U.S. patent application number 11/089191 was filed with the patent office on 2005-11-24 for antisense modulation of interleukin 12 p35 subunit expression.
Invention is credited to Ackermann, Elizabeth J., Anderson, Kevin P., Baker, Brenda F., Bennett, C. Frank, Bhanot, Sanjay, Brown-Driver, Vickie L., Chiang, Ming-Yi, Cowsert, Lex M., Dean, Nicholas M., Ecker, David J., Freier, Susan M., Gregory, Susan, Hanecak, Ronnie C., Marcusson, Eric G., Vickers, Timothy, Wyatt, Jacqueline R..
Application Number | 20050261228 11/089191 |
Document ID | / |
Family ID | 35375960 |
Filed Date | 2005-11-24 |
United States Patent
Application |
20050261228 |
Kind Code |
A1 |
Bennett, C. Frank ; et
al. |
November 24, 2005 |
Antisense modulation of interleukin 12 P35 subunit expression
Abstract
Compounds, compositions and methods are provided for modulating
the expression of Interleukin 12 p35 subunit. The compositions
comprise chemically modified antisense compounds, particularly
antisense oligonucleotides, targeted to nucleic acids encoding
Interleukin 12 p35 subunit. Methods of using these compounds for
modulation of Interleukin 12 p35 subunit expression and for
treatment of diseases associated with expression of Interleukin 12
p35 subunit are provided.
Inventors: |
Bennett, C. Frank;
(Carlsbad, CA) ; Baker, Brenda F.; (Carlsbad,
CA) ; Freier, Susan M.; (San Diego, CA) ;
Gregory, Susan; (San Diego, CA) ; Hanecak, Ronnie
C.; (San Clemente, CA) ; Anderson, Kevin P.;
(Carlsbad, CA) ; Chiang, Ming-Yi; (San Diego,
CA) ; Brown-Driver, Vickie L.; (Solana Beach, CA)
; Ecker, David J.; (Encinitas, CA) ; Vickers,
Timothy; (Oceanside, CA) ; Wyatt, Jacqueline R.;
(Sundance, WY) ; Marcusson, Eric G.; (San Diego,
CA) ; Dean, Nicholas M.; (Olivenhain, CA) ;
Bhanot, Sanjay; (Carlsbad, CA) ; Ackermann, Elizabeth
J.; (Del Mar, CA) ; Cowsert, Lex M.;
(Pittsburgh, PA) |
Correspondence
Address: |
COZEN O'CONNOR, P.C.
1900 MARKET STREET
PHILADELPHIA
PA
19103-3508
US
|
Family ID: |
35375960 |
Appl. No.: |
11/089191 |
Filed: |
March 23, 2005 |
Related U.S. Patent Documents
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Application
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Filing Date |
Patent Number |
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11089191 |
Mar 23, 2005 |
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10476960 |
Nov 5, 2003 |
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10476960 |
Nov 5, 2003 |
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PCT/US02/13871 |
May 1, 2002 |
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10476960 |
Nov 5, 2003 |
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09851520 |
May 7, 2001 |
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6399379 |
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11089191 |
Mar 23, 2005 |
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10667236 |
Sep 17, 2003 |
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11089191 |
Mar 23, 2005 |
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10038335 |
Jan 2, 2002 |
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10038335 |
Jan 2, 2002 |
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09299058 |
Apr 23, 1999 |
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09299058 |
Apr 23, 1999 |
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08403888 |
Jun 12, 1995 |
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5952490 |
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08403888 |
Jun 12, 1995 |
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PCT/US93/09297 |
Sep 29, 1993 |
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08403888 |
Jun 12, 1995 |
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07954185 |
Sep 29, 1992 |
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11089191 |
Mar 23, 2005 |
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10515546 |
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10515546 |
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PCT/US03/18312 |
Jun 10, 2003 |
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11089191 |
Mar 23, 2005 |
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10512739 |
Oct 27, 2004 |
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10512739 |
Oct 27, 2004 |
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PCT/US03/18320 |
Jun 10, 2003 |
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11089191 |
Mar 23, 2005 |
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10515545 |
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10515545 |
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PCT/US03/18258 |
Jun 10, 2003 |
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11089191 |
Mar 23, 2005 |
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10188883 |
Jul 2, 2002 |
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11089191 |
Mar 23, 2005 |
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10464158 |
Jun 18, 2003 |
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10464158 |
Jun 18, 2003 |
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09857278 |
Sep 24, 2001 |
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09857278 |
Sep 24, 2001 |
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PCT/US99/13624 |
Jun 16, 1999 |
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PCT/US99/13624 |
Jun 16, 1999 |
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09205204 |
Dec 3, 1998 |
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5958772 |
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11089191 |
Mar 23, 2005 |
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11048271 |
Feb 1, 2005 |
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11048271 |
Feb 1, 2005 |
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10197290 |
Jul 16, 2002 |
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10197290 |
Jul 16, 2002 |
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09857299 |
Oct 4, 2001 |
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09857299 |
Oct 4, 2001 |
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PCT/US99/22083 |
Sep 23, 1999 |
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09857299 |
Oct 4, 2001 |
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09205144 |
Dec 3, 1998 |
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5958771 |
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11089191 |
Mar 23, 2005 |
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10070789 |
Aug 6, 2002 |
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10070789 |
Aug 6, 2002 |
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PCT/US00/00583 |
Jan 11, 2000 |
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10070789 |
Aug 6, 2002 |
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09392580 |
Sep 9, 1999 |
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6087173 |
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60388100 |
Jun 11, 2002 |
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60388074 |
Jun 11, 2002 |
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60388118 |
Jun 11, 2002 |
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Current U.S.
Class: |
514/44A ;
435/455; 536/23.5 |
Current CPC
Class: |
C12N 2310/346 20130101;
C12N 15/1136 20130101; C12N 2310/341 20130101; C12N 2310/315
20130101; C12N 2310/321 20130101; C12N 2310/3525 20130101; A61K
38/00 20130101; C12N 2310/321 20130101; C12N 2310/3341 20130101;
Y02P 20/582 20151101 |
Class at
Publication: |
514/044 ;
435/455; 536/023.5 |
International
Class: |
A61K 048/00; C07H
021/04; C12N 015/85 |
Claims
What is claimed is:
1. A compound comprising a chemically modified antisense
oligonucleotide compound 15 to 30 nucleobases in length targeted to
an active site of a nucleic acid molecule encoding Interleukin 12
p35 subunit.
2. The compound of claim 1 comprising SEQ ID NO: 23, 24 or 44.
3. The compound of claim 1 further comprising at least one chemical
modification selected from the group consisting of: a modified
nucleobase, a substituted sugar moiety, a modified oligonucleotide
backbone or a conjugate.
4. The compound of claim 3 further comprising a sense strand such
that the antisense oligonucleotide is double stranded siRNA.
5. The compound of claim 3 comprising a chimeric oligonucleotide of
15 to 30 nucleobases in length targeted to a nucleic acid molecule
encoding Interleukin 12 p35 subunit comprising: a 5' region of
nucleobases, each containing a 2'-MOE modification; a central
region containing deoxynucleotides; and a 3' region of nucleobases,
each containing a 2'-MOE modification.
6. The chimeric oligonucleotide of claim 4 comprising SEQ ID NO:
23, 24 or 44.
7. A method of inhibiting the expression of Interleukin 12 p35
subunit in cells or tissues comprising contacting said cells or
tissues with the compound of claim 1 so that expression of
Interleukin 12 p35 subunit is inhibited.
8. A method of treating an animal having a disease or condition
associated with Interleukin 12 p35 subunit comprising administering
to said animal a therapeutically or prophylactically effective
amount of the compound of claim 1 so that expression of Interleukin
12 p35 subunit is inhibited.
9. The method of claim 8 wherein the disease or condition is
selected from the group consisting of an autoimmune disorder,
cancer, a metabolic disorder, or a viral or bacterial
infection.
10. The method of claim 9 wherein the autoimmune disorder is
multiple sclerosis, diabetes or Crohn's disease.
11. The method of claim 9 wherein the infection is endotoxemia.
12. The method of claim 9 wherein the metabolic disorder is
selected from the group consisting of obesity, cardiovascular
disease, metabolic syndrome, diabetes, or insulin resistance.
13. A method for inhibiting the differentiation of an adipocyte
cell comprising contacting a preadipocyte cell with an effective
amount of a compound of claim 1, whereby adipocyte differentiation
is inhibited.
14. A method for inhibiting lipid accumulation in a cell comprising
contacting a cell with a compound of claim 1, whereby lipid
accumulation in the cell is inhibited.
Description
RELATED APPLICATIONS
[0001] This application is a continuation-in-part of U.S. patent
application Ser. No. 10/476,960, filed Nov. 7, 2003, which is a
United States National Phase of PCT/US02/13871, filed May 1, 2002,
which claims priority to and is a continuation (PCT) of U.S. patent
application Ser. No. 09/851,520, filed May 7, 2001 now issued as
U.S. Pat. No. 6,399,379. This application is also a
continuation-in-part of U.S. patent application Ser. No.
10/667,236, filed Sep. 17, 2003. This application is also a
continuation-in-part of U.S. patent application Ser. No.
10/038,335, filed Jan. 2, 2002, which is a continuation-in-part of
U.S. patent application Ser. No. 09/299,058, filed Apr. 23, 1999,
which is a continuation of U.S. patent application Ser. No.
08/403,888, filed Jun. 12, 1995 now issued as U.S. Pat. No.
5,952,490, which is a United States National Phase of
PCT/US93/09297, filed Sep. 29, 1993, which claims priority to and
is a continuation (PCT) of U.S. patent application Ser. No.
07/954,185, filed Sep. 29, 1992. This application is also a
continuation-in-part of U.S. patent application Ser. No.
10/515,546, filed Nov. 23, 2004, which is a United States National
Phase of PCT/US03/18312, filed Jun. 10, 2003, which claims priority
to and is a continuation (PCT) of U.S. patent application Ser. No.
60/388,100, filed Jun. 11, 2002. This application is also a
continuation-in-part of U.S. patent application Ser. No.
10/512,739, filed Oct. 27, 2004, which is a United States National
Phase of PCT/US03/18320, filed Jun. 10, 2003, which claims priority
to and is a continuation (PCT) of U.S. patent application Ser. No.
60/388,074, filed Jun. 11, 2002. This application is also a
continuation-in-part of U.S. patent application Ser. No.
10/515,545, filed Nov. 23, 2004, which is a United States National
Phase of PCT/US03/18258, filed Jun. 10, 2003, which claims priority
to and is a continuation (PCT) of U.S. patent application Ser. No.
60/388,118, filed Jun. 11, 2002. This application is also a
continuation-in-part of U.S. patent application Ser. No.
10/188,883, filed Jul. 2, 2002. This application is also a
continuation-in-part of U.S. patent application Ser. No.
10/464,158, filed Jun. 18, 2003, which is a continuation-in-part of
U.S. patent application Ser. No. 09/857,278, filed Sep. 24, 2001,
which is a United States National Phase of PCT/US99/13624, filed
Jun. 16, 1999, which claims priority to and is a continuation (PCT)
of U.S. patent application Ser. No. 09/205,204, filed Dec. 3, 1998
now issued as U.S. Pat. No. 5,958,772. This application also claims
priority to U.S. patent application Ser. No. 10/070,789, filed Aug.
6, 2002, which is a United States National Phase of PCT/US00/00583,
filed Jan. 11, 2000, which claims priority to and is a continuation
(PCT) of U.S. patent application Ser. No. 09/392,580, filed Sep. 9,
1999 now issued as U.S. Pat. No. 6,087,173. This application is
also a continuation-in-part of U.S. patent application Ser. No.
11/048,271, filed Feb. 1, 2005, which is a continuation of U.S.
patent application Ser. No. 10/197,290, filed Jul. 16, 2002, which
is a continuation-in-part of U.S. patent application Ser. No.
09/857,299, filed Oct. 4, 2001, which is a United States National
Phase of PCT/US99/22083, filed Sep. 23, 1999, which claims priority
to and is a continuation (PCT) of U.S. patent application Ser. No.
09/205,144, filed Dec. 3, 1998 now issued as U.S. Pat. No.
5,958,771. The entire contents of each the above applications and
patents are herein incorporated by reference.
FIELD OF THE INVENTION
[0002] The present invention provides compositions and methods for
modulating the expression of Interleukin 12 p35 subunit. In
particular, this invention relates to compounds, particularly
oligonucleotides, specifically hybridizable with nucleic acids
encoding Interleukin 12 p35 subunit. Such compounds have been shown
to modulate the expression of Interleukin 12 p35 subunit.
BACKGROUND OF THE INVENTION
[0003] Cytokines are soluble factors produced by lymphocytes that
regulate the survival, proliferation, differentiation, and
homeostasis of cells involved in mediating the immune response.
These factors do not only activate other lymphocytes, they also
relay signals to non-lymphoid cells including macrophages,
epithelial and stromal cells, creating a broad spectrum of cytokine
activity that is critical to the maintenance of health.
Consequently, much effort has been devoted to the study of these
proteins.
[0004] Interleukin 12 (IL-12; formerly NKSF, for natural killer
cell stimulatory factor, or CLMF, for cytotoxic lymphocyte
maturation factor) is a cytokine produced by monocytes,
macrophages, neutrophils, dendritic cells and antibody-producing B
cells (Hall, Science, 1995, 268, 1432-1434) as well as
keratinocytes and epidermoid carcinoma cell lines (Aragane et al.,
J. Immunol., 1994, 153, 5366-5372).
[0005] Interleukin 12 is responsible for activation of natural
killer (NK) cells, T cells and induction of increased levels of
interferon-gamma, a cytokine that helps to shape the immune
response (Hall, Science, 1995, 268, 1432-1434). The combination of
interferon-gamma and interleukin 12 sends a powerful signal to
native precursor cells of the T helper lineage, shifting the immune
system to a T.sub.H1-type immune response (Hall, Science, 1995,
268, 1432-1434). Generally, resistance to pathogens increases when
interleukin 12 is present to drive a T.sub.H1 response (Hall,
Science, 1995, 268, 1432-1434).
[0006] Interleukin 12 is unique among the cytokines because it is a
disulfide-linked heterodimer composed of unrelated 40-kD (p40) and
35-kD (p35) subunits that are encoded by genes on separate
chromosomes. The p35 and p40 subunits are localized to chromosomes
3p12-3q13.2 and 5q31-q33 respectively (Sieburth et al., Genomics,
1992, 14, 59-62). The p35 subunit shares structural similarities
with the cytokines interleukin 6 and granulocyte colony-stimulating
factor (Merberg et al., Immunol. Today, 1992, 13, 77-78).
Alternatively, the p40 subunit is structurally related to the
interleukin 6 receptor (Gearing and Cosman, Cell, 1991, 66,
9-10).
[0007] Disclosed and claimed in U.S. Pat. No. 5,457,038 and PCT
publication WO 92/05206 is a DNA sequence coding for interleukin 12
or a subunit thereof (Trinchieri et al., 1995; Trinchieri et al.,
1992).
[0008] cDNAs for both subunits of interleukin 12 were cloned in
1991 from a lymphoblastoid B-cell line (Gubler et al., Proc. Natl.
Acad. Sci. USA, 1991, 88, 4143-4147). Both subunits are required to
obtain the biologically active heterodimer (Gubler et al., Proc.
Natl. Acad. Sci. USA, 1991, 88, 4143-4147) and p35 is only secreted
as part of the heterodimer (D'Andrea et al., J Exp. Med., 1992,
176, 1387-1398) whereas p40 can be induced and secreted
independently (Snijders et al., J. Immunol., 1996, 156, 1207-1212)
and has no biological activity (Ling et al., J. Immunol., 1995,
154, 116-127). Bioactive murine and human single chain interleukin
12 fusion proteins expressed from retroviral constructs have been
demonstrated to retain antitumor activity in vivo (Lieschke et al.,
Nat. Biotechnol., 1997, 15, 35-40).
[0009] Interleukin 12 has been found to be upregulated in vivo
during murine lipopolysaccharide-induced endotoxemia and to
stimulate the synthesis of interferon-gamma (Heinzel et al.,
Infect. Immun., 1994, 62, 4244-4249). However, pretreatment of the
mice with anti-interleukin 12 antibodies caused a reduction in
interferon-gamma levels after lipopolysaccharide injection (Heinzel
et al., Infect. Immun., 1994, 62, 4244-4249).
[0010] Astrocyte-targeted expression of both interleukin 12 p35 and
p40 genes in mice promoted the spontaneous development of a severe
neuroimmunological disorder with many features resembling those of
experimental allergic encephalomyelitis (EAE) (Pagenstecher et al.,
J. Immunol., 2000, 164, 4481-4492).
[0011] Analysis of the cytokine pattern expressed in situ in
inhalant allergen patch test reactions of atopic dermatitis
patients indicate increased expression of interleukin 12 p35
subunit. This upregulation of the p35 subunit may contribute to the
observed switch of the cytokine secretion pattern (Grewe et al., J.
Invest. Dermatol., 1995, 105, 407-410).
[0012] Structure-function analysis of the mouse interleukin 12 p35
subunit has indicated that p35 participates in both receptor
binding and signaling (Zou et al., J. Biol. Chem., 1995, 270,
5864-5871).
[0013] Tone et al. have determined that the murine interleukin 12
p35 subunit has multiple transcription start sites and can initiate
from either of two 5' exons, resulting in mRNA isoforms with
different 5' untranslated regions (Tone et al., Eur. J. Immunol.,
1996, 26, 1222-1227). In a separate study, the same research group
found that p35 subunit mRNA was up-regulated by lipopolysaccharide
stimulation of murine B cell lymphoma line A20 and in bone
marrow-derived dendritic cells (Babik et al., J. Immunol., 1999,
162, 4069-4078). Four p35 subunit mRNA isoforms were found in both
cell types and transcription was found to initiate from alternate
positions after lipopolysaccharide stimulation. Further regulation
of p35 subunit was observed at the translational level in addition
to the transcriptional level (Babik et al., J. Immunol., 1999, 162,
4069-4078).
[0014] Interleukin 12 p35 and p40 antisense probes were used in in
situ hybridization studies that identified enhanced interleukin 12
transcription in the gastric mucosa of pediatric patients with
Crohn's disease (Berrebi et al., Am. J. Pathol., 1998, 152,
667-672).
[0015] The homodimer of the interleukin 12 p40 subunit (also known
as (p40).sub.2) has been found to be a very potent inhibitor of
interleukin 12 activity (Gillessen et al., Eur. J. Immunol., 1995,
25, 200-206; Ling et al., J. Immunol., 1995, 154, 116-127) and
functions by binding to the interleukin 12 receptor (Ling et al.,
J. Immunol., 1995, 154, 116-127). The p40 homodimer was used as an
antagonist of interleukin 12 in investigative treatments of mice
with cyclophosphamide-induced diabetes and found to dampen islet
formation (Rothe et al., Diabetologia, 1997, 40, 641-646). The p40
homodimer was found to inhibit the antitumor activity of the
interleukin 12 heterodimer and the induction of interferon-gamma in
murine bladder carcinoma in vivo. (Chen et al., J. Immunol., 1997,
159, 351-359).
[0016] Carter et al. have produced antibodies to recombinant human
interleukin 12 which have been demonstrated to neutralize the
biological activity of interleukin 12. However, essentially all
antibodies were generated to the p40 subunit, possibly due to
conformational limitations of the intact interleukin 12 heterodimer
(Carter et al., Hybridoma, 1997, 16, 363-369). Larsson et al. have
reported an immunoassay that only recognized the bioactive human
interleukin 12 heterodimer and not the individual p35 and p40
subunits (Larsson and Linden, Cytokine, 1998, 10, 786-789).
Disclosed and claimed in PCT publication WO 99/37682 are anti-human
interleukin 12 antibodies that are characterized by specificity to
the interleukin 12 heterodimer but do not bind to the interleukin
12 p40 subunit (Gately and Presky, 1999).
[0017] Disclosed and claimed in PCT Publication WO 00/28000 is a
genetically modified immature dendritic cell which is capable of
maturation, in which one or more endogenous gene(s) have been
inactivated, and wherein the inactivated endogenous gene(s)
comprise any of: B7-1, IL-12, the p35 or p40 subunit of IL-12.
Further claimed is a composition comprising said cell, use of the
cell of any one of the preceding claims for the manufacture of a
medicament for use in therapy or prophylaxis, a process for the
manufacture of a medicament for use in therapy of said cell, a
method for producing dendritic cells which method comprises
providing a population of embryonic stem (ES) cells, culturing the
ES cells in the presence of a cytokine or combination of cytokines
which bring about differentiation of the ES cells into dendritic
cells, and recovering the dendritic cells from the culture, wherein
the ES cells are genetically modified so as to inactivate at least
one copy of at least one gene, for example by homologous
recombination or antisense technology (Waldmann, et al., 2000).
[0018] In investigations of the mechanisms of anti-inflammatory
effects of corticosteriods budesonide was found to inhibit
production of bioactive interleukin 12 in human monocytes (Larsson
and Linden, Cytokine, 1998, 10, 786-789).
[0019] Pentoxifylline, a non-specific phosphodiesterase inhibitor
exhibited complex effects on the expression of interleukin 12. The
production of interleukin 12 p35 subunit was inhibited but, the
production of the p40 subunit was enhanced (Marcinkiewicz et al.,
Immunopharmacology, 2000, 49, 335-343).
[0020] The involvement of interleukin 12 p35 subunit in immune
system regulation and as well as viral and bacterial infections
make it a potentially useful therapeutic target for intervention in
autoimmune diseases. Currently, inhibitors of the interleukin 12
p35 subunit and/or the interleukin 12 heterodimer include the p40
homodimer, antibodies and small molecules such as corticosteroids
and the phosphodiesterase inhibitor pentoxyfylline. Consequently,
there remains a long felt need for additional agents capable of
effectively and selectively inhibiting the function of the
interleukin 12 p35 subunit.
[0021] Antisense technology is emerging as an effective means for
reducing the expression of specific gene products and may therefore
prove to be uniquely useful in a number of therapeutic, diagnostic,
and research applications for the modulation of expression of the
interleukin 12 p35 subunit.
[0022] The present invention provides compositions and methods for
modulating expression of the interleukin 12 p35 subunit, including
modulation of alternative splice variants of the p35 subunit.
SUMMARY OF THE INVENTION
[0023] The present invention is directed to compounds, particularly
chemically modified antisense oligonucleotides, which are targeted
to a nucleic acid encoding Interleukin 12 p35 subunit, and which
modulate the expression of Interleukin 12 p35 subunit.
Pharmaceutical and other compositions comprising the compounds of
the invention are also provided. Further provided are methods of
modulating the expression of Interleukin 12 p35 subunit in cells or
tissues comprising contacting said cells or tissues with one or
more of the antisense compounds or compositions of the invention.
