y1N1ZN2Y23'.
In some embodiments the immunostimulatory nucleic acid having an
unmethylated CG dinucleotide, a TG dinucleotide or a Py-rich sequence has a

completely phosphodiester backbone and in other embodiments the immunostimulatory
nucleic acid having an unmethylated CG dinucleotide, a TG dinucleotide or a Py-rich
sequence has a modified backbone, which optionally may have internucleotide linkages
selected from the group consisting of phosphorothioate, phosphorodithioate, and p- .
ethoxy.
In one embodiment immunostimulatory nucleic acid having an unmethylated CG
dinucleotide has a formula comprising: 5'X1X2CGX3X43' wherein X1, X2, X3 and X4
are nucleotides. In other embodiments the immunostimulatory nucleic acid sequence
includes at least the following formula: 5' TCNTX1X2CGX3X4 3' wherein N is a nucleic
acid sequence composed of from about 0-25 nucleotides, wherein at least one nucleotide
has a modified internucleotide linkage, and wherein the nucleic acid has less than or
equal to 100 nucleotides. According to some embodiments X1X2 are nucleotides
selected from the group consisting of: GT, GG, GA and AA and X3X4 are nucleotides
selected from the group consisting of: TT, CT or GT. In a preferred embodiment X1X2
are GA and X3X4 are TT.
In another embodiment the immunostimulatory nucleic acid sequence having an
unmethylated CG dinucleotide includes at least one of the following sequences:
ATCGACTCTCGAGCGTTCTC (SEQ ID No. 15); TCCATGTCGGTCCTGCTGAT
(SEQ ID No. 32); TCCATGTCGGTZCTGATGCT (SEQ ID No. 31);
ATCGACTCTCGAGCGTTZTC (SEQ ID No. 18); TCCATGTCGGTCCTGATGCT
(SEQ ID No. 28); GGGGGG (SEQ ID No. 12); TCCATGACGGTCCTGATGCT (SEQ
ID No. 35); TCCATGGCGGTCCTGATGCT (SEQ ID No. 34);
TCCATGACGTTCCTGATGCT (SEQ ID No. 7); TCCATGTCGTTCCTGATGCT
(SEQ ID No. 38); GGGGTCAGTCTTGACGGGG (SEQ ID No. 41);
TCCATGTCGCTCCTGATGCT (SEQ ID No. 37); TCCATGTCGATCCTGATGCT
(SEQ ID No. 36); TCCATGCCGGTCCTGATGCT (SEQ ID No. 33);
TCCATAACGTTCCTGATGCT (SEQ ID No. 3); TCCATGACGTTCCTGATGCT
(SEQ ID No. 7); TCCATGACGTCCCTGATGCT (SEQ ID No 39);
TCCATCACGTGCCTGATGCT (SEQ ID No. 48); TCCATGACGTTCCTGACGTT
(SEQ ID No. 10); ATGACGTTCCTGACGTT (SEQ ID No. 70);
TCTCCCAGCGCGCGCCAT (SEQ ID No. 72); TCCATGTCGTTCCTGTCGTT (SEQ
ID No. 73); TCCATAGCGTTCCTAGCGTT (SEQ ID No. 74);

TCCTGACGTTCCTGACGTT (SEQ ID No. 76); TCCTGTCGTTCCTGTCGTT (SEQ
ID No. 77); TCCTGTCGTTCCTTGTCGTT (SEQ ID No. 52);
TCCTTGTCGTTCCTGTCGTT (SEQ ID No 121); TCCTGTCGTTTTTTGTCGTT
(SEQ ID No. 208); TCGTCGCTGTTGTCGTTTCTT (SEQ ID No. 120);
TCCATGCGTTGCGTTGCGTT (SEQ ID No. 81); TCCACGACGTTTTCGACGTT
(SEQ ID No. 82); TCGTCGTTGTCGTTGTCGTT (SEQ ID No. 47);
TCGTCGTTTTGTCGTTTTGTCGTT (SEQ ID No. 46);
TCGTCGTTGTCGTTTTGTCGTT (SEQ ID No. 49);
GCGTGCGTTGTCGTTGTCGTT (SEQ ID No. 56); TGTCGTTTGTCGTTTGTCGTT
(SEQ ID No. 48); TGTCGTTGTCGTTGTCGTTGTCGTT (SEQ ID No. 84);
TGTCGTTGTCGTTGTCGTT (SEQ ID No. 50); TCGTCGTCGTCGTT (SEQ ID No.
51); and TGTCGTTGTCGTT (SEQ ID No. 85). In another embodiment the
immunostimulatory nucleic acid having a Py-rich or TG sequence is a nucleic acid as
described above.
In another aspect the invention relates to pharmaceutical compositions and kits
which contain both an oligonucleotide having the formula Y1N1ZN2Y2 and a CpG
oligonucleotide (which optionally may be free of poly T and TG motifs and not be Py-
rich), a Py-rich and/or TG oligonucleotide physically separate from the oligonucleotide
having the formula Y1N1ZN2Y2. The pharmaceutical preparations are in effective
amounts and typically include pharmaceutically acceptable carriers, all as set forth in
detail herein. The kits include at least one container containing an oligonucleotide
having the formula Y1N1ZN2Y2. The same container, or in other embodiments, a second
container, may contain an oligonucleotide with a CpG motif, which optionally may be
free of Py-rich and/or TG motifs and/or a Py-rich or TG oligonucleotide (or some
combination thereof). The kit also contains instructions for administering the
oligonucleotides to a subject. The kits also may include a container containing a solvent
or a diluent.
In summary, as if fully recited herein, an oligonucleotide having the formula
Y1N1ZN2Y2 which is physically separate from the CpG, Py-rich or TG oligonucleotide
can be used together with the CpG, Py-rich, TG oligonucleotides, in the methods,
compositions and products described herein.

In another aspect the invention relates to a pharmaceutical composition including
at least two oligonucleotides of the invention, wherein the at least two oligonucleotides
have different sequences from one another and a pharmaceutically acceptable-carrier.
A vaccine formulation is provided according to another aspect of the invention.
The vaccine includes any of the compositions of the invention in combination with an
antigen.
According to another aspect of the invention a method of stimulating an immune
response is provided. The method involves administering a Py-rich or a TG
immunostimulatory nucleic acid to a non-rodent subject in an amount effective to induce
an immune response in the non-rodent subject. Preferably the Py-rich or TG
immunostimulatory nucleic acid is administered orally, locally, in a sustained release
device, mucosally to a mucosal surface, systemically, parenterally, or intramuscularly.
When the Py-rich or TG immunostimulatory nucleic acid is administered to the mucosal
surface it may be delivered in an amount effective for inducing a mucosal immune
response or a systemic immune response. In preferred embodiments the mucosal surface
is selected from the group consisting of an oral, nasal, rectal, vaginal, and ocular surface.
In some embodiments the method includes exposing the subject to an antigen
wherein the immune response is an antigen-specific immune response. The antigen may
be encoded by a nucleic acid vector which can be delivered to the subject. In some
embodiments the antigen is selected from the group consisting of a tumor antigen, a viral
antigen, a bacterial antigen, a parasitic antigen and a peptide antigen.
Py-rich and TG immunostimulatory nucleic acids are capable of provoking a
broad spectrum of immune response. For instance these immunostimulatory nucleic
acids can be used to redirect a Th2 to a Thl immune response. Py-rich and TG nucleic
acids may also be used to activate an immune cell, such as a leukocyte, a dendritic cell,
and an NK cell. The activation can be performed in vivo, in vitro, or ex vivo, i.e., by
isolating an immune cell from the subject, contacting the immune cell with an effective
amount to activate the immune cell of the Py-rich or TG immunostimulatory nucleic acid
and re-administering the activated immune cell to the subject. In some embodiments the
dendritic cell expresses a cancer antigen. The dendritic cell can be exposed to the cancer
antigen ex vivo.

The immune response produced by Py-rich or TG nucleic acids may also result in
induction of cytokine production, e.g., production of IL-6, IL-12, IL-18 TNF, IFN-α and
IFN-γ.
In still another embodiment, the Py-rich and TG nucleic acids are useful for
treating cancer. The Py-rich and TG nucleic acids are also useful according to other
aspects of the invenion in preventing cancer (e.g., reducing a risk of developing cancer)
in a suject at risk of developing a cancer. The cancer may be selected from the group
consisting of biliary tract cancer, breast cancer, cervical cancer, choriocarcinoma, colon
cancer, endometrial cancer, gastric cancer, intraepithelial neoplasms, lymphomas, liver
cancer, lung cancer (e.g. small cell and non-small cell), melanoma, neuroblastomas, oral
cancer, ovarian cancer, pancreas cancer, prostate cancer, rectal cancer, sarcomas, thyroid
cancer, and renal cancer, as well as other carcinomas and sarcomas. In some important
embodiments, the cancer is selected from the group consisting of bone cancer, brain and
CNS cancer, connective tissue cancer, esophageal cancer, eye cancer, Hodgkin's
lymphoma, larynx cancer, oral cavity cancer, skin cancer, and testicular cancer.
Py-rich and TG nucleic acids may also be used for increasing the responsiveness
of a cancer cell to a cancer therapy (e.g., an anti-cancer therapy), optionally when the Py-
rich or TG immunostimulatory nucleic acid is administered in conjunction with an anti-
cancer therapy. The anti-cancer therapy may be a chemotherapy, a vaccine (e.g., an in
vitro primed dendritic cell vaccine or a cancer antigen vaccine) or an antibody based
therapy. This latter therapy may also involve administering an antibody specific for a
cell surface antigen of, for example, a cancer cell, wherein the immune response results
in antigen dependent cellular cytotoxicity (ADCC). In one embodiment, the antibody
may be selected from the group consisting Ributaxin, Herceptin, Quadramet, Panorex,
IDEC-Y2B8, BEC2, C225, Oncolym, SMART Ml95, ATRAGEN, Ovarex, Bexxar,
LDP-03, ior t6, MDX-210, MDX-11, MDX-22, OV103, 3622W94, anti-VEGF,
Zenapax, MDX-220, MDX-447, MELIMMUNE-2, MELIMMUNE-3, CEACIDE,
Pretarget, NovoMAb-G2, TNT, Gliomab-H, GNI-250, EMD-72000, LymphoCide, CMA
676, Monopharm-C, 4B5, ior egf.r3, ior c5, BABS, anti-FLK-2, MDX-260, ANA Ab,
SMART 1D10 Ab, SMART ABL 364 Ab and ImmuRAIT-CEA.
Thus, according to some aspects of the invention, a subject having cancer Or at
risk of having a cancer is administered an immunostimulatory nulceic acid and an anti-

cancer therapy. In some embodiments, the anti-cancer therapy is selected from the group
consisting of a chemotherapeutic agent, an immunotherapeutic agent and a cancer
vaccine. The chemotherapeutic agent may be selected from the group consisting of
methotrexate, vincristine, adriamycin, cisplatin, non-sugar containing
chforoethylnitrosoureas, 5-fiuorouracil, mitomycin C, bleomycin, doxorubicin,
dacarbazine, taxol, fragyline, Meglamine GLA, valrubicin, carmustaine and
poliferposan, MMI270, BAY 12-9566, RAS famesyl transferase inhibitor, famesyl
transferase inhibitor, MMP, MTA/LY231514, LY264618/Lometexol, Glamolec, CI-994,
TNP-470, Hycamtin/Topotecan, PKC412, VaIspodar/PSC833,
Novantrone/Mitroxantrone, Metaret/Suramin, Batimastat, E7070, BCH-4556, CS-682, 9-
AC, AG3340, AG3433, Incel/VX-710, VX-853, ZD0101, ISI641, ODN 698, TA
2516/Marmistat, BB2516/Marmistat, CD? 845, D2163, PD183805, DX8951f, Lemonal
DP 2202, FK 317, Picibanil/OK-432, AD 32/Valrubicin, Metastron/strontium derivative,
Temodal/Temozolomide, Evacet/liposomal doxorubicin, Yevrtaxan/Placlitaxel,
Taxol/Paclitaxel, Xeload/Capecitabine, Furtulon/Doxifluridine, Cyclopax/oral paclitaxel,
Oral Taxoid, SPU-077/Cisplatin, HMR 1275/Flavopiridol, CP-358 (774)/EGFR, CP-609
(754)/RAS oncogene inhibitor, BMS-182751/oral platinum, UFT(Tegafur/Uracil),
Ergamisol/Levamisole, Eniluracil/776C85/5FU enhancer, Campto/Levamisole,
Camptosar/Irinotecan, Tumodex/Ralitrexed, Leustatin/Cladribine, Paxex/Paclitaxel,
Doxil/liposomal doxorubicin, Caelyx/liposomal doxorubicin, Fludara/Fludarabine,
Pharmarubicin/Epirubicin, DepoCyt, ZD1839, LU 79553/Bis-Naphtalimide, LU
103793/Dolastain, Caetyx/liposomal doxorubicin, Gemzar/Gemcitabine, ZD
0473/Anorrned, YM 116, Iodine seeds, CDK4 and CDK2 inhibitors, PARP inhibitors,
D4809/Dexifosamide, Ifes/Mesnex/Ifosamide, Vumon/Teniposide,
Paraplatin/Carboplatin, Plantinol/cisplatin, Vepeside/Etoposide, ZD 9331,
Taxctere/Docetaxel, prodrug of guanine arabinoside, Taxane Analog, nitrosoureas,
alkylating agents such as melphelan and cyclophosphamide, Aminoglutethimide,
Asparaginase, Busulfan, Carboplatin, Chlorombucil, Cytarabine HCI, Dactinomycin,
Daunorubicin HCI, Estramustine phosphate sodium, Etoposide (VP16-213), Floxuridine,
Fluorouracil (5-FU), Flutamide, Hydroxyurea (hydroxycarbamide), Ifosfamide,
Interferon Alfa-2a, Alfa-2b, Leuprolide acetate (LHRH-releasing factor analogue),
Lomustine (CCNU), Mechlorethamine HCI (nitrogen mustard), Mercaptopurine, Mesna,

Mitotane (o.p'-DDD), Mitoxantrone HC1, Octreotide, Plicamycin, Procarbazine HC1,
Streptozocin, Tamoxifen citrate, Thioguanine, Thiotepa, Vinblastine sulfate, Amsaerine
(m-AMSA), Azacitidine, Erthropoietin, Hexamethylmelamine (HMM), Interleukin 2,
Mitoguazorie (methyl-GAG; methyl glyoxai bis-guanylhydrazone; MGBG), Pentostatin
(2'deoxycoformycin), Semustine (methyl-CCNU), Teniposide (VM-26) and Vindesine
sulfate, but it is not so limited.
The immunotherapeutic agent may be selected from the group consisting of
Ributaxin, Herceptin, Quadramet, Panorex, 1DEC-Y2B8, BEC2, C225, Oncolym,
SMART Ml 95, ATRAGEN, Ovarex, Bexxar, LDP-03, ior t6, MDX-210, MDX-11,
MDX-22, OV103, 3622W94, anti-VEGF, Zenapax, MDX-220, MDX-447,
MELIMMUNE-2, MELIMMUNE-1, CEACIDE, Pretarget, NovoMAb-G2, TNT,
Gliomab-H, GNI-250, EMD-72000, LymphoCide, CMA 676, Monopharm-C, 4B5, ior
egf.r3, ior c5, BABS, anti-FLK-2, MDX-260, ANA Ab, SMART 1D10 Ab, SMART
ABL 364 Ab and ImmuRAIT-CEA, but it is not so limited.
The cancer vaccine may be selected from the group consisting of EGF, Anti-
idiotypic cancer vaccines, Gp75 antigen, GMK melanoma vaccine, MGV ganglioside
conjugate vaccine, Her2/neu, Ovarex, M-Vax, O-Vax, L-Vax, STn-KHL theratope,
BLP25 (MUC-1), liposomal idiotypic vaccine, Melacine, peptide antigen vaccines,
toxin/antigen vaccines, MVA-based vaccine, PACIS, BCG vacine, TA-HPV, TA-CIN,
DISC-virus and ImmuCyst/TheraCys, but it is not so limited.
In still another embodiment of the methods directed to preventing or treating
cancer, the subject may be further adminsitered interferon-α.
The invention in other aspects relates to methods for preventing disease in a
subject. The method involves administering to the subject a Py-rich or a TG
immunostimulatory nucleic acid on a regular basis to promote immune system
responsiveness to prevent disease in the subject. Examples of diseases or conditions
sought to be prevented using the prophylactic methods of the invention include microbial
infections (e.g., sexually transmitted diseases) and anaphylactic shock from food
allergies.
In other aspects, the invention is a method for inducing an innate immune
response by administering to the subject a Py-rich or a TG immunostimulatory nucleic
acid in an amount effective for activating an innate immune response.

According to another aspect of the invention a method for treating or preventing a
viral or rerroviral infection is provided. The method involves administering to a subject
having or at risk of having a viral or retroviral infection, an effective amount for treating
or preventing the viral or retroviral infection of any of the compositions of the invention.
In some embodiments the virus is caused by a hepatitis virus, HIV, hepatitis B, hepatitis
C, herpes virus, or papillomavirus.
A method for treating or preventing a bacterial infection is provided according to
another aspect of the invention. The method involves administering to a subject having
or at risk of having a bacterial infection, an effective amount for treating or preventing
the bacterial infection of any of the compositions of the invention. In one embodiment
the bacterial infection is due to an intiacellular bacteria.
In another aspect the invention is a method for treating or preventing a parasite
infection by administering to a subject having or at risk of having a parasite infection, an
effective amount for treating or preventing the parasite infection of any of the
compositions of the invention. In one embodiment the parasite infection is due to an
intracellular parasite. In another embodiment the parasite infection is due to a non-
helminthic parasite.
In some embodiments the subject is a human and in other embodiments the
subject is a non-human vertebrate selected from the group consisting of a dog, cat, horse,
cow, pig, goat, fish, monkey, chicken, and sheep.
In yet another aspect, the invention is a method for treating or preventing asthma,
by administering to a subject having or at risk of having asthma, an effective amount for
treating or preventing the asthma of any of the compositions of the invention. In one
embodiment the asthma is allergic asthma.
In another aspect the invention relates to a method for treating or preventing
allergy. The method involves administering to a subject having or at risk of having
allergy, an effective amount for treating or preventing the allergy of any of the
compositions of the invention.
A method for treating or preventing an immune deficiency is provided according
to another aspect of the invention. The method involves administering to a subject
having or at risk of an immune deficiency, an effective amount for treating or preventing
the immune deficiency of any of the compositions of the invention.

In another aspect the invention relates to a method for inducing a TH1 immune
response by administering to a subject any of the compositions of the invention in an
effective amount to produce a TH1 immune response.
In one embodiment the methods of the invention involve administering an
oligonucleotide of formula 5' Y1N1ZN2Y2 3' and an irnmunostimulatory nucleic acid
having an unmethylated CG dinucleotide a TG dinucleotide or a T-rich sequence. In an
embodiment the oligonucleotide comprising 5' Y1N1ZN2Y2 3' is administered separately
from the immunostimulatory nucleic acid. In some embodiments the oligonucleotide
comprising 5' Y1N1ZN2Y2 3' and the immunostimulatory nucleic acid are administered
on an alternating weekly schedule and in other embodiments the oligonucleotide
comprising 5' Y1N1ZN2Y2 3' and the immunostimulatory nucleic acid are administered
on an alternating biweekly schedule.
The invention provides in another aspect a composition, comprising an
immunostimulatory nucleic acid and an anti-cancer therapy, formulated in a
pharmaceutically-acceptable carrier and in an effective amount to treat a cancer or to
reduce the risk of developing a cancer. In important embodiments, the
immunostimulatory nucleic acid is selected from the group consisting of a T-rich nucleic
acid, a TG nucleic acid and a C-rich nucleic acid.
The invention further provides a kit comprising a first container housing an
immunostimulatory nucleic acid and at least one other container (e.g., a second
container) housing a an anti-cancer therapy, and instructions for use. In one
embodiment, the kit further comprises interferon-α, which may be separately housed in
yet another container (e.g., a third container). In an important embodiment, the kit
comprises a sustained-release vehicle containing an immunostimulatory nucleic acid, and
at least one container housing an anti-cancer therapy, and instructions instructions for
timing of administration of the anti-cancer therapy. The immunostimulatory nucleic
acid may be selected from the group consisting of a Py-rich nucleic acid, a TG nucleic
acid and a CpG nucleic acid, wherein the CpG nucleic acid has a nulceotide sequence
comprising SEQ ID NO: 246.
The invention further provides a method for preventing or treating asthma or
allergy, comprising administering an immunostimulatory nucleic acid and an
asthma/allergy medicament in an effective amount to treat or prevent the asthma or

allergy. In important embodiments, the immunostimulatory nucleic acid is selected from
the group consisting of a T-rich nucleic acid, a TG nucleic acid and a C-rich nucleic acid.
In one embodiment the immunostimulatory nucleic acid is a T-rich nucleic acid
In a related embodiment, the T-rich nucleic acid has a nucleotide sequence selected from
the group consisting of SEQ ID NO: 59-63, 73-75,142,215,226,241,267-269,282,
301, 304, 330, 342, 358, 370-372, 393, 433, 471,479, 486, 491, 497, 503, 556-558, 567,
694, 793-794, 797, 833, 852, 861, 867, 868, 882, 886, 905, 907,908, and 910-913. In
other embodiments the T-rich nucleic acids are sequence selected from the group
consisting of SEQ ID NO: 64,98,112,146,185,204, 208,214,224, 233,244,246, 247,
258, 262, 263, 265, 270-273, 300, 305, 316, 317, 343, 344, 350, 352, 354, 374, 376, 392,
407,411-413,429-432, 434,435,443,474, 475, 498-501, 518, 687, 692, 693, 804, 862,
883, 884, 888, 890, and 891.
In yet a further related embodiment, the T-rich nucleic acid is not a TG nucleic
acid. In yet still another embodiment, the T-rich nucleic acid is not a CpG nucleic acid.
In one embodiment, the immunostimulatory nucleic acid is a TG nucleic acid. In
a further related embodiment, the TG nucleic acid is not a T-rich nucleic acid. In another
related embodiment, the TG nucleic acid is not a CpG nucleic acid.
In one embodiment, the immunostimulatory nucleic acid is a CpG nucleic acid,
wherein the CpG nucleic acid has a nucleotide sequence comprising SEQ ID NO: 246.
In another embodiment, the asthma/allergy medicament is a medicament selected
from the group consisting of PDE-4 inhibitor, Bronchodilator/beta-2 agonist, K+ channel
opener, VLA-4 antagonist, Neurokin antagonist, TXA2 synthesis inhibitor, Xanthanine,
Arachidonic acid antagonist, 5 lipoxygenase inhibitor, Thromboxin A2 receptor
antagonist, Thromboxane A2 antagonist, Inhibitor of 5-lipox activation protein, and
Protease inhibitor, but is not so limited. In some important embodiments, the
asthma/allergy medicament is a Bronchodilator/beta-2 agonist selected from the group
consisting of salmeterol, salbutamol, terbutaline, D2522/formoterol, fenoterol, and
orciprenaline.
In another embodiment, the asthma/allergy medicament is a medicament selected
from the group consisting of Anti-histamines and Prostaglandin inducers. In one
embodiment, the anti-histamine is selected from the group consisting of loratidine,
cetirizine, buclizine, ceterizine analogues, fexofenadine, terfenadine, desloratadine,

norastemizole, epinastine, ebastine, ebastine, astemizole, levocabastine, azelastine,
tranilast, terfenadine, mizolastine, betatastine, CS 560, and HSR 609. In another
embodiment, the Prostaglandin inducer is S-5751.
In yet another embodiment, the asthma/allergy medicament is selected from the
group consisting of Steroids and Immunomodulators. The immunomodulators may be
selected from the group consisting of anti-inflammatory agents, leukotriene antagonists,
1L4 muteins, Soluble IL-4 receptors, Immunosuppressants, anti-IL-4 antibodies, IL-4
antagonists, anti-IL-5 antibodies, soluble IL-13 receptor-Fc fusion proteins, anti-IL-9
antibodies, CCR3 antagonists, CCR5 antagonists, VLA-4 inhibitors, and Downregulators
of IgE, but are not so limited. In one embodiment, the downregulator of IgE is an anti-
IgE.
In another embodiment, the Steroid is selected from the group consisting of
beclomethasone, fluticasone, tramcinolone, budesonide, and budesonide. In still a
furhter embodiment, the Immunosuppressant is a Tolerizing peptide vaccine.
In one embodiment, the immunostimulatory nucleic acid is administered
concurrently with the asthma/allergy medicament. In another embodiment, the subject is
an immunocompromised subject
The immunostimulatory nucleic acids to be administered to a subject in the
methods disclosed herein relating to the prevention and treatment of asthma/allergy are
as described for other method aspects of the invention.
In another aspect, the invention provides a kit comprising a first container
housing an immunostimulatory nucleic acid, and at least another container (e.g., a second
container) housing an asthma/allergy medicament, and instructions for use. The
immunostimulatory nucleic acid useful in the kit is as described herein. In important
embodiments, the immunostimulatory nucleic acid is selected from the group consisting
of a T-rich nucleic acid, a TG nucleic acid and a C-rich nucleic acid. In another
important embodiment, the kit comprises a sustained-release vehicle containing an
immunostimulatory nucleic acid, and at least one container housing an asthma/allergy
medicament, and instructions for timing of administration of the asthma/allergy
medicament. The asthma/allergy medicament may be selected from the group of
asthma/allergy medicaments described in the foregoing methods directed towards the
prevention or treatment of asthma/allergy.

In yet another aspect, the invention provides a composition, comprising an
immunostimulatory nucleic acid and an asthma/allergy medicament, formulated in a
pharmaceutically-acceptable carrier and in an effective amount for preventing or treating
an immune response associated with exposure to a mediator of asthma or allergy. The
immunostimulatory nucleic acid may be selected from the group of immunostimulatory
nucleic acids described for the foregoing methods and compositions. In important
embodiments, the immunostimulatory nucleic acid is selected from the group consisting
of a T-rich nucleic acid, a TG nucleic acid and a C-rich nucleic acid. The asthma/allergy
medicament may be selected from the group consisting of asthma medicaments and
allergy medicaments as described in the foregoing methods and compositions.
In still a further aspect, the invention provides a composition comprising an
immunostimulatory nucleic acid selected from the group consisting of SEQ ID NO: 95-
136, SEQ ID NO: 138-152, SEQ ID NO: 154-222, SEQ ID NO: 224-245, SEQ ID NO:
247-261, SEQ ID NO: 263-299, SEQ ID NO: 301, SEQ ID NO: 303-4109, SEQ ID NO:
414-420, SEQ ID NO: 424, SEQ ID NO: 426-947, SEQ ID NO: 959-1022, SEQ ID NO:
1024-1093, and a pharmaceutically acceptable carrier. Preferably the
immunostimulatory nucleic acid is present in the composition in an effective amount. la
one embodiment, the immunostimulatory nucleic acid is present in an effective amount
to induce an immune response. In another embodiment, the immunostimulatory nucleic
acid is present in an effective amount to prevent or treat cancer. In yet a further
embodiment, the immunostimulatory nucleic acid is present in an effective amount to
prevent or treat asthma/allergy. The invention also provides kits comprising any of the
foregoing immunostimulatory nucleic acid compositions, and instructions for use.
In another aspect the invention includes a composition of an immunostimulatory
nucleic acid consisting essentially of: 5' M1TCGTCGTTM2 3' wherein at least one of the
Cs is unmethylated, wherein M1 is a nucleic acid having at least one nucleotide, wherein
M2 is a nucleic acid having between 0 and 50 nucleotides, and wherein the
immunostimulatory nucleic acid has less than 100 nucleotides.
In yet other aspects the invention relates to a pharmaceutical composition of an
immunostimulatory nucleic acid comprising: 5' TCGTCGTT 3' wherein at least one of
the Cs is unmethylated, wherein the immunostimulatory nucleic acid has less than 100
nucleotides and a phosphodiester backbone, and a sustained release device. In some

embodiments the sustained release device is a microparticle. In other embodiments the
composition includes an antigen.
Each of the limitations of the invention can encompass various embodiments of
the invention. It is, therefore, anticipated that each of the limitations of the invention
involving any one element or combinations of elements can be included in each aspect of
the invention.
BRIEF DESCRIPTION OF THE ACCOMPANYING DRAWINGS
Figure 1A is a histogram of the expression of CD 8 6 (Y-axis) by CD19+ cells
following exposure of these cells to the oligonucleotides shown on the X-axis at a
concentration of 0.15 g/ml.
Figure IB is a histogram of the expression of CD86 (Y-axis) by CD19+ cells
following exposure of these cells to the oligonucleotides shown on the X-axis at a
concentration of 0.30 g/ml.
Figure 2 is a graph comparing the abilities of ODN 2137, ODN 2177, ODN 2200
and ODN 2202 to stimulate B cell proliferation at concentrations ranging from 0.2 g/ml
to 20 g/ml.
Figure 3 is a graph comparing the abilities of ODN 2188, ODN 2189, ODN 2190
and ODN 2182 to stimulate B cell proliferation at concentrations ranging from 0.2 g/ml
to 20 g/ml.
Fig. 4 is a bar graph depicting dose-dependent B cell activation induced by non-
CpG ODN. PBMC of a blood donor were incubated with the indicated concentrations of
ODNs 2006 (SEQ ID NO.: 246), 2117 (SEQ ID NO.: 358), 2137 (SEQ ID NO.: 886),
5125 (SEQ ID NO.: 1058) and 5162 (SEQ ID NO.: 1094) and stained with mAb for
CD 19 (B cell marker) and CD86 (B cell activation marker, B7-2). Expression was
measured by flow cytometry.
Fig. 5 is a bar graph depicting stimulation of B cells by a diverse set of non-CpG
ODNs. PBMC of one representative donor were stimulated by 0.4g/ml, l.Oug/ml or
lO.0g/ml of the following ODNs: 2006 (SEQ ID NO.: 246), 2196 (SEQ ID NO.: 913),
2194 (SEQ ID NO.: 911), 5162 (SEQ ID NO.: 1094), 5163 (SEQ ID "NO.: 1095), 5168
(SEQ ID NO.: 1096) and 5169 (SEQ ID NO.: 1097) and expression of the activation
marker CD86 (B7-2) on CD19-positive B cells was measured by flow cytometry.

Fig 6 is a bar graph depicting B cell activation by non-CpG ODNs 1982 and
2041. PBMC were incubated with the indicated concentrations of ODN 2006 (SEQ ID
NO.: 246), 1982 (SEQ ID NO.: 225) and 2041 (SEQ ID NO.: 282) and B cell activation
(expression of the activation marker CD86) was measured by flow cytometry.
Fig. 7 is a bar graph depicting NK cells are activated by non-CpG ODNs. PBMC
were incubated with 6g/ml of the following ODNs: 2006 (SEQ ID NO.: 246), 2117
(SEQ ID NO.: 358), 2137 (SEQ ID NO.: 886), 2183 (SEQ ID NO.: 433), 2194 (SEQ ID
NO.: 911) and 5126 (SEQ ID NO.: 1058) and stained with mAb for CD3 (J cell
marker), CD56 (NK cell marker) and CD69 (early activation marker). Expression of
CD69 on CD56-positive NK cells was measured by flow cytometry.
Fig. 8 is a bar graph depicting NK-mediated cytotoxicity is enhanced by non-
CpG ODN. NK-mediated lysis of K-562 target cells was measured after over night
incubation of PBMC with 6g/ml of the ODN 2006 (SEQ ID NO.: 246), 2194 (SEQ ID
NO.: 911) and 5126 (SEQ ID NO.: 1058).
Fig. 9 is a bar graph depicting NKT cells can be activated by non-CpG ODN.
PBMC of one representative donor were incubated with 6g/ml ODN 2006 (SEQ ID
NO.: 246), 2117 (SEQ ID NO.: 358), 2137 (SEQ ID NO.: 886), 2183 (SEQ ID NO.:
433), 2194 (SEQ ID NO.: 911) and 5126 (SEQ ID NO.: 1058) for 24h and activation of
NKT cells was measured by flow cytometry after staining of cells with mAb for CD3 (T
cell marker), CD56 (NK cell marker) and CD69 (early activation marker).
Fig. 10 is a bar graph depicting stimulation of monocytes by different CpG and
non-CpGODN. PBMC were incubated with 6ug/ml 2006 (SEQ ID NO.: 246), 2117
(SEQ ID NO.: 358), 2137 (SEQ ID NO.: 886), 2178 (SEQ ID NO.: 428), 2183 (SEQ ID
NO.: 433), 2194 (SEQ ID NO.: 911), 5126 (SEQ ID NO.: 1058)and 5163 (SEQ ID NO.:
1095) and stained for CD14 (monocyte marker) and CD80 (B7-1, activation marker).
Expression was measured by flow cytometry.
Fig. 11 is a bar graph depicting release of TNFα upon culture of human cells with
non-CpG ODN. PBMC were cultured for 24h with or without 6g/ml of the indicated
ODNs or 1 ng/ml LPS as positive control and TNFct measured by ELISA.
Fig. 12 is a bar graph depicting release of IL-6 after culture with non-CpG ODNs
shows the same pattern, as for TNFα. PBMC were cultured with the indicated ODNs
(1.0g/ml) and IL-6 was measured in the supernatants by ELISA.

