# Patent

## Title
Compositions and their uses directed to PTPR alpha

## Abstract

Disclosed herein are compounds, compositions and methods for modulating the expression of PTPR.alpha. in a cell, tissue or animal. Also provided are methods of target validation. Also provided are uses of disclosed compounds and compositions in the manufacture of a medicament for treatment of diseases and disorders. Also provided are methods for the prevention, amelioration and/or treatment of airway hyperresponsiveness and pulmonary inflammation by administration of antisense compounds targeted to PTPR.alpha.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is related to U.S. patent application Ser. No. 11/502,251, filed Aug. 9, 2006; which is a continuation-in-part of U.S. patent application Ser. No. 11/036,095, filed on Jan. 14, 2005, which is a continuation in part of U.S. patent application Ser. No. 10/210,556, filed on Jul. 31, 2002 now abandoned. The entire contents of these applications and patents are incorporated herein by reference in their entirety.


SEQUENCE LISTING
The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled BIOL0084WOSEQ.TXT, created on May 7, 2007 which is 508 Kb in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.
BACKGROUND OF THE INVENTION
The process of protein phosphorylation represents one course by which intracellular signals are propagated in a cellular response. Within the cell, proteins can be phosphorylated on serine, threonine or tyrosine residues and the extent of phosphorylation is regulated by the opposing action of phosphatases, which remove the phosphate moieties.
PTPR.alpha. (also known as protein tyrosine phosphatase receptor type alpha, LCA-related phosphatase; LRP, HLPR, HPTPA, PTPRA, PTPA, PTP-R alpha, PTPRL2 and RPTPA) is a widely expressed member of the family of receptor-like phosphatases. It was cloned from a human hepatoblastoma cell line (Jirik et al., FEBS Lett., 1990, 273, 239-242) and a brain stem cell line (Kaplan et al., Proc. Natl. Acad. Sci. U.S.A., 1990, 87, 7000-7004) and was mapped to chromosome 20p13, a chromosomal region involved in translocations and deletions in myeloid disorders and neoplasms (Jirik et al., Cytogenet. Cell Genet., 1992, 60, 117-118; Kaplan et al., Proc. Natl. Acad. Sci. U.S.A., 1990, 87, 7000-7004).
Kaplan et al. have presented evidence for the existence of two major PTPR.alpha. RNA transcripts of approximately 4.3 and 6.3 kb (Kaplan et al., Proc. Natl. Acad. Sci. U.S.A., 1990, 87, 7000-7004) whose proteins differ in a stretch of 9 amino acid residues situated in the external juxtamembrane segment (Daum et al., J. Biol. Chem., 1994, 269, 10524-10528). The larger of the two species appears to be more prevalent in fetal tissues, suggesting that the differential expression of the two transcripts is developmentally regulated and/or a result of alternative splicing mechanisms (Kaplan et al., Proc. Natl. Acad. Sci. U.S.A., 1990, 87, 7000-7004). Four additional variants have been subsequently identified.
PTPR.alpha. has been identified as a negative regulator of insulin receptor signaling indicating that it may play a key role in insulin action and in the pathophysiology of non-insulin-dependent diabetes (Moeller et al., J. Biol. Chem., 1995, 270, 23126-23131). However, the importance of PTPR.alpha.'s role in insulin signaling is considered unclear. (Cheng, A., et al., Eur. J. Biochem. (2002) 269:1050-1059).
There is a need in the art for compositions that modulate the activity of PTPR.alpha. and methods for their use as a treatment of prophylactic for diseases and conditions associated with alterations in plasma glucose and in insulin levels as well as insulin action, such as for type 2 diabetes.
SUMMARY OF THE INVENTION
Provided are antisense compounds, particularly oligomeric compounds, especially nucleic acid and nucleic acid-like oligomers, which are targeted to a nucleic acid encoding PTPR.alpha. Preferably, the antisense compounds are antisense oligonucleotides targeted to PTPR.alpha., particularly human PTPR.alpha., and are capable of modulating the expression of PTPR.alpha. Prefered compounds comprise at least an 8 nucleobase portion, preferably a 12 nucleobase portion, more preferably at least a 15 nucleobase portion, of the sequences listed in Table 3 or 4, or are at least 80% identical to the complement of validated target segments, or to the antisense oligonucleotide sequences listed in Table 3 or 4.
Provided are methods for modulating the expression of PTPR.alpha. in cells or tissues comprising contacting the cells with at least one antisense compound, as described, and analyzing the cells for indicators of a decrease in expression of PTPR.alpha. mRNA and/or protein by direct measurement of mRNA and/or protein levels, and/or indirect indicators of a disease or condition such as measuring plasma triglyceride levels, plasma glucose levels, plasma transaminase levels, plasma insulin levels, hepatic triglyceride levels or similar indicators of type 2 diabetes, fatty liver, obesity or metabolic syndrome.
Provided are methods for the prevention, amelioration, and/or treatment of type 2 diabetes, fatty liver disease or metabolic syndrome comprising administering at least one antisense compound of this invention to an individual in need of such intervention.
Provided are methods for using the antisense compounds disclosed herein to prepare a medicament for the prevention, amelioration, and/or treatment of a disease or condition, especially a those associated with at least one indicator of type 2 diabetes, fatty liver disease, obesity or metabolic syndrome.
Further Methods and Compositions are Provided as Follows:


    
    
        1. An antisense compound of 15 to 35 nucleobases targeted to a nucleic acid molecule encoding human PTPR.alpha. wherein the nucleic acid molecule encoding human PTPR.alpha. is SEQ ID NO: 18 and wherein the antisense compound hybridizes with nucleotides 716 to 894, nucleotides 1063 to 1229, nucleotides 1818 to 2045, nucleotides 2328 to 2779, nucleotides 2982 to 3211, nucleotides 1210 to 1905 of SEQ ID NO: 18 or nucleotides 2860 to 2990 of SEQ ID NO: 11.
        2. Any one of the antisense compounds described herein can be targeted to at least two or more nucleic acid molecules encoding human PTPR.alpha.
        3. Any one of the antisense compounds described herein, wherein the compound is at least about 80% complementary to a target region of the nucleic acid encoding PTPR.alpha.
        4. Any one of the antisense compounds described herein, wherein the compound optionally includes a complementary strand 15 to 35 nucleobases in length.
        5. Any one of the antisense compounds described herein, wherein the compound is an antisense oligonucleotide.
        6. Any one of the compounds described herein having at least one modified internucleoside linkage, sugar moiety, or nucleobase.
        7. Any one of the compounds described herein comprising a chimeric oligonucleotide.
        8. Any one of the compounds described herein wherein the modified internucleoside linkage comprises a phosphorothioate linkage.
        9. Any one of the compounds described herein wherein the at least one modified sugar moiety comprises a 2′-MOE, a LNA, a 2′-OMe, an ENA, a 2′-F or combinations thereof.
        10. Any one of the compounds described herein wherein the modified nucleobase comprises 5-methylcytosine.
        11. A pharmaceutical composition comprising one or more compounds described herein and a pharmaceutically acceptable penetration enhancer, carrier, or diluent.
        12. A method for the prevention, amelioration, or treatment of a disease or condition wherein indicators of the disease or condition comprise increased plasma glucose levels, increased plasma lipid levels, increased hepatic triglyceride levels, increased plasma transaminase levels, reduced hepatic function, reduced insulin sensitivity or combinations thereof comprising administration of one or more compounds described herein to an individual in need of such intervention.
        13. The methods described herein wherein the disease or condition is fatty liver disease and wherein administration of compounds described herein results in a decrease in plasma lipid levels, a decrease in plasma transaminase levels, a decrease in hepatic triglyceride levels or combinations thereof.
        14. The methods described herein wherein the disease or condition is type-2 diabetes and wherein administration of one or more compounds described herein results in a decrease in plasma glucose levels, an improvement in insulin sensitivity or combinations thereof.
        15. The methods described herein wherein the disease or condition is metabolic syndrome and wherein administration of one or more compounds described herein results in a decrease in plasma glucose levels, a decrease in plasma lipid levels, a decrease in hepatic triglyceride levels, an improvement in insulin sensitivity, an improvement in hepatic function, a decrease in plasma transaminase levels or combinations thereof.
        16. Use of an antisense compounds described herein in the manufacture of a medicament for the treatment, prevention or amelioration of a disease or condition wherein indicators of the disease or condition comprise increased plasma glucose levels, increased plasma lipid levels, increased hepatic triglyceride levels, increased plasma transaminase levels, reduced hepatic function, reduced insulin sensitivity or combinations thereof wherein the medicament reduces the expression of a nucleic acid molecule encoding PTPR.alpha.
        17. The use of the compounds described herein wherein the disease or condition comprises type-2 diabetes, fatty liver, metabolic syndrome or combinations thereof.
        18. The use of the compounds described herein wherein the antisense compounds optionally further comprises a complementary strand 15 to 35 nucleobases in length.
        19. A method for lowering blood glucose levels in an animal in need thereof by administering one or more compounds provided herein.
        20. A method for lowering triglyceride levels in an animal in need thereof by administering one or more compounds provided herein.
        21. The method of lowering triglyceride levels wherein the triglyceride levels are lowered in the plasma.
        22. The method of lowering triglyceride levels wherein the triglyceride levels are lowered in the liver.
        23. The methods as provided wherein the animal suffers from type-2 diabetes, fatty liver disease, obesity, metabolic syndrome of combinations thereof.
    
    





BRIEF DESCRIPTION OF THE FIGURES
FIGS. 1a and 1b illustrate that administration of the disclosed antisense compounds is useful for clearing fat from the liver. FIG. 1a is an oil red stained liver section of an ob/ob mouse treated with saline and showing no clearing. FIG. 1b is an oil red stained liver section of an ob/ob mouse treated with an antisense inhibitor of PTPR.alpha and showing clearing of fat from the liver.
FIG. 2 is a graph illustrating weekly body weights for DIO mice receiving treatment oligo, control oligo or saline.
FIG. 3 is a graph illustrating food intake for DIO receiving treatment oligo, control oligo or saline.



DETAILED DESCRIPTION OF THE INVENTION
Provided are antisense compounds for the prevention, amelioration, and/or treatment of diseases or conditions associated with increases in plasma triglyceride levels, plasma glucose levels, plasma transaminase levels, plasma insulin levels hepatic triglyceride levels and further associated with PTPR.alpha activity. As used herein, the term “prevention” means to delay or forestall onset or development of a condition or disease for a period of time from hours to days, preferably weeks to months. As used herein, the term “amelioration” means a lessening of at least one indicator of the severity of a condition or disease. The severity of indicators may be determined by subjective or objective measures which are known to those skilled in the art. As used herein, “treatment” means to administer an antisense composition to effect an alteration or improvement of the disease or condition. Prevention, amelioration, and/or treatment may require administration of multiple doses at regular intervals, or prior to exposure to an agent to alter the course of the condition or disease. Moreover, a single agent may be used in a single individual for each prevention, amelioration, and treatment of a condition or disease sequentially, or concurrently.
Disclosed herein are antisense compounds, including antisense oligonucleotides and other antisense compounds for use in modulating the expression of nucleic acid molecules encoding PTPR.alpha. This is accomplished by providing antisense compounds that hybridize with one or more target nucleic acid molecules encoding PTPR.alpha. As used herein, the terms “target nucleic acid” and “nucleic acid molecule encoding PTPR.alpha. ”have been used for convenience to encompass RNA (including pre-mRNA and mRNA or portions thereof) transcribed from DNA encoding PTPR.alpha., and also cDNA derived from such RNA. In a preferred embodiment, the target nucleic acid is an mRNA encoding human PTPR.alpha.
Target Nucleic Acids
“Targeting” an antisense compound to a particular target nucleic acid molecule can be a multistep process. The process usually begins with the identification of a target nucleic acid whose expression is to be modulated. For example, the target nucleic acid can be 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. As disclosed herein, the target nucleic acid encodes PTPR.alpha.
Variants
It is also known in the art that alternative RNA transcripts can be produced from the same genomic region of DNA. These alternative transcripts are generally known as “variants.” More specifically, “pre-mRNA variants” are transcripts produced from the same genomic DNA that differ from other transcripts produced from the same genomic DNA in either their start or stop position and contain both intronic and exonic sequence. Variants can result in mRNA variants including, but not limited to, those with alternate splice junctions, or alternate initiation and termination codons. Variants in genomic and mRNA sequences can result in disease.
Target Names, Synonyms, Features
Accordingly, there are provided compositions and methods for modulating the expression of PTPR.alpha. Table 1 lists the GenBank accession numbers of sequences corresponding to nucleic acid molecules encoding PTPR.alpha. (nt=nucleotide), the date the version of the sequence was entered in GenBank, and the corresponding SEQ ID NO in the instant application, when assigned, each of which is incorporated herein by reference.