Further provided are methods of treating an animal, particularly a
human, suspected of having or being prone to a disease or condition
associated with expression of Interleukin 12 p35 subunit by
administering a therapeutically or prophylactically effective
amount of one or more of the antisense compounds or compositions of
the invention.
DETAILED DESCRIPTION OF THE INVENTION
[0024] The present invention employs oligomeric compounds,
particularly antisense oligonucleotides, for use in modulating the
function of nucleic acid molecules encoding Interleukin 12 p35
subunit, ultimately modulating the amount of Interleukin 12 p35
subunit produced. This is accomplished by providing antisense
compounds which specifically hybridize with one or more nucleic
acids encoding Interleukin 12 p35 subunit. As used herein, the
terms "target nucleic acid" and "nucleic acid encoding Interleukin
12 p35 subunit" encompass DNA encoding Interleukin 12 p35 subunit,
RNA (including pre-mRNA and mRNA) transcribed from such DNA, and
also cDNA derived from such RNA. The specific hybridization of an
oligomeric compound with its target nucleic acid interferes with
the normal function of the nucleic acid. This modulation of
function of a target nucleic acid by compounds which specifically
hybridize to it is generally referred to as "antisense". The
functions of DNA to be interfered with include replication and
transcription. The functions of RNA to be interfered with include
all vital functions such as, for example, translocation of the RNA
to the site of protein translation, translation of protein from the
RNA, splicing of the RNA to yield one or more mRNA species, and
catalytic activity which may be engaged in or facilitated by the
RNA. The overall effect of such interference with target nucleic
acid function is modulation of the expression of Interleukin 12 p35
subunit. In the context of the present invention, "modulation"
means either an increase (stimulation) or a decrease (inhibition)
in the expression of a gene. In the context of the present
invention, inhibition is the preferred form of modulation of gene
expression and mRNA is a preferred target.
[0025] It is preferred to target specific nucleic acids for
antisense. "Targeting" an antisense compound to a particular
nucleic acid, in the context of this invention, is a multistep
process. The process usually begins with the identification of a
nucleic acid sequence whose function is to be modulated. This may
be, for example, a cellular gene (or mRNA transcribed from the
gene) whose expression is associated with a particular disorder or
disease state, or a nucleic acid molecule from an infectious agent.
In the present invention, the target is a nucleic acid molecule
encoding Interleukin 12 p35 subunit. The targeting process also
includes determination of a site or sites within this gene for the
antisense interaction to occur such that the desired effect, e.g.,
detection or modulation of expression of the protein, will result.
Within the context of the present invention, a preferred intragenic
site is the region encompassing the translation initiation or
termination codon of the open reading frame (ORF) of the gene.
Since, as is known in the art, the translation initiation codon is
typically 5'-AUG (in transcribed mRNA molecules; 5'-ATG in the
corresponding DNA molecule), the translation initiation codon is
also referred to as the "AUG codon," the "start codon" or the "AUG
start codon". A minority of genes have a translation initiation
codon having the RNA sequence 5'-GUG, 5'-UUG or 5'-CUG, and 5'-AUA,
5'-ACG and 5'-CUG have been shown to function in vivo. Thus, the
terms "translation initiation codon" and "start codon" can
encompass many codon sequences, even though the initiator amino
acid in each instance is typically methionine (in eukaryotes) or
formylmethionine (in prokaryotes). It is also known in the art that
eukaryotic and prokaryotic genes may have two or more alternative
start codons, any one of which may be preferentially utilized for
translation initiation in a particular cell type or tissue, or
under a particular set of conditions. In the context of the
invention, "start codon" and "translation initiation codon" refer
to the codon or codons that are used in vivo to initiate
translation of an mRNA molecule transcribed from a gene encoding
Interleukin 12 p35 subunit, regardless of the sequence(s) of such
codons.
[0026] It is also known in the art that a translation termination
codon (or "stop codon") of a gene may have one of three sequences,
i.e., 5'-UAA, 5'-UAG and 5'-UGA (the corresponding DNA sequences
are 5'-TAA, 5'-TAG and 5'-TGA, respectively). The terms "start
codon region" and "translation initiation codon region" refer to a
portion of such an mRNA or gene that encompasses from about 25 to
about 50 contiguous nucleotides in either direction (i.e., 5' or
3') from a translation initiation codon. Similarly, the terms "stop
codon region" and "translation termination codon region" refer to a
portion of such an mRNA or gene that encompasses from about 25 to
about 50 contiguous nucleotides in either direction (i.e., 5' or
3') from a translation termination codon.
[0027] The open reading frame (ORF) or "coding region," which is
known in the art to refer to the region between the translation
initiation codon and the translation termination codon, is also a
region which may be targeted effectively. Other target regions
include the 5' untranslated region (5'UTR), known in the art to
refer to the portion of an mRNA in the 5' direction from the
translation initiation codon, and thus including nucleotides
between the 5' cap site and the translation initiation codon of an
mRNA or corresponding nucleotides on the gene, and the 3'
untranslated region (3'UTR), known in the art to refer to the
portion of an mRNA in the 3' direction from the translation
termination codon, and thus including nucleotides between the
translation termination codon and 3' end of an mRNA or
corresponding nucleotides on the gene. The 5' cap of an mRNA
comprises an N7-methylated guanosine residue joined to the 5'-most
residue of the mRNA via a 5'-5' triphosphate linkage. The 5' cap
region of an mRNA is considered to include the 5' cap structure
itself as well as the first 50 nucleotides adjacent to the cap. The
5' cap region may also be a preferred target region.
[0028] Although some eukaryotic mRNA transcripts are directly
translated, many contain one or more regions, known as "introns,"
which are excised from a transcript before it is translated. The
remaining (and therefore translated) regions are known as "exons"
and are spliced together to form a continuous mRNA sequence. mRNA
splice sites, i.e., intron-exon junctions, may also be preferred
target regions, and are particularly useful in situations where
aberrant splicing is implicated in disease, or where an
overproduction of a particular mRNA splice product is implicated in
disease. Aberrant fusion junctions due to rearrangements or
deletions are also preferred targets. It has also been found that
introns can also be effective, and therefore preferred, target
regions for antisense compounds targeted, for example, to DNA or
pre-mRNA.
[0029] Once one or more target sites have been identified,
oligonucleotides are chosen which are sufficiently complementary to
the target, i.e., hybridize sufficiently well and with sufficient
specificity, to give the desired effect.
[0030] In the context of this invention, "hybridization" means
hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed
Hoogsteen hydrogen bonding, between complementary nucleoside or
nucleotide bases. For example, adenine and thymine are
complementary nucleobases which pair through the formation of
hydrogen bonds. "Complementary," as used herein, refers to the
capacity for precise pairing between two nucleotides. For example,
if a nucleotide at a certain position of an oligonucleotide is
capable of hydrogen bonding with a nucleotide at the same position
of a DNA or RNA molecule, then the oligonucleotide and the DNA or
RNA are considered to be complementary to each other at that
position. The oligonucleotide and the DNA or RNA are complementary
to each other when a sufficient number of corresponding positions
in each molecule are occupied by nucleotides which can hydrogen
bond with each other. Thus, "specifically hybridizable" and
"complementary" are terms which are used to indicate a sufficient
degree of complementarity or precise pairing such that stable and
specific binding occurs between the oligonucleotide and the DNA or
RNA target. It is understood in the art that the sequence of an
antisense compound need not be 100% complementary to that of its
target nucleic acid to be specifically hybridizable. An antisense
compound is specifically hybridizable when binding of the compound
to the target DNA or RNA molecule interferes with the normal
function of the target DNA or RNA to cause a loss of utility, and
there is a sufficient degree of complementarity to avoid
non-specific binding of the antisense compound to non-target
sequences under conditions in which specific binding is desired,
i.e., under physiological conditions in the case of in vivo assays
or therapeutic treatment, and in the case of in vitro assays, under
conditions in which the assays are performed.
[0031] Antisense and other compounds of the invention which
hybridize to the target and inhibit expression of the target are
identified through experimentation, and the sequences of these
compounds are hereinbelow identified as preferred embodiments of
the invention. The target sites to which these preferred sequences
are complementary are hereinbelow referred to as "active sites" and
are therefore preferred sites for targeting. Therefore another
embodiment of the invention encompasses compounds which hybridize
to these active sites.
[0032] Antisense compounds are commonly used as research reagents
and diagnostics. For example, antisense oligonucleotides, which are
able to inhibit gene expression with exquisite specificity, are
often used by those of ordinary skill to elucidate the function of
particular genes. Antisense compounds are also used, for example,
to distinguish between functions of various members of a biological
pathway. Antisense modulation has, therefore, been harnessed for
research use.
[0033] For use in kits and diagnostics, the antisense compounds of
the present invention, either alone or in combination with other
antisense compounds or therapeutics, can be used as tools in
differential and/or combinatorial analyses to elucidate expression
patterns of a portion or the entire complement of genes expressed
within cells and tissues.
[0034] Expression patterns within cells or tissues treated with one
or more antisense compounds are compared to control cells or
tissues not treated with antisense compounds and the patterns
produced are analyzed for differential levels of gene expression as
they pertain, for example, to disease association, signaling
pathway, cellular localization, expression level, size, structure
or function of the genes examined. These analyses can be performed
on stimulated or unstimulated cells and in the presence or absence
of other compounds which affect expression patterns.
[0035] Examples of methods of gene expression analysis known in the
art include DNA arrays or microarrays (Brazma and Vilo, FEBS Lett.,
2000, 480, 17-24; Celis, et al., FEBS Lett., 2000, 480, 2-16), SAGE
(serial analysis of gene expression)(Madden, et al., Drug Discov.
Today, 2000, 5, 415-425), READS (restriction enzyme amplification
of digested cDNAs) (Prashar and Weissman, Methods Enzymol., 1999,
303, 258-72), TOGA (total gene expression analysis) (Sutcliffe, et
al., Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 1976-81), protein
arrays and proteomics (Celis, et al., FEBS Lett., 2000, 480, 2-16;
Jungblut, et al., Electrophoresis, 1999, 20, 2100-10), expressed
sequence tag (EST) sequencing (Celis, et al., FEBS Lett., 2000,
480, 2-16; Larsson, et al., J. Biotechnol., 2000, 80, 143-57),
subtractive RNA fingerprinting (SuRF) (Fuchs, et al., Anal.
Biochem., 2000, 286, 91-98; Larson, et al., Cytometry, 2000, 41,
203-208), subtractive cloning, differential display (DD) (Jurecic
and Belmont, Curr. Opin. Microbiol, 2000, 3, 316-21), comparative
genomic hybridization (Carulli, et al., J. Cell Biochem. Suppl.,
1998, 31, 286-96), FISH (fluorescent in situ hybridization)
techniques (Going and Gusterson, Eur. J. Cancer, 1999, 35,
1895-904) and mass spectrometry methods (reviewed in (To, Comb.
Chem. High Throughput Screen, 2000, 3, 23541).
[0036] The specificity and sensitivity of antisense is also
harnessed by those of skill in the art for therapeutic uses.
Antisense oligonucleotides have been employed as therapeutic
moieties in the treatment of disease states in animals and man.
Antisense oligonucleotide drugs, including ribozymes, have been
safely and effectively administered to humans and numerous clinical
trials are presently underway. It is thus established that
oligonucleotides can be useful therapeutic modalities that can be
configured to be useful in treatment regimes for treatment of
cells, tissues and animals, especially humans.
[0037] In the context of this invention, the term "oligonucleotide"
refers to an oligomer or polymer of ribonucleic acid (RNA) or
deoxyribonucleic acid (DNA) or mimetics thereof. This term includes
single-stranded and double-stranded oligonucleotides composed of
naturally-occurring nucleobases, sugars and covalent intemucleoside
(backbone) linkages as well as oligonucleotides having
non-naturally-occurring portions which function similarly. Such
modified or substituted oligonucleotides are often preferred over
native forms because of desirable properties such as, for example,
enhanced cellular uptake, enhanced affinity for nucleic acid target
and increased stability in the presence of nucleases.
[0038] While the one form of antisense compound is a
single-stranded antisense oligonucleotide, in many species the
introduction of double-stranded structures, such as double-stranded
RNA (dsRNA) molecules, has been shown to induce potent and specific
antisense-mediated reduction of the function of a gene or its
associated gene products. This phenomenon occurs in both plants and
animals and is believed to have an evolutionary connection to viral
defense and transposon silencing.
[0039] The first evidence that dsRNA could lead to gene silencing
in animals came in 1995 from work in the nematode, Caenorhabditis
elegans (Guo and Kempheus, Cell, 1995, 81, 611-620). Montgomery et
al. have shown that the primary interference effects of dsRNA are
posttranscriptional (Montgomery et al., Proc. Natl. Acad. Sci. USA,
1998, 95, 15502-15507). The posttranscriptional antisense mechanism
defined in Caenorhabditis elegans resulting from exposure to
double-stranded RNA (dsRNA), also refered to as small interfering
RNA (siRNA), has since been designated as RNA interference (RNAi).
This term has been generalized to mean antisense-mediated gene
silencing involving the introduction of dsRNA leading to the
sequence-specific reduction of endogenous targeted mRNA levels
(Fire et al., Nature, 1998, 391, 806-811). It has further been
confirmed that it is, in fact, the single-stranded RNA oligomers of
antisense polarity of the dsRNAs which are the potent inducers of
RNAi (Tijsterman et al., Science, 2002, 295, 694-697).
[0040] While antisense oligonucleotides are a preferred form of
antisense compound, the present invention comprehends other
oligomeric antisense compounds, including but not limited to
oligonucleotide mimetics such as are described below. The antisense
compounds in accordance with this invention preferably comprise
from about 8 to about 50 nucleobases (i.e. from about 8 to about 50
linked nucleosides). Particularly preferred antisense compounds are
antisense oligonucleotides, even more preferably are antisense
compounds comprising from about 15 to about 30 nucleobases.
Antisense compounds include single-stranded and double-stranded
oligonucleotides (including siRNA), ribozymes, external guide
sequence (EGS) oligonucleotides (oligozymes), and other short
catalytic RNAs or catalytic oligonucleotides which hybridize to the
target nucleic acid and modulate its expression, such antisense
compounds can have chemical modifications such as those described
below. A preferred form of the invention is an antisense compound
which further comprises a sense strand such that the antisense
compound is double-stranded, even more preferably such
double-stranded antisense compound is chemically modified
siRNA.
[0041] As is known in the art, a nucleoside is a base-sugar
combination. The base portion of the nucleoside is normally a
heterocyclic base. The two most common classes of such heterocyclic
bases are the purines and the pyrimidines. Nucleotides are
nucleosides that further include a phosphate group covalently
linked to the sugar portion of the nucleoside. For those
nucleosides that include a pentoftiranosyl sugar, the phosphate
group can be linked to either the 2', 3' or 5' hydroxyl moiety of
the sugar. In forming oligonucleotides, the phosphate groups
covalently link adjacent nucleosides to one another to form a
linear polymeric compound. In turn the respective ends of this
linear polymeric structure can be further joined to form a circular
structure, however, open linear structures are generally preferred.
Within the oligonucleotide structure, the phosphate groups are
commonly referred to as forming the internucleoside backbone of the
oligonucleotide. The normal linkage or backbone of RNA and DNA is a
3' to 5' phosphodiester linkage.
[0042] Specific examples of preferred antisense compounds useful in
this invention include oligonucleotides containing modified
backbones or non-natural internucleoside linkages. As defined in
this specification, oligonucleotides having modified backbones
include those that retain a phosphorus atom in the backbone and
those that do not have a phosphorus atom in the backbone. For the
purposes of this specification, and as sometimes referenced in the
art, modified oligonucleotides that do not have a phosphorus atom
in their internucleoside backbone can also be considered to be
oligonucleosides.
[0043] Preferred modified oligonucleotide backbones include, for
example, phosphorothioates, chiral phosphorothioates,
phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters,
methyl and other alkyl phosphonates including 3'-alkylene
phosphonates, 5'-alkylene phosphonates and chiral phosphonates,
phosphinates, phosphoramidates including 3'-amino phosphoramidate
and aminoalkylphosphoramidates, thionophosphoramidates,
thionoalkylphosphonates, thionoalkylphosphotriest- ers,
selenophosphates and boranophosphates having normal 3'-5' linkages,
2'-5' linked analogs of these, and those having inverted polarity
wherein one or more internucleotide linkages is a 3' to 3', 5' to
5' or 2' to 2' linkage. Preferred oligonucleotides having inverted
polarity comprise a single 3' to 3' linkage at the 3'-most
internucleotide linkage i.e. a single inverted nucleoside residue
which may be abasic (the nucleobase is missing or has a hydroxyl
group in place thereof). Various salts, mixed salts and free acid
forms are also included.
[0044] Representative U.S. patents that teach the preparation of
the above phosphorus-containing linkages include, but are not
limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301;
5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302;
5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233;
5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111;
5,563,253; 5,571,799; 5,587,361; 5,194,599; 5,565,555; 5,527,899;
5,721,218; 5,672,697 and 5,625,050, certain of which are commonly
owned with this application, and each of which is herein
incorporated by reference.
[0045] Preferred modified oligonucleotide backbones that do not
include a phosphorus atom therein have backbones that are formed by
short chain alkyl or cycloalkyl intemucleoside linkages, mixed
heteroatom and alkyl or cycloalkyl internucleoside linkages, or one
or more short chain heteroatomic or heterocyclic internucleoside
linkages. These include those having morpholino linkages (formed in
part from the sugar portion of a nucleoside); siloxane backbones;
sulfide, sulfoxide and sulfone backbones; formacetyl and
thioformacetyl backbones; methylene formacetyl and thioformacetyl
backbones; riboacetyl backbones; alkene containing backbones;
sulfamate backbones; methyleneimino and methylenehydrazino
backbones; sulfonate and sulfonamide backbones; amide backbones;
and others having mixed N, O, S and CH.sub.2 component parts.
[0046] Representative U.S. patents that teach the preparation of
the above oligonucleosides include, but are not limited to, U.S.
Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141;
5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677;
5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240;
5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070;
5,663,312; 5,633,360; 5,677,437; 5,792,608; 5,646,269 and
5,677,439, certain of which are commonly owned with this
application, and each of which is herein incorporated by
reference.
[0047] In other preferred oligonucleotide mimetics, both the sugar
and the internucleoside linkage, i.e., the backbone, of the
nucleotide units are replaced with novel groups. The base units are
maintained for hybridization with an appropriate nucleic acid
target compound. One such oligomeric compound, an oligonucleotide
mimetic that has been shown to have excellent hybridization
properties, is referred to as a peptide nucleic acid (PNA). In PNA
compounds, the sugar-backbone of an oligonucleotide is replaced
with an amide containing backbone, in particular an
aminoethylglycine backbone. The nucleobases are retained and are
bound directly or indirectly to aza nitrogen atoms of the amide
portion of the backbone. Representative U.S. patents that teach the
preparation of PNA compounds include, but are not limited to, U.S.
Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is
herein incorporated by reference. Further teaching of PNA compounds
can be found in Nielsen et al., Science, 1991, 254, 1497-1500.
[0048] Most preferred embodiments of the invention are
oligonucleotides with phosphorothioate backbones and
oligonucleosides with heteroatom backbones, and in particular
--CH.sub.2--NH--O--CH.sub.2--,
--CH.sub.2--N(CH.sub.3)--O--CH.sub.2-- [known as a methylene
(methylimino) or MMI backbone],
--CH.sub.2--O--N(CH.sub.3)--CH.sub.2--,
--CH.sub.2--N(CH.sub.3)--N(CH.sub.3)--CH.sub.2-- and
--O--N(CH.sub.3)--CH.sub.2--CH.sub.2--[wherein the native
phosphodiester backbone is represented as --O--P--O--CH.sub.2--] of
the above referenced U.S. Pat. No. 5,489,677, and the amide
backbones of the above referenced U.S. Pat. No. 5,602,240. Also
preferred are oligonucleotides having morpholino backbone
structures of the above-referenced U.S. Pat. No. 5,034,506.
[0049] Modified oligonucleotides may also contain one or more
substituted sugar moieties. Preferred oligonucleotides comprise one
of the following at the 2' position: OH; F; O--, S--, or N-alkyl;
O--, S--, or N-alkenyl; O--, S--or N-alkynyl; or O-alkyl-O-alkyl,
wherein the alkyl, alkenyl and alkynyl may be substituted or
unsubstituted C.sub.1 to C.sub.10 alkyl or C.sub.2 to C.sub.10
alkenyl and alkynyl. Particularly preferred are
O[(CH.sub.2).sub.nO].sub.mCH.sub.3, O(CH.sub.2).sub.nOCH.sub.3,
O(CH.sub.2).sub.nNH.sub.2, O(CH.sub.2).sub.nCH.sub.3,
O(CH.sub.2).sub.nONH.sub.2, and
O(CH.sub.2).sub.nON[(CH.sub.2).sub.nCH.su- b.3)].sub.2, where n and
m are from 1 to about 10. Other preferred oligonucleotides comprise
one of the following at the 2' position: C.sub.1 to C.sub.10 lower
alkyl, substituted lower alkyl, alkenyl, alkynyl, alkaryl, aralkyl,
O-alkaryl or O-aralkyl, SH, SCH.sub.3, OCN, Cl, Br, CN, CF.sub.3,
OCF.sub.3, SOCH.sub.3, SO.sub.2CH.sub.3, ONO.sub.2, NO.sub.2,
N.sub.3, NH.sub.2, heterocycloalkyl, heterocycloalkaryl,
aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving
group, a reporter group, an intercalator, a group for improving the
pharmacokinetic properties of an oligonucleotide, or a group for
improving the pharmacodynamic properties of an oligonucleotide, and
other substituents having similar properties. A preferred
modification includes 2'-methoxyethoxy
(2'-O--CH.sub.2CH.sub.2OCH.sub.3, also known as
2'-O-(2-methoxyethyl) or 2'-MOE) (Martin et al., Helv. Chim. Acta,
1995, 78, 486-504) i.e., an alkoxyalkoxy group. A further preferred
modification includes 2'-dimethylaminooxyethoxy, i.e., a
O(CH.sub.2).sub.2ON(CH.sub.3).sub.2 group, also known as 2'-DMAOE,
as described in examples hereinbelow, and
2'-dimethylaminoethoxyethoxy (also known in the art as
2'-O-dimethylaminoethoxyethyl or 2'-DMAEOE), i.e.,
2'-O--CH.sub.2--O--CH.sub.2--N(CH.sub.2).sub.2, also described in
examples hereinbelow.