DETAILED DESCRIPTION
The invention in one aspect involves the finding that pyrimidine (Py) rich and
preferably thymidine (T) rich nucleic acids as well as nucleic acids that contain TG
dirtucleotide motifs are effective in mediating immune stimulatory effects. It was known
in the prior art that CpG containing nucleic acids are therapeutic and prophylactic
compositions that stimulate the immune system to treat cancer, infectious diseases,
allergy, asthma and other disorders and to help protect against opportunistic infections
following cancer chemotherapies. The strong yet balanced, cellular and humoral
immune responses that result from CpG stimulation reflect the body's own natural
defense system against invading pathogens and cancerous cells. CpG sequences, while
relatively rare in human DNA are commonly found in the DNA of infectious organisms
such as bacteria. The human immune system has apparently evolved to recognize CpG
sequences as an early warning sign of infection, and to initiate an immediate and
powerful immune response against invading pathogens without causing adverse reactions
frequently seen with other immune stimulatory agents. Thus CpG containing nucleic
acids, relying on this innate immune defense mechanism, can utilize a unique and natural
pathway for immune therapy. The effects of CpG nucleic acids on immune modulation
were discovered by the inventor of the instant patent application and have been described
extensively in co-pending patent applications, such as U.S. Patent Application Serial
Nos: 08/386,063 filed on 02/07/95 (and related PCT US95/0I570); 08/738,652 filed on
10/30/96; 08/960,774 filed on 10/30/97 (and related PCT/US97/19791, WO 98/18810);
09/191,170 filed on 11/13/98; 09/030,701 filed on 02/25/98 (and related
PCT/US98/03678; 09/082,649 filed on 05/20/98 (and related PCT/US98/10408);
09/325,193 filed on 06/03/99 (and related PCT/US98/04703); 09/286,098 filed on
04/02/99 (and related PCT/US99/07335); 09/306,281 filed on 05/06/99 (and related
PCT/US99/09863). The entire contents of each of these patents and patent applications
is hereby incorporated by reference.
The findings of the instant invention are applicable to all of the above described
uses of CpG containing nucleic acids as well as any other known use for CpG nucleic
acids. The invention involves, in one aspect, the discovery that Py-rich and preferably T-
rich and TG nucleic acids have similar immune stimulatory properties to CpG
oligonucleotides regardless of whether a CpG motif is present. Thus the invention is

useful for any method for stimulating the immune system using Py-rich or TG nucleic
acids. It was also discovered surprisingly according to the invention that chimeric
oligonucleotides which lack a CpG motif are immune stimulatory and have many of the
same prophylactic and therapeutic activities as a CpG oligonucleotide.
A Py-rich nucleic acid is a T-rich or C-rich immunostimulatory nucleic acid. In
some embodiments T-rich nucleic acids are preferred. A T-rich nucleic acid is a nucleic
acid, which includes at least one poly T sequence and/or which has a nucleotide
composition of greater than 25% T nucleotide residues. A nucleic acid having a poly-T
sequence includes at least four Ts in a row, such as 5'TTTT3\ Preferably the T-rich
nucleic acid includes more than one poly T sequence. In preferred embodiments the T-
rich nucleic acid may have 2, 3, 4, etc poly T sequences, such as oligonucleotide #2006
(SEQ ID NO:246). One of the most highly immunostimulatory T-rich oligonucleotides
discovered according to the invention is a nucleic acid composed entirely of T nucleotide
residues, e.g., oligonucleotide #2183 (SEQ ID NO.-433). Other T-rich nucleic acids
according to the invention have a nucleotide composition of greater than 25% T
nucleotide residues, but do not necessarily include a poly T sequence. In these T-rich
nucleic acids the T nucleotide resides may be separated from one another by other types
of nucleotide residues, i.e., G, C, and A. In some embodiments the T-rich nucleic acids
have a nucleotide composition of greater than 35%, 40%, 50%, 60%, 70%, 80%, 90%,
and 99%, T nucleotide residues and every integer % in between. Preferably the T-rich
nucleic acids have at least one poly T sequence and a nucleotide composition of greater
than 25% T nucleotide residues.
It was discovered according to the invention that the T content of an ODN has a
dramatic effect on the immune stimulatory effect of the ODN and that T-rich ODN can
activate multiple human immune cell types in the absence of any CpG motifs. An
oligonucleotide having a 3' poly-T region and 2 5'CGs e.g., ODN 2181 (SEQ ID
NO:431) is highly immune stimulatory. An oligonucleotide of similar length, ODN
2116 (SEQ ID NO:357) which contains two CG dinucleotides at the 5* end and a poly-C
region at the 3' end was also immune stimulatory but to a lesser extent than the T-rich
oligonucleotide using standard experimental conditions. Thus, although C and T have
almost identical structures, their effects on the immune properties of an ODN are varied.
They both are capable of inducing an immune response but to different extents. Thus

both T-rich and C-rich oligonucleotides are useful according to the invention, but T-rich
oligonucleotides are preferred. Furthermore, if the T content of the ODN is reduced by
incorporating other bases such as G, A, or C, then the immune stimulatory effects are
reduced (ODN #2188 (SEQ ID NO:905), 2190 (SEQ ID NO.907), 2191 (SEQ ID
NO:908), and 2193 (SEQ ID NO:910)).
A C-rich nucleic acid is a nucleic acid molecule having at least one or preferably
at least two poly-C regions or which is composed of at least 50% C nucleotides. A poly-
C region is at least four C residues in a row. Thus a poly-C region is encompassed by
the formula 5'CCCC 3'. In some embodiments it is preferred that the poly-C region
have the formula 5'CCCCCC 3'. Other C-rich nucleic acids according to the invention
have a nucleotide composition of greater than 50% C nucleotide residues, but do not
necessarily include a poly C sequence. In these C-rich nucleic acids the C nucleotide
residues may be separated from one another by other types of nucleotide residues, i.e., G,
T, and A. In some embodiments the C-rich nucleic acids have a nucleotide composition
of greater than 60%, 70%, 80%, 90%, and 99%, C nucleotide residues and every integer
% in between. Preferably the C-rich nucleic acids have at least one poly C sequence and
a nucleotide composition of greater than 50% C nucleotide residues, and in some
embodiments are also T-rich.
As shown in the Examples, several ODN previously believed to be non-
immunostimulatory, including two ODNs SEQ ID NO.: 225 and SEQ ID NO.: 282
previously described to be non-stimulatory and mainly used as control ODNs
(Takahashi, T et al 2000. J. Immunol 164:4458) were found to be immunostimulatory.
Our experiments, demonstrated that these ODNs can stimulate B cells, although at higher
concentrations compared to CpG ODNs (Fig. 6). A long Poly T ODN (30mer) induced,
at least in some experiments, comparable strong activation of B cells to one of the
strongest CpG ODN activators of B cells. These experiments also revealed the
surprising finding that even Poly C ODNs can lead to stimulation of B cells.
Immunostimulation by these ODNs, however, was not limited to human B cells.
Different experimental assays clearly demonstrated in addition that monocytes, NK cells
and even NKT cells can be activated by such non-CpG ODNs (Fig. 7-10). In contrast
to Poly T and Poly C sequences, immunostimulation by Poly A sequences (at least for
monocytes, B and NK cells) was not achieved. Interestingly it was found that the

introduction of a CpG motif into SEQ ID NO.: 225 enhanced the immunostimulatory
activity whereas the elongation with a Poly T stretch did not enhance
immunostimulation. This suggests that CpG and T-rich ODN may operate through
different mechanisms or pathways. It is also possible that insertion of a poly-T motif
into a different position of SEQ ID NO.: 225 may result in a change in
immunostimulatory properties.
A "TG nucleic acid" or a "TG immunostimulatory nucleic acid" as used herein is
a nucleic acid containing at least one TpG dinucleotide (thymidine-guanine dinucleotide
sequence, i.e. "TG DNA" or DNA containing a 5' thymidine followed by 3' guanosine
and linked by a phosphate bond) and activates a component of the immune system.
In one embodiment the invention provides a TG nucleic acid represented by at
least the formula:
wherein X1 and X2 are nucleotides and N is any nucleotide and N1 and N2 are
nucleic acid sequences composed of any number of N provided that the sum total of N1
and N2 is in the range of 11 to 21. As an example, if N1 is 5, then N2 may be 6 (leading
to a total length for the oligonucleotide of 15 nucleotides). The TG may be located
anywhere within the oligonucleotide stretch, including the 5' end, the center and the 3'
end. Thus, N1 may be zero through to 21, inclusive, provided that N2 is appropriately
chosen to give a sum of N2 and N1 equal to 11 through to 21, inclusive. Similarly, N2
may be zero through to 21, inclusive, provided that the sum total of N1 and N2 equals 11
to 21, inclusive. In some embodiments X1 is adenine, guanine, or thymidine and X2 is
cytosine, adenine, or thymidine. In one preferred embodiment, X2 is thymidine. In other
embodiments X1 is cytosine and/or X2 is guanine. In other embodiments, as discussed
herein, the nucleic acid may encompass other motifs, provided it is long enough to do so.
In other embodiments the TG nucleic acid is represented by at least the formula:
5'N1X1X2TGX3X4N23'
wherein X1, X2, X3, and X4 are nucleotides. In some embodiments, X1X2 are
nucleotides selected from the group consisting of: GpT, GpG, GpA, ApA, ApT, ApG,
CpT, CpA, TpA and TpT; and X3X4 are nucleotides selected from the group consisting
of: TpT, CpT, ApT, ApG, TpC, ApC, CpC, TpA, ApA, and CpA; N is any nucleotide
and N1 and N2 are nucleic acid sequences composed of any number of nucleotides

provide that the sum total of N, and N2 is in the range of 9 to 19. In some embodiments,
X1X2 are GpA or GpT and X3X4 are TpT. In other embodiments X1 or X2 or both are
purines and X3 or X4 or both are pyrimidines or X,X2 are GpA and X3 or X4 or both are
pyrimidines. In one preferred embodiment, X3X4 are nucleotides selected from the
group consisting of: TpT, TpC and TpA.
The immunostimulatory nucleic acid may be any size (i.e., length) provided it is
at least 4 nucleotides. In important embodiments, the immunostimulatory nucleic acids
have a length in the range of between 6 and 100. In still other embodiments, the length
is in the range of between 8 and 35 nucleotides. Preferably, the TG oligonucleotides
range in size from 15 to 25 nucleotides.
The size (i.e., the number of nucleotide residues along the length of the nucleic
acid) of the immunostimulatory nucleic acid may also contribute to the stimulatory
activity of the nucleic acid. It has been discovered, surprisingly that even for highly
immune stimulating immunostimulatory nucleic acids, the length of the nucleic acid
influences the extent of immunostimulation that can be achieved. It has been
demonstrated that increasing the length of a T-rich nucleic acid up to 24 nucleotides
causes increased immune stimulation. The experiments presented in the examples
demonstrate that when the length of the T-rich nucleic acid is increased from 18 to 27
nucleotides the ability of the nucleic acid to stimulate an immune response is increased
significantly (compare ODN #2194,2183,2195, and 2196 decreasing in size from 27-18
nucleotides). Increasing the length of the nucleic acid up to 30 nucleotides had a
dramatic impact on the biological properties of the nucleic acid but increasing the length
beyond 30 nucleotides did not appear to further influence the immune stimulatory effect
(e.g., compare ODN 2179 to 2006).
It has been shown that TG nucleic acids ranging in length from 15 to 25
nucleotides in length may exhibit an increased immune stimulation. Thus, in one aspect,
the invention provides an oligonucleotide that is 15-27 nucleotides in length (i.e., an
oligonucleotide that is 15,16,17, 18,19,20, 21,22, 23, 24, 25,26 or 27 nucleotides in
length) that may be a T-rich nucleic acid or may be a TG nucleic acid, or may be both a
T-rich and a TG nucleic acid. In one embodiment, the oligonucleotide is not a T-rich
nucleic acid nor is it a TG nucleic acid. In other embodiments, the oligonucleotide does
not have a CG motif. The invention similarly provides oligonucleotides that are 15-27

nucleotides in length, oligonucleotides that are 18-25 nucleotides in length,
oligonucleotides that are 20-23 nucleotides in length, and oligonucleotides that are 23-
25 nucleotides in length. Any of the foregoing embodiments relating to oligonucleotides
15-27 in length also relate to the oligonucleotides of these differing lengths. The
invention further embraces the use of any of these foregoing oligonucleotides in the
methods recited herein.
Although a maximal level of immune stimulation is achieved with some T-rich
nucleic acids when the nucleic acid is 24-30 nucleotide residues in length, as well as with
some TG nucleic acids that range from 15 to 25 nucleotides in length, shorter or longer
immunostimulatory nucleic acids can also be used according to the methods of the
invention. For facilitating uptake into cells immunostimulatory nucleic acids preferably
have a minimum length of 6 nucleotide residues. Nucleic acids of any size greater than 6
nucleotides (even many kb long) are capable of inducing an immune response according
to the invention if sufficient immunostimulatory motifs are present, since larger nucleic
acids are degraded inside of cells. Preferably the immunostimulatory nucleic acids are in
the range of between 8 and 100 and in some embodiments T-rich containing
irnmunostirnulatory nucleic acids are between 24 and 40 nucleotides in length and TG
containing immunostimulatory nucleic acids are between 15 and 25 nucleotides in
length.
In one embodiment the T-rich nucleic acid is represented by at least the formula:
5lX1X2TTTTX3X43'
wherein X1, X2,X3, and X4 are nucleotides. In one embodiment X1X2 is TT
and/or X3X4 is TT. In another embodiment X1X2 are any one of the following nucleotides
TA, TG, TC, AT, AA, AG, AC, CT, CC, CA, GT, GG, GA, and GC; and X3X4 are any
one of the following nucleotides TA, TG, TC, AT, AA, AG, AC, CT, CC, CA, GT, GG,
GA, and GC.
In some embodiments it is preferred that the immunostimulatory nucleic acids do
not contain poly-C (CCCC), or poly-A (AAAA). In other embodiments it is preferred
that the immunostimulatory nucleic acid include poly-C, poly-A, poly-G (GGGG) or
multiple GGs. In particular poly-G or multiple GG motifs have dramatic effects on some
immunostimulatory nucleic acids. The effect of these non-T sequences depends in part
on the status of the nucleic acid backbone. For instance, if the nucleic acid has a

phosphodiester backbone or a chimeric backbone the inclusion of these sequences in the
nucleic acid will only have minimal if any effect on the biological activity of the nucleic
acid. If the backbone is completely phosphorothioate (or other phosphate modification)
or significantly phosphorothioate then the inclusion of these sequences may have more
influence on the biological activity or the kinetics of the biological activity, causing a
decrease in potency of the T-rich and TG immunostimulatory nucleic acids.
Although C-rich nucleic acids have been demonstrated to have immune
stimulating properties, insertion of Poly-C sequences into a T-rich nucleic acid in a
manner that would reduce the relative proportion of T nucleotides in the nucleic acid can
have a negative impact on the nucleic acid. Although applicants are not bound by a
proposed mechanism, it is believed that the immune system has developed a mechanism
for distinguishing nucleic acids having different nucleotide properties, possibly resulting
from different sets of binding proteins which recognize different sequences or specific
binding proteins which recognize all the immunostimulatory sequences but with different
affinities. In general nucleic acids including unmethylated CpG motifs are the most
immunostimulatory, followed by T-rich nucleic acids, TG nucleic acids and C-rich
nucleic acids. This generalization, however, has many exceptions. For instance a strong
T-rich nucleic acid like SEQ ID NO.: 886 is more immune stimulatory in some assays
than some CpG containing nucleic acids (e.g., a phosphorothioate CpG nucleic acid
containing a single CpG motif).
It has also been discovered that the addition of a poly-A tail to an
immunostimulatory nucleic acid can enhance the activity of the nucleic acid. It was
discovered that when a highly immune stimulatory CpG nucleic acid (SEQ ID NO.: 246)
was modified with the addition of a poly-A tail (AAAAAA) or a poly-T tail (TTTTTT),
the resultant oligonucleotides increased in immune stimulatory activity. The ability of
the poly-A tail and the poly-T tail to increase the immunostimulating properties of the
oligonucleotide was very similar. SEQ ID NO.: 246 is a T-rich oligonucleotide. It is
likely that if poly-A and poly-T tails are added to a nucleic acid which is not T-rich, it
would have a bigger impact on the immune stimulating capability of the nucleic acid.
Since the poly-T tail was added to a nucleic acid that was already highly T-rich the
immune stimulating properties of the poly-T addition was diluted somewhat, although
not completely. This finding has important implications for the use of poly-A regions.

Thus in some embodiments the immunostimulatory nucleic acids include a poly-A
region and in other embodiments they do not.
Some of the immunostimulatory nucleic acids of the invention include one or
more CG motifs. The presence of CG motifs in the immunostimulatory nucleic acids
also has an influence on the biological activity of the nucleic acids. If the total length of
an immunostimulatory nucleic acid is 20 nucleotide residues or less, then CpG motifs are
important in determining the immune effect of the nucleic acid, and methylation of these
motifs reduces the potency of the immune stimulatory effects of the nucleic acid. If the
length of the immunostimulatory nucleic acid is increased to 24, then the immune
stimulatory effects of the nucleic acid become less dependent on the CpG motifs, and are
no longer abolished by methylation of the CpG motifs or by their inversion to GC
dinucleotides, provided the other immune-stimulatory properties described herein are
present.
For example, ODN 2006 (SEQ ID NO:246) is a highly immune stimulatory T-
rich nucleic acid of 24 nucleotide residues in length with four CpG dinucleotides.
However, ODN 2117 (SEQ ID NO.358), in which the CpG motifs are methylated is also
highly immune stimulatory. ODN 2137 (SEQ ID NO:886), in which the CpG motifs of
ODN 2006 are inverted to GpC, and which as a result possesses six TG dinucleotides is
also immune stimulatory. The immune stimulatory effects of nucleic acids such as ODN
2117 and 2137 are regulated by their T and TG content. Each of these three nucleic
acids is T-rich and ODN 2137 is additionally TG rich. If their T content is reduced by
inserting other bases such as A (ODN 2117 (SEQ ID NO:358)) or if their TG content is
reduced by substituting TG with AG, then the immune stimulatory effects are somewhat
reduced. In another example, a nucleic acid 24 nucleotides in length in which all of the
positions are randomized has only a modest immune stimulatory effect (ODN 2182
(SEQ ID NO:432)). Likewise, a nucleic acid 24 nucleotides in length with other,
nucleotide compositions have variable immune stimulatory effects, depending on their T
content (ODN 2188 (SEQ ID NO:905), 2189 (SEQ ID NO:906), 2190 (SEQ ID
NO:907), 2191 (SEQ ID NO:908), 2193 (SEQ ID NO:910), 2183 (SEQ ID NO:433), and
2178 (SEQ ID NO:428)). ODN 2190 which contains TGT motifs is more immune
stimulatory than ODN 2202 which possesses TGG motifs. Thus, in some embodiments,
TGT motifs are preferred. In still other embodiments, the number of TG motifs is

important in that an increase in the number of TG motifs leads to an increase in immune
stimulation. Some preferred TG nucleic acids contain at least three TG motifs.
Examples of CpG nucleic acids include but are not limited to those listed in Table
A, such as SEQ ID NO: 1, 3, 4, 14-16, 18-24, 28, 29, 33-46, 49, 50, 52-56, 58, 64-67, 69,
71, 72, 76-87, 90, 91, 93, 94, 96, 98, 102-124, 126-128, 131-133, 136-141, 146-150,
152-153,155-171,173-178,180-186,188-198,201,203-214,216-220,223,224,227-
240., 242-256, 258, 260-265, 270-273,275, 277-281, 286-287, 292, 295-296, 300, 302,
305-307, 309-312, 314-317, 320-327, 329, 335, 337-341, 343-352, 354, 357, 361-365,
367-369,373-376, 378-385, 388-392, 394, 395, 399, 401-404, 406-426, 429-433, 434-
437: 439,441-443, 445, 447,448,450,453-456, 460-464, 466-469, 472-475, 477, 478,
480, 483-485, 488,489, 492, 493, 495-502, 504-505, 507-509, 511, 513-529, 532-541,
543-555, 564-566, 568-576, 578, 580, 599, 601-605, 607-611, 613-615, 617, 619-622,
625-646, 648-650, 653-664, 666-697, 699-706, 708, 709, 711-716, 718-732, 736, 737,
739-744, 746, 747, 749-761, 763, 766-767, 769, 772-779, 781-783, 785-786, 7900792,
798-799, 804-808, 810, 815, 817, 818, 820-832, 835-846, 849-850, 855-859, 862, 865,
872, 874-877, 879-881, 883-885, 888-904, and 909-913.
In some embodiments of the invention the immunostimulatory nucleic acids
include CpG dinucleotides and in other embodiments the immunostimulatory nucleic
acids are free of CpG dinucleotides. The CpG dinucleotides may be methylated or
unmethylated. A nucleic acid containing at least one unmethylated CpG dinucleotide is
a nucleic acid molecule which contains an unmethylated cytosine-guanine dinucleotide
sequence (i.e. "CpG DNA" or DNA containing an unmethylated 5' cytosine followed by
3' guanosine and linked by a phosphate bond) and activates the immune system. A
nucleic acid containing at least one methylated CpG dinucleotide is a nucleic acid which
contains a methylated cytosine-guanine dinucleotide sequence (i.e., a methylated 5'
cytosine followed by a 3' guanosine and linked by a phosphate bond).
Examples of T rich nucleic acids that are free of CpG nucleic acids include but
are not limited to those listed in Table A, such as SEQ ID NO: 59-63,73-75,142,215,
226,241,267-269,282, 301,304,330,342,358, 370-372, 393,433,471,479,486,491,
497, 503, 556-558, 567, 694, 793-794, 797, 833, 852, 861, 867, 868, 882, 886, 905, 907,
908, and 910-913. Examples of T rich nucleic acids that include CpG nucleic acids
include but are not limited to those listed in Table A, such as SEQ ID NO: 64,98,112,

146, 185, 204, 208, 214, 224,233,244,246, 247,258, 262,263,265,270-273, 300, 305,
316, 317, 343, 344, 350, 352,354, 374, 376, 392, 407, 411-413,429-432,434,435,443,
474,475, 498-501, 518, 687, 692, 693, 804, 862, 883, 884, 888, 890, and 891.
The immunostimulatory nucleic acids can be double-stranded or single-stranded.
Generally, double-stranded molecules are more stable in vivo, while single-stranded
molecules have increased immune activity. Thus in some aspects of the invention it is
preferred that the nucleic acid be single stranded and in other aspects it is preferred that
the nucleic acid be double stranded.
The term T-rich nucleic acid and TG nucleic acid, as used herein, refers to an
immunostimulatory T-rich nucleic acid and an immunostimulatory TG nucleic acid,
respectively, unless otherwise indicated. The T-rich nucleic acid sequences of the
invention are those broadly described above as well as the nucleic acids shown in Table
A that have at least one poly T motif and/or have a composition of greater than 25% T
or preferably 35% nucleotide residues. The C-rich nucleic acids are those having at least
one and preferably at least two poly-C regions. The TG nucleic acids of the invention
are those broadly described above as well as the specific nucleic acids shown in Table A
that have at least one TG motif.
The nucleic acids of the invention may, but need not, also include a poly G motif.
Poly G containing nucleic acids are also immunostimulatory. A variety of references,
including Pisetsky and Reich, 1993 Mol Biol. Reports, 18:217-221; Krieger and Herz,
1994, Ann. Rev. Biochem., 63:601-637; Macaya et al., 1993, PNAS, 90:3745-3749;
Wyatt et al., 1994, PNAS, 91:1356-1360; Rando and Hogan, 1998, In Applied Antisense
Oligonucleotide Technology, ed. Krieg and Stein, p. 335-352; and Kimura et al., 1994, J.
Biochem. 116, 991-994 also describe the immunostimulatory properties of poly G
nucleic acids.
Poly G nucleic acids preferably are nucleic acids having the following formulas:
5'X1X2GGGX3X4 3'
wherein X1, X2,X3, and X4 are nucleotides. In preferred embodiments at least one of X3
and X4 are a G. In other embodiments both of X3 and X4 are a G. In yet other
embodiments the preferred formula is 5' GGGNGGG3', or 5' GGGNGGGNGGG 3'
wherein N represents between 0 and 20 nucleotides. In other embodiments the poly G
nucleic acid is free of unmethylated CG dinucleotides, such as, for example, the nucleic

acids listed below as SEQ ID NO: 5, 6, 73, 215,267-269,276,282,288,297-299,355,
359, 386, 387, 444,476, 531, 557-559, 733, 768, 795, 796, 914-925, 928-931, 933-936,
and 938. In other embodiments the poly G nucleic acid includes at least one
unmethylated CG dinucleotide, such as, for example, the nucleic acids listed above as
SEQ ID NO: 67, 80-82, 141,,147, 148, 173, 178, 183, 185,214,224,264,265,315,329,
434, 435, 475, 519, 521-524, 526, 527, 535, 554, 565, 609, 628, 660, 661, 662, 725, 767,
825, 856, 857, 876, 892,909, 926, 927, 932, and 937.
The terms "nucleic acid" and "oligonucleotide" are used interchangeably to mean
multiple nucleotides (i.e. molecules comprising a sugar (e.g. ribose or deoxyribose)
linked to a phosphate group and to an exchangeable organic base, which is either a
substituted pyrimidine (e.g. cytosine (C), thymidine (T) or uracil (U)) or a substituted
purine (e.g. adenine (A) or guanine (G)). As used herein, the terms refer to
oligoribonucleotides as well as oligodeoxyribonucleotides. The terms shall also include
polynucleosides (i.e. a polynucleotide minus the phosphate) and any other organic base
containing polymer. Nucleic acid molecules can be obtained from existing nucleic acid
sources (e.g., genomic or cDNA), but are preferably synthetic (e.g. produced by nucleic
acid synthesis).
The terms nucleic acid and oligonucleotide also encompass nucleic acids or
oligonucleotides with substitutions or modifications, such as in the bases and/or sugars.
For example, they include nucleic acids having backbone sugars which are covalently
attached to low molecular weight organic groups other than a hydroxyl group at the 3'
position and other than a phosphate group at the 5' position. Thus modified nucleic acids
may include a 2'-O-alkylated ribose group. In addition, modified nucleic acids may
include sugars such as arabinose instead of ribose. Thus the nucleic acids may be
heterogeneous in backbone composition thereby containing any possible combination of
polymer units linked together such as peptide- nucleic acids (which have amino acid
backbone with nucleic acid bases). In some embodiments, the nucleic acids are
homogeneous in backbone composition. Nucleic acids also include substituted purines
and pyrimidines such as C-5 propyne modified bases (Wagner et al., Nature
Biotechnology 14:840- 844,1996). Purines and pyrimidines include but are not limited
to adenine, cytosine, guanine, thymidine, 5-methylcytosine, 2-aminopurine,
2-amino-6-chloropurine, 2,6-diaminopurine, hypoxanthine, and other naturally and

non-naturally occurring nucleobases, substituted and unsubstituted aromatic moieties.
Other such modifications are well known to those of skill in the art.
For use in the instant invention, the nucleic acids of the invention can be
synthesized de novo using any of a number of procedures well known in the art. For
example, the b-cyanoethyl phosphoramidite method (Beaucage, S.L., and Caruthers,
M.H., Tet. Let. 22:1859,1981); nucleoside H-phosphonate method (Garegg etai, Tet.
Let. 27:4051-4054,1986; Froehler etal.,Nucl Acid. Res. J4:5399-5407, 1986,; Garegg
etai, Tet. Let. 27:4055-4058, 1986, Gaffney etal., Tet. Let. 29:2619-2622, 1988).
These chemistries can be performed by a variety of automated nucleic acid synthesizers
available in the market. These nucleic acids are referred to as synthetic nucleic acids.
Alternatively, T-rich and/or TG dinucleotides can be produced on a large scale in
plasmids, (see Sambrook, T., et al, "Molecular Cloning: A Laboratory Manual", Cold
Spring Harbor laboratory Press, New York, 1989) and separated into smaller pieces or
administered whole. Nucleic acids can be prepared from existing nucleic acid sequences
{e.g., genomic or cDNA) using known techniques, such as those employing restriction
enzymes, exonucleases or endonucleases. Nucleic acids prepared in this mariner are
referred to as isolated nucleic acid. An isolated nucleic acid generally refers to a nucleic
acid which is separated from components which it is normally associated with in nature.
As an example, an isolated nucleic acid may be one which is separated from a cell, from
a nucleus, from mitochondria or from chromatin. The terms Py-rich nucleic acids and
TG nucleic acids encompasses both synthetic and isolated Py-rich nucleic acids and TG
nucleic acids.
For use in vivo, the Py-rich and TG nucleic acids may optionally be relatively
resistant to degradation (e.g., are stabilized). A "stabilized nucleic acid molecule" shall
mean a nucleic acid molecule that is relatively resistant to in vivo degradation (e.g. via an
exo- or endo-nuclease). Stabilization can be a function of length or secondary structure.
Nucleic acids that are tens to hundreds of kbs long are relatively resistant to in vivo
degradation. For shorter nucleic acids, secondary structure can stabilize and increase
their effect. For example, if the 3' end of an nucleic acid has self-complementarity to an
upstream region, so that it can fold back and form a sort of stem loop structure, then the
nucleic acid becomes stabilized and therefore exhibits more activity.

Alternatively, nucleic acid stabilization can be accomplished via phosphate
backbone modifications. Preferred stabilized nucleic acids of the instant invention have
a modified backbone. It has been demonstrated that modification of the nucleic acid
backbone provides enhanced activity of the Py-rich and TG nucleic acids when
administered in vivo. These stabilized structures are preferred because the Py-rich and
TG molecules of the invention have at least a partial modified backbone. Py-rich and
TG constructs having phosphorothioate linkages provide maximal activity and protect
the nucleic acid from degradation by intracellular exo- and endo-nucleases. Other
modified nucleic acids include phosphodiester modified nucleic acids, combinations of
phosphodiester and phosphorothioate nucleic acid, methylphosphonate,
methylphosphorothioate, phosphorodithioate, p-ethoxy, and combinations thereof. Each
of these combinations and their particular effects on immune cells is discussed in more
detail with respect to CpG nucleic acids in PCT Published Patent Applications
PCT/US95/01570 (WO 96/02555) and PCT/US97/19791 (WO 98/18810) claiming
priority to U.S. Serial Nos. 08/386,063 and 08/960,774, filed on February 7, 1995 and
October 30, 1997 respectively, the entire contents of which are hereby incorporated by
reference. It is believed that these modified nucleic acids may show more stimulatory
activity due to enhanced nuclease resistance, increased cellular uptake, increased protein
binding, and/or altered intracellular localization.
The compositions of the invention may optionally be chimeric oligonucleotides.
The chimeric oligonucleotides are oligonucleotides having a formula: 5' Y1N1ZN2Y2 3'.
Y1 and Y2 are nucleic acid molecules having between 1 and 10 nucleotides. Y1 and Y2
each include at least one modified intemucleotide linkage. Since at least 2 nucleotides of
the chimeric oligonucleotides include backbone modifications these nucleic acids are an
example of one type of "stabilized immunostimulatory nucleic acids."
With respect to the chimeric oligonucleotides, Y1 and Y2 are considered
independent of one another. This means that each of Y1 and Y2 may or may not have
different sequences and different backbone linkages from one anther in the same
molecule. The sequences vary, but in some cases Y1 and Y2 have a poly-G sequence. A
poly-G sequence refers to at least 3 Gs in a row. In other embodiments the poly-G
sequence refers to at least 4, 5, 6, 7, or 8 Gs in a row. In other embodiments Y1 and Y2
may be TCGTCG, TCGTCGT, or TCGTCGTT (SEQ ID NO:1145). Y1 and Y2 may also

have a poly-C, poIy-T, or poly-A sequence. In some embodiments Y1 and/or Y2 have
between 3 and 8 nucleotides.
N1 and N2 are nucleic acid molecules having between 0 and 5 nucleotides as long
as N1ZN2 has at least 6 nucleotides in total. The nucleotides of N1ZN2 have a
phosphodiester backbone and do not include nucleic acids having a modified backbone.
Z is an immunostimulatory nucleic acid motif but does not include a CG. For
instance, Z may be a nucleic acid a T-rich sequence, e.g. including a TTTT motif or a
sequence wherein at least 50% of the bases of the sequence are Ts or Z may be a TG
sequence.
The center nucleotides (N1ZN2) of the formula Y1N1ZN2Y2 have phosphodiester
intemucleotide linkages and Y1 and Y2 have at least one, but may have more than one or
even may have all modified intemucleotide linkages. In preferred embodiments Y!
and/or Y2 have at least two or between two and five modified intemucleotide linkages or
Y1 has two modified intemucleotide linkages and Y2 has five modified intemucleotide
linkages or Y\ has five modified intemucleotide linkages and Y2 has two modified
intemucleotide linkages. The modified intemucleotide linkage, in some embodiments is
a phosphorothioate modified linkage, a phosphorodithioate modified linkage or a p-
ethoxy modified linkage.
Modified backbones such as phosphorothioates may be synthesized using
automated techniques employing either phosphoramidate or H-phosphonate chemistries.
Aryl-and alkyl-phosphonates can be made, e.g., as described in U.S. Patent No.
4,469,863; and alkylphosphotriesters (in which the charged oxygen moiety is alkylated
as described in U.S. Patent No. 5,023,243 and European Patent No. 092,574) can be
prepared by automated solid phase synthesis using commercially available reagents.
Methods for making other DNA backbone modifications and substitutions have been
described (Uhlmann, E. and Peyman, A., Chem. Rev. 90:544,1990; Goodchild, J.,
Bioconjugate Chem. 1:165, 1990).
Other stabilized nucleic acids include: nonionic DNA analogs, such as alkyl- and
aryl-phosphates (in which the charged phosphonate oxygen is replaced by an alkyl or
aryl group), phosphodiester and alkylphosphotriesters, in which the charged oxygen
moiety is alkylated. Nucleic acids which contain diol, such as tetraethyleneglycol or

hexaethylenegjycol, at either or both termini have also been shown to be substantially
resistant to nuclease degradation.
In the case when the Py-rich or TG nucleic acid is administered in conjunction
with an antigen which is encoded in a nucleic acid vector, it is preferred that the
backbone of the Py-rich or TG nucleic acid be a chimeric combination of phosphodiester
and phosphorothioate (or other phosphate modification). The cell may have a problem
taking up a plasmid vector in the presence of completely phosphorothioate nucleic acid.
Thus when both a vector and a nucleic acid are delivered to a subject, it is preferred that
the nucleic acid have a chimeric backbone or have a phosphorothioate backbone but that
the plasmid be associated with a vehicle that delivers it directly into the cell, thus
avoiding the need for cellular uptake. Such vehicles are known in the art and include, for
example, liposomes and gene guns.
The nucleic acids described herein as well as various control nucleic acids are
presented below in Table A.













