TABLE 1







Gene Targets












Genbank



Species
Genbank #
Date
SEQ ID NO





human
NM_080841.1
Jan. 31, 2002
SEQ ID NO: 4


human
M34668.1
Apr. 27, 1993
SEQ ID NO: 18


human
a consensus sequence

SEQ ID NO: 19



constructed from GenBank



accession numbers



AL161656.15 and



AL121905.23


human
X54890.1
Apr. 21, 1993
SEQ ID NO: 20


human
X53364.1
Apr. 21, 1993
SEQ ID NO: 21


human
AF121183.1
May 24, 1999
SEQ ID NO: 22


human
the complement
Jan. 21, 2000
SEQ ID NO: 23



of GenBank



accession number



BE168541.1


human
the complement
Sept. 13, 1999
SEQ ID NO: 24



of GenBank



accession number



AW024120.1


human
the complement
Apr. 9, 1998
SEQ ID NO: 25



of GenBank



accession number



AA903762.1


human
the complement
May 19, 1999
SEQ ID NO: 26



of GenBank



accession number



AI674319.1


human
residues 2749000-2925000
Oct. 17, 2001
SEQ ID NO: 27



of GenBank accession



number NT_011387.6


mouse
NM_008980.1
Jan. 6, 2000
SEQ ID NO: 11


mouse
AW323517.1
Jan. 26, 2000
SEQ ID NO: 93


mouse
L13686.1
Jun. 12, 1993
SEQ ID NO: 94


mouse
L13668.1
Jun. 12, 1993
SEQ ID NO: 95


mouse
L13670.1
Jun. 12, 1993
SEQ ID NO: 96


mouse
L13672.1
Jun. 12, 1993
SEQ ID NO: 97


mouse
L13674.1
Jun. 12, 1993
SEQ ID NO: 98


mouse
L13675.1
Jun. 12, 1993
SEQ ID NO: 99


mouse
L13676.1
Jun. 12, 1993
SEQ ID NO: 100


mouse
L13608.1
Jun. 12, 1993
SEQ ID NO: 101


mouse
BE372094.1
Jul. 21, 2000
SEQ ID NO: 102









Modulation of Target Expression

Modulation of expression of a target nucleic acid can be achieved through alteration of any number of nucleic acid (DNA or RNA) functions. “Modulation” or “Modulation of Expression” means a perturbation of function, for example, either an increase (stimulation or induction) or a decrease (inhibition or reduction) in expression of the target mRNA. As another example, modulation of expression can include perturbing splice site selection of pre-mRNA processing. “Expression” includes all the functions by which a gene's coded information is converted into structures present and operating in a cell. These structures include the products of transcription and translation. The functions of RNA to be modulated can include translocation functions, which include, but are not limited to, translocation of the RNA to a site of protein translation, translocation of the RNA to sites within the cell which are distant from the site of RNA synthesis, and translation of protein from the RNA. RNA processing functions that can be modulated include, but are not limited to, splicing of the RNA to yield one or more RNA species, capping of the RNA, 3′ maturation of the RNA and catalytic activity or complex formation involving the RNA which may be engaged in or facilitated by the RNA. Modulation of expression can result in the increased level of one or more nucleic acid species or the decreased level of one or more nucleic acid species, either temporally or by net steady state level. One result of such interference with target nucleic acid function is modulation of the expression of PTPR.alpha. Thus, in one embodiment, modulation of expression can mean increase or decrease in target RNA or protein levels. In another embodiment modulation of expression can mean an increase or decrease of one or more RNA splice products, or a change in the ratio of two or more splice products.
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 and can be routinely determined using, for example, PCR or Northern blot analysis. Cell lines are derived from both normal tissues and cell types and from cells associated with various disorders (e.g. hyperproliferative disorders). Cell lines derived from multiple tissues and species can be obtained from American Type Culture Collection (ATCC, Manassas, Va.) and other public sources. Primary cells, or those cells which are isolated from an animal and not subjected to continuous culture, can be prepared according to methods known in the art, or obtained from various commercial suppliers. Additionally, primary cells include those obtained from donor human subjects in a clinical setting (i.e. blood donors, surgical patients). These techniques are well known to those skilled in the art.
Assaying Modulation of Expression
Modulation of PTPR.alpha. expression can be assayed in a variety of ways known in the art. PTPR.alpha. mRNA levels can be quantitated by, e.g., Northern blot analysis, competitive polymerase chain reaction (PCR), or real-time PCR. RNA analysis can be performed on total cellular RNA or poly(A)+mRNA by methods known in the art. 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 PRISMTM 7700 Sequence Detection System, available from PE-Applied Biosystems, Foster City, Calif. and used according to manufacturer's instructions. The method of analysis of modulation of RNA levels is not a limitation of the instant invention.
Levels of a protein encoded by PTPR.alpha. 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 a protein encoded by PTPR.alpha. 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.
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.
Active Target Segments
The locations on the target nucleic acid defined by having one or more active antisense compounds targeted thereto are referred to as “active target segments.” There may be substantial variation in activity (e.g., as defined by percent inhibition) of the antisense compounds within an active target segment. Active antisense compounds are those that are determined to modulate the expression of their target RNA. Preferably, active antisense compounds inhibit expression of their target RNA at least about 50%, more preferably at least about 70% and most preferably at least about 80%. In a more preferred embodiment, the level of inhibition required to define an active antisense compound is defined based on the results from the screen used to define the active target segments. Those skilled in the art understand that the percent inhibition by an antisense compound on a target mRNA will vary between assays due to factors relating to assay conditions.
Hybridization
As used herein, “hybridization” means the pairing of complementary strands of antisense compounds to their target sequence. While not limited to a particular mechanism, the most common mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases (nucleobases). For example, the natural base adenine is complementary to the natural nucleobases thymidine and uracil which pair through the formation of hydrogen bonds. The natural base guanine is complementary to the natural base 5-methyl cytosine and the artificial base known as a G-clamp. Hybridization can occur under varying circumstances.
An antisense compound is specifically hybridizable when there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target nucleic acid 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 under conditions in which assays are performed in the case of in vitro assays.
As used herein, “stringent hybridization conditions” or “stringent conditions” refers to conditions under which an antisense compound will hybridize to its target sequence, but to a minimal number of other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances, and “stringent conditions” under which antisense compounds hybridize to a target sequence are determined by the nature and composition of the antisense compounds and the assays in which they are being investigated.
Complementarity
“Complementarity,” as used herein, refers to the capacity for precise pairing between two nucleobases on either two oligomeric compound strands or an antisense compound with its target nucleic acid. For example, if a nucleobase at a certain position of an antisense compound is capable of hydrogen bonding with a nucleobase at a certain position of a target nucleic acid, then the position of hydrogen bonding between the oligonucleotide and the target nucleic acid is considered to be a complementary position. The antisense compound and the further DNA or RNA are complementary to each other when a sufficient number of complementary positions in each molecule are occupied by nucleobases which can hydrogen bond with each other. Thus, “specifically hybridizable” and “complementary” are terms which are used to indicate a sufficient degree of precise pairing or complementarity over a sufficient number of nucleobases such that stable and specific binding occurs between the antisense compound and a target nucleic acid.
Identity
Antisense compounds, or a portion thereof, may have a defined percent identity to a SEQ ID NO, or a compound having a specific Isis number. As used herein, a sequence is identical to the sequence disclosed herein if it has the same nucleobase pairing ability. For example, a RNA which contains uracil in place of thymidine in the disclosed sequences would be considered identical as they both pair with adenine. Similarly, a G-clamp modified heterocyclic base would be considered identical to a cytosine or a 5-Me cytosine in the sequences of the instant application as it pairs with a guanine. This identity may be over the entire length of the oligomeric compound, or in a portion of the antisense compound (e.g., nucleobases 1-20 of a 27-mer may be compared to a 20-mer to determine percent identity of the oligomeric compound to the SEQ ID NO.) It is understood by those skilled in the art that an antisense compound need not have an identical sequence to those described herein to function similarly to the antisense compound described herein. Shortened versions of antisense compound taught herein, or non-identical versions of the antisense compound taught herein fall within the scope of this disclosure. Non-identical versions are those wherein each base does not have the same pairing activity as the antisense compounds disclosed herein. Bases do not have the same pairing activity by being shorter or having at least one abasic site. Alternatively, a non-identical version can include at least one base replaced with a different base with different pairing activity (e.g., G can be replaced by C, A, or T). Percent identity is calculated according to the number of bases that have identical base pairing corresponding to the SEQ ID NO or antisense compound to which it is being compared. The non-identical bases may be adjacent to each other, dispersed through out the oligonucleotide, or both.
For example, a 16-mer having the same sequence as nucleobases 2-17 of a 20-mer is 80% identical to the 20-mer. Alternatively, a 20-mer containing four nucleobases not identical to the 20-mer is also 80% identical to the 20-mer. A 14-mer having the same sequence as nucleobases 1-14 of an 18-mer is 78% identical to the 18-mer. Such calculations are well within the ability of those skilled in the art.
The percent identity is based on the percent of nucleobases in the original sequence present in a portion of the modified sequence. Therefore, a 30 nucleobase antisense compound comprising the full sequence of the complement of a 20 nucleobase active target segment would have a portion of 100% identity with the complement of the 20 nucleobase active target segment, while further comprising an additional 10 nucleobase portion. The complement of an active target segment may constitute a single portion. In a preferred embodiment, the oligonucleotides are at least about 80%, more preferably at least about 85%, even more preferably at least about 90%, most preferably at least 95% identical to at least a portion of the complement of the active target segments presented herein.
It is well known by those skilled in the art that it is possible to increase or decrease the length of an antisense compound and/or introduce mismatch bases without eliminating activity. For example, in Woolf et al. (Proc. Natl. Acad. Sci. USA 89:7305-7309, 1992, incorporated herein by reference), a series of ASOs 13-25 nucleobases in length were tested for their ability to induce cleavage of a target RNA. ASOs 25 nucleobases in length with 8 or 11 mismatch bases near the ends of the ASOs were able to direct specific cleavage of the target mRNA, albeit to a lesser extent than the ASOs that contained no mismatches. Similarly, target specific cleavage was achieved using a 13 nucleobase ASOs, including those with 1 or 3 mismatches. Maher and Dolnick (Nuc. Acid. Res. 16:3341-3358,1988, incorporated herein by reference) tested a series of tandem 14 nucleobase ASOs, and a 28 and 42 nucleobase ASOs comprised of the sequence of two or three of the tandem ASOs, respectively, for their ability to arrest translation of human DHFR in a rabbit reticulocyte assay. Each of the three 14 nucleobase ASOs alone were able to inhibit translation, albeit at a more modest level than the 28 or 42 nucleobase ASOs. Antisense compounds having a contiguous nucleobase composition that is shorter or longer or that comprises mismatches are contemplated in this invention so long as the antisense oligonucleotide activity is maintained.
Therapeutics
Antisense compounds can be used to modulate the expression of PTPR.alpha. in an animal, such as a human. In one non-limiting embodiment, the methods comprise the step of administering to said animal in need of therapy for a disease or condition associated with, increased plasma glucose levels, increased plasma lipid levels, increased hepatic triglyceride levels, increased plasma transaminase levels, reduced hepatic function, reduced insulin sensitivity or combinations thereof, an effective amount of an antisense compound that inhibits expression of PTPR.alpha. A disease or condition associated with PTPR.alpha. includes, but is not limited to, increased plasma glucose levels, increased plasma lipid levels, increased hepatic triglyceride levels, increased plasma transaminase levels, reduced hepatic function, reduced insulin sensitivity or combinations thereof. In one embodiment, the antisense compounds effectively inhibit the levels or function of PTPR.alpha. RNA. Because reduction in PTPR.alpha. mRNA levels can lead to alteration in PTPR.alpha. protein products of expression as well, such resultant alterations can also be measured. Antisense compounds that effectively inhibit the level or function of PTPR.alpha. RNA or protein products of expression are considered an active antisense compounds. In one embodiment, the antisense compounds inhibit the expression of PTPR.alpha. causing a reduction of RNA by at least 10%, by at least 20%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, by at least 98%, by at least 99%, or by 100%.
For example, the reduction of the expression of PTPR.alpha. can be measured in a bodily fluid, tissue or organ of the animal. Methods of obtaining samples for analysis, such as body fluids (e.g., plasma), tissues (e.g., biopsy), or organs, and methods of preparation of the samples to allow for analysis are well known to those skilled in the art. Methods for analysis of RNA and protein levels are discussed above and are well known to those skilled in the art. The effects of treatment can be assessed by measuring biomarkers associated with the PTPR.alpha. expression in the aforementioned fluids, tissues or organs, collected from an animal contacted with one or more compounds, by routine clinical methods known in the art. These biomarkers include but are not limited to: liver transaminases, body weight, organ weight, percent fat, lipids, non-esterified fatty acids, glucose, insulin and other markers of diabetes, fatty liver and metabolic syndrome.
The antisense compounds can be utilized in pharmaceutical compositions by adding an effective amount of a compound to a suitable pharmaceutically acceptable diluent or carrier. Acceptable carriers and diluents are well known to those skilled in the art. Selection of a diluent or carrier is based on a number of factors, including, but not limited to, the solubility of the compound and the desired route of administration. Such considerations are well understood by those skilled in the art. In one aspect, the compounds inhibit the expression of PTPR.alpha. The antisense compounds can also be used in the manufacture of a medicament for the treatment of diseases and conditions related to PTPR.alpha. expression.
Methods whereby bodily fluids, organs or tissues are contacted with an effective amount of one or more of the antisense compounds or compositions are also contemplated. Bodily fluids, organs or tissues can be contacted with one or more of the compounds disclosed herein resulting in modulation of PTPR.alpha. expression in the cells of bodily fluids, organs or tissues.
Thus, provided herein is the use of an isolated single- or double-stranded antisense compound targeted to PTPR.alpha. in the manufacture of a medicament for the treatment of a disease or disorder by means of the method described above. In a preferred embodiment, the antisense compound is a single stranded antisense compound.
Kits, Research Reagents, and Diagnostics
The antisense compounds disclosed herein can be utilized for diagnostics, and as research reagents and kits. Furthermore, antisense compounds, which are able to inhibit gene expression with specificity, are often used by those of ordinary skill to elucidate the function of particular genes or to distinguish between functions of various members of a biological pathway.
For use in kits and diagnostics, the antisense compounds, either alone or in combination with other 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. Methods of gene expression analysis are well known to those skilled in the art.
Compounds
The term “oligomeric compound” refers to a polymeric structure capable of hybridizing to a region of a nucleic acid molecule. Generally, oligomeric compounds comprise a plurality of monomeric subunits linked together by internucleoside linking groups and/or internucleoside linkage mimetics. Each of the monomeric subunits comprises a sugar, abasic sugar, modified sugar, or a sugar mimetic, and except for the abasic sugar includes a nucleobase, modified nucleobase or a nucleobase mimetic. Preferred monomeric subunits comprise nucleosides and modified nucleosides.
An “antisense compound” or “antisense oligomeric compound” refers to an oligomeric compound that is at least partially complementary to the region of a target nucleic acid molecule to which it hybridizes and which modulates (increases or decreases) its expression. This term includes oligonucleotides, oligonucleosides, oligonucleotide analogs, oligonucleotide mimetics, antisense compounds, antisense oligomeric compounds, and chimeric combinations of these. Consequently, while all antisense compounds can be said to be oligomeric compounds, not all oligomeric compounds are antisense compounds. An “antisense oligonucleotide” is an antisense compound that is a nucleic acid-based oligomer. An antisense oligonucleotide can, in some cases, include one or more chemical modifications to the sugar, base, and/or internucleoside linkages. Nonlimiting examples of antisense compounds include primers, probes, antisense compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, and siRNAs. As such, these compounds can be introduced in the form of single-stranded, double-stranded, circular, branched or hairpins and can contain structural elements such as internal or terminal bulges or loops. Antisense double-stranded compounds can be two strands hybridized to form double-stranded compounds or a single strand with sufficient self complementarity to allow for hybridization and formation of a fully or partially double-stranded compound. The compounds are not auto-catalytic. As used herein, “auto-catalytic” means a compound has the ability to promote cleavage of the target RNA in the absence of accessory factors, e.g. proteins.
In one embodiment, the antisense compound comprises a single stranded oligonucleotide. In some embodiments the antisense compound contains chemical modifications. In a preferred embodiment, the antisense compound is a single stranded, chimeric oligonucleotide wherein the modifications of sugars, bases, and internucleoside linkages are independently selected.
The antisense compounds disclosed herein may comprise an antisense compound from about 12 to about 35 nucleobases (i.e. from about 12 to about 35 linked nucleosides). In other words, a single-stranded compound comprises from about 12 to about 35 nucleobases, and a double-stranded antisense compound (such as a siRNA, for example) comprises two strands, each of which is independently from about 12 to about 35 nucleobases. This includes oligonucleotides 15 to 35 and 16 to 35 nucleobases in length. Contained within the antisense compounds (whether single or double stranded and on at least one strand) are antisense portions. The “antisense portion” is that part of the antisense compound that is designed to work by one of the aforementioned antisense mechanisms. One of ordinary skill in the art will appreciate that about 12 to about 35 nucleobases includes 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 nucleobases.
Antisense compounds about 12 to 35 nucleobases in length, preferably about 15 to 35 nucleobases in length, comprising a complementary stretch of at least 8, preferably at least 12, more preferably at least 15 consecutive nucleobases selected from within the active target regions, are considered to be suitable antisense compounds as well.
Modifications can be made to the antisense compounds and may include conjugate groups attached to one of the termini, selected nucleobase positions, sugar positions or to one of the internucleoside linkages. Possible modifications include, but are not limited to, 2′-fluoro (2′-F), 2′-OMethyl (2′-OMe), 2′-Methoxy ethoxy (2′-MOE) sugar modifications, inverted abasic caps, deoxynucleobases, and bicyclice nucleobase analogs such as locked nucleic acids (including LNA) and ENA.
In one embodiment, double-stranded antisense compounds encompass short interfering RNAs (siRNAs). As used herein, the term “siRNA” is defined as a double-stranded compound having a first and second strand, each strand having a central portion and two independent terminal portions. The central portion of the first strand is complementary to the central portion of the second strand, allowing hybridization of the strands. The terminal portions are independently, optionally complementary to the corresponding terminal portion of the complementary strand. The ends of the strands may be modified by the addition of one or more natural or modified nucleobases to form an overhang