[0050] A further prefered modification includes Locked Nucleic
Acids (LNAs) in which the 2'-hydroxyl group is linked to the 3' or
4' carbon atom of the sugar ring thereby forming a bicyclic sugar
moiety. The linkage is preferably a methelyne (--CH.sub.2--).sub.n
group bridging the 2' oxygen atom and the 4' carbon atom wherein n
is 1 or 2. LNAs and preparation thereof are described in WO
98/39352 and WO 99/14226.
[0051] Other preferred modifications include 2'-methoxy
(2'-O-CH.sub.3), 2'-aminopropoxy
(2'-OCH.sub.2CH.sub.2CH.sub.2NH.sub.2), 2'-allyl
(2'-CH.sub.2--CH.dbd.CH.sub.2), 2'-O-allyl
(2'-O--CH.sub.2--CH.dbd.CH.sub- .2) and 2'-fluoro (2'-F). The
2'-modification may be in the arabino (up) position or ribo (down)
position. A preferred 2'-arabino modification is 2'-F. Similar
modifications may also be made at other positions on the
oligonucleotide, particularly the 3' position of the sugar on the
3' terminal nucleotide or in 2'-5' linked oligonucleotides and the
5' position of 5' terminal nucleotide. Oligonucleotides may also
have sugar mimetics such as cyclobutyl moieties in place of the
pentofuranosyl sugar. Representative U.S. patents that teach the
preparation of such modified sugar structures include, but are not
limited to, U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080;
5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134;
5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053;
5,639,873; 5,646,265; 5,658,873; 5,670,633; 5,792,747; and
5,700,920, certain of which are commonly owned with the instant
application, and each of which is herein incorporated by reference
in its entirety.
[0052] Oligonucleotides may also include nucleobase (often referred
to in the art simply as "base") modifications or substitutions. As
used herein, "unmodified" or "natural" nucleobases include the
purine bases adenine (A) and guanine (G), and the pyrimidine bases
thymine (T), cytosine (C) and uracil (U). Modified nucleobases
include other synthetic and natural nucleobases such as
5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine,
hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives
of adenine and guanine, 2-propyl and other alkyl derivatives of
adenine and guanine, 2-thiouracil, 2-thiothymine and
2-thiocytosine, 5-halouracil and cytosine, 5-propynyl
(--C.ident.C--CH.sub.3) uracil and cytosine and other alkynyl
derivatives of pyrimidine bases, 6-azo uracil, cytosine and
thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino,
8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines
and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and
other 5-substituted uracils and cytosines, 7-methylguanine and
7-methyladenine, 2-F-adenine, 2-amino-adenine, 8-azaguanine and
8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine
and 3-deazaadenine. Further modified nucleobases include tricyclic
pyrimidines such as phenoxazine
cytidine(1H-pyrimido[5,4-b][1,4]benzoxazi- n-2(3H)-one),
phenothiazine cytidine (1H-pyrimido[5,4-b][1,4]benzothiazin--
2(3H)-one), G-clamps such as a substituted phenoxazine cytidine
(e.g.
9-(2-aminoethoxy)-H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one),
carbazole cytidine (2H-pyrimido[4,5-b]indol-2-one), pyridoindole
cytidine (H-pyrido[3',2':4,5]pyrrolo[2,3-d]pyrimidin-2-one).
Modified nucleobases may also include those in which the purine or
pyrimidine base is replaced with other heterocycles, for example
7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone.
Further nucleobases include those disclosed in U.S. Pat. No.
3,687,808, those disclosed in The Concise Encyclopedia Of Polymer
Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John
Wiley & Sons, 1990, those disclosed by Englisch et al.,
Angewandte Chemie, International Edition, 1991, 30, 613, and those
disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and
Applications, pages 289-302, Crooke, S. T. and Lebleu, B., ed., CRC
Press, 1993. Certain of these nucleobases are particularly useful
for increasing the binding affinity of the oligomeric compounds of
the invention. These include 5-substituted pyrimidines,
6-azapyrimidines and N-2, N-6 and O-6 substituted purines,
including 2-aminopropyladenine, 5-propynyluracil and
5-propynylcytosine. 5-methylcytosine substitutions have been shown
to increase nucleic acid duplex stability by 0.6-1.2.degree. C.
(Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., eds., Antisense
Research and Applications, CRC Press, Boca Raton, 1993, pp.
276-278) and are presently preferred base substitutions, even more
particularly when combined with 2'-O-methoxyethyl sugar
modifications.
[0053] Representative U.S. patents that teach the preparation of
certain of the above noted modified nucleobases as well as other
modified nucleobases include, but are not limited to, the above
noted U.S. Pat. No. 3,687,808, as well as U.S. Pat. Nos. 4,845,205;
5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187;
5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469;
5,594,121, 5,596,091; 5,614,617; 5,645,985; 5,830,653; 5,763,588;
6,005,096; and 5,681,941, certain of which are commonly owned with
the instant application, and each of which is herein incorporated
by reference, and U.S. Pat. No. 5,750,692, which is commonly owned
with the instant application and also herein incorporated by
reference.
[0054] Another modification of the oligonucleotides of the
invention involves chemically linking to the oligonucleotide one or
more moieties or conjugates which enhance the activity, cellular
distribution or cellular uptake of the oligonucleotide. The
compounds of the invention can include conjugate groups covalently
bound to functional groups such as primary or secondary hydroxyl
groups. Conjugate groups of the invention include intercalators,
reporter molecules, polyamines, polyamides, polyethylene glycols,
polyethers, groups that enhance the pharmacodynamic properties of
oligomers, and groups that enhance the pharmacokinetic properties
of oligomers. Typical conjugates groups include cholesterols,
lipids, phospholipids, biotin, phenazine, folate, phenanthridine,
anthraquinone, acridine, fluoresceins, rhoda-mines, coumarins, and
dyes. Groups that enhance the pharmacodynamic properties, in the
context of this invention, include groups that improve oligomer
uptake, enhance oligomer resistance to degradation, and/or
strengthen sequence-specific hybridization with RNA. Groups that
enhance the pharmacokinetic properties, in the context of this
invention, include groups that improve oligomer uptake,
distribution, metabolism or excretion. Representative conjugate
groups are disclosed in International Patent Application
PCT/US92/09196, filed Oct. 23, 1992 the entire disclosure of which
is incorporated herein by reference. Conjugate moieties include but
are not limited to lipid moieties such as a cholesterol moiety
(Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86,
6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let.,
1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol
(Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309;
Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a
thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20,
533-538), an aliphatic chain, e.g., dodecandiol or undecyl residues
(Saison-Behmoaras et al., EMBO J., 1991, 10, 1111-1118; Kabanov et
al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie,
1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol
or triethylammonium 1,2-di-O-hexadecyl-rac-glyc-
ero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36,
3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a
polyamine or a polyethylene glycol chain (Manoharan et al.,
Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane
acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36,
3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys.
Acta, 1995, 1264, 229-237), or an octadecylamine or
hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J.
Pharmacol. Exp. Ther., 1996, 277, 923-937. Oligonucleotides of the
invention may also be conjugated to active drug substances, for
example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen,
fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen,
dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid,
folinic acid, a benzothiadiazide, chlorothiazide, a diazepine,
indomethicin, a barbiturate, a cephalosporin, a sulfa drug, an
antidiabetic, an antibacterial or an antibiotic.
Oligonucleotide-drug conjugates and their preparation are described
in U.S. patent application Ser. No. 09/334,130 (filed Jun. 15,
1999) which is incorporated herein by reference in its
entirety.
[0055] Representative U.S. patents that teach the preparation of
such oligonucleotide conjugates include, but are not limited to,
U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465;
5,541,313; 5,545,730; 5,552,538; 5,578,717,5,580,731; 5,580,731;
5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603;
5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025;
4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582;
4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963;
5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250;
5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463;
5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142;
5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928
and 5,688,941, certain of which are commonly owned with the instant
application, and each of which is herein incorporated by
reference.
[0056] It is not necessary for all positions in a given compound to
be uniformly modified, and in fact more than one of the
aforementioned modifications may be incorporated in a single
compound or even at a single nucleoside within an oligonucleotide.
The present invention also includes antisense compounds which are
chimeric compounds. "Chimeric" antisense compounds or "chimeras,"
in the context of this invention, are antisense compounds,
particularly oligonucleotides, which contain two or more chemically
distinct regions, each made up of at least one monomer unit, i.e.,
a nucleotide in the case of an oligonucleotide compound. These
oligonucleotides typically contain at least one region wherein the
oligonucleotide is modified so as to confer upon the
oligonucleotide increased resistance to nuclease degradation,
increased cellular uptake, and/or increased binding affinity for
the target nucleic acid. An additional region of the
oligonucleotide may serve as a substrate for enzymes capable of
cleaving RNA:DNA or RNA:RNA hybrids. By way of example, RNase H is
a cellular endonuclease which cleaves the RNA strand of an RNA:DNA
duplex. Activation of RNase H, therefore, results in cleavage of
the RNA target, thereby greatly enhancing the efficiency of
oligonucleotide inhibition of gene expression. Consequently,
comparable results can often be obtained with shorter
oligonucleotides when chimeric oligonucleotides are used, compared
to phosphorothioate deoxyoligonucleotides hybridizing to the same
target region. Cleavage of the RNA target can be routinely detected
by gel electrophoresis and, if necessary, associated nucleic acid
hybridization techniques known in the art.
[0057] Chimeric antisense compounds of the invention may be formed
as composite structures of two or more oligonucleotides, modified
oligonucleotides, oligonucleosides and/or oligonucleotide mimetics
as described above. Such compounds have also been referred to in
the art as hybrids or gapmers. Representative U.S. patents that
teach the preparation of such hybrid structures include, but are
not limited to, U.S. Pat. Nos. 5,013,830; 5,149,797; 5,220,007;
5,256,775; 5,366,878; 5,403,711; 5,491,133; 5,565,350; 5,623,065;
5,652,355; 5,652,356; and 5,700,922, certain of which are commonly
owned with the instant application, and each of which is herein
incorporated by reference in its entirety.
[0058] The antisense compounds used in accordance with this
invention may be conveniently and routinely made through the
well-known technique of solid phase synthesis. Equipment for such
synthesis is sold by several vendors including, for example,
Applied Biosystems (Foster City, Calif.). Any other means for such
synthesis known in the art may additionally or alternatively be
employed. It is well known to use similar techniques to prepare
oligonucleotides such as the phosphorothioates and alkylated
derivatives.
[0059] The antisense compounds of the invention are synthesized in
vitro and do not include antisense compositions of biological
origin, or genetic vector constructs designed to direct the in vivo
synthesis of antisense molecules. The compounds of the invention
may also be admixed, encapsulated, conjugated or otherwise
associated with other molecules, molecule structures or mixtures of
compounds, as for example, liposomes, receptor targeted molecules,
oral, rectal, topical or other formulations, for assisting in
uptake, distribution and/or absorption. Representative U.S. patents
that teach the preparation of such uptake, distribution and/or
absorption assisting formulations include, but are not limited to,
U.S. Pat. Nos. 5,108,921; 5,354,844; 5,416,016; 5,459,127;
5,521,291; 5,543,158; 5,547,932; 5,583,020; 5,591,721; 4,426,330;
4,534,899; 5,013,556; 5,108,921; 5,213,804; 5,227,170; 5,264,221;
5,356,633; 5,395,619; 5,416,016; 5,417,978; 5,462,854; 5,469,854;
5,512,295; 5,527,528; 5,534,259; 5,543,152; 5,556,948; 5,580,575;
and 5,595,756, each of which is herein incorporated by
reference.
[0060] The antisense compounds of the invention encompass any
pharmaceutically acceptable salts, esters, or salts of such esters,
or any other compound which, upon administration to an animal
including a human, is capable of providing (directly or indirectly)
the biologically active metabolite or residue thereof. Accordingly,
for example, the disclosure is also drawn to prodrugs and
pharmaceutically acceptable salts of the compounds of the
invention, pharmaceutically acceptable salts of such prodrugs, and
other bioequivalents.
[0061] The term "prodrug" indicates a therapeutic agent that is
prepared in an inactive form that is converted to an active form
(i.e., drug) within the body or cells thereof by the action of
endogenous enzymes or other chemicals and/or conditions. In
particular, prodrug versions of the oligonucleotides of the
invention are prepared as SATE [(S-acetyl-2-thioethyl)phosphate]
derivatives according to the methods disclosed in WO 93/24510 to
Gosselin et al., published Dec. 9, 1993 or in WO 94/26764 and U.S.
Pat. No. 5,770,713 to Imbach et al.
[0062] The term "pharmaceutically acceptable salts" refers to
physiologically and pharmaceutically acceptable salts of the
compounds of the invention: i.e., salts that retain the desired
biological activity of the parent compound and do not impart
undesired toxicological effects thereto.
[0063] Pharmaceutically acceptable base addition salts are formed
with metals or amines, such as alkali and alkaline earth metals or
organic amines. Examples of metals used as cations are sodium,
potassium, magnesium, calcium, and the like. Examples of suitable
amines are N,N'-dibenzylethylenediamine, chloroprocaine, choline,
diethanolamine, dicyclohexylamine, ethylenediamine,
N-methylglucamine, and procaine (see, for example, Berge et al.,
"Pharmaceutical Salts," J. of Pharma Sci., 1977, 66, 1-19). The
base addition salts of said acidic compounds are prepared by
contacting the free acid form with a sufficient amount of the
desired base to produce the salt in the conventional manner. The
free acid form may be regenerated by contacting the salt form with
an acid and isolating the free acid in the conventional manner. The
free acid forms differ from their respective salt forms somewhat in
certain physical properties such as solubility in polar solvents,
but otherwise the salts are equivalent to their respective free
acid for purposes of the present invention. As used herein, a
"pharmaceutical addition salt" includes a pharmaceutically
acceptable salt of an acid form of one of the components of the
compositions of the invention. These include organic or inorganic
acid salts of the amines. Preferred acid salts are the
hydrochlorides, acetates, salicylates, nitrates and phosphates.
Other suitable pharmaceutically acceptable salts are well known to
those skilled in the art and include basic salts of a variety of
inorganic and organic acids, such as, for example, with inorganic
acids, such as for example hydrochloric acid, hydrobromic acid,
sulfuric acid or phosphoric acid; with organic carboxylic,
sulfonic, sulfo or phospho acids or N-substituted sulfamic acids,
for example acetic acid, propionic acid, glycolic acid, succinic
acid, maleic acid, hydroxymaleic acid, methylmaleic acid, fumaric
acid, malic acid, tartaric acid, lactic acid, oxalic acid, gluconic
acid, glucaric acid, glucuronic acid, citric acid, benzoic acid,
cinnamic acid, mandelic acid, salicylic acid, 4-aminosalicylic
acid, 2-phenoxybenzoic acid, 2-acetoxybenzoic acid, embonic acid,
nicotinic acid or isonicotinic acid; and with amino acids, such as
the 20 alpha-amino acids involved in the synthesis of proteins in
nature, for example glutamic acid or aspartic acid, and also with
phenylacetic acid, methanesulfonic acid, ethanesulfonic acid,
2-hydroxyethanesulfonic acid, ethane-1,2-disulfonic acid,
benzenesulfonic acid, 4-methylbenzenesulfonic acid,
naphthalene-2-sulfonic acid, naphthalene-1,5-disulfonic acid, 2- or
3-phosphoglycerate, glucose-6-phosphate, N-cyclohexylsulfamic acid
(with the formation of cyclamates), or with other acid organic
compounds, such as ascorbic acid. Pharmaceutically acceptable salts
of compounds may also be prepared with a pharmaceutically
acceptable cation. Suitable pharmaceutically acceptable cations are
well known to those skilled in the art and include alkaline,
alkaline earth, ammonium and quaternary ammonium cations.
Carbonates or hydrogen carbonates are also possible.
[0064] For oligonucleotides, preferred examples of pharmaceutically
acceptable salts include but are not limited to (a) salts formed
with cations such as sodium, potassium, ammonium, magnesium,
calcium, polyamines such as spermine and spermidine, etc.; (b) acid
addition salts formed with inorganic acids, for example
hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric
acid, nitric acid and the like; (c) salts formed with organic acids
such as, for example, acetic acid, oxalic acid, tartaric acid,
succinic acid, maleic acid, fumaric acid, gluconic acid, citric
acid, malic acid, ascorbic acid, benzoic acid, tannic acid,
palmitic acid, alginic acid, polyglutamic acid, naphthalenesulfonic
acid, methanesulfonic acid, p-toluenesulfonic acid,
naphthalenedisulfonic acid, polygalacturonic acid, and the like;
and (d) salts formed from elemental anions such as chlorine,
bromine, and iodine.
[0065] The antisense compounds of the present invention can be
utilized for diagnostics, therapeutics, prophylaxis and as research
reagents and kits. For therapeutics, an animal, preferably a human,
suspected of having a disease or disorder which can be treated by
modulating the expression of Interleukin 12 p35 subunit is treated
by administering antisense compounds in accordance with this
invention. The compounds of the invention can be utilized in
pharmaceutical compositions by adding an effective amount of an
antisense compound to a suitable pharmaceutically acceptable
diluent or carrier. Use of the antisense compounds and methods of
the invention may also be useful prophylactically, e.g., to prevent
or delay infection, inflammation or tumor formation, for
example.
[0066] The antisense compounds of the invention are useful for
research and diagnostics, because these compounds hybridize to
nucleic acids encoding Interleukin 12 p35 subunit, enabling
sandwich and other assays to easily be constructed to exploit this
fact. Hybridization of the antisense oligonucleotides of the
invention with a nucleic acid encoding Interleukin 12 p35 subunit
can be detected by means known in the art. Such means may include
conjugation of an enzyme to the oligonucleotide, radiolabelling of
the oligonucleotide or any other suitable detection means. Kits
using such detection means for detecting the level of Interleukin
12 p35 subunit in a sample may also be prepared.
[0067] The present invention also includes pharmaceutical
compositions and formulations which include the antisense compounds
of the invention. The pharmaceutical compositions of the present
invention may be administered in a number of ways depending upon
whether local or systemic treatment is desired and upon the area to
be treated. Administration may be topical (including ophthalmic and
to mucous membranes including vaginal and rectal delivery),
pulmonary, e.g., by inhalation or insufflation of powders or
aerosols, including by nebulizer; intratracheal, intranasal,
epidermal and transdermal), oral or parenteral. Parenteral
administration includes intravenous, intraarterial, subcutaneous,
intraperitoneal or intramuscular injection or infusion; or
intracranial, e.g., intrathecal or intraventricular,
administration. Oligonucleotides with at least one
2'-O-methoxyethyl modification are believed to be particularly
useful for oral administration.
[0068] Pharmaceutical compositions and formulations for topical
administration may include transdermal patches, ointments, lotions,
creams, gels, drops, suppositories, sprays, liquids and powders.
Conventional pharmaceutical carriers, aqueous, powder or oily
bases, thickeners and the like may be necessary or desirable.
Coated condoms, gloves and the like may also be useful. Preferred
topical formulations include those in which the oligonucleotides of
the invention are in admixture with a topical delivery agent such
as lipids, liposomes, fatty acids, fatty acid esters, steroids,
chelating agents and surfactants. Preferred lipids and liposomes
include neutral (e.g. dioleoylphosphatidyl DOPE ethanolamine,
dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl
choline) negative (e.g. dimyristoylphosphatidyl glycerol DMPG) and
cationic (e.g. dioleoyltetramethylaminopropyl DOTAP and
dioleoylphosphatidyl ethanolamine DOTMA). Oligonucleotides of the
invention may be encapsulated within liposomes or may form
complexes thereto, in particular to cationic liposomes.
Alternatively, oligonucleotides may be complexed to lipids, in
particular to cationic lipids. Preferred fatty acids and esters
include but are not limited arachidonic acid, oleic acid,
eicosanoic acid, lauric acid, caprylic acid, capric acid, myristic
acid, palmitic acid, stearic acid, linoleic acid, linolenic acid,
dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate,
1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or
a C.sub.1-10 alkyl ester (e.g. isopropylmyristate IPM),
monoglyceride, diglyceride or pharmaceutically acceptable salt
thereof. Topical formulations are described in detail in U.S.
patent application Ser. No. 09/315,298 filed on May 20, 1999 which
is incorporated herein by reference in its entirety.
[0069] Compositions and formulations for oral administration
include powders or granules, microparticulates, nanoparticulates,
suspensions or solutions in water or non-aqueous media, capsules,
gel capsules, sachets, tablets or minitablets. Thickeners,
flavoring agents, diluents, emulsifiers, dispersing aids or binders
may be desirable. Preferred oral formulations are those in which
oligonucleotides of the invention are administered in conjunction
with one or more penetration enhancers surfactants and chelators.
Preferred surfactants include fatty acids and/or esters or salts
thereof, bile acids and/or salts thereof. Prefered bile acids/salts
include chenodeoxycholic acid (CDCA) and ursodeoxychenodeoxycholic
acid (UDCA), cholic acid, dehydrocholic acid, deoxycholic acid,
glucholic acid, glycholic acid, glycodeoxycholic acid, taurocholic
acid, taurodeoxycholic acid, sodium tauro-24,25-dihydro-fusid- ate,
sodium glycodihydrofusidate,. Prefered fatty acids include
arachidonic acid, undecanoic acid, oleic acid, lauric acid,
caprylic acid, capric acid, myristic acid, palmitic acid, stearic
acid, linoleic acid, linolenic acid, dicaprate, tricaprate,
monoolein, dilaurin, glyceryl 1-monocaprate,
1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or
a monoglyceride, a diglyceride or a pharmaceutically acceptable
salt thereof (e.g. sodium). Also prefered are combinations of
penetration enhancers, for example, fatty acids/salts in
combination with bile acids/salts. A particularly prefered
combination is the sodium salt of lauric acid, capric acid and
UDCA. Further penetration enhancers include
polyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether.
Oligonucleotides of the invention may be delivered orally in
granular form including sprayed dried particles, or complexed to
form micro or nanoparticles. Oligonucleotide complexing agents
include poly-amino acids; polyimines; polyacrylates;
polyalkylacrylates, polyoxethanes, polyalkylcyanoacrylates;
cationized gelatins, albumins, starches, acrylates,
polyethyleneglycols (PEG) and starches; polyalkylcyanoacrylates;
DEAE-derivatized polyimines, pollulans, celluloses and starches.
Particularly preferred complexing agents include chitosan,
N-trimethylchitosan, poly-L-lysine, polyhistidine, polyornithine,
polyspermines, protamine, polyvinylpyridine,
polythiodiethylamino-methylethylene P(TDAE), polyaminostyrene (e.g.
p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate),
poly(butylcyanoacrylate), poly(isobutylcyanoacrylate),
poly(isohexylcynaoacrylate), DEAE-methacrylate, DEAE-hexylacrylate,
DEAE-acrylamide, DEAE-albumin and DEAE-dextran, polymethylacrylate,
polyhexylacrylate, poly(D,L-lactic acid),
poly(DL-lactic-co-glycolic acid (PLGA), alginate, and
polyethyleneglycol (PEG). Oral formulations for oligonucleotides
and their preparation are described in detail in U.S. application
Ser. No. 08/886,829 (filed Jul. 1, 1997), Ser. No. 09/108,673
(filed Jul. 1, 1998), Ser. No. 09/256,515 (filed Feb. 23, 1999),
Ser. No. 09/082,624 (filed May 21, 1998) and Ser. No. 09/315,298
(filed May 20, 1999) each of which is incorporated herein by
reference in their entirety.