While CpG effects in mice are well characterized, information regarding the
human system is limited. CpG phosphorothioate oligonucleotides with strong stimulatory
activity in the mouse system show lower activity on human and other non-rodent
immune cells. In the examples the development of a potent human CpG motif and the
characterization of its effects and mechanisms of action on human primary B-cells is
described. DNA containing this CpG motif strongly stimulated primary human B-cells
to proliferate, to produce IL-6 and to express increased levels of CD86, CD40, CD54 and
MHC II. It increased DNA binding activity of the transcription factors NFKB and AP-1,
as well as phosphorylation of the stress activated protein kinases JNK and p38, and the
transcription factor ATF-2. B-cell signaling pathways activated by CpG DNA were
different from those activated by the B-cell receptor which activated ERK and a different
isoform of JNK, but did not activate p38 and ATF-2. In general the data on CpG DNA-
initiated signal transduction are consistent with those obtained in mice (Hacker H., et al.
1998. Embo J 17:6230, Yi A. K., and Krieg A. M. 1998. JImmunol 161:4493).
The preferred non-rodent motif is 5' TCGTCGTT 3'. Base exchanges within the
most potent 8mer CpG motif (5' TCGTCGTT 3') diminished the activity of the
oligonucleotide. The thymidines at the 5' and the 3' position of this motif were more
important than the thymidine at the middle position. An adenine or guanosine at the
middle position produced a decrease in the activity.
Of note, our studies demonstrate that one human CpG motif within a
phosphodiester oligonucleotide (2080) is sufficient to produce the maximal effect, and
that additional CpG motifs (2059) did not further enhance the activity. The
oligonucleotide with the 8mer motif 5' TCG TCG TT 3' (2080) containing two CpG
dinucleotides showed the highest activity in the studies. Replacement of the bases
flanking the two CpG dinucleotides (5' position, middle position, 3' position) reduced
the activity of this sequence. Both CpG dinucleotides within the 8mer CpG motif were
required for the optimal activity (2108, 2106). Cytidine methylation of the CpG
dinucleotides (2095) abolished the activity of 2080, while methylation of an unrelated

cytidine (2094) did not. The addition of two CpG motifs into the sequence of 2080
resulting in 2059 did not further increase the activity of the phosphodiester
oligonucleotide. The sequence of 2080 with a phosphorothioate backbone (2116)
• demonstrated less activity, suggesting that additional CpG motifs are preferred for a
potent phosphorothioate oligonucleotide.
It has been discovered according to the invention that the immunostimulatory
nucleic acids have dramatic immune stimulatory effects on human cells such as NK
cells, B cells, and DCs in vitro. It has been demonstrated that that the in vitro assays
used herein predict in vivo effectiveness as a vaccine adjuvant in non-rodent vertebrates
(Example 12), suggesting that immunostimulatory nucleic acids are effective therapeutic
agents for human vaccination, cancer immunotherapy, asthma immunotherapy, general
enhancement of immune function, enhancement of hematopoietic recovery following
radiation or chemotherapy, and other immune modulatory applications.
Thus the immunostimulatory nucleic acids are useful in some aspects of the
invention as a prophylactic vaccine for the treatment of a subject at risk of developing an
infection with an infectious organism or a cancer in which a specific cancer antigen has
been identified or an allergy or asthma where the allergen or predisposition to asthma is
known. The immunostimulatory nucleic acids can also be given without the antigen or
allergen for shorter term protection against infection, allergy or cancer, and in this case
repeated doses will allow longer term protection. A subject at risk as used herein is a
subject who has any risk of exposure to an infection causing pathogen or a cancer or an
allergen or a risk of developing cancer. For instance, a subject at risk may be a subject
who is planning to travel to an area where a particular type of infectious agent is found or
it may be a subject who through lifestyle or medical procedures is exposed to bodily
fluids which may contain infectious organisms or directly to the organism or even any
subject living in an area where an infectious organism or an allergen has been identified.
Subjects at risk of developing infection also include general populations to which a
medical agency recommends vaccination with a particular infectious organism antigen.
If the antigen is an allergen and the subject develops allergic responses to that particular
antigen and the subject may be exposed to the antigen, i.e., during pollen season, then
that subject is at risk of exposure to the antigen. A subject at risk of developing an
allergy to asthma includes those subjects that have been identified as having an allergy or

asthma but that don't have the active disease during the immunostimulatory nucleic acid
treatment as well as subjects that are considered to be at risk of developing these diseases
because of genetic or environmental factors.
A subject at risk of developing a cancer is one who is who has a high probability
of developing cancer. These subjects include, for instance, subjects having a genetic
abnormality, the presence of which has been demonstrated to have a correlative relation
to a higher likelihood of developing a cancer and subjects exposed to cancer causing
agents such as tobacco, asbestos, or other chemical toxins, or a subject who has
previously been treated for cancer and is in apparent remission. When a subject at risk of
developing a cancer is treated with an antigen specific for the type of cancer to which the
subject is at risk of developing and a immunostimulatory nucleic acid, the subject may be
able to kill the cancer cells as they develop. If a tumor begins to form in the subject, the
subject will develop a specific immune response against the tumor antigen.
In addition to the use of the immunostimulatory nucleic acids for prophylactic
treatment, the invention also encompasses the use of the immunostimulatory nucleic
acids for the treatment of a subject having an infection, an allergy, asthma, or a cancer.
A subject having an infection is a subject that has been exposed to an infectious
pathogen and has acute or chronic detectable levels of the pathogen in the body. The
imrnunostimulatory nucleic acids can be used with an antigen to mount an antigen
specific systemic or mucosal immune response that is capable of reducing the level of or
eradicating the infectious pathogen. An infectious disease, as used herein, is a disease
arising from the presence of a foreign microorganism in the body. It is particularly
important to develop effective vaccine strategies and treatments to protect the body's
mucosal surfaces, which are the primary site of pathogenic entry.
A subject having an allergy is a subject that has or is at risk of developing an
allergic reaction in response to an allergen. An allergy refers to acquired
hypersensitivity to a substance (allergen). Allergic conditions include but are not limited
to eczema, allergic rhinitis or coryza, hay fever, conjunctivitis, bronchial asthma,
urticaria (hives) and food allergies, and other atopic conditions.
Currently, allergic diseases are generally treated by the injection of small doses of
antigen followed by subsequent increasing dosage of antigen. It is believed that this
procedure induces tolerization to the allergen to prevent further allergic reactions. These

methods, however, can take several years to be effective and are associated with the risk
of side effects such as anaphylactic shock. The methods of the invention avoid these
problems.
Allergies are generally caused by IgE antibody generation against harmless
allergens. The cytokines that are induced by systemic or mucosal administration of
immunostimulatory nucleic acids are predominantly of a class called Thl (examples are
IL-12 and IFN-γ) and these induce both humoral and cellular immune responses. The
types of antibodies associated with a Thl response are generally more protective because
they have high neutralization and opsonization capabilities. The other major type of
immune response, which is associated with the production of IL-4, IL-5 and IL-10
cytokines, is termed a Th2 immune response. Th2 responses involve predominately
antibodies and these have less protective effect against infection and some Th2 isotypes
(e.g., IgE) are associated with allergy. In general, it appears that allergic diseases are
mediated by Th2 type immune responses while Thl responses provide the best
protection against infection, although excessive Thl responses are associated with
autoimmune disease. Based on the ability of the immunostimulatory nucleic acids to
shift the immune response in a subject from a Th2 (which is associated with production
of IgE antibodies and allergy) to a Thl response (which is protective against allergic
reactions), an effective dose for inducing an immune response of a immunostimulatory
nucleic acid can be administered to a subject to treat or prevent an allergy.
Thus, the immunostimulatory nucleic acids have significant therapeutic utility in
the treatment of allergic and non-allergic conditions such as asthma. Th2 cytokines,
especially IL-4 and IL-5 are elevated in the airways of asthmatic subjects. These
cytokines promote important aspects of the asthmatic inflammatory response, including
IgE isotope switching, eosinophil chemotaxis and activation and mast cell growth. Thl
cytokines, especially IFN-γ and IL-12, can suppress the formation of Th2 clones and
production of Th2 cytokines. Asthma refers to a disorder of the respiratory system
characterized by inflammation, narrowing of the airways and increased reactivity of the
airways to inhaled agents. Asthma is frequently, although not exclusively associated
with atopic or allergic symptoms.
A subject having a cancer is a subject that has detectable cancerous cells. The
cancer may be a malignant or non-malignant cancer. Cancers or tumors include but are

not limited to biliary tract cancer; brain cancer; breast cancer; cervical cancer;
choriocarcinoma; colon cancer; endometrial cancer; esophageal cancer; gastric cancer;
intracpithelial neoplasms; Iymphomas; liver cancer; lung cancer (e.g. small cell and
non-small cell); melanoma; neuroblastomas; oral cancer; ovarian cancer; pancreas
cancer; prostate cancer; rectal cancer; sarcomas; skin cancer; testicular cancer; thyroid
cancer; and renal cancer, as well as other carcinomas and sarcomas. In one embodiment
the cancer is hairy cell leukemia, chronic myelogenous leukemia, cutaneous T-cell
leukemia, multiple myeloma, follicular lymphoma, malignant melanoma, squamous cell
carcinoma, renal cell carcinoma, prostate carcinoma, bladder cell carcinoma, or colon
carcinoma.
A subject according to the invention is a non-rodent subject. A non-rodent
subject shall mean a human or vertebrate animal including but not limited to a dog, cat,
horse, cow, pig, sheep, goat, chicken, primate, e.g., monkey, and fish (aquaculture
species), e.g. salmon, but specifically excluding rodents such as rats and mice.
Thus, the invention can also be used to treat cancer and tumors in non human
subjects. Cancer is one of the leading causes of death in companion animals (i.e., cats
and dogs). Cancer usually strikes older animals which, in the case of house pets, have
become integrated into the family. Forty-five % of dogs older than 10 years of age, are
likely to succumb to the disease. The most common treatment options include surgery,
chemotherapy and radiation therapy. Others treatment modalities which have been used
with some success are laser therapy, cryotherapy, hyperthermia and immunotherapy.
The choice of treatment depends on type of cancer and degree of dissemination. Unless
the malignant growth is confined to a discrete area in the body, it is difficult to remove
only malignant tissue without also affecting normal cells.
Malignant disorders commonly diagnosed in dogs and cats include but are not
limited to lymphosarcoma, osteosarcoma, mammary tumors, mastocytoma, brain tumor,
melanoma, adenosquamous carcinoma, carcinoid lung tumor, bronchial gland tumor,
bronchiolar adenocarcinoma, fibroma, myxochondroma, pulmonary sarcoma,
neurosarcoma, osteoma, papilloma, retinoblastoma, Ewing's sarcoma, Wilm's tumor,
Burkitt's lymphoma, microglioma, neuroblastoma, osteoclastoma, oral neoplasia,
fibrosarcoma, osteosarcoma and rhabdomyosarcoma. Other neoplasias in dogs include
genital squamous cell carcinoma, transmissable veneral tumor, testicular tumor,

seminoma, Sertoli cell tumor, hemangiopericytoma, histiocytoma, chloroma
(granulocytic sarcoma), corneal papilloma, corneal squamous cell carcinoma,
hemangiosarcoma, pleural mesothelioma, basal cell tumor, thymoma, stomach tumor,
adrenal gland carcinoma, oral papillomatosis, hemangioendothelioma and cystadenoma.
Additional malignancies diagnosed in cats include follicular lymphoma, intestinal
lymphosarcoma, fibrosarcoma and pulmonary squamous cell carcinoma. The ferret, an
ever-more popular house pet is known to develop insulinoma, lymphoma, sarcoma,
neuroma, pancreatic islet cell tumor, gastric MALT lymphoma and gastric
adenocarcinoma.
Neoplasias affecting agricultural livestock include leukemia,
hemangiopericytoma and bovine ocular neoplasia (in cattle); preputial fibrosarcoma,
ulcerative squamous cell carcinoma, preputial carcinoma, connective tissue neoplasia
and mastocytoma (in horses); hepatocellular carcinoma (in swine); lymphoma and
pulmonary adenomatosis (in sheep); pulmonary sarcoma, lymphoma, Rous sarcoma,
reticulendotheliosis, fibrosarcoma, nephroblastoma, B-cell lymphoma and lymphoid
leukosis (in avian species); retinoblastoma, hepatic neoplasia, lymphosarcoma
(lymphoblastic lymphoma), plasmacytoid leukemia and swimbladder sarcoma (in fish),
caseous lumphadenitis (CLA): chronic, infectious, contagious disease of sheep and goats
caused by the bacterium Corynebacterium pseudotuberculosis, and contagious lung
tumor of sheep caused by jaagsiekte.
The subject is exposed to the antigen. As used herein, the term exposed to refers
to either the active step of contacting the subject with an antigen or the passive exposure
of the subject to the antigen in vivo. Methods for the active exposure of a subject to an
antigen are well-known in the art. In general, an antigen is administered directly to the
subject by any means such as intravenous, intramuscular, oral, transdermal, mucosal,
intranasal, intratracheal, or subcutaneous administration. The antigen can be
administered systemically or locally. Methods for administering the antigen and the
immunostimulatory nucleic acid are described in more detail below. A subject is
passively exposed to an antigen if an antigen becomes available for exposure to the
immune cells in the body. A subject may be passively exposed to an antigen, for
instance, by entry of a foreign pathogen into the body or by the development of a tumor
cell expressing a foreign antigen on its surface.

The methods in which a subject is passively exposed to an antigen can be
particularly dependent on timing of administration of the immunostimulatory nucleic
acid. For instance, in a subject at risk of developing a cancer or an infectious disease or
an allergic or asthmatic response, the subject may be administered the
immunostimulatory nucleic acid on a regular basis when that risk is greatest, i.e., during
allergy season or after exposure to a cancer causing agent. Additionally the
immunostimulatory nucleic acid may be administered to travelers before they travel to
foreign lands where they are at risk of exposure to infectious agents. Likewise the
immunostimulatory nucleic acid may be administered to soldiers or civilians at risk of
exposure to biowarfare to induce a systemic or mucosal immune response to the antigen
when and if the subject is exposed to it.
An antigen as used herein is a molecule capable of provoking an immune
response. Antigens include but are not limited to cells, cell extracts, proteins,
polypeptides, peptides, polysaccharides, polysaccharide conjugates, peptide and non-
peptide mimics of polysaccharides and other molecules, small molecules, lipids,
glycolipids, carbohydrates, viruses and viral extracts and muticellular organisms such as
parasites and allergens. The term antigen broadly includes any type of molecule which is
recognized by a host immune system as being foreign. Antigens include but are not
limited to cancer antigens, microbial antigens, and allergens.
A cancer antigen as used herein is a compound, such as a peptide or protein,
associated with a tumor or cancer cell surface and which is capable of provoking an
immune response when expressed on the surface of an antigen presenting cell in the
context of an MHC molecule. Cancer antigens can be prepared from cancer cells either
by preparing crude extracts of cancer cells, for example, as described in Cohen, et al.,
1994, Cancer Research, 54:1055, by partially purifying the antigens, by recombinant
technology, or by de novo synthesis of known antigens. Cancer antigens include but are
not limited to antigens that are recombinantly expressed, an immunogenic portion of, or
a whole tumor or cancer. Such antigens can be isolated or prepared recombinantly or by
any other means known in the art.
A microbial antigen as used herein is an antigen of a microorganism and includes
but is not limited to virus, bacteria, parasites, and fungi. Such antigens include the intact
microorganism as well as natural isolates and fragments or derivatives thereof and also

synthetic compounds which are identical to or similar to natural microorganism antigens
and induce an immune response specific for that microorganism. A compound is similar
to a natural microorganism antigen if it induces an immune response (humoral and/or
cellular) to a natural microorganism antigen. Such antigens are used routinely in the art
and are well known to those of ordinary skill in the art.
Examples of viruses that have been found in humans include but are not limited
to: Retroviridae (e.g. human immunodeficiency viruses, such as HIV-1 (also referred to
as HTLV-III, LAV or HTLV-III/LAV, or HIV-III; and other isolates, such as HIV-LP;
Picornaviridae (e.g. polio viruses, hepatitis A virus; enteroviruses, human Coxsackie
viruses, rhinoviruses, echoviruses); Calciviridae (e.g. strains that cause gastroenteritis);
Togaviridae (e.g. equine encephalitis viruses, rubella viruses); Flaviridae (e.g. dengue
viruses, encephalitis viruses, yellow fever viruses); Coronoviridae (e.g. coronaviruses);
Rhabdoviradae (e.g. vesicular stomatitis viruses, rabies viruses); Coronaviridae (e.g.
coronaviruses); Rhabdoviridae (e.g. vesicular stomatitis viruses, rabies viruses);
Filoviridae (e.g. ebola viruses); Paramyxoviridae (e.g. parainfluenza viruses, mumps
virus, measles virus, respiratory syncytial virus); Orthomyxoviridae (e.g. influenza
viruses); Bungaviridae (e.g. Hantaan viruses, bunga viruses, phleboviruses and Nairo
viruses); Arena viridae (hemorrhagic fever viruses); Reoviridae (e.g. reoviruses,
orbiviurses and rotaviruses); Birnaviridae; Hepadnaviridae (Hepatitis B virus);
Parvovirida (parvoviruses); Papovaviridae (papilloma viruses, polyoma viruses);
Adenoviridae (most adenoviruses); Herpesviridae (herpes simplex virus (HSV) 1 and 2,
varicella zoster virus, cytomegalovirus (CMV), herpes virus; Poxviridae (variola viruses,
vaccinia viruses, pox viruses); and Iridoviridae (e.g. African swine fever virus); and
unclassified viruses (e.g. the etiological agents of Spongiform encephalopathies, the
agent of delta hepatitis (thought to be a defective satellite of hepatitis B virus), the agents
of non-A, non-B hepatitis (class 1 = internally transmitted; class 2 = parenterally
transmitted (i.e. Hepatitis C); Norwalk and related viruses, and astroviruses).
Both gram negative and gram positive bacteria serve as antigens in vertebrate
animals. Such gram positive bacteria include, but are not limited to, Pasteurella species,
Staphylococci species, and Streptococcus species. Gram negative bacteria include, but
are not limited to, Escherichia coll, Pseudomonas species, and Salmonella species.
Specific examples of infectious bacteria include but are not limited to, Helicobacter

pyloris, Borelia burgdorferi, Legionella pneumophilia, Mycobacteria sps (e.g. M.
tuberculosis, M. avium, M. intracellulare, M. kansaii, M. gordo/iae), Staphylococcus
aureus, Neisseria gonorrhoeae, Neisseria meningitidis, Listeria monocytogenes,
Streptococcus pyogenes (Group A Streptococcus), Streptococcus agalactiae (Group B
Streptococcus), Streptococcus (viridans group), Streptococcus faecalis, Streptococcus
bovis, Streptococcus (anaerobic sps.), Streptococcus pneumoniae, pathogenic
Campylobacter sp., Enterococcus sp., Haemophilus influenzae, Bacillus antracis,
corynebacterium diphtheriae, corynebacterium sp., Erysipelothrix rhusiopathiae,
Clostridium perjringers, Clostridium tetani, Enterobacter aerogenes, Klebsiella
pneumoniae, Pasturella multocida, Bacteroides sp., Fusobacterium nucleatum,
Streptobacillus moniliformis, Treponema pallidium, Treponema pertenue, Leptospira,
Rickettsia, and Actinomyces israelli.
Examples of fungi include Cryptococcus neoformans, Histoplasma capsulatum,
Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Candida
albicans.
Other infectious organisms (i.e., protists) include Plasmodium spp. such as
Plasmodiumfalciparum, Plasmodium malariae, Plasmodium ovale, and Plasmodium
vivax and Toxoplasma gondii. Blood-bome and/or tissues parasites include Plasmodium
spp., Babesia microti, Babesia divergens, Leishmania tropica, Leishmania spp.,
Lcishmania braziliensis, Leishmania donovani, Trypanosoma gambiense and
Trypanosoma rhodesiense (African sleeping sickness), Trypanosoma cruzi (Chagas'
disease), and Toxoplasma gondii.
Other medically relevant microorganisms have been described extensively in the
literature, e.g., see C.G.A Thomas, Medical Microbiology, Bailliere Tindall, Great
Britain 1983, the entire contents of which is hereby incorporated by reference.
Although many of the microbial antigens described above relate to human
disorders, the invention is also useful for treating other nonhuman vertebrates.
Nonhuman vertebrates are also capable of developing infections which can be prevented
or treated with the Imrnunostimulatory nucleic acids disclosed herein. For instance, in
addition to the treatment of infectious human diseases, the methods of the invention are
useful for treating infections of animals.

As used herein, the term treat, treated, or treating when used with respect to an
infectious disease refers to a prophylactic treatment which increases the resistance of a
subject (a subject at risk of infection) to infection with a pathogen or, in other words,
decreases the likelihood that the subject will become infected with the pathogen as well
as a treatment after the subject (a subject who has been infected) has become infected in
order to fight the infection, e.g., reduce or eliminate the infection or prevent it from
becoming worse.
Many vaccines for the treatment of non-human vertebrates are disclosed in
Bennett, K. Compendium of Veterinary Products, 3rd ed. North American
Compendiums, Inc., 1995. As discussed above, antigens include infectious microbes
such as virus, parasite, bacteria and fungi and fragments thereof, derived from natural
sources or synthetically. Infectious viruses of both human and non-human vertebrates,
include retroviruses, RNA viruses and DNA viruses. This group of retroviruses includes
both simple retroviruses and complex retroviruses. The simple retroviruses include the
subgroups of B-type retroviruses, C-type retroviruses and D-type retroviruses. An.
example of a B-type retrovirus is mouse mammary tumor virus (MMTV). The C-type
retroviruses include subgroups C-type group A (including Rous sarcoma virus (RSV),
avian leukemia virus (ALV), and avian myeloblastosrs virus (AMV)) and C-type group
B (including feline leukemia virus (FeLV), gibbon ape leukemia virus (GALV), spleen
necrosis virus (SNV), reticuloendotheliosis virus (RV) and simian sarcoma virus (SSV)).
The D-type retroviruses include Mason-Pfizer monkey virus (MPMV) and simian
retrovirus type 1 (SRV-1). The complex retroviruses include the subgroups of
lentiviruses, T-cell leukemia viruses and the foamy viruses. Lentiviruses include HIV-1,
but also include HIV-2, SIV, Visna virus, feline immunodeficiency virus (FIV), and
equine infectious anemia virus (EIAV). The T-cell leukemia viruses include HTLV-1,
HTLV-II, simian T-cell leukemia virus (STLV), and bovine leukemia virus (BLV). The
foamy viruses include human foamy virus (HFV), simian foamy virus (SFV) and bovine
foamy virus (BFV).
Examples of other RNA viruses that are antigens in vertebrate animals include,
but are not limited to, members of the family Reoviridae, including the genus
Orthoreovirus (multiple serotypes of both mammalian and avian retroviruses), the genus
Orbivirus (Bluetongue virus, Eugenangee virus, Kemerovo virus, African horse sickness

virus, and Colorado Tick Fever virus), the genus Rotavirus (human rotavirus, Nebraska
calf diarrhea virus, simian rotavirus, bovine or ovine rotavirus, avian rotavirus); the
family Picornaviridae, including the genus Enterovirus (poliovirus, Coxsackie virus A
and B, enteric cytopathic human orphan (ECHO) viruses, hepatitis A virus, Simian
enteroviruses, Murine encephalomyelitis (ME) viruses, Poliovirus muris, Bovine
enteroviruses, Porcine enteroviruses, the genus Cardiovirus (Encephalomyocarditis virus
(EMC), Mengovirus), the genus Rhinovirus (Human rhinoviruses including at least 113
subtypes; other rhinoviruses), the genus Apthovirus (Foot and Mouth disease (FMDV);
the family Calciviridae, including Vesicular exanthema of swine virus, San Miguel sea
lion virus, Feline picomavirus and Norwalk virus; the family Togaviridae, including the
genus Alphavirus (Eastern equine encephalitis virus, Semliki forest virus, Sindbis virus,
Chikungunya virus, O'Nyong-Nyong virus, Ross river virus, Venezuelan equine
encephalitis virus, Western equine encephalitis virus), the genus Flavirius (Mosquito
borne yellow fever virus, Dengue virus, Japanese encephalitis virus, St. Louis
encephalitis virus, Murray Valley encephalitis virus, West Nile virus, Kunjin virus,
Central European tick borne virus, Far Eastern tick borne virus, Kyasanur forest virus,
Louping III virus, Powassan virus, Omsk hemorrhagic fever virus), the genus Rubivirus
(Rubella virus), the genus Pestivirus (Mucosal disease virus, Hog cholera virus, Border
disease virus); the family Bunyaviridae, including the genus Bunyvirus (Bunyamwera
and related viruses, California encephalitis group viruses), the genus Phlebovirus
(Sandfly fever Sicilian virus, Rift Valley fever virus), the genus Nairovirus
(Crimean-Congo hemorrhagic fever virus, Nairobi sheep disease virus), and the genus
Uukuvirus (Uukuniemi and related viruses); the family Orthomyxoviridae, including the
genus Influenza virus (Influenza virus type A, many human subtypes); Swine influenza
virus, and Avian and Equine Influenza viruses; influenza type B (many human subtypes),
and influenza type C (possible separate genus); the family paramyxoviridae, including
the genus Paramyxovirus (Parainfluenza virus type 1, Sendai virus, Hemadsorption virus,
Parainfluenza viruses types 2 to 5, Newcastle Disease Virus, Mumps virus), the genus
Morbillivirus (Measles virus, subacute sclerosing panencephalitis virus, distemper virus,
Rinderpest virus), the genus Pneumovirus (respiratory syncytial virus (RSV), Bovine
respiratory syncytial virus and Pneumonia virus); the family Rhabdoviridae, including
the genus Vesiculovirus (VSV), Chandipura virus, Flanders-Hart Park virus), the genus

Lyssavirus (Rabies virus), fish Rhabdoviruses, and two probable Rhabdoviruses
(Marburg virus and Ebola virus); the family Arenaviridae, including Lymphocytic
choriomeningitis virus (LCM), Tacaribe virus complex, and Lassa virus; the family
Coronoaviridae, including Infectious Bronchitis Virus (IBV), Hepatitis virus, Human
enteric corona virus, and Feline infectious peritonitis (Feline coronavirus).
Illustrative DNA viruses that are antigens in vertebrate animals include, but are
not limited to, the family Poxviridae, including the genus Orthopoxvirus (Variola major,
Variola minor, Monkey pox Vaccinia, Cowpox, Buffalopox, Rabbitpox, Ectromelia), the
genus Leporipoxvirus (Myxoma, Fibroma), the genus Avipoxvirus (Fowlpox, other
avian poxvirus), the genus Capripoxvirus (sheeppox, goatpox), the genus Suipoxvirus
(Swinepox), the genus Parapoxvirus (contagious postular dermatitis virus,
pseudocowpox, bovine papular stomatitis virus); the family Iridoviridae (African swine
fever virus, Frog viruses 2 and 3, Lymphocystis virus offish); the family Herpesviridae,
including the alpha-Herpesviruses (Herpes Simplex Types 1 and 2, Varicella-Zoster,
Equine abortion virus, Equine herpes virus 2 and 3, pseudorabies virus, infectious bovine
keratoconjunctivitis virus, infectious bovine rhinotracheitis virus, feline rhinotracheitis
virus, infectious laryngotracheitis virus) the Beta-herpesviruses (Human cytomegalovirus
and cytomegaloviruses of swine and monkeys); the gamma-herpesviruses (Epstein-Barr
virus (EB V), Marek's disease virus, Herpes saimiri, Herpesvirus ateles, Herpesvirus
sylvilagus, guinea pig herpes virus, Lucke tumor virus); the family Adenoviridae,
including the genus Mastadenovirus (Human subgroups A,B,C,D,E and ungrouped;
simian adenoviruses (at least 23 serotypes), infectious canine hepatitis, and adenoviruses
of cattle, pigs, sheep, frogs and many other species, the genus Aviadenovirus (Avian
adenoviruses); and non-cultivatable adenoviruses; the family Papoviridae, including the
genus Papillomavirus (Human papilloma viruses, bovine papilloma viruses, Shope rabbit
papilloma virus, and various pathogenic papilloma viruses of other species), the genus
Polyomavirus (polyomavirus, Simian vacuolating agent (SV-40), Rabbit vacuolating
agent (RKV), K virus, BK virus, JC virus, and other primate polyoma viruses such as
Lymphotrophic papilloma virus); the family Parvoviridae including the genus
Adeno-associated viruses, the genus Parvovirus (Feline panleukopenia virus, bovine
parvovirus, canine parvovirus, Aleutian mink disease virus, etc). Finally, DNA viruses
may include viruses which do not fit into the above families such as Kuru and

Creutzfeldt-Jacob disease viruses and chronic infectious neuropathic agents (CHINA
virus).
Each of the foregoing lists is illustrative, and is not intended to be limiting.
In addition to the use of the immunostimulatory nucleic acids to induce an
antigen specific immune response in humans, the methods of the preferred embodiments
are particularly well suited for treatment of birds such as hens, chickens, turkeys, ducks,
geese, quail, and pheasant. Birds are prime targets for many types of infections.
Hatching birds are exposed to pathogenic microorganisms shortly after birth.
Although these birds are initially protected against pathogens by maternal derived
antibodies, this protection is only temporary, and the bird's own immature immune
system must begin to protect the bird against the pathogens. It is often desirable to
prevent infection in young birds when they are most susceptible. It is also desirable to
prevent against infection in older birds, especially when the birds are housed in closed
quarters, leading to the rapid spread of disease. Thus, it is desirable to administer the
Immunostimulatory nucleic acid and the non-nucleic acid adjuvant of the invention to
birds to enhance an antigen-specific immune response when antigen is present.
An example of a common infection in chickens is chicken infectious anemia
virus (CIAV). CIAV was first isolated in Japan in 1979 during an investigation of a
Marek's disease vaccination break (Yuasa et al., 1979, Avian Dis. 23:366-385). Since
that time, CIAV has been detected in commercial poultry in all major poultry producing
countries (van Bulow et al., 1991, pp.690-699) in Diseases of Poultry, 9th edition, Iowa
State University Press).
CIAV infection results in a clinical disease, characterized by anemia,
hemorrhage and immunosuppression, in young susceptible chickens. Atrophy of the
thymus and of the bone marrow and consistent lesions of CIAV-infected chickens are
also characteristic of CIAV infection. Lymphocyte depletion in the thymus, and
occasionally in the bursa of Fabricius, results in immunosuppression and increased
susceptibility to secondary viral, bacterial, or fungal infections which then complicate the
course of the disease. The immunosuppression may cause aggravated disease after
infection with one or more of Marek's disease virus (MDV), infectious bursal disease
virus, reticuloendotheliosis virus, adenovirus, or reovirus. It has been reported that
pathogenesis of MDV is enhanced by CIAV (DeBoer et al., 1989, p. 28 In Proceedings

of the 38th Western Poultry Diseases Conference, Tempe, Ariz.). Further, it has been
reported that CIAV aggravates the signs of infectious bursal disease (Rosenberger et al.,
1989, Avian Dis. 33:707-713). Chickens develop an age resistance to experimentally
induced disease due to CAA. This is essentially complete by the age of 2 weeks, but
older birds are still susceptible to infection (Yuasa, N. et al., 1979 supra; Yuasa, N. et al.,
Arian Diseases 24,202-209, 1980). However, if chickens are dually infected with CAA
and an immunosuppressive agent (IBDV, MDV etc.), age resistance against the disease
is delayed (Yuasa, N. et al., 1979 and 1980 supra; Bulow von V. et al., J. Veterinary
Medicine 33, 93-116, 1986). Characteristics of CIAV that may potentiate disease
transmission include high resistance to environmental inactivation and some common
disinfectants. The economic impact of CIAV infection on the poultry industry is clear
from the fact that 10% to 30% of infected birds in disease outbreaks die.
Vaccination of birds, like other vertebrate animals can be performed at any age.
Normally, vaccinations are performed at up to 12 weeks of age for a live microorganism
and between 14-18 weeks for an inactivated microorganism or other type of vaccine.
For in ovo vaccination, vaccination can be performed in the last quarter of embryo
development. The vaccine may be administered subcutaneously, by spray, orally,
intraocularly, intratracheally, nasally, or by other mucosal delivery methods described
herein. Thus, the immunostimulatory nucleic acids of the invention can be administered
to birds and other non-human vertebrates using routine vaccination schedules and the
antigen can be administered after an appropriate time period as described herein.
Cattle and livestock are also susceptible to infection. Diseases which affect these
animals can produce severe economic losses, especially amongst cattle. The methods of
the invention can be used to protect against infection in livestock, such as cows, horses,
pigs, sheep, and goats.
Cows can be infected by bovine viruses. Bovine viral diarrhea virus (BVDV) is a
small enveloped positive-stranded RNA virus and is classified, along with hog cholera
virus (HOCV) and sheep border disease virus (BDV), in the pestivirus genus. Although,
Pestiviruses were previously classified in the Togaviridae family, some studies have
suggested their reclassification within the Flaviviridae family along with the flavivirus
and hepatitis C virus (HCV) groups (Francki, et al., 1991).

BVDV, which is an important pathogen of cattle can be distinguished, based on
cell culture analysiS, into cytopathogenic (CP) and noncytopathogenic (NCP) biotypes.
The NCP biotype is more widespread although both biotypes can be found in cattle. If a
pregnant caw becomes infected with an NCP strain, the cow can give birth to a
persistently infected and specifically immunotolerant calf that will spread virus during
its lifetime. The persistently infected cattle can succumb to mucosal disease and both
biotypes can then be isolated from the animal. Clinical manifestations can include
abortion, teratogenesis, and respiratory problems, mucosal disease and mild diarrhea. In
addition, severe thrombocytopenia, associated with herd epidemics, that may result in
the death of the animal has been described and strains associated with this disease seem
more virulent than the classical BVDVs.
Equine herpes viruses (EHV) comprise a group of antigenically distinct
biological agents which cause a variety of infections in horses ranging from subclinical
to fatal disease. These include Equine herpesvirus-1 (EHV-1), a ubiquitous pathogen in
horses. EHV-1 is associated with epidemics of abortion, respiratory tract disease, and
central nervous system disorders. Primary infection of upper respiratory tract of young
horses results in a febrile illness which lasts for 8 to 10 days. Immunologically
experienced mares may be re-infected via the respiratory tract without disease becoming
apparent, so that abortion usually occurs without warning. The neurological syndrome is
associated with respiratory disease or abortion and can affect animals of either sex at any
age, leading to lack of co-ordination, weakness and posterior paralysis (Telford, E. A. R.
et al., Virology 189,304-316, 1992). Other EHV's include EHV-2, or equine
cytomegalovirus, EHV-3, equine coital exanthema virus, and EHV-4, previously
classified as EHV-1 subtype 2.
Sheep and goats can be infected by a variety of dangerous microorganisms
including visna-maedi.
Primates such as monkeys, apes and macaques can be infected by simian
immunodeficiency virus. Inactivated cell-virus and cell-free whole simian
immunodeficiency vaccines have been reported to afford protection in macaques (Stott et
al. (1990) Lancet 36:1538-1541; Desrosiers et al. PNAS USA (1989) 86:6353-6357;
Murphey-Corb et al. (1989) Science 246:1293-1297; and Carlson et al. (1990) AIDS
Res. Human Retroviruses 6:1239-1246). A recombinant HIV gpl20 vaccine has been

reported to afford protection in chimpanzees (Berman et al. (1990) Nature
345:622-625).
Cats, both domestic and wild, are susceptible to infection with a variety of
microorganisms. For instance, feline infectious peritonitis is a disease which occurs in
both domestic and wild cats, such as lions, leopards, cheetahs, and jaguars. When it is
desirable to prevent infection with this and other types of pathogenic organisms in cats,
the methods of the invention can be used to vaccinate cats to protect them against
infection.
Domestic cats may become infected with several retroviruses, including but not
limited to feline leukemia virus (FeLV), feline sarcoma virus (FeSV), endogenous type
Concornavirus (RD-114), and feline syncytia-forming virus (FeSFV). Of these, FeLV is
the most significant pathogen, causing diverse symptoms, including lymphoreticular and
myeloid neoplasms, anemias, immune mediated disorders, and an immunodeficiency
syndrome which is similar to human acquired immune deficiency syndrome (AIDS).
Recently, a particular replication-defective FeLV mutant, designated FeLV-AIDS, has
been more particularly associated with immunosuppressive properties.
The discovery of feline T-lymphotropic lentivirus (also referred to as feline
immunodeficiency) was first reported in Pedersen et al. (1987) Science 235:790-793.
Characteristics of FIV have been reported in Yamamoto et al. (1988) Leukemia,
December Supplement 2:204S-215S; Yamamoto et al. (1988) Am. J. Vet. Res.
49:1246-1258; and Ackley et al. (1990) J. Virol. 64:5652-5655. Cloning and sequence
analysis of FIV have been reported in Olmsted et al. (1989) Proc. Natl. Acad. Sci. USA
86:2448-2452 and 86:4355-4360.
Feline infectious peritonitis (FIP) is a sporadic disease occurring unpredictably in
domestic and wild Felidae. While FIP is primarily a disease of domestic cats, it has been
diagnosed in lions, mountain lions, leopards, cheetahs, and the jaguar. Smaller wild cats
that have been afflicted with FIP include the lynx and caracal, sand cat, and pallas cat.
In domestic cats, the disease occurs predominantly in young animals, although cats of all
ages are susceptible. A peak incidence occurs between 6 and 12 months of age. A
decline in incidence is noted from 5 to 13 years of age, followed by an increased
incidence in cats 14 to 15 years old.

Viral, bacterial, and parasitic diseases in fin-fish, shellfish or other aquatic life
forms pose a serious problem for the aquaculture industry. Owing to the high density of
animals in the hatchery tanks or enclosed marine farming areas, infectious diseases may
eradicate a large proportion of the stock in, for example, a fin-fish, shellfish, or other
aquatic life forms facility. Prevention of disease is a more desired remedy to these
threats to fish than intervention once the disease is in progress. Vaccination of fish is the
only preventative method which may offer long-term protection through immunity.
Nucleic acid based vaccinations are described in US Patent No. 5,780,448 issued to
Davis.
The fish immune system has many features similar to the mammalian immune
system, such as the presence of B cells, T cells, lymphokines, complement, and
immunoglobulins. Fish have lymphocyte subclasses with roles that appear similar in
many respects to those of the B and T cells of mammals. Vaccines can be administered
by immersion or orally.
Aquaculture species include but are not limited to fin-fish, shellfish, and other
aquatic animals. Fin-fish include all vertebrate fish, which may be bony or cartilaginous
fish, such as, for example, salmonids, carp, catfish, yellowtail, seabream, and seabass.
Salmonids are a family of fin-fish which include trout (including rainbow trout), salmon,
and Arctic char. Examples of shellfish include, but are not limited to, clams, lobster,
shrimp, crab, and oysters. Other cultured aquatic animals include, but are not limited to
eels, squid, and octopi.
Polypeptides of viral aquaculture pathogens include but are not limited to
glycoprotein (G) or nucleoprotein (N) of viral hemorrhagic septicemia virus (VHSV); G
or N proteins of infectious hematopoietic necrosis virus (IHNV); VP1, VP2, VP3 or N
structural proteins of infectious pancreatic necrosis virus (IPNV); G protein of spring
viremia of carp (SVC); and a membrane-associated protein, tegumin or capsid protein or
glycoprotein of channel catfish virus (CCV).
Typical parasites infecting horses are Gasterophilus spp.; Eimeria huckarti,
Giardia spp.; Tritrichomonas equi; Babesia spp. (RBC's), Theileria equi; Trypanosoma
spp.; Klossiella equi; Sarcocystis spp.