Each strand of the siRNA duplex may be from about 12 to about 35 nucleobases. In a preferred embodiment, each strand of the siRNA duplex is about 17 to about 25 nucleobases. The two strands may be fully complementary (i.e., form a blunt ended compound), or include a 5′ or 3′ overhang on one or both strands. Double-stranded compounds can be made to include chemical modifications as discussed herein.
Chemical Modifications
As is known in the art, a nucleoside is a base-sugar combination. The base portion of the nucleoside is normally a heterocyclic base (sometimes referred to as a “nucleobase” or simply a “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 pentofuranosyl sugar, the phosphate group can be linked to 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. Within oligonucleotides, 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. It is often preferable to include chemical modifications in oligonucleotides to alter their activity. Chemical modifications can alter oligonucleotide activity by, for example: increasing affinity of an antisense oligonucleotide for its target RNA, increasing nuclease resistance, and/or altering the pharmacokinetics of the oligonucleotide. The use of chemistries that increase the affinity of an oligonucleotide for its target can allow for the use of shorter oligonucleotide compounds.
The term “nucleobase” or “heterocyclic base moiety” as used herein, refers to the heterocyclic base portion of a nucleoside. In general, a nucleobase is any group that contains one or more atom or groups of atoms capable of hydrogen bonding to a base of another nucleic acid. In addition to “unmodified” or “natural” nucleobases such as the purine nucleobases adenine (A) and guanine (G), and the pyrimidine nucleobases thymine (T), cytosine (C) and uracil (U), many modified nucleobases or nucleobase mimetics known to those skilled in the art are amenable to the disclosed antisense compounds. The terms modified nucleobase and nucleobase mimetic can overlap but generally a modified nucleobase refers to a nucleobase that is fairly similar in structure to the parent nucleobase, such as for example a 7-deaza purine or a 5-methyl cytosine, whereas a nucleobase mimetic would include more complicated structures, such as for example a tricyclic phenoxazine nucleobase mimetic. Methods for preparation of the above noted modified nucleobases are well known to those skilled in the art.
Antisense compounds disclosed herein may also contain one or more nucleosides having modified sugar moieties. The furanosyl sugar ring of a nucleoside can be modified in a number of ways including, but not limited to, addition of a substituent group, bridging of two non-geminal ring atoms to form a bicyclic nucleic acid (BNA) and substitution of an atom or group such as —S—, —N(R)— or —C(R.sub.1)(R.sub.2) for the ring oxygen at the 4′-position. Modified sugar moieties are well known and can be used to alter, typically increase, the affinity of the antisense compound for its target and/or increase nuclease resistance. A representative list of preferred modified sugars includes but is not limited to bicyclic modified sugars (BNA's), including LNA and ENA (4′-(CH.sub.2).sub.2-O-2′ bridge); and substituted sugars, especially 2′-substituted sugars having a 2′-F, 2′-OCH.sub.2 or a 2′-O(CH.sub.2).sub.2-OCH3 substituent group. Sugars can also be replaced with sugar mimetic groups among others. Methods for the preparations of modified sugars are well known to those skilled in the art.
Also included are internucleoside linking groups that link the nucleosides or otherwise modified monomer units together thereby forming an antisense compound. The two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters, phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates. Representative non-phosphorus containing internucleoside linking groups include, but are not limited to, methylenemethylimino (—CH.sub.2-N(CH.sub.3)—O—CH.sub.2-), thiodiester (—O—C(O)—S—), thionocarbamate (—O—C(O)(NH)—S—); siloxane (—O—Si(H)2-O—); and N,N′-dimethylhydrazine (—CH.sub.2-N(CH.sub.3)—N(CH.sub.3)-). Antisense compounds having non-phosphorus internucleoside linking groups are referred to as oligonucleosides. Modified internucleoside linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the antisense compound. Internucleoside linkages having a chiral atom can be prepared racemic, chiral, or as a mixture. Representative chiral internucleoside linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing linkages are well known to those skilled in the art.
As used herein the term “mimetic” refers to groups that are substituted for a sugar, a nucleobase, and/ or internucleoside linkage. Generally, a mimetic is used in place of the sugar or sugar-internucleoside linkage combination, and the nucleobase is maintained for hybridization to a selected target. Representative examples of a sugar mimetic include, but are not limited to, cyclohexenyl or morpholino. Representative examples of a mimetic for a sugar-internucleoside linkage combination include, but are not limited to, peptide nucleic acids (PNA) and morpholino groups linked by uncharged achiral linkages. In some instances a mimetic is used in place of the nucleobase. Representative nucleobase mimetics are well known in the art and include, but are not limited to, tricyclic phenoxazine analogs and universal bases (Berger et al., Nuc Acid Res. 2000, 28:2911-14, incorporated herein by reference). Methods of synthesis of sugar, nucleoside and nucleobase mimetics are well known to those skilled in the art.
As used herein the term “nucleoside” includes, nucleosides, abasic nucleosides, modified nucleosides, and nucleosides having mimetic bases and/or sugar groups.
The term “oligonucleotide” refers to an oligomeric compound which is an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). This term includes oligonucleotides composed of naturally- and non-naturally-occurring nucleobases, sugars and covalent internucleoside linkages, possibly further including non-nucleic acid conjugates.
Compounds having reactive phosphorus groups are used for forming internucleoside linkages including for example phosphodiester and phosphorothioate internucleoside linkages. Methods of preparation and/or purification of precursors or antisense compounds are not a limitation of the compositions or methods disclosed herein. Methods for synthesis and purification of DNA, RNA, and the antisense compounds are well known to those skilled in the art.
As used herein the term “chimeric antisense compound” refers to an antisense compound, having at least one sugar, nucleobase and/or internucleoside linkage that is differentially modified as compared to the other sugars, nucleobases and internucleoside linkages within the same oligomeric compound. The remainder of the sugars, nucleobases and internucleoside linkages can be independently modified or unmodified. In general a chimeric oligomeric compound will have modified nucleosides that can be in isolated positions or grouped together in regions that will define a particular motif. Any combination of modifications and or mimetic groups can comprise a chimeric oligomeric compound.
Chimeric oligomeric compounds typically contain at least one region modified so as to confer increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid. An additional region of the oligomeric compound 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 that 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 inhibition of gene expression. Consequently, comparable results can often be obtained with shorter oligomeric compounds when chimeras are used, compared to for example 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.
Certain chimeric as well as non-chimeric oligomeric compounds can be further described as having a particular motif. As used herein, the term “motif” refers to the orientation of modified sugar moieties and/or sugar mimetic groups in an antisense compound relative to like or differentially modified or unmodified nucleosides. As used herein, the terms “sugars”, “sugar moieties” and “sugar mimetic groups” are used interchangeably. Such motifs include, but are not limited to, gapped motifs, alternating motifs, fully modified motifs, hemimer motifs, blockmer motifs, and positionally modified motifs. The sequence and the structure of the nucleobases and type of internucleoside linkage is not a factor in determining the motif of an antisense compound.
As used herein, the term “gapped motif” refers to an antisense compound comprising a contiguous sequence of nucleosides that is divided into 3 regions, an internal region (gap) flanked by two external regions (wings). The regions are differentiated from each other at least by having differentially modified sugar groups that comprise the nucleosides. In some embodiments, each modified region is uniformly modified (e.g. the modified sugar groups in a given region are identical); however, other motifs can be applied to regions. For example, the wings in a gapmer could have an alternating motif. The nucleosides located in the gap of a gapped antisense compound have sugar moieties that are different than the modified sugar moieties in each of the wings.
As used herein, the term “alternating motif” refers to an antisense compound comprising a contiguous sequence of nucleosides comprising two differentially sugar modified nucleosides that alternate for essentially the entire sequence of the antisense compound, or for essentially the entire sequence of a region of an antisense compound.
As used herein, the term “fully modified motif” refers to an antisense compound comprising a contiguous sequence of nucleosides wherein essentially each nucleoside is a sugar modified nucleoside having uniform modification.
As used herein, the term “hemimer motif” refers to a sequence of nucleosides that have uniform sugar moieties (identical sugars, modified or unmodified) and wherein one of the 5′-end or the 3′-end has a sequence of from 2 to 12 nucleosides that are sugar modified nucleosides that are different from the other nucleosides in the hemimer modified antisense compound.
As used herein, the term “blockmer motif” refers to a sequence of nucleosides that have uniform sugars (identical sugars, modified or unmodified) that is internally interrupted by a block of sugar modified nucleosides that are uniformly modified and wherein the modification is different from the other nucleosides. Methods of preparation of chimeric oligonucleotide compounds are well known to those skilled in the art.
As used herein, the term “positionally modified motif” comprises all other motifs. Methods of preparation of positionally modified oligonucleotide compounds are well known to those skilled in the art.
The compounds described herein contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), alpha or beta, or as (D) or (L) such as for amino acids et al. All such possible isomers, as well as their racemic and optically pure forms, are included herein.
In one aspect, antisense compounds are modified by covalent attachment of one or more conjugate groups. Conjugate groups may be attached by reversible or irreversible attachments. Conjugate groups may be attached directly to antisense compounds or by use of a linker. Linkers may be mono- or bifunctional linkers. Such attachment methods and linkers are well known to those skilled in the art. In general, conjugate groups are attached to antisense compounds to modify one or more properties. Such considerations are well known to those skilled in the art.
Oligomer Synthesis
Oligomerization of modified and unmodified nucleosides can be routinely performed according to literature procedures for DNA (Protocols for Oligonucleotides and Analogs, Ed. Agrawal (1993), Humana Press) and/or RNA (Scaringe, Methods (2001), 23, 206-217. Gait et al., Applications of Chemically synthesized RNA in RNA: Protein Interactions, Ed. Smith (1998), 1-36. Gallo et al., Tetrahedron (2001), 57, 5707-5713).
Antisense compounds can 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. The invention is not limited by the method of antisense compound synthesis.
Oligomer Purification and Analysis
Methods of oligonucleotide purification and analysis are known to those skilled in the art. Analysis methods include capillary electrophoresis (CE) and electrospray-mass spectroscopy. Such synthesis and analysis methods can be performed in multi-well plates. The method of the invention is not limited by the method of oligomer purification.
Salts, Prodrugs and Bioequivalents
The antisense compounds disclosed herein may comprise any pharmaceutically acceptable salts, esters, or salts of such esters, or any other functional chemical equivalent 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 antisense compounds, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents.
The term “prodrug” indicates a therapeutic agent that is prepared in an inactive or less active form that is converted to an active form (i.e., drug) within the body or cells thereof by the action of endogenous enzymes, chemicals, and/or conditions. In particular, prodrug versions of the oligonucleotides are prepared as SATE ((S-acetyl-2-thioethyl)phosphate) derivatives according to the methods disclosed in WO 93/24510 or WO 94/26764. Prodrugs can also include antisense compounds wherein one or both ends comprise nucleobases that are cleaved (e.g., by incorporating phosphodiester backbone linkages at the ends) to produce the active compound.
The term “pharmaceutically acceptable salts” refers to physiologically and pharmaceutically acceptable salts of the compounds: i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto. Sodium salts of antisense oligonucleotides are useful and are well accepted for therapeutic administration to humans. In another embodiment, sodium salts of dsRNA compounds are also provided.
Formulations
The antisense compounds may also be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds.
Also included are pharmaceutical compositions and formulations which include the antisense compounds. The pharmaceutical compositions may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated
The pharmaceutical formulations, 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, finely divided solid carriers, or both, and then, if necessary, shaping the product (e.g., into a specific particle size for delivery).
A “pharmaceutical carrier” or “excipient” can be a pharmaceutically acceptable solvent, suspending agent or any other pharmacologically inert vehicle for delivering one or more nucleic acids to an animal and are known in the art. 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.
Combinations
Pharmaceutical compositions may comprise two or more antisense compounds. In another related embodiment, pharmaceutical compositions may comprise 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. Alternatively, pharmaceutical compositions may comprise two or more antisense compounds targeted to different regions of the same nucleic acid target. Two or more combined compounds may be used together or sequentially. Pharmaceutical compositions may comprise an antisense compound combined with other non-antisense compound therapeutic agents.
Nonlimiting Disclosure and Incorporation by Reference
While certain compounds, compositions and are being described herein with specificity in accordance with certain embodiments, the following examples serve only as illustrations and not as limitations. Each of the references, GenBank accession numbers, and the like recited in the present application is incorporated herein by reference in its entirety.
EXAMPLE 1
Cell Types and Transfection Methods
Example 1—Cell types—The effect of oligomeric compounds on target nucleic acid expression was tested in one or more of the following cell types.
T-24 cells: 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 (Invitrogen Corporation, Carlsbad, Calif.) supplemented with 10% fetal calf serum (Invitrogen Corporation, Carlsbad, Calif.), penicillin 100 units per mL, and streptomycin 100 micrograms per mL (Invitrogen Corporation, Carlsbad, Calif.). Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence. Cells were seeded into 96-well plates (Falcon-Primaria #353872) at a density of 7000 cells/well for use in RT-PCR analysis.
b.END cells: The mouse brain endothelial cell line b.END was obtained from Dr. Werner Risau at the Max Plank Institute (Bad Nauheim, Germany). b.END cells were routinely cultured in DMEM, high glucose (Gibco/Life Technologies, Gaithersburg, Md.) supplemented with 10% fetal calf serum (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 3000 cells/well for use in RT-PCR analysis.
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.
NHDF cells: 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.
HEK cells: 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.
Treatment with oligomeric compounds: When cells reach appropriate confluency, they are treated with oligonucleotide using a transfection method as described.
LipofectinTM When cells reached 65-75% confluency, they were treated with oligonucleotide. Oligonucleotide was mixed with LIPOFECTINTM Invitrogen Life Technologies, Carlsbad, Calif.) in Opti-MEMTM-1 reduced serum medium (Invitrogen Life Technologies, Carlsbad, Calif.) to achieve the desired concentration of oligonucleotide and a LIPOFECTINTM concentration of 2.5 or 3.micro.g/mL per 100 nM oligonucleotide. This transfection mixture was incubated at room temperature for approximately 0.5 hours. For cells grown in 96-well plates, wells were washed once with 100 .micro.L OPTI-MEMTM-1 and then treated with 130 .micro.L of the transfection mixture. Cells grown in 24-well plates or other standard tissue culture plates are treated similarly, using appropriate volumes of medium and oligonucleotide. Cells are treated and data are obtained in duplicate or triplicate. After approximately 4-7 hours of treatment at 37.deg.C., the medium containing the transfection mixture was replaced with fresh culture medium. Cells were harvested 16-24 hours after oligonucleotide treatment.
Control Oligonucleotides
Control oligonucleotides are used to determine the optimal oligomeric compound concentration for a particular cell line. Furthermore, when oligomeric compounds are tested in oligomeric compound screening experiments or phenotypic assays, control oligonucleotides are tested in parallel.
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. The concentration of positive control oligonucleotide that results in 80% inhibition of the target 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 the target 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. The concentrations of antisense oligonucleotides used herein are from 50 nM to 300 nM when the antisense oligonucleotide is transfected using a liposome reagent and 1 μM to 40 μM when the antisense oligonucleotide is transfected by electroporation.
EXAMPLE 2
Real-time Quantitative PCR Analysis of PTPR.alpha. mRNA Levels
Quantitation of PTPR.alpha. mRNA levels was accomplished by real-time quantitative PCR using the ABI PRISMTM 7600, 7700, or 7900 Sequence Detection System (PE-Applied Biosystems, Foster City, Calif.) according to manufacturer's instructions.
Prior to quantitative PCR analysis, primer-probe sets specific to the PTPR.alpha. being measured were evaluated for their ability to be “multiplexed” with a GAPDH amplification reaction. After isolation the RNA is subjected to sequential reverse transcriptase (RT) reaction and real-time PCR, both of which are performed in the same well. RT and PCR reagents were obtained from Invitrogen Life Technologies (Carlsbad, Calif.). RT, real-time PCR was carried out in the same by adding 20 .micro.L PCR cocktail (2.5× PCR buffer minus MgCl.sub.2, 6.6 mM MgCl.sub.2, 375. micro.M each of dATP, dCTP, dCTP and dGTP, 375 nM each of forward primer and reverse primer, 125 nM of probe, 4 Units RNase inhibitor, 1.25 Units PLATINUM® Taq, 5 Units MuLV reverse transcriptase, and 2.5× ROX dye) to 96-well plates containing 30 .micro.L total RNA solution (20-200 ng). The RT reaction was carried out by incubation for 30 minutes at 48.deg.C. Following a 10 minute incubation at 95.deg.C. to activate the PLATINUM® Taq, 40 cycles of a two-step PCR protocol were carried out: 95.deg.C. for 15 seconds (denaturation) followed by 60.deg.C. for 1.5 minutes (annealing/extension).
Gene target quantities obtained by RT, real-time PCR were normalized using either the expression level of GAPDH, a gene whose expression is constant, or by quantifying total RNA using RiboGreenTM (Molecular Probes, Inc. Eugene, Oreg.). GAPDH expression was quantified by RT, real-time PCR, by being run simultaneously with the target, multiplexing, or separately. Total RNA was quantified using RiboGreenTM RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.).
170 .micro.L of RiboGreenTM working reagent (RiboGreenTM reagent diluted 1:350 in 10 mM Tris-HCl, 1 mM EDTA, pH 7.5) was pipetted into a 96-well plate containing 30 .micro.L purified cellular RNA. The plate was read in a CytoFluor 4000 (PE Applied Biosystems) with excitation at 485 nm and emission at 530 nm.
The GAPDH PCR probes have JOE covalently linked to the 5′ end and TAMRA or MGB covalently linked to the 3′ end, where JOE is the fluorescent reporter dye and TAMRA or MGB is the quencher dye. In some cell types, primers and probe designed to a GAPDH sequence from a different species are used to measure GAPDH expression. For example, a human GAPDH primer and probe set is used to measure GAPDH expression in monkey-derived cells and cell lines.
Probes and primers for use in real-time PCR were designed to hybridize to target-specific sequences. The primers and probes and the target nucleic acid sequences to which they hybridize are presented in Table 2. The target-specific PCR probes have FAM covalently linked to the 5′ end and TAMRA or MGB covalently linked to the 3′ end, where FAM is the fluorescent dye and TAMRA or MGB is the quencher dye.







TABLE 2







PTPR.alpha.-specific primers and


probes for use in real-time PCR












Target


SEQ



SEQ
Sequence

ID


Species
ID NO
Description
Sequence 5′ to3′)
NO














Human
4
Fwd Primer
GGTGGACTACACAGTACGGAA
5





GTTC


 


Human
4
Rev Primer
GATGAGGCGCTGTGGCTTT
6


 


Human
4
Probe
FAM-CATCCAGCAGGTGGGCG
7





ACATG-TAMRA


 


Mouse
11
Fwd Primer
GATATAATGAAATCCTCAGCC
12





TGGA


 


Mouse
11
Rev Primer
GAATGAGTCTTAGGTTTATCT
13





TCTTTAGGAA


 


Mouse
11
Probe
FAM-TGGGCCAGATTGTTCCT
14





TGCTTCAAAT-TAMRA









EXAMPLE 3
Antisense Inhibition of Human PTPR.alpha. Expression by Oligomeric Compounds
Accordingly, a series of oligonucleotides were designed to target different regions of the human PTPR.alpha. RNA, using published sequences (GenBank accession number NM—080841.1, representing a human PTPR.alpha. variant herein designated hPTPRA-3, incorporated herein as SEQ ID NO: 4; GenBank accession number M34668.1, representing the main mRNA of human PTPR.alpha., herein designated hPTPRA, incorporated herein as SEQ ID NO: 18; a consensus sequence constructed from GenBank accession numbers AL161656.15 and AL121905.23, representing a genomic sequence of human PTPR.alpha., incorporated herein as SEQ ID NO: 19; GenBank accession number X54890.1, representing a human PTPR.alpha. variant herein designated hPTPRA-4, incorporated herein as SEQ ID NO: 20; GenBank accession number X53364.1, representing a human PTPR.alpha. variant herein designated hPTPRA-5, incorporated herein as SEQ ID NO: 21; GenBank accession number AF121183.1, representing a 5′-extension of SEQ ID NO: 18, incorporated herein as SEQ ID NO: 22; the complement of GenBank accession number BE168541.1, representing a 5′-extenstion of SEQ ID NO: 22 incorporated herein as SEQ ID NO: 23; the complement of GenBank accession number AW024120.1, representing a 5′-extension of SEQ ID NO: 20, incorporated herein as SEQ ID NO: 24; the complement of GenBank accession number AA903762.1, representing a 3′-extension of SEQ ID NO: 18, incorporated herein as SEQ ID NO: 25; the complement of GenBank accession number AI674319.1, representing a variant of human PTPR.alpha. herein designated hPTPRA-7, incorporated herein as SEQ ID NO: 26, and residues 2749000-2925000 of GenBank accession number NT—011387.6, representing a genomic sequence of human PRPTA, incorporated herein as SEQ ID NO: 27). The oligonucleotides are shown in Table 3. “Target site” indicates the first (5′-most) nucleotide number on the particular target sequence to which the oligonucleotide binds. All compounds in Table 3 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═S) throughout the oligonucleotide. All cytidine residues are 5-methylcytidines. The compounds were analyzed for their effect on human PTPR.alpha. mRNA levels by quantitative real-time PCR as described in other examples herein. Data are averages from two experiments in which T-24 cells were treated with the antisense oligonucleotides. The positive control for each data point is identified in the table by sequence ID number. If present, “N.D.” indicates “no data”.