[0070] Compositions and formulations for parenteral, intrathecal or
intraventricular administration may include sterile aqueous
solutions which may also contain buffers, diluents and other
suitable additives such as, but not limited to, penetration
enhancers, carrier compounds and other pharmaceutically acceptable
carriers or excipients.
[0071] Pharmaceutical compositions of the present invention
include, but are not limited to, solutions, emulsions, and
liposome-containing formulations. These compositions may be
generated from a variety of components that include, but are not
limited to, preformed liquids, self-emulsifying solids and
self-emulsifying semisolids.
[0072] The pharmaceutical formulations of the present invention,
which may conveniently be presented in unit dosage form, may be
prepared according to conventional techniques well known in the
pharmaceutical industry. Such techniques include the step of
bringing into association the active ingredients with the
pharmaceutical carrier(s) or excipient(s). In general the
formulations are prepared by uniformly and intimately bringing into
association the active ingredients with liquid carriers or finely
divided solid carriers or both, and then, if necessary, shaping the
product.
[0073] The compositions of the present invention may be formulated
into any of many possible dosage forms such as, but not limited to,
tablets, capsules, gel capsules, liquid syrups, soft gels,
suppositories, and enemas. The compositions of the present
invention may also be formulated as suspensions in aqueous,
non-aqueous or mixed media. Aqueous suspensions may further contain
substances which increase the viscosity of the suspension
including, for example, sodium carboxymethylcellulose, sorbitol
and/or dextran. The suspension may also contain stabilizers.
[0074] In one embodiment of the present invention the
pharmaceutical compositions may be formulated and used as foams.
Pharmaceutical foams include formulations such as, but not limited
to, emulsions, microemulsions, creams, jellies and liposomes. While
basically similar in nature these formulations vary in the
components and the consistency of the final product. The
preparation of such compositions and formulations is generally
known to those skilled in the pharmaceutical and formulation arts
and may be applied to the formulation of the compositions of the
present invention.
[0075] Emulsions
[0076] The compositions of the present invention may be prepared
and formulated as emulsions. Emulsions are typically heterogenous
systems of one liquid dispersed in another in the form of droplets
usually exceeding 0.1 .mu.m in diameter. (Idson, in Pharmaceutical
Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel
Dekker, Inc., New York, N.Y., volume 1, p. 199; Rosoff, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New York, N.Y., Volume 1, p. 245; Block
in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker
(Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 2, p.
335; Higuchi et al., in Remington's Pharmaceutical Sciences, Mack
Publishing Co., Easton, Pa., 1985, p. 301). Emulsions are often
biphasic systems comprising of two immiscible liquid phases
intimately mixed and dispersed with each other. In general,
emulsions may be either water-in-oil (w/o) or of the oil-in-water
(o/w) variety. When an aqueous phase is finely divided into and
dispersed as minute droplets into a bulk oily phase the resulting
composition is called a water-in-oil (w/o) emulsion. Alternatively,
when an oily phase is finely divided into and dispersed as minute
droplets into a bulk aqueous phase the resulting composition is
called an oil-in-water (o/w) emulsion. Emulsions may contain
additional components in addition to the dispersed phases and the
active drug which may be present as a solution in either the
aqueous phase, oily phase or itself as a separate phase.
Pharmaceutical excipients such as emulsifiers, stabilizers, dyes,
and anti-oxidants may also be present in emulsions as needed.
Pharmaceutical emulsions may also be multiple emulsions that are
comprised of more than two phases such as, for example, in the case
of oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w)
emulsions. Such complex formulations often provide certain
advantages that simple binary emulsions do not. Multiple emulsions
in which individual oil droplets of an o/w emulsion enclose small
water droplets constitute a w/o/w emulsion. Likewise a system of
oil droplets enclosed in globules of water stabilized in an oily
continuous provides an o/w/o emulsion.
[0077] Emulsions are characterized by little or no thermodynamic
stability. Often, the dispersed or discontinuous phase of the
emulsion is well dispersed into the external or continuous phase
and maintained in this form through the means of emulsifiers or the
viscosity of the formulation. Either of the phases of the emulsion
may be a semisolid or a solid, as is the case of emulsion-style
ointment bases and creams. Other means of stabilizing emulsions
entail the use of emulsifiers that may be incorporated into either
phase of the emulsion. Emulsifiers may broadly be classified into
four categories: synthetic surfactants, naturally occurring
emulsifiers, absorption bases, and finely dispersed solids (Idson,
in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker
(Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p.
199).
[0078] Synthetic surfactants, also known as surface active agents,
have found wide applicability in the formulation of emulsions and
have been reviewed in the literature (Rieger, in Pharmaceutical
Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel
Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199).
Surfactants are typically amphiphilic and comprise a hydrophilic
and a hydrophobic portion. The ratio of the hydrophilic to the
hydrophobic nature of the surfactant has been termed the
hydrophile/lipophile balance (HLB) and is a valuable tool in
categorizing and selecting surfactants in the preparation of
formulations. Surfactants may be classified into different classes
based on the nature of the hydrophilic group: nonionic, anionic,
cationic and amphoteric (Rieger, in Pharmaceutical Dosage Forms,
Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New
York, N.Y., volume 1, p. 285).
[0079] Naturally occurring emulsifiers used in emulsion
formulations include lanolin, beeswax, phosphatides, lecithin and
acacia. Absorption bases possess hydrophilic properties such that
they can soak up water to form w/o emulsions yet retain their
semisolid consistencies, such as anhydrous lanolin and hydrophilic
petrolatum. Finely divided solids have also been used as good
emulsifiers especially in combination with surfactants and in
viscous preparations. These include polar inorganic solids, such as
heavy metal hydroxides, nonswelling clays such as bentonite,
attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum
silicate and colloidal magnesium aluminum silicate, pigments and
nonpolar solids such as carbon or glyceryl tristearate.
[0080] A large variety of non-emulsifying materials are also
included in emulsion formulations and contribute to the properties
of emulsions. These include fats, oils, waxes, fatty acids, fatty
alcohols, fatty esters, humectants, hydrophilic colloids,
preservatives and antioxidants (Block, in Pharmaceutical Dosage
Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker,
Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical
Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel
Dekker, Inc., New York, N.Y., volume 1, p. 199).
[0081] Hydrophilic colloids or hydrocolloids include naturally
occurring gums and synthetic polymers such as polysaccharides (for
example, acacia, agar, alginic acid, carrageenan, guar gum, karaya
gum, and tragacanth), cellulose derivatives (for example,
carboxymethylcellulose and carboxypropylcellulose), and synthetic
polymers (for example, carbomers, cellulose ethers, and
carboxyvinyl polymers). These disperse or swell in water to form
colloidal solutions that stabilize emulsions by forming strong
interfacial films around the dispersed-phase droplets and by
increasing the viscosity of the external phase.
[0082] Since emulsions often contain a number of ingredients such
as carbohydrates, proteins, sterols and phosphatides that may
readily support the growth of microbes, these formulations often
incorporate preservatives. Commonly used preservatives included in
emulsion formulations include methyl paraben, propyl paraben,
quaternary ammonium salts, benzalkonium chloride, esters of
p-hydroxybenzoic acid, and boric acid. Antioxidants are also
commonly added to emulsion formulations to prevent deterioration of
the formulation. Antioxidants used may be free radical scavengers
such as tocopherols, alkyl gallates, butylated hydroxyanisole,
butylated hydroxytoluene, or reducing agents such as ascorbic acid
and sodium metabisulfite, and antioxidant synergists such as citric
acid, tartaric acid, and lecithin.
[0083] The application of emulsion formulations via dermatological,
oral and parenteral routes and methods for their manufacture have
been reviewed in the literature (Idson, in Pharmaceutical Dosage
Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker,
Inc., New York, N.Y., volume 1, p. 199). Emulsion formulations for
oral delivery have been very widely used because of reasons of ease
of formulation, efficacy from an absorption and bioavailability
standpoint. (Rosoff, in Pharmaceutical Dosage Forms, Lieberman,
Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York,
N.Y., volume 1, p. 245; Idson, in Pharmaceutical Dosage Forms,
Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New
York, N.Y., volume 1, p. 199). Mineral-oil base laxatives,
oil-soluble vitamins and high fat nutritive preparations are among
the materials that have commonly been administered orally as o/w
emulsions.
[0084] In one embodiment of the present invention, the compositions
of oligonucleotides and nucleic acids are formulated as
microemulsions. A microemulsion may be defined as a system of
water, oil and amphiphile which is a single optically isotropic and
thermodynamically stable liquid solution (Rosoff, in Pharmaceutical
Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel
Dekker, Inc., New York, N.Y., volume 1, p. 245). Typically
microemulsions are systems that are prepared by first dispersing an
oil in an aqueous surfactant solution and then adding a sufficient
amount of a fourth component, generally an intermediate
chain-length alcohol to form a transparent system. Therefore,
microemulsions have also been described as thermodynamically
stable, isotropically clear dispersions of two immiscible liquids
that are stabilized by interfacial films of surface-active
molecules (Leung and Shah, in: Controlled Release of Drugs:
Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH
Publishers, N.Y., pages 185-215). Microemulsions commonly are
prepared via a combination of three to five components that include
oil, water, surfactant, cosurfactant and electrolyte. Whether the
microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w)
type is dependent on the properties of the oil and surfactant used
and on the structure and geometric packing of the polar heads and
hydrocarbon tails of the surfactant molecules (Schott, in
Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton,
Pa., 1985, p. 271).
[0085] The phenomenological approach utilizing phase diagrams has
been extensively studied and has yielded a comprehensive knowledge,
to one skilled in the art, of how to formulate microemulsions
(Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and
Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1,
p. 245; Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger
and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y.,
volume 1, p. 335). Compared to conventional emulsions,
microemulsions offer the advantage of solubilizing water-insoluble
drugs in a formulation of thermodynamically stable droplets that
are formed spontaneously.
[0086] Surfactants used in the preparation of nicroemulsions
include, but are not limited to, ionic surfactants, non-ionic
surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol
fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol
monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol
pentaoleate (PO500), decaglycerol monocaprate (MCA750),
decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750),
decaglycerol decaoleate (DAO750), alone or in combination with
cosurfactants. The cosurfactant, usually a short-chain alcohol such
as ethanol, 1-propanol, and 1-butanol, serves to increase the
interfacial fluidity by penetrating into the surfactant film and
consequently creating a disordered film because of the void space
generated among surfactant molecules. Microemulsions may, however,
be prepared without the use of cosurfactants and alcohol-free
self-emulsifying microemulsion systems are known in the art. The
aqueous phase may typically be, but is not limited to, water, an
aqueous solution of the drug, glycerol, PEG300, PEG400,
polyglycerols, propylene glycols, and derivatives of ethylene
glycol. The oil phase may include, but is not limited to, materials
such as Captex 300, Captex 355, Capmul MCM, fatty acid esters,
medium chain (C8-C12) mono, di, and tri-glycerides,
polyoxyethylated glyceryl fatty acid esters, fatty alcohols,
polyglycolized glycerides, saturated polyglycolized C8-C 10
glycerides, vegetable oils and silicone oil.
[0087] Microemulsions are particularly of interest from the
standpoint of drug solubilization and the enhanced absorption of
drugs. Lipid based microemulsions (both o/w and w/o) have been
proposed to enhance the oral bioavailability of drugs, including
peptides (Constantinides et al., Pharmaceutical Research, 1994, 11,
1385-1390; Ritschel, Meth. Find. Exp. Clin. Pharmacol., 1993, 13,
205). Microemulsions afford advantages of improved drug
solubilization, protection of drug from enzymatic hydrolysis,
possible enhancement of drug absorption due to surfactant-induced
alterations in membrane fluidity and permeability, ease of
preparation, ease of oral administration over solid dosage forms,
improved clinical potency, and decreased toxicity (Constantinides
et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J.
Pharm. Sci., 1996, 85, 138-143). Often microemulsions may form
spontaneously when their components are brought together at ambient
temperature. This may be particularly advantageous when formulating
thermolabile drugs, peptides or oligonucleotides. Microemulsions
have also been effective in the transdermal delivery of active
components in both cosmetic and pharmaceutical applications. It is
expected that the microemulsion compositions and formulations of
the present invention will facilitate the increased systemic
absorption of oligonucleotides and nucleic acids from the
gastrointestinal tract, as well as improve the local cellular
uptake of oligonucleotides and nucleic acids within the
gastrointestinal tract, vagina, buccal cavity and other areas of
administration.
[0088] Microemulsions of the present invention may also contain
additional components and additives such as sorbitan monostearate
(Grill 3), Labrasol, and penetration enhancers to improve the
properties of the formulation and to enhance the absorption of the
oligonucleotides and nucleic acids of the present invention.
Penetration enhancers used in the microemulsions of the present
invention may be classified as belonging to one of five broad
categories--surfactants, fatty acids, bile salts, chelating agents,
and non-chelating non-surfactants (Lee et al., Critical Reviews in
Therapeutic Drug Carrier Systems, 1991, p. 92). Each of these
classes has been discussed above.
[0089] Liposomes
[0090] There are many organized surfactant structures besides
microemulsions that have been studied and used for the formulation
of drugs. These include monolayers, micelles, bilayers and
vesicles. Vesicles, such as liposomes, have attracted great
interest because of their specificity and the duration of action
they offer from the standpoint of drug delivery. As used in the
present invention, the term "liposome" means a vesicle composed of
amphiphilic lipids arranged in a spherical bilayer or bilayers.
[0091] Liposomes are unilamellar or multilamellar vesicles which
have a membrane formed from a lipophilic material and an aqueous
interior. The aqueous portion contains the composition to be
delivered. Cationic liposomes possess the advantage of being able
to fuse to the cell wall. Non-cationic liposomes, although not able
to fuse as efficiently with the cell wall, are taken up by
macrophages in vivo.
[0092] In order to cross intact mammalian skin, lipid vesicles must
pass through a series of fine pores, each with a diameter less than
50 nm, under the influence of a suitable transdermal gradient.
Therefore, it is desirable to use a liposome which is highly
deformable and able to pass through such fine pores.
[0093] Further advantages of liposomes include; liposomes obtained
from natural phospholipids are biocompatible and biodegradable;
liposomes can incorporate a wide range of water and lipid soluble
drugs; liposomes can protect encapsulated drugs in their internal
compartments from metabolism and degradation (Rosoff, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245).
Important considerations in the preparation of liposome
formulations are the lipid surface charge, vesicle size and the
aqueous volume of the liposomes.
[0094] Liposomes are useful for the transfer and delivery of active
ingredients to the site of action. Because the liposomal membrane
is structurally similar to biological membranes, when liposomes are
applied to a tissue, the liposomes start to merge with the cellular
membranes. As the merging of the liposome and cell progresses, the
liposomal contents are emptied into the cell where the active agent
may act.
[0095] Liposomal formulations have been the focus of extensive
investigation as the mode of delivery for many drugs. There is
growing evidence that for topical administration, liposomes present
several advantages over other formulations. Such advantages include
reduced side-effects related to high systemic absorption of the
administered drug, increased accumulation of the administered drug
at the desired target, and the ability to administer a wide variety
of drugs, both hydrophilic and hydrophobic, into the skin.
[0096] Several reports have detailed the ability of liposomes to
deliver agents including high-molecular weight DNA into the skin.
Compounds including analgesics, antibodies, hormones and
high-molecular weight DNAs have been administered to the skin. The
majority of applications resulted in the targeting of the upper
epidermis.
[0097] Liposomes fall into two broad classes. Cationic liposomes
are positively charged liposomes which interact with the negatively
charged DNA molecules to form a stable complex. The positively
charged DNA/liposome complex binds to the negatively charged cell
surface and is internalized in an endosome. Due to the acidic pH
within the endosome, the liposomes are ruptured, releasing their
contents into the cell cytoplasm (Wang et al., Biochem. Biophys.
Res. Commun., 1987, 147, 980-985).
[0098] Liposomes which are pH-sensitive or negatively-charged,
entrap DNA rather than complex with it. Since both the DNA and the
lipid are similarly charged, repulsion rather than complex
formation occurs. Nevertheless, some DNA is entrapped within the
aqueous interior of these liposomes. pH-sensitive liposomes have
been used to deliver DNA encoding the thymidine kinase gene to cell
monolayers in culture. Expression of the exogenous gene was
detected in the target cells (Zhou et al., Journal of Controlled
Release, 1992, 19, 269-274).
[0099] One major type of liposomal composition includes
phospholipids other than naturally-derived phosphatidylcholine.
Neutral liposome compositions, for example, can be formed from
dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl
phosphatidylcholine (DPPC). Anionic liposome compositions generally
are formed from dimyristoyl phosphatidylglycerol, while anionic
fusogenic liposomes are formed primarily from dioleoyl
phosphatidylethanolamine (DOPE). Another type of liposomal
composition is formed from phosphatidylcholine (PC) such as, for
example, soybean PC, and egg PC. Another type is formed from
mixtures of phospholipid and/or phosphatidylcholine and/or
cholesterol.
[0100] Several studies have assessed the topical delivery of
liposomal drug formulations to the skin. Application of liposomes
containing interferon to guinea pig skin resulted in a reduction of
skin herpes sores while delivery of interferon via other means
(e.g. as a solution or as an emulsion) were ineffective (Weiner et
al., Journal of Drug Targeting, 1992, 2, 405-410). Further, an
additional study tested the efficacy of interferon administered as
part of a liposomal formulation to the administration of interferon
using an aqueous system, and concluded that the liposomal
formulation was superior to aqueous administration (du Plessis et
al., Antiviral Research, 1992, 18, 259-265).
[0101] Non-ionic liposomal systems have also been examined to
determine their utility in the delivery of drugs to the skin, in
particular systems comprising non-ionic surfactant and cholesterol.
Non-ionic liposomal formulations comprising Novasome.TM. I
(glyceryl dilaurate/cholesterol/po- lyoxyethylene-10-stearyl ether)
and Novasome.TM. II (glyceryl distearate/
cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver
cyclosporin-A into the dermis of mouse skin. Results indicated that
such non-ionic liposomal systems were effective in facilitating the
deposition of cyclosporin-A into different layers of the skin (Hu
et al. S.T.P. Pharma. Sci., 1994, 4, 6, 466).
[0102] Liposomes also include "sterically stabilized" liposomes, a
term which, as used herein, refers to liposomes comprising one or
more specialized lipids that, when incorporated into liposomes,
result in enhanced circulation lifetimes relative to liposomes
lacking such specialized lipids. Examples of sterically stabilized
liposomes are those in which part of the vesicle-forming lipid
portion of the liposome (A) comprises one or more glycolipids, such
as monosialoganglioside G.sub.M1, or (B) is derivatized with one or
more hydrophilic polymers, such as a polyethylene glycol (PEG)
moiety. While not wishing to be bound by any particular theory, it
is thought in the art that, at least for sterically stabilized
liposomes containing gangliosides, sphingomyelin, or
PEG-derivatized lipids, the enhanced circulation half-life of these
sterically stabilized liposomes derives from a reduced uptake into
cells of the reticuloendothelial system (RES) (Allen et al., FEBS
Letters, 1987, 223, 42; Wu et al., Cancer Research, 1993, 53,
3765).
[0103] Various liposomes comprising one or more glycolipids are
known in the art. Papahadjopoulos et al. (Ann. N.Y. Acad. Sci.,
1987, 507, 64) reported the ability of monosialoganglioside
G.sub.M1, galactocerebroside sulfate and phosphatidylinositol to
improve blood half-lives of liposomes. These findings were
expounded upon by Gabizon et al. (Proc. Natl. Acad. Sci. U.S.A.,
1988, 85, 6949). U.S. Pat. No. 4,837,028 and WO 88/04924, both to
Allen et al., disclose liposomes comprising (1) sphingomyelin and
(2) the ganglioside G.sub.M1 or a galactocerebroside sulfate ester.
U.S. Pat. No. 5,543,152 (Webb et al.) discloses liposomes
comprising sphingomyelin. Liposomes comprising
1,2-sn-dimyristoylphosphat- idylcholine are disclosed in WO
97/13499 (Lim et al.).
[0104] Many liposomes comprising lipids derivatized with one or
more hydrophilic polymers, and methods of preparation thereof, are
known in the art. Sunamoto et al. (Bull. Chem. Soc. Jpn., 1980, 53,
2778) described liposomes comprising a nonionic detergent,
2C.sub.1215G, that contains a PEG moiety. Illum et al. (FEBS Lett.,
1984, 167, 79) noted that hydrophilic coating of polystyrene
particles with polymeric glycols results in significantly enhanced
blood half-lives. Synthetic phospholipids modified by the
attachment of carboxylic groups of polyalkylene glycols (e.g., PEG)
are described by Sears (U.S. Pat. Nos. 4,426,330 and 4,534,899).
Klibanov et al. (FEBS Lett., 1990, 268, 235) described experiments
demonstrating that liposomes comprising phosphatidylethanolamine
(PE) derivatized with PEG or PEG stearate have significant
increases in blood circulation half-lives. Blume et al. (Biochimica
et Biophysica Acta, 1990, 1029, 91) extended such observations to
other PEG-derivatized phospholipids, e.g., DSPE-PEG, formed from
the combination of distearoylphosphatidylethanolamine (DSPE) and
PEG. Liposomes having covalently bound PEG moieties on their
external surface are described in European Patent No. EP 0 445 131
B1 and WO 90/04384 to Fisher. Liposome compositions containing 1-20
mole percent of PE derivatized with PEG, and methods of use
thereof, are described by Woodle et al. (U.S. Pat. Nos. 5,013,556
and 5,356,633) and Martin et al. (U.S. Pat. No. 5,213,804 and
European Patent No. EP 0 496 813 B1). Liposomes comprising a number
of other lipid-polymer conjugates are disclosed in WO 91/05545 and
U.S. Pat. No. 5,225,212 (both to Martin et al.) and in WO 94/20073
(Zalipsky et al.) Liposomes comprising PEG-modified ceramide lipids
are described in WO 96/10391 (Choi et al.). U.S. Pat. No. 5,540,935
(Miyazaki et al.) and U.S. Pat. No. 5,556,948 (Tagawa et al.)
describe PEG-containing liposomes that can be further derivatized
with functional moieties on their surfaces.