Typical parasites infecting swine include Eimeria bebliecki, Eimeria scabra,
Isospora suis, Giardia spp.; Balantidium coli, Entamoeba histolytica; Toxoplasma gondii
and Sarcocystis spp., and Trichinella spiralis.
The major parasites of dairy and beef cattle include Eimeria spp.,
Cryptosporidium sp., Giardia spp.; Toxoplasma gondii', Babesia bovis (RBC), Babesia
bigemina (RBC), Trypanosoma spp. (plasma), Theileria spp. (RBC); Theileriaparva
(lymphocytes); Tritrichomonas foetus; and Sarcocystis spp.
The major parasites of raptors include Trichomonas gallinae; Coccidia (Eimeria
spp.); Plasmodium relictum, Leucocytozoon danilewskyi (owls), Haemoproteus spp.,
Trypanosoma spp.; Histomonas; Cryptosporidium meleagridis, Cryptosporidium
baileyi, Giardia, Eimeria; Toxoplasma.
Typical parasites infecting sheep and goats include Eimeria spp.,
Cryptosporidium sp., Giardia sp.; Toxoplasma gondii; Babesia spp. (RBC),
Trypanosoma spp. (plasma), Theileria spp. (RBC); and Sarcocystis spp.
Typical parasitic infections in poultry include coccidiosis caused by Eimeria
acervulina, E. necatrix, E. tenella, Isospora spp. and Eimeria truncata; histomoniasis,
caused by Histomonas meleagridis and Histomonas gallinarum; trichomoniasis caused
by Trichomonas gallinae; and hexamitiasis caused by Hexamita meleagridis. Poultry
can also be infected Emeria maxima, Emeria meleagridis, Eimeria adenoeides, Eimeria
meleagrimitis, Cryptosporidium, Eimeria brunetti, Emeria adenoeides, Leucocytozoon
spp., Plasmodium spp., Hemoproteus meleagridis, Toxoplasma gondii and Sarcocystis.
The methods of the invention can also be applied to the treatment and/or
prevention of parasitic infection in dogs, cats, birds, fish and ferrets. Typical parasites of
birds include Trichomonas gallinae; Eimeria spp., Isospora spp., Giardia;
Cryptosporidium; Sarcocystis spp., Toxoplasma gondii,
Haemoproteus/Parahaemoproteus, Plasmodium spp., Leucocytozoon/Akiba,
Atoxoplasma, Trypanosoma spp. Typical parasites infecting dogs include Trichinella
spiralis; Isopora spp., Sarcocystis spp., Cryptosporidium spp., Hammondia spp., Giardia
duodenalis (canis); Balantidium coli, Entamoeba histolytica; Hepatozoon canis;
Toxoplasma gondii, Trypanosoma cruzi; Babesia canis; Leishmania amastigotes;
Neospora caninum.

Typical parasites infecting feline species include Isospora spp., Toxoplasma
gondii, Sarcocystis spp., Hammondia hammondi, Besnoitia spp., Giardia spp.;
Entamoeba histolytica; Hepatozoon canis, Cytauxzoon sp., Cytauxzoon sp., Cytauxzoon
sp. (red cells, RE cells).
Typical parasites infecting fish include Hexamita spp., Eimeria spp.; Cryptobia
spp., Nosema spp., Myxosoma spp., Chilodonella spp., Trichodina spp.; Plistophora
spp., Myxosoma Henneguya; Costia spp., Ichthyophithirius spp., and Oodinium spp.
Typical parasites of wild mammals include Giardia spp. (carnivores, herbivores),
Isospora spp. (carnivores), Eimeria spp. (carnivores, herbivores); Theileria spp.
(herbivores), Babesia spp. (carnivores, herbivores), Trypanosoma spp. (carnivores,
herbivores); Schistosoma spp. (herbivores); Fasciola hepatica (herbivores),
Fascioloides magna (herbivores), Fasciola gigantica (herbivores), Trichinella spiralis
(carnivores, herbivores).
Parasitic infections in zoos can also pose serious problems. Typical parasites of
the bovidae family (blesbok, antelope, banteng, eland, gaur, impala, klipspringer, kudu,
gazelle) include Eimeria spp. Typical parasites in the pinnipedae family (seal, sea lion)
include Eimeria phocae. Typical parasites in the camelidae family (camels, llamas)
include Eimeria spp. Typical parasites of the giraffidae family (giraffes) include Eimeria
spp. Typical parasites in the elephantidae family (African and Asian) include Fasciola
spp. Typical parasites of lower primates (chimpanzees, orangutans, apes, baboons,
macaques, monkeys) include Giardia sp.; Balantidium coli, Entamoeba histolytica,
Sarcocystis spp., Toxoplasma gondii; Plasmodim spp. (RBC), Babesia spp. (RBC),
Trypanosoma spp. (plasma), Leishmania spp. (macrophages).
Polypeptides of bacterial pathogens include but are not limited to an
iron-regulated outer membrane protein, (IROMP), an outer membrane protein (OMP),
and an A-protein of Aeromonis salmonicida which causes furunculosis, p57 protein of
Renibacterium salmoninarum which causes bacterial kidney disease (BKD), major
surface associated antigen (msa), a surface expressed cytotoxin (mpr), a surface
expressed hemolysin (ish), and a flagellar antigen of Yersiniosis; an extracellular protein
(ECP), an iron-regulated outer membrane protein (IROMP), and a structural protein of
Pasteurellosis; an OMP and a flagellar protein of Vibrosis anguillarum and V. ordalii; a
flagellar protein, an OMP protein, aroA, and purA of Edwardsiellosis ictaluri and E.

tarda; and surface antigen of Ichthyophthirius; and a structural and regulatory protein of
Cytophaga columnari; and a structural and regulatory protein of Rickettsia.
Polypeptides of a parasitic pathogen include but are not limited to the surface
antigens of Ichthyophthirius.
An allergen refers to a substance (antigen) that can induce an allergic or
asthmatic response in a susceptible subject. The list of allergens is enormous and can
include pollens, insect venoms, animal dander dust, fungal spores and drugs (e.g.
penicillin). Examples of natural, animal and plant allergens include but are not limited to
proteins specific to the following genuses: Canine (Canis familiaris); Dermatophagoides
(e.g. Dermatophagoides farinae); Felis (Felis domesticus); Ambrosia {Ambrosia
artemiisfolia; Lolium (e.g. Lolium perenne or Lolium multiflorum); Cryptomeria
(Cryptomeriajaponica); Alternaria {Alternaria alternata); Alder; Alnus (Alnus
gultinoasa); Betula {Betula verrucosa); Quercus (Quercus alba); Olea (Olea europa);
Artemisia (Artemisia vulgaris); Plantago (e.g. Plantago lanceolata); Parietaria (e.g.
Parietaria officinalis or Parietaria judaica); Blattella (e.g. Blattella germanica); Apis
(e.g. Apis multiflorum); Cupressus (e.g. Cupressus sempervirens, Cupressus arizonica
and Cupressus macrocarpd); Juniperus (e.g. Juniperus sabinoides, Juniperus virginiana,
Juniperus communis and Juniperus ashei); Thuya (e.g. Thuya orientalis);
Chamaecyparis (e.g. Chamaecyparis obtusa); Periplaneta (e.g. Periplaneta americana);
Agropyron (e.g. Agropyron repens); Secale (e.g. Secale cereale); Triticum (e.g. Triticum
aestivum); Dactylis (e.g. Dactylis glomerata); Festuca (e.g. Festuca elatior); Poa (e.g.
Poapratensis or Poa compressd); Avena (e.g. Avena sativa); Holcus (e.g. Holcus
lanatus); Anthoxanthum (e.g. Anthoxanthum odoratum); Arrhenatherum (e.g.
Arrhenatherum elatius); Agrostis (e.g. Agrostis alba); Phleum (e.g. Phleum pratense);
Phalaris (e.g. Phalaris arundinacea); Paspalum (e.g. Paspalum notatum); Sorghum (e.g.
Sorghum halepensis); and Bromus (e.g. Bromus inermis).
The antigen may be an antigen that is encoded by a nucleic acid vector or it may
be not encoded in a nucleic acid vector. In the former case the nucleic acid vector is
administered to the subject and the antigen is expressed in vivo. In the latter case the
antigen may be administered directly to the subject. An antigen not encoded in a nucleic
acid vector as used herein refers to any type of antigen that is not a nucleic acid. For
instance, in some aspects of the invention the antigen not encoded in a nucleic acid

vector is a polypeptide. Minor modifications of the primary amino acid sequences of
polypeptide antigens may also result in a polypeptide which has substantially equivalent
antigenic activity as compared to the unmodified counterpart polypeptide. Such
modifications may be deliberate, as by site-directed mutagenesis, or may be spontaneous.
All of the polypeptides produced by these modifications are included herein as long as
antigenicity still exists. The polypeptide may be, for example, a viral polypeptide.
The term substantially purified as used herein refers to a polypeptide which is
substantially free of other proteins, lipids, carbohydrates or other materials with which it
is naturally associated. One skilled in the art can purify viral or bacterial polypeptides
using standard techniques for protein purification. The substantially pure polypeptide
will often yield a single major band on a non-reducing polyacrylamide gel. In the case of
partially glycosylated polypeptides or those that have several start codons, there may be
several bands on a non-reducing polyacrylamide gel, but these will form a distinctive
pattern for that polypeptide. The purity of the viral or bacterial polypeptide can also be
determined by ammo-terminal amino acid sequence analysis. Other types of antigens not
encoded by a nucleic acid vector such as polysaccharides, small molecule, mimics etc are
described above, and included within the invention.
The invention also utilizes polynucleotides encoding the antigenic polypeptides.
It is envisioned that the antigen may be delivered to the subject in a nucleic acid
molecule which encodes for the antigen such that the antigen must be expressed in vivo.
Such antigens delivered to the subject in a nucleic acid vector are referred to as antigens
encoded by a nucleic acid vector. The nucleic acid encoding the antigen is operatively
linked to a gene expression sequence which directs the expression of the antigen nucleic
acid within a eukaryotic cell. The gene expression sequence is any regulatory nucleotide
sequence, such as a promoter sequence or promoter-enhancer combination, which
facilitates the efficient transcription and translation of the antigen nucleic acid to which it
is operatively linked. The gene expression sequence may, for example, be a mammalian
or viral promoter, such as a constitutive or inducible promoter. Constitutive mammalian
promoters include, but are not limited to, the promoters for the following genes:
hypoxanthine phosphoribosyl transferase (HPTR), adenosine deaminase, pyruvate
kinase, b-actin promoter and other constitutive promoters. Exemplary viral promoters
which function constitutively in eukaryotic cells include, for example, promoters from

the cytomegalovjrus (CMV), simian virus (e.g., SV40), papilloma virus, adenovirus,
human immunodeficiency virus (HIV), Rous sarcoma virus, cytomegalovirus, the long
terminal repeats (LTR) of Moloney leukemia virus and other retroviruses, and the
thymidine kinase promoter of herpes simplex virus. Other constitutive promoters are
known to those of ordinary skill in the art. The promoters useful as gene expression
sequences of the invention also include inducible promoters. Inducible promoters are
expressed in the presence of an inducing agent. For example, the metallothionein
promoter is induced to promote transcription and translation in the presence of certain
metal ions. Other inducible promoters are known to those of ordinary skill in the art.
In general, the gene expression sequence shall include, as necessary, 5'
non-transcribing and 5' non-translating sequences involved with the initiation of
transcription and translation, respectively, such as a TATA box, capping sequence,
CAAT sequence, and the like. Especially, such 5' non-transcribing sequences will
include a promoter region which includes a promoter sequence for transcriptional control
; of the operably joined antigen nucleic acid. The gene expression sequences optionally
include enhancer sequences or upstream activator sequences as desired.
The antigen nucleic acid is operatively linked to the gene expression sequence.
As used herein, the antigen nucleic acid sequence and the gene expression sequence are
said to be operably linked when they are covalently linked in such a way as to place the
expression or transcription and/or translation of the antigen coding sequence under the
influence or control of the gene expression sequence. Two DNA sequences are said to
be operably linked if induction of a promoter in the 5' gene expression sequence results
in the transcription of the antigen sequence and if the nature of the linkage between the
two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2)
interfere with the ability of the promoter region to direct the transcription of the antigen
sequence, or (3) interfere with the ability of the corresponding RNA transcript to be
translated into a protein. Thus, a gene expression sequence would be operably linked to
an antigen nucleic acid sequence if the gene expression sequence were capable of
effecting transcription of that antigen nucleic acid sequence such that the resulting
transcript is translated into the desired protein or polypeptide.
The antigen nucleic acid of the invention may be delivered to the immune system
alone or in association with a vector. In its broadest sense, a vector is any vehicle

capable of facilitating the transfer of the antigen nucleic acid to the cells of the immune
system so that the antigen can be expressed and presented on the surface of the immune
cell. The vector generally transports the nucleic acid to the immune cells with reduced
degradation relative to the extent of degradation that would result in the absence of the
vector. The vector optionally includes the above-described gene expression sequence to
enhance expression of the antigen nucleic acid in immune cells. In general, the vectors
useful in the invention include, but are not limited to, plasmids, phagemids, viruses,
other vehicles derived from viral or bacterial sources that have been manipulated by the
insertion or incorporation of the antigen nucleic acid sequences. Viral vectors are a
preferred type of vector and include, but are not limited to, nucleic acid sequences from
the following viruses: retrovirus, such as Moloney murine leukemia virus, Harvey
murine sarcoma virus, murine mammary tumor virus, and Rous sarcoma virus;
adenovirus, adeno-associated virus; SV40-type viruses; polyoma viruses; Epstein-Barr
viruses; papilloma viruses; herpes virus; vaccinia virus; polio virus; and RNA virus such
as a retrovirus. One can readily employ other vectors not named but known in the art.
Preferred viral vectors are based on non-cytopathic eukaryotic viruses in which
non-essential genes have been replaced with the gene of interest. Non-cytopathic viruses
include retroviruses, the life cycle of which involves reverse transcription of genomic
viral RNA into DNA with subsequent proviral integration into host cellular DNA.
Retroviruses have been approved for human gene therapy trials. Most useful are those
retroviruses that are replication-deficient (i.e., capable of directing synthesis of the
desired proteins, but incapable of manufacturing an infectious particle). Such genetically
altered retroviral expression vectors have general utility for the high-efficiency
transduction of genes in vivo. Standard protocols for producing replication-deficient
retroviruses (including the steps of incorporation of exogenous genetic material into a
plasmid, transfection of a packaging cell lined with plasmid, production of recombinant
retroviruses by the packaging cell line, collection of viral particles from tissue culture
media, and infection of the target cells with viral particles) are provided in Kriegler, M.,
Gene Transfer and Expression, A Laboratory Manual W.H. Freeman CO., New York
(1990) and Murry, E.J. Methods in Molecular Biology, vol. 7, Humana Press, Inc.,
Cliffton, New Jersey (1991).

A preferred virus for certain applications is the adeno-associated virus, a
double-stranded DNA virus. The adeno-associated virus can be engineered to be
replication -deficient and is capable of infecting a wide range of cell types and species.
It further has advantages such as, heat and lipid solvent stability; high transduction
frequencies in cells of diverse lineages, including hemopoietic cells; and lack of
superinfection inhibition thus allowing multiple series of transductions. Reportedly, the
adeno-associated virus can integrate into human cellular DNA in a site-specific manner,
thereby minimizing the possibility of insertional mutagenesis and variability of inserted
gene expression characteristic of retroviral infection. In addition, wild-type
adeno-associated virus infections have been followed in tissue culture for greater than
100 passages in the absence of selective pressure, implying that the adeno-associated
virus genomic integration is a relatively stable event. The adeno-associated virus can
also function in an extrachromosomal fashion.
Other vectors include plasmid vectors. Plasmid vectors have been extensively
described in the art and are well-known to those of skill in the art. See e,g., Sambrook et
ah, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor
Laboratory Press, 1989. In the last few years, plasmid vectors have been found to be
particularly advantageous for delivering genes to cells in vivo because of their inability to
replicate within and integrate into a host genome. These plasmids, however, having a
promoter compatible with the host cell, can express a peptide from a gene operatively
encoded within the plasmid. Some commonly used plasmids include pBR322, pUC18,
pUC19, pRC/CMV, SV40, and pBlueScript. Other plasmids are well-known to those of
ordinary skill in the art. Additionally, plasmids may be custom designed using
restriction enzymes and ligation reactions to remove and add specific fragments of DNA.
It has recently been discovered that gene carrying plasmids can be delivered to
the immune system using bacteria. Modified forms of bacteria such as Salmonella can
be transfected with the plasmid and used as delivery vehicles. The bacterial delivery
vehicles can be administered to a host subject orally or by other administration means.
The bacteria deliver the plasmid to immune cells, e.g. B cells, dendritic cells, likely by
passing through the gut barrier. High levels of immune protection have been established
using this methodology. Such methods of delivery are useful for the aspects of the

invention utilizing systemic delivery of antigen, Immunostimulatory nucleic acid and/or
other therapeutic agent.
Thus, the immunostimulatory nucleic acids are useful as vaccine adjuvants. It
was previously established that CpG oligonucleotides are excellent vaccine adjuvants. It
was also demonstrated, however, that CpG ODN which are superb vaccine adjuvants in
mice are not the preferred adjuvants in non-rodent animals. In order to identify the best
immunostimulatory nucleic acids for use as a vaccine adjuvant in humans and other non-
rodent animals, in vivo screening of different nucleic acids for this purpose was
conducted. Several in vitro assays were evaluated in mice for their predictive value of
adjuvant activity in vivo in mice. During the course of this study, an in vitro test that is
predictive of in vivo efficacy was identified. It was discovered, rather surprisingly, that
both B cell and NK cell activation correlated particularly well with the ability of an
immunostimulatory nucleic acid to enhance an in vivo immune response against an
antigen.
The good predictive value of B cell activation for in vivo vaccine adjuvant
activity is most likely linked to the central role of B cells in the establishment of a
specific immune response. Polyclonal proliferation of B cells (induced by
immunostimulatory nucleic acids) increases the likelihood of an antigen specific B cell/T
helper cell match. Furthermore, enhanced expression of the co-stimulatory molecule
CD86 on polyclonally expanded B cells activates antigen specific T helper cells. B cells
also increase their CD40 expression in response to immunostimulatory nucleic acids
improving the capability of CD40L expressing activated T helper cells to stimulate B
cells. Increased ICAM-1 synthesis on B cells facilitates the cell to cell contact. Thus,
the activation status of polyclonal B cells plays a critical role during the initiation of a
specific antibody response.
The contribution of NK cell activity for the establishment of specific antibodies
was, however, surprising. NK cells are part of the innate immune system and as such are
involved in the first line of defense against pathogens. Most likely the cytokine pattern
produced by NK cells upon activation is closely related to the initiation of a specific
immune response. Thus, in one aspect the invention relates to a method of identifying an
adjuvant, by detecting NK cell activation. The NK cell activation assay may be carried
out as described in the Examples below or using other known NK cell activity assays. It

is preferred, however that a mixed cell population such as PBMC be used because of the
likelihood that NK cell activation is an indirect effect. The assay is preferably useful for
identifying immunostimulatory nucleic acids which are useful as adjuvants in human and
other non-rodent animals.
Cytokine induction was also identified as an important predictor of in vivo
adjuvant activity. As there is a 2 log higher endotoxin sensitivity of human than mouse
primary monocytes, some caution, however, is required to avoid endotoxin
contamination of immunostimulatory nucleic acids used for testing in the human system
(Hartmann G., and Krieg A. M. 1999. Gene Therapy 6:893). Since TNF-α, IL-6 and IL-
12 are produced by human monocytes in response to even low amounts of endotoxin,
their value for high throughput in vitro screening assays is limited. On the other hand,
human B cells and NK cells show only minor activation by endotoxin and thus are far
more useful in testing for immunostimulatory activity.
Stimulation of cellular function in either NK or B cells (i.e., lytic activity,
proliferation) requires a stronger immunostimulatory nucleic acid than the induction of
activation markers at their surface (CD69, CD86). For both cell types, the use of cell
surface activation markers showed a higher nonspecific background attributable to the
phosphorothioate backbone compared to the functional assays. This high sensitivity of
surface markers requires the use of low immunostimulatory nucleic acid concentrations
for optimal discrimination between immunostimulatory nucleic acid of similar activity.
Thus, the use of surface markers allows the comparison of immunostimulatory nucleic
acids with weak activity, while functional assays are preferred for comparing
immunostimulatory nucleic acids with high activity. It is of note that the optimal
immunostimulatory nucleic acid concentrations for stimulating B cells and NK cells
differ. While 0.6 ug/ml ODN is already maximal to stimulate B cells, optimal NK cell
activation may Tequire 6 ug/ml ODN. Both B cell activation and NK cell functional
activity were measured within freshly isolated PBMC. It was previously found that
highly purified human primary B cells are activated by CpG DNA. The existence of a
direct effect of CpG DNA on NK cells is less clear, and a secondary mechanism
mediated by another cell type within PBMC might contribute to CpG-induced functional
activity of NK cells.

The nucleic acids of the invention may be administered to a subject with an anti-
microbial agent. An anti-microbial agent, as used herein, refers to a naturally-occurring
or synthetic compound which is capable of killing or inhibiting infectious
microorganisms. The type of anti-microbial agent useful according to the invention will
depend upon the type of microorganism with which the subject is infected or at risk of
becoming infected. Anti-microbial agents include but are not limited to anti-bacterial
agents, anti-viral agents, anti-fungal agents and anti-parasitic agents. Phrases such as
"anti-infective agent", "anti-bacterial agent", "anti-viral agent", "anti-fungal agent",
"anti-parasitic agent" and "parasiticide" have well-established meanings to those of
ordinary skill in the art and are defined in standard medical texts. Briefly, anti-bacterial
agents kill or inhibit bacteria, and include antibiotics as well as other synthetic or natural
compounds having similar functions. Antibiotics are low molecular weight molecules
which are produced as secondary metabolites by cells, such as microorganisms. In
general, antibiotics interfere with one or more bacterial functions or structures which are
specific for the microorganism and which are not present in host cells. Anti-viral agents
can be isolated from natural sources or synthesized and are useful for killing or inhibiting
viruses. Anti-fungal agents are used to treat superficial fungal infections as well as
opportunistic and primary systemic fungal infections. Anti-parasite agents kill or inhibit
parasites.
Examples of anti-parasitic agents, also referred to as parasiticides useful for
human administration include but are not limited to albendazole, amphotericin B,
benznidazole, bithionol, chloroquine HC1, chloroquine phosphate, clindamycin,
dehydroemetine, diethylcarbamazine, diloxanide furoate, eflornithine, furazolidaone,
glucocorticoids, halofantrine, iodoquinol, ivermectin, mebendazole, mefloquine,
meglumine antimoniate, melarsoprol, metrifonate, metronidazole, niclosamide,
nifurtimox, oxamniquine, paromomycin, pentamidine isethionate, piperazine,
praziquantel, primaquine phosphate, proguanil, pyrantel pamoate, pyrimethanmine-
sulfonamides, pyrimethanmine-sulfadoxine, quinacrine HC1, quinine sulfate, quinidine
gluconate, spiramycin, stibogluconate sodium (sodium antimony gluconate), suramin,
tetracycline, doxycycline, thiabendazole, tinidazole, trimethroprim-sulfamethoxazole,
and tryparsamide some of which are used alone or in combination with others.

Parasiticides used in non-human subjects include piperazine,
diethylcarbamazine, thiabendazole, fenbendazole, albendazole, oxfendazole,
oxibendazole, febantel, levamisole, pyrantel tartrate, pyrantel pamoate, dichlorvos,
ivermectin, doramectic, milbemycin oxime, iprinomectin, moxidectin, N-butyl chloride,
toluene, hygromycin B thiacetarseniide sodium, melarsomine, praziquantel, epsiprantel,
benzimidazoles such as fenbendazole, albendazole, oxfendazole, clorsulon, albendazole,
amprolium; decoquinate, lasalocid, monensin sulfadimethoxine; sulfamethazine,
sulfaquinoxaline, metronidazole.
Parasiticides used in horses include mebendazole, oxfendazole, febantel,
pyrantel, dichlorvos, trichlorfon, ivermectin, piperazine; for S. wesleri: ivermectin,
benzimiddazoles such as thiabendazole, cambendazole, oxibendazole and fenbendazole.
Useful parasiticides in dogs include milbemycin oxine, ivermectin, pyrantel pamoate and
the combination of ivermectin and pyrantel. The treatment of parasites in swine can
include the use of levamisole, piperazine, pyrantel, thiabendazole, dichlorvos and
fenbendazole. In sheep and goats anthelmintic agents include levamisole or ivermectin.
Caparsolate has shown some efficacy in the treatment of D. immitis (heartworm) in cats.
Antibacterial agents kill or inhibit the growth or function of bacteria. A large
class of antibacterial agents is antibiotics. Antibiotics, which are effective for killing or
inhibiting a wide range of bacteria, are referred to as broad spectrum antibiotics. Other
types of antibiotics are predominantly effective against the bacteria of the class gram-
positive or gram-negative. These types of antibiotics are referred to as narrow spectrum
antibiotics. Other antibiotics which are effective against a single organism or disease
and not against other types of bacteria, are referred to as limited spectrum antibiotics.
Antibacterial agents are sometimes classified based on their primary mode of action. In
general, antibacterial agents are cell wall synthesis inhibitors, cell membrane inhibitors,
protein synthesis inhibitors, nucleic acid synthesis or functional inhibitors, and
competitive inhibitors.
Anti-bacterial agents useful in the invention include but are not limited to natural
penicillins, semi-synthetic penicillins, clavulanic acid, cephalolsporins, bacitracin,
ampicillin, carbenicillin, oxacillin, azlocillin, mezlocillin, piperacillin, methicillin,
dicloxacillin, nafcillin, cephalothin, cephapirin, cephalexin, cefamandole, cefaclor,
cefazolin, cefuroxine, cefoxitin, cefotaxime, cefsulodin, cefetamet, cefixime, ceftriaxone,

cefoperazone, ceftazidine, moxalactam, carbapenems, imipenems, monobactems,
euztreonam, vancomycin, polymyxin, amphotericin B, nystatin, imidazoles,
clotrimazole, miconazole, ketoconazole, itraconazole, fluconazole, rifampins,
ethambutol, tetracyclines, chloramphenicol, macrolides, aminoglycosides, streptomycin,
kanamycin, tobramycin, amikacin, gentamicin, tetracycline, minocycline, doxycycline,
chlortetracycline, erythromycin, roxithromycin, clarithromycin, oleandomycin,
azithromycin, chloramphenicol, quinolones, co-trimoxazole, norfloxacin, ciprofloxacin,
enoxacin, nalidixic acid, temafloxacin, sulfonamides, gantrisin, and trimethoprim;
Acedapsone ; Acetosulfone Sodium; Alamecin; Alexidine; Amdinocillin; Amdinocillin
Pivoxil; Amicycline; Amifloxacin; Amifloxacin Mesylate; Amikacin; Amikacin Sulfate;
Aminosalicylic acid; Aminosalicylate sodium; Amoxicillin; Amphomycin; Ampicillin;
Ampicillin Sodium; Apalcillin Sodium; Apramycin; Aspartocin; Astromicin Sulfate;
Avilamycin; Avoparcin; Azithromycin; Azlocillin; Azlocillin Sodium; Bacampicillin
Hydrochloride; Bacitracin; Bacitracin Methylene Disalicylate; Bacitracin Zinc;
Bambermycins; Benzoylpas Calcium; Berythromycin ; Betamicin Sulfate; Biapenem;
Biniramycin; Biphenamine Hydrochloride ; Bispyrithione Magsulfex ; Butikacin;
Butirosin Sulfate; Capreomycin Sulfate; Carbadox; Carbenicillin Disodium;
Carbenicillin Indanyl Sodium; Carbenicillin Phenyl Sodium; Carbenicillin Potassium;
Carumonam Sodium; Cefaclor; Cefadroxil; Cefamandole; Cefamandole Nafate;
Cefamandole Sodium; Cefaparole; Cefatrizine; Cefazaflur Sodium; Cefazolin; Cefazolin
Sodium; Cefbuperazone; Cefdinir; Cefepime; Cefepime Hydrochloride; Cefetecol;
Cefixime; Cefmenoxime Hydrochloride; Cefinetazole; Cefmetazole Sodium; Cefonicid
Monosodium; Cefonicid Sodium; Cefoperazone Sodium; Ceforanide; Cefotaxime
Sodium; Cefotetan; Cefotetan Disodium; Cefotiam Hydrochloride; Cefoxitin; Cefoxitin
Sodium; Cefpimizole; Cefpimizole Sodium; Cefpiramide; Cefpiramide Sodium;
Cefpirome Sulfate; Cefpodoxime Proxetil; Cefprozil; Cefroxadine; Cefsulodin Sodium;
Ceftazidime; Ceftibuten; Ceftizoxime Sodium; Ceftriaxone Sodium; Cefuroxime;
Cefuroxime Axetil; Cefuroxime Pivoxetil; Cefuroxime Sodium; Cephacetrile Sodium;
Cephalexin; Cephalexin Hydrochloride; Cephaloglycin; Cephaloridine; Cephalothin
Sodium; Cephapirin Sodium; Cephradine; Cetocycline Hydrochloride; Cetophenicol;
Chloramphenicol; Chloramphenicol Palmitate ; Chloramphenicol Pantothenate Complex
; Chloramphenicol Sodium Succinate; Chlorhexidine Phosphanilate; Chloroxylenol;

Chlortetracycline Bisulfate ; Chlortetracycline.Hydrochloride ; Cinoxacin;
Ciprofloxacin; Ciprofloxacin Hydrochloride; Cirolemycin; Clarithromycin;
Clinafloxacin Hydrochloride; Clindamycin; Clindamycin Hydrochloride; Clindamycin
Palmitate Hydrochloride; Clindamycin Phosphate; Clofazimine ; Cloxacillin Benzathine;
Cloxacillin Sodium; Cloxyquin; Colistimethate Sodium; Colistin Sulfate; Coumermycin;
Coumermycin Sodium; Cyclacillin; Cycloserine; Dalfopristin; Dapsone ; Daptomycin;
Demeclocycline; Demeclocycline Hydrochloride; Demecycline; Denofungin;
Diaveridine; Dicloxacillin; Dicloxacillin Sodium; Dihydrostreptomycin Sulfate;
Dipyrithione; Dirithromycin; Doxycycline; Doxycycline Calcium ; Doxycycline
Fosfatex; Doxycycline Hyclate; Droxacin Sodium; Enoxacin; Epicillin; Epitetracycline
Hydrochloride; Erythromycin; Erythromycin Acistrate; Erythromycin Estolate;
Erythromycin Ethylsuccinate; Erythromycin Gluceptate; Erythromycin Lactobionate;
Erythromycin Propionate; Erythromycin Stearate; Ethambutol Hydrochloride;
Ethionamide; Fleroxacin; Floxacillin; Fludalanine; Flumequine; Fosfomycin;
Fosfomycin Tromethamine; Fumoxicillin; Furazolium Chloride; Furazolium Tartrate;
Fusidate Sodium; Fusidic Acid; Gentamicin Sulfate; Gloximonam; Gramicidin;
Haloprogin; Hetacillin; Hetacillin Potassium; Hexedine; Ibafloxacin; Imipenem;
Isoconazole; Isepamicin; Isoniazid; Josamycin; Kanamycin Sulfate; Kitasamycin;
Levofuraltadone; Levopropylcillin Potassium; Lexithromycin; Lincomycin; Lincomycin
Hydrochloride; Lomefloxacin; Lomefloxacin Hydrochloride; Lomefloxacin Mesylate;
Loracarbef; Mafenide; Meclocycline; Meclocycline Sulfosalicylate; Megalomicin
Potassium Phosphate; Mequidox; Meropenem; Methacycline; Methacycline
Hydrochloride; Methenamine; Methenamine Hippurate; Methenamine Mandelate;
Methicillin Sodium; Metioprim; Metronidazole Hydrochloride; Metronidazole
Phosphate; Mezlocillin; Mezlocillin Sodium; Minocycline; Miriocycllne Hydrochloride;
Mirincamycin Hydrochloride ; Monensin ; Monensin Sodium ; Nafcillin Sodium;
Nalidixate Sodium; Nalidixic Acid; Natamycin; Nebramycin; Neomycin Palmitate;
Neomycin Sulfate; Neomycin Undecylenate ; Netilmicin Sulfate; Neutramycin;
Nifuradene; Nifuraldezone; Nifuratel; Nifuratrone; Nifurdazil; Nifurimide; Nifurpirinol;
Nifurquinazol; Nifurthiazole; Nitrocycline; Nitrofurantoin; Nitromide; Norfloxacin;
Novobiocin Sodium; Ofloxacin; Ormetoprim; Oxacillin Sodium; Oximonam; Oximonam
Sodium; Oxolinic Acid; Oxytetracycline; Oxytetracycline Calcium; Oxytetracycline