TABLE 3







Inhibition of human PTPR.alpha. mRNA levels



by chimeric phosphorothioate oligonucleotides


having 2′-MOE wings and a deoxy gap

















TARGET




CONTROL





SEQ ID
TARGET


SEQ ID
SEQ ID


ISIS #
REGION
NO
SITE
SEQUENCE
% INHIB
NO
NO


















147239
Coding
27
101612
ttggtgccacagaaagagaa
83
28
2



 


147240
Coding
27
101621
ggctgaatgttggtgccaca
82
29
2


 


147244
Coding
27
123433
agggccaccatcaccgcaat
72
30
2


 


147246
Coding
27
123448
actagcagagaggacagggc
83
31
2


 


147247
Coding
4
706
cttaaaccttaacatgtaca
62
32
2


 


147252
Coding
27
141723
acaggtggcctggataggac
91
33
2


 


147253
Coding
27
141728
gcctcacaggtggcctggat
81
34
2


 


147256
Coding
27
144039
ttgatgtaatcagaatctgg
94
35
2


 


147259
Coding
27
158044
cgtactgtgtagtccaccag
95
36
2


 


147260
Coding
4
1338
cccacctgctggatgcagaa
98
37
2


 


147262
Coding
27
158737
ggaactgagtgatgaggcgc
89
38
2


 


147263
Coding
27
158815
aggccttcaccttcttgagg
87
39
2


 


147267
Coding
27
161150
agataatgctccagaagggc
66
40
2


 


147269
Coding
27
163359
cgcatcttgtcattctggat
87
41
2


 


147270
Coding
27
163783
actggaatgatcactctgtt
90
42
2


 


147272
Coding
27
164391
tggagaagagggccctggct
89
43
2


 


147273
Coding
27
164429
tccactcccagatcattcgc
78
44
2


 


147274
Coding
4
2104
ggcacacttctcctggcctc
80
45
2


 


147275
Intron:
27
172236
tactgggcacacttctcctg
77
46
2



Exon



Junction


 


147276
Intron:
27
172246
agatggccagtactgggcac
93
47
2



Exon



Junction


 


147278
Coding
27
172302
cattcctcctccttcttcag
78
48
2


 


147279
Coding
27
172336
ggtgaccaggaggtctcgga
75
49
2


 


147280
Coding
27
172341
gtgttggtgaccaggaggtc
84
50
2


 


147281
Coding
4
2223
ttctccctggtgttggtgac
71
51
2


 


147282
Coding
27
172462
tggaagtggaactgccggat
66
52
2


 


147283
Coding
27
173896
agccgcaggctcttgacagt
70
53
2


 


147285
Coding
27
174766
acttgaagttggcataatct
74
54
2


 


147288
Coding
27
174875
ttctaaaacagttataagat
65
55
2


 


147291
Coding
27
174937
agtgctaacacatttacata
35
56
2


 


147297
Coding
27
175134
agagctctgagaactttgtg
78
57
2


 


194483
5′UTR
18
20
acctgctcccctgagcgtgt
47
58
2


 


194484
5′UTR
18
470
gtgtcatgtagagacaggtc
22
59
2


 


194485
Start
18
685
ggaatccatgcttgttagct
52
60
2



Codon


 


194486
Coding
18
716
gaccactgccgagcagaaca
91
61
2


 


194487
Coding
18
1063
tgctgcggtgctggaattcc
82
62
2


 


194488
Coding
18
2026
acctgtacgccctacacctg
84
63
2


 


194489
Stop
18
3094
tgttgccgcttacttgaagt
83
64
2



Codon


 


194490
3′UTR
18
3338
aatttctcggctgaggattt
63
65
2


 


194491
Exon:
19
2575
tgggccaaaccttggctgca
7
66
2



Intron



Junction


 


194492
Exon:
19
11234
gaacactcacagagtcgggc
81
67
2



Intron



Junction


 


194493
Intron
19
30977
cataatatattaagtacagc
1
68
2


 


194494
Intron:
19
60678
gttgtgtcacctgcaacaaa
66
69
2



Exon



Junction


 


194495
Intron
19
85496
cagtacttactagcttcttt
85
70
2


 


194496
Intron:
19
93080
tgaagaagtcctagaacacc
57
71
2



Exon



Junction


 


194497
Intron:
19
101743
ccatgcttatctggaaaata
72
72
2



Exon



Junction


 


194498
Exon:
19
124321
gtaggctcaccttaacatgt
68
73
2



Intron



Junction


 


194499
Intron:
19
125366
gacaggtcatgcacaccctg
86
74
2



Exon



Junction


 


194500
Intron:
19
125503
tttcttaaacctaatgagaa
94
75
2



Exon



Junction


 


194501
Exon:
19
125577
aatgccttacccacatcctc
52
76
2



Intron



Junction


 


194502
Intron
19
127990
caggctggtttcgaactcct
87
77
2


 


194503
Intron
19
132617
ttaaagccaaatttcttttc
76
78
2


 


194504
Intron
19
151456
gcccagccccaaagtgcttc
92
79
2


 


194505
5′UTR
20
49
gttgtgtcacagagtcgggc
6
80
2


 


194506
Coding
20
592
ggtgtctcatctgaaggagg
91
81
2


 


194507
5′UTR
21
73
tgaagaagtctagcttcttt
9
82
2


 


194508
Start
21
165
atccatgcttatcaccaggg
31
83
2



Codon


 


194509
5′UTR
22
51
ggctcgagccacatccccat
13
84
2


 


194510
5′UTR
22
148
acaccttgatggccagctcc
35
85
2


 


194511
5′UTR
23
115
agcagcacctggatggtgag
36
86
2


 


194512
5′UTR
23
218
ccagtgggccaggatcctgc
46
87
2


 


194513
5′UTR
24
20
gttcattgctgttcagagac
14
88
2


 


194514
5′UTR
24
183
cctcgcctccatggcgaggg
39
89
2


 


194515
3′UTR
25
115
cccatgatatcagtggtggg
69
90
2


 


194516
3′UTR
25
190
ctcagggagtcaaagctttt
49
91
2


 


194517
Exon:
26
197
gggctccacatcctcagtgc
86
92
2



Exon



Junction









As shown in Table 3, SEQ ID NOS: 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57, 60, 61, 62, 63, 64, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 90 and 92 demonstrated at least 50% inhibition of human PTPR.alpha. expression in this assay and are therefore preferred. The target sites to which these preferred sequences are complementary are herein referred to as “preferred target sites” and are therefore preferred sites for targeting by antisense compounds. These preferred target sites are shown in Table 5.
EXAMPLE 4
Antisense Inhibition of Mouse PTPR.alpha. Expression by Oligomeric Compounds
Accordingly, a second series of oligonucleotides were designed to target different regions of the mouse PTPR.alpha. RNA, using published sequences (GenBank accession number NM—008980.1, representing a variant of mouse PTPR.alpha. herein designated mPTPRA-2, incorporated herein as SEQ ID NO: 11; GenBank accession number AW323517.1, representing a 5′-extension of SEQ ID NO: 11, incorporated herein as SEQ ID NO: 93; GenBank accession numbers L13686.1, L13668.1, L13670.1, L13672.1, L13674.1, L13675.1, L13676.1 and L13608.1, representing partial genomic sequences of mouse PTPR.alpha., incorporated herein as SEQ ID NOs: 94, 95, 96, 97, 98, 99, 100 and 101 respectively; and GenBank accession number BE372094.1, representing the main mRNA of mouse PTPR.alpha., herein designated mPTPRA, incorporated herein as SEQ ID NO: 102). The oligonucleotides are shown in Table 4. “Target site” indicates the first (5′-most) nucleotide number on the particular target sequence to which the oligonucleotide binds. All compounds in Table 4 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. It is expected that antisense oligonucleotides with mismatches or varying nucleotide lengths will have similar profiles to those described herein. The internucleoside (backbone) linkages are phosphorothioate (P═S) throughout the oligonucleotide. All cytidine residues are 5-methylcytidines. The compounds were analyzed for their effect on mouse PTPR.alpha. mRNA levels by quantitative real-time PCR as described in other examples herein. Data are averages from two experiments. The positive control for each data point is identified in the table by sequence ID number. If present, “N.D.” indicates “no data”.








TABLE 4







Inhibition of mouse PTPR.alpha. mRNA levels



by chimeric phosphorothioate oligonucleotides


having 2′-MOE wings and a deoxy gap

















TARGET




CONTROL





SEQ ID
TARGET


SEQ ID
SEQ ID


ISIS #
REGION
NO
SITE
SEQUENCE
% INHIB
NO
NO


















147237
Start
11
17
caggaatccatgctgaccga
77
103
1




Codon


 


147238
Start
11
25
gaatgaaccaggaatccatg
1
104
1



Codon


 


147241
Coding
11
376
tcccctcccagggttctgtt
1
105
1


 


147242
Coding
11
407
gtttctggagtggttgctgc
54
106
1


 


147243
Coding
11
445
tcaccgcaataattggtgtc
49
107
1


 


147245
Coding
11
460
aggacagggccaccatcacc
73
108
1


 


147248
Coding
11
519
gtatttcttaaaccttaaca
25
109
1


 


147249
Coding
11
531
cccagcttgcttgtatttct
73
110
1


 


147250
Coding
11
665
tcctcttccagcttgtccac
52
111
1


 


147251
Coding
11
735
aggacaagcagggagagcgt
57
112
1


 


147254
Coding
11
876
tctttctaacaatggagtgg
4
113
1


 


147255
Coding
11
926
gagtggtcatctgagagaca
0
114
1


 


147257
Coding
11
1040
tcttttggtccttgtgcagc
39
115
1


 


147258
Coding
11
1177
tcccataggtccagcagcct.
83
116
1


 


147261
Coding
11
1258
cgtcgcccacctgctggatg
71
117
1


 


147264
Coding
11
1385
tgagggttacaggccttcac
52
118
1


 


147265
Coding
11
1489
ctttgcgttccgaatgcatc
52
119
1


 


147266
Coding
11
1523
gcccggatccggctcacaaa
0
120
1


 


147268
Coding
11
1711
aagttaatttcttaaactcc
14
121
1


 


147271
Coding
11
1903
tggcaatgtaggagtctttc
56
122
1


 


147277
Coding
11
2039
ccatcagatggccagtactg
27
123
1


 


147284
Coding
11
2430
atactgttccagtgtctgga
38
124
1


 


147286
Stop
11
2504
gtcacctgtcacttgaagtt
63
125
1



Codon


 


147287
3′UTR
11
2585
aagatatatacaattttggg
0
126
1


 


147289
3′UTR
11
2606
tgccatttctaaaacagtta
66
127
1


 


147290
3′UTR
11
2627
aacaggtaatagaagcctat
66
128
1


 


147292
3′UTR
11
2670
aggactatcagtgctaacac
75
129
1


 


147293
3′UTR
11
2763
gcaaggaacaatctggccca
96
130
1


 


147294
3′UTR
11
2788
tcttctttaggaaaagatat
37
131
1


 


147295
3′UTR
11
2805
aatgagtcttaggtttatct
48
132
1


 


147296
3′UTR
11
2830
ttttagttggcactgagcta
40
133
1


 


147298
3′UTR
11
2860
cctcaagagctctgagaact
78
134
1


 


147299
3′UTR
11
2867
accatttcctcaagagctct
76
135
1


 


147300
3′UTR
11
2971
tgcctgaggtggctgatctt
55
136
1


 


147301
3′UTR
11
3024
ctgacgatccctgctgtggt
60
137
1


 


147302
3′UTR
11
3039
aagagtgtttattacctgac
35
138
1


 


147303
5′UTR
93
28
atgcccccgcgagtccctgt
71
139
1


 


147304
5′UTR
93
93
gaagcggcagagagaggact
35
140
1


 


147305
Intron
94
2
agagtggtcatctgcaaaca
15
141
1


 


147306
Intron:
95
1
cacatttacactacaatgaa
14
142
1



Exon



Junction


 


147307
Intron:
96
1
tacacctgcactgtagccag
49
143
1



Exon



Junction


 


147308
Intron:
97
3
tgaagttaatttctgaatga
0
144
1



Exon



Junction


 


147309
Exon:
98
136
ttgaactcacctggcctctc
61
145
1



Intron



Junction


 


147310
Exon:
99
122
ctcaccctggtgttggtgac
18
146
1



Intron



Junction


 


147311
Intron:
100
1
tcttgttctcctttggaaga
19
147
1



Exon



Junction


 


147312
3′UTR
101
138
ataagactgctctgcccaag
65
148
1


 


147313
3′UTR
101
167
taggaacaacccaggagagc
58
149
1


 


147314
Exon:
102
633
tagagtgttcttagggcagg
28
150
1



Intron



Junction









As shown in Table 4, SEQ ID NOs 103, 106, 108, 110, 111, 112, 116, 117, 118, 119, 122, 125, 127, 128, 129, 130, 134, 135, 136, 137, 139, 145, 148 and 149 demonstrated at least 50% inhibition of mouse PTPR.alpha. expression in this experiment and are therefore preferred. The target sites to which these preferred sequences are complementary are herein referred to as “preferred target sites” and are therefore preferred sites for targeting antisense oligonucleotides. These preferred target sites are shown in Table 5. Moreover, nucleotides 2860 to 2990 of SEQ ID NO: 11 form a region wherein the screened oligonucleotides inhibited expression of PTPR.alpha. by an average of about 70%, and thus is designated as an active target segment (active target segment E).








TABLE 5







Sequence and position of preferred



target sites identified in PTPR.alpha..















TARGET









SEQ ID
TARGET

REV COMP

SEQ ID


SITEID
NO
SITE
SEQUENCE
OF SEQ ID
ACTIVE IN
NO

















62483
27
101612
ttctctttctgtggcaccaa
28
H. sapiens
151



 


62484
27
101621
tgtggcaccaacattcagcc
29
H. sapiens
152


 


62488
27
123433
attgcggtgatggtggccct
30
H. sapiens
153


 


62490
27
123448
gccctgtcctctctgctagt
31
H. sapiens
154


 


62491
4
706
tgtacatgttaaggtttaag
32
H. sapiens
155


 


62496
27
141723
gtcctatccaggccacctgt
33
H. sapiens
156


 


62497
27
141728
atccaggccacctgtgaggc
34
H. sapiens
157


 


62500
27
144039
ccagattctgattacatcaa
35
H. sapiens
158


 


62503
27
158044
ctggtggactacacagtacg
36
H. sapiens
159


 


62504
4
1338
ttctgcatccagcaggtggg
37
H. sapiens
160


 


62506
27
158737
gcgcctcatcactcagttcc
38
H. sapiens
161


 


62507
27
158815
cctcaagaaggtgaaggcct
39
H. sapiens
162


 


62511
27
161150
gcccttctggagcattatct
40
H. sapiens
163


 


62513
27
163359
atccagaatgacaagatgcg
41
H. sapiens
164


 


62514
27
163783
aacagagtgatcattccagt
42
H. sapiens
165


 


62516
27
164391
agccagggccctcttctcca
43
H. sapiens
166


 


62517
27
164429
gcgaatgatctgggagtgga
44
H. sapiens
167


 


62518
4
2104
gaggccaggagaagtgtgcc
45
H. sapiens
168


 


62519
27
172236
caggagaagtgtgcccagta
46
H. sapiens
169


 


62520
27
172246
gtgcccagtactggccatct
47
H. sapiens
170


 


62522
27
172302
ctgaagaaggaggaggaatg
48
H. sapiens
171


 


62523
27
172336
tccgagacctcctggtcacc
49
H. sapiens
172


 


62524
27
172341
gacctcctggtcaccaacac
50
H. sapiens
173


 


62525
4
2223
gtcaccaacaccagggagaa
51
H. sapiens
174


 


62526
27
172462
atccggcagttccacttcca
52
H. sapiens
175


 


62527
27
173896
actgtcaagagcctgcggct
53
H. sapiens
176


 


62529
27
174766
agattatgccaacttcaagt
54
H. sapiens
177


 


62532
27
174875
atcttataactgttttagaa
55
H. sapiens
178


 


62541
27
175134
cacaaagttctcagagctct
57
H. sapiens
179


 


112597
18
685
agctaacaagcatggattcc
60
H. sapiens
180


 


112598
18
716
tgttctgctcggcagtggtc
61
H. sapiens
181


 


112599
18
1063
ggaattccagcaccgcagca
62
H. sapiens
182


 


112600
18
2026
caggtgtagggcgtacaggt
63
H. sapiens
183


 


112601
18
3094
acttcaagtaagcggcaaca
64
H. sapiens
184


 


112602
18
3338
aaatcctcagccgagaaatt
65
H. sapiens
185


 


112604
19
11234
gcccgactctgtgagtgttc
67
H. sapiens
186


 


112606
19
60678
tttgttgcaggtgacacaac
69
H. sapiens
187


 


112607
19
85496
aaagaagctagtaagtactg
70
H. sapiens
188


 


112608
19
93080
ggtgttctaggacttcttca
71
H. sapiens
189


 


112609
19
101743
tattttccagataagcatgg
72
H. sapiens
190


 


112610
19
124321
acatgttaaggtgagcctac
73
H. sapiens
191


 


112611
19
125366
cagggtgtgcatgacctgtc
74
H. sapiens
192


 


112612
19
125503
ttctcattaggtttaagaaa
75
H. sapiens
193


 


112613
19
125577
gaggatgtgggtaaggcatt
76
H. sapiens
194


 


112614
19
127990
aggagttcgaaaccagcctg
77
H. sapiens
195


 


112615
19
132617
gaaaagaaatttggctttaa
78
H. sapiens
196


 


112616
19
151456
gaagcactttggggctgggc
79
H. sapiens
197


 


112618
20
592
cctccttcagatgagacacc
81
H. sapiens
198


 


112627
25
115
cccaccactgatatcatggg
90
H. sapiens
199


 


112629
26
197
gcactgaggatgtggagccc
92
H. sapiens
200


 


62481
11
17
tcggtcagcatggattcctg
103
M. musculus
201


 


62486
11
407
gcagcaaccactccagaaac
106
M. musculus
202


 


62489
11
460
ggtgatggtggccctgtcct
108
M. musculus
203


 


62493
11
531
agaaatacaagcaagctggg
110
M. musculus
204


 


62494
11
665
gtggacaagctggaagagga
111
M. musculus
205


 


62495
11
735
acgctctccctgcttgtcct
112
N. musculus
206


 


62502
11
1177
aggctgctggacctatggga
116
M. musculus
207


 


62505
11
1258
catccagcaggtgggcgacg
117
M. musculus
208


 


62508
11
1385
gtgaaggcctgtaaccctca
118
M. musculus
209


 


62509
11
1489
gatgcattcggaacgcaaag
119
M. musculus
210


 


62515
11
1903
gaaagactcctacattgcca
122
M. musculus
211


 


62530
11
2504
aacttcaagtgacaggtgac
125
M. musculus
212


 


62533
11
2606
taactgttttagaaatggca
127
M. musculus
213


 


62534
11
2627
ataggcttctattacctgtt
128
M. musculus
214


 


62536
11
2670
gtgttagcactgatagtcct
129
M. musculus
215


 


62537
11
2763
tgggccagattgttccttgc
130
M. musculus
216


 


62542
11
2860
agttctcagagctcttgagg
134
M. musculus
217


 


62543
11
2867
agagctcttgaggaaatggt
135
M. musculus
218


 


62544
11
2971
aagatcagccacctcaggca
136
M. musculus
219


 


62545
11
3024
accacagcagggatcgtcag
137
M. musculus
220


 


62547
93
28
acagggactcgcgggggcat
139
M. musculus
221


 


62553
98
136
gagaggccaggtgagttcaa
145
M. musculus
222


 


62556
101
138
cttgggcagagcagtcttat
148
M. musculus
223


 


62557
101
167
gctctcctgggttgttccta
149
M. musculus
224









As these “preferred target regions” have been found by experimentation to be open to, and accessible for, hybridization with the antisense compounds, one of skill in the art will recognize or be able to ascertain, using no more than routine experimentation, further embodiments encompassing other compounds that specifically hybridize to these sites and consequently inhibit the expression of PTPR.alpha.
In one embodiment, the “preferred target region” may be employed in screening candidate antisense compounds. “Candidate antisense compounds” are those that inhibit the expression of a nucleic acid molecule encoding PTPR.alpha. and which comprise at least an 8-nucleobase portion which is complementary to a preferred target region. The method comprises the steps of contacting a preferred target region of a nucleic acid molecule encoding PTPR.alpha. with one or more candidate antisense compounds, and selecting for one or more candidate antisense compounds which inhibit the expression of a nucleic acid molecule encoding PTPR.alpha. Once it is shown that the candidate antisense compound or compounds are capable of inhibiting the expression of a nucleic acid molecule encoding PTPR.alpha., the candidate antisense compound may be employed as an antisense compound as described herein.
Accordingly, antisense compounds include 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.
EXAMPLE 5
Targeting of Individual Oligonucleotides to Specific Variants of Human PTPR.alpha.
In some instances it is advantageous to selectively inhibit the expression of one or more variants of PTPR.alpha. Consequently, there are provided oligonucleotides that selectively target, hybridize to, and specifically inhibit one or more, but fewer than all of the variants of human PTPR.alpha. A summary of the target sites of the PTPR.alpha. main mRNA and variants is shown in Table 6 and includes GenBank accession number NM—080841.1, representing hPTPRA-3, incorporated herein as SEQ ID NO: 4; GenBank accession number M34668.1, representing hPTPR.alpha. main mRNA, incorporated herein as SEQ ID NO: 18; GenBank accession number X54890.1, representing hPTPRA-4, incorporated herein as SEQ ID NO: 20; GenBank accession number X53364.1, representing hPTPRA-5, incorporated herein as SEQ ID NO: 21; the complement of GenBank accession number AI674319.1, representing hPTPRA-7, incorporated herein as SEQ ID NO: 26; GenBank accession number NM—002836.1 (entered Mar. 24, 1999), representing hPTPRA-1, incorporated herein as SEQ ID NO: 225; GenBank accession number NM—080840.1 (entered Jan. 31, 2002), representing hPTPRA-2, incorporated herein as SEQ ID NO: 226; and GenBank accession number X54130.1 (entered Apr. 21, 1993), representing hPTPRA-6, incorporated herein as SEQ ID NO: 227.







TABLE 6







Targeting of individual oligonucleotides to specific variants


of human PTPR.alpha.












OLIGO SEQ


VARIANT


ISIS #
ID NO.
TARGET SITE
VARIANT
SEQ ID NO.














147239
28
389
hPTPRA-3
4


147239
28
866
hPTPRA
18


147239
28
357
hPTPRA-4
20


147239
28
349
hPTPR-5
21


147239
28
857
hPTPRA-1
225


147239
28
520
hPTPRA-2
226


147239
28
201
hPTPRA-6
227


147240
29
398
hPTPRA-3
4


147240
29
875
hPTPRA
18


147240
29
366
hPTPRA-4
20


147240
29
358
hPTPR-5
21


147240
29
866
hPTPRA-1
225


147240
29
529
hPTPRA-2
226


147240
29
210
hPTPRA-6
227


147244
30
648
hPTPRA-3
4


147244
30
1152
hPTPRA
18


147244
30
616
hPTPRA-4
20


147244
30
608
hPTPR-5
21


147244
30
1143
hPTPRA-1
225


147244
30
779
hPTPRA-2
226


147244
30
460
hPTPRA-6
227


147246
31
663
hPTPRA-3
4


147246
31
1167
hPTPRA
18


147246
31
631
hPTPRA-4
20


147246
31
623
hPTPR-5
21


147246
31
1158
hPTPRA-1
225


147246
31
794
hPTPRA-2
226


147246
31
475
hPTPRA-6
227


147247
32
706
hPTPRA-3
4


147247
32
1210
hPTPRA
18


147247
32
674
hPTPRA-4
20


147247
32
666
hPTPR-5
21


147247
32
1201
hPTPRA-1
225


147247
32
837
hPTPRA-2
226


147247
32
518
hPTPRA-6
227


147259
36
1818
hPTPRA
18


147259
36
1282
hPTPRA-4
20


147259
36
1274
hPTPR-5
21


147259
36
1809
hPTPRA-1
225


147259
36
1445
hPTPRA-2
226


147259
36
1126
hPTPRA-6
227


147260
37
1338
hPTPRA-3
4


147260
37
1842
hPTPRA
18


147260
37
1306
hPTPRA-4
20


147260
37
1298
hPTPR-5
21


147260
37
1833
hPTPRA-1
225


147260
37
1469
hPTPRA-2
226


147260
37
1150
hPTPRA-6
227


147262
38
1382
hPTPRA-3
4


147262
38
1886
hPTPRA
18


147262
38
1350
hPTPRA-4
20


147262
38
1342
hPTPR-5
21


147262
38
1877
hPTPRA-1
225


147262
38
1513
hPTPRA-2
226


147262
38
1194
hPTPRA-6
227


147263
39
1460
hPTPRA-3
4


147263
39
1964
hPTPRA
18


147263
39
1428
hPTPRA-4
20


147263
39
1420
hPTPR-5
21


147263
39
1955
hPTPRA-1
225


147263
39
1591
hPTPRA-2
226


147263
39
1272
hPTPRA-6
227


147267
40
1680
hPTPRA-3
4


147267
40
2184
hPTPRA
18


147267
40
1648
hPTPRA-4
20


147267
40
1640
hPTPR-5
21


147267
40
2175
hPTPRA-1
225


147267
40
1811
hPTPRA-2
226


147267
40
1492
hPTPRA-6
227


147269
41
1824
hPTPRA-3
4


147269
41
2328
hPTPRA
18


147269
41
1792
hPTPRA-4
20


147269
41
1784
hPTPR-5
21


147269
41
2319
hPTPRA-1
225


147269
41
1955
hPTPRA-2
226


147269
41
1636
hPTPRA-6
227


147270
42
1908
hPTPRA-3
4


147270
42
2412
hPTPRA
18


147270
42
1876
hPTPRA-4
20


147270
42
1868
hPTPR-5
21


147270
42
2403
hPTPRA-1
225


147270
42
2039
hPTPRA-2
226


147270
42
1720
hPTPRA-6
227


147272
43
2007
hPTPRA-3
4


147272
43
2511
hPTPRA
18


147272
43
1975
hPTPRA-4
20


147272
43
1967
hPTPR-5
21


147272
43
2502
hPTPRA-1
225


147272
43
2138
hPTPRA-2
226


147272
43
1819
hPTPRA-6
227


147273
44
2045
hPTPRA-3
4


147273
44
2549
hPTPRA
18


147273
44
2013
hPTPRA-4
20


147273
44
2005
hPTPR-5
21


147273
44
2540
hPTPRA-1
225


147273
44
2176
hPTPRA-2
226


147273
44
1857
hPTPRA-6
227


147274
45
2104
hPTPRA-3
4


147274
45
2608
hPTPRA
18


147274
45
2072
hPTPRA-4
20


147274
45
2064
hPTPR-5
21


147274
45
2599
hPTPRA-1
225


147274
45
2235
hPTPRA-2
226


147274
45
1916
hPTPRA-6
227


147275
46
2109
hPTPRA-3
4


147275
46
2613
hPTPRA
18


147275
46
2077
hPTPRA-4
20


147275
46
2069
hPTPR-5
21


147275
46
2604
hPTPRA-1
225


147275
46
2240
hPTPRA-2
226


147275
46
1921
hPTPRA-6
227


147276
47
2119
hPTPRA-3
4


147276
47
2623
hPTPRA
18


147276
47
2087
hPTPRA-4
20


147276
47
2079
hPTPR-5
21


147276
47
2614
hPTPRA-1
225


147276
47
2250
hPTPRA-2
226


147276
47
1931
hPTPRA-6
227


147278
48
2175
hPTPRA-3
4


147278
48
2679
hPTPRA
18


147278
48
2143
hPTPRA-4
20


147278
48
2135
hPTPR-5
21


147278
48
2670
hPTPRA-1
225


147278
48
2306
hPTPRA-2
226


147278
48
1987
hPTPRA-6
227


147279
49
2209
hPTPRA-3
4


147279
49
2713
hPTPRA
18


147279
49
2177
hPTPRA-4
20


147279
49
2169
hPTPR-5
21


147279
49
2704
hPTPRA-1
225


147279
49
2340
hPTPRA-2
226


147279
49
2021
hPTPRA-6
227


147280
50
2214
hPTPRA-3
4


147280
50
2718
hPTPRA
18


147280
50
2182
hPTPRA-4
20


147280
50
2174
hPTPR-5
21


147280
50
2709
hPTPRA-1
225


147280
50
2345
hPTPRA-2
226


147280
50
2026
hPTPRA-6
227


147281
51
2223
hPTPRA-3
4


147281
51
2727
hPTPRA
18


147281
51
2191
hPTPRA-4
20


147281
51
2183
hPTPR-5
21


147281
51
2718
hPTPRA-1
225


147281
51
2354
hPTPRA-2
226


147281
51
2035
hPTPRA-6
227


147282
52
2256
hPTPRA-3
4


147282
52
2760
hPTPRA
18


147282
52
2224
hPTPRA-4
20


147282
52
2216
hPTPR-5
21


147282
52
2751
hPTPRA-1
225


147282
52
2387
hPTPRA-2
226


147282
52
2068
hPTPRA-6
227


147283
53
2478
hPTPRA-3
4


147283
53
2982
hPTPRA
18


147283
53
2446
hPTPRA-4
20


147283
53
2438
hPTPR-5
21


147283
53
2973
hPTPRA-1
225


147283
53
2609
hPTPRA-2
226


147283
53
2290
hPTPRA-6
227


147285
54
2579
hPTPRA-3
4


147285
54
3083
hPTPRA
18


147285
54
2547
hPTPRA-4
20


147285
54
2539
hPTPR-5
21


147285
54
3074
hPTPRA-1
225


147285
54
2710
hPTPRA-2
226


147285
60
2391
hPTPRA-6
227


147288
55
2688
hPTPRA-3
4


147288
55
3192
hPTPRA
18


147288
55
2655
hPTPRA-4
20


147288
55
3183
hPTPRA-1
225


147288
55
2819
hPTPRA-2
226


147291
56
2750
hPTPRA-3
4


147291
56
3254
hPTPRA
18


147291
56
2717
hPTPRA-4
20


147291
56
3245
hPTPRA-1
225


147291
56
2881
hPTPRA-2
226


147297
57
2947
hPTPRA-3
4


147297
57
3451
hPTPRA
18


147297
57
3442
hPTPRA-1
225


147297
57
3078
hPTPRA-2
226


194483
58
20
hPTPRA
18


194484
59
470
hPTPRA
18


194484
59
461
hPTPRA-1
225


194485
60
685
hPTPRA
18


194486
61
239
hPTPRA-3
4


194486
61
716
hPTPRA
18


194486
61
207
hPTPRA-4
20


194486
61
199
hPTPR-5
21


194486
61
707
hPTPRA-1
225


194486
61
370
hPTPRA-2
226


194486
61
51
hPTPRA-6
227


194487
62
586
hPTPRA-3
4


194487
62
1063
hPTPRA
18


194487
62
554
hPTPRA-4
20


194487
62
546
hPTPR-5
21


194487
62
1054
hPTPRA-1
225


194487
62
717
hPTPRA-2
226


194487
62
398
hPTPRA-6
227


194488
63
1522
hPTPRA-3
4


194488
63
2026
hPTPRA
18


194488
63
1490
hPTPRA-4
20


194488
63
1482
hPTPR-5
21


194488
63
2017
hPTPRA-1
225


194488
63
1653
hPTPRA-2
226


194488
63
1334
hPTPRA-6
227


194489
64
2590
hPTPRA-3
4


194489
64
3094
hPTPRA
18


194489
64
2558
hPTPRA-4
20


194489
64
3085
hPTPRA-1
225


194489
64
2721
hPTPRA-2
226


194489
64
2402
hPTPRA-6
227


194490
65
2834
hPTPRA-3
4


194490
65
3338
hPTPRA
18


194490
65
3329
hPTPRA-1
225


194490
65
2965
hPTPRA-2
226


194500
75
128
hPTPRA-7
26


194505
80
49
hPTPRA-4
20


194505
80
212
hPTPRA-2
226


194506
81
624
hPTPRA-3
4


194506
81
592
hPTPRA-4
20


194506
81
584
hPTPR-5
21


194506
81
755
hPTPRA-2
226


194506
81
436
hPTPRA-6
227


194507
82
113
hPTPRA-3
4


194507
82
73
hPTPR-5
21


194508
83
205
hPTPRA-3
4


194508
83
165
hPTPR-5
21


194514
89
64
hPTPRA-2
226


194515
90
3043
hPTPRA-3
4


194515
90
3547
hPTPRA
18


194515
90
3538
hPTPRA-1
225


194515
90
3174
hPTPRA-2
226


194517
92
778
hPTPRA-3
4


194517
92
1282
hPTPRA
18


194517
92
738
hPTPR-5
21


194517
92
197
hPTPRA-7
26


194517
92
1273
hPTPRA-1
225


194517
92
909
hPTPRA-2
226


194517
92
590
hPTPRA-6
227









Human PTPR.alpha. mRNA sequences from Table 1 were aligned and the screened human oligos were determined to have a complementary sequence to a common PTPR.alpha. mRNA, specifically (SEQ ID NO: 18). Antisense compounds targeting SEQ ID NO: 18 are shown in Table 6b. The antisense compounds were then grouped according to activity and active target segments were determined. An active target segment is used herein to describe a region of the PTPR.alpha. mRNA that has one or more active antisense compounds targeted thereto. Each of the following active target segment was targeted by multiple, active antisense oligonucleotides. These regions include nucleotides 716 to 894, nucleotides 1063 to 1229, nucleotides 1818 to 2045 and nucleotides 2328 to 2779 of SEQ ID NO: 18. Each of the oligonucleotides tested within each of these regions inhibited expression of human PTPR.alpha. by at least 60% in this assay. In active target segment A (nucleotides 716 to 894) the screened oligonucleotides inhibited expression of PTPR.alpha. by an average of about 85%. In active target segment B (nucleotides 1063 to 1229) the screened oligonucleotides inhibited expression of PTPR.alpha. by an average of about 75%. In active target segment C (nucleotides 1818 to 2045) the screened oligonucleotides inhibited expression of PTPR.alpha. by an average of about 90%. In active target segment D (nucleotides 2328 to 2779) the screened oligonucleotides inhibited expression of PTPR.alpha. by an average of about 80%. In active target segment F (nucleotides 1210-1905) the screened oligonucleotides inhibited expression of PTPR.alpha. by an average of about 87%. In active target segment G (nucleotides 2982-3211) the screened oligonucleotides inhibited expression of PTPR.alpha. by an average of about 73%.Identification of these regions allows for the design of antisense oligonucleotides that modulate the expression of PTPR.alpha.







TABLE 6b







Exemplary human PTPR.alpha. oligos targeting SEQ ID NO: 18



















Oligo








SEQ



ISIS
Target
Start
Stop

ID



No:
Site
Codon
Codon
Length
NO:


















194483
112595
20
39
20
58



194484
112596
470
489
20
59



194485
112597
685
704
20
60



194486
112598
716
735
20
61



147239
62483
866
885
20
28



147240
62484
875
894
20
29



194487
112599
1063
1082
20
62



147244
62488
1152
1171
20
30



147246
62490
1167
1186
20
31



147247
62491
1210
1229
20
32



147252
62496
1447
1466
20
33



147253
62497
1452
1471
20
34



147256
62500
1566
1585
20
35



147259
62503
1818
1837
20
36



147260
62504
1842
1861
20
37



147262
62506
1886
1905
20
38



147263
62507
1964
1983
20
39



194488
112600
2026
2045
20
63



147267
62511
2184
2203
20
40



147269
62513
2328
2347
20
41



147270
62514
2412
2431
20
42



147272
62516
2511
2530
20
43



147273
62517
2549
2568
20
44



147274
62518
2608
2627
20
45



147275
62519
2613
2632
20
46



147276
62520
2623
2642
20
47



147278
62522
2679
2698
20
48



147279
62523
2713
2732
20
49



147280
62524
2718
2737
20
50



147281
62525
2727
2746
20
51



147282
62526
2760
2779
20
52



147283
62527
2982
3001
20
53



147285
62529
3083
3102
20
54



194489
112601
3094
3113
20
64



147288
62532
3192
3211
20
55



147291
62535
3254
3273
20
56



194490
112602
3338
3357
20
65



147297
62541
3451
3470
20
57










EXAMPLE 6
Targeting of Individual Oligonucleotides to Specific Variants of Mouse PTPR.alpha.
It is advantageous to selectively inhibit the expression of one or more variants of PTPR.alpha. Oligonucleotides are provided that selectively target, hybridize to, and specifically inhibit one or more, but fewer than all of the variants of mouse PTPR.alpha. A summary of the target sites of the PTPR.alpha. main mRNA and variants is shown in Table 7 and includes GenBank accession number NM—008980.1, representing mPTPRA-2, incorporated herein as SEQ ID NO: 11 and GenBank accession number BE372094.1, representing mPTPR.alpha. main mRNA, incorporated herein as SEQ ID NO: 102.







TABLE 7







Targeting of individual oligonucleotides to specific variants


of mouse PTPR.alpha.












OLIGO SEQ


VARIANT SEQ


ISIS #
ID NO.
TARGET SITE
VARIANT
ID NO.














147237
103
17
mPTPRA-2
11


147238
104
25
mPTPRA-2
11


147254
113
876
mPTPRA-2
11


147255
114
926
mPTPRA-2
11


147257
115
1040
mPTPRA-2
11


147258
116
1177
mPTPRA-2
11


147261
117
1258
mPTPRA-2
11


147264
118
1385
mPTPRA-2
11


147265
119
1489
mPTPRA-2
11


147266
120
1523
mPTPRA-2
11


147268
121
1711
mPTPRA-2
11


147271
122
1903
mPTPRA-2
11


147277
123
2039
mPTPRA-2
11


147284
124
2430
mPTPRA-2
11


147286
125
2504
mPTPRA-2
11


147287
126
2585
mPTPRA-2
11


147289
127
2606
mPTPRA-2
11


147290
128
2627
mPTPRA-2
11


147292
129
2670
mPTPRA-2
11


147293
130
2763
mPTPRA-2
11


147294
131
2788
mPTPRA-2
11


147295
132
2805
mPTPRA-2
11


147296
133
2830
mPTPRA-2
11


147298
134
2860
mPTPRA-2
11


147299
135
2867
mPTPRA-2
11


147300
136
2971
mPTPRA-2
11


147301
137
3024
mPTPRA-2
11


147302
138
3039
mPTPRA-2
11


147314
150
633
mPTPRA
102









EXAMPLE 7
Effect of Antisense Inhibitors of PTPR.alpha. in ob/ob Mice: a Model of Obesity and Diabetes
ob/ob mice are used as a model of obesity and of type-2 diabetes. These mice have a deficiency in the Leptin hormone produced by fat that regulates appetite. Deficiencies in this hormone in both humans and non-human animals lead to obesity. The ob/ob mice have a mutation in the leptin gene which results in obesity and hyperglycemia. ob/ob mice have higher circulating levels of insulin and are less hyperglycemic than db/db mice, which harbor a mutation in the leptin receptor. ISIS 147299 (SEQ ID NO: 135) was tested in the ob/ob model of obesity and diabetes.
Male C57B1/6J-Lep ob/ob mice (Jackson Laboratory, Bar Harbor, Me.) were fed a diet with a fat content of 10-15% and were subcutaneously injected with ISIS 147299 at a dose of 25 mg/kg two times per week for 4 weeks. The mice received a final dose at 12.5 mg/kg at day 30. Saline-injected animals served as controls. After the treatment period, mice were sacrificed and target levels were evaluated in liver and fat. RNA isolation and target mRNA expression level quantitation were performed as described by other examples herein. Animals treated with ISIS 147299 on average showed about a 75% reduction in liver PTPR.alpha. mRNA levels (n=5), and on average about a 50% reduction in fat PTPR.alpha. (n=5) compared to saline controls.
To assess the physiological effects resulting from inhibition of PTPR.alpha. mRNA, the ob/ob mice were further evaluated throughout the treatment period and at the end of the treatment period for body weight, percent fat from body weight, organ weight, chemistries, including serum transaminase, cholesterol, triglycerides and non-esterified fatty acids, liver triglycerides, plasma glucose levels, fed plasma insulin levels and glucose tolerance. Triglycerides, lipoproteins, cholesterol and transaminases were measured by routine clinical analyzer instruments (e.g. Olympus Clinical Analyzer, Melville, N.Y.). Serum free fatty acids were measured using a Wako Chemicals kit for non-esterified free fatty acids (Richmond, Va.). Serum apolipoproteins were measured using apolipoprotein-specific ELISA or by protein immunoblot with apolipoprotein-specific antibodies. Tissue triglyceride levels were measured using a Triglyceride GPO Assay from Roche Diagnostics (Indianapolis, Ind.). Liver triglyceride levels were used to assess hepatic steatosis, or clearing of lipids from the liver. Hepatic steatosis was also assessed by routine histological analysis of frozen liver tissue sections stained with oil red O stain.
The effects of target inhibition on glucose and insulin metabolism were evaluated in the ob/ob mice treated with the oligomeric compounds. Plasma glucose was measured at the start of the treatment and after 2 weeks, 3 weeks and 4.5 weeks of treatment. Mice were sacrificed at day 33 and plasma glucose was measured. (Table 8) Plasma insulin is similarly measured at the beginning of the treatment, and at 2 weeks, at 3 weeks and at 4.5 weeks of treatment. (Table 9)







TABLE 8







Fed Plasma Glucose Levels












Base


Week 4.5



Line
Wk 2
Wk 3
Sacrifice















Saline (sem)
406.6 mg/dl
419.9 mg/dl
394.0 mg/dl
516.4 mg/dl



(24.29)
(23.60)
(36.00)
(42.37)


PTPR.alpha.
403.3 mg/dl
376.7 mg/dl
330.0 mg/dl
295.7 mg/dl


antisense oligo
(25.85)
(24.80)
(19.49)
(22.17)


(sem)
















TABLE 9







Fed Plasma Insulin Levels












Wk 0
Wk 2
Wk 3
Wk 4.5





Saline (sem)
21.29 ng/ml
35.19 ng/ml
29.41 ng/ml
18.7 ng/ml



(2.08)
(3.78)
(3.19)
(6.96)


PTPR.alpha.
21.57 ng/ml
31.37 ng/ml
25.08 ng/ml
15.2 ng/ml


antisense oligo
(1.66)
(3.22)
(3.00)
(2.34)


(sem)









In ob/ob mice treated with ISIS 147299, fed plasma glucose levels were approximately 403.3 mg/dl at base line, 376.7 mg/dl at week 2, 330.0 mg/dl at week 3 and 295.7 mg/dl at sacrifice. Fed plasma insulin levels were approximately 21.57 ng/ml at baseline, 31.37 at week 2, 25.08 at week 3 and 15.2 at week 4.5. Compared to saline control animals, plasma glucose levels are reduced in animals following treatment with an antisense oligonucleotide that inhibit PTPR.alpha.
Plasma lipids in ob/ob mice were also measured throughout the treatment period and at the end of the treatment period. Table 10. Cholesterol levels were approximately 179.3 mg/dl at baseline, 240.3 mg/dl after 2 weeks, 242.9 mg.dl after 3 weeks and 247.3 mg/dl at sacrifice for the ice receiving an antisense inhibitor of PTPR.alpha. There was no significant change in plasma cholesterol levels for mice receiving an antisense inhibitor of PTPR.alpha. Triglycerides were approximately 165.7 mg/dl at base line, 107.9 mg/dl after 2 weeks, 87.4 mg/dl after 3 weeks and 88.9 mg/dl at sacrifice for ISIS 147299-treated mice. For mice receiving treatment with an antisense inhibitor of PTPR.alpha. there was a decrease in fed plasma triglyceride levels.







TABLE 10







Plasma Lipid Levels in ob/ob mice















Wk 4.5



Base Line
Wk 2
Wk 3
Sacrifice















Cholesterol






(sem)


Saline
174.6 mg/dL
209.7 mg/dL
218.3 mg/dL
258.0 mg/dL



 (4.40)
(9.28)
(8.86)
(5.07)


PTPR.alpha.
179.3 mg/dL
240.3 mg/dL
242.9 mg/dL
247.3 mg/dL


antisense oligo
 (4.19)
(6.01)
(7.48)
(10.87) 


Triglycerides


(sem)


Saline
136.6 mg/dL
132.0 mg/dL
129.7 mg/dL
119.3 mg/dL



(10.98)
(7.54)
(9.33)
(3.09)


PTPR.alpha.
165.7 mg/dL
107.9 mg/dL
 87.4 mg/dL
 88.9 mg/dL


antisense oligo
(17.17)
(14.70) 
(5.04)
(4.03)









Treatment of the ob/ob mice with ISIS 147299 decreased hepatic triglyceride levels and improved hepatic function. Liver triglycerides were approximately 109.71 mg/g after 4.5 weeks of treatment. (Table 11) Oil Red-O staining of liver sections showed a marked clearing of lipid deposits for the treated group compared to control. (FIGS. 1a and 1b.) Plasma transaminase levels were reduced in the mice receiving treatment compared to those receiving saline. Plasma Alanine Aminotransferase (ALT) levels were approximately 86.3 IU/L at baseline, 244.1 after 2 weeks, 258.3 IU/l after 3 weeks and 137.7 IU/L at sacrifice for the treated group. Plasma Aspartate Aminotransferase (AST) levels were approximately 71.1 IU/L at base line, 128.4 IU/L after 2 weeks, 144.0 IU/L after 3 weeks and 134.4 IU/L at sacrifice following treatment. Fasted transaminase levels were determined after 4 weeks of treatment and were approximately 246.9 IU/L for ALT and 139.1 for AST. Table 12. These values show that treatment with an antisense inhibitor of PTPR.alpha. reduced hepatic and plasma triglyceride levels and improved hepatic function compared to the saline control group.







TABLE 11







Liver Triglyceride Levels









mg/g (sem)














Saline
151.26 (11.11)



PTPR.alpha. antisense oligo
109.71 (6.24)

















TABLE 12







Plasma Transaminase Levels













Base Line
Wk 2
Wk 3
Wk 4 Fasted
Wk 4.5 Sacrifice
















ALT (sem)







Saline
90.6 IU/L
147.6 IU/L
209.7 IU/L
189.7 IU/L
209.4 IU/L



(6.51)
 (9.08)
(14.71)
(15.26)
(20.65)


PTPR.alpha.
86.3 IU/L
244.1 IU/L
258.3 IU/L
246.9 IU/L
137.7 IU/L


antisense oligo
(3.19)
(23.14)
(27.97)
(26.73)
(14.75)


AST (sem)


Saline
73.4 IU/L
112.3 IU/L
164.9 IU/L
176.3 IU/L
218.6 IU/L



(4.50)
 (7.79)
(11.63)
(11.44)
(26.21)


PTPR.alpha.
71.1 IU/L
128.4 IU/L
144.0 IU/L
139.1 IU/L
134.4 IU/L


antisense oligo
(2.01)
(11.65)
(15.12)
(16.14)
 (9.28)









No changes in body weight, fat content, plasma cholesterol or plasma free fatty acid levels were observed for mice receiving treatment with ISIS 147299 compared to saline controls.
These results indicate that antisense inhibition of PTPR.alpha. expression improves plasma glucose levels, glucose tolerance and plasma and hepatic triglycerides levels in the ob/ob mouse model of diabetes and obesity. Consequently, antisense inhibitors of PTPR.alpha. are useful for preventing, ameliorating or treating conditions and disorders associated with these factors.
EXAMPLE 8
Effect of Antisense Inhibitors of PTPR.alpha. on Diet-induced Obesity in Mice
Antisense inhibitors of PTPR.alpha. expression are expected to reduce obesity or weight gain. This is tested in the high fat diet (HFD) model, also known as the DIO (diet-induced obesity) model.
Four week old male C57b1/6 mice were fed a high fat diet (60% kCal) ad libitum beginning at 4 weeks of age and continuing for 10 weeks. After the 10 weeks the mice were maintained on the diet as described and were treated with either an antisense inhibitor of PTPR.alpha., a control oligonucleotide having similar chemistry to the treatment oligonucleotide but not having a sequence that is complementary to the target mRNA, or saline. During this feeding schedule, animals were weighed at regular intervals and body weight and percent fat measurements were determined. At sacrifice, organ weights were determined as well.
Mice in the treatment group received 25 mg/kg of ISIS 147299 (SEQ ID NO: 135) twice a week by subcutaneous injection. Control group mice received a same treatment routine except using saline or, 25 mg/kg of control oligonucleotide that is not an antisense inhibitor of PTPR.alpha (CCTTCCCTGAAGGTTCCTCC-SEQ ID NO: 228). A further control group received no treatment and was fed normal chow. Food consumption was determined for mice in each of the groups. Mice treated with the antisense PTPR.alpha. inhibitor had reduced body weight gains and reduced food consumption. FIGS. 2 and 3. There were no differences in organ weight and percent fat between the groups.
Blood was drawn weekly and transaminase levels, plasmid glucose levels, NEFA levels, and plasma lipid levels were determined. There was a decrease in plasma lipid levels for the mice receiving an antisense inhibitor of PTPR.alpha. After five weeks of treatment plasma triglyceride levels for mice receiving an antisense inhibitor of PTPR.alpha. were 59.9 IU/l (sem=3.57) compared to 75.9 IU/L (sem=2.20) for saline, 77.2 IU/L (sem=4.81) for control oligo and 91.80 IU/L (sem=5.92) for normal chow.
Insulin levels are presented in Table 13. For mice treated with an antisense inhibitor of PTPR.alpha. fed plasma insulin levels were approximately 2.66 ng/ml at base line, 2.96 ng/ml after 2 weeks, 2.71 ng/ml after 3 weeks and 1.95 ng/ml after 5 weeks. At week four fasted insulin levels were approximately 0.58 ng/ml for the mice receiving treatment with an antisense inhibitor of PTPR.alpha.







TABLE 13







Insulin Levels in DIO mice












ng/ml (sem)
BL
Wk 2
Wk 3
Fasted Wk 4
Wk 5





Saline
2.63 (0.30)
3.91 (0.40)
5.07 (0.73)
1.75 (0.47)
6.97 (1.03)


PTPR.alpha.
2.66 (0.29)
2.96 (0.27)
2.71 (0.36)
0.58 (0.15)
1.95 (0.18)


Control
2.53 (0.56)
2.23 (0.46)
2.01 (0.46)
0.63 (0.16)
2.42 (0.57)


Oligo


Normal
0.96 (0.20)
1.10 (0.31)
1.37 (0.43)
0.57 (0.17)
1.28 (0.24)


Chow









At day 41 of the treatment period the DIO mice were given an insulin tolerance test. Insulin tolerance tests are a good measure of insulin sensitivity. Mice were fasted for 3 hours and then received 0.35 U/kg of humilin (Lilly, Indianapolis, Ind.) via gavage of a 0.1 U/ml solution in saline. Blood glucose was measured at time point 0 and at 15, 20 or 30 minute intervals for up to 2 hours. Glucose levels are measured using a YSI glucose analyzer (YSI Scientific, Yellow Springs, Ohio). Results of the insulin tolerance test are shown in Table 14.







TABLE 14







Glucose During Insulin Tolerance Test in DIO Mice












mg/dL (sem)
0
30
60
90
120





Saline
194.4 (7.20)
175.3 (9.13) 
182.9 (7.60) 
216.7 (11.68)
242.9 (13.72)


PTPR.alpha.
179.7 (7.18)
142.0 (8.91) 
149.3 (11.36)
165.3 (12.38)
200.1 (12.35)


Control Oligo
161.8 (6.61)
121.0 (11.84)
126.8 (6.34) 
150.8 (10.71)
186.0 (12.29)


Normal Chow
 106.6 (20.56)
100.8 (18.50)
113.2 (22.18)
125.0 (23.58)
127.4 (24.27)









Insulin levels were reduced for the animals receiving ISIS 147299 antisense inhibitor to PTPR.alpha. In addition, there was a reduction in plasma glucose levels seen during the insulin tolerance test for animals receiving ISIS 147229. A similar decrease was seen with control oligo, but not in the groups receiving saline.
The results from the ob/ob mouse studies and the DIO mouse studies indicate that antisense inhibition of PTPR.alpha. results in a reduction of plasma glucose levels and triglyceride levels in the plasma and liver. Antisense inhibition of PTPR.alpha. may provide a therapeutic strategy for conditions and diseases associated with these factors, such as type II diabetes, fatty liver disease and metabolic syndrome.

## Claims

1. A method for the prevention, amelioration, or treatment of a disease or condition wherein indicators of the disease or condition comprise increased plasma glucose levels, increased plasma lipid levels, increased hepatic triglyceride levels, increased plasma transaminase levels, reduced hepatic function, reduced insulin sensitivity or combinations thereof comprising administering an antisense compound 12 to 35 linked nucleosides in length targeted to a nucleic acid molecule encoding human PTPR alpha to an individual in need of such intervention, wherein plasma glucose levels, plasma lipid levels, hepatic triglyceride levels or plasma transaminase levels are decreased, hepatic function or insulin sensitivity is improved or combinations thereof.

2. The method of claim 1 wherein the disease or condition is fatty liver disease and wherein administration of the compound results in a decrease in plasma lipid levels, a decrease in plasma transaminase levels, a decrease in hepatic triglyceride levels or combinations thereof.

3. The method of claim 1 wherein the disease or condition is type-2 diabetes and wherein administration of the compound results in a decrease in plasma glucose levels, an improvement in insulin sensitivity or combinations thereof.

4. The method of claim 1 wherein the disease or condition is metabolic syndrome and wherein administration of the compound results in a decrease in plasma glucose levels, a decrease in plasma lipid levels, a decrease in hepatic triglyceride levels, an improvement in insulin sensitivity, an improvement in hepatic function, a decrease in plasma transaminase levels or combinations thereof.

5. The method of claim 1 wherein the disease or condition comprises type-2 diabetes, fatty liver, metabolic syndrome or combinations thereof.

6. The method of claim 1 wherein the antisense compound optionally further comprises a complementary strand 15 to 35 nucleobases in length.

7. A method for lowering blood glucose levels in an animal in need thereof by administering an antisense compound 12 to 35 nucleosides in length targeted to a nucleic acid molecule encoding human PTPR alpha.

8. A method for lowering triglyceride levels in an animal in need thereof by administering an antisense compound 12 to 35 nucleosides in length targeted to a nucleic acid molecule encoding human PTPR alpha.

9. The method of claim 8 wherein the triglyceride levels are lowered in the plasma.

10. The method of claim 8 wherein the triglyceride levels are lowered in the liver.

11. The method of claim 7, 8, 9 or 10 wherein the animal suffers from type-2 diabetes, fatty liver disease, obesity, metabolic syndrome of combinations thereof.

12. The method of claim 1, wherein the compound is at least 80% complementary to a target region of the nucleic acid encoding PTPRalpha.

13. The method of claim 1, wherein the compound optionally includes a complementary strand 15 to 35 nucleobases in length.

14. The method of claim 1, wherein the compound is an antisense oligonucleotide.

15. The compound of claim 14, wherein the compound has at least one modified internucleoside linkage, sugar moiety, or nucleobase.

16. The compound of claim 14, wherein the compound comprises a chimeric oligonucleotide.

17. The compound of claim 15, wherein the modified internucleoside linkage comprises a phosphorothioate linkage.

18. The compound of claim 15, wherein the at least one modified sugar moiety comprises a 2′-MOE, a LNA, a 2′-OMe, an ENA, a 2′-F or combinations thereof.

19. The compound of claim 15, wherein the modified nucleobase comprises 5-methylcytosine.

20. The method of claim 12, wherein the compound is administered in a pharmaceutical composition comprising the compound and a pharmaceutically acceptable penetration enhancer, carrier, or diluent.