WO2008070858A1 - Inhibiting translation of abrerrant dnmt3b transcripts in cancer cells using inhibitory nucleic acids - Google Patents

Abstract

The present invention provides new methods of inhibiting aberrant DNA methyltransferase 3B (DNMT3B) transcripts containing abnormal splicing. Inhibitory nucleic acids, such as interfering RNAs and antisense molecules target improperly retained introns, thereby selectively inhibiting aberrant transcripts. Methods of treating cancers that involve aberrant DNMT3B transcripts also are provided.

Description

DESCRIPTION

INHIBITING TRANSLATION OF ABERRANT DNMT3B TRANSCRIPTS IN CANCER CELLS USING INHIBITORY NUCLEIC ACIDS

BACKGROUND OF THE INVENTION

This application claims priority to U.S. provisional patent application 60/869,266 filed on December 8, 2006 and 60/992,041 filed on December 3, 2007, which are hereby incorporated by reference in their entirety.

A. Field of the Invention

The present invention relates to the fields of molecular biology, nucleic acid biochemistry, and/or oncology. More particularly, the invention provides for methods and compositions involving inhibitory nucleic acids that target aberrant DNA methyltransfera.se 3B (DNMT3B) transcripts in a cancer cell.

B. Related Art

Cytosine methylation and histone modifications play an important role in the transcriptional regulation of cellular genes (Robertson, 2005). DNA is methylated at the 5-C position of cytosines that are part of CpG dinucleotides. In normal cells, repetitive DNA is highly methylated and transcriptionally silenced, effectively inactivating transposable elements that could mediate genomic rearrangements. Open chromatin associated with actively transcribed genes is hypomethylated. DNA methylation is used to control gene expression in normal cellular processes (e.g. , X chromosome inactivation, genomic imprinting, aging).

Cancer cells are characterized by abnormal patterns of DNA methylation (Robertson, 2005). Repetitive DNA sequences are hypomethylated and transcriptionally active, and the altered chromatin structure of these regions is thought to contribute to the formation of some of the chromosomal rearrangements seen in cancer cells. Additionally, some gene promoters are hypermethylated in tumor cells, resulting in transcriptional silencing of tumor suppressor genes without accompanying inactivating mutations.

Three DNA methyltransferase (DNMT) enzymes have been identified in eukaryotic cells (Bestor, 2000; Rountree et α/., 2001). DNMTl is generally considered to be a maintenance methylase, although it also has de novo methylase activity (Bestor, 2000; Robertson, 2002). Both DNMT3A and DNMT3B catalyze de novo methylation of DNA sequences (Li, 2002). Each of these three enzymes is essential for life, since homozygous knock-out alleles of Dnmtl and Dnmt3b cause embryonic lethality in mice, and mice with homozygous knock-out alleles of Dnmt3 a die several weeks after birth (Li et al, 1992; Okano et al, 1999). Dnmtl V- embryonic stem cells display extensive demethylation of endogenous retroviral DNA (Li et al, 1992), and murine embryonic stem cells lacking Dnmt3b demonstrate hypomethylation of minor satellite sequences (Okano et al, 1999). Patients with a rare autosomal recessive syndrome, the Immunodeficiency; Centromere instability; Facial anomalies (ICF) Syndrome, have germline mutations in the DNMT3B gene (Hansen et al, 1999; Shirohzu et al, 2002; Xu et al, 1999), and lymphocytes from affected individuals display hypomethylation of repetitive DNA sequences. Furthermore, mice expressing Dnmt3b alleles similar to those found in ICF Syndrome are small with abnormal craniofacial development and hypomethylation of repetitive elements, suggesting that these alleles encode hypomorphic proteins (Ueda et al, 2006).

Numerous studies have implicated both DNMTl and DNMT3B in the altered distribution of DNA methylation in cancer cells. (Beaulieu et al, 2002; Robert et al, 2003). A human colon cancer cell line, HCTl 16 deficient in DNMTl following targeted recombination, demonstrates demethylation of pericentromeric satellite sequences (Rhee et al, 2000), whereas HCTl 16 cells lacking both DNMTl and DNMT3B contain demethylated satellite 2 and AIu repetitive sequences (Rhee et al, 2002) and demonstrate increased chromosomal instability (Karpf & Matsui, 2005). Additional studies of the doubly-targeted cells suggest that at least some histone modifications occur prior to alterations in DNA methylation (Bachman et al, 2003). Mice expressing a hypomorphic Dnmtl protein develop T-cell lymphomas (Gaudet et al, 2003), and when this deficiency is crossed into other tumor models, tumor incidence increases (Eden et al, 2003; Yamada et al, 2005). Dnmt3b deficiency inhibits the formation of macroadenomas in the murine Ape Minl+ colon cancer model, indicating a requirement for Dnmt3b activity in the transition from microadenoma to tumor (Lin et al, 2006).

Experiments designed to understand the mechanism by which cancer cells have altered patterns of DNA methylation have not yielded a simple explanation. Mutations of the DNA methyltransferase genes are rare in cancer cells (Kanai et al , 2003). Several groups have examined the expression of DNMT transcripts and have not found a correlation with DNA methylation levels in cancer cells (Robertson et al, 1999; Saito et al, 2002; Ehrlich et al, 2006). However, expression of transcripts that originate from a promoter within intron 4, ADNMT3B1-7, correlates with the DNA methylation states of the pi 6 and RASSFlA promoters in non-small cell lung cancers (Wang et al, 2006a). Interestingly, several DNMT3B transcripts are predicted to encode proteins lacking critical parts of or the entire catalytic domain and therefore would produce catalytically inactive proteins: DNMT3B4 and DNMT3B5 encode proteins lacking the final two methyltransferase domains (Robertson et al, 1999), and three of the recently described transcripts from non-small cell lung cancers, ADNMT3B5-7, also encode truncated DNMT3B proteins (Wang et al, 2006a; Wang et al, 2006b).

SUMMARY OF THE INVENTION The present invention is based on the observation of aberrant DNMT3B transcripts in cancer cells and their effect on DNA methylation. Therefore, the present invention provides methods and compositions concerning a DNMT3B transcript in cancer cells.

Thus, in accordance with the present invention, there is provided a method of inhibiting a cancer cell comprising contacting said cell with a nucleic acid that hybridizes to an intronic region of an aberrantly spliced DNMT3B transcript comprising a retained intron. Inhibition may comprise inhibiting cancer cell growth, inhibiting cancer cell proliferation, inhibiting cancer cell survival, inhibiting cancer cell invasion, inhibiting cancer cell migration, restoring cancer cell growth control, or inducing cancer cell death.

The cancer cell may be a brain cancer cell, a head & neck cancer cell, a lung cancer cell, an esophageal cancer cell, a stomach cancer cell, a pancreatic cancer cell, a liver cancer cell, a colon cancer cell, a breast cancer cell, an ovarian cancer cell, a testicular cancer cell, a prostate cancer cell, a cervical cancer cell, a rectal cancer cell, a skin cancer cell, a leukemia cell, or a lymphoma cell. The hybridizing nucleic acid may be an antisense molecule or an interfering nucleic acid molecule, such as a siRN A, a dsRNA or a shRNA. The DNMT3B may be DNMT3B7, DNMT3B8, DNMT3B9 or DNMT3B11-30. The method may further comprise contacting said cell with a second anti-cancer agent, such as a chemotherapy, radiotherapy, hormonal therapy, immunotherapy or toxin therapy. The term "inhibitory nucleic acids" (e.g., siRNA and antisense nucleic acids), is used herein to include both interfering nucleic acids and antisense molecules that target improperly retained introns, thereby selectively inhibiting aberrant transcripts. Whereas, "interfering nucleic acids" (e.g., siRNA, shRNA and dsRNA) is a more specific term that refers to those nucleic acids that act by post-transcriptional gene silencing via a double stranded RNA intermediates.