Hydrochloride; Paldimycin; Parachlorophenol; Paulomycin; Pefloxacin; Pefloxacin
Mesylate; Penamecillin; Penicillin G Benzathine; Penicillin G Potassium; Penicillin G
Procaine; Penicillin G Sodium; Penicillin V; Penicillin V Benzathine; Penicillin V
Hydrabamine; Penicillin V Potassium; Pentizidone Sodium; Phenyl Aminosalicylate;
Piperacillin Sodium; Pirbenicillin Sodium; Piridicillin Sodium; Pirlimycin
Hydrochloride; Pivampicillin Hydrochloride; Pivampicillin Pamoate; Pivampicillin
Probenate; Polymyxin B Sulfate; Porfiromycin ; Propikacin; Pyrazinamide; Pyrithione
Zinc; Quindecamine Acetate; Quinupristin; Racephenicol; Ramoplanin; Ranimycin;
Relomycin; Repromicin; Rifabutin; Rifametane; Rifamexil; Rifamide; Rifampin;
Rifapentine; Rifaximin; Rolitetracycline; Rolitetracycline Nitrate; Rosaramicin;
Rosaramicin Butyrate; Rosaramicin Propionate; Rosaramicin Sodium Phosphate;
Rosaramicin Stearate; Rosoxacin; Roxarsone; Roxithromycin; Sancycline; Sanfetrinem
Sodium; Sarmoxicillin; Sarpicillin; Scopafungin; Sisomicin; Sisomicin Sulfate;
Sparfloxacin; Spectinomycin Hydrochloride; Spiramycin; Stallimycin Hydrochloride;
Steffimycin; Streptomycin Sulfate; Streptonicozid; Sulfabenz; Sulfabenzamide;
Sulfacetamide; Sulfacetamide Sodium; Sulfacytine; Sulfadiazine; Sulfadiazine Sodium;
Sulfadoxine; Sulfalene; Sulfamerazine; Sulfameter; Sulfamethazine; Sulfamethizole;
Sulfamethoxazole; Sulfamonomethoxine; Sulfamoxole; Sulfanilate Zinc; Sulfanitran ;
Sulfasalazine; Sulfasomizole; Sulfathiazole; Sulfazamet; Sulfisoxazole; Sulfisoxazole
Acetyl; Sulfisoxazole Diolamine; Sulfomyxin; Sulopenem; Sultamicillin; Suncillin
Sodium; Talampicillin Hydrochloride; Teicoplanin; Temafloxacin Hydrochloride;
Temocillin; Tetracycline; Tetracycline Hydrochloride; Tetracycline Phosphate Complex;
Tetroxoprim; Thiamphenicol; Thiphencillin Potassium; Ticarcillin Cresyl Sodium;
Ticarcillin Disodium; Ticarcillin Monosodium; Ticlatone; Tiodonium Chloride;
Tobramycin; Tobramycin Sulfate; Tosufloxacin; Trimethoprim; Trimethoprim Sulfate;
Trisulfapyrimidines; Troleandomycin; Trospectomycin Sulfate; Tyrothricin;
Vancomycin; Vancomycin Hydrochloride; Virginiamycin; and Zorbamycin.
Antiviral agents are compounds which prevent infection of cells by viruses or
replication of the virus within the cell. There are many fewer antiviral drugs than
antibacterial drugs because the process of viral replisation is so closely related to DNA
replication within the host cell, that non-specific antiviral agents would often be toxic to
the host. There are several stages within the process of viral infection which can be

blocked or inhibited by antiviral agents. These stages include, attachment of the virus to
the host cell (immunoglobulin or binding peptides), uncoating of the virus (e.g.
amantadine), synthesis or translation of viral mRNA (e.g. interferon), replication of viral
RNA or DNA (e.g. nucleoside analogues), maturation of new virus proteins (e.g.
protease inhibitors), and budding and release of the virus.
Nucleotide analogues are synthetic compounds which are similar to nucleotides,
but which have an incomplete or abnormal deoxyribose or ribose group. Once the
nucleotide analogues are in the cell, they are phosphorylated, producing the triphosphate
formed which competes with normal nucleotides for incorporation into the viral DNA or
RNA. Once the triphosphate form of the nucleotide analogue is incorporated into the
growing nucleic acid chain, it causes irreversible association with the viral polymerase
and thus chain termination. Nucleotide analogues include, but are not limited to,
acyclovir (used for the treatment of herpes simplex virus and varicella-zoster virus),
gancyclovir (useful for the treatment of cytomegalovirus), idoxuridine, ribavirin (useful
for the treatment of respiratory syncitial virus), dideoxyinosine, dideoxycytidine, and
zidovudine (azidothymidine).
The interferons are cytokines which are secreted by virus-infected cells as well as
immune cells. The interferons function by binding to specific receptors on cells adjacent
to the infected cells, causing the change in the cell which protects it from infection by the
virus, a and p-interferon also induce the expression of Class I and Class IIMHC
molecules on the surface of infected cells, resulting in increased antigen presentation for
host immune cell recognition, a and P-interferons are available as recombinant forms
and have been used for the treatment of chronic hepatitis B and C infection. At the
dosages which are effective for anti-viral therapy, interferons have severe side effects
such as fever, malaise and weight loss.
Immunoglobulin therapy is used for the prevention of viral infection.
Immunoglobulin therapy for viral infections is different than bacterial infections, because
rather than being antigen-specific, the immunoglobulin therapy functions by binding to
extracellular virions and preventing them from attaching to and entering cells which are
susceptible to the viral infection. The therapy is useful for the prevention of viral
infection for the period of time that the antibodies are present in the host. In general
there are two types of immunoglobulin therapies, normal immunoglobulin therapy and

hyper-immunoglobulin therapy. Normal immune globulin therapy utilizes a antibody
product which is prepared from the serum of normal blood donors and pooled. This
pooled product contains low titers of antibody to a wide range of human viruses, such as
hepatitis A, parvovirus, enterovirus (especially in neonates). Hyper-immune globulin
therapy utilizes antibodies which are prepared from the serum of individuals who have
high titers of an antibody to a particular virus. Those antibodies are then used against a
specific virus. Examples of hyper-immune globulins include zoster immune globulin
(useful for the prevention of varicella in immuno-compromised children and neonates),
human rabies immunoglobulin (useful in the post-exposure prophylaxis of a subject
bitten by a rabid animal), hepatitis B immune globulin (useful in the prevention of
hepatitis B virus, especially in a subject exposed to the virus), and RSV immune globulin
(useful in the treatment of respiratory syncitial virus infections).
Another type of immunoglobulin therapy is active immunization. This involves
the administration of antibodies or antibody fragments to viral surface proteins. Two
types of vaccines which are available for active immunization of hepatitis B include
serum-derived hepatitis B antibodies and recombinant hepatitis B antibodies. Both are
prepared from HBsAg. The antibodies are administered in three doses to subjects at high
risk of infection with hepatitis B virus, such as health care workers, sexual partners of
chronic carriers, and infants.
Thus, anti-viral agents useful in the invention include but are not limited to
immunoglobulins, amantadine, interferon, nucleoside analogues, and protease inhibitors.
Specific examples of anti-virals include but are not limited to Acemannan; Acyclovir;
Acyclovir Sodium; Adefovir; Alovudine; Alvircept Sudotox; Amantadine
Hydrochloride; Aranotin; Arildone; Atevirdine Mesylate; Avridine; Cidofovir;
Cipamfylline; Cytarabine Hydrochloride; Delavirdine Mesylate; Desciclovir;
Didanosine; Disoxaril; Edoxudine; Enviradene; Enviroxime; Famciclovir; Famotine
Hydrochloride; Fiacitabine; Fialuridine; Fosarilate; Foscarnet Sodium; Fosfonet Sodium;
Ganciclovir; Ganciclovir Sodium; Idoxuridine; Kethoxal; Lamivudine; Lobucavir;
Memotine Hydrochloride; Methisazone; Nevirapine; Penciclovir; Pirodavir; Ribavirin;
Rimantadine Hydrochloride; Saquinavir Mesylate; Somantadine Hydrochloride;
Sorivudine; Statolon; Stavudine; Tilorone Hydrochloride; Trifluridine; Valacyclovir

Hydrochloride; Vidarabine; Vidarabine Phosphate; Vidarabine Sodium Phosphate;
Viroxime; Zalcitabine; Zidovudine; and Zinviroxime.
Anti-fungal agents are useful for the treatment and prevention of infective fungi.
Anti-fungal agents are sometimes classified by their mechanism of action. Some anti-
fungal agents function as cell wall inhibitors by inhibiting glucose synthase. These
include, but are not limited to, basiungin/ECB. Other anti-fungal agents function by
destabilizing membrane integrity. These include, but are not limited to, immidazoles,
such as clotrimazole, sertaconzole, fiuconazole, itraconazole, ketoconazole, miconazole,
and voriconacole, as well as FK 463, amphotericin B, BAY 38-9502, MK 991,
pradimicin, UK 292, butenafine, and terbinafine. Other anti-fungal agents function by
breaking down chitin (e.g. chitinase) or immunosuppression (501 cream). Some
examples of commercially-available agents are shown in Table B


Carbol-Fuchsin; Chlordantoin; Ciclopirox; Ciclopirox Olamine; Cilofiingin;
Cisconazole; Clotrimazole; Cuprimyxin; Denofungin ; Dipyrithione; Doconazole;
Econazole; Econazole Nitrate; Enilconazole; Ethonam Nitrate; Fenticonazole Nitrate;
Filipin; Fluconazole; Flucytosine; Fungimycin; Griseofulvin; Hamycin; Isoconazole ;
Itraconazole; Kalafungin; Ketoconazole; Lomofungin; Lydimycin; Mepartricin ;
Miconazole; Miconazole Nitrate; Monensin; Monensin Sodium; Naftifine
Hydrochloride; Neomycin Undecylenate; Nifuratel; Nifurmerone; Nitralamine
Hydrochloride; Nystatin; Octanoic Acid; Orconazole Nitrate; Oxiconazole Nitrate;
Oxifungin Hydrochloride; Parconazole Hydrochloride; Partricin ; Potassium Iodide ;
Proclonol; Pyrithione Zinc ; Pyrrolnitrin; Rutamycin; Sanguinarium Chloride ;
Saperconazole; Scopafungin ; Selenium Sulfide ; Sinefungin; Sulconazole Nitrate;
Terbinafine; Terconazole; Thiram; Ticlatone ; Tioconazole; Tolciclate; Tolindate;
Tolnaftate; Triacetin; Triafungin; Undecylenic Acid; Viridofulvin; Zinc Undecylenate;
and Zinoconazole Hydrochloride.
Immunostimulatory nucleic acids can be combined with other therapeutic agents
such as adjuvants to enhance immune responses. The immunostimulatory nucleic acid
and other therapeutic agent may be administered simultaneously or sequentially. When
the other therapeutic agents are administered simultaneously they can be administered in
the same or separate formulations, but are administered at the same time. The other
therapeutic agents are administered sequentially with one another and with
immunostimulatory nucleic acid, when the administration of the other therapeutic agents
and the immunostimulatory nucleic acid is temporally separated. The separation in time
between the administration of these compounds may be a matter of minutes or it may be
longer. Other therapeutic agents include but are not limited to adjuvants, cytokines,
antibodies, antigens, etc.
The immunostimulatory nucleic acids are useful as adjuvants for inducing a
systemic immune response. Thus either can be delivered to a subject exposed to an
antigen to produce an enhanced immune response to the antigen.
In addition to the immunostimulatory nucleic acids, the compositions of the
invention may also be administered with non-nucleic acid adjuvants. A non-nucleic acid
adjuvant is any molecule or compound except for the immunostimulatory nucleic acids
described herein which can stimulate the humoral and/or cellular immune response.

Non-nucleic acid adjuvants include, for instance, adjuvants that create a depo effect,
immune stimulating adjuvants, and adjuvants that create a depo effect and stimulate the
immune system.
An adjuvant that creates a depo effect as used herein is an adjuvant that causes
the antigen to be slowly released in the body, thus prolonging the exposure of immune
cells to the antigen. This class of adjuvants includes but is not limited to alum (e.g.,
aluminum hydroxide, aluminum phosphate); or emulsion-based formulations including
mineral oil, non-mineral oil, water-in-oil or oil-in-water-in oil emulsion, oil-in-water
emulsions such as Seppic ISA series of Montanide adjuvants (e.g., Montanide ISA 720,
AirLiquide, Paris, France); MF-59 (a squalene-in-water emulsion stabilized with Span 85
and Tween 80; Chiron Corporation, Emeryville, CA; and PRO VAX (an oil-in-water
emulsion containing a stabilizing detergent and a micelle-forming agent; IDEC,
Pharmaceuticals Corporation, San Diego, CA).
An immune stimulating adjuvant is an adjuvant that causes activation of a cell of
the immune system. It may, for instance, cause an immune cell to produce and secrete
cytokines. This class of adjuvants includes but is not limited to saponins purified from
the bark of the Q. saponaria tree, such as QS21 (a glycolipid that elutes in the 21st peak
with HPLC fractionation; Aquila Biopharmaceuticals, Inc., Worcester, MA);
poly[di(carboxylatophenoxy)phosphazene (PCPP polymer; Virus Research Institute,
USA); derivatives of lipopolysaccharides such as monophosphoryl lipid A (MPL; Ribi
ImmunoChem Research, Inc., Hamilton, MT), muramyl dipeptide (MDP; Ribi) and
threonyl-muramyl dipeptide (t-MDP; Ribi); OM-174 (a glucosamine disaccharide related
to lipid A; OM Pharma SA, Meyrin, Switzerland); and Leishmania elongation factor (a
purified Leishmania protein; Corixa Corporation, Seattle, WA).
Adjuvants that create a depo effect and stimulate the immune system are those
compounds which have both of the above- identified functions. This class of adjuvants
includes but is not limited to ISCOMS (Immunostimulating complexes which contain
mixed saponins, lipids and form virus-sized particles with pores that can hold antigen;
CSL, Melbourne, Australia); SB-AS2 (SmithKline Beecham adjuvant system #2 which
is an oil-in-water emulsion containing MPL and QS21: SmithKline Beecham Biologicals
[SBB], Rixensart, Belgium); SB-AS4 (SmithKline Beecham adjuvant system #4 which
contains alum and MPL; SBB, Belgium); non-ionic block copolymers that form micelles

such as CRL 1005 (these contain a linear chain of hydrophobic polyoxpropylene flanked
by chains of polyoxyethylene; Vaxcel, Inc., Norcross, GA); and Syntex Adjuvant
Formulation (SAF, an oil-in-water emulsion containing Tween 80 and a nonionic block
copolymer; Syntex Chemicals, Inc., Boulder, CO).
The immunostimulatory nucleic acids are also useful as mucosal adjuvants. It
has previously been discovered that both systemic and mucosal immunity are induced by
mucosal delivery of CpG nucleic acids. The systemic immunity induced in response to
CpG nucleic acids included both humoral and cell-mediated responses to specific
antigens that were not capable of inducing systemic immunity when administered alone
to the mucosa. Furthermore, both CpG nucleic acids and cholera toxin (CT, a mucosal
adjuvant that induces a Th2-like response) induced CTL. This was surprising since with
systemic immunization, the presence of Th2-like antibodies is normally associated with a
lack of CTL (Schirmbeck et al, 1995). Based on the results presented herein it is
expected that the immunostimulatory nucleic acids will function in a similar manner.
Additionally, the immunostimulatory nucleic acids induce a mucosal response at
both local (e.g., lung) and remote (e.g., lower digestive tract) mucosal sites. Significant
levels of IgA antibodies are induced at distant mucosal sites by the immunostimulatory
nucleic acids. CT is generally considered to be a highly effective mucosal adjuvant. As
has been previously reported (Snider 1995), CT induces predominantly IgGl isotype of
antibodies, which are indicative of Th2-type response. In contrast, the
immunostimulatory nucleic acids are more Thl with predominantly IgG2a antibodies,
especially after boost or when the two adjuvants are combined. Thl-type antibodies in
general have better neutralizing capabilities, and furthermore, a Th2 response in the lung
is highly undesirable because it is associated with asthma (Kay, 1996, Hogg, 1997).
Thus the use of immunostimulatory nucleic acids as a mucosal adjuvant has benefits that
other mucosal adjuvants cannot achieve. The immunostimulatory nucleic acids of the
invention also are useful as mucosal adjuvants for induction of both a systemic and a
mucosal immune response.
Mucosal adjuvants referred to as non-nucleic acid mucosal adjuvants may also be
administered with the Immunostimulatory nucleic acids. A non-nucleic acid mucosal
adjuvant as used herein is an adjuvant other than a immunostimulatory nucleic acid that
is capable of inducing a mucosal immune response in a subject when administered to a

mucosal surface in conjunction with an antigen. Mucosal adjuvants include but are not
limited to Bacterial toxins e.g., Cholera toxin (CT), CT derivatives including but not
limited to CT B subunit (CTB) (Wu et al., 1998, Tochikubo et al., 1998); CTD53 (Val to
Asp) (Fontana et al., 1995); CTK97 (Val to Lys) (Fontana et al., 1995); CTK104 (Tyr to
Lys) (Fontana et al., 1995); CTD53/K63 (Val to Asp, Ser to Lys) (Fontana et al., 1995);
CTH54 (Arg to His) (Fontana et al., 1995); CTN107 (His to Asn) (Fontana et al., 1995);
CTE114 (Ser to Glu) (Fontana et al., 1995); CTE112K (Glu to Lys) (Yamamoto et al.,
1997a); CTS61F (Ser to Phe) (Yamamoto et al., 1997a, 1997b); CTS106 (Pro to Lys)
(Douce et al., 1997, Fontana et al., 1995); and CTK63 (Ser to Lys) (Douce et al., 1997,
Fontana et al., 1995), Zonula occludens toxin, zot, Escherichia coli heat-labile
enterotoxin, Labile Toxin (LT), LT derivatives including but not limited to LT B subunit
(LTB) (Verweij et al., 1998); LT7K (Arg to Lys) (Komase et al., 1998, Douce et al.,
1995); LT61F (Ser to Phe) (Komase et al., 1998); LT112K (Glu to Lys) (Komase et al.,
1998); LT118E (Gly to Glu) (Komase et al., 1998); LT146E (Arg to Glu) (Komase et al.,
1998); LT192G (Arg to Gly) (Komase et al., 1998); LTK63 (Ser to Lys) (Marchetti et
al., 1998, Douce et al., 1997,1998, Di Tommaso et al., 1996); and LTR72 (Ala to Arg)
(Giuliani et al., 1998), Pertussis toxin, PT. (Lycke et al., 1992", Spangler BD, 1992,
Freytag and Clemments, 1999, Roberts et al., 1995, Wilson et al., 1995) including PT-
9K/129G (Roberts et al., 1995, Cropley et al., 1995); Toxin derivatives (see below)
(Holmgren et al., 1993, Verweij et al., 1998, Rappuoli et al., 1995, Freytag and
Clements, 1999); Lipid A derivatives (e.g., monophosphoryl lipid A, MPL) (Sasaki et al.,
1998, Vancott et al., 1998; Muramyl Dipeptide (MDP) derivatives (Fukushima et al.,
1996, Ogawa et al., 1989, Michalek et al., 1983, Morisaki et al., 1983); Bacterial outer
membrane proteins (e.g., outer surface protein A (OspA) lipoprotein of Borrelia
burgdorferi, outer membrane protine of Neisseria meningitidis)(Mairinaio et al., 1999,
Van de Verg et al., 1996); Oil-in-water emulsions (e.g., MF59) (Barchfield et al., 1999,
Verschoor et al., 1999,0'Hagan, 1998); Aluminum salts (Isaka et al., 1998,1999); and
Saponins (e.g., QS21) Aquila Biopharmaceuticals, Inc., Worster, MA) (Sasaki et al.,
1998, MacNeal et al., 1998), ISCOMS, MF-59 (a squalene-in-water emulsion stabilized
with Span 85 and Tween 80; Chiron Corporation, Emeryville, CA); the Seppic ISA
series of Montanide adjuvants (e.g., Montanide ISA 720; AirLiquide, Paris, France);
PROVAX (an oil-in-water emulsion containing a stabilizing detergent and a micelle-

forming agent; IDEC Pharmaceuticals Corporation, San Diego, CA); Syntext Adjuvant
Formulation (SAP; Syntex Chemicals, Inc., Boulder, CO);
poly[di(carboxylatophenoxy)phosphazene (PCPP polymer; Virus Research Institute,
USA) and Leishmania elongation factor (Corixa Corporation, Seattle, WA)_
Immune responses can also be induced or augmented by the co-administration or
co-linear expression of cytokines (Bueler & Mulligan, 1996; Chow et al, 1997; Geissler
et al, 1997; Iwasaki et al, 1997; Kim et al, 1997) or B-7 co-stimulatory molecules
(Iwasaki et al, 1997; Tsuji et al, 1997) with the Immunostimulatory nucleic acids. The
cytokines can be administered directly with Immunostimulatory nucleic acids or may be
administered in the form of a nucleic acid vector that encodes the cytokine, such that the
cytokine can be expressed in vivo. In one embodiment, the cytokine is administered in
the form of a plasmid expression vector. The term cytokine is used as a generic name for
a diverse group of soluble proteins and peptides which act as humoral regulators at nano-
to picomolar concentrations and which, either under normal or pathological conditions,
modulate the functional activities of individual cells and tissues. These proteins also
mediate interactions between cells directly and regulate processes taking place in the
extracellular environment. Examples of cytokines include, but are not limited to IL-1,
IL-2, IL-4, IL-5, IL-6, IL-7, IL-10, IL-12, IL-15, IL-18, granulocyte-macrophage colony
stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), interferon-
γ (γ-IFN), IFN-α, tumor necrosis factor (TNF), TGF-p, FLT-3 ligand, and CD40 ligand.
Cytokines play a role in directing the T cell response. Helper (CD4+) T cells
orchestrate the immune response of mammals through production of soluble factors that
act on other immune system cells, including other T cells. Most mature CD4+ T helper
cells express one of two cytokine profiles: Thl or Th2. The Thl subset promotes
delayed-type hypersensitivity, cell-mediated immunity, and immunoglobulin class
switching to IgG2a. The Th2 subset induces humoral immunity by activating B cells,
promoting antibody production, and inducing class switching to IgG1 and IgE. In some
embodiments, it is preferred that the cytokine be a Thl cytokine.
The nucleic acids are also useful for redirecting an immune response from a Th2
immune response to a Thl immune response. Redirection of an immune response from a
Th2 to a Thl immune response can be assessed by measuring the levels of cytokines
produced in response to the nucleic acid (e.g., by inducing monocytic cells and other

cells to produce Thl cytokines, including IL-12, IFN-y and GM-CSF). The redirection
or rebalance of the immune response from a Th2 to a Thl response is particularly useful
for the treatment or prevention of asthma. For instance, an effective amount for treating
asthma can be that amount; useful for redirecting a Th2 type of immune response that is
associated with asthma to a Thl type of response. Th2 cytokines, especially IL-4 and IL-
5 are elevated in the airways of asthmatic subjects. These cytokines promote important
aspects of the asthmatic inflammatory response, including IgE isotype switching,
eosinophil chemotaxis and activation and mast cell growth. Thl cytokines, especially
IFN-y and IL-12, can suppress the formation of Th2 clones and production of Th2
cytokines. The immunostimulatory nucleic acids of the invention cause an increase in
Thl cytokines which helps to rebalance the immune system, preventing or reducing the
adverse effects associated with a predominately Th2 immune response.
The nucleic acids are also useful for improving survival, differentiation,
activation and maturation of dendritic cells. The immunostimulatory nucleic acids have
the unique capability to promote cell survival, differentiation, activation and maturation
of dendritic cells. Dendritic precursor cells isolated from blood by immunomagnetic cell
sorting develop morphologic and functional characteristics of dendritic cells during a two
day incubation with GM-CSF. Without GM-CSF these cells undergo apoptosis. The
immunostimulatory nucleic acids are superior to GM-CSF in promoting survival and
differentiation of dendritic cells (MHCII expression, cell size, granularity). The
immunostimulatory nucleic acids also induce maturation of dendritic cells. Since
dendritic cells form the link between the innate and the acquired immune system, by
presenting antigens as well as through their expression of pattern recognition receptors
which detect microbial molecules like LPS in their local environment, the ability to
activate dendritic cells with immunostimulatory nucleic acids supports the use of these
immunostimulatory nucleic acid based strategies for in vivo and ex-vivo immunotherapy
against disorders such as cancer and allergic or infectious diseases. The
immunostimulatory nucleic acids are also useful for activating and inducing maturation
of dendritic cells.
Immunostimulatory nucleic acids also increase natural killer cell lytic activity
and antibody dependent cellular cytotoxicity (ADCC). ADCC can be performed using a
immunostimulatory nucleic acid in combination with an antibody specific for a cellular

target, such as a cancer cell. When the immunostimulatory nucleic acid is administered
to a subject in conjunction with the antibody the subject's immune system is induced to
kill the tumor cell. The antibodies useful in the ADCC procedure include antibodies
which interact with a cell in the hody. Many such antibodies specific for cellular targets
have been described in the art and many are commercially available. Examples of these
antibodies are listed below among the list of cancer immunotherapies.
The immunostimulatory nucleic acids may also be administered in conjunction
with an anti-cancer therapy. Anti-cancer therapies include cancer medicaments,
radiation and surgical procedures. As used herein, a "cancer medicament" refers to a
agent which is administered to a subject for the purpose of treating a cancer. As used
herein, "treating cancer" includes preventing the development of a cancer, reducing the
symptoms of cancer, and/or inhibiting the growth of an established cancer. In other
aspects, the cancer medicament is administered to a subject at risk of developing a cancer
for the purpose of reducing the risk of developing the cancer. Various types of
medicaments for the treatment of cancer are described herein. For the purpose of this
specification, cancer medicaments are classified as chemotherapeutic agents,
immunotherapeutic agents, cancer vaccines, hormone therapy, and biological response
modifiers.
As used herein, a "cancer medicament" refers to an agent which is administered
to a subject for the purpose of treating a cancer. As used herein, "treating cancer"
includes preventing the development of a cancer, reducing the symptoms of cancer,
and/or inhibiting the growth of an established cancer. In other aspects, the cancer
medicament is administered to a subject at risk of developing a cancer for the purpose of
reducing the risk of developing the cancer. Various types of medicaments for the
treatment of cancer are described herein. For the purpose of this specification, cancer
medicaments are classified as chemotherapeutic agents, immunotherapeutic agents,
cancer vaccines, hormone therapy, and biological response modifiers. Additionally, the
methods of the invention are intended to embrace the use of more than one cancer
medicament along with the immunostimulatory nucleic acids. As an example, where
appropriate, the immunostimulatory nucleic acids may be administered with a both a
chemotherapeutic agent and an immunotherapeutic agent. Alternatively, the cancer
medicament may embrace an immunotherapeutic agent and a cancer vaccine, or a

chemotherapeutic agent and a cancer vaccine, or a chemotherapeutic agent, an
immunotherapeutic agent and a cancer vaccine all administered to one subject for the
purpose of treating a subject having a cancer or at risk of developing a cancer.
Cancer medicaments function in a variety of ways. Some cancer medicaments
work by targeting physiological mechanisms that are specific to tumor cells. Examples
include the targeting of specific genes and their gene products (i.e., proteins primarily)
which are mutated in cancers. Such genes include but are not limited to oncogenes (e.g.,
Ras, Her2, bcl-2), tumor suppressor genes (e.g., EGF, p53, Rb), and cell cycle targets
(e.g., CDK4, p21, telomerase). Cancer medicaments can alternately target signal
transduction pathways and molecular mechanisms which are altered in cancer cells.
Targeting of cancer cells via the epitopes expressed on their cell surface is accomplished
through the use of monoclonal antibodies. This latter type of cancer medicament is
generally referred to herein as immunotherapy.
Other cancer medicaments target cells other than cancer cells. For example,
some medicaments prime the immune system to attack tumor cells (i.e., cancer
vaccines). Still other medicaments, called angiogenesis inhibitors, function by attacking
the blood supply of solid tumors. Since the most malignant cancers are able to
metastasize (i.e., exist the primary tumor site and seed a distal tissue, thereby forming a
secondary tumor), medicaments that impede this metastasis are also useful in the
treatment of cancer. Angiogenic mediators include basic FGF, VEGF, angiopoietins,
angiostatin, endostatin, TNFoc, TNP-470, thrombospandin-l, platelet factor 4, CAI, and
certain members of the integrin family of proteins. One category of this type of
medicament is a metalloproteinase inhibitor, which inhibits the enzymes used by the
cancer cells to exist the primary tumor site and extravasate into another tissue.
Some cancer cells are antigenic and thus can be targeted by the immune system.
In one aspect, the combined administration of immunostimulatory nucleic acids and
cancer medicaments, particularly those which are classified as cancer immunotherapies,
is useful for stimulating a specific immune response against a cancer antigen. A "cancer
antigen" as used herein is a compound, such as a peptide, associated with a tumor or
cancer cell surface and which is capable of provoking an immune response when
expressed on the surface of an antigen presenting cell in the context of an MHC
molecule. Cancer antigens, such as those present in cancer vaccines or those used to

prepare cancer immunotherapies, can be prepared from crude cancer cell extracts, as
described in Cohen, et al., 1994, Cancer Research, 54:1055, or by partially purifying the
antigens, using recombinant technology, or de novo synthesis of known antigens.
Cancer antigens can be used in the form of immunogenic portions of a particular antigen
or in some instances a whole cell or a tumor mass can be used as the antigen. Such
antigens can be isolated or prepared recombinantly or by any other means known in the
art.
The theory of immune surveillance is that a prime function of the immune system
is to detect and eliminate neoplastic cells before a tumor forms. A basic principle of this
theory is that cancer cells are antigenically different from normal cells and thus elicit
immune reactions that are similar to those that cause rejection of immunologically
incompatible allografts. Studies have confirmed that tumor cells differ, either
qualitatively or quantitatively, in their expression of antigens. For example, "tumor-
specific antigens" are antigens that are specifically associated with tumor cells but not
normal cells. Examples of tumor specific antigens are viral antigens in tumors induced
by DNA or RNA viruses. "Tumor-associated" antigens are present in both tumor cells
and normal cells but are present in a different quantity or a different form in tumor cells.
Examples of such antigens are oncofetal antigens (e.g., carcinoembryonic antigen),
differentiation antigens (e.g., T and Tn antigens), and oncogene products (e.g.,
HERAieu).
Different types of cells that can kill tumor targets in vitro and in vivo have been
identified: natural killer cells (NK cells), cytolytic T lymphocytes (CTLs), lymphokine-
activated killer cells (LAKs), and activated macrophages. NK cells can kill tumor cells
without having been previously sensitized to specific antigens, and the activity does not
require the presence of class I antigens encoded by the major histocompatibility complex
(MHC) on target cells. NK cells are thought to participate in the control of nascent
tumors and in the control of metastatic growth. In contrast to NK cells, CTLs can kill
tumor cells only after they have been sensitized to tumor antigens and when the target
antigen is expressed on the tumor cells that also express MHC class I. CTLs are thought
to be effector cells in the rejection of transplanted tumors and of tumors caused by DNA
viruses. LAK cells are a subset of null lymphocytes distinct from the NK and CTL
populations. Activated macrophages can kill tumor cells in a manner that is not antigen

dependent nor MHC restricted once activated. Activated macrophages are through to
decrease the growth rate of the tumors they infiltrate. In vitro assays have identified
other immune mechanisms such as antibody-dependent, cell-mediated cytotoxic
reactions and lysis by antibody plus complement. However, these immune effector
mechanisms are thought to be less important in vivo than the function of NK, CTLs,
LAK, and macrophages in vivo (for review see Piessens, W.F., and David, J., "Tumor
Immunology", In: Scientific American Medicine. Vol. 2, Scientific American Books,
N.Y.,pp. 1-13,1996.
The goal of immunotherapy is to augment a patient's immune response to an
established tumor. One method of immunotherapy includes the use of adjuvants.
Adjuvant substances derived from microorganisms, such as bacillus Calmette-Guerin,
heighten the immune response and enhance resistance to tumors in animals.
Immunotherapeutic agents are medicaments which derive from antibodies or
antibody fragments which specifically bind or recognize a cancer antigen. As used
herein a cancer antigen is broadly defined as an antigen expressed by a cancer cell.
Preferably, the antigen is expressed at the cell surface of the cancer cell. Even more
preferably, the antigen is one which is not expressed by normal cells, or at least not
expressed to the same level as in cancer cells. Antibody-based immunotherapies may
function by binding to the cell surface of a cancer cell and thereby stimulate the
endogenous immune system to attack the cancer cell. Another way in which antibody-
based therapy functions is as a delivery system for the specific targeting of toxic
substances to cancer cells. Antibodies are usually conjugated to toxins such as ricin
(e.g., from castor beans), calicheamicin and maytansinoids, to radioactive isotopes such
as Iodine-131 and Yttrium-90, to chemotherapeutic agents (as described herein), or to
biological response modifiers. In this way, the toxic substances can be concentrated in
the region of the cancer and non-specific toxicity to normal cells can be minimized. In
addition to the use of antibodies which are specific for cancer antigens, antibodies which
bind to vasculature, such as those which bind to endothelial cells, are also useful in the
invention. This is because generally solid tumors are dependent upon newly formed
blood vessels to survive, and thus most tumors are capable of recruiting and stimulating
the growth of new blood vessels. As a result, one strategy of many cancer medicaments

is to attack the blood vessels feeding a tumor and/or the connective tissues (or stroma)
supporting such blood vessels.
The use of immunostimulatory nucleic acids in conjunction with
immunotherapeutic agents such as monoclonal antibodies is able to increase long-term
survival through a number of mechanisms including significant enhancement of ADCC
(as discussed above), activation of natural killer (NK) cells and an increase in IFNα
levels. The nucleic acids when used in combination with monoclonal antibodies serve to
reduce the dose of the antibody required to achieve a biological result.
Examples of cancer immunotherapies which are currently being used or which
are in development are listed in Table C.







Yet other types of chemotherapeutic agents which can be used according to the
invention include Aminoglutethimide, Asparaginase, Busulfan, Carboplatin,
Chlorombucil, Cytarabine HCI, Dactinomycin, Daunorubicin HC1, Estramustine
phosphate sodium, Etoposide (VP16-213), Floxuridine, Fluorouracil (5-FU), Flutamide,
Hydroxyurea (hydroxycarbamide), Ifosfamide, Interferon Alfa-2a, Alfa-2b, Leuprolide
acetate (LHRH-releasing factor analogue), Lomustine (CCNU), Mechlorethamine HCI
(nitrogen mustard), Mercaptopurine, Mesna, Mitotane (o.p'-DDD), Mitoxantrone HCI,
Octreotide, Plicamycin, Procarbazine HCI, Streptozocin, Tamoxifen citrate,
Thioguanine, Thiotepa, Vinblastine sulfate, Amsacrine (m-AMSA), Azacitidine,
Erthropoietin, Hexamethylmelamine (HMM), Interleukin 2, Mitoguazone (methyl-GAG;
methyl glyoxal bis-guanylhydrazone; MGBG), Pentostatin (2'deoxycoformycin),
Semustine (methyl-CCNU), Teniposide (VM-26) and Vindesine suifate.
Cancer vaccines are medicaments which are intended to stimulate an endogenous
immune response against cancer cells. Currently produced vaccines predominantly
activate the humoral immune system (i.e., the antibody dependent immune response).
Other vaccines currently in development are focused on activating the cell-mediated
immune system including cytotoxic T lymphocytes which are capable of killing tumor
cells. Cancer vaccines generally enhance the presentation of cancer antigens to both
antigen presenting cells (e.g., macrophages and dendritic cells) and/or to other immune
cells such as T cells, B cells, and NK cells.
Although cancer vaccines may take one of several forms, as discussed infra, their
purpose is to deliver cancer antigens and/or cancer associated antigens to antigen
presenting cells (APC) in order to facilitate the endogenous processing of such antigens
by APC and the ultimate presentation of antigen presentation on the cell surface in the
context of MHC class I molecules. One form of cancer vaccine is a whole cell vaccine
which is a preparation of cancer cells which have been removed from a subject, treated
ex vivo and then reintroduced as whole cells in the subject. Lysates of tumor cells can

also be used as cancer vaccines to elicit an immune response. Another form cancer
vaccine is a peptide vaccine which uses cancer-specific or cancer-associated small
proteins to activate T cells. Cancer-associated proteins are proteins which are not
exclusively expressed by cancer cells (i.e., other normal cells may still express these
antigens). However, the expression of cancer-associated antigens is generally
consistently upregulated with cancers of a particular type. Yet another form of cancer
vaccine is a dendritic cell vaccine which includes whole dendritic cells which have been
exposed to a cancer antigen or a cancer-associated antigen in vitro. Lysates or
membrane fractions of dendritic cells may also be used as cancer vaccines. Dendritic
cell vaccines are able to activate antigen-presenting cells directly. Other cancer vaccines
include ganglioside vaccines, heat-shock protein vaccines, viral and bacterial vaccines,
and nucleic acid vaccines.
The use of immunostimulatory nucleic acids in conjunction with cancer vaccines
provides an improved antigen-specific humoral and cell mediated immune response, in
addition to activating NK cells and endogenous dendritic cells, and increasing IFNcc
levels. This enhancement allows a vaccine with a reduced antigen dose to be used to
achieve the same beneficial effect. In some instances, cancer vaccines may be used
along with adjuvants, such as those described above.
As used herein, the terms "cancer antigen" and "tumor antigen" are used
interchangeably to refer to antigens which are differentially expressed by cancer cells
and can thereby be exploited in order to target cancer cells. Cancer antigens are antigens
which can potentially stimulate apparently tumor-specific immune responses. Some of
these antigens are encoded, although not necessarily expressed, by normal cells. These
antigens can be characterized as those which are normally silent (i.e., not expressed) in
normal cells, those that are expressed only at certain stages of differentiation and those
that are temporally expressed such as embryonic and fetal antigens. Other cancer
antigens are encoded by mutant cellular genes, such as oncogenes (e.g., activated ras
oncogene), suppressor genes (e.g., mutant p53), fusion proteins resulting from internal
deletions or chromosomal translocations. Still other cancer antigens can be encoded by
viral genes such as those carried on RNA and DNA tumor viruses.
Other vaccines take the form of dendritic cells which have been exposed to
cancer antigens in vitro, have processed the antigens and are able to express the cancer

antigens at their cell surface in the context of MHC molecules for effective antigen
presentation to other immune system cells.
The immunostimulatory nucleic acids are used in one aspect of the invention in
conjunction with cancer vaccines which are dendritic cell based. A dendritic-cell is a
professional antigen presenting cell. Dendritic cells form the link between the innate and
the acquired immune system by presenting antigens and through their expression of
pattern recognition receptors which detect microbial molecules like LPS in their local
environment. Dendritic cells efficiently internalize, process, and present soluble specific
antigen to which it is exposed. The process of internalizing and presenting antigen
causes rapid upregulation of the expression of major histocompatibility complex (MHC)
and costimulatory molecules, the production of cytokines, and migration toward
lymphatic organs where they are believed to be involved in the activation of T cells.
Table D lists a variety of cancer vaccines which are either currently being used or
are in development.