[0105] A limited number of liposomes comprising nucleic acids are
known in the art. WO 96/40062 to Thierry et al. discloses methods
for encapsulating high molecular weight nucleic acids in liposomes.
U.S. Pat. No. 5,264,221 to Tagawa et al. discloses protein-bonded
liposomes and asserts that the contents of such liposomes may
include an antisense RNA. U.S. Pat. No. 5,665,710 to Rahman et al.
describes certain methods of encapsulating oligodeoxynucleotides in
liposomes. WO 97/04787 to Love et al. discloses liposomes
comprising antisense oligonucleotides targeted to the raf gene.
[0106] Transfersomes are yet another type of liposomes, and are
highly deformable lipid aggregates which are attractive candidates
for drug delivery vehicles. Transfersomes may be described as lipid
droplets which are so highly deformable that they are easily able
to penetrate through pores which are smaller than the droplet.
Transfersomes are adaptable to the environment in which they are
used, e.g. they are self-optimizing (adaptive to the shape of pores
in the skin), self-repairing, frequently reach their targets
without fragmenting, and often self-loading. To make transfersomes
it is possible to add surface edge-activators, usually surfactants,
to a standard liposomal composition. Transfersomes have been used
to deliver serum albumin to the skin. The transfersome-mediated
delivery of serum albumin has been shown to be as effective as
subcutaneous injection of a solution containing serum albumin.
[0107] Surfactants find wide application in formulations such as
emulsions (including microemulsions) and liposomes. The most common
way of classifying and ranking the properties of the many different
types of surfactants, both natural and synthetic, is by the use of
the hydrophile/lipophile balance (HLB). The nature of the
hydrophilic group (also known as the "head") provides the most
useful means for categorizing the different surfactants used in
formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel
Dekker, Inc., New York, N.Y., 1988, p. 285).
[0108] If the surfactant molecule is not ionized, it is classified
as a nonionic surfactant. Nonionic surfactants find wide
application in pharmaceutical and cosmetic products and are usable
over a wide range of pH values. In general their HLB values range
from 2 to about 18 depending on their structure. Nonionic
surfactants include nonionic esters such as ethylene glycol esters,
propylene glycol esters, glyceryl esters, polyglyceryl esters,
sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic
alkanolamides and ethers such as fatty alcohol ethoxylates,
propoxylated alcohols, and ethoxylated/propoxylated block polymers
are also included in this class. The polyoxyethylene surfactants
are the most popular members of the nonionic surfactant class.
[0109] If the surfactant molecule carries a negative charge when it
is dissolved or dispersed in water, the surfactant is classified as
anionic. Anionic surfactants include carboxylates such as soaps,
acyl lactylates, acyl amides of amino acids, esters of sulfuric
acid such as alkyl sulfates and ethoxylated alkyl sulfates,
sulfonates such as alkyl benzene sulfonates, acyl isethionates,
acyl taurates and sulfosuccinates, and phosphates. The most
important members of the anionic surfactant class are the alkyl
sulfates and the soaps.
[0110] If the surfactant molecule carries a positive charge when it
is dissolved or dispersed in water, the surfactant is classified as
cationic. Cationic surfactants include quaternary ammonium salts
and ethoxylated amines. The quaternary ammonium salts are the most
used members of this class.
[0111] If the surfactant molecule has the ability to carry either a
positive or negative charge, the surfactant is classified as
amphoteric. Amphoteric surfactants include acrylic acid
derivatives, substituted alkylamides, N-alkylbetaines and
phosphatides.
[0112] The use of surfactants in drug products, formulations and in
emulsions has been reviewed (Rieger, in Pharmaceutical Dosage
Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).
[0113] Penetration Enhancers
[0114] In one embodiment, the present invention employs various
penetration enhancers to effect the efficient delivery of nucleic
acids, particularly oligonucleotides, to the skin of animals. Most
drugs are present in solution in both ionized and nonionized forms.
However, usually only lipid soluble or lipophilic drugs readily
cross cell membranes. It has been discovered that even
non-lipophilic drugs may cross cell membranes if the membrane to be
crossed is treated with a penetration enhancer. In addition to
aiding the diffusion of non-lipophilic drugs across cell membranes,
penetration enhancers also enhance the permeability of lipophilic
drugs.
[0115] Penetration enhancers may be classified as belonging to one
of five broad categories, i.e., surfactants, fatty acids, bile
salts, chelating agents, and non-chelating non-surfactants (Lee et
al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.
92). Each of the above mentioned classes of penetration enhancers
are described below in greater detail.
[0116] Surfactants: In connection with the present invention,
surfactants (or "surface-active agents") are chemical entities
which, when dissolved in an aqueous solution, reduce the surface
tension of the solution or the interfacial tension between the
aqueous solution and another liquid, with the result that
absorption of oligonucleotides through the mucosa is enhanced. In
addition to bile salts and fatty acids, these penetration enhancers
include, for example, sodium lauryl sulfate,
polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether)
(Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems,
1991, p. 92); and perfluorochemical emulsions, such as FC43.
Takahashi et al., J. Pharm. Pharmacol, 1988, 40, 252).
[0117] Fatty acids: Various fatty acids and their derivatives which
act as penetration enhancers include, for example, oleic acid,
lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic
acid, stearic acid, linoleic acid, linolenic acid, dicaprate,
tricaprate, monoolein (1-monooleoyl-rac-glycerol), dilaurin,
caprylic acid, arachidonic acid, glycerol 1-monocaprate,
1-dodecylazacycloheptan-2-one, acylcarnitines, acylcholines,
C.sub.1-10 alkyl esters thereof (e.g., methyl, isopropyl and
t-butyl), and mono- and di-glycerides thereof (i.e., oleate,
laurate, caprate, myristate, palmitate, stearate, linoleate, etc.)
(Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems,
1991, p. 92; Muranishi, Critical Reviews in Therapeutic Drug
Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm.
Pharmacol., 1992, 44, 651-654).
[0118] Bile salts: The physiological role of bile includes the
facilitation of dispersion and absorption of lipids and fat-soluble
vitamins (Brunton, Chapter 38 in: Goodman & Gilman's The
Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al.
Eds., McGraw-Hill, New York, 1996, pp. 934-935). Various natural
bile salts, and their synthetic derivatives, act as penetration
enhancers. Thus the term "bile salts" includes any of the naturally
occurring components of bile as well as any of their synthetic
derivatives. The bile salts of the invention include, for example,
cholic acid (or its pharmaceutically acceptable sodium salt, sodium
cholate), dehydrocholic acid (sodium dehydrocholate), deoxycholic
acid (sodium deoxycholate), glucholic acid (sodium glucholate),
glycholic acid (sodium glycocholate), glycodeoxycholic acid (sodium
glycodeoxycholate), taurocholic acid (sodium taurocholate),
taurodeoxycholic acid (sodium taurodeoxycholate), chenodeoxycholic
acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA),
sodium tauro-24,25-dihydro-fusidate (STDHF), sodium
glycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (Lee
et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991,
page 92; Swinyard, Chapter 39 In: Remington's Pharmaceutical
Sciences, 18th Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa.,
1990, pages 782-783; Muranishi, Critical Reviews in Therapeutic
Drug Carrier Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharm.
Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm. Sci., 1990,
79, 579-583).
[0119] Chelating Agents: Chelating agents, as used in connection
with the present invention, can be defined as compounds that remove
metallic ions from solution by forming complexes therewith, with
the result that absorption of oligonucleotides through the mucosa
is enhanced. With regards to their use as penetration enhancers in
the present invention, chelating agents have the added advantage of
also serving as DNase inhibitors, as most characterized DNA
nucleases require a divalent metal ion for catalysis and are thus
inhibited by chelating agents (Jarrett, J. Chromatogr., 1993, 618,
315-339). Chelating agents of the invention include but are not
limited to disodium ethylenediaminetetraacetate (EDTA), citric
acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate and
homovanilate), N-acyl derivatives of collagen, laureth-9 and
N-amino acyl derivatives of beta-diketones (enamines)(Lee et al.,
Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page
92; Muranishi, Critical Reviews in Therapeutic Drug Carrier
Systems, 1990, 7, 1-33; Buur et al., J. Control Rel., 1990, 14,
43-51).
[0120] Non-chelating non-surfactants: As used herein, non-chelating
non-surfactant penetration enhancing compounds can be defmed as
compounds that demonstrate insignificant activity as chelating
agents or as surfactants but that nonetheless enhance absorption of
oligonucleotides through the alimentary mucosa (Muranishi, Critical
Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33). This
class of penetration enhancers include, for example, unsaturated
cyclic ureas, 1-alkyl- and 1-alkenylazacyclo-alkanone derivatives
(Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems,
1991, page 92); and non-steroidal anti-inflammatory agents such as
diclofenac sodium, indomethacin and phenylbutazone (Yamashita et
al., J. Pharm. Pharmacol., 1987, 39, 621-626).
[0121] Agents that enhance uptake of oligonucleotides at the
cellular level may also be added to the pharmaceutical and other
compositions of the present invention. For example, cationic
lipids, such as lipofectin (Junichi et al, U.S. Pat. No.
5,705,188), cationic glycerol derivatives, and polycationic
molecules, such as polylysine (Lollo et al., PCT Application WO
97/30731), are also known to enhance the cellular uptake of
oligonucleotides.
[0122] Other agents may be utilized to enhance the penetration of
the administered nucleic acids, including glycols such as ethylene
glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and
terpenes such as limonene and menthone.
[0123] Carriers
[0124] Certain compositions of the present invention also
incorporate carrier compounds in the formulation. As used herein,
"carrier compound" or "carrier" can refer to a nucleic acid, or
analog thereof, which is inert (i.e., does not possess biological
activity per se) but is recognized as a nucleic acid by in vivo
processes that reduce the bioavailability of a nucleic acid having
biological activity by, for example, degrading the biologically
active nucleic acid or promoting its removal from circulation. The
coadministration of a nucleic acid and a carrier compound,
typically with an excess of the latter substance, can result in a
substantial reduction of the amount of nucleic acid recovered in
the liver, kidney or other extracirculatory reservoirs, presumably
due to competition between the carrier compound and the nucleic
acid for a common receptor. For example, the recovery of a
partially phosphorothioate oligonucleotide in hepatic tissue can be
reduced when it is coadministered with polyinosinic acid, dextran
sulfate, polycytidic acid or
4-acetamido-4'isothiocyano-stilbene-2,2'-disulfonic acid (Miyao et
al., Antisense Res. Dev., 1995, 5, 115-121; Takakura et al.,
Antisense & Nucl. Acid Drug Dev., 1996, 6, 177-183).
[0125] Excipients
[0126] In contrast to a carrier compound, a "pharmaceutical
carrier" or "excipient" is a pharmaceutically acceptable solvent,
suspending agent or any other pharmacologically inert vehicle for
delivering one or more nucleic acids to an animal. The excipient
may be liquid or solid and is selected, with the planned manner of
administration in mind, so as to provide for the desired bulk,
consistency, etc., when combined with a nucleic acid and the other
components of a given pharmaceutical composition. Typical
pharmaceutical carriers include, but are not limited to, binding
agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or
hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and
other sugars, microcrystalline cellulose, pectin, gelatin, calcium
sulfate, ethyl cellulose, polyacrylates or calcium hydrogen
phosphate, etc.); lubricants (e.g., magnesium stearate, talc,
silica, colloidal silicon dioxide, stearic acid, metallic
stearates, hydrogenated vegetable oils, corn starch, polyethylene
glycols, sodium benzoate, sodium acetate, etc.); disintegrants
(e.g., starch, sodium starch glycolate, etc.); and wetting agents
(e.g., sodium lauryl sulphate, etc.).
[0127] Pharmaceutically acceptable organic or inorganic excipient
suitable for non-parenteral administration which do not
deleteriously react with nucleic acids can also be used to
formulate the compositions of the present invention. Suitable
pharmaceutically acceptable carriers include, but are not limited
to, water, salt solutions, alcohols, polyethylene glycols, gelatin,
lactose, amylose, magnesium stearate, talc, silicic acid, viscous
paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the
like.
[0128] Formulations for topical administration of nucleic acids may
include sterile and non-sterile aqueous solutions, non-aqueous
solutions in common solvents such as alcohols, or solutions of the
nucleic acids in liquid or solid oil bases. The solutions may also
contain buffers, diluents and other suitable additives.
Pharmaceutically acceptable organic or inorganic excipients
suitable for non-parenteral administration which do not
deleteriously react with nucleic acids can be used.
[0129] Suitable pharmaceutically acceptable excipients include, but
are not limited to, water, salt solutions, alcohol, polyethylene
glycols, gelatin, lactose, amylose, magnesium stearate, talc,
silicic acid, viscous paraffin, hydroxymethylcellulose,
polyvinylpyrrolidone and the like.
[0130] Other Components
[0131] The compositions of the present invention may additionally
contain other adjunct components conventionally found in
pharmaceutical compositions, at their art-established usage levels.
Thus, for example, the compositions may contain additional,
compatible, pharmaceutically-active materials such as, for example,
antipruritics, astringents, local anesthetics or anti-inflammatory
agents, or may contain additional materials useful in physically
formulating various dosage forms of the compositions of the present
invention, such as dyes, flavoring agents, preservatives,
antioxidants, opacifiers, thickening agents and stabilizers.
However, such materials, when added, should not unduly interfere
with the biological activities of the components of the
compositions of the present invention. The formulations can be
sterilized and, if desired, mixed with auxiliary agents, e.g.,
lubricants, preservatives, stabilizers, wetting agents,
emulsifiers, salts for influencing osmotic pressure, buffers,
colorings, flavorings and/or aromatic substances and the like which
do not deleteriously interact with the nucleic acid(s) of the
formulation.
[0132] Aqueous suspensions may contain substances which increase
the viscosity of the suspension including, for example, sodium
carboxymethylcellulose, sorbitol and/or dextran. The suspension may
also contain stabilizers.
[0133] Certain embodiments of the invention provide pharmaceutical
compositions containing (a) one or more antisense compounds and (b)
one or more other chemotherapeutic agents which function by a
non-antisense mechanism. Examples of such chemotherapeutic agents
include but are not limited to daunorubicin, daunomycin,
dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin,
bleomycin, mafosfamide, ifosfamide, cytosine arabinoside,
bis-chloroethylnitrosurea, busulfan, mitomycin C, actinomycin D,
mithramycin, prednisone, hydroxyprogesterone, testosterone,
tamoxifen, dacarbazine, procarbazine, hexamethylmelamine,
pentamethylmelamine, mitoxantrone, amsacrine, chlorambucil,
methylcyclohexylnitrosurea, nitrogen mustards, melphalan,
cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine,
5-azacytidine, hydroxyurea, deoxycoformycin,
4-hydroxyperoxycyclophosphor- amide, 5-fluorouracil (5-FU),
5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine,
taxol, vincristine, vinblastine, etoposide (VP-16), trimetrexate,
irinotecan, topotecan, gemcitabine, teniposide, cisplatin and
diethylstilbestrol (DES). See, generally, The Merck Manual of
Diagnosis and Therapy, 15th Ed. 1987, pp. 1206-1228, Berkow et al.,
eds., Rahway, N.J. When used with the compounds of the invention,
such chemotherapeutic agents may be used individually (e.g., 5-FU
and oligonucleotide), sequentially (e.g., 5-FU and oligonucleotide
for a period of time followed by MTX and oligonucleotide), or in
combination with one or more other such chemotherapeutic agents
(e.g., 5-FU, MTX and oligonucleotide, or 5-FU, radiotherapy and
oligonucleotide). Anti-inflammatory drugs, including but not
limited to nonsteroidal anti-inflammatory drugs and
corticosteroids, and antiviral drugs, including but not limited to
ribivirin, vidarabine, acyclovir and ganciclovir, may also be
combined in compositions of the invention. See, generally, The
Merck Manual of Diagnosis and Therapy, 15th Ed., Berkow et al.,
eds., 1987, Rahway, N.J., pages 2499-2506 and 46-49, respectively).
Other non-antisense chemotherapeutic agents are also within the
scope of this invention. Two or more combined compounds may be used
together or sequentially.
[0134] In another related embodiment, compositions of the invention
may contain one or more antisense compounds, particularly
oligonucleotides, targeted to a first nucleic acid and one or more
additional antisense compounds targeted to a second nucleic acid
target. Numerous examples of antisense compounds are known in the
art. Two or more combined compounds may be used together or
sequentially.
[0135] The formulation of therapeutic compositions and their
subsequent administration is believed to be within the skill of
those in the art. Dosing is dependent on severity and
responsiveness of the disease state to be treated, with the course
of treatment lasting from several days to several months, or until
a cure is effected or a diminution of the disease state is
achieved. Optimal dosing schedules can be calculated from
measurements of drug accumulation in the body of the patient.
Persons of ordinary skill can easily determine optimum dosages,
dosing methodologies and repetition rates. Optimum dosages may vary
depending on the relative potency of individual oligonucleotides,
and can generally be estimated based on EC.sub.50s found to be
effective in in vitro and in vivo animal models. In general, dosage
is from 0.01 ug to 100 g per kg of body weight, and may be given
once or more daily, weekly, monthly or yearly, or even once every 2
to 20 years. Persons of ordinary skill in the art can easily
estimate repetition rates for dosing based on measured residence
times and concentrations of the drug in bodily fluids or tissues.
Following successful treatment, it may be desirable to have the
patient undergo maintenance therapy to prevent the recurrence of
the disease state, wherein the oligonucleotide is administered in
maintenance doses, ranging from 0.01 ug to 100 g per kg of body
weight, once or more daily, to once every 20 years.
[0136] While the present invention has been described with
specificity in accordance with certain of its preferred
embodiments, the following examples serve only to illustrate the
invention and are not intended to limit the same. Each of the
references, GenBank accession numbers, U.S. patents and the like
recited in the present application is incorporated herein by
reference in its entirety.
EXAMPLES
Example 1
[0137] Synthesis of Nucleoside Phosphoramidites
[0138] The following compounds, including amidites and their
intermediates were prepared as described in U.S. Pat. No. 6,426,220
and published PCT WO 02/36743; 5'-O-Dimethoxytrityl-thymidine
intermediate for 5-methyl dC amidite,
5'-O-Dimethoxytrityl-2'-deoxy-5-methylcytidine intermediate for
5-methyl-dC amidite,
5'-O-Dimethoxytrityl-2'-deoxy-N4-benzoyl-5-methylcyt- idine
penultimate intermediate for 5-methyl dC amidite,
[5'-O-(4,4'-Dimethoxytriphenylmethyl)-2'-deoxy-N4-benzoyl-5-methylcytidin-
-3'-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite (5-methyl dC
amidite), 2'-Fluorodeoxyadenosine, 2'-Fluorodeoxyguanosine,
2'-Fluorouridine, 2'-Fluorodeoxycytidine, 2'-O-(2-Methoxyethyl)
modified amidites, 2'-O-(2-methoxyethyl)-5-methyluridine
intermediate, 5'-O-DMT-2'-O-(2-methoxyethyl)-5-methyluridine
penultimate intermediate,
[5'-O-(4,4'-Dimethoxytriphenylmethyl)-2'-O-(2-methoxyethyl)-5-methyluridi-
n-3'-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite (MOE T
amidite),
5'-O-Dimethoxytrityl-2'-O-(2-methoxyethyl)-5-methylcytidine
intermediate,
5'-O-dimethoxytrityl-2'-O-(2-methoxyethyl)-N4-benzoyl-5-methyl-cytidine
penultimate intermediate,
[5'-O-(4,4'-Dimethoxytriphenylmethyl)-2'-O-(2-m-
ethoxyethyl)-N4-benzoyl-5-methylcytidin-3'-O-yl]-2-cyanoethyl-N,N-diisopro-
pylphosphoramidite (MOE 5-Me-C amidite),
[5'-O-(4,4'-Dimethoxytriphenylmet-
hyl)-2'-O-(2-methoxyethyl)-N6-benzoyladenosin-3'-O-yl]-2-cyanoethyl-N,N-di-
isopropylphosphoramidite (MOE A amdite),
[5'-O-(4,4'-Dimethoxytriphenylmet-
hyl)-2'-O-(2-methoxyethyl)-N4-isobutyrylguanosin-3'-O-yl]-2-cyanoethyl-N,N-
-diisopropylphosphoramidite (MOE G amidite), 2'-O-(Aminooxyethyl)
nucleoside amidites and 2'-O-(dimethylaminooxyethyl) nucleoside
amidites, 2'-(Dimethylaminooxyethoxy) nucleoside amidites,
5'-O-tert-Butyldiphenyls- ilyl-O2-2'-anhydro-5-methyluridine,
5'-O-tert-Butyldiphenylsilyl-2'-O-(2-h-
ydroxyethyl)-5-methyluridine,
2'-O-([2-phthalimidoxy)ethyl]-5'-t-butyldiph-
enylsilyl-5-methyluridine,
5'-O-tert-butyldiphenylsilyl-2'-O-[(2-formadoxi-
minooxy)ethyl]-5-methyluridine,
5'-O-tert-Butyldiphenylsilyl-2'-O-[N,N
dimethylaminooxyethyl]-5-methyluridine,
2'-O-(dimethylaminooxyethyl)-5-me- thyluridine,
5'-O-DMT-2'-O-(dimethylaminooxyethyl)-5-methyluridine,
5'-O-DMT-2'-O-(2-N,N-dimethylaminooxyethyl)-5-methyluridine-3'-[(2-cyanoe-
thyl)-N,N-diisopropylphosphoramidite], 2'-(Aminooxyethoxy)
nucleoside amidites,
N2-isobutyryl-6-O-diphenylcarbamoyl-2'-O-(2-ethylacetyl)-5'-O-(-
4,4'-dimethoxytrityl)guanosine-3'-[(2-cyanoethyl)-N,N-diisopropylphosphora-
midite], 2'-dimethylaminoethoxyethoxy (2'-DMAEOE) nucleoside
amidites, 2'-O-[2(2-N,N-dimethylaminoethoxy)ethyl]-5-methyl
uridine,
5'-O-dimethoxytrityl-2'-O-[2(2-N,N-dimethylaminoethoxy)-ethyl)]-5-methyl
uridine and
5'-O-Dimethoxytrityl-2'-O-[2(2-N,N-dimethylaminoethoxy)-ethyl-
)]-5-methyl
uridine-3'-O-(cyanoethyl-N,N-diisopropyl)phosphoramidite.
Example 2
[0139] Oligonucleotide and Oligonucleoside Synthesis
[0140] The antisense compounds used in accordance with this
invention may be conveniently and routinely made through the
well-known technique of solid phase synthesis. Equipment for such
synthesis is sold by several vendors including, for example,
Applied Biosystems (Foster City, Calif.). Any other means for such
synthesis known in the art may additionally or alternatively be
employed. It is well known to use similar techniques to prepare
oligonucleotides such as the phosphorothioates and alkylated
derivatives.
[0141] Oligonucleotides: Unsubstituted and substituted
phosphodiester (P.dbd.O) oligonucleotides are synthesized on an
automated DNA synthesizer (Applied Biosystems model 394) using
standard phosphoramidite chemistry with oxidation by iodine.
[0142] Phosphorothioates (P.dbd.S) are synthesized similar to
phosphodiester oligonucleotides with the following exceptions:
thiation was effected by utilizing a 10% w/v solution of
3,H-1,2-benzodithiole-3-o- ne 1,1-dioxide in acetonitrile for the
oxidation of the phosphite linkages. The thiation reaction step
time was increased to 180 sec and preceded by the normal capping
step. After cleavage from the CPG column and deblocking in
concentrated ammonium hydroxide at 55.quadrature.C (12-16 hr), the
oligonucleotides were recovered by precipitating with >3 volumes
of ethanol from a 1 M NH4OAc solution. Phosphinate oligonucleotides
are prepared as described in U.S. Pat. No. 5,508,270, herein
incorporated by reference.
[0143] Alkyl phosphonate oligonucleotides are prepared as described
in U.S. Pat. No. 4,469,863, herein incorporated by reference.
[0144] 3'-Deoxy-3'-methylene phosphonate oligonucleotides are
prepared as described in U.S. Pat. Nos. 5,610,289 or 5,625,050,
herein incorporated by reference.
[0145] Phosphoramidite oligonucleotides are prepared as described
in U.S. Pat. No. 5,256,775 or U.S. Pat. No. 5,366,878, herein
incorporated by reference.
[0146] Alkylphosphonothioate oligonucleotides are prepared as
described in published PCT applications PCT/US94/00902 and
PCT/US93/06976 (published as WO 94/17093 and WO 94/02499,
respectively), herein incorporated by reference.
[0147] 3'-Deoxy-3'-amino phosphoramidate oligonucleotides are
prepared as described in U.S. Pat. No. 5,476,925, herein
incorporated by reference.
[0148] Phosphotriester oligonucleotides are prepared as described
in U.S. Pat. No. 5,023,243, herein incorporated by reference.
[0149] Borano phosphate oligonucleotides are prepared as described
in U.S. Pat. Nos. 5,130,302 and 5,177,198, both herein incorporated
by reference.
[0150] Oligonucleosides: Methylenemethylimino linked
oligonucleosides, also identified as MMI linked oligonucleosides,
methylenedimethylhydrazo linked oligonucleosides, also identified
as MDH linked oligonucleosides, and methylenecarbonylamino linked
oligonucleosides, also identified as amide-3 linked
oligonucleosides, and methyleneaminocarbonyl linked
oligonucleosides, also identified as amide-4 linked
oligonucleosides, as well as mixed backbone compounds having, for
instance, alternating MMI and P.dbd.O or P.dbd.S linkages are
prepared as described in U.S. Pat. Nos. 5,378,825, 5,386,023,
5,489,677, 5,602,240 and 5,610,289, all of which are herein
incorporated by reference.
[0151] Formacetal and thioformacetal linked oligonucleosides are
prepared as described in U.S. Pat. Nos. 5,264,562 and 5,264,564,
herein incorporated by reference.
[0152] Ethylene oxide linked oligonucleosides are prepared as
described in U.S. Pat. No. 5,223,618, herein incorporated by
reference.
Example 3
[0153] RNA Synthesis
[0154] In general, RNA synthesis chemistry is based on the
selective incorporation of various protecting groups at strategic
intermediary reactions. Although one of ordinary skill in the art
will understand the use of protecting groups in organic synthesis,
a useful class of protecting groups includes silyl ethers. In
particular bulky silyl ethers are used to protect the 5'-hydroxyl
in combination with an acid-labile orthoester protecting group on
the 2'-hydroxyl. This set of protecting groups is then used with
standard solid-phase synthesis technology. It is important to
lastly remove the acid labile orthoester protecting group after all
other synthetic steps. Moreover, the early use of the silyl
protecting groups during synthesis ensures facile removal when
desired, without undesired deprotection of 2' hydroxyl. Following
this procedure for the sequential protection of the 5 '-hydroxyl in
combination with protection of the 2'-hydroxyl by protecting groups
that are differentially removed and are differentially chemically
labile, RNA oligonucleotides were synthesized. RNA oligonucleotides
are synthesized in a stepwise fashion. Each nucleotide is added
sequentially (3'- to 5'-direction) to a solid support-bound
oligonucleotide. The first nucleoside at the 3'-end of the chain is
covalently attached to a solid support. The nucleotide precursor, a
ribonucleoside phosphoramidite, and activator are added, coupling
the second base onto the 5'-end of the first nucleoside. The
support is washed and any unreacted 5'-hydroxyl groups are capped
with acetic anhydride to yield 5'-acetyl moieties. The linkage is
then oxidized to the more stable and ultimately desired P(V)
linkage. At the end of the nucleotide addition cycle, the 5'-silyl
group is cleaved with fluoride. The cycle is repeated for each
subsequent nucleotide.
[0155] Following synthesis, the methyl protecting groups on the
phosphates are cleaved in 30 minutes utilizing 1 M
disodium-2-carbamoyl-2-cyanoethyl- ene-1,1-dithiolate trihydrate
(S2Na2) in DMF. The deprotection solution is washed from the solid
support-bound oligonucleotide using water. The support is then
treated with 40% methylamine in water for 10 minutes at 55.degree.
C. This releases the RNA oligonucleotides into solution, deprotects
the exocyclic amines, and modifies the 2'-groups. The
oligonucleotides can be analyzed by anion exchange HPLC at this
stage. The 2'-orthoester groups are the last protecting groups to
be removed. The ethylene glycol monoacetate orthoester protecting
group developed by Dharmacon Research, Inc. (Lafayette, Colo.), is
one example of a useful orthoester protecting group which, has the
following important properties. It is stable to the conditions of
nucleoside phosphoramidite synthesis and oligonucleotide synthesis.
However, after oligonucleotide synthesis the oligonucleotide is
treated with methylamine which not only cleaves the oligonucleotide
from the solid support but also removes the acetyl groups from the
orthoesters. The resulting 2-ethyl-hydroxyl substituents on the
orthoester are less electron withdrawing than the acetylated
precursor. As a result, the modified orthoester becomes more labile
to acid-catalyzed hydrolysis. Specifically, the rate of cleavage is
approximately 10 times faster after the acetyl groups are removed.
Therefore, this orthoester possesses sufficient stability in order
to be compatible with oligonucleotide synthesis and yet, when
subsequently modified, permits deprotection to be carried out under
relatively mild aqueous conditions compatible with the final RNA
oligonucleotide product. Additionally, methods of RNA synthesis are
well known in the art (Scaringe, S. A. Ph. D. Thesis, University of
Colorado, 1996; Scaringe, S. A., et al., J. Am. Chem. Soc., 1998,
120, 11820-11821; Matteucci, M. D. and Caruthers, M. H. J. Am.
Chem. Soc., 1981, 103, 3185-3191; Beaucage, S. L. and Caruthers, M.
H. Tetrahedron Lett., 1981, 22, 1859-1862; Dahl, B. J., et al.,
Acta Chem. Scand,. 1990, 44, 639-641; Reddy, M. P., et al.,
Tetrahedrom Lett., 1994, 25, 4311-4314; Wincott, F. et al., Nucleic
Acids Res., 1995, 23, 2677-2684; Griffin, B. E., et al.,
Tetrahedron, 1967, 23, 2301-2313; Griffin, B. E., et al.,
Tetrahedron, 1967, 23, 2315-2331). RNA antisense compounds (RNA
oligonucleotides) of the present invention can be synthesized by
the methods herein or purchased from Dharmacon Research, Inc
(Lafayette, Colo.). Once synthesized, complementary RNA antisense
compounds can then be annealed by methods known in the art to form
double stranded (duplexed) antisense compounds. For example,
duplexes can be formed by combining 30 .mu.l of each of the
complementary strands of RNA oligonucleotides (50 uM RNA
oligonucleotide solution) and 15 .mu.l of 5.times. annealing buffer
(100 mM potassium acetate, 30 mM HEPES-KOH pH 7.4, 2 mM magnesium
acetate) followed by heating for 1 minute at 90.degree. C., then 1
hour at 37.degree. C. The resulting duplexed antisense compounds
can be used in kits, assays, screens, or other methods to
investigate the role of a target nucleic acid, or for diagnostic or
therapeutic purposes.
Example 4
[0156] Synthesis of Chimeric Compounds
[0157] Chimeric oligonucleotides, oligonucleosides or mixed
oligonucleotides/oligonucleosides of the invention can be of
several different types. These include a first type wherein the
"gap" segment of linked nucleosides is positioned between 5' and 3'
"wing" segments of linked nucleosides and a second "open end" type
wherein the "gap" segment is located at either the 3' or the 5'
terminus of the oligomeric compound. Oligonucleotides of the first
type are also known in the art as "gapmers" or gapped
oligonucleotides. Oligonucleotides of the second type are also
known in the art as "hemimers" or "wingmers".
[2'-O-Me]-[2'-deoxy]-[2'-O-Me] Chimeric Phosphorothioate
Oligonucleotides
[0158] Chimeric oligonucleotides having 2'-O-alkyl phosphorothioate
and 2'-deoxy phosphorothioate oligonucleotide segments are
synthesized using an Applied Biosystems automated DNA synthesizer
Model 394, as above. Oligonucleotides are synthesized using the
automated synthesizer and
2'-deoxy-5'-dimethoxytrityl-3'-O-phosphoramidite for the DNA
portion and 5'-dimethoxytrityl-2'-O-methyl-3'-O-phosphoramidite for
5' and 3' wings. The standard synthesis cycle is modified by
incorporating coupling steps with increased reaction times for the
5'-dimethoxytrityl-2'-O-methyl-3'-O- -phosphoramidite. The fully
protected oligonucleotide is cleaved from the support and
deprotected in concentrated ammonia (NH4OH) for 12-16 hr at
55.degree. C. The deprotected oligo is then recovered by an
appropriate method (precipitation, column chromatography, volume
reduced in vacuo and analyzed spetrophotometrically for yield and
for purity by capillary electrophoresis and by mass
spectrometry.
[2'-O-(2-Methoxyethyl)]-[2'-deoxy]-[2'-O-(Methoxyethyl)] Chimeric
Phosphorothioate Oligonucleotides
[0159] [2'-O-(2-methoxyethyl)]-[2'-deoxy]-[-2'-O-(methoxyethyl)]
chimeric phosphorothioate oligonucleotides were prepared as per the
procedure above for the 2'-O-methyl chimeric oligonucleotide, with
the substitution of 2'-O-(methoxyethyl) amidites for the
2'-O-methyl amidites.
[2'-O-(2-Methoxyethyl)Phosphodiester]-[2'-deoxy
Phosphorothioate]-[2'-O-(2- -Methoxyethyl)Phosphodiester] Chimeric
Oligonucleotides
[0160] [2'-O-(2-methoxyethyl phosphodiester]-[2'-deoxy
phosphorothioate]-[2'-O-(methoxyethyl)phosphodiester] chimeric
oligonucleotides are prepared as per the above procedure for the
2'-O-methyl chimeric oligonucleotide with the substitution of
2'-O-(methoxyethyl) amidites for the 2'-O-methyl amidites,
oxidation with iodine to generate the phosphodiester
internucleotide linkages within the wing portions of the chimeric
structures and sulfurization utilizing 3,H-1,2 benzodithiole-3-one
1,1 dioxide (Beaucage Reagent) to generate the phosphorothioate
intemucleotide linkages for the center gap.
[0161] Other chimeric oligonucleotides, chimeric oligonucleosides
and mixed chimeric oligonucleotides/oligonucleosides are
synthesized according to U.S. Pat. No. 5,623,065, herein
incorporated by reference.
Example 5
[0162] PNA Synthesis
[0163] Peptide nucleic acids (PNAs) are prepared in accordance with
any of the various procedures referred to in Peptide Nucleic Acids
(PNA): Synthesis, Properties and Potential Applications, Bioorganic
& Medicinal Chemistry, 1996, 4, 5-23. They may also be prepared
in accordance with U.S. Pat. Nos. 5,539,082, 5,700,922, and
5,719,262, herein incorporated by reference.
Example 6
[0164] Oligonucleotide Isolation
[0165] After cleavage from the controlled pore glass column
(Applied Biosystems) and deblocking in concentrated ammonium
hydroxide at 55.degree. C. for 18 hours, the oligonucleotides or
oligonucleosides are purified by precipitation twice out of 0.5 M
NaCl with 2.5 volumes ethanol. Synthesized oligonucleotides were
analyzed by polyacrylamide gel electrophoresis on denaturing gels
and judged to be at least 85% full length material. The relative
amounts of phosphorothioate and phosphodiester linkages obtained in
synthesis were periodically checked by .sup.31P nuclear magnetic
resonance spectroscopy, and for some studies oligonucleotides were
purified by HPLC, as described by Chiang et al., J. Biol. Chem.
1991, 266, 18162-18171. Results obtained with HPLC-purified
material were similar to those obtained with non-HPLC purified
material.
Example 7
[0166] Oligonucleotide Synthesis--96 Well Plate Format
[0167] Oligonucleotides were synthesized via solid phase P(III)
phosphoramidite chemistry on an automated synthesizer capable of
assembling 96 sequences simultaneously in a standard 96 well
format. Phosphodiester intemucleotide linkages were afforded by
oxidation with aqueous iodine. Phosphorothioate intemucleotide
linkages were generated by sulfurization utilizing 3,H-1,2
benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) in anhydrous
acetonitrile. Standard base-protected beta-cyanoethyldiisopropyl
phosphoramidites were purchased from commercial vendors (e.g.
PE-Applied Biosystems, Foster City, Calif., or Pharmacia,
Piscataway, N.J.). Non-standard nucleosides are synthesized as per
known literature or patented methods. They are utilized as base
protected beta-cyanoethyldiisopropyl phosphoramidites.
[0168] Oligonucleotides were cleaved from support and deprotected
with concentrated NH.sub.4OH at elevated temperature (55-60.degree.
C.) for 12-16 hours and the released product then dried in vacuo.
The dried product was then re-suspended in sterile water to afford
a master plate from which all analytical and test plate samples are
then diluted utilizing robotic pipettors.
Example 8
[0169] Oligonucleotide Analysis--96 Well Plate Format
[0170] The concentration of oligonucleotide in each well was
assessed by dilution of samples and UV absorption spectroscopy. The
full-length integrity of the individual products was evaluated by
capillary electrophoresis (CE) in either the 96 well format
(Beckman P/ACE.TM. MDQ) or, for individually prepared samples, on a
commercial CE apparatus (e.g., Beckman P/ACE.TM. 5000, ABI 270).
Base and backbone composition was confirmed by mass analysis of the
compounds utilizing electrospray-mass spectroscopy. All assay test
plates were diluted from the master plate using single and
multi-channel robotic pipettors. Plates were judged to be
acceptable if at least 85% of the compounds on the plate were at
least 85% full length.
Example 9
[0171] Cell culture and Oligonucleotide Treatment
[0172] The effect of antisense compounds on target nucleic acid
expression can be tested in any of a variety of cell types provided
that the target nucleic acid is present at measurable levels. This
can be routinely determined using, for example, PCR or Northern
blot analysis. The following 5 cell types are provided for
illustrative purposes, but other cell types can be routinely used,
provided that the target is expressed in the cell type chosen. This
can be readily determined by methods routine in the art, for
example Northern blot analysis, Ribonuclease protection assays, or
RT-PCR.
[0173] T-24 Cells:
[0174] The human transitional cell bladder carcinoma cell line T-24
was obtained from the American Type Culture Collection (ATCC)
(Manassas, Va.). T-24 cells were routinely cultured in complete
McCoy's 5A basal media (Gibco/Life Technologies, Gaithersburg, Md.)
supplemented with 10% fetal calf serum (Gibco/Life Technologies,
Gaithersburg, Md.), penicillin 100 units per mL, and streptomycin
100 micrograms per mL (Gibco/Life Technologies, Gaithersburg, Md.).
Cells were routinely passaged by trypsinization and dilution when
they reached 90% confluence. Cells were seeded into 96-well plates
(Falcon-Primaria #3872) at a density of 7000 cells/well for use in
RT-PCR analysis.
[0175] For Northern blotting or other analysis, cells may be seeded
onto 100 mm or other standard tissue culture plates and treated
similarly, using appropriate volumes of medium and
oligonucleotide.
[0176] A549 Cells:
[0177] The human lung carcinoma cell line A549 was obtained from
the American Type Culture Collection (ATCC) (Manassas, Va.). A549
cells were routinely cultured in DMEM basal media (Gibco/Life
Technologies, Gaithersburg, Md.) supplemented with 10% fetal calf
serum (Gibco/Life Technologies, Gaithersburg, Md.), penicillin 100
units per mL, and streptomycin 100 micrograms per mL (Gibco/Life
Technologies, Gaithersburg, Md.). Cells were routinely passaged by
trypsinization and dilution when they reached 90% confluence.
[0178] NHDF Cells:
[0179] Human neonatal dermal fibroblast (NHDF) were obtained from
the Clonetics Corporation (Walkersville Md.). NHDFs were routinely
maintained in Fibroblast Growth Medium (Clonetics Corporation,
Walkersville Md.) supplemented as recommended by the supplier.
Cells were maintained for up to 10 passages as recommended by the
supplier.
[0180] HEK Cells:
[0181] Human embryonic keratinocytes (HEK) were obtained from the
Clonetics Corporation (Walkersville Md.). HEKs were routinely
maintained in Keratinocyte Growth Medium (Clonetics Corporation,
Walkersville Md.) formulated as recommended by the supplier. Cells
were routinely maintained for up to 10 passages as recommended by
the supplier.
[0182] HepG2 Cells:
[0183] The human hepatoblastoma cell line HepG2 was obtained from
the American Type Culure Collection (Manassas, Va.). HepG2 cells
were routinely cultured in Eagle's MEM supplemented with 10% fetal
calf serum, non-essential amino acids, and 1 mM sodium pyruvate
(Gibco/Life Technologies, Gaithersburg, Md.). Cells were routinely
passaged by trypsinization and dilution when they reached 90%
confluence. Cells were seeded into 96-well plates (Falcon-Primaria
#3872) at a density of 7000 cells/well for use in RT-PCR
analysis.
[0184] For Northern blotting or other analyses, cells may be seeded
onto 100 mm or other standard tissue culture plates and treated
similarly, using appropriate volumes of medium and
oligonucleotide.
[0185] Treatment With Antisense Compounds:
[0186] When cells reached 80% confluency, they were treated with
oligonucleotide. For cells grown in 96-well plates, wells were
washed once with 200 .mu.L OPTI-MEM.TM.-1 reduced-serum medium
(Gibco BRL) and then treated with 130 .mu.L of OPTI-MEM.TM.-1
containing 3.75 .mu.g/mL LIPOFECTIN.TM. (Gibco BRL) and the desired
concentration of oligonucleotide. After 4-7 hours of treatment, the
medium was replaced with fresh medium. Cells were harvested 16-24
hours after oligonucleotide treatment.
[0187] The concentration of oligonucleotide used varies from cell
line to cell line. To determine the optimal oligonucleotide
concentration for a particular cell line, the cells are treated
with a positive control oligonucleotide at a range of
concentrations. For human cells the positive control
oligonucleotide is ISIS 13920, TCCGTCATCGCTCCTCAGGG, SEQ ID NO: 1,
a 2'-O-methoxyethyl gapmer (2'-O-methoxyethyls shown in bold) with
a phosphorothioate backbone which is targeted to human H-ras. For
mouse or rat cells the positive control oligonucleotide is ISIS
15770, ATGCATTCTGCCCCCAAGGA, SEQ ID NO: 2, a 2'-O-methoxyethyl
gapmer (2'-O-methoxyethyls shown in bold) with a phosphorothioate
backbone which is targeted to both mouse and rat c-raf. The
concentration of positive control oligonucleotide that results in
80% inhibition of c-Ha-ras (for ISIS 13920) or c-raf (for ISIS
15770) mRNA is then utilized as the screening concentration for new
oligonucleotides in subsequent experiments for that cell line. If
80% inhibition is not achieved, the lowest concentration of
positive control oligonucleotide that results in 60% inhibition of
H-ras or c-raf mRNA is then utilized as the oligonucleotide
screening concentration in subsequent experiments for that cell
line. If 60% inhibition is not achieved, that particular cell line
is deemed as unsuitable for oligonucleotide transfection
experiments.
Example 10
[0188] Analysis of Oligonucleotide Inhibition of Interleukin 12 p35
Subunit Expression
[0189] Antisense modulation of Interleukin 12 p35 subunit
expression can be assayed in a variety of ways known in the art.
For example, Interleukin 12 p35 subunit mRNA levels can be
quantitated by, e.g., Northern blot analysis, competitive
polymerase chain reaction (PCR), or real-time PCR (RT-PCR).
Real-time quantitative PCR is presently preferred. RNA analysis can
be performed on total cellular RNA or poly(A)+ mRNA. Methods of RNA
isolation are taught in, for example, Ausubel, F. M. et al.,
Current Protocols in Molecular Biology, Volume 1, pp. 4.1.1-4.2.9
and 4.5.1-4.5.3, John Wiley & Sons, Inc., 1993. Northern blot
analysis is routine in the art and is taught in, for example,
Ausubel, F. M. et al., Current Protocols in Molecular Biology,
Volume 1, pp. 4.2.1-4.2.9, John Wiley & Sons, Inc., 1996.
Real-time quantitative (PCR) can be conveniently accomplished using
the commercially available ABI PRISM.TM. 7700 Sequence Detection
System, available from PE-Applied Biosystems, Foster City, Calif.
and used according to manufacturer's instructions.
[0190] Protein levels of Interleukin 12 p35 subunit can be
quantitated in a variety of ways well known in the art, such as
immunoprecipitation, Western blot analysis (immunoblotting), ELISA
or fluorescence-activated cell sorting (FACS). Antibodies directed
to Interleukin 12 p35 subunit can be identified and obtained from a
variety of sources, such as the MSRS catalog of antibodies (Aerie
Corporation, Birmingham, Mich.), or can be prepared via
conventional antibody generation methods. Methods for preparation
of polyclonal antisera are taught in, for example, Ausubel, F. M.
et al., Current Protocols in Molecular Biology, Volume 2, pp.
11.12.1-11.12.9, John Wiley & Sons, Inc., 1997. Preparation of
monoclonal antibodies is taught in, for example, Ausubel, F. M. et
al., Current Protocols in Molecular Biology, Volume 2, pp.
11.4.1-11.11.5, John Wiley & Sons, Inc., 1997.
[0191] Immunoprecipitation methods are standard in the art and can
be found at, for example, Ausubel, F. M. et al., Current Protocols
in Molecular Biology, Volume 2, pp. 10.16.1-10.16.11, John Wiley
& Sons, Inc., 1998. Western blot (immunoblot) analysis is
standard in the art and can be found at, for example, Ausubel, F.
M. et al., Current Protocols in Molecular Biology, Volume 2, pp.
10.8.1-10.8.21, John Wiley & Sons, Inc., 1997. Enzyme-linked
immunosorbent assays (ELISA) are standard in the art and can be
found at, for example, Ausubel, F. M. et al., Current Protocols in
Molecular Biology, Volume 2, pp. 11.2.1-11.2.22, John Wiley &
Sons, Inc., 1991.
Example 11
[0192] Poly(A)+ mRNA Isolation
[0193] Poly(A)+ mRNA was isolated according to Miura et al., Clin.
Chem., 1996, 42, 1758-1764. Other methods for poly(A)+ mRNA
isolation are taught in, for example, Ausubel, F. M. et al.,
Current Protocols in Molecular Biology, Volume 1, pp. 4.5.1-4.5.3,
John Wiley & Sons, Inc., 1993. Briefly, for cells grown on
96-well plates, growth medium was removed from the cells and each
well was washed with 200 .mu.L cold PBS. 60 .mu.L lysis buffer (10
mM Tris-HCl, pH 7.6, 1 mM EDTA, 0.5 M NaCl, 0.5% NP-40, 20 mM
vanadyl-ribonucleoside complex) was added to each well, the plate
was gently agitated and then incubated at room temperature for five
minutes. 55 .mu.L of lysate was transferred to Oligo d(T) coated
96-well plates (AGCT Inc., Irvine Calif.). Plates were incubated
for 60 minutes at room temperature, washed 3 times with 200 .mu.L
of wash buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA, 0.3 M NaCl).
After the final wash, the plate was blotted on paper towels to
remove excess wash buffer and then air-dried for 5 minutes. 60
.mu.L of elution buffer (5 mM Tris-HCl pH 7.6), preheated to
70.degree. C. was added to each well, the plate was incubated on a
90.degree. C. hot plate for 5 minutes, and the eluate was then
transferred to a fresh 96-well plate.
[0194] Cells grown on 100 mm or other standard plates may be
treated similarly, using appropriate volumes of all solutions.
Example 12
[0195] Total RNA Isolation
[0196] Total RNA was isolated using an RNEASY 96.TM. kit and
buffers purchased from Qiagen Inc. (Valencia Calif.) following the
manufacturer's recommended procedures. Briefly, for cells grown on
96-well plates, growth medium was removed from the cells and each
well was washed with 200 .mu.L cold PBS. 100 .mu.L Buffer RLT was
added to each well and the plate vigorously agitated for 20
seconds. 100 .mu.L of 70% ethanol was then added to each well and
the contents mixed by pipetting three times up and down. The
samples were then transferred to the RNEASY 96.TM. well plate
attached to a QIAVAC.TM. manifold fitted with a waste collection
tray and attached to a vacuum source. Vacuum was applied for 15
seconds. 1 mL of Buffer RW1 was added to each well of the RNEASY
96.TM. plate and the vacuum again applied for 15 seconds. 1 mL of
Buffer RPE was then added to each well of the RNEASY 96.TM. plate
and the vacuum applied for a period of 15 seconds. The Buffer RPE
wash was then repeated and the vacuum was applied for an additional
10 minutes. The plate was then removed from the QIAVAC.TM. manifold
and blotted dry on paper towels. The plate was then re-attached to
the QIAVAC.TM. manifold fitted with a collection tube rack
containing 1.2 mL collection tubes. RNA was then eluted by
pipetting 60 .mu.L water into each well, incubating 1 minute, and
then applying the vacuum for 30 seconds. The elution step was
repeated with an additional 60 .mu.L water.
[0197] The repetitive pipetting and elution steps may be automated
using a QIAGEN Bio-Robot 9604 (Qiagen, Inc., Valencia Calif.).
Essentially, after lysing of the cells on the culture plate, the
plate is transferred to the robot deck where the pipetting, DNase
treatment and elution steps are carried out.
Example 13
[0198] Real-time Quantitative PCR Analysis of Interleukin 12 p35
Subunit mRNA Levels
[0199] Quantitation of Interleukin 12 p35 subunit mRNA levels was
determined by real-time quantitative PCR using the ABI PRISM.TM.
7700 Sequence Detection System (PE-Applied Biosystems, Foster City,
Calif.) according to manufacturer's instructions. This is a
closed-tube, non-gel-based, fluorescence detection system which
allows high-throughput quantitation of polymerase chain reaction
(PCR) products in real-time. As opposed to standard PCR, in which
amplification products are quantitated after the PCR is completed,
products in real-time quantitative PCR are quantitated as they
accumulate. This is accomplished by including in the PCR reaction
an oligonucleotide probe that anneals specifically between the
forward and reverse PCR primers, and contains two fluorescent dyes.
A reporter dye (e.g., JOE, FAM, or VIC, obtained from either Operon
Technologies Inc., Alameda, Calif. or PE-Applied Biosystems, Foster
City, Calif.) is attached to the 5' end of the probe and a quencher
dye (e.g., TAMRA, obtained from either Operon Technologies Inc.,
Alameda, Calif. or PE-Applied Biosystems, Foster City, Calif.) is
attached to the 3' end of the probe. When the probe and dyes are
intact, reporter dye emission is quenched by the proximity of the
3' quencher dye. During amplification, annealing of the probe to
the target sequence creates a substrate that can be cleaved by the
5'-exonuclease activity of Taq polymerase. During the extension
phase of the PCR amplification cycle, cleavage of the probe by Taq
polymerase releases the reporter dye from the remainder of the
probe (and hence from the quencher moiety) and a sequence-specific
fluorescent signal is generated. With each cycle, additional
reporter dye molecules are cleaved from their respective probes,
and the fluorescence intensity is monitored at regular intervals by
laser optics built into the ABI PRISM.TM. 7700 Sequence Detection
System. In each assay, a series of parallel reactions containing
serial dilutions of mRNA from untreated control samples generates a
standard curve that is used to quantitate the percent inhibition
after antisense oligonucleotide treatment of test samples.
[0200] Prior to quantitative PCR analysis, primer-probe sets
specific to the target gene being measured are evaluated for their
ability to be "multiplexed" with a GAPDH amplification reaction. In
multiplexing, both the target gene and the internal standard gene
GAPDH are amplified concurrently in a single sample. In this
analysis, mRNA isolated from untreated cells is serially diluted.
Each dilution is amplified in the presence of primer-probe sets
specific for GAPDH only, target gene only ("single-plexing"), or
both (multiplexing). Following PCR amplification, standard curves
of GAPDH and target mRNA signal as a function of dilution are
generated from both the single-plexed and multiplexed samples. If
both the slope and correlation coefficient of the GAPDH and target
signals generated from the multiplexed samples fall within 10% of
their corresponding values generated from the single-plexed
samples, the primer-probe set specific for that target is deemed
multiplexable. Other methods of PCR are also known in the art.
[0201] PCR reagents were obtained from PE-Applied Biosystems,
Foster City, Calif. RT-PCR reactions were carried out by adding 25
.mu.L PCR cocktail (1.times. TAQMAN.TM. buffer A, 5.5 mM
MgCl.sub.2, 300 .mu.M each of dATP, dCTP and dGTP, 600 .mu.M of
dUTP, 100 nM each of forward primer, reverse primer, and probe, 20
Units RNAse inhibitor, 1.25 Units AMPLITAQ GOLD.TM., and 12.5 Units
MuLV reverse transcriptase) to 96 well plates containing 25 .mu.L
total RNA solution. The RT reaction was carried out by incubation
for 30 minutes at 48.degree. C. Following a 10 minute incubation at
95.degree. C. to activate the AMPLITAQ GOLD.TM., 40 cycles of a
two-step PCR protocol were carried out: 95.degree. C. for 15
seconds (denaturation) followed by 60.degree. C. for 1.5 minutes
(annealing/extension).
[0202] Gene target quantities obtained by real time RT-PCR are
normalized using either the expression level of GAPDH, a gene whose
expression is constant, or by quantifying total RNA using
RiboGreen.TM. (Molecular Probes, Inc. Eugene, Oreg.). GAPDH
expression is quantified by real time RT-PCR, by being run
simultaneously with the target, multiplexing, or separately. Total
RNA is quantified using RiboGreen.TM. RNA quantification reagent
from Molecular Probes. Methods of RNA quantification by
RiboGreen.TM. are taught in Jones, L. J., et al, Analytical
Biochemistry, 1998, 265, 368-374.
[0203] In this assay, 175 .mu.L of RiboGreen.TM. working reagent
(RiboGreen.TM. reagent diluted 1:2865 in 10 mM Tris-HCl, 1 mM EDTA,
pH 7.5) is pipetted into a 96-well plate containing 25 uL purified,
cellular RNA. The plate is read in a CytoFluor 4000 (PE Applied
Biosystems) with excitation at 480 nm and emission at 520 nm.
[0204] Probes and primers to human Interleukin 12 p35 subunit were
designed to hybridize to a human Interleukin 12 p35 subunit
sequence, using published sequence information (GenBank accession
number M65291, incorporated herein as SEQ ID NO:3). For human
Interleukin 12 p35 subunit the PCR primers were:
[0205] forward primer: GCCACTCCAGACCCAGGAAT (SEQ ID NO: 4)
[0206] reverse primer: TGTCTGGCCTTCTGGAGCAT (SEQ ID NO: 5) and the
PCR probe was: FAM-TCCCATGCCTTCACCACTCCCAA-TAMRA (SEQ ID NO: 6)
where FAM (PE-Applied Biosystems, Foster City, Calif.) is the
fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster
City, Calif.) is the quencher dye. For human GAPDH the PCR primers
were:
[0207] forward primer: GAAGGTGAAGGTCGGAGTC (SEQ ID NO: 7)
[0208] reverse primer: GAAGATGGTGATGGGATTTC (SEQ ID NO: 8) and the
PCR probe was: 5' JOE-CAAGCTTCCCGTTCTCAGCC-TAMRA 3' (SEQ ID NO: 9)
where JOE (PE-Applied Biosystems, Foster City, Calif.) is the
fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster
City, Calif.) is the quencher dye.
Example 14
[0209] Northern Blot Analysis of Interleukin 12 p35 Subunit mRNA
Levels
[0210] Eighteen hours after antisense treatment, cell monolayers
were washed twice with cold PBS and lysed in 1 mL RNAZOL.TM.
(TEL-TEST "B" Inc., Friendswood, Tex.). Total RNA was prepared
following manufacturer's recommended protocols. Twenty micrograms
of total RNA was fractionated by electrophoresis through 1.2%
agarose gels containing 1.1% formaldehyde using a MOPS buffer
system (AMRESCO, Inc. Solon, Ohio). RNA was transferred from the
gel to HYBOND.TM.-N+ nylon membranes (Amersham Pharmacia Biotech,
Piscataway, N.J.) by overnight capillary transfer using a
Northern/Southern Transfer buffer system (TEL-TEST "B" Inc.,
Friendswood, Tex.). RNA transfer was confirmed by UV visualization.
Membranes were fixed by UV cross-linking using a STRATALINKER.TM.
UV Crosslinker 2400 (Stratagene, Inc, La Jolla, Calif.) and then
robed using QUICKHYB.TM. hybridization solution (Stratagene, La
Jolla, Calif.) using manufacturer's recommendations for stringent
conditions.
[0211] To detect human Interleukin 12 p35 subunit, a human
Interleukin 12 p35 subunit specific probe was prepared by PCR using
the forward primer GCCACTCCAGACCCAGGAAT (SEQ ID NO: 4) and the
reverse primer TGTCTGGCCTTCTGGAGCAT (SEQ ID NO: 5). To normalize
for variations in loading and transfer efficiency membranes were
stripped and probed for human glyceraldehyde-3-phosphate
dehydrogenase (GAPDH) RNA (Clontech, Palo Alto, Calif.).
[0212] Hybridized membranes were visualized and quantitated using a
PHOSPHORIMAGER.TM. and IMAGEQUANT.TM. Software V3.3 (Molecular
Dynamics, Sunnyvale, Calif.). Data was normalized to GAPDH levels
in untreated controls.
Example 15
[0213] Antisense Inhibition of Human Interleukin 12 p35 Subunit
Expression By Chimeric Phosphorothioate Oligonucleotides Having
2'-MOE Wings and a Deoxy Gap
[0214] In accordance with the present invention, a series of
oligonucleotides were designed to target different regions of the
human Interleukin 12 p35 subunit RNA, using published sequences
(GenBank accession number M65291, incorporated herein as SEQ ID NO:
3, and GenBank accession number AF050083, incorporated herein as
SEQ ID NO: 10). The oligonucleotides are shown in Table 1. "Target
site" indicates the first (5'-most) nucleotide number on the
particular target sequence to which the oligonucleotide binds. All
compounds in Table 1 are chimeric oligonucleotides ("gapmers") 20
nucleotides in length, composed of a central "gap" region
consisting of ten 2'-deoxynucleotides, which is flanked on both
sides (5' and 3' directions) by five-nucleotide "wings". The wings
are composed of 2'-methoxyethyl (2'-MOE)nucleotides. The
internucleoside (backbone) linkages are phosphorothioate (P.dbd.S)
throughout the oligonucleotide. All cytidine residues are
5-methylcytidines. The compounds were analyzed for their effect on
human Interleukin 12 p35 subunit mRNA levels by quantitative
real-time PCR as described in other examples herein. Data are
averages from two experiments. If present, "N.D." indicates "no
data".
1TABLE 1 Inhibition of human Interleukin 12 p35 subunit mRNA levels
by chimeric phosphorothioate oligonucleotides having 2'-MOE wings
and a deoxy gap TARGET SEQ ID TARGET % SEQ ID ISIS # REGION NO.
SITE SEQUENCE INHIB NO 138957 5'UTR 3 1 acatcagcttctcggtgacc 79 11
138958 5'UTR 3 10 tctctctctacatcagcttc 49 12 138959 5'UTR 3 61
cggcaggactttcccgggac 45 13 138960 5'UTR 3 66 aggcgcggcaggactttccc
65 14 138961 Coding 3 148 tggatgcagacctgtggccg 32 15 138962 Coding
3 183 ctgagccggcactgcaggga 78 16 138963 Coding 3 191
gacacatgctgagccggcac 71 17 138964 Coding 3 201 ctgcgcgctggacacatgct
43 18 138965 Coding 3 217 agcgacaaggaggaggctgc 52 19 138966 Coding
3 230 ggaggaccagggtagcgaca 58 20 138967 Coding 3 255
tttctggccaaactgaggtg 59 21 138968 Coding 3 282 cctgggtctggagtggccac
73 22 138969 Coding 3 290 ggaacattcctgggtctgga 100 23 138970 Coding
3 305 agtggtgaaggcatgggaac 94 24 138971 Coding 3 311
tttgggagtggtgaaggcat 94 25 138972 Coding 3 332 tgctgacggccctcagcagg
88 26 138973 Coding 3 356 tttgtctggccttctggagc 61 27 138974 Coding
3 362 ctagagtttgtctggccttc 53 28 138975 Coding 3 375
caagggtaaaattctagagt 38 29 138976 Coding 3 390 atctcttcagaagtgcaagg
85 30 138977 Coding 3 435 gcctccactgtgctggtttt 79 31 138978 Coding
3 441 aaacaggcctccactgtgct 66 32 138979 Coding 3 448
caatggtaaacaggcctcca 82 33 138980 Coding 3 453 aattccaatggtaaacaggc
52 34 138981 Coding 3 462 ttcttggttaattccaatgg 62 35 138982 Coding
3 482 tggaatttaggcaactctca 74 36 138983 Coding 3 490
ggtctctctggaatttaggc 70 37 138984 Coding 3 503 tagttatgaaagaggtctct
49 38 138985 Coding 3 522 gaggccaggcaactcccatt 54 39 138986 Coding
3 529 ctttctggaggccaggcaac 58 40 138987 Coding 3 535
agaggtctttctggaggcca 67 41 138988 Coding 3 540 ataaaagaggtctttctgga
68 42 138989 Coding 3 553 gcacagggccatcataaaag 24 43 138990 Coding
3 587 ggtacatcttcaagtcttca 96 44 138991 Coding 3 598
gaactccacctggtacatct 44 45 138992 Coding 3 614 ttgcattcatggtcttgaac
64 46 138993 Coding 3 624 atcagaagctttgcattcat 49 47 138994 Coding
3 636 ctcttaggatccatcagaag 83 48 138995 Coding 3 645
aagatctgcctcttaggatc 56 49 138996 Coding 3 651 tctagaaagatctgcctctt
60 50 138997 Coding 3 657 ttttgatctagaaagatctg 20 51 138998 Coding
3 661 catgttttgatctagaaaga 80 52 138999 Coding 3 675
tcaataactgccagcatgtt 67 53 139000 Coding 3 686 gcatcagctcatcaataact
46 54 139001 Coding 3 727 ggatttttgtggcacagtct 42 55 139002 Coding
3 740 gttcttcaagggaggatttt 48 56 139003 Coding 3 757
agttttataaaaatccggtt 57 57 139004 Coding 3 790 gaaagcatgaagaagtatgc
55 58 139005 Coding 3 799 ccgaattctgaaagcatgaa 62 59 139006 Coding
3 804 actgcccgaattctgaaagc 77 60 139007 Coding 3 828
tagctcatcactctatcaat 52 61 139008 Stop 3 853 cctcgctttttaggaagcat
60 62 Codon 139009 3'UTR 3 877 aaaaatgacaacggtttgga 91 63 139010
3'UTR 3 908 ctatcaaagtttcctcattt 26 64 139011 3'UTR 3 913
acatcctatcaaagtttcct 37 65 139012 3'UTR 3 926 tagttcttaatccacatcct
47 66 139013 3'UTR 3 934 cccctccctagttcttaatc 20 67 139014 3'UTR 3
953 atagtcccatccttctttcc 35 68 139015 3'UTR 3 959
gatgtaatagtcccatcctt 58 69 139016 3'UTR 3 964 atgtggatgtaatagtccca
84 70 139017 3'UTR 3 987 aaaaatacttgatcagaggt 56 71 139018 3'UTR 3
1035 gcaattcattcatgaaaact 60 72 139019 3'UTR 3 1041
ttcttagcaattcattcatg 74 73 139020 3'UTR 3 1066 acaccttcaggatggatatt
76 74 139021 3'UTR 3 1073 atgaaaaacaccttcaggat 47 75 139022 3'UTR 3
1099 aaatatttgcccttctatta 61 76 139023 3'UTR 3 1117
ggtacagaaatagcttataa 74 77 139024 3'UTR 3 1123 cactttggtacagaaatagc
62 78 139025 3'UTR 3 1131 tccacaaacactttggtaca 76 79 139026 3'UTR 3
1141 catgtttgtttccacaaaca 73 80 139027 3'UTR 3 1158
aaaataagttatgcttacat 25 81 139028 3'UTR 3 1194 ctttcatgattaccaagtta
71 82 139029 3'UTR 3 1212 tataagttagctcagatgct 60 83 139030 3'UTR 3
1284 tatttttagaacacttaaaa 28 84 139031 Intron 10 1434
gcgctttcggattaactccc 47 85 139032 Coding 10 1575
gggccacatttttataattg 24 86 139033 Coding 10 1597
gtggctgggaggctgaccca 41 87 139034 Coding 10 1678
ctggacacatgctgagccgg 51 88
[0215] As shown in Table 1, SEQ ID NOs 11, 12, 13, 14, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36,
37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55,
56, 57, 58, 59, 60, 61, 62, 63, 66, 69, 70, 71, 72, 73, 74, 75, 76,
77, 78, 79, 80, 82, 83, 85, 87 and 88 demonstrated at least 40%
inhibition of human Interleukin 12 p35 subunit expression in this
assay and are therefore preferred. The target sites to which these
preferred sequences are complementary are herein referred to as
"active sites" and are therefore preferred sites for targeting by
compounds of the present invention.
Example 16
[0216] Western Blot Analysis of Interleukin 12 p35 Subunit Protein
Levels
[0217] Western blot analysis (immunoblot analysis) is carried out
using standard methods. Cells are harvested 16-20 h after
oligonucleotide treatment, washed once with PBS, suspended in
Laemmli buffer (100 ul/well), boiled for 5 minutes and loaded on a
16% SDS-PAGE gel. Gels are run for 1.5 hours at 150 V, and
transferred to membrane for western blotting. Appropriate primary
antibody directed to Interleukin 12 p35 subunit is used, with a
radiolabelled or fluorescently labeled secondary antibody directed
against the primary antibody species. Bands are visualized using a
PHOSPHORIMAGER.TM. (Molecular Dynamics, Sunnyvale Calif.).
Example 17
[0218] Triglyceride Accumulation Assay:
[0219] This assay measures the accumulation of triglyceride by
newly differentiated adipocytes. The in vitro triglyceride assay
model used here is a good representation of an in vivo model
because a time-dependent increase in triglyceride accumulation by
the adipocytes has been shown to increase concomitantly with
increasing leptin secretion. Furthermore, an increased in
triglyceride content is a well established marker for adipocyte
differentiation.
[0220] Triglyceride accumulation is measured using the Infinity.TM.
Triglyceride reagent kit (Sigma-Aldrich, St. Louis, Mo.). Human
white preadipocytes (Zen-Bio Inc., Research Triangle Park, N.C.)
are grown in preadipocyte media (ZenBio Inc.) One day before
transfection, 96-well plates are seeded with 3000 cells/well. Cells
are treated according to standard published procedures with
Interleukin 12 p35 inhibitor (in this experiment, 250 nM
oligonucleotide) in lipofectin (Gibco). Monia et al., J. Biol.
Chem., 1993, 268, 14514-22. Inhibitors are tested in triplicate on
each 96-well plate, and the effects of TNF-.alpha., a positive drug
control that inhibits adipocyte differentiation, are also measured
in triplicate. Negative controls and transfectant-only controls may
be measured up to six times per plate. After the cells have reached
confluence (approximately three days), they are exposed to
differentiation media (Zen-Bio, Inc.; differentiation media
contains a PPAR-.gamma. agonist, IBMX, dexamethasone and insulin)
for three days. Cells are then fed adipocyte media (Zen-Bio, Inc.),
which is replaced at 2 to 3 day intervals. On day nine
post-transfection, cells are washed and lysed at RT, and the
triglyceride assay reagent is added. Triglyceride accumulation is
measured based on the amount of glycerol liberated from
triglycerides by the enzyme lipoprotein lipase. Liberated glycerol
is phosphorylated by glycerol kinase. Next, glycerol-1-phosphate is
oxidized to dihydroxyacetone phosphate by glycerol phosphate
oxidase. Hydrogen peroxide is generated during this reaction.
Horseradish peroxidase (HRP) uses H.sub.2O.sub.2 to oxidize
4-aminoantipyrine and 3,5 dichloro-2-hydroxybenzene sulfonate to
produce a red-colored dye. Dye absorbance, which is proportional to
the concentration of glycerol, is measured at 515 nm using an UV
spectrophotometer. Glycerol concentration is calculated from a
standard curve for each assay, and data are normalized to total
cellular protein as determined by a Bradford assay (Bio-Rad
Laboratories, Hercules, Calif.). Results are expressed as a percent
+standard deviation relative to transfectant-only control.
[0221] The Interleukin 12 p35 inhibitor employed in this assay is
an antisense oligomer, ISIS 138969; SEQ ID NO: 23, and the control
(or negative control) employed in this assay is a nonsense
oligomer, ISIS 29848, NNNNNNNNNNNNNNNNNNNN, SEQ ID NO. 89, where N
is a mixture of A, C, G and T. Other antisense inhibitors of
Interleukin 12 p35, their synthesis and uses are disclosed in U.S.
Pat. No. 6,399,379.
[0222] At 250 nM of Interleukin 12 p35 inhibitor, the triglyceride
accumulation was reduced by 94% as compared to control. This
indicates that differentiation of preadipocytes to adipocytes was
inhibited by treatment with Interleukin 12 p35 inhibitor.
Example 18
[0223] Leptin Secretion Assay for Differentiated Adipocytes:
[0224] Leptin is a marker for differentiated adipocytes. In this
assay, leptin secretion into the media above the newly
differentiated adipocytes is measured by protein ELISA. Cell
growth, treatment with Interleukin 12 p35 inhibitor and
differentiation procedures are carried out as described for the
triglyceride accumulation assay (see above). On day nine
post-transfection, 96-well plates are coated with a monoclonal
antibody to human leptin (R&D Systems, Minneapolis, Minn.) and
are left at 4 oC overnight. The plates are blocked with bovine
serum albumin (BSA), and a dilution of the media is incubated in
the plate at room temperature for 2 hours. After washing to remove
unbound components, a second monoclonal antibody to human leptin
(conjugated with biotin) is added. The plate is then incubated with
strepavidin-conjugated horseradish peroxidase (HRP) and enzyme
levels are determined by incubation with
3,3',5,5'-Tetramethylbenzidine, which turns blue when cleaved by
HRP. The OD450 is read for each well, where the dye absorbance is
proportional to the leptin concentration in the cell lysate.
Results are expressed as a percent .+-.standard deviation relative
to transfectant-only controls.
Example 19
[0225] Hallmark Gene Expression:
[0226] During adipocyte differentiation, the gene expression
patterns in adipocytes change considerably. This gene expression
pattern is controlled by several different transcription factors,
including glucose transporter-4 (GLUT4), hormone-sensitive lipase
(HSL) and adipocyte lipid binding protein (aP2). These genes play
important roles in the uptake of glucose and the metabolism and
utilization of fats. Cell growth, treatment with Interleukin 12 p35
inhibitor and differentiation procedures are carried out as
described for the triglyceride accumulation assay. On day nine
post-transfection, cells are lysed in a guanidinium-containing
buffer and total RNA is harvested. The amount of total RNA in each
sample is determined using a RIBOGREEN assay (Molecular Probes,
Eugene, Oreg.). Real-time PCR is performed on the total RNA using
primer/probe sets for three adipocyte differentiation hallmark
genes: glucose transporter-4 (GLUT4), hormone-sensitive lipase
(HSL) and adipocyte lipid binding protein (aP2). Expression levels
for each gene are normalized to total RNA, and values .+-. standard
deviation relative to transfectant-only controls are entered into
the database.
[0227] The Interleukin 12 p35 inhibitor employed in this assay is
an antisense oligomer, ISIS 138969; SEQ ID NO. 23; and the control
(or negative control) employed in this assay is an nonsense
oligomer, ISIS 29848, NNNNNNNNNNNNNNNNNNNN, SEQ ID NO: 89; where N
is a mixture of A, C, G and T. Other antisense inhibitors of
Interleukin 12 p35, their synthesis and uses are disclosed in U.S.
Pat. No. 6,399,379.
[0228] At 250 nM of Interleukin 12 p35 inhibitor, aP2 was reduced
by 67% and GLUT4 was reduced by 89% as compared to control. This
indicates that differentiation of preadipocytes to adipocytes was
inhibited by treatment with Interleukin 12 p35 inhibitor.
Sequence CWU 1
1
88 1 20 DNA Artificial Sequence Antisense Oligonucleotide 1
tccgtcatcg ctcctcaggg 20 2 20 DNA Artificial Sequence Antisense
Oligonucleotide 2 atgcattctg cccccaagga 20 3 1316 DNA Homo sapiens
CDS (102)...(863) 3 ggtcaccgag aagctgatgt agagagagac acagaaggag
acagaaagca agagaccaga 60 gtcccgggaa agtcctgccg cgcctcggga
caattataaa a atg tgg ccc cct ggg 116 Met Trp Pro Pro Gly 1 5 tca
gcc tcc cag cca ccg ccc tca cct gcc gcg gcc aca ggt ctg cat 164 Ser
Ala Ser Gln Pro Pro Pro Ser Pro Ala Ala Ala Thr Gly Leu His 10 15
20 cca gcg gct cgc cct gtg tcc ctg cag tgc cgg ctc agc atg tgt cca
212 Pro Ala Ala Arg Pro Val Ser Leu Gln Cys Arg Leu Ser Met Cys Pro
25 30 35 gcg cgc agc ctc ctc ctt gtc gct acc ctg gtc ctc ctg gac
cac ctc 260 Ala Arg Ser Leu Leu Leu Val Ala Thr Leu Val Leu Leu Asp
His Leu 40 45 50 agt ttg gcc aga aac ctc ccc gtg gcc act cca gac
cca gga atg ttc 308 Ser Leu Ala Arg Asn Leu Pro Val Ala Thr Pro Asp
Pro Gly Met Phe 55 60 65 cca tgc ctt cac cac tcc caa aac ctg ctg
agg gcc gtc agc aac atg 356 Pro Cys Leu His His Ser Gln Asn Leu Leu
Arg Ala Val Ser Asn Met 70 75 80 85 ctc cag aag gcc aga caa act cta
gaa ttt tac cct tgc act tct gaa 404 Leu Gln Lys Ala Arg Gln Thr Leu
Glu Phe Tyr Pro Cys Thr Ser Glu 90 95 100 gag att gat cat gaa gat
atc aca aaa gat aaa acc agc aca gtg gag 452 Glu Ile Asp His Glu Asp
Ile Thr Lys Asp Lys Thr Ser Thr Val Glu 105 110 115 gcc tgt tta cca
ttg gaa tta acc aag aat gag agt tgc cta aat tcc 500 Ala Cys Leu Pro
Leu Glu Leu Thr Lys Asn Glu Ser Cys Leu Asn Ser 120 125 130 aga gag
acc tct ttc ata act aat ggg agt tgc ctg gcc tcc aga aag 548 Arg Glu
Thr Ser Phe Ile Thr Asn Gly Ser Cys Leu Ala Ser Arg Lys 135 140 145
acc tct ttt atg atg gcc ctg tgc ctt agt agt att tat gaa gac ttg 596
Thr Ser Phe Met Met Ala Leu Cys Leu Ser Ser Ile Tyr Glu Asp Leu 150
155 160 165 aag atg tac cag gtg gag ttc aag acc atg aat gca aag ctt
ctg atg 644 Lys Met Tyr Gln Val Glu Phe Lys Thr Met Asn Ala Lys Leu
Leu Met 170 175 180 gat cct aag agg cag atc ttt cta gat caa aac atg
ctg gca gtt att 692 Asp Pro Lys Arg Gln Ile Phe Leu Asp Gln Asn Met
Leu Ala Val Ile 185 190 195 gat gag ctg atg cag gcc ctg aat ttc aac
agt gag act gtg cca caa 740 Asp Glu Leu Met Gln Ala Leu Asn Phe Asn
Ser Glu Thr Val Pro Gln 200 205 210 aaa tcc tcc ctt gaa gaa ccg gat
ttt tat aaa act aaa atc aag ctc 788 Lys Ser Ser Leu Glu Glu Pro Asp
Phe Tyr Lys Thr Lys Ile Lys Leu 215 220 225 tgc ata ctt ctt cat gct
ttc aga att cgg gca gtg act att gat aga 836 Cys Ile Leu Leu His Ala
Phe Arg Ile Arg Ala Val Thr Ile Asp Arg 230 235 240 245 gtg atg agc
tat ctg aat gct tcc taa aaagcgaggt ccctccaaac 883 Val Met Ser Tyr
Leu Asn Ala Ser 250 cgttgtcatt tttataaaac tttgaaatga ggaaactttg
ataggatgtg gattaagaac 943 tagggagggg gaaagaagga tgggactatt
acatccacat gatacctctg atcaagtatt 1003 tttgacattt actgtggata
aattgttttt aagttttcat gaatgaattg ctaagaaggg 1063 aaaatatcca
tcctgaaggt gtttttcatt cactttaata gaagggcaaa tatttataag 1123
ctatttctgt accaaagtgt ttgtggaaac aaacatgtaa gcataactta ttttaaaata
1183 tttatttata taacttggta atcatgaaag catctgagct aacttatatt
tatttatgtt 1243 atatttatta aattatttat caagtgtatt tgaaaaatat
ttttaagtgt tctaaaaata 1303 aaagtattga att 1316 4 20 DNA Artificial
Sequence PCR Primer 4 gccactccag acccaggaat 20 5 20 DNA Artificial
Sequence PCR Primer 5 tgtctggcct tctggagcat 20 6 23 DNA Artificial
Sequence PCR Probe 6 tcccatgcct tcaccactcc caa 23 7 19 DNA
Artificial Sequence PCR Primer 7 gaaggtgaag gtcggagtc 19 8 20 DNA
Artificial Sequence PCR Primer 8 gaagatggtg atgggatttc 20 9 20 DNA
Artificial Sequence PCR Probe 9 caagcttccc gttctcagcc 20 10 1703
DNA Homo sapiens CDS (1586)...(1703) CDS (1688)...(1703) 10
gaattctcag acagcagcat tagaaggggc cttagagatc aaccatttct cttattttac
60 acacacctaa aactccctac agccgtgctt catcagcttc gagcagatga
gccacccaga 120 aggcagctcc agttattagg tcctagggcc tgggtgtagt
caggcccttt ggaagctcca 180 agtcagagat caaacacatc ctccccacta
cccacgccta gggtgactaa tgcctgtggg 240 aaaaacaact gaactaaaaa
gtcccacagg aacctcaaac ccagcacatc caaaatggaa 300 cttctcacca
tctcctccaa actcagtcct cttatacagt aatccctgta aagctagaac 360
aatctccatt ccccattctc agggccttcc tctcccgctc acctgaggag ctaccaagcc
420 ttggcccaca agccctctga gagtccctcc tgcccaccct gtgttctcca
tactgaataa 480 ggacttggcc acaccttgtc aactcttccc tctgctctac
tcctgacccc tggatccccc 540 catcatgcaa attctgccac atctcccgcc
taaaacccag gaagactccc cactactctc 600 agcacagaaa gtacactcct
tagtatggca tcccctgccc tcatggcatg gcccatccag 660 ccctccagcc
tcacaccctg caaggacacc tagaccccca cctccctcaa cccttcatga 720
ctgcgcttct gatccctgtt tcccctggct agaccctgcg tgccctcccg ctggaagcgg
780 tctaatgcct gcttgttttt aacactcagg ttggggcccc tgcctgctcc
cgggagcctt 840 tgctgactcc tggaccccgt tgctccggct gagcgtgggc
tctttctcta ggtctttcct 900 cccaggactc tgtgtattca tcctatcgtt
aaactggatt ctctacaaga gtaataattg 960 cagagtcagc cagctctcat
cccttttcag gtttcagaaa agacctgtga acaaaacgcc 1020 ttgagtctga
tttagtgtgg caatgcccca agggtcctgt tctccctggg tgtcctgcac 1080
ctggtgcaac gtcggcctgg catctagtga gccatctaaa ggaacgatga tgagtgaatg
1140 atttgcctac cccttccagt actaggctgg aggtcgtggt tagggcccat
ccctacgcag 1200 gacatgcaaa gtgggaggca ctcctctctc tacgtcggca
gggggcgctg cacagctgcg 1260 gggcggggta gcttagacac ggggcgtccg
gctaaggccg gggacccagg gtggtgggcg 1320 gggtgtcccg cccgcctgtg
gaccccgcgc agtaactgcg aacatttcgc tttcattttg 1380 ggccgagctg
gaggcggcgg ggccgtcccg gaacggctgc ggccgggcac cccgggagtt 1440
aatccgaaag cgccgcaagc ccccggggcc ggccgcaccg cacgtgtcac cgagaagctg
1500 atgtagagag agacacagaa ggagacagaa agcaagagac cagagtcccg
ggaaagtcct 1560 gccgcgcctc gggacaatta taaaa atg tgg ccc cct ggg tca
gcc tcc cag 1612 Met Trp Pro Pro Gly Ser Ala Ser Gln 1 5 cca ccg
ccc tca cct gcc gcg gcc aca ggt ctg cat cca gcg gct cgc 1660 Pro
Pro Pro Ser Pro Ala Ala Ala Thr Gly Leu His Pro Ala Ala Arg 10 15
20 25 cct gtg tcc ctg cag tgc cgg ctc agc atg tgt cca gcg cgc a
1703 Pro Val Ser Leu Gln Cys Arg Leu Ser Met Cys Pro Ala Arg 30 35
1703 11 20 DNA Artificial Sequence Antisense Oligonucleotide 11
acatcagctt ctcggtgacc 20 12 20 DNA Artificial Sequence Antisense
Oligonucleotide 12 tctctctcta catcagcttc 20 13 20 DNA Artificial
Sequence Antisense Oligonucleotide 13 cggcaggact ttcccgggac 20 14
20 DNA Artificial Sequence Antisense Oligonucleotide 14 aggcgcggca
ggactttccc 20 15 20 DNA Artificial Sequence Antisense
Oligonucleotide 15 tggatgcaga cctgtggccg 20 16 20 DNA Artificial
Sequence Antisense Oligonucleotide 16 ctgagccggc actgcaggga 20 17
20 DNA Artificial Sequence Antisense Oligonucleotide 17 gacacatgct
gagccggcac 20 18 20 DNA Artificial Sequence Antisense
Oligonucleotide 18 ctgcgcgctg gacacatgct 20 19 20 DNA Artificial
Sequence Antisense Oligonucleotide 19 agcgacaagg aggaggctgc 20 20
20 DNA Artificial Sequence Antisense Oligonucleotide 20 ggaggaccag
ggtagcgaca 20 21 20 DNA Artificial Sequence Antisense
Oligonucleotide 21 tttctggcca aactgaggtg 20 22 20 DNA Artificial
Sequence Antisense Oligonucleotide 22 cctgggtctg gagtggccac 20 23
20 DNA Artificial Sequence Antisense Oligonucleotide 23 ggaacattcc
tgggtctgga 20 24 20 DNA Artificial Sequence Antisense
Oligonucleotide 24 agtggtgaag gcatgggaac 20 25 20 DNA Artificial
Sequence Antisense Oligonucleotide 25 tttgggagtg gtgaaggcat 20 26
20 DNA Artificial Sequence Antisense Oligonucleotide 26 tgctgacggc
cctcagcagg 20 27 20 DNA Artificial Sequence Antisense
Oligonucleotide 27 tttgtctggc cttctggagc 20 28 20 DNA Artificial
Sequence Antisense Oligonucleotide 28 ctagagtttg tctggccttc 20 29
20 DNA Artificial Sequence Antisense Oligonucleotide 29 caagggtaaa
attctagagt 20 30 20 DNA Artificial Sequence Antisense
Oligonucleotide 30 atctcttcag aagtgcaagg 20 31 20 DNA Artificial
Sequence Antisense Oligonucleotide 31 gcctccactg tgctggtttt 20 32
20 DNA Artificial Sequence Antisense Oligonucleotide 32 aaacaggcct
ccactgtgct 20 33 20 DNA Artificial Sequence Antisense
Oligonucleotide 33 caatggtaaa caggcctcca 20 34 20 DNA Artificial
Sequence Antisense Oligonucleotide 34 aattccaatg gtaaacaggc 20 35
20 DNA Artificial Sequence Antisense Oligonucleotide 35 ttcttggtta
attccaatgg 20 36 20 DNA Artificial Sequence Antisense
Oligonucleotide 36 tggaatttag gcaactctca 20 37 20 DNA Artificial
Sequence Antisense Oligonucleotide 37 ggtctctctg gaatttaggc 20 38
20 DNA Artificial Sequence Antisense Oligonucleotide 38 tagttatgaa
agaggtctct 20 39 20 DNA Artificial Sequence Antisense
Oligonucleotide 39 gaggccaggc aactcccatt 20 40 20 DNA Artificial
Sequence Antisense Oligonucleotide 40 ctttctggag gccaggcaac 20 41
20 DNA Artificial Sequence Antisense Oligonucleotide 41 agaggtcttt
ctggaggcca 20 42 20 DNA Artificial Sequence Antisense
Oligonucleotide 42 ataaaagagg tctttctgga 20 43 20 DNA Artificial
Sequence Antisense Oligonucleotide 43 gcacagggcc atcataaaag 20 44
20 DNA Artificial Sequence Antisense Oligonucleotide 44 ggtacatctt
caagtcttca 20 45 20 DNA Artificial Sequence Antisense
Oligonucleotide 45 gaactccacc tggtacatct 20 46 20 DNA Artificial
Sequence Antisense Oligonucleotide 46 ttgcattcat ggtcttgaac 20 47
20 DNA Artificial Sequence Antisense Oligonucleotide 47 atcagaagct
ttgcattcat 20 48 20 DNA Artificial Sequence Antisense
Oligonucleotide 48 ctcttaggat ccatcagaag 20 49 20 DNA Artificial
Sequence Antisense Oligonucleotide 49 aagatctgcc tcttaggatc 20 50
20 DNA Artificial Sequence Antisense Oligonucleotide 50 tctagaaaga
tctgcctctt 20 51 20 DNA Artificial Sequence Antisense
Oligonucleotide 51 ttttgatcta gaaagatctg 20 52 20 DNA Artificial
Sequence Antisense Oligonucleotide 52 catgttttga tctagaaaga 20 53
20 DNA Artificial Sequence Antisense Oligonucleotide 53 tcaataactg
ccagcatgtt 20 54 20 DNA Artificial Sequence Antisense
Oligonucleotide 54 gcatcagctc atcaataact 20 55 20 DNA Artificial
Sequence Antisense Oligonucleotide 55 ggatttttgt ggcacagtct 20 56
20 DNA Artificial Sequence Antisense Oligonucleotide 56 gttcttcaag
ggaggatttt 20 57 20 DNA Artificial Sequence Antisense
Oligonucleotide 57 agttttataa aaatccggtt 20 58 20 DNA Artificial
Sequence Antisense Oligonucleotide 58 gaaagcatga agaagtatgc 20 59
20 DNA Artificial Sequence Antisense Oligonucleotide 59 ccgaattctg
aaagcatgaa 20 60 20 DNA Artificial Sequence Antisense
Oligonucleotide 60 actgcccgaa ttctgaaagc 20 61 20 DNA Artificial
Sequence Antisense Oligonucleotide 61 tagctcatca ctctatcaat 20 62
20 DNA Artificial Sequence Antisense Oligonucleotide 62 cctcgctttt
taggaagcat 20 63 20 DNA Artificial Sequence Antisense
Oligonucleotide 63 aaaaatgaca acggtttgga 20 64 20 DNA Artificial
Sequence Antisense Oligonucleotide 64 ctatcaaagt ttcctcattt 20 65
20 DNA Artificial Sequence Antisense Oligonucleotide 65 acatcctatc
aaagtttcct 20 66 20 DNA Artificial Sequence Antisense
Oligonucleotide 66 tagttcttaa tccacatcct 20 67 20 DNA Artificial
Sequence Antisense Oligonucleotide 67 cccctcccta gttcttaatc 20 68
20 DNA Artificial Sequence Antisense Oligonucleotide 68 atagtcccat
ccttctttcc 20 69 20 DNA Artificial Sequence Antisense
Oligonucleotide 69 gatgtaatag tcccatcctt 20 70 20 DNA Artificial
Sequence Antisense Oligonucleotide 70 atgtggatgt aatagtccca 20 71
20 DNA Artificial Sequence Antisense Oligonucleotide 71 aaaaatactt
gatcagaggt 20 72 20 DNA Artificial Sequence Antisense
Oligonucleotide 72 gcaattcatt catgaaaact 20 73 20 DNA Artificial
Sequence Antisense Oligonucleotide 73 ttcttagcaa ttcattcatg 20 74
20 DNA Artificial Sequence Antisense Oligonucleotide 74 acaccttcag
gatggatatt 20 75 20 DNA Artificial Sequence Antisense
Oligonucleotide 75 atgaaaaaca ccttcaggat 20 76 20 DNA Artificial
Sequence Antisense Oligonucleotide 76 aaatatttgc ccttctatta 20 77
20 DNA Artificial Sequence Antisense Oligonucleotide 77 ggtacagaaa
tagcttataa 20 78 20 DNA Artificial Sequence Antisense
Oligonucleotide 78 cactttggta cagaaatagc 20 79 20 DNA Artificial
Sequence Antisense Oligonucleotide 79 tccacaaaca ctttggtaca 20 80
20 DNA Artificial Sequence Antisense Oligonucleotide 80 catgtttgtt
tccacaaaca 20 81 20 DNA Artificial Sequence Antisense
Oligonucleotide 81 aaaataagtt atgcttacat 20 82 20 DNA Artificial
Sequence Antisense Oligonucleotide 82 ctttcatgat taccaagtta 20 83
20 DNA Artificial Sequence Antisense Oligonucleotide 83 tataagttag
ctcagatgct 20 84 20 DNA Artificial Sequence Antisense
Oligonucleotide 84 tatttttaga acacttaaaa 20 85 20 DNA Artificial
Sequence Antisense
Oligonucleotide 85 gcgctttcgg attaactccc 20 86 20 DNA Artificial
Sequence Antisense Oligonucleotide 86 gggccacatt tttataattg 20 87
20 DNA Artificial Sequence Antisense Oligonucleotide 87 gtggctggga
ggctgaccca 20 88 20 DNA Artificial Sequence Antisense
Oligonucleotide 88 ctggacacat gctgagccgg 20
* * * * *