In some embodiments of the invention, an inhibitory nucleic acid is provided to a cell by providing to it a plasmid or vector that contains or encodes for the inhibitory nucleic acid.

In certain embodiments of the invention, an inhibitory nucleic acid comprises a region has 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 272, 28, 29, 30 or more contiguous nucleic acid residues that are complementary or identical to any of SEQ ID NOs: 1-52. The complementarity or identity across these lengths may be at least or at most 80, 85, 90, 95, 96, 97, 98, 99, or 100%. It is contemplated that an inhibitory nucleic acid may comprise more than one such region.

In another embodiment, there is provided a method of altering DNA methylation in a cancer cell comprising contacting said cell with an inhibitory nucleic acid that targets an intronic region of an aberrantly spliced DNMT3B transcript comprising a retained intron. In some embodiments, methylation of a particular gene is increased. In other embodiments, methylation of a particular gene is decreased. In other embodiments, overall methylation in the cell is increased, while in other embodiments, overall methylation of the cell is decreased. In the case of overall methylation, it may be that the methylation of certain genes is the same as the cell's overall change in methylation, though in other cases the methylation of other genes is the opposite as the cell's overall change in methylation.

In yet another embodiment, there is provided a method of preventing hypomethylation in a cancer cell comprising contacting said cell with an inhibitory nucleic acid that targets an intronic region of an aberrantly spliced DNMT3B transcript comprising a retained intron. In another embodiment, there is provided a method of preventing hypermethylation in a cancer cell comprising contacting said cell with an inhibitory nucleic acid that targets an intronic region of an aberrantly spliced DNMT3B transcript comprising a retained intron.

In still yet another embodiment, there is provided a method of treating cancer in a subject comprising administering to a cancer cell in said subject a hybridizing nucleic acid that targets an intronic region of an aberrantly spliced DNMT3B transcript comprising a retained intron. Inhibiting may comprise inhibiting cancer cell growth, inhibiting cancer cell proliferation, inhibiting cancer cell survival, inhibiting cancer cell invasion, inhibiting cancer cell migration, restoring growth control of said cancer cell, or inducing cancer cell death. The cancer cell may be a brain cancer cell, a head & neck cancer cell, a lung cancer cell, an esophageal cancer cell, a stomach cancer cell, a pancreatic cancer cell, a liver cancer cell, a colon cancer cell, a breast cancer cell, an ovarian cancer cell, a testicular cancer cell, a prostate cancer cell, a cervical cancer cell, a rectal cancer cell, a skin cancer cell, a leukemia cell, or a lymphoma cell. The hybridizing nucleic acid may be an antisense molecule or an interfering nucleic acid such as an siRNA, a dsRNA or a shRNA. The DNMT3B transcript may be DNMT3B7, DNMT3B8, DNMT3B9 or DNMT3B 11-30. The method may further comprise administering to said cell a second anti-cancer therapy, such as a chemotherapeutic, a radiotherapeutic, a hormone therapy, an immunotherapy, or surgery. In yet a further embodiment, there is provided an oligonucleotide consisting of

10 to 50 bases and comprising a segment of at least 10 consecutive bases of a DNMT3B intron or an intron-exon boundary. The oligonucleotide may be single- stranded, double- stranded, may comprise phosphodiester bases, and may be an antisense molecule or an interfering nucleic acid or a short hairpin RNA. The number of consecutive bases from the DNMT3B gene may be 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 or 50 bases, or any range derivable therein. It is contemplated that embodiments of the invention may involve any such number of consecutive bases from any of SEQ ID NO: 1 through SEQ ID NO:52. Any embodiment discussed in the context of shRNA may be implemented with any interfering RNA, such as an siRNA, and vice versa.

It is contemplated that any method or composition described herein can be implemented with respect to any other method or composition described herein. The use of the word "a" or "an" when used in conjunction with the term "comprising" in the claims and/or the specification may mean "one," but it is also consistent with the meaning of "one or more," "at least one," and "one or more than one." These, and other, embodiments of the invention will be better appreciated and understood when considered in conjunction with the following description and the accompanying drawings. It should be understood, however, that the following description, while indicating various embodiments of the invention and numerous specific details thereof, is given by way of illustration and not of limitation. Many substitutions, modifications, additions and/or rearrangements may be made within the scope of the invention without departing from the spirit thereof, and the invention includes all such substitutions, modifications, additions and/or rearrangements. BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to these drawings and the detailed description presented below.

FIGS. IA-B. Cancer cells express aberrant DNMT3B transcripts as demonstrated by reverse-transcription PCR (RT-PCR). (FIG. IA) DNMT3B cDNA was amplified from exon 9 to exon 13 in several cancer cell lines. DNA sizing is shown at the left. The cDNA sources were: water, negative control; normal human peripheral blood; MDA-MB-231, a breast cancer cell line; K562, a cell line derived from chronic myeloid leukemia in myeloid blast phase; Jurkat, a T-cell leukemia cell line; and H526, a small cell lung cancer cell line. Product A is derived from a normal DNMT3B transcript that lacks exon 10, either DNMT3B2 or DNMT3B3. Product B is derived from DNMT3B1, which contains exon 10. Product C is an abnormally- migrating species, the DNMT3B7 transcript. Amplification of the GAPD cDNA served as a loading control demonstrating equal amounts of input cDNA from each cDNA source (bottom panel). (FIG. IB) Alternative splicing of the DNMT3B gene. The protein-encoding exons of the DNMT3B gene are indicated at the top of the figure. Six major splice forms of the DNMT3B gene have been described, DNMT3B1-6. The exons contained in a particular transcript are shown in solid black rectangles. Exons excluded through alternative splicing are indicated by rectangular outlines. Premature translational stop codons are indicated by stop signs. The structure of the 5' ends of the DNMT3B4 and DNMT3B5 transcripts are not known (Robertson et al., 1999). The most widely expressed aberrant DNMT3B transcript in cancer cells, DNMT3B7, is indicated in the middle of the figure. The retained intron sequence is indicated with a solid grey rectangle. The ADNMT3BI-4 transcripts identified recently in non-small cell lung cancer differ from each other with respect to alternative splicing of exons 7 and 10 (numbering according to exons in DNMT3B1-3 transcripts), and ADNMT3B5-6 differ from each other with respect to alternative splicing of exon 7, indicated by hatched bars (Wang et al., 2006a; Wang et al., 2006b).