As used herein, chemotherapeutic agents embrace all other forms of cancer
medicaments which do not fall into the categories of immunotherapeutic agents or cancer
vaccines. Chemotherapeutic agents as used herein encompass both chemical and
biological agents. These agents function to inhibit a cellular activity which the cancer
cell is dependent upon for continued survival. Categories of chemotherapeutic agents
include alkylating/alkaloid agents, antimetabolites, hormones or hormone analogs, and
miscellaneous antineoplastic drugs. Most if not all of these agents are directly toxic to
cancer cells and do not require immune stimulation. Combination chemotherapy and

immunostimulatory nucleic acid administration increases the maximum tolerable dose of
chemotherapy.
Chemotherapeutic agents which are currently in development or in use in a
clinical setting are shown in Table E.






administration of some immunostimulatory nucleic acids, these nucleic acids can be used
to generate IFNα endogenously.
The invention also includes a method for inducing antigen non-specific innate
immune activation and broad spectrum resistance to infectious challenge using the
immunostimulatory nucleic acids. The term antigen non-specific innate immune
activation as used herein refers to the activation of immune cells other than B cells and
for instance can include the activation of NK cells, T cells or other immune cells that can
respond in an antigen independent fashion or some combination of these cells. A broad
spectrum resistance to infectious challenge is induced because the immune cells are in
active form and are primed to respond to any invading compound or microorganism.
The cells do not have to be specifically primed against a particular antigen. This is
particularly useful in biowarfare, and the other circumstances described above such as
travelers.
The stimulation index of a particular immunostimulatory nucleic acid can be
tested in various immune cell assays. Preferably, the stimulation index of the
immunostimulatory nucleic acid with regard to B cell proliferation is at least about 5,
preferably at least about 10, more preferably at least about 15 and most preferably at
least about 20 as determined by incorporation of 3H uridine in a murine B cell culture,
which has been contacted with 20 uM of nucleic acid for 20h at 37°C and has been
pulsed with 1 Ci of 3H uridine; and harvested and counted 4h later as described in detail
in PCT Published Patent Applications PCT/US95/01570 (WO 96/02555) and
PCT/US97/19791 (WO 98/18810) claiming priority to U.S. Serial Nos. 08/386,063 and
08/960,774, filed on February 7, 1995 and October 30,1997 respectively. For use in
vivo, for example, it is important that the immunostimulatory nucleic acids be capable of
effectively inducing an immune response, such as, for example, antibody production.
Immunostimulatory nucleic acids are effective in non-rodent vertebrate.
Different immunostimulatory nucleic acid can cause optimal immune stimulation
depending on the type of subject and the sequence of the immunostimulatory nucleic
acid. Many vertebrates have been found according to the invention to be responsive to
the same class of immunostimulatory nucleic acids, sometimes referred to as human
specific immunostimulatory nucleic acids. Rodents, however, respond to different
nucleic acids. As shown herein an immunostimulatory nucleic acid causing optimal "

stimulation in humans may not generally cause optimal stimulation in a mouse and vice
versa. An immunostimulatory nucleic acid causing optimal stimulation in humans often
does, however, cause optimal stimulation in other animals such as cow, horses, sheep,
etc. One of skill in the art can identify the optimal nucleic acid sequences useful for a
particular species of interest using routine assays described herein and/or known in the
art, using the guidance supplied herein.
The immunostimulatory nucleic acids may be directly administered to the subject
or may be administered in conjunction with a nucleic acid delivery complex. A nucleic
acid delivery complex shall mean a nucleic acid molecule associated with (e.g. ionically
or covalently bound to; or encapsulated within) a targeting means (e.g. a molecule that
results in higher affinity binding to target cell (e.g., B cell surfaces and/or increased
cellular uptake by target cells). Examples of nucleic acid delivery complexes include
nucleic acids associated with a sterol (e.g. cholesterol), a lipid (e.g. a cationic Iipid,
virosome or liposome), or a target cell specific binding agent (e.g. a ligand recognized by
target cell specific receptor). Preferred complexes may be sufficiently stable in vivo to
prevent significant uncoupling prior to internalization by the target cell. However, the
complex can be cleavable under appropriate conditions within the cell so that the nucleic
acid is released in a functional form.
Delivery vehicles or delivery devices for delivering antigen and nucleic acids to
surfaces have been described. The Immunostimulatory nucleic acid and/or the antigen
and/or other therapeutics may be administered alone (e.g., in saline or buffer) or using
any delivery vehicles known in the art. For instance the following delivery vehicles have
been described: Cochleates (Gould-Fogerite et al., 1994,1996); Emulsomes (Vancott et
al., 1998, Lowell et al., 1997); ISCOMs (Mowat et al., 1993, Carlsson et al., 1991, Hu
et., 1998, Morein et al., 1999); Liposomes (Childers et al., 1999, Michalek etal., 1989,
1992, de Haan 1995a, 1995b); Live bacterial vectors (e.g., Salmonella, Escherichia coli,
Bacillus calmatte-guerin, Shigella, Lactobacillus) (Hone et al., 1996, Pouwels et al.,
1998, Chatfield et al., 1993, Stover et al., 1991, Nugent et al., 1998); Live viral vectors
(e.g., Vaccinia, adenovirus, Herpes Simplex) (Gallichan et al., 1993, 1995, Moss et al.,
1996, Nugent et al., 1998, Flexner et al., 1988, Morrow et al., 1999); Microspheres
(Gupta et al., 1998, Jones et al., 1996, Maloy et al., 1994, Moore et al., 1995, O'Hagan et
al., 1994, Eldridge et al., 1989); Nucleic acid vaccines (Fynan et al., 1993, Kuklin et al.,

1997, Sasaki et al., 1998, Okada et al., 1997, Ishii et al., 1997); Polymers (e.g.
carboxymethylcellulose, chitosan) (Hamajima et al., 1998, Jabbal-Gill et al., 1998);
Polymer rings (Wyatt et al., 1998); Proteosomes (Vancott et al., 1998, Lowell et al.,
1988, 1996, 1997); Sodium Fluoride (Hashi et al., 1998); Transgenic plants (Tacket et
al., 1998, Mason et al., 1998, Haq et al., 1995); Virosomes (Gluck et al., 1992,
Mengiardi et al., 1995, Cryz et al., 1998); Virus-like particles (Jiang et al., 1999, Leibl et
al., 1998). Other delivery vehicles are known in the art and some additional examples
are provided below in the discussion of vectors.
The term effective amount of a immunostimulatory nucleic acid refers to the
amount necessary or sufficient to realize a desired biologic effect. For example, an
effective amount of a immunostimulatory nucleic acid for inducing mucosal immunity is
that amount necessary to. cause the development of IgA in response to an antigen upon
exposure to the antigen, whereas that amount required for inducing systemic immunity is
that amount necessary to cause the development of IgG in response to an antigen upon
exposure to the antigen. Combined with the teachings provided herein, by choosing
among the various active compounds and weighing factors such as potency, relative
bioavailability, patient body weight, severity of adverse side-effects and preferred mode
of administration, an effective prophylactic or therapeutic treatment regimen can be
planned which does not cause substantial toxicity and yet is entirely effective to treat the
particular subject. The effective amount for any particular application can vary
depending on such factors as the disease or condition being treated, the particular
immunostimulatory nucleic acid being administered, the antigen, the size of the subject,
or the severity of the disease or condition. One of ordinary skill in the art can
empirically determine the effective amount of a particular immunostimulatory nucleic
acid and/or antigen and/or other therapeutic agent without necessitating undue
experimentation.
Subject doses of the compounds described herein for mucosal or local delivery
typically range from about 0.1 g to 10 mg per administration, which depending on the
application could be given daily, weekly, or monthly and any other amount of time
therebetween. More typically mucosal or local doses range from about 10 g to 5 mg
per administration, and most typically from about 100 g to 1 mg, with 2-4
administrations being spaced days or weeks apart. More typically, immune stimulant

doses range from 1 g to 10 mg per administration, and most typically 10g to 1 mg,
with daily or weekly administrations. Subject doses of the compounds described herein
for parenteral delivery for the purpose of inducing an antigen-specific immune response,
wherein the compounds are delivered with an antigen but not another therapeutic agent
are typically 5 to 10,000 times higher than the effective mucosal dose for vaccine
adjuvant or immune stimulant applications, and more typically 10 to 1,000 times higher,
and most typically 20 to 100 times higher. Doses of the compounds described herein for
parenteral delivery for the purpose of inducing an innate immune response or for
increasing ADCC or for inducing an antigen specific immune response when the
immunostimulatory nucleic acids are administered in combination with other therapeutic
agents or in specialized delivery vehicles typically range from about 0.1 g to 10 mg per
administration, which depending on the application could be given daily, weekly, or
monthly and any other amount of time therebetween. More typically parenteral doses for
these purposes range from about 10 g to 5 mg per administration, and most typically
from about 100 g to 1 mg, with 2-4 administrations being spaced days or weeks apart.
In some embodiments, however, parenteral doses for these purposes may be used in a
range of 5 to 10,000 times higher than the typical doses described above.
For any compound described herein the therapeutically effective amount can be
initially determined from animal models. A therapeutically effective dose can also be
determined from human data for CpG oligonucleotides which have been tested in
humans (human clinical trials have been initiated) and for compounds which are known
to exhibit similar pharmacological activities, such as other mucosal adjuvants, e.g., LT
and other antigens for vaccination purposes, for the mucosal or local administration.
Higher doses are required for parenteral administration. The applied dose can be
adjusted based on the relative bioavailability and potency of the administered compound.
Adjusting the dose to achieve maximal efficacy based on the methods described above
and other methods as are well-known in the art is well within the capabilities of the
ordinarily skilled artisan.
The formulations of the invention are administered in pharmaceutically
acceptable solutions, which may routinely contain pharmaceutically acceptable
concentrations of salt, buffering agents, preservatives, compatible carriers, adjuvants,
and optionally other therapeutic ingredients.

For use in therapy, an effective amount of the immunostimulatory nucleic acid
can be administered to a subject by any mode that delivers the nucleic acid to the desired
surface, e.g., mucosal, systemic. Administering the pharmaceutical composition of the
present invention may be accomplished by any means known to the skilled artisan.
Preferred routes of administration include but are not limited to oral, parenteral,
intramuscular, intranasal, intratracheal, inhalation, ocular, vaginal, and rectal.
For oral administration, the compounds (i.e., immunostimulatory nucleic acids,
antigens and other therapeutic agents) can be formulated readily by combining the active
compound(s) with pharmaceutically acceptable carriers well known in the art. Such
carriers enable the compounds of the invention to be formulated as tablets, pills, dragees,
capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a
subject to be treated. Pharmaceutical preparations for oral use can be obtained as solid
excipient, optionally grinding a resulting mixture, and processing the mixture of
granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores.
Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose,
mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat
starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose,
hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or
polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the
cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium
alginate. Optionally the oral formulations may also be formulated in saline or buffers for
neutralizing internal acid conditions or may be administered without any carriers.
Dragee cores are provided with suitable coatings. For this purpose, concentrated
sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl
pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer
solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may
be added to the tablets or dragee coatings for identification or to characterize different
combinations of active compound doses.
Pharmaceutical preparations which can be used orally include push-fit capsules
made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as
glycerol or sorbitol. The push-fit capsules can contain the active ingredients in
admixture with filler such as lactose, binders such as starches, and/or lubricants such as

talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active
compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid
paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added.
Microspheres formulated for oral administration may also be used. Such microspheres
have been well defined in the art. All formulations for oral administration should be in
dosages suitable for such administration.
For buccal administration, the compositions may take the form of tablets or
lozenges formulated in conventional manner.
For administration by inhalation, the compounds for use according to the present
invention may be conveniently delivered in the form of an aerosol spray presentation
from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g.,
dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon
dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be
determined by providing a valve to deliver a metered amount. Capsules and cartridges of
e.g. gelatin for use in an inhaler or insufflator may be formulated containing a powder
mix of the compound and a suitable powder base such as lactose or starch.
The compounds, when it is desirable to deliver them systemically, may be
formulated for parenteral administration by injection, e.g., by bolus injection or
continuous infusion. Formulations for injection may be presented in unit dosage form,
e.g., in ampoules or in multi-dose containers, with an added preservative. The
compositions may take such forms as suspensions, solutions or emulsions in oily or
aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing
and/or dispersing agents.
Pharmaceutical formulations for parenteral administration include aqueous
solutions of the active compounds in water-soluble form. Additionally, suspensions of
the active compounds may be prepared as appropriate oily injection suspensions.
Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic
fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection
suspensions may contain substances which increase the viscosity of the suspension, such
as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may
also contain suitable stabilizers or agents which increase the solubility of the compounds
to allow for the preparation of highly concentrated solutions.

Alternatively, the active compounds may be in powder form for constitution with
a suitable vehicle, e.g., sterile pyrogen-free water, before use.
The compounds may also be formulated in rectal or vaginal compositions such as
suppositories or retention enemas, e.g., containing conventional suppository bases such
as cocoa butter or other glycerides.
In addition to the formulations described previously, the compounds may also be
formulated as a depot preparation. Such long acting formulations may be formulated
with suitable polymeric or hydrophobic materials (for example as an emulsion in an
acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example,
as a sparingly soluble salt.
The pharmaceutical compositions also may comprise suitable solid or gel phase
carriers or excipients. Examples of such carriers or excipients include but are not limited
to calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives,
gelatin, and polymers such as polyethylene glycols.
Suitable liquid or solid pharmaceutical preparation forms are, for example,
aqueous or saline solutions for inhalation, microencapsulated, encochleated, coated onto
microscopic gold particles, contained in liposomes, nebulized, aerosols, pellets for
implantation into the skin, or dried onto a sharp object to be scratched into the skin. The
pharmaceutical compositions also include granules, powders, tablets, coated tablets,
(micro)capsules, suppositories, syrups, emulsions, suspensions, creams, drops or
preparations with protracted release of active compounds, in whose preparation
excipients and additives and/or auxiliaries such as disintegrants, binders, coating agents,
swelling agents, lubricants, flavorings, sweeteners or solubilizers are customarily used as
described above. The pharmaceutical compositions are suitable for use in a variety of
drug delivery systems. For a brief review of methods for drug delivery, see Langer,
Science 249:1527-1533, 1990, which is incorporated herein by reference.
The immunostimulatory nucleic acids and optionally other therapeutics and/or
antigens may be administered per se (neat) or in the form of a pharmaceutically
acceptable salt. When used in medicine the salts should be pharmaceutically acceptable,
but non-pharmaceutically acceptable salts may conveniently be used to prepare
pharmaceutically acceptable salts thereof. Such salts include, but are not limited to,
those prepared from the following acids: hydrochloric, hydrobromic, sulphuric, nitric,

phosphoric, maleic, acetic, salicylic, p-toluene sulphonic, tartaric, citric, methane
sulphonic, formic, malonic, succinic, naphthalene-2-sulphonic, and benzene sulphonic.
Also, such salts can be prepared as alkaline metal or alkaline earth salts, such as sodium,
potassium or calcium salts of the carboxylic acid group.
Suitable buffering agents include: acetic acid and a salt (1-2% w/v); citric acid
and a salt (1-3% w/v); boric acid and a salt (0.5-2.5% w/v); and phosphoric acid and a
salt (0.8-2% w/v). Suitable preservatives include benzalkonium chloride (0.003-0.03%
w/v); chlorobutanol (0.3-0.9% w/v); parabens (0.01-0.25% w/v) and thimerosal (0.004-
0.02% w/v).
The pharmaceutical compositions of the invention contain an effective amount of
a Immunostimulatory nucleic acid and optionally antigens and/or other therapeutic
agents optionally included in a pharmaceutically-acceptable carrier. The term
pharmaceutically-acceptable carrier means one or more compatible solid or liquid filler,
diluents or encapsulating substances which are suitable for administration to a human or
other vertebrate animal. The term carrier denotes an organic or inorganic ingredient,
natural or synthetic, with which the active ingredient is combined to facilitate the
application. The components of the pharmaceutical compositions also are capable of
being commingled with the compounds of the present invention, and with each other, in
a manner such that there is no interaction which would substantially impair the desired
pharmaceutical efficiency.
The immunostimulatory nucleic acids useful in the invention may be delivered in
mixtures with additional adjuvant(s), other therapeutics, or antigen(s). A mixture may
consist of several adjuvants in addition to the Immunostimulatory nucleic acid or several
antigens or other therapeutics.
A variety of administration routes are available. The particular mode selected
will depend, of course, upon the particular adjuvants or antigen selected, the particular
condition being treated and the dosage required for therapeutic efficacy. The methods of
this invention, generally speaking, may be practiced using any mode of administration
that is medically acceptable, meaning any mode that produces effective levels of an
immune response without causing clinically unacceptable adverse effects. Preferred
modes of administration are discussed above.

The compositions may conveniently be presented in unit dosage form and may be
prepared by any of the methods well known in the art of pharmacy. All methods include
the step of bringing the compounds into association with a carrier which constitutes one
or more accessory ingredients. In general, the compositions are prepared by uniformly
and intimately bringing the compounds into association with a liquid carrier, a finely
divided solid carrier, or both, and then, if necessary, shaping the product. Liquid dose
units are vials or ampoules. Solid dose units are tablets, capsules and suppositories. For
treatment of a patient, depending on activity of the compound, manner of administration,
purpose of the immunization (i.e., prophylactic or therapeutic), nature and severity of the
disorder, age and body weight of the patient, different doses may be necessary. The
administration of a given dose can be carried out both by single administration in the
form of an individual dose unit or else several smaller dose units. Multiple
administration of doses at specific intervals of weeks or months apart is usual for
boosting the antigen-specific responses.
Other delivery systems can include time-release, delayed release or sustained
release delivery systems. Such systems can avoid repeated administrations of the
compounds, increasing convenience to the subject and the physician. Many types of
release delivery systems are available and known to those of ordinary skill in the art.
They include polymer base systems such as poly(lactide-glycolide), copolyoxalates,
polycaprolactones, polyesteramides, polyorthoesters, polyhydroxybutyric acid, and
polyanhydrides. Microcapsules of the foregoing polymers containing drugs are
described in, for example, U.S. Patent 5,075,109. Delivery systems also include
non-polymer systems that are: lipids including sterols such as cholesterol, cholesterol
esters and fatty acids or neutral fats such as mono-di-and tri-glycerides; hydrogel release
systems; sylastic systems; peptide based systems; wax coatings; compressed tablets
using conventional binders and excipients; partially fused implants; and the like.
Specific examples include, but are not limited to: (a) erosional systems in which an agent
of the invention is contained in a form within a matrix such as those described in U.S.
Patent Nos. 4,452,775,4,675,189, and 5,736,152, and (b) diffusional systems in which
an active component permeates at a controlled rate from a polymer such as described in
U.S. Patent Nos. 3,854,480,5,133,974 and 5,407,686. In addition, pump-based hardware
delivery systems can be used, some of which are adapted for implantation.

The present invention is further illustrated by the following Examples, which in
no way should be construed as further limiting. The entire contents of all of the
references (including literature references, issued patents, published patent applications,
and co-pending patent applications) cited throughout this application are hereby
expressly incorporated by reference.
Examples
Materials and Methods:
Oligodeoxynucleotides: Native phosphodiester and phosphorothioate-modified
ODN were purchased from Operon Technologies (Alameda, CA) and Hybridon
Specialty Products (Milford, MA). ODN were tested for endotoxin using the LAL-assay
(LAL-assay BioWhittaker, Walkersville, MD; lower detection limit 0.1 EU/ml). For in
vitro assays, ODN were diluted in TE-buffer (10 mM Tris, pH 7.0, 1 mM EDTA), and
stored at -20° C. For in vivo use, ODN were diluted in phosphate buffered saline (0.1 M
PBS, pH 7.3) and stored at 4°C. All dilutions were carried out using pyrogen-free
reagents.
Isolation of human PBMC and cell culture: Peripheral blood mononuclear
cells (PBMC) were isolated from peripheral blood of healthy volunteers by Ficoll-Paque
density gradient centrifugation (Histopaque-1077, Sigma Chemical Co., St. Louis, MO)
as described (Hartmann et al., 1999 Proc. Natl. Acad. Sci USA 96:9305-10). Cells were
suspended in RPMI 1640-culture medium supplemented with 10% (v/v) heat-inactivated
(56°C, 1 h) FCS (HyClone, Logan, UT), 1.5 mM L-glutamine, 100 U/ml penicillin and
100 g/ml streptomycin (all from Gibco BRL, Grand Island, NY) (complete medium).
Cells (final concentration 1 x 106 cells/ml) were cultured in complete medium in a 5%
CO2 humidified incubator at 37°C. ODN and LPS (from Salmonella typhimurium, Sigma
Chemical Co., St. Louis, MO) or anti-IgM were used as stimuli. For measurement of
human NK lytic activity, PBMC were incubated at 5 x 106/well in 24-well plates.
Cultures were harvested after 24 hours, and cells were used as effectors in a standard 4
hours 51Cr-release assay against K562 target cells as previously described (Ballas et al.,
1996 J. Immunol. 157:1840-1845). For B cell proliferation, 1 Ci of 3H thymidine was
added 18 hours before harvest, and the amount of 3H thymidine incorporation was
determined by scintillation counting at day 5. Standard deviations of the triplicate wells
were
Flow cytometry on human PBMC: Surface antigens on primate PBMC were
stained as previously described (Hartmann et al., 1998 J. Pharmacol. Exp. Ther. 285:920-
928). Monoclonal antibodies to CD3 (UCHT1), CD14 (M5E2), CD19 (B43), CD56
(B159), CD69 (FN50) and CD86 (2331 [FUN-1]) were purchased from Pharmingen, San
Diego, CA. IgG,,K (MOPC-21) and IgG2b,K (Hartmann et al., 1999 Proc. Natl. Acad. Sci
USA 96:9305-10) were used to control for non-specific staining. NK cells were
identified by CD56 expression on CD3, CD14 and CD19 negative cells, whereas B cells
were identified by expression of CD19. Flow cytometric data of 10000 cells per sample
were acquired on a FACScan (Beckton Dickinson Immunocytometry Systems, San Jose,
CA). The viability of cells within the FSC/SSC gate used for analysis was examined by
propidium iodide staining (2 ug/ml) and found to be higher than 98%. Data were
analyzed using the computer program FlowJo (version 2.5.1, Tree Star, Inc., Stanford,
CA).
Results:
Example 1: CpG-dependent stimulation of human B cells depends on
methylation and ODN length.
Human PBMC were obtained from normal donors and cultured for five days at 2
x 105 cells/well with the indicated concentrations of the indicated ODN sequences. As
shown in Table F, human PBMCs proliferate above the background when cultured with a
variety of different CpG ODN, but also show some proliferation even with ODN that do
not contain any CpG motifs. The importance of unmethylated CpG motifs in providing
optimal immune stimulation with these ODN is demonstrated by the fact that ODN 1840
(SEQ ID NO. 83) induces 56,603 counts of ^H-thymidine incorporation whereas the
same T-rich ODN with the CpG motifs methylated (non-CpG), 1979 (SEQ ID NO. 222),
induces lower, but still increased over background, activity (only 18,618 counts) at the
same concentration of 0.6 g/ml. The reduced proliferation at higher ODN
concentrations may be an artifact of the cells becoming exhausted under these
experimental conditions or could reflect some toxicity of the higher ODN concentrations.
Interestingly, shorter ODN containing CpG motifs, such as the 13-14 mers 2015 and
2016, are less stimulatory despite the fact that their molar concentration would actually
be higher since the ODNs were added on the basis of mass rather than molarity. This
demonstrates that ODN length may also be an important determinant in the immune

effects of the ODN. A non-CpG ODN but slight T-rich ODN (about 30% T), 1982 (SEQ
ID NO. 225), caused only a small amount of background cell proliferation.


Human PBMCs were cultured for 24 hours with a panel of different CpG or non-
CpG ODN at two different concentrations, and then tested for their ability to kill NK
target cells as described previously (Ballas et al., 1996 J. Immunol. 157:1840-1845).
Killing is measured as lytic units, or L.U. The human donor used in this experiment had
a background level of 3.69 L.U. which increased to 180.36 L.U. using the positive
control, IL-2. A CpG oligo, 2006 (SEQ ID NO. 246), induced high levels of NK lytic
function at a low concentration of 0.6, and a lower level at a concentration of 6.0.
Surprisingly, a T-rich ODN in which the CpG motifs of 2006 were methylated (ODN at
2117 (SEQ ID NO. 358)) or inverted to GpCs (ODN 2137 (SEQ ID NO. 886)) retained
strong immune stimulatory function at the higher ODN concentrations, as shown in
Table G. These concentration-dependent immune stimulatory effects are not a general
property of the phosphorothioate backbone since the experiments described below
demonstrate that a poly-A ODN, is nonstimulatory above background levels. Some
stimulation is seen with a 24-base long ODN in which all of the base positions are
randomized so that A, C, G, and T will occur at a frequency of 25% in each of the base
positions (ODN 2182 (SEQ ID NO. 432)). However, the stimulatory effect of such a 24-
base ODN is greatly enhanced if it is pure poly-T, in which case stimulation is also seen
at the lowest concentration of 0.6 g/ml (ODN 2183 (SEQ ID NO. 433)). In fact, the
stimulatory activity of ODN SEQ ID NO. 433 at this low concentration is higher than
that of any other ODN tested at this low concentration, aside from the optimal human
immune stimulatory ODN of SEQ ID NO. 246. In fact, the higher concentration of ODN
SEQ ID NO. 433 stimulated more NK activity than any other phosphorothioate ODN
except for the strong CpG ODN 2142 (SEQ ID NO. 890), which was marginally higher.
If the G content of ODN SEQ ID NO. 246 is increased relative to the T content by
addition of more Gs, thus resulting in a decrease in the proportion of T nucleotides the
immune stimulatory effect of the ODN is reduced (see ODN 2132 (SEQ ID NO. 373)).
Thus, the T content of an ODN is an important determinant of its immune stimulatory
effect. Although a poly-T ODN is the most stimulatory of the non-CpG ODN, other
bases are also important in determining the immune stimulatory effect of a non-CpG
ODN. ODN 2131 (SEQ ID NO. 372), in which slightly more than half of the bases are T
and in which there are no Gs, is immune stimulatory at a concentration of 6 g/ml but
has less activity than other T-rich ODN. If the 6 A's in ODN 2131 (SEQ ID NO. 372)

are replaced by 6 Gs, the immune stimulatory effect of the ODN can be increased (see
ODN 2130 (SEQ ID NO. 371)).





Example 3: Induction ofB cell proliferation by T-rich non-CpGODN.
To assess the ability of T-rich ODN to activate B cell proliferation, human
PBMCs were stained with the cytoplasmic dye CSFE, incubated with five days with the
indicated ODN at either 0.15 or 0.3 g/ml, and then analyzed by flow cytometry. B
cells were identified by gating on cells positive for the lineage marker CD19). CpG
ODN 2006 was a strong inducer of B cell proliferation, and this effect was reduced if the
CpG motifs were methylated or inverted to GpC as shown in Figure 1 at an ODN
concentration of 0.3 ug/ml. The base composition of the ODN appears to be important in
determining the immune stimulatory effect. Reducing the T content of an ODN
substantially reduces immune stimulatory effect, as exemplified by ODN 2177 (SEQ ID
NO. 427) in which 6 of the Ts present in ODN 2137 (SEQ ID NO. 886) have been
switched to A's, resulting in a greatly reduced immune stimulatory effect. The
importance of T's in the immune stimulatory effect of an ODN is also shown by
comparison of ODN 2116 (SEQ ID NO. 357) and 2181 (SEQ ID NO. 431), which differ
in the 3' end of the ODN. ODN 2181, in which the 3' end is poly-T is more stimulatory

than ODN 2116, in which the 3' end is poly-C, despite the fact that both ODN have a
TCGTCG at the 5' end.
Example 4: B Cell Proliferation Induced by TG Oligonucleotides
The stimulatory effects of TG motifs are shown in Figure 2. ODN 2137 has the
identical base composition as ODN 2006, but the CG motifs have all been inverted to
GC's resulting in a CG-free nucleic acid. ODN does however contain 6 TG
dinucleotides. In ODN 2177, all the TG dinucleotides of ODN 2137 have been changed
to AG. Although ODN 2177 contains only 6 adenines, it is virtually nonstimulatory at a
concentration of 0.2 g/ml. For comparison, an ODN 24 bases in length in which each
position is randomized to be any of the four bases (ODN 2182) induces > 12% of B cells
to proliferate at a concentration of 0.2 g/ml. These results indicate that the stimulatory
effects of ODN 2137 are not simply those of a phosphorothioate backbone, but relate to
the presence of TG dinucleotides.
In order to determine the effect of varying the number of TG dinucleotide motifs,
ODN 2200 and ODN 2202 were compared, as shown in Figure 2. Both ODN contain 18
Ts and 6 Gs, but in ODN 2200 all of the Gs are consecutive, so that there is only one TG
dinucleotide, whereas in ODN 2202, the Gs are split up as GG dinucleotides throughout
the ODN so that there are three TGs. ODN 2202 is significantly more stimulatory than
ODN 2200, consistent with the model that at least three TG motifs in an ODN are
required for optimal stimulatory activity. It is likely that even higher levels of
stimulation could be achieved if the TG motifs had been optimized as taught herein.
Example 5: Effects of TTG versus TTG motifs.
Figure 3 shows the results of experiments conducted to study TG content in terms
of the relative levels of Ts versus Gs as it relates to the stimulatory effect of an ODN.
The Figure shows that an ODN in which all of the bases are randomized to be either T or
G (ODN 2188 (SEQ ID NO. 905)) is nonstimulatory at a concentration of 0.2 jag/ml,
similar to an ODN in which all of the bases are randomized to be either A or G (ODN
2189 (SEQ ID NO. 906)). However, at the higher concentration of 2 jig/ml, the
randomized T/G ODN 2188 is significantly more stimulatory. This latter level of
stimulation is still lower than that which occurs with a totally randomized ODN (ODN
2182 (SEQ ID NO. 432)). The highest stimulation at low concentrations is seen with an

ODN in which half of the bases are fixed at T and the other half of the bases are
randomized to be either T or G (ODN 2190 (SEQ ID NO. 907)). Since every other' base
is fixed to be a T, there cannot be any TG motifs. The data in Figure 3 show that
increasing the TG content of an ODN improves its stimulatory activity.
In yet other experiments, the results of which are not diagrammed herein, ODN
2190 (SEQ ID NO. 907) exhibited a stimulation, of NK activity compared to ODN 2188
(SEQ ID NO. 905) or ODN 2189 (SEQ ID NO. 906).
Examples 6-8
Introduction:
Above, we demonstrated that Poly T sequences are able to enhance stimulation of
B and NK cells. Here and below we investigate the effect of a variety of non-CpG T-
rich ODN as well as Poly C ODN for their ability to stimulate human B cells, NK cells
and monocytes.


Cell preparation and cell culture: Human PBMC were isolated from peripheral
blood of healthy volunteers, obtained by the German Red Cross (Ratingen, Germany), as
described above in Example 1, but all material were purchased from Life Technologies,
Germany and were endotoxin-tested., For the B cell, NK cell and monocyte activation
assays PBMC were cultured in complete medium at a concentration of 2x106 cells/ml in
200l in 96 round bottom plates in a humidified incubator at 37°C. Different ODNs,
LPS (Sigma) or IL-2 (R&D Systems, USA) were used as stimuli. At the indicated time
points, cells were harvested for flow cytometry.
Flow cytometry: MAbs used for staining of surface antigens were: CD3, CD14,
CD19, CD56, CD69, CD80 and CD86 (all obtained from Pharmingen/Becton Dickinson,
Germany). For monocytes Fc receptors were blocked using human IgG (Myltenyi,
Germany) as previously described (Bauer, M et al 1999 Immunology 97:699). Flow
cytometric data of at least 1000 cells of a specified subpopulation (B cells, monocytes,
NK cells, NKT cells or T cells) were acquired on a FACSCalibur (Becton Dickinson).
Data were analyzed using the program CellQuest (Becton Dickinson).
NK-mediated cytotoxicity: PBMC were cultured overnight with or without
6g/ml ODN or 100U/ml IL-2 at 37°C, 5% CO2. The next morning, K-562 target cells
were labeled with a fluorescent dye, CFSE, as described previously for human B cells
(Hartmann, G., and A. M. Krieg. 2000 J. Immunol 164:944). PBMC were added in
different ratios (50:1, 25:1 and 12.5:1) to 2x105 target cells and incubated for 4h at 37°C.
Cells were harvested and incubated with the DNA-specific dye 7-AAD (Pharmingen) for
detection of apoptotic cells. Results were measured by flow cytometry.
ELISA: PBMC (3x106 cells/ml) were cultured with the specified concentrations
of ODN or LPS for 24h (IL-6,-IFNγ and TNFα) or 8h (IL-1β) in 48 well plates in a
humidified atmosphere at 37°C. Supernatants were collected and cytokines were
measured using OPTeia ELISA Kits (Pharmingen) for IL-6, IFNy and TNFa or an Eli-
pair ELISA assay (Hoelzel, Germany) for IL-1β according to the manufacturer protocols.
Example 6: B cell activation induced by ODNs lacking CpG motifs
In the Experiments described above in Example 3, we demonstrate that T-rich
ODN were capable of activating B cells. We expand those studies here using additional
ODN and different cell and reagent sources. In a first set of experiments, we compared
the activation potential of different non-CpG T-rich ODNs with the very potent known

CpG ODN 2006 (SEQ ID NO.: 246). PBMC (2xl06cells/ml) of a blood donor (n=2)
were incubated with the indicated concentrations of ODNs 2006 (SEQ ID NO.: 246),
2117 (SEQ ID NO.: 358), 2137 (SEQ ID NO.: 886), 5126 (SEQ ID NO.: 1058), an9
5162 (SEQ ID NO.: 1094). Cells were incubated for 48h at 37°C as described above and
stained with mAb for CD 19 (B cell marker) and CD86 (B cell activation marker, B7-2).
Expression was measured by flow cytometry.
Using different concentrations of ODNs, we showed (Fig. 4) that T-rich ODNs
without a CpG motif, can induce stimulation of human B cells. ODN 5126 (SEQ ID
NO.: 1058) which contains only a single poly-T sequence but is greater than 50% T,
caused high levels of human B cell activation. Although there are some similarities to
SEQ ID NO.: 246 (e.g. more than 80% TIG content), this ODN clearly lacks any known
immunostimulatory CpG motif. Surprisingly, for all tested T-rich ODNs, the highest
stimulatory index was obtained at concentrations between 3 and lOug/ml. The highest
stimulatory index of the tested ODNs was achieved by CpG/T-rich ODN SEQ ID NO.:
246 at 0.4μg/ml. Interestingly, the activity decreased at high concentrations.
Poly A, Poly C and Poly T sequences were synthesized and tested for biological
activity. PBMC (2xl06cells/ml) of one representative donor (n=3) were stimulated as
described above by 0.4fig/ml, 1.0μg/ml or 10.0μg/ml of the following ODNs: 2006 (SEQ
ID NO.: 246), 2196 (SEQ ID NO.: 913) (Poly T, 18 bases), 2194 (SEQ ID NO.: 911)
(Poly T, 27 bases), 5162 (SEQ ID NO.: 1094) (Poly T, 30 bases), 5163 (SEQ ID NO.:
1095) (Poly A, 30 bases), 5168 (SEQ ID NO.: 1096) (Poly C, 30 bases) and 5169 (SEQ
ID NO.: 1097) (Poly CG, 30 bases). Expression of the activation marker CD86 (B7-2)
on CD19-positive B cells was measured by flow cytometry.
Fig. 5 demonstrates that the length of the sequence, at least for Poly T ODNs, has
an important impact on its activity. A Poly T sequence containing only 18 bases (SEQ
ID NO.: 913) was shown to be less stimulatory than one with 27 bases (SEQ ID NO.:
911) or one with 30 bases (SEQ ID NO.: 1094) with a clear rank of stimulation: SEQ ID
NO.: 1094> SEQ ID NO.: 911> SEQ ID NO.: 913. Poly A (SEQ ID NO.: 1095) or Poly
CG (SEQ ID NO.: 1097) sequences, in contrast, do not induce activation of human B
cells. Surprisingly it was also discovered that Poly C sequences (SEQ ID NO.: 1096)
can activate human B cells at least at high concentrations (lOug/ml) (Fig. 5).

Two other T-rich ODNs, namely 1982 (SEQ ID NO.: 225) and 2041 (SEQ ID
NO.: 282) lacking CpG motifs were tested for their effect on human B cells. PBMC
(n=2) were incubated with the indicated concentrations of ODN 2006 (SEQ ID NO.:
246), 1982 (SEQ ID NO.: 225) and 2041 (SEQ ID NO.: 282) as described above. B cell
activation (expression of the activation marker CD86) was measured by flow cytometry.
Fig. 6 demonstrates that T-rich non-CpG ODN are immunostimulatory at
concentrations higher than 1μg/ml. Incorporation of a CpG motif into 1982 enhanced the
immunostimulatory activity. Elongation with a Poly T sequence did not enhance the
immunostimulatory activity of this already T-rich ODN but rather, decreased the
activation potential slightly.
Example 7: Immunostimulation of non-CpG ODNs is reflected in the
enhancement of NK activation, NK cytotoxicity and monocyte activation
NK cells as well as monocytes were tested for their response to non-CpG ODNs.
PBMC (2x106 cells/ml) were incubated with 6μg/ml of the following ODNs (n=4): 2006
(SEQ ID NO.: 246), 2117 (SEQ ID NO.: 358), 2137 (SEQ ID NO.: 886), 2183 (SEQ ID
NO.: 433), 2194 (SEQ ID NO.: 911) and 5126 (SEQ ID NO.: 1058). After 24h of
cultivation at 37°C cells were harvested and stained with mAb for CD3 (T cell marker),
CD56 (NK cell marker) and CD69 (early activation marker) as described above.
Expression of CD69 on CD56-positive NK cells was measured by flow cytometry.
Fig. 7 shows that for Poly T ODNs similar effects can be observed as described
in Fig. 5. The stimulation of NK cells, like B cells, may be influenced by the length of
the ODN. ODN 2183 (SEQ ID NO.: 433) (21 bases) induced activation of NK cells but
to a lesser extent than the longer ODN 2194 (SEQ ID NO.: 911) (27 bases), as measured
by enhanced expression of the early activation marker CD69. ODN 5126 (SEQ ID NO.:
1058) was also demonstrated to activate human NK cells (Fig. 7).
It is believed that the anti-tumor activity of CpG ODNs can be assessed by the
ability of the ODN to enhance NK-mediated cytotoxicity in vitro. ODNs containing at
the 5' and 3' ends stretches of Poly G were shown to result in the highest induction of
cytotoxicity (Ballas, Z. K., et al. 1996 J. Immunol. 157:1840). To investigate the
influence of non-CpG T-rich ODN on NK cytotoxicity, we analyzed the effect of the

ODNs 2194 (SEQ ID NO.: 911) and 5126 (SEQ ID NO.: 1058) on NK-mediated lysis
(Fig. 8). NK-mediated lysis of K.-562 target cells was measured after over night
incubation of PBMC with 6μg/ml of the ODN 2006 (SEQ ID NO.: 246), SEQ ID NO.:
911 (SEQ ID NO.: 911 ) (Poly T, 27 bases) and 5126 (SEQ ID NO.: 1058) as described
above. SEQ ID NO.: 1058 demonstrated small increases in lysis by human NK cells as
compared to no ODN. SEQ ID NO.: 911 and SEQ ID NO.: 246 enhanced human NK
cell cytotoxicity to an even higher extent.
Previous reports demonstrated that not only NK cells but also NKT cells are
mediators of cytotoxic responses to tumor cells (14). We, therefore, looked at the
potential activation of human NKT cells by T-rich non-CpG ODN. PBMC of one
representative donor (n=2) were incubated with 6ng/ml ODN 2006 (SEQ ID NO.: 246),
2117 (SEQ ID NO.: 358), 2137 (SEQ ID NO.: 886), 2183 (SEQ ID NO.: 433), 2194
(SEQ ID NO.: 913) and 5126 (SEQ ID NO.: 1058) for 24h as described above.
Activation of NKT cells was measured by flow cytometry after staining of cells with
mAb for CD3 (T cell marker), CD56 (NK cell marker) and CD69 (early activation
marker). Shown is the expression of CD69 on CD3 and CD56 double-positive cells
(NKT cells).
In Fig. 9, SEQ ID NO.: 911 as well as SEQ ID NO.: 1058 were found to
stimulate NKT cells. Similar to NK cells SEQ ID NO.: 911 (Poly T) was more active
than SEQ ID NO. 1058. In addition, as described above for B cells and NK cells, the
length of the ODN has some influence on the immunostimulatory potential, with the
longer ODN having stronger effects on NKT cells. Similar results were observed for
human T cells.
Another type of cell of the immune system involved in fighting infections is the
monocytes. These cells release upon activation a variety of cytokines and can mature
into dendritic cells (DC), professional antigen-presenting cells (Roitt, I., J. Brostoff, and
D. Male. 1998. Immunology. Mosby, London). Fig. 10 shows activation of human
monocytes after culturing of PBMC with different ODNs. PBMC (2x106 cells/ml) were
incubated with 6μg/ml 2006 (SEQ ID NO.: 246), 2117 (SEQ ID NO.: 358), 2137 (SEQ
ID NO.: 886), 2178 (SEQ ID NO.:1096), 2183 (SEQ ID NO.: 433), 2194 (SEQ ID NO.:
911), 5126 (SEQ ID NO.: 1058) and 5163 (SEQ ID NO.: 1095) overnight at 37°C as

described above (n=3). Cells were harvested and stained for CD 14 (monocyte marker)
and CD80 (B7-1, activation marker). Expression was measured by flow cytometry.
As demonstrated above for NK and B cells, T-rich sequences (e.g., SEQ ID NO.:
433, SEQ ID NO.: 911) of different length induce monocyte stimulation but have
different levels of activity e.g., SEQ ID NO.: 433> SEQ ID NO.: 911. Poly A (SEQ ID
NO.: 1095) as well as Poly C (SEQ ID NO.: 1096 (2178) sequences, in contrast, did not
lead to activation of monocytes (measured by the upregulation of CD80 at a
concentration of 6ug/ml ODN).
Example 8: Induction ofcytokine release by non-CpG ODNs
Next the ability of different T-rich ODNs to influence the cytokine milieu was
examined. PBMC (3xl06cells/ml) were cultured for 24h with or without 6μg/ml of the
indicated ODNs or 1μg/ml LPS as positive control (n=2). After incubation supematants
were collected and TNFα measured by ELISA as described above and the results are
shown in Fig. 11. PBMC were cultured with the indicated ODNs (1.0g/ml) as
described in Fig. 11 and IL-6 was measured in the supematants by ELISA and the results
are shown in Fig. 12.
Fig. 11 and 12 demonstrate that T-rich non-CpG and T-rich/CpG ODNs can
induce the secretion of the pro-inflammatory cytokines TNFa and IL-6. For both
cytokines, ODN 5126 (SEQ ID NO.: 1058) was found in most assays to be as potent as
ODN 2194 (SEQ ID NO.: 911). It is known that CpG ODNs influence the Thl/Th2
balance by preferentially inducing Thl cytokines (Krieg, A. M. 1999 Biochemica et
Biophysica Acta 93321:1). To test whether T-rich ODN caused a similar shift to Thl
cytokines, IFNy production in PBMC was measured. In a first set of experiments, it was
demonstrated that, as described for IL-6 and TNFa, ODNs SEQ ID NO.: 1058 and SEQ
ID NO.: 911 induced the release of comparable amounts of this Thl cytokine IFNy. In
addition, it was demonstrated that another pro-inflammatory cytokine, IL-1, was
released upon culture of PBMC with these two ODNs. Although the amount of these
cytokines induced by the T-rich ODN lacking CpG motifs was less than when CpG ODN
SEQ ID NO.: 246 was used the amounts induced by T-rich ODN were significantly
higher than the-control.

Examples 9-11
Introduction:
An optimal CpG motif for immune system activation in non-rodent vertebrates is
described herein. A phosphodiester oligonucleotide containing this motif was found to
strongly stimulate CD86, CD40, CD54 and MHCII expression, IL-6 synthesis and
proliferation of primary human B-cells. These effects required internalisation of the
oligonucleotide and endosomal maturation. This CpG motif was associated with the
sustained induction of the NFKB p50/p65 heterodimer and of the transcription factor
complex activating protein-1 (AP-1). Transcription factor activation by CpG DNA was
preceded by increased phosphorylation of the stress kinases c-jun NH2 terminal kinase
(JNK) and p38, and of activating transcription factor-2 (ATF-2). In contrast to CpG,
signaling through the B-cell receptor led to activation of extracellular receptor kinase
(ERK) and to phosphorylation of a different isoform of JNK.
Materials and Methods:
Oligodeoxynudeotides: Unmodified (phosphodiester, PE)and modified
nuclease-resistant (phosphorothioate, PS) ODN were purchased from Operon
Technologies (Alameda, CA) and Hybridon Specialty Products (Milford, MA). The
sequences used are provided in Table H. E. coli DNA and calf thymus DNA were
purchased from Sigma Chemical Co., St. Louis, MO. Genomic DNA samples were
purified by extraction with phenol-chloroform-isoamyl alcohol (25/24/1) and ethanol
precipitation. DNA was purified from endotoxin by repeated extraction with triton x-114
(Sigma Chemical Co., St. Louis, MO) and tested for endotoxin using the LAL-assay
(LAL-assay BioWhittaker, Walkersville, MD; lower detection limit 0.1 EU/ml) and the
high sensitivity assay for endotoxin described earlier (lower detection limit 0.0014
EU/ml) (Hartmann G., and Krieg A. M. 1999. CpG DNA and LPS induce distinct
patterns of activation in human monocytes. Gene Therapy 6:893). Endotoxin content of
DNA samples was below 0.0014 U/ml. E. coli and calf thymus DNA were made single
stranded before use by boiling for 10 minutes, followed by cooling on ice for 5 minutes.
DNA samples were diluted in TE-buffer using pyrogen-free reagents.
Table H: Oligonucleotide panel used1



Cell preparation and cell culture: Human peripheral blood mononuclear cells
(PBMC) were isolated from peripheral blood of healthy volunteers by Ficoll-Paque
density gradient centrifugation (Histopaque-1077, Sigma Chemical Co., St. Louis, MO)
as described (Hartmann G., et al 1996 Antisense Nucleic Acid Drug Dev 6:291)). Cells
were suspended in RPMI 1640 culture medium supplemented with 10 % (v/v) heat-
inactivated (56°C, 1 h) FCS (HyClone, Logan, UT), 1.5 mM L-glutamine, 100 U/ml
penicillin and 100 g/ml streptomycin (all from Gibco BRL, Grand Island, NY)
(complete medium). All compounds were purchased endotoxin-tested. Viability was
determined before and after incubation with ODN by trypan blue exclusion
(conventional microscopy) or by propidium iodide exclusion (flow cytometric analysis).
In all experiments, 96 % to 99 % of PBMC were viable. Cells (final concentration 1 x
106 cells/ml) were cultured in complete medium in a 5 % CO2 humidified incubator at
37°C. Different oligonucleotides (see table I, concentration as indicated in the figure
legends), LPS (from salmonella typhimurium, Sigma Chemical Co., St. Louis, MO) or
anti-IgM were used as stimuli. Chloroquine (5 g/ml; Sigma Chemical Co., St. Louis,
MO) was used to block endosomal maturation/acidification. At the indicated time points,
cells were harvested for flow cytometry as described below.
For signal transduction studies, human primary B-cells were isolated by
immunomagnetic cell sorting using the VARIOMACS technique (Miltenyi Biotec Inc.,
Auburn, CA) as described by the manufacturer. In brief, PBMC obtained from buffy
coats of healthy blood donors (Elmer L. DeGowin Blood Center, University of Iowa)
were incubated with a microbeads-conjugated antibody to CD 19 and passed over a
positive selection column. Purity of B-cells was higher than 95%. After stimulation,
whole cellular extracts (Western blot) and nuclear extracts (EMSA) for signal
transduction studies were prepared.
For CpG binding protein studies, Ramos cells (human Burkitt lymphoma B cell
line, ATCC CRL-1923 or CRL-1596; Intervirology 5: 319-334,1975) were grown in
complete medium. Untreated cells were harvested and cytosolic protein extracts were
prepared and analyzed for the presence of CpG oligonucleotide binding proteins by
EMSA and UV-crosslink as described below.
Flow cytometry: Staining of surface antigens was performed as previously
described (Hartmann G. et al. 1998 J Pharmacol Exp Ther 285:920). Monoclonal

antibodies to HLA-DR were purchased from Immunotech, Marseille, France. All other
antibodies were purchased from Pharmingen, San Diego, CA: mABs to CD 19 (B43),
CD40 (5C3), CD54 (HA58), CD86 (2331 (FUN-1)). IgG1,k (MOPC-21) and IgG2b,k
were used to control for specific staining. Intracellular cytokine staining for IL-6 was
performed as described (Hartmann G., and Krieg A. M. 1999. CpG DNA and LPS
induce distinct patterns of activation in human monocytes. Gene Therapy 6:893). In
brief, PBMC (final concentration 1 x 106 cells/ml) were incubated in the presence of
brefeldin A (final concentration 1 ug/ml, Sigma Chemical Co., St. Louis, MO). After
incubation, cells were harvested and stained using a FITC-labeled mAB to CD 19 (B43),
a PE-labeled rat anti-human IL-6 mAb (MQ2-6A3, Pharmingen) and the Fix and Perm
Kit (Caltag Laboratories, Burlingame, CA). Flow cytometric data of 5000 cells per
sample were acquired on a FACScan (Beckton Dickinson Immunocytometry Systems,
San Jose, CA). Non-viable cells were excluded from analysis by propidium iodide
staining (2 ug/ml). Data were analyzed using the computer program FlowJo (version
2.5.1, Tree Star, Inc., Stanford, CA).
Proliferation assay: CFSE (5-(and-6-) carboxyfluorescein diacetate
succinimidyl ester, Molecular Probes, USA) is a fluorescein-derived intracellular
fluorescent label which is divided equally between daughter cells upon cell division.
Staining of cells with CFSE allows both quantification and immunophenotyping
(phycoerythrin-labeled antibodies) of proliferating cells in a mixed cell suspension.
Briefly, PBMC were washed twice in PBS, resuspended in PBS containing CFSE at a
final concentration of 5 uM, and incubated at 37°C for 10 minutes. Cells were washed
three times with PBS and incubated for five days as indicated in the figure legends.
Proliferating CD19-positive B-cells were identified by decreased CFSE content using
flow cytometry.
Preparation of whole cell, nuclear and cytosolic protein extracts: For Western
blot analysis, whole cell extracts were prepared. Primary B-cells were treated with
medium, the phosphodiester oligonucleotides 2080 (SEQ ID NO.: 321) or 2078 (SEQ ID
NO.: 319) at 30 ug/ml, or anti-IgM (10 ug/ml). Cells were harvested, washed twice with
ice-cold PBS containing 1 mM Na3VO4, resuspended in lysis buffer (150 mM NaCl, 10
mM TRIS pH 7.4, 1 % NP40, 1 mM Na3VO4, 50 mM NaF, 30 mg/ml leupeptin, 50
mg/ml aprotinin, 5 mg/ml antipain, 5 mg/ml pepstatin, 50 g/ml

phenylmethylsulfonylfluoride (PMSF)), incubated for 15 min on ice and spun at 14000
rpm for 10 min. The supernatant was frozen at -80 C. For the preparation of nuclear
extracts, primary B-cells were resuspended in hypotonic buffer (10 mM HEPES/KOH
(pH 7.9), 10 mM KC1, 0.05 % NP40,1.5 mM MgCl2, 0.5 mM dithiothfeitol (DTT), 0.5
mM PMSF, 30 mg/ml leupeptin, 50 mg/ml aprotinin, 5 mg/ml antipain, 5 mg/ml
pepstatin). After 15 minutes incubation on ice, the suspension was centrifuged at 1000 x
g for 5 minutes. The pelleted nuclei were resuspended in extraction buffer (20 mM
HEPES (pH 7.9), 450 mM NaCl, 50 mM NaF, 20% glycerol, 1 mM EDTA, 1 mM
EGTA, 1 mM DTT, 1 mM PMSF, 30 mg/ml leupeptin, 50 mg/ml aprotinin, 5 mg/ml
antipain, 5 mg/ml pepslatin) and incubated on ice for one hour. The nuclear suspension
was centrifuged for 10 minutes at 16,000 g at 4°C. Supernatant was collected and stored
at -80°C. Cytosolic extracts for the CpG binding protein studies were prepared from
unstimulated Ramos cells, which were lysed with hypotonic buffer as described for the
preparation of the nuclear extract. After centrifugation, the supernatant was removed as
cytoplasmic fraction and stored at -80°C. Protein concentrations were measured using a
Bradford protein assay (Bio-Rad, Hercules, CA) according to the manufacturer.
Western blot analysis: Equal concentrations of whole cell protein extracts (25
fig/lane) were boiled in SDS sample buffer (50 mM Tris-Cl, pH 6.8; 1% p-
mercaptoethanol; 2% SDS; 0.1% bromphenolblue; 10% glycerol) for 4 min before being
subjected to electrophoresis on a 10 % polyacrylamide gel containing 0.1 % SDS (SDS-
PAGE). After electrophoresis; proteins were transferred to Immobilion-P transfer
membranes (Millipore Corp. Bedford, MA). Blots were blocked with 5 % nonfat dry
milk. Specific antibodies against the phosphorylated form of extracellular receptor kinase
(ERK), c-jun NH2-terminal kinase (JNK), p38 and activating transcription factor-2
(ATF-2) were used (New England BioLabs, Beverly, MA). Blots were developed in
enhanced chemiluminescence reagent (ECL; Amersham International, Aylesbury, U.K.)
according to the manufacturer's recommended procedure.
Electrophoretic mobility shift assay (EMSA): To detect the DNA-binding
activity of the transcription factor activator protein-1 (AP-1) and NFKB, nuclear extracts
(1 jig/lane) were analyzed by EMSA using the dsODNs 5' GAT CTA GTG ATG AGT
CAG CCG GAT C 3' (SEQ ID NO.: 838) containing the AP-1 binding sequence, and the
NFKB URE from the c-myc promotor region 5' TGC AGG AAG TCC GGG TTT TCC

CCA ACC CCC C 3' (SEQ ID NO.: 1142), as probes. ODNs were end labeled with T4-
polynucleotide kinase (New England Biolabs) and (- P) ATP (Amersham, Arlington
Heights, IL). Binding reactions were performed with 1 ug nuclear protein extract in
DNA-binding buffer (10 mM Tris-HCl (pH 7.5), 40 mM MgCl2, 20 mM EDTA, 1 mM
dithiothreitol, 8% glycerol and 100 - 400 ng of poly (dI-dC) with 20.000 - 40.000 cpm
labeled ODN in 10 l total volume. Specificity of the NFKB bands was confirmed by
competition studies with cold oligonucleotides from unrelated transcription factor
binding sites (10-100 ng). For the supershift assay, 2 ug of specific antibodies for c-Rel,
p50 and p65 (Santa Cruz Biotechnology, Inc., Santa Cruz, CA) were added into the
reaction mixture for 30 min before the radiolabeled probe was added. Following
incubation for 30 minutes at room temperature loading buffer was added and the probes
were electrophoresed on a 6 % polyacrylamide gel in Tris-borate-EDTA running buffer
(90 mM Tris, 90 mM boric acid, 2 mM EDTA, pH 8.0). Gels were dried and then
autoradiographed.
UV-crossIinking and denaturing protein electrophoresis: Nuclear extracts
were incubated with labeled phosphodiester oligonucleotide as described for the EMSA.
DNA-protein complexes were crosslinked with UV-light in a Stratalinker (Stratagene)
for 10 minutes. Probes were mixed with SDS-sample buffer, boiled for 10 minutes and
loaded on a 7.5% SDS-PAGE. The gel was dried on Whatman paper and
autoradiographed. Plotting the distance against the molecular weight of the marker
proteins yielded a standard curve which was used to calculate the approximate molecular
weight of the crosslinked protein-ODN complexes. The molecular weight of the
oligonucleotide was subtracted from this value to give the size.
Example 9: Identification of an Optimal CpG motif for use alone or in
combination with a T-rich ODN
Phosphorothioate oligonucleotides containing the murine CpG motif GACGTT
(SEQ ID NO.: 1143) (for example 1826 (SEQ ID NO.: 69)) and used at concentrations
which are active in murine B-cells (Yi A. K., Chang M., Peckham D. W., Krieg A. M.,
and Ashman R. F. 1998. CpG oligodeoxyribonucleotides rescue mature spleen B cells
from spontaneous apoptosis and promote cell cycle entry. J Immunol 160:5898), have
showed little or no immunostimulatory activity on human immune cells. At higher

concentrations this ODN was found to demonstrate some stimulatory effect on human B
cells.
In earlier studies on B-cell activation in mice, it was found that a CpG-
dinucleotide flanked by two 5' purines and two 3' pyrimidines and preferably the 6mer
motif 5' GACGTT 3' (SEQ ID NO: 1143) was optimal for a phosphodiester
oligonucleotide to be active (Krieg A. M., et al. 1995 Nature 374:546, Yi A. K., Chang
M.,etaL 1998 J Immunol 160:5898).
In order to identify an optimal motif for stimulation of an immune response in
humans and non-rodent vertebrates we designed a series of ODN and tested their
activity. First we designed a 20 mer phosphodiester oligonucleotide with a TC
dinucleotide at the 5' end preceding the optimal murine CpG motif 5* GACGTT 3'
(SEQ ID NO.: 1143) and foHowed by a poly C tail (2079: 5' TCG ACG TTC CCC CCC
CCC CC 3'(SEQ ID NO.: 320)). This oligonucleotide if added to human primary B-cells
under the same conditions as found to be optimal for E. coli DNA (repeated addition at 0
hours, 4 hours and 18 hours; 30 g/ml for each time point) stimulated high levels of
CD86 expression on human primary B-cells after two days. To determine the structure-
function relationship of the CpG motifs, we replaced the bases adjacent to the CpG
dinucleotides while maintaining the two CpG dinucleotides within the sequence.
Exchange of the adenine located between both CpG dinucleotides by thymidine (2080
(SEQ ID NO.: 321)) resulted in slightly higher activity. Replacement by guanosine
(2100 (SEQ ID NO.: 341)) or cytidine (2082 (SEQ ID NO.: 323)) at this position showed
no major changes compared to 2079 (SEQ ID NO.: 320). In contrast, replacement of the
thymidine 3' to the second CpG dinucleotide by the purines guanosine (2099 (SEQ ID
NO.: 340)) or adenine (2083 (SEQ ID NO.: 324)) resulted in a major drop in activity of
the oligonucleotide, while the pyrimidine cytidine caused only a minor decrease. The
thymidine immediately 5' to the first CpG dinucleotide was also important.
Replacement of the thymidine by any other base (2105 (SEQ ID NO.: 346), guanosine;
2107 (SEQ ID NO.: 348), adenine; 2104 (SEQ ID NO.: 345), cytidine) led to a marked
decrease in activity of the oligonucleotide. Elimination of the first (2108 (SEQ ID NO.:
349)) or the second (2106 (SEQ ID NO.: 347)) CpG dinucleotide also partially reduced
the activity.

The addition of more 5' GTCGTT 3' (SEQ ID NO.: 1144) CpG motifs to the
phosphodiester oligonucleotide containing the 8mer duplex CpG motif (5' TCGTCGTT
3' (SEQ ID NO:1145) , 2080 (SEQ ID NO.: 321)) did not further enhance CD86
expression on B-cells (2059 (SEQ ID NO.: 300)). An oligonucleotide with the same
sequence as 2080 (SEQ ID NO.: 321) but with a phosphorothioate backbone showed no
activity above background (2116 (SEQ ID NO.: 357)). This was surprising since the
phosphorothioate backbone has been reported to greatly stabilize oligonucleotides and
enhance CpG-induced stimulation (Krieg A. M., Yi A. K., Matson S., Waldschmidt T. J.,
Bishop G. A., Teasdale R., Koretzky G. A., and Klinman D. M. 1995. CpG motifs in
bacterial DNA trigger direct B-cell activation. Nature 374:546). We therefore performed
further structure-function analysis of phosphorothioate oligonucleotides containing the 5'
GTCGTT 3' (SEQ ID NO:1144) and 5' TCGTCGTT 3' (SEQ ID NO:1145) motifs,
which showed that additional CpG motifs (2006 (SEQ ID NO.: 246)) tended to increase
the activity of phosphorothioate oligonucleotides.
Purified B-cells isolated from peripheral blood by immunomagnetic cell sorting
were activated by CpG DNA to the same extent as unpurified B-cells within PBMC.
Thus, activation of B-cells is a primary response and not a secondary effect caused by
cytokines secreted by other cells.
In addition to the co-stimulatory molecule CD86, the functional stage of B-cells
is characterized by other surface markers. For example, activated T helper cells stimulate
B-cells by CD40 ligation, the intercellular adhesion molecule-1 (ICAM-1, CD54)
mediates binding to other immune cells, and major histocompatibility complex II (MHC
II) is responsible for antigen presentation. We found that B cell expression of CD40,
CD54 and MHC II was upregulated by the CpG oligonucleotide 2080 (SEQ ID NO.:
321). The non-CpG control oligonucleotide 2078 (SEQ ID NO.: 319) showed no activity
compared to medium alone.
When PBMC were incubated for 5 days in the presence of 2080 (SEQ ID NO.:
321) (added at 0 hours, 4 hours, 18 hours and every subsequent morning), it was
intriguing that a subpopulation of lymphocytes increased in cell size (FSC) and became
more granular (SSC). To examine if this subpopulation represented proliferating B-cells,
we stained freshly isolated PBMC with CFSE (5-(and-6-) carboxyfluorescein diacetate
succinimidyl ester) at day 0 and incubated them for 5 days with 2080 (SEQ ID NO.: 321)

as above. CFSE is a fluorescent molecule that binds irreversibly to cell proteins. Each
cell division decreases CFSE stain by 50 %. Cells staining low with CFSE (proliferating
cells) were found to be mainly CD 19-positive B-cells. Thcoligonucleotide 2080 (SEQ
ID NO.: 321) induced 60 to 70 % of CD} 9 positive B-cells to proliferate within 5 days.
The control oligonucleotide 2078 (SEQ ID NO.: 319) induced less than 5 % of B-cells to
proliferate. Proliferating B-cells (CFSE low) showed a larger cell size (FSC) and higher
granularity.
Proliferating B-cells expressed higher levels of CD86 than non-proliferating cells
(not shown). In agreement with this finding, the oligonucleotide panel tested above for
induction of CD86 expression resulted in an almost identical pattern of B-cell
proliferation. Replacement of the 3' thymidine reduced activity more than changing the
thymidine in the middle position.
Example 10: B-cell activation requires endosomal maturation/acidification
It has previously been shown that chloroquine, an inhibitor of endosomal
acidification, blocks CpG-mediated stimulation of murine antigen presenting cells and B-
cells, while not influencing LPS-mediated effects (Hacker H., et al 1998 Embo J
17:6230, Yi A. K.et al 1998 J Immunol 160:4755, Macfarlane D. E., and Manzel L.
1998 J Immunol 160:1122). We found that the addition of 5 g/ml chloroquine
completely blocked CpG DNA-mediated induction of CD86 expression on primary B-
cells (MFI CD86: 2006 (SEQ ID NO.: 246), 4.7 vs 1.4; E. coH DNA, 3.4 vs. 1.4;
medium only, 0.9; n=4). Furthermore, chloroquine completely inhibited the induction of
B-cell proliferation by the phosphorothioate oligonucleotide 2006 (SEQ ID NO.: 246)
measured with the CFSE proliferation assay as well as with the standard . These results
suggest that as with murine cells, activation of human B-cells by CpG DNA requires the
uptake of DNA in endosomes and subsequent endosomal acidification.
Example 11: Analysis of sub-cellular events resulting upon human B cell
stimulation with optimal human ODN.
Since the CpG motif requirement for maximal B-cell activation is substantially
different between mouse (GACGTT) (SEQ ID NO: 1143) and humans (TCGTCGTT)
(SEQ ID NO: 1145), we were interested if the basic intracellular signaling events are

comparable. Rapid induction of NFKB binding activity has been found earlier in murine
B-cells and macrophages (Stacey K. J., et al 1996 J Immunol 157:2116, Yi A. K et al
1998 J Immunol 160:4755). To investigate the NFKB response to CpG DNA in humans,
human primary B-cells were isolated from peripheral blood by immunomagnetic cell
sorting and incubated with the CpG oligonucleotide 2080 (SEQ ID NO.: 321), the non-
CpG control oligonucleotide 2078 (SEQ ID NO.: 319), or medium. At the indicated time
points, cells were harvested and nuclear extracts were prepared. In the presence of CpG
oligonucleotide, NFKB binding activity was increased within one hour and maintained up
to 18 hours (latest time point examined). The non-CpG control oligonucleotide 2078
(SEQ ID NO.: 319) did not show enhanced NFKB activity compared to cells incubated
with medium only. The NFKB band was identified by cold competition, and shown to
consist of p50 and p65 subunits by supershift assay.
The activating protein-1 (AP-1) transcription factor is involved in the regulation
of immediate early genes and cytokine expression (Karin M. 1995. The regulation of AP-
1 activity by mitogen-activated protein kinases. J Biol Chem 270:16483). In murine B-
cells, AP-1 binding activity is induced in response to CpG DNA (Yi A. K., and Krieg A.
M. 1998. Rapid induction of mitogen-activated protein kinases by immune stimulatory
CpG DNA. J Immunol 161:4493). To determine whether this transcription factor would
also be induced by CpG DNA in humans, we examined AP-1 DNA binding activity in
human primary B-cells. Cells were incubated with the CpG oligonucleotide 2080 (SEQ
ID NO.: 321) or the control oligonucleotide 2078 (SEQ ID NO.: 319). Nuclear extracts
were prepared and the AP-1 binding activity was analyzed by EMS A. AP-1 binding
activity was enhanced within one hour, and increased up to 18 hours (latest time point
examined), showing a sustained response.
Since AP-1 activity is induced by many stimuli (Angel P., and Karin M. 1991.
The role of Jun, Fos and the AP-1 complex in cell-proliferation and transformation.
Biochim Biophys Acta 1072:129), we were interested in signal transduction pathways
upstream of AP-1. The AP-1 transcription factor complex integrates different mitogen
activated protein kinase (MAPK) pathways (Karin M. 1995. The regulation of AP-1
activity by mitogen-activated protein kinases. J Biol Chem 270:16483). Western blots
were performed using whole cell extracts from primary B-cells incubated with the CpG
oligonucleotide 2080 (SEQ ID NO.: 321), the controf 2078 (SEQ ID NO.: 319), or

medium only. Specific antibodies to the phosphorylated form of JNK, p38, ATF-2 and
ERK were used. Strong induction of JNK phosphorylation was found 30 min and 60 min
after exposure to CpG-DNA, while the non-CpG oligonucleotide showed no activity
above background. The protein kinase p38, another stress activated protein kinase
(SAPK), was also phosphorylated in response to CpG DNA within 60 min. ATF-2, a
substrate of both p38 and JNK (Gupta S., Campbell D., Derijard B., and Davis R. J.
1995. Transcription factor ATF2 regulation by the JNK signal transduction pathway.
Science 267:389) and a component of the AP-1 complex, showed weak phosphorylation
after 30 min which increased after 60 min. CpG DNA failed to induce substantial
phosphorylation of ERK. In contrast, anti-IgM, stimulating the B-cell receptor, did
trigger phosphorylation of ERK. Anti-IgM activated different isoforms of JNK than CpG
DNA.
Example 12: Assay for in vivo adjuvant activity.
An in vitro screening assay to identify ODN useful as an adjuvant in vivo in
humans and other non-rodent animals was developed. Since we saw not only
quantitative but also qualitative differences in activities of different CpG ODN in mice,
we first screened a panel of CpG and non-CpG control ODN on mouse cells to find in
vitro assays with reliable and strong correlation to in vivo adjuvant activity with hepatitis
B surface antigen (HBsAg). We then systematically tested a panel of more than 250
ODN in corresponding human assays to identify sequences with in vitro
immunostimulatory activity. We next examined if the ODN with the highest activity in
these human assays also activate B cell proliferation in chimpanzees and monkeys, and
finally, if they are active as adjuvants with HBsAg in chimpanzees and cynomolgus
monkeys in vivo. These studies revealed that the sequence, number and spacing of
individual CpG motifs contribute to the immunostimulatory activity of a CpG
phosphorothioate ODN. An ODN with a TC dinucleotide at the 5' end followed by three
6mer CpG motifs (5' GTCGTT 3') separated by TT dinucleotides consistently showed
the highest activity for human, chimpanzee, and rhesus monkey leukocytes.
Chimpanzees or monkeys vaccinated once against hepatitis B with this CpG ODN
adjuvant developed 15 times higher anti-HBs antibody titers than those receiving vaccine
alone.

Materials and Methods
Oligodeoxynucleotides: Phosphorothioate-modified ODN were purchased from
Operon Technologies (Alameda, CA) and Hybridon Specialty Products (Milford, MA).
ODN were tested for endotoxin using the LAL-assay (LAL-assay BioWhittaker,
Walkersville, MD; lower detection limit 0.1 EU/ml). For in vitro assays, ODN were
diluted in TE-buffer (10 mM Tris, pH 7.0, 1 mM EDTA), and stored at -20° C. For in
vivo use, ODN were diluted in phosphate buffered saline (0.1 M PBS, pH 7.3) and stored
at 4°C. All dilutions were carried out using pyrogen-free reagents.
Mouse spleen cell cultures: Spleens were removed from 6-12 week old female
BALB/c (The Jackson Laboratory), 2 x 106 splenocytes were cultured with 0.2 M ODN
for 4 hours (TNF-a) or 24 hours (IL-6, IFN-, IL-12), and cytokines were detected by
ELISA as previously described (Yi A. K., Klinman D. M., Martin T. L., Matson S., and
Krieg A. M. 1996. Rapid immune activation by CpG motifs in bacterial DNA. Systemic
induction of IL-6 transcription through an antioxidant-sensitive pathway. J Immunol
157:5394). To evaluate CpG-induced B cell proliferation, spleen cells were depleted of T
cells with anti-Thy-1.2 and complement and centrifugation over lympholyte M®
(Cedarlane Laboratories, Hornby, ON, Canada), cultured for 44 hours with the indicated
ODN, and then pulsed for 4 hours with 1 Ci of 3H thymidine as described previously
(Krieg A. M., Yi A. K., Matson S., Waldschmidt T. J., Bishop G. A., Teasdale R.,
Koretzky G. A., and Klinman D. M. 1995. CpG motifs in bacterial DNA trigger direct B-
cell activation. Nature 374:546). To examine NK cell lytic activity murine spleen cells
were depleted of B cells using magnetic beads coated with goat anti-mouse Ig as
previously detailed (Ballas Z. K., and Rasmussen W. 1993. Lymphokine-activated killer
cells. VII. IL-4 induces anNKl.l+CD8 ct+P' TCR-ap B220+ lymphokine-activated killer
subset. J Immunol 150:17). Cells were cultured at 5 x 106/well in 24-well plates and
harvested at 18 hours for use as effector cells in a standard 4 hour 51Cr-release assay
against YAC-1 target cells. One unit (LU) was defined as the number of cells needed to
effect 30 % specific lysis.
Immunization of mice against HBsAg and evaluation of the humoral
response: Groups of 6-8 week old female BALB/c mice (n = 5 or 10, Charles River,
Montreal, QC) were immunized against HBsAg as previously described (Davis H. L., et

al 1998 J Immunol 160:870). In brief, each mouse Teceived a single IM injection of 50
l PBS containing 1 g recombinant HBsAg (Medix Biotech, Foster City, CA) and 10
jag of CpG ODN or non-CpG ODN as a sole adjuvant or combined with alum
(AlhydrogeL"85'; Superfos Biosector, Vedbaek, Denmark; 25 mg Al34Ymg HBsAg).
Control mice were immunized with HBsAg without adjuvant or with alum. Plasma was
recovered from mice at various times after immunization and Abs specific to HBsAg
(anti-HBs) were quantified by end-point dilution ELISA assay (in triplicate) as described
previously (Davis H. L et al 1998 J Immunol 160:870). End-point titers were defined as
the highest plasma dilution that resulted in an absorbance value (OD450) two times
higher than that of non-immune plasma with a cut-off value of 0.05.
Isolation of primate PBMC and cell culture: Peripheral blood mononuclear
cells (PBMC) were isolated from peripheral blood of healthy volunteers, chimpanzees or
rhesus or cynomolgus monkeys by Ficoll-hypaque density gradient centrifugation
(Histopaque-1077, Sigma Chemical Co., St. Louis, MO) as described (Hartmann G., et al
1996 Antisense Nucleic Acid Drug Dev 6:291). Cells were suspended in RPMI1640
culture medium supplemented with 10 % (v/v) heat-inactivated (56°C, 1 h) FCS
(HyClone, Logan, UT), 1.5 mM L-glutamine, 100 U/ml penicillin and 100 g/ml
streptomycin (all from Gibco BRL, Grand Island, NY) (complete medium). Cells (final
concentration 1 x 106 cells/ml) were cultured in complete medium in a 5 % CO2
humidified incubator at 37°C. GDN and LPS (from Salmonella typhimurium, Sigma
Chemical Co., St. Louis, MO) or anti-IgM were used as stimuli. For measurement of
human NK lytic activity, PBMC were incubated at 5 x 106/well in 24-well plates.
Cultures were harvested after 24 hours, and cells were used as effectors in a standard 4
hours 51Cr-release assay against K562 target cells as previously described (Ballas Z. K.,
Rasmussen W. L., and Krieg A. M. 1996. Induction of NK activity in murine and human
cells by CpG motifs in oligodeoxymicleotides and bacterial DNA. J Immunol 157:1840;
Ballas Z. K., and Rasmussen W. 1993. Lymphokine-activated killer cells. VII. IL-4
induces an NK1.1+CD8 +( TCR-aP B220+ lymphokine-activated killer subset. J
Immunol 150:17). For B cell proliferation, 1 Ci of 3H thymidine was added 18 hours
before harvest, and the amount of 3H thymidine incorporation was determined by
scintillation counting at day 5. Standard deviations of the triplicate wells were
Flow cytometry on primate PBMC: Surface antigens on primate PBMC were
stained as previously described (Hartmann G et al 1998 JPharmacol Exp Ther
285:920). Monoclonal antibodies to CD3 (UCHT1), CD14 (M5E2), CD19 (B43), CD56
(B159), CD69 (FN50) and CD86 (2331 (FUN-1)) were purchased from Pharmingen, San
Diego, CA. IgG1,K (MOPC-21) and IgG2b,K (Hartmann G et al 1999 PNAS 96:9305)
were used to control for non-specific staining. NK cells were identified by CD56
expression on CD3, CD14 and CD19 negative cells, whereas B cells were identified by
expression of CD 19. Flow cytometric data from 10000 cells per sample were acquired on
a FACScan (Beckton Dickinson Immunocytometry Systems, San Jose, CA). The
viability of cells within the FSC/SSC gate used for analysis was examined by propidium
iodide staining (2 ug/ml) and found to be higher than 98 %. Data were analyzed using
the computer program FlowJo (version 2.5.1, Tree Star, Inc., Stanford, CA).
Immunization of chimpanzees and cynomolgus monkeys against HBsAg and
evaluation of the humoral response: Fourteen cynomolgus monkeys (2.0-3.5 kg) were
immunized with a pediatric dose of Engerix-B (SmithKline Beecham Biologicals,
Rixensart, BE) containing 10 g HBsAg adsorbed to alum (25 mg Al3+/mg HBsAg).
This was administered alone (n=5), or combined with CpG ODN 1968 (n=5, 500 g) or
CpG ODN 2006 (SEQ ID NO.: 246) (n=4, 150 g). Four chimpanzees (10-20 kg) were
immunized in the same fashion with two receiving control vaccine (Engerix-B only) and
two receiving experimental vaccine (Engerix-B plus 1 mg CpG ODN 2006). All vaccines
were administered IM in the right anterior thigh in a total volume of 1 ml. Monkeys were
maintained in the animal facility of the Primate Research Center (Bogor, Indonesia) and
chimpanzees were housed at Bioqual (Rockville, MD). Animals were monitored daily by
animal care specialists. No symptoms of general ill health or local adverse reactions at
the injection site were noted. Plasma was recovered by IV puncture prior to and at
various times after immunization and was stored frozen (-20°C) until assayed for
antibodies. Anti-HBs antibodies were detected using a commercial ELISA kit (Monolisa
Anti-HBs; Sanofi-Pasteur, Montreal, QC) and titers were expressed in mlU/ml based on
comparison with WHO defined standards (Monolisa Anti-HBs Standards; Sanofi-
Pasteur).
Results

Identification of CpG ODN with different profiles of in vitro immune activities:
Our studies showed that the precise bases on the 5' and 3' sides of a CpG dinucleotide
within a CpG motif may have an impact on the level of immune activation of a synthetic
ODN, but it has been unclear whether different CpG motifs might display different
immune effects. To evaluate this possibility, we tested a panel of CpG ODN for their
ability to induce NK lytic activity, B cell proliferation, and to stimulate synthesis of
TNF-, IL-6, IFN-Γ and IL-12 in murine spleen cells . Immunostimulatory activity of
ODN without CpG motifs (ODN 1982 (SEQ ID NO.: 225), ODN 1983 (SEQ ID NO.:
226)) was negative or weak compared to CpG ODN. ODN with non optimal CpG
motifs (ODN 1628 (SEQ ID NO.: 767), ODN 1758 (SEQ ID NO.: 1)) were less active
than ODN containing CpG motifs flanked by two 5' purines and two 3' pyrimidines
(ODN 1760 (SEQ ID NO.: 3), ODN 1826 (SEQ ID NO.: 69), ODN 1841 (SEQ ID NO.:
84)). ODN 1826 containing two optimal murine CpG motifs (5' GACGTT 3') (SEQ ID
NO:1143) had the highest activity for 5 of 6 measured endpoints. Except for ODN 1628,
all ODN showed a generally similar pattern of activity (NK cell-mediated lysis, B cell
proliferation, IL-12, IL-6, TNF a, IFN-Γ). Of note, ODN 1628, which was unique in this
panel for containing two G-rich regions, showed preferential induction of IFN-γ
synthesis but relatively low stimulation of the other activities.
Identification of in vitro assays which correlate with in vivo adjuvant activity:
Since adjuvant activity is an in vivo endpoint, we were interested in identifying in vitro
assays that would predict the adjuvant activity of a CpG ODN in vivo. The same ODN
used for in vitro endpoints therefore were tested for their adjuvant activity to immunize
mice against HBsAg. This was carried out both with ODN alone and with ODN
combined with alum, since earlier studies had shown strong synergy for CpG ODN and
alum adjuvants (PCT Published Patent Application WO98/40100).
B ALB/c mice immunized with HBsAg without adjuvant attained only low titers
of anti-HBs by 4 weeks, and this was not affected by addition of control ODN. In
contrast, addition of CpG ODN raised anti-HBs titers by 5 to 40 fold, depending on the
sequence used. When alum was added, titers of anti HBs were approximately 6 times
higher than with HBsAg alone. Specifically, control ODN had no effect and the various
CpG ODN augmented these titers 2 to 36 fold. Results obtained with the different ODN

alone correlated very strongly (r = 0.96) with those obtained using the same ODN plus
alum. When linear regression was performed, a very high degree of correlation was
found between certain in vitro assays and in vivo augmentation of anti-HBs titers. Of all
the in vitro endpoints examined, the induction of NK lytic activity showed the best
correlation to in vivo adjuvant activity (without alum, r = 0.98; with alum, r = 0.95; p 0.0001). A good correlation regarding adjuvant activity was also obtained for B-cell
stimulation (r= 0.84 and 0.7), as well as secretion of TNF-a (r= 0.9 and 0.88), IL-12 (r=
0.88 and 0.86) and IL-6 (r= 0.85 and 0.91). The one in vitro assay that did not correlate
well with the in vivo results was IFN-y secretion (r = 0.57 and 0.68). These data
demonstrate that in vitro assays for NK lytic activity, B cell activation and production of
TNF-a, IL-6 and IL-12 provide valuable information in vitro to predict the adjuvant
activity of a given ODN in vivo.
Screening of a phosphorothioate ODN panel to activate human NK cells: In
previous studies we found that synthesis of inflammatory cytokines by human PBMC is
induced by extremely low amounts of endotoxin (induced TNF-a secretion is detectable
with just 6 pg/ml endotoxin, 2 logs more sensitive than murine immune cells). In
contrast, activation of human B cells and induction of human NK cell lytic activity with
endotoxin is low even at high endotoxin concentrations. Based on these results we
selected activation of NK cells (lytic activity and CD69 expression) and B cells
(proliferation and CD86 expression) as the most highly specific and reproducible assays
with low inter-subject variability and used these assays for in vitro screening of a pool of
ODN.
First we studied the effect of phosphorothioate ODN containing various
combinations and permutations of CpG motifs on NK cell-mediated lysis of target cells.
For clarity and ease of presentation, only data with selected representative CpG and
control ODN are shown. Human PBMC were incubated with different phosphorothioate
ODN (6 ng/ml) for 24 hours and tested for their ability to lyse 51Cr-labeled K562 cells.
ODN with two 6-mer CpG motifs (either 5' GACGTT 3' (SEQ ID NO.: 1143) or 5'
GTCGTT 3' (SEQ ID NO.: 1144)) in combination with a TpC at the 5'end of the ODN
(ODN 1840 5' TCCATGTCGTTCCTGTCGTT 3' (SEQ ID NO.: 83), ODN 1851 5'
TCCTGACGTTCCTGACGTT 3' (SEQ ID NO.: 94) or with at least three 6-mer motifs
without a TpC at the 5' end (ODN 2013 (SEQ ID NO.: 253)) show intermediate activity.

High activity was found when the 5' TpC directly preceded a 6-mer human CpG motif
(5' TCGTCGTT 3' (SEQ ID NO.: 1145)) and was followed by two 6-mer motifs (ODN
2005 (SEQ ID NO.: 245), ODN 2006 (SEQ ID NO.: 246) and ODN 2007 (SEQ ID NO.:
247)). The best results were obtained when the 6-mer CpG motifs were separated from
each other and from the 5' 8-mer CpG motif by TpT (ODN 2006 (SEQ ID NO.: 246)).
Expression of the activation marker CD69 is rapidly upregulatedon the surface
of NK cells subsequent to stimulation. To confirm the results from the NK cell lysis
assay, PBMC were incubated for 18 hours with ODN (2 ug/ml). CD69 expression was
examined on CD56 positive NK cells (CD3, CD14 and CD19 negative). Although
induction of CD69 expression was less sequence restricted than stimulation of NK cell
functional activity, control ODN (ODN 1982, ODN 2116, ODN 2117, ODN 2010)
showed only low activity similar to background levels. ODN with two human CpG
motifs separated by 5' TTTT 3' (ODN 1965 (SEQ ID NO.: 208)) or four human CpG
motifs without spacing (ODN 2013 (SEQ ID NO.: 253)) were relatively more active at
inducing CD69 expression than at stimulating NK cell lytic activity. Optimal NK cell
functional activity, as well as CD69 expression, was obtained with ODNs containing a
TpC dinucleotide preceding the human CpG motif, and additional human motifs within
the sequence (ODN 2006 (SEQ ID NO.: 246), ODN 2007 (SEQ ID NO.: 247)).
Activity of phosphorothioate ODN for stimulating human B cells: In preliminary
experiments we found that the percentage of proliferating B cells (CFSE assay, see
methods section) correlated with the surface expression of the co-stimulatory CD86 B
cells, as measured by flow cytometry. Thus we used CD86 expression on B cells to
screen a panel of ODN for their immunostimulatory activity. PBMC were incubated with
0.6 g/ml ODN. Expression of CD86 (mean fluorescence intensity, MFI) was examined
on CD19 positive B cells. A poly C ODN (ODN 2017 (SEQ ID NO.: 257)) or ODN
without CpG cHnucleotides (ODN 1982 (SEQ ID NO.: 225)) failed to stimulate human B
cells under these experimental conditions. A phosphorothioate ODN (ODN 2116 (SEQ
ID NO.: 256)) with one optimal human CpG motif preceded by a TpC (5' TCGTCGTT
3' (SEQ ID NO.: 1145)) had low activity. The presence of one human 6-mer CpG motif
(5' GTCGTT 3' (SEQ ID NO.: 1144)) had no activating effect. Two of these CpG
motifs within the sequence showed no (ODN 1960 (SEQ ID NO.: 203), ODN 2016 (SEQ
ID NO.: 256)) or intermediate (ODN 1965 (SEQ ID NO.: 208)) activity dependent on the

sequence context. If the ODN was composed of three or four copies of this motif (ODN
2012 (SEQ ID NO.: 252), ODN 2013 (SEQ ID NO.: 253), ODN 2014 (SEQ ID NO.:
254)), intermediate activity on B cells could be detected. The combination of the human
8-mer CpG motif on the 5' end of the ODN with two 6-mer CpG motifs (ODN 2005
(SEQ ID NO.: 245), ODN 2006 (SEQ ID NO.: 246), ODN 2007 (SEQ ID NO.: 247),
ODN 2102 (SEQ ID NO.: 343), ODN 2103 (SEQ ID NO.: 344)) led to a considerable
increase in the ability of the ODN to stimulate B cells. The spacing between the single
motifs was critical. The separation of CpG motifs by TpT was preferable (ODN 2006
(SEQ ID NO.: 246)) compared to unseparated CpG motifs (ODN 2005 (SEQ ID NO.:);
also compare ODN 1965 (SEQ ID NO.: 208) to ODN 1960 (SEQ ID NO.: 203)). The
human 6-mer CpG motif (5' GTCGTT 3') was better than the optimal mouse 6-mer CpG
motif (5' GACGTT 3' (SEQ ID NO.: 246)) when combined with the human 8-mer CpG
motif on the 5' end (ODN 2006 vs. ODN 2102 (SEQ ID NO.: 343) and ODN 2103 (SEQ
ID NO.: 344)). A (TCG)poly ODN was inactive or only weakly active, as were ODN
containing CpG dinucleotides flanked by guanines or other CpG dinucleotides (ODN
2010 (SEQ ID NO.: 250)). Taken together, the findings for NK cells and B cells showed
consistently that of the ODN tested, ODN 2006 (SEQ ID NO.: 246) has the highest
immunostimulatory activity on human immune cells.
Comparative analysis of potency of CpG phosphorothioate ODNs in different
primates: Different CpG motifs are optimal to activate murine and human immune cells.
Furthermore, the number and location of CpG motifs within an active phosphorothioate
ODN is different in mice and humans. We were interested to know if CpG
phosphorothioate ODN show a similar activity among different species of primates. We
compared a panel of CpG ODN for their ability to induce B cell proliferation in humans,
chimpanzees and rhesus or cynomolgus monkeys. The capability of ODN to stimulate
human B cell proliferation (Table J) correlated well with their ability to induce CD86
expression on B cells. ODN 2006 (SEQ ID NO.: 246), which showed the highest activity
in human B cells and NK cells, was also the most active in stimulating chimpanzee and
rhesus monkey B cell proliferation (Table J). ODN 1968 (SEQ ID NO.: 211) and ODN
2006 (SEQ ID NO.: 246) gave the highest activation of cynomolgus monkey B-cells in
vitro (SI of 25 and 29 respectively at 6 g ODN/ml). Surprisingly, CpG ODN 2007
(SEQ ID NO.: 247), which displayed similarly high activity as the optimal ODN 2006

(SEQ ID NO.: 246) in human cells, did not stimulate Rhesus monkey or chimpanzee B
cell proliferation, and the ODN 1968 (SEQ ID NO.: 211) showed low activity. CpG
ODN originally identified with high activity in mice (ODN 1760 (SEQ ID NO.: 3), ODN
1826 (SEQ ID NO.: 69)) showed little activity in monkeys (Table J).
Table J: Proliferative response of PBMC to phosphorothioate CpG ODN in primates

PBMC were prepared from peripheral blood and incubated with ODN (0.6 jig/ml) as
indicated for five days. Proliferation was measured by uptake of 3H/thymidm5
(cpm/1000) during the last 18 hours. More than 95 % of proliferating cells were B-cells
10 as determined using the CFSE assay. Four human probands, six chimpanzees and two
rhesus monkeys were tested.
In vivo adjuvant activity of CpG ODN in chimpanzees and cynomolgus
monkeys: In order to evaluate whether CpG ODN with strong in vitro stimulatory
effects on primate cells had detectable adjuvant activity in vivo, Cynomolgus monkeys
15 and chimpanzees were immunized with Engerix B, which comprises HBsAg adsorbed to

alum, alone or with added ODN 1968 (500 g) or ODN 2006 (SEQ ID NO.: 246) (1 mg)
respectively. Compared to controls not receiving CpG ODN, anti-HBs titers at 4 weeks
post-prime and 2 weeks post-boost were 66- and 16-fold higher respectively in the
monkeys, and 15- and 3-fold higher in the chimpanzees (Table K). Thus a clear adjuvant
effect of CpG ODN was seen, and this was particularly striking after a single

3Animals were immunized by IM injection of Engerix B containing 10 g HBsAg
adsorbed to alum, alone or with added CpG ODN. Cynomolgus monkeys were boosted
at 10 wks and chimpanzees were boosted at 4 wks post-prime. Anti-HBs was determined
by ELISA assay; values for monkeys are GMT ± SEM (n=5) whereas individual values
for the two chimpanzees in each group are provided.
I claim:

WE CLAIM:
1. A Py-rich immunostimulatory nucleic acid that is greater than 60% T and contains a CpG
dinucleotide and wherein the immunostimulatory nucleic acid is between 8 and 100 nucleotides.
2. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
iminunostimulatory nucleic acid is a poly T nucleic acid comprising
5"TTTT3'.
3. The immunostimulatory nucleic acid as claimed in claim 2, wherein the poly T nucleic
acid comprises 5' X1X2TTTTX3X4 3'wherein Xi, X2, X3 and X4 are nucleotides.
4. The immunostimulatory nucleic acid as claimed in claim 2, wherein the- Py-rich
immunostimulatory nucleic acid comprises a plurality of poly T nucleic acid motifs.
5. The immunostimulatory nucleic acid as claimed in claim 3, wherein X1X2 is TT.
6. The- immunostimulatory nucleic acid as claimed in claim 3, wherein X3X4 is TT.

7. The immunostimulatory nucleic acid as claimed in claim 3, wherein X1X2 is selected
from the group consisting of TA, TG, TC, AT, AA, AG, AC, CT, CC, CA, GT, GG, GA, and
GC.
8. The immunostimulatory nucleic acid as claimed in claim 3, wherein X3X4 is selected
from the group consisting of TA, TG, TC, AT, AA, AG, AC, CT, CC, CA, GT, GG, GA, and
GC.
9. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid comprises a nucleotide composition of greater than 80% T.

10. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid comprises at least 20 nucleotides.
11. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid comprises at least 24 nucleotides.
12. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid has a nucleotide backbone which includes at least one backbone
modification.
13. The immunostimulatory nucleic acid as claimed in claim 1, wherein the backbone
modification is a phosphorothioate modification.
14. The immunostimulatory nucleic acid as claimed in claim 1, wherein the nucleotide
backbone is chimeric.
15. The immunostimulatory nucleic acid as claimed in claim 1, wherein the nucleotide
backbone is entirely modified.
16. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid is free of methylated CpG dinucleotides.
17. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid is free of poly-C sequences.
18. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid comprises a poly-A sequence.
19. The immunostimulatory nucleic acid as claimed in claim 14, wherein the
immunostimulatory nucleic acid comprises a poly-G sequence.

20. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid comprises a nucleotide composition of greater than 25% C.
21. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid comprises a nucleotide composition of greater than 25% A.
22. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid is formulated for oral administration.
23. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid is formulated for local administration.
24 The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid is formulated as a sustained release device.
25. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid is formulated for mucosal administration-to a mucosal surface.
26. The immunostimulatory nucleic acid as claimed in claim 25, wherein the mucosal
surface is selected from the group consisting of an oral, nasal, rectal, vaginal, and ocular
surface.
27. The immunostimulatory nucleic acid as claimed in claim 1, comprising an antigen.
28. The immunostimulatory nucleic acid as claimed in claim 27, wherein a nucleic acid
vector -encodes the antigen, and wherein the nucleic acid vector is separate from the
iramunostimulatory nucleic acid.
29. The immunostimulatory nucleic acid as claimed in claim 27, wherein the antigen is a
peptide antigen.

30. The immunostimulatory nucleic acid as claimed in claim 27, wherein the antigen is
selected from the group consisting of a tumor antigen, a viral antigen, a bacterial antigen, a
fungal antigen, and a parasitic antigen.
31. The immunostimulatory nucleic acid as claimed in claim 1, comprising an anti-cancer
therapy.
32. The immunostimulatory nucleic acid as claimed in claim 31, wherein the anti-cancer
theiapy is an antibody.
33. The immunostimulatory nucleic acid as claimed in claim 1, comprising an antibody
specific for a cell surface antigen which results in antigen dependent cellular cytotoxicity
(ADCC).
34. The immunostimulatory nucleic acid as claimed in claim 27, wherein the antigen is
deri ved from a microorganism selected from the group consisting of herpesviridae, retroviridae,
orthomyroviridae, toxoplasma, haemophilus, campylobacter, clostridium, E.coli, and
staphylococcus.
35. The immunostimulatory nucleic acid as claimed in claim 1, wherein the
immunostimulatory nucleic acid comprises a TG motif.
36. The immunostimulatory nucleic acid as claimed in claim 35, wherein the TG nucleic
acid comprises 5'N1X1TGX2N23'.
37. The immunostimulatory nucleic acid as claimed in claim 35, wherein the TG nucleic
acid comprises 5'N1X1X2TGX3X4N23'.
38. The immunostimulatory nucleic acid as claimed in claim 36, wherein N1 is a nucleic
acid sequence composed of a number of nucleotides ranging from (11-N2) to (21-N2).

39. The immunostimulatory nucleic acid as claimed in claim 36, wherein N2 is a nucleic
acid sequence composed of a number of nucleotides ranging from (11-N1) to (21-N1).
40. The immunostimulatory nucleic acid as claimed in claim 37, wherein Ni is a nucleic
aciil sequence composed of a number of nucleotides ranging from (9-N2) to (19-N2).
41. The immunostimulatory nucleic acid as claimed in claim 37, wherein N2 is a nucleic
acid sequence composed of a number of nucleotides ranging from (9-N1) to (19-N1).
42 The immunostimulatory nucleic acid as claimed in claim 36, wherein X2 is thymidine.
43. The immunostimulatory nucleic acid as claimed in claim 37, wherein X3 is thymidine.
44. The immunostimulatory nucleic acid as claimed in claim 37, wherein X1X2 are
nucieotides selected from the group consisting of GT, GG, GA, AA, AT, AG, CT, CA, CG,
TA and TT.
At. The immunostimulatory nucleic acid as claimed in claim 37, wherein X3X4 are
nucleotides selected from the group consisting of TT, CT, AT, AG, CG, TC, AC, CC, TA,
AA, and CA.
46. The immunostimulatory nucleic acid as claimed in claim 36, wherein X3X4 are
nudeotides selected from the group consisting of TT, TC, TA and TG.
47. The immunostimulatory nucleic acid as claimed in claim 31, wherein the anti-
cancer therapy is selected from the group consisting of a chemotherapeutic agent, an
immunotherapeutic agent and a cancer vaccine.
48. A composition comprising a sustained release device comprising an immunostimulatory
nucleic acid, wherein the immunostimulatory nucleic acid is free of unmethylated CpG motifs
end is selected from the group consisting of a T-rich nucleic acid and a TG nucleic acid, and

wherein the immunostimulatory nucleic acid is between 8 and 100 nucleotides.
49. The composition as claimed in claim 48, wherein the immunostimulatory nucleic acid
has a phosphodiester backbone.
50. A composition of a nutritional supplement comprising an immunostimulatory nucleic
acid in a delivery device selected from the group consisting of a capsule, a pill, and a sublingual
tablet, wherein the immunostimulatory nucleic acid is free of ummethylated CpG motifs and is
selected from the group consisting of a T-rich nucleic acid and a TG nucleic acid, and wherein
the immunostimulatory nucleic acid is between 8 and 100 nucleotides.
51. The composition as claimed in claim 50, wherein the immunostimulatory nucleic acid
has a phosphorothioate backbone.
52. A composition comprising an immunostimulatory nucleic acid and an antigen, wherein
the immunostimulatory nucleic acid is free of unmethylated CpG motifs and is selected from the
group consisting of a TG immunostimulatory nucleic acid comprising the sequence
5' N1X1X2TGX3X4N2 3'
wherein X1X2 is selected from the group consisting of TA, AA, AG, CA, GG, GT, AT, CT, TT
and GA, and X3X4 is selected from the group consisting of AT, AA, AG, AC, CT, CC, CA, TT,
TC, and TA. and N1 is a nucleic acid composed of a number of nucleotides ranging from (9-N2)
to (19-N2) and N2 is a nucleic acid sequence composed of a number of nucleotides ranging from
(9-N1) to (19-N1), and a Py-rich immunostimulatory nucleic acid comprising the sequence
5' X1X2TTTTX3X4 3'
wherein X1X2 is selected from the group consisting of TA, TG, TC, AA, AG, AC, CC, CA,
GG, GA, and GC, and X3X4 is selected from the group consisting of AT, AA, AG, AC, CT,
CC, CA, GT, GG, GA, and GC.
53. A composition comprising an immunostimulatory nucleic acid and an anti-microbial
agent, wherein the immunostimulatory nucleic acid is free of unmethylated CpG motifs and is

selected from the group consisting of a T-rich nucleic acid and a TG nucleic acid, and wherein
the immunostimulatory nucleic acid is between 8 and 100 nucleotides.
54. The composition as claimed in claim 53, wherein the anti-microbial agent is selected
from the group consisting of an anti-viral agent, an anti-fungal agent, an anti-parasitic agent, and
an anti-bacterial agent.
55. The immunostimulatory nucleic acid as claimed in claim 4, wherein the
immunostimulatory nucleic acid comprises at least 3, at least 4, at least 5, at least 6, at least 7, or
at least 8 poly T motifs.
56. The immunostimulatory nucleic acid as claimed in claim 4, wherein at least two of the
plurality of poly T nucleic acid motifs each comprises at least three contiguous T nucleotide
residues.
57. The immunostimulatory nucleic acid as claimed in claim 4, wherein at least two of the
poly T nucleic acid motifs each comprises at least four contiguous T nucleotide residues.
58. The immunostimulatory nucleic acid of claim 4, wherein the plurality of poly T
nacleic acid motifs is at least 3 poly T nucleic acid motifs and wherein the at least 3 poly T
nucleic acid motifs each comprises at least 3 contiguous T nucleotide residues.
59. The immunostimulatory nucleic acid as claimed in claim 4, wherein the plurality of
poly T nucleic acid motifs is at least 4 poly T nucleic acid motifs and wherein the at least 4
poly T nucleic acid motifs each comprises at least 3 contiguous T nucleotide residues.
60. The immunostimulatory nucleic acid as claimed in claim 4, wherein at least one of the
plurality of poly T nucleic acid motifs comprises at least 5, at least 6, at least 7, or at least 8
contiguous T nucleotide residues.
61. The immunostimulatory nucleic acid as claimed in claim 1, wherein the

immunostimulatory nucleic acid comprises at least two poly C sequences of at least 3
contiguous C nucleotide residues.
62 The immunostimulatory nucleic acid as claimed in claim 1, wherein the
imtnunostimulatory nucleic acid is free of two poly A sequences of at least 3 contiguous A
nucleotide residues.
63. A pharmaceutical composition comprising an effective amount for stimulating an
immune response of an isolated immunostimulatory nucleic acid as claimed in claims 1-21, 35 -
46, 55 - 61 or 62 and a pharmaceutically acceptable carrier.
64. A composition of matter, comprising an isolated immunostimulatory nucleic acid as
churned in claims 1-21,35- 46, 55-61 or 62 and a pharmaceutically acceptable carrier.
65. The immunostimulatory nucleic acid as claimed in claim 60, wherein the nucleic acid
further comprises a plurality of CpG motifs, and wherein the plurality is at least 3 motifs, at least
4 motifs and wherein the at least 4 motifs each comprises at least 3 contiguous T nucleotide
residues.

66. The immunostimulatory nucleic acid as claimed in claim 57, wherein the plurality of
CpG motifs and poly T motifs are interspersed.
67. A composition; comprising:
an immunostimulatory nucleic acid and an anti-cancer therapy, formulated in a
pharmaceutically-acceptable carrier, wherein the immunostimulatory nucleic acid is selected
from the group consisting of a T-rich nucleic acid that is greater than 60% T and contains a CpG
dinucleotide. and a TG nucleic acid that is free of CpG dinucleotides, wherein the
immunostimulatory nucleic acid is between 8 and 100 nucleotides.
68. A composition, comprising:
an immunostimulatory nucleic acid and an asthma/allergy medicament, formulated in a

phamiaceutically-acceptable carrier, wherein the immunostimulatory nucleic acid is selected
from the group consisting of a T-rich nucleic acid that is greater than 60% T and contains a CpG
dinucleotide, and a TG nucleic acid that is free of CpG dinucleotides. wherein the
immunostimulatory nucleic acid is between 8 and 100 nucleotides.
69. A composition comprising
an immunostimulatory nucleic acid selected from the group consisting of SEQ ID NO:95-119,
SEQ ID NO: 121-136, SEQ ID NO: 138-152, SEQ ID NO:154-210, SEQ ID NO:212-222, SEQ
ID NO:224-244, SEQ ID NO:247-260, SEQ ID NO:263-272, SEQ ID NO:274-299, SEQ ID
NO:301, SEQ ID NO:303-409, SEQ ID NO:414-420, SEQ ID NO:424,SEQ ID NO:427-758,
SEQ rD NO.760-947, SEQ ID NO:959-963, SEQ ID NO:968-1022, and SEQ ID NO: 1024-
1093, and a pharmaceutical ly acceptable carrier.
70. A composition comprising an immunostimulatory nucleic acid consisting essentially of:
5'M1TCGTCGTTM23'
wherein at least one of the Cs is unmethylated, wherein M1 is a nucleic acid having at least one
nucleotide, wherein M2 is a nucleic acid having between 0 and 50 nucleotides, and wherein the
immunostimulatory nucleic acid has less than 100 nucleotides.
71. A pharmaceutical composition comprising an immunostimulatory nucleic acid
comprising:
5' TCGTCGTT 3'
wherein at least one of the Cs is unmethylated, wherein the immunostimulatory nucleic acid has
less than 100 nucleotides and a phosphodiester backbone, and
a sustained release device.
72. The pharmaceutical composition as claimed in claim 71, wherein the sustained release
device is a microparticle.
73. The pharmaceutical composition as claimed in claim 71, comprising an antigen.

74. A composition comprising an oligonucleotide having a nucleic acid sequence of TCG
TCG TTT TGA CGT TTT GTC GTT (SEQ ID NO: 343).
75. A TG immunostimulatory nucleic acid, wherein the nucleic acid comprises the sequence
5' N1X1X2TGX3X4N23'
wherein X1X2 is selected from the group consisting of TA, AA, AG, CA. GG, GT, AT, CT, TT
and GA, and X3X4 is selected from the group consisting of AT, AA, AG, AC, CT, CC, CA, TT,
TC, and TA, and N1 and N2 are nucleic acid sequences composed of any number of nucleotides
pro\ iding that the sum total of N1 and N2 is in the range of 9 to 19, and wherein the nucleic acid
is live of a CpG dinucleotide, and wherein the immunostimulatory nucleic acid is between 8 and
100 nucleotides.
76. The immunostimulatory nucleic acid as claimed in claims 41 or 67, wherein the
immunostimulatory nucleic acid has a phosphorothioate backbone.
77. The composition as claimed in claims 47, 59, 60 or 61, wherein the immunostimulatory
nucleic acid has a phosphorothioate backbone.

Immunostimulatory nucleic acids having a T nucleotide content greater than 60% and
having a CpG dinucleotide or a TG motif and being free of CpG dinucleotides are provided. The
invention also relates in part to compositions or nutritional supplements that include a sustained
delivery device or other delivery device having an immunostimulatory nucleic acid of the
invention. Compositions having an immunostimulatory nucleic acid of the invention that include
an antigen, an anti-microbial agent, an anti-cancer therapy, or an asthma/allergy medicament are
also provided.

Documents:

IN-PCT-2002-351-KOL-CORRESPONDENCE.pdf

IN-PCT-2002-351-KOL-FORM 27.pdf

IN-PCT-2002-351-KOL-FORM-27-1.pdf

in-pct-2002-351-kol-granted-abstract.pdf

in-pct-2002-351-kol-granted-assignment.pdf

in-pct-2002-351-kol-granted-claims.pdf

in-pct-2002-351-kol-granted-correspondence.pdf

in-pct-2002-351-kol-granted-description (complete).pdf

in-pct-2002-351-kol-granted-drawings.pdf

in-pct-2002-351-kol-granted-examination report.pdf

in-pct-2002-351-kol-granted-form 1.pdf

in-pct-2002-351-kol-granted-form 13.pdf

in-pct-2002-351-kol-granted-form 18.pdf

in-pct-2002-351-kol-granted-form 3.pdf

in-pct-2002-351-kol-granted-form 5.pdf

in-pct-2002-351-kol-granted-gpa.pdf

in-pct-2002-351-kol-granted-reply to examination report.pdf

in-pct-2002-351-kol-granted-sequence listing.pdf

in-pct-2002-351-kol-granted-specification.pdf


Patent Number 228099
Indian Patent Application Number IN/PCT/2002/351/KOL
PG Journal Number 05/2009
Publication Date 30-Jan-2009
Grant Date 28-Jan-2009
Date of Filing 14-Mar-2002
Name of Patentee UNIVERSITY OF IOWA RESEARCH FOUNDATION
Applicant Address 214 TECHNOLOGY INNOVATION CENTER, OAKDALE RESEARCH, CAMPUS, IOWA CITY, IA
Inventors:
# Inventor's Name Inventor's Address
1 KRIEG ARTHUR M UNIVERCITY IF IOWA, DEPARTMENT OF INTERNAL MEDICINE, 540 EM RB. IOWA CITY, IA 52242
2 SCHETTER CHRISTIAN COLEY PHARMACEUTICAL GROUP GMBH, QIAGEN GMBH, MAX-VOLMER STRABE 4, D-40724
3 VOLLMER JORG COLEY PHARMACEUTICAL GROUP GMBH, QIAGEN GMBH, MAX-VOLMER STRABE 4, D-40724
PCT International Classification Number A61K 31/7088
PCT International Application Number PCT/US00/26383
PCT International Filing date 2000-09-25
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/156,113 1999-09-25 U.S.A.
2 60/156,135 1999-09-27 U.S.A.
3 60/227,436 2000-08-23 U.S.A.