The data reported in this figure and other figures is described in Ostler et al. , Oncogene 26:5553-5563, 2007, which is hereby incorporated by reference in its entirety. FIGS. 2A-B. Identification of truncated DNMT3B proteins by Western blotting. (FIG. 2A) Identification of truncated DNMT3B proteins in extracts from cancer cell lines. Top panel, Cytosolic and nuclear extracts (60 μg each) from SK- BR-3 (breast cancer cells) and HeLa (cervical carcinoma cells) were probed by Western blotting using the DNMT3B T-16 antibody (Santa Cruz Biotechnology). The positions of full-length DNMT3B and truncated DNMT3B7 are indicated to the right. The positions of the molecular weight markers are given at the left. C, cytoplasmic extract; N, nuclear extract. Middle panel, Parallel blot to that shown in the top panel probed with the same antibody plus the antigenic peptide. Bottom panel, Equal loading of cytosolic extracts and integrity of nuclear extracts as demonstrated by Western blotting using an anti-GAPDH antibody (AbCam). (FIG. 2B) Expression of DNMT3B7 in stable 293 cell lines. Top panel, Cytosolic and nuclear extracts (40- 50 μg each) from vector-transfected or DNMT3B7-transfected 293 cells demonstrate expression of DNMT3B7 in the nuclear fraction. Middle panel, Parallel blot to that shown in the top panel probed with the same antibody plus the antigenic peptide. Bottom panel, Equal loading of cytosolic extracts and integrity of nuclear extracts as demonstrated by Western blotting using an anti-GAPDH antibody (AbCam).

FIG. 3. Gene expression changes in DNMT3B7-expressing 293 cells. A heat map shows the 51 genes whose expression changed with DNMT3B7 expression (black outlined, underexpression; not outlined, overexpression). Four samples of vector-transfected cells were compared to three samples each of DNMT3B7- expressing cells, and the average-fold change for each probe is listed. Gene names are in bold for the genes whose expression changes were validated by semi- quantitative RT-PCR (data not shown). The chromosomal locus of each gene is given at the right, and the genes located on chromosomes 1, 9, and 16, and the X chromosome are indicated by highlighting. Some genes (e.g., PRKCBl and MIDI) are listed more than once in the figure, because the microarray contained multiple probes for these genes. FIGS. 4A-D. 293 cells overexpressing DNMT3B7 demonstrate gene expression changes that correspond with altered DNA methyl ation within some CpG islands as determined by sodium bisulfite analysis. Methylated CpG dinucleotides are represented by filled-in black circles, and unmethylated CpG dinucleotides are represented by open circles. Each numbered row represents an individual clone, and the CpG dinucleotide number is given across the top of each section. The number of identical clones is given in parentheses after a representative row. (FIG. 4A) Analysis of the methylation state of 18 individual CpG dinucleotides from the portion of the CDHl CpG island that is located just 5' to the gene's transcriptional start. Hypermethylation of particular CpG dinucleotides in both Line 1 and Line 2 were statistically-significant and are indicated by daggers. (FIG. 4B) Analysis of the methylation state of 12 individual CpG dinucleotides from the portion of the MAGEA3 CpG island that is located overlapping with the gene's transcriptional start. (FIG. 4C) Analysis of the methylation state of two portions of the PLP2 CpG island. At the left, the figure shows the methylation state of 19 individual CpG dinucleotides from a part of the CpG island located just 5' to the gene's transcriptional start, and at the right, the figure indicates the methylation state of 24 additional CpG dinucleotides located just 3' to the translational start. Hypomethylation of one particular CpG residue in the 3 ' portion of the CpG island is indicated with an asterisk. (FIG. 4D) Analysis of the methylation state of 7 individual CpG dinucleotides from the portion of the SH2D1A CpG island that is located within exon 2.

FIG. 5. The splicing patterns of the aberrant DNMT3B transcripts, DNMT3B 7-DNMT3B30. The exons present in each transcript are indicated by solid black boxes. The intron-derived sequences that are contained within aberrant transcripts are indicated by solid grey rectangles. Inclusion of part of an exon is indicated by a grey dashed bar in front of the exon when the beginning of the exon is missing and at the end of the exon when the end of the exon is missing in a particular transcript. The locations of the premature translational stops are indicated by stop signs. Intron sequences are indicated by thin lines. FIG. 6. shRNAs directed against the 94 base pairs of retained intron sequence target destruction of PNMT3B7, but not full-length DNMT3B. Lane 1, 293 cells stably expressing DNMT3B7 + RNAi #1; Lane 2, 293 cells stably expressing DNMT3B7 + RNAi #2; Lane 3, 293 cells stably expressing DNMT3B7 + Luciferase shRNA; Lane 4, 293 cells stably expressing DNMT3B7 + RNAi #3. FIGS. 7A-C. Identification of DNMT3B Intron-Exon Boundaries. (FIG. 7A)

Exons 1-12 and Introns 1-11. (FIG. 7B) Exons 13-23 and Introns 12-23. (FIG. 7C) Exon 24.

FIGS. 8A-B. Introduction of DNMT3B7 shRNA #1 slows the growth of MDA-MB-231 cells. A. RT-PCR confirmation that MDA-MB-231 cells expressing DNMT3B7 shRNA#l lack DNMT3B7. Total RNA was made from several cell lines (from left to right): 293 cells expressing DNMT3B7, MDA-MB-231 cells, MDA-MB- 231 cells expressing an shRNA against Luciferase, and MDA-MB-231 cells expressing DNMT3B7 shRNA #1. Amplifications for DNMT3B7 (top panel) and GAPD (bottom panel) were performed. The negative control (water, dH2O) is shown in the left-most lane. DNA sizing ladders are shown to the right. These reactions were run on the same agarose gel, but the lanes were re-ordered here for ease of presentation. B. MDA-MB-231 cells expressing DNMT3B7 shRNA#l (triangles) grow more slowly after passage 8 than parental cells (circles) or MDA-MB-231 cells expressing the control Luciferase shRNA (squares). Duplicate plates were counted at each passage, and the fold increase in cell number was plotted on a logarithmic scale. The Student's t-test was used to compare the rate of growth of the cells, P<0.02 after passage 8. DETAILED DESCRIPTION OF THE INVENTION

As discussed above, studies have implicated DNMT3B in the altered distribution of DNA methylation in cancer cells. The inventors have now demonstrated that cancer cells express numerous aberrant splice variants of the DNMT3B gene, all of which are predicted to encode truncated proteins lacking the catalytic C-terminus. Western blotting of cancer cell extracts demonstrates that truncated DNMT3B proteins are present in nuclear protein extracts, despite low levels of aberrant DNMT3B transcripts. When expressed in 293 cells, DNMT3B7, the most frequently observed truncated protein, causes altered gene expression with corresponding changes in the DNA methylation states of several CpG islands. These findings suggest that truncated DNMT3B proteins could influence the DNA methylation state of cancer cells.

The inventors' extensive analysis of 25 cancer cell lines indicates that aberrant DNMT3B transcription is extremely widespread in cancer. The only tumor type in which the inventors did not observe novel DNMT3B transcripts was hepatocellular carcinoma. Interestingly, Alexander cells, derived from hepatocellular carcinomas, are known to express DNMT3B4, which encodes a catalytically-inactive DNMT3B isoform (Saito et al, 2002). Furthermore, recently described transcripts from non- small cell lung cancers, ADNMT3B5-7, are also predicted to encode truncated DNMT3B proteins lacking the catalytic domain (Wang et al, 2006a; Wang et al, 2006b). Therefore, all of the cancer cell lines studied by the inventors express DNMT3B transcripts that encode catalytically active as well as truncated DNMT3B proteins that are predicted to be catalytically inactive.

The inventors used microarray analysis to indicate which genes showed altered transcription in DNMT3B7-expressing cells, and some of these changes in gene expression correlated with DNA methylation of corresponding CpG islands. Almost all of the changes in DNA methylation levels were stronger in the 293 cells that expressed higher DNMT3B7 levels (Line 2), suggesting that subtle changes in levels of catalytically-inactive DNMT3B proteins could have significant effects in cells over the many generations of cell divisions that occur during tumor formation and growth.

The inventors' studies show that the most common of the truncated proteins, DNMT3B7, is concentrated in the nucleus, suggesting that the nucleus is the major site of its activity. DNMT3B7 may localize to the nucleus via the retention of one weak nuclear localization signal or via binding to a protein that could shuttle it into the nucleus. The inventors envision several models by which DNMT3B7 could affect DNA methylation, and consequently, gene expression. First, DNMT3B7 may interfere with the normal DNA methylation machinery by binding one or more of the known DNMT3B binding partners. Several proteins have been shown to bind DNMT3B, including SUMO-I and UBC-9, two components of the sumoylation pathway (Kang et al, 2001); h-CAP-C and hCAP-E, two components of the condensin complex; KIF4A, a chromokinesin homolog; hSNF2H, an ATP-dependent chromatin remodeling enzyme; HDACl, a histone deacetylase; and SIN3A, a transcriptional co-repressor (German et al, 2004a). DNMT3B is also known to interact with HDAC2 (Geiman et al, 2004b) and DNMTl (Kim et al, 2002), although the precise binding regions have not been defined. In addition, the PHD domain of murine Dnmt3b, which is located in the N-terminus, mediates binding to Suv39hl and HPl proteins, both of which are components of the histone methylation machinery (Geiman et al, 2004b).

Second, DNMT3B7 may bind DNA directly and affect the activity of active DNMTs. And third, DNMT3B7 may affect DNA methylation as outlined above, which could in turn, lead to alterations in histone modifications. Mice lacking histone Hl showed alterations in DNA methylation levels and consequent gene expression changes in relatively few genes, often in imprinted genes or genes located on the X chromosome (Fan et al, 2005). In addition, histone H3 and H4 acetylation levels increased after patients received 5-azacytidine, a global hypomethylating agent (Gore et al, 2006). Interestingly, the genes that were overexpressed in DNMT3B7-expressing cells were over-represented on chromosomes 1, 9, 16, and X. Cells from patients with ICF Syndrome contain dramatically hypomethylated repetitive DNA sequences of the satellite 2 repeats concentrated at the pericentromeric regions of chromosomes 1 and 16 and of the satellite 3 repeats found near the centromere of chromosome 9 (Ehrlich, 2003) as well as hypomethylation of the LINE-I elements located on the inactive X chromosome (Hansen, 2003). The inventors did not observe significant hypomethylation of repetitive elements in their DNMT3B7-expressing 293 cells, possibly because they have relatively undermethylated repetitive sequences at baseline (data not shown). Aberrant processing of mRNAs in tumor cells has been described for the MDM2, RasGRP4, SLP-65, TLEl, TLE4, MTAl, and CD44 genes and is emerging as an important characteristic of tumor cells (Bartel et al, 2002; Jumaa et al, 2003; Kumar et al, 2002; Reuther et al, 2002; Venables, 2004; Watermann et al, 2006; Yang et al, 2002). Aberrant mRNA processing has also been observed in other diseases, such as myotonic dystrophy (Charlet-B. et al, 2002). In aberrant splicing, portions of exons, portions of introns, or both are retained within transcripts that fail to be purged by the cellular pathways designed to scavenge abnormal mRNAs, such as nonsense-mediated decay (Culbertson, 1999; Wilkinson & Shyu, 2002). Often, the aberrant mRNAs produce truncated proteins that in some cases allow them to function in a dominant-negative manner. The aberrant transcripts do not represent intermediates of the normal splicing reaction, because they are found in the cytoplasm and are translated. The cellular abnormalities that lead to aberrant mRNA processing and possible defects in nonsense-mediated decay are not clear, but represent an exciting opportunity for future studies.

In summary, the data presented here are the first to demonstrate that a wide variety of cancer cells exhibit aberrant splicing of the DNMT3B gene, producing transcripts that encode truncated proteins lacking the C-terminal catalytic domain. These data support a model in which aberrations in mRNA splicing in cancer cells give rise to truncated DNMT3B proteins, resulting in changes in DNA methylation patterns and gene expression. The results suggest that the abnormal patterns of DNA methylation present in nearly all cancer cells may be regulated in part by the presence of catalytically-inactive DNMT3B proteins. Further work in which levels of aberrant DNMT3B transcripts and/or truncated DNMT3B proteins are varied within cancer cells may help to confirm this model. Future experiments could also address whether truncated DNMT3B proteins affect epigenetic modifications in addition to DNA methylation, such as histone alterations. Overall, this work supports growing evidence that aberrant gene splicing in cancer cells affects cellular phenotype.

These findings, and the use of inhibitors of aberrant DNMTSB transcripts in the treatment of cancer is described in detail in the following sections of this document. I. DNMT3B and Inhibitors of Aberrant DNMT3B Transcripts and Proteins A. DNMT3B

DNA (cytosine-5-)-methyltransferase 3B is a 770 to 853 amino acid protein (SEQ ID NO:2), the gene for which is located at 20ql 1.2. Transcripts range in size from just under 4100 bp to over 4300 bp. At least two transcriptional start points exist, and expression is controlled by different promoters (lacking typical TATA sequences, where one promoter contains a CpG-rich area near the transcription start site, and the other promoter is CpG-poor). It is expressed abundantly in ES cells, but is barely detectable in differentiated cells. Accession numbers for genomic sequences are NC_000020.9 and NT_028392.5.

The N-terminus is characterized by a PWWP domain. A central cysteine-rich region with homology to ATRX (XNP) is also found, along with a PHD domain and five C-terminal conserved catalytic domains functioning in the transmethylation reaction. It is known to co-localize with condensin and KIF4A on condensed chromosomes throughout mitosis. It also interacts with HDACl, HDA C2, HPl proteins, SUV39H1, and components of the histone methylation system as well as the ATP-dependent chromatin remodeling enzyme SMARC A5. Four different transcripts give rise to four distinct protein products:

NP__008823.1, NPJ787044.1, NP_787045.1 and NP_787046.1 The genomic sequence has introns located on chromosome 20 at positions 30,814,012-30,860,823 (numbering is according to www.ensembl.org; gene DNMT3B, OTTHUMG00000032226, the sequence of which is hereby incorporated by reference). Hybridizing nucleic acids, described below, will be modeled off the genomic sequence to target the introns and intron-exon boundaries, shown in FIGS. 7A-C.

The inventors amplified the cDNAs encoding the three DNA methyltransferase enzymes from several cancer cell lines using a high-fidelity polymerase. Although amplicons derived from the DNMTl and DNMT3A cDNAs were wild-type in sequence (data not shown), PCR amplification of DNMT3B cDNA from exon 9 to exon 13 produced the two expected amplification products (Products A and B in FIG. IA in Examples) as well as an unexpected amplicon (Product C in FIG. IA in Examples). Sequence analysis demonstrated that this novel transcript contained an aberrant splicing event from exon 9 to the 3' end of intron 10, resulting in an insertion of 94 base pairs that is normally part of intron 10, located just 5' to exon 11. The inventors designated this transcript DNMT3B7 (Genbank accession number DQ321787; FIG. IB in Examples).

The inventors looked at 25 established cancer cell lines derived from both hematopoietic malignancies (11 cell lines) as well as solid tumors (14 cell lines), and 30 primary acute leukemia samples (27 acute myeloid leukemia samples and 3 acute lymphoblastic leukemia samples) (Table 1 and FIG. 5 in Examples). DNMT3B transcripts involving aberrant splicing events at the 5' end of the gene could be detected in all of the samples tested, except in HepG2 and Alexander cells, derived from hepatocellular carcinomas. Alexander cells are known to express DNMT3B4, which encodes a catalytically-inactive DNMT3B isoform (Saito et al, 2002). All of the primary leukemia samples expressed a transcript containing aberrant splicing between exons 9 and 13 as originally observed, confirming that the expression of these novel mRNAs was not due to an artifact of in vitro culture. Notably, there was expression of at least one of the three wild-type DNMT3B transcripts in all of the tumor cell line-derived cDNAs as well as in all of the primary leukemia samples, in keeping with previous data that complete loss of DNMT3B activity is incompatible with viability (Li et al, 1992; Okano et al, 1999).

Most of the aberrantly- spliced DNMT3B transcripts contain sequences that are normally intronic and lack various exons, and all of them encode truncated DNMT3B proteins containing novel amino acids but lacking the catalytic C-terminus. Table 3 (in Examples) lists the properties of each aberrant transcript. The inventors noted alternative splicing of several 5' exons, including exon 5 (Xu et al, 1999). The 5' half of each transcript could be amplified using a primer derived from exon IA (data not shown), suggesting that the promoter originally identified for DNMT3B is used to generate the aberrant transcripts (Yanagisawa et al, 2002).

B. Antisense

Antisense methodology takes advantage of the fact that nucleic acids tend to pair with "complementary" sequences. By complementary, it is meant that polynucleotides are those which are capable of base-pairing or "hybridizing" according to the standard Watson-Crick complementarity rules. That is, the larger purines will base pair with the smaller pyrimidines to form combinations of guanine paired with cytosine (G:C) and adenine paired with either thymine (A:T) in the case of DNA, or adenine paired with uracil (A:U) in the case of RNA. Inclusion of less common bases such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others in hybridizing sequences does not interfere with pairing.

Targeting double-stranded (ds) DNA with polynucleotides leads to triple-helix formation; targeting RNA will lead to double-helix formation. Antisense polynucleotides, when introduced into a target cell, specifically bind to their target polynucleotide and interfere with transcription, RNA processing, transport, translation and/or stability. Antisense RNA constructs, or DNA encoding such antisense RNA' s, may be employed to inhibit gene transcription or translation or both within a host cell, either in vitro or in vivo, such as within a host animal, including a human subject. "Complementary," as that term is used herein, refers to the capacity for precise pairing between two nucleotides. For example, if a nucleotide at a certain position of a polynucleotide is capable of hydrogen bonding with a nucleotide at the same position of a DNA or RNA molecule, then the polynucleotide and the DNA or RNA are complementary to each other at that position. The polynucleotide and the DNA or RNA are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleotides that can hydrogen bond with each other. "Specifically hybridize" means that a particular sequence has a sufficient degree of complementarity or precise pairing with a DNA or RNA target sequence that stable and specific binding occurs between the polynucleotide and the DNA or RNA target. It is understood in the art that the sequence of an antisense compound need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable. Typically, for specific hybridization in vitro, moderate stringency conditions are used such that hybridization occurs between substantially similar nucleic acids, but not between dissimilar nucleic acids. In in vitro systems, stringency conditions are dependent upon time, temperature and salt concentration as can be readily determined by the skilled artisan (see, e.g., Sambrook et al, 1989). For in vivo antisense methods, the hybridization conditions consist of intracellular conditions which govern the hybridization of the antisense polynucleotide with the target sequence. An antisense compound specifically hybridizes to the target sequence when binding of the compound to the target DNA or RNA molecule interferes with the normal translation of the target DNA or RNA such that a functional gene product is not produced, and there is a sufficient degree of complementarity to avoid nonspecific binding. While antisense polynucleotides are one form of antisense compound, the present invention contemplates other oligomeric antisense compounds, including, but not limited to, polynucleotide mimetics, those containing modified backbones (which may be referred to herein as "modified internucleoside linkages"), and/or 3' and 5' terminal moieties that provide physiological stability or other types of stability. As defined herein, polynucleotides having modified backbones include those that retain a phosphorous atom in the backbone, as well as those that do not have a phosphorous atom in the backbone.

Modified polynucleotide backbones which are useful in the subject antisense polynucleotides include, for example, phosphorothioates, chiral phosphorofhioates, phosphorodithioates, phosphotriesters, amino alkylkphosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3^r-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, and boranophosphonates having normal 3'-5' linkages, 2'-5' linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'. Various salts, mixed salts and free acid forms are also included. References that teach the preparation of such modified backbone polynucleotides are provided, for example, in U.S. Patent 5,945,290, incorporated by reference.

Modified polynucleotide backbones that do not include a phosphorous atom therein may comprise short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages; siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene-containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂ component parts. Preparation of the polynucleotides listed above is described in U.S. Patent 5,945,290.

Other useful polynucleotide mimetics, which are useful in the subject antisense polynucleotides, comprise replacement of both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units with novel groups. One such oligomeric compound that has excellent hybridization properties is a peptide nucleic acid. See, e.g., Nielsen et al. (1991); and U.S. Patents 5,539,082; 5,714,331; and 5,719,262, incorporated by reference. In such peptide nucleic acid compounds, the sugar-backbone of a polynucleotide is replaced with an amide containing backbone, in particular with an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza-nitrogen atoms of the amide portion of the backbone.

Other useful modified polynucleotides are those having phosphorothioate backbones and polynucleotides with heteroatom backbones, and in particular --CH₂- NH-O-CH₂-, -CH₂-N(CH₃)-O-CH₂-, -CH₂-O-N(CH₃)-CH₂~, --CH₂- N(CH₃)~N(CH₃)~CH₂-, and ~O-N(CH₃)-CH₂~CH₂-, wherein the native phosphodiester backbone is represented as --0--P-O-CH₂-, as disclosed in U.S. Patent 5,489,677, and the amide backbones disclosed in U.S. Patent 5,602,240. Also useful are polynucleotides having morpholino backbone structures as taught in U.S. Patent 5,304,506. Each of the preceding patents is incorporated by reference.

Modified polynucleotides can also contain one or more substituted sugar moieties (which may be referred to herein as "modified sugar moieties"). Useful polynucleotides comprise one of the following at the 2' position: OH; F; O, S, N- alkyl; N-alkenyl; N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl, or alkynyl may be substituted or unsubstituted Ci to Ci₀ alkyl, or C₂ to Ci₀ alkenyl and alkynyl; 0(CH₂)O(CH₃); O(CH₂)O(CH₂)_nCH₃; O(CH₂)_nNH₂; or O(CH₂)_nCH₃ (where n = 1 to 10); Cl; Br; CNB; CF₃; OCF₃; NO₂; N₃; NH₂; heterocycloalkyl; heterocycloalkaryl; amino alkylamino; polyalkylamino; substituted silyl; an RNA cleaving group; a cholesterol group; a reporter group; an intercalator; a group for improving the pharmacokinetic properties of an polynucleotide; or a group for improving other substituents having similar properties. Polynucleotides can also have sugar mimetics such as cyclobutyls in place of the pentafuranosyl group. A particular modified sugar moiety is a 2'-O-methoxyethyl sugar moiety.

Other useful antisense compounds may include at least one nucleobase modification or substitution. As used herein, "unmodified" or "natural" nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases, such as 5-methylcytosine, 5- hydroxyrnethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocystine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil, 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo, particularly 5-bromo, 5-trifluromethyl and other 5- substitutes uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3- deazaadenine.

C. RNA Interference

RNA interference (also referred to as "RNA-mediated interference" or RNAi) is a mechanism by which gene expression can be reduced or eliminated. Double- stranded RNA (dsRNA) has been observed to mediate the reduction, which is a multi- step process. dsRNA activates post-transcriptional gene expression surveillance mechanisms that appear to function to defend cells from virus infection and transposon activity (Fire et al, 1998; Grishok et al, 2000; Ketting et al, 1999; Lin and Avery et al, 1999; Montgomery et al, 1998; Sharp and Zamore, 2000; Tabara et al, 1999). Activation of these mechanisms targets mature, dsRNA-complementary mRNA for destruction. RNAi offers major experimental advantages for study of gene function. These advantages include a very high specificity, ease of movement across cell membranes, and prolonged down-regulation of the targeted gene (Fire et al, 1998; Grishok et al, 2000; Ketting et al, 1999; Lin and Avery et al, 1999; Montgomery et al, 1998; Sharp et al, 1999; Sharp and Zamore, 2000; Tabara et al, 1999). It is generally accepted that RNAi acts post-transcriptionally, targeting RNA transcripts for degradation. It appears that both nuclear and cytoplasmic RNA can be targeted (Bosher and Labouesse, 2000).

1. siRNA siRNAs must be designed so that they are specific and effective in suppressing the expression of the genes of interest. Methods of selecting the target sequences, i.e., those sequences present in the gene or genes of interest to which the siRNAs will guide the degradative machinery, are directed to avoiding sequences that may interfere with the siRNA's guide function while including sequences that are specific to the gene or genes. Typically, siRNA target sequences of about 21 to 23 nucleotides in length are most effective. This length reflects the lengths of digestion products resulting from the processing of much longer RNAs as described above (Montgomery et al, 1998).

Several further modifications to siRNA sequences have been suggested in order to alter their stability or improve their effectiveness. It is suggested that synthetic complementary 21-mer RNAs having di-nucleotide overhangs (i.e., 19 complementary nucleotides + 3' non-complementary dimers) may provide the greatest level of suppression. These protocols primarily use a sequence of two (2'-deoxy) thymidine nucleotides as the di-nucleotide overhangs. These dinucleotide overhangs are often written as dTdT to distinguish them from the typical nucleotides incorporated into RNA. The literature has indicated that the use of dT overhangs is primarily motivated by the need to reduce the cost of the chemically synthesized

RNAs. It is also suggested that the dTdT overhangs might be more stable than UU overhangs, though the data available shows only a slight (< 20%) improvement of the dTdT overhang compared to an siRNA with a UU overhang.

In some embodiments of the invention, siRNA or candidate siRNA is directed to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more portions of the same target gene. In particular aspects of the present invention, there is disclosed an isolated RNA of from about 5 to about 20 nucleotides that mediates RNA interference of a target mRNA. In other non- limiting aspects, the RNA can inactivate a corresponding gene by transcriptional silencing. In certain embodiments, the RNA can be 5, 6, 7, 8, 9, 20, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more nucleotides in length. The RNA can correspond to, be identical to, or be complementary to any of SEQ ID NOs: 1-52. The isolated RNA can further comprise a terminal 3' hydroxyl group or a 5' phosphate group, or both. The isolated RNA can be an siRNA. The siRNA can be a single or double stranded RNA. In particular aspects, the 3' or 5' or both ends of the double stranded RNA comprises a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 or more nucleotide overhang. In certain embodiments, the nucleotide overhang is a 2 nucleotide overhang. The nucleotide overhang can include any combination of a thymine, uracil, adenine, guanine, or cytosine, or derivatives or analogues thereof. The nucleotide overhang in certain aspects is a 2 nucleotide overhang, where both nucleotides are thymine.

The isolated RNA can be made by any of methods known to those of skill in the art or discussed herein. In particular embodiments the isolated RNA is chemically synthesized or is an analog of a naturally occurring RNA. In other embodiments, the isolated RNA is formulated into a pharmaceutically acceptable composition.

The isolated RNA can also associate with a protein complex. In certain aspects, the isolated RNA is associated with or bound to a protein complex. In non- limiting embodiments, the protein complex is RNA-induced silencing complex (RISC).

In more particular aspects, the isolated RNA comprises a nucleotide sequence selected from the group consisting of any sequence identified herein, whether it is an shRNA or siRNA. Any embodiment discussed below as an siRNA may be implemented with any interfering RNA disclosed herein, such as an shRNA, and vice versa.

The inventors also contemplate analogs of the RNAs described throughout the specification. The analog can differ from the RNA by the addition, deletion, substitution or alteration of one or more nucleotides. Non-limiting examples of the different types of nucleotides that can be use with the present invention are described throughout the specification.

In yet another embodiment of the present invention there is provided a method of reducing expression of a target gene in a cell comprising obtaining at least one siRNA of 5-100 or more nucleotides in length and delivering the siRNA into the cell. The siRNA can be from about 10 to about 90, 20, to about 80, 30 to about 70, 40 to about 60, to about 50 nucleotides in length. In specific aspects, the siRNA is from about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 to about 20 nucleotides in length. The siRNAs may be directed to, be complementary to, or be identical to at least or at most 80%, 85, 90, 95, 96, 97, 98, 99, or 100% of any of SEQ ID NOs: 1-52. Delivery of the siRNA into a cell can be performed by any numerous ways that are known to a person of ordinary skill in the art and that are described throughout this specification. There are certain embodiments where at least two siRNAs are obtained and are subsequently delivered into the cell. Other aspects include obtaining a pool of siRNAs and delivering the pool into the cell. As noted above and throughout the specification, the siRNAs of the present invention can be made by many methods. In particular aspects, the siRNAs are chemically synthesized or are an analog of a naturally occurring siRNA. There are certain instances of the invention where the siRNA is isolated prior to its delivery into the cell. Isolating and purifying siRNAs are known in the art and are described throughout the specification. Isolating the siRNA can be done prior to or after delivery into the cell. In non-limiting embodiments, the cell can be comprised in an organism. The organism, in non- limiting examples, can be a human, dog, rat, mouse, pig, rabbit, or cow. The cell can be a human or non-human cell. In certain aspects, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, or more siRNA molecules are delivered into the cell. The siRNAs can be the same or different siRNAs with different target mRNAs.

In still another aspect of the present invention, there is provided a method of mediating RNA interference of mRNA of a gene in a cell or organism comprising (a) introducing RNA of from about 5 to about 20 nucleotides which targets the mRNA of the gene for degradation into the cell or organism and (b) maintaining the cell or organism under conditions under which degradation of the mRNA occurs, thereby mediating RNA interference of the mRNA of the gene in the cell or organism. The RNA can be a chemically synthesized RNA or an analog of naturally occurring RNA. The RNA can be an siRNA that is from about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, or more nucleotides in length. The gene of interest is the DNMT3B transcript, as discussed throughout the specification.

Another embodiment includes a method of mediating RNA interference of mRNA of a gene in a cell or organism in which RNA interference occurs, comprising introducing into the cell or organism RNA of from about 5 to about 20 nucleotides that mediates RNA interference of mRNA of the gene, thereby producing a cell or organism that contains the RNA; and maintaining the cell or organism that contains the RNA under conditions under which RNA interference occurs, thereby mediating RNA interference of mRNA of the gene in the cell or organism. As discussed throughout, in non-limiting examples, the RNA can be an siRNA that is from about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, or more nucleotides in length. The siRNA can be chemically synthesized or an analog of RNA that mediates RNA interference.

As discussed above, various embodiments of the present invention involve siRNAs that target DNMT3B transcripts. In certain embodiments, the siRNAs are rationally designed. siRNAs of the invention may be functional or hyperfunctional, meaning that these molecules are observed to (1) induce greater than 95% silencing of a specific target when they are transfected at subnanomolar concentrations (i.e., less than one nanomolar); and/or (2) induce functional (or better) levels of silencing for greater than 96 hours.

In various embodiments, an siRNA that targets DNMT3B transcripts is provided, wherein the siRNA is selected from the group consisting of various siRNA sequences targeting DNMT3B transcripts that are disclosed herein. In various embodiments, the siRNA sequence is selected from the group consisting of any nucleic acid sequence identified herein.

In various embodiments, siRNA comprising a sense region and an antisense region are provided, wherein (1) the sense region and the antisense region are at least 90% complementary to each other, wherein the sense region and the antisense region together form a duplex region comprising 18-30 base pairs and (2) the sense region comprises a sequence that is at least 90% identical to a DNMT3B sequence of that length. In various embodiments, the siRNA sequence is selected from the group consisting of any nucleic acid sequence identified herein. In various embodiments, an siRNA comprising a sense region and an antisense region is provided, wherein the sense region and the antisense region are at least 90% complementary to each other, wherein (1) the sense region and the antisense region together form a duplex region comprising 18-30 base pairs and (2) the sense region comprises a sequence that is identical to a contiguous stretch of at least 18 bases of the DNMT3B sequence disclosed herein. In various embodiments, the duplex region is 19-30 base pairs, and the sense region comprises a sequence that is identical to a sequence selected from the group consisting of any nucleic acid sequence identified herein.

In various embodiments, a pool of at least two different siRNAs is provided. In particular embodiments, the pool comprises at least or at most 2, 3, 4, 5, 6, 7, 8, 9, 10 or more different siRNAs targeting DNMT3B, as discussed above.

According to another embodiment, the present invention provides a pool of at least two siRNAs in the form of a kit or therapeutic reagent, wherein one strand of each of the siRNAs comprises a sequence that is at least 90% identical to a sequence of that length within a target mRNA. The opposite strand, the antisense strand, will preferably comprise a sequence that is at least 90% complementary to that length of region of the target mRNA. In some embodiments, one strand of each siRNA will comprise a sequence that is identical to a sequence that is contained in the target mRNA. In additional embodiments, each siRNA will be 19 base pairs in length, and one strand of each of the siRNAs will be 100% complementary to a portion of the target mRNA.

By increasing the number of siRNAs directed to a particular target using a pool or kit, one is able both to increase the likelihood that at least one siRNA with satisfactory functionality will be included, as well as to benefit from additive or synergistic effects. Further, when two or more siRNAs directed against a single gene do not have satisfactory levels of functionality alone, if combined, they may satisfactorily promote degradation of the target messenger RNA and successfully inhibit translation. By including multiple siRNAs in the system, not only is the probability of silencing increased, but the economics of operation are also improved when compared to adding different siRNAs sequentially. This effect is contrary to the conventional wisdom that the concurrent use of multiple siRNA will negatively impact gene silencing (e.g., Holen et al. (2003)..

In fact, when two siRNAs were pooled together, 54% of the pools of two siRNAs induced more than 95% gene silencing. Thus, a 2.5-fold increase in the percentage of functionality was achieved by randomly combining two siRNAs. Further, over 84% of pools containing two siRNAs induced more than 80% gene silencing.

In further embodiments, the kit is comprised of at least three siRNAs, wherein one strand of each siRNA comprises a sequence that is at least 90% identical to a sequence of that length in the target mRNA and the other strand comprises a sequence that is at least 90% complementary to the region of the target mRNA.

Additionally, there may be overhangs on either the sense strand or the antisense strand, and these overhangs may be at either the 5' end or the 3' end of either of the strands, for example there may be one or more overhangs of 1-6 bases. When overhangs are present, they are not included in the calculation of the number of base pairs. The two nucleotide 3' overhangs mimic natural siRNAs and are commonly used but are not essential. In some embodiments, the overhangs should consist of two nucleotides, most often dTdT or UU at the 3' end of the sense and antisense strand that are not complementary to the target sequence. The siRNAs may be produced by any method that is now known or that comes to be known for synthesizing double stranded RNA that one skilled in the art would appreciate would be useful in the present invention. Methods for synthesizing siRNAs are well known to persons skilled in the art and include, but are not limited to, any chemical synthesis of RNA oligonucleotides, ligation of shorter oligonucleotides, in vitro transcription of RNA oligonucleotides, the use of vectors for expression within cells, recombinant Dicer products and PCR products.

The siRNA duplexes within the aforementioned pools of siRNAs may correspond to overlapping sequences within a particular mRNA, or non-overlapping sequences of the mRNA. However, preferably they correspond to non-overlapping sequences. Further, each siRNA may be selected randomly, or one or more of the siRNA may be selected according to the criteria discussed above for maximizing the effectiveness of siRNA. There are a number of published patent application regarding the synthesis, use, manipulation, and design of siRNAs. These include, but are not limited to: 2007/0265438, 2007/0191294, 2007/0135372, 2007/0039072, 2006/0217327, 2006/0166913, 2006/142228, 2006/0134787, 2006/0122139, 2005/0233994, 2005/0214851, 2005/0164970, 2005/0089902, 2005/0060771, 2005/0020521, 2004/0248841, 2004/0241854, 2004/0235171, 2004/0224405, 2004/0162235, 2004/0146858, 2004/0115815, 2004/0091918, 2004/0029275, 2004/0023390, 2004/0018176, 2004/0005593, 2004/0002077, 2003/0198627, 2003/0166282, 2003/0125281, which are hereby incorporated by reference in their entireties. 2. shRNA Short hairpin RNA (shRNA) is a sequence of RNA that makes a tight hairpin turn that can be used to silence gene expression. shRNA is transcribed by RNA polymerase III. shRNA production in a mammalian cell can sometimes cause the cell to mount an interferon response as the cell seeks to defend itself from what it perceives as viral attack. Paddison et al. (2002) examined the importance of stem and loop length, sequence specificity, and presence of overhangs in determining shRNA activity. The authors found some interesting results. For example, they showed that the length of the stem and loop of functional shRNAs could vary. Stem lengths could range anywhere from 25 to 29 nt and loop size could range between 4 to 23 nt without affecting silencing activity. Presence of G-U mismatches between the 2 strands of the shRNA stem did not lead to a decrease in potency. Complementarity between the portion of the stem that binds to the target mRNA (antisense strand) and the mRNA, on the other hand, was shown to be critical. Single base mismatches between the antisense strand of the stem and the mRNA abolished silencing. It has been reported that presence of 2 nt 3 '-overhangs is critical for siRNA activity (Elbashir et al., 2001). Presence of overhangs on shRNAs, however, did not seem to be important. Some of the functional shRNAs that were either chemically synthesized or in vitro transcribed, for example, did not have predicted 3' overhangs.

II. Production of Inhibitory Nucleic Acids

A. Antisense

Oligonucleotide synthesis is performed according to standard methods. See, for example, Itakura and Riggs (1980). Oligonucleotide synthesis is well known to those of skill in the art. Various different mechanisms of oligonucleotide synthesis have been disclosed in for example, U.S. Patents 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is incorporated herein by reference. Basically, chemical synthesis can be achieved by the diester method, the triester method polynucleotides phosphorylase method and by solid-phase chemistry. These methods are discussed in further detail below. A number of other methods are disclosed in the identified published patent applications listed above.

1. Diester Method

The diester method was the first to be developed to a usable state, primarily by Khorana and co-workers. (Khorana, 1979). The basic step is the joining of two suitably protected nucleotides to form a dinucleotide containing a phosphodiester bond. The diester method is well established and has been used to synthesize oligonucleotide molecules (Khorana, 1979).

2. Triester Method

The main difference between the diester and triester methods is the presence in the latter of an extra protecting group on the phosphate atoms of the reactants and products (Itakura et al, 1975). The phosphate protecting group is usually a chlorophenyl group, which renders the nucleotides and polynucleotide intermediates soluble in organic solvents. Therefore purification's are done in chloroform solutions. Other improvements in the method include (i) the block coupling of trimers and larger oligomers, (ii) the extensive use of high-performance liquid chromatography for the purification of both intermediate and final products, and (iii) solid-phase synthesis. 3. Polynucleotide Phosphorylase Method

This is an enzymatic method of oligonucleotide synthesis that can be used to synthesize many useful oligonucleotides (Gillam et al, 1978; Gillam et al, 1979). Under controlled conditions, polynucleotide phosphorylase adds predominantly a single nucleotide to a short oligonucleotide. Chromatographic purification allows the desired single adduct to be obtained. At least a trimer is required to start the procedure, and this primer must be obtained by some other method. The polynucleotide phosphorylase method works and has the advantage that the procedures involved are familiar to most biochemists.

4. Solid-Phase Methods

Drawing on the technology developed for the solid-phase synthesis of polypeptides, it has been possible to attach the initial nucleotide to solid support material and proceed with the stepwise addition of nucleotides. AU mixing and washing steps are simplified, and the procedure becomes amenable to automation. These syntheses are now routinely carried out using automatic DNA and RNA synthesizers.

Phosphoramidite chemistry (Beaucage and Lyer, 1992) has become by far the most widely used coupling chemistry for the synthesis of oligonucleotides. As is well known to those skilled in the art, phosphoramidite synthesis of oligonucleotides involves activation of nucleoside phosphoramidite monomer precursors by reaction with an activating agent to form activated intermediates, followed by sequential addition of the activated intermediates to the growing oligonucleotide chain (generally anchored at one end to a suitable solid support) to form the oligonucleotide product.

B. Interfering RNAs dsRNA can be synthesized using well-described methods (Fire et al, 1998). Briefly, sense and antisense RNA are synthesized from DNA templates using T7 polymerase (MEGAscript, Ambion). After the synthesis is complete, the DNA template is digested with DNaseI and RNA purified by phenol/chloroform extraction and isopropanol precipitation. RNA size, purity and integrity are assayed on denaturing agarose gels. Sense and antisense RNA are diluted in potassium citrate buffer and annealed at 8O⁰C for 3 min to form dsRNA. As with the construction of DNA template libraries, additional procedures may be used to aid this time intensive procedure. The sum of the individual dsRNA species is designated as a "dsRNA library." The making of siRNAs has been mainly through direct chemical synthesis; through processing of longer, double stranded RNAs through exposure to Drosophila embryo lysates; or through an in vitro system derived from S2 cells. Use of cell lysates or in vitro processing may further involve the subsequent isolation of the short, 21-23 nucleotide siRNAs from the lysate, etc., making the process somewhat cumbersome and expensive. Chemical synthesis proceeds by making two single- stranded RNA-oligomers followed by the annealing of the two single stranded oligomers into a double-stranded RNA. Methods of chemical synthesis are diverse. Non-limiting examples are provided in U.S. Patents 5,889,136, 4,415,723, and 4,458,066, expressly incorporated herein by reference, and in Wincott et al. (1995). WO 99/32619 and WO 01/68836 suggest that RNA for use in siRNA may be chemically or enzymatically synthesized. Both of these texts are incorporated herein in their entirety by reference. The enzymatic synthesis contemplated in these references is by a cellular RNA polymerase or a bacteriophage RNA polymerase (e.g., T3, T7, SP6) via the use and production of an expression construct as is known in the art. For example, see U.S. Patent 5,795,715. The contemplated constructs provide templates that produce RNAs that contain nucleotide sequences identical to a portion of the target gene. The length of identical sequences provided by these references is at least 25 bases, and may be as many as 400 or more bases in length. An important aspect of this reference is that the authors contemplate digesting longer dsRNAs to 21-25mer lengths with the endogenous nuclease complex that converts long dsRNAs to siRNAs in vivo. They do not describe or present data for synthesizing and using in vitro transcribed 21-25mer dsRNAs. No distinction is made between the expected properties of chemical or enzymatically synthesized dsRNA in its use in RNA interference. Similarly, WO 00/44914, incorporated herein by reference, suggests that single strands of RNA can be produced enzymatically or by partial/total organic synthesis. Preferably, single-stranded RNA is enzymatically synthesized from the PCR products of a DNA template, preferably a cloned cDNA template and the RNA product is a complete transcript of the cDNA, which may comprise hundreds of nucleotides. WO 01/36646, incorporated herein by reference, places no limitation upon the manner in which the siRNA is synthesized, providing that the RNA may be synthesized in vitro or in vivo, using manual and/or automated procedures. This reference also provides that in vitro synthesis may be chemical or enzymatic, for example using cloned RNA polymerase {e.g., T3, T7, SP6) for transcription of the endogenous DNA (or cDNA) template, or a mixture of both. Again, no distinction in the desirable properties for use in RNA interference is made between chemically or enzymatically synthesized siRNA. U.S. Patent 5,795,715 reports the simultaneous transcription of two complementary DNA sequence strands in a single reaction mixture, wherein the two transcripts are immediately hybridized. The templates used are preferably of between 40 and 100 base pairs, and which is equipped at each end with a promoter sequence. The templates are preferably attached to a solid surface. After transcription with RNA polymerase, the resulting dsRNA fragments may be used for detecting and/or assaying nucleic acid target sequences.

Several groups have developed expression vectors that continually express siRNAs in stably transfected mammalian cells (Brumrnelkamp et al, 2002; Lee et al, 2002; Miyagishi and Taira, 2002; Paddison et al, 2002; Paul et al, 2002; Sui et al, 2002; Yu et al, 2002). Some of these plasmids are engineered to express shRNAs lacking poly (A) tails (Brummelkamp et al, 2002; Paddison et al, 2002; Paul et al, 2002; Yu et al, 2002). Transcription of shRNAs is initiated at a polymerase III (pol III) promoter and is believed to be terminated at position 2 of a 4-5-thymine transcription termination site. shRNAs are thought to fold into a stem-loop structure with 3' UU-overhangs. Subsequently, the ends of these shRNAs are processed, converting the shRNAs into ~21 nt siRNA-like molecules (Brummelkamp et al, 2002). The siRNA-like molecules can, in turn, bring about gene-specific silencing in the transfected mammalian cells.

III. Treatment of Cancers The present invention also involves the treatment of cancer. The types of cancer that may be treated, according to the present invention, is limited only by the involvement of DNMT3B. Thus, it is contemplated that a wide variety of tumors may be treated using these therapies, including cancers of the brain, lung, liver, spleen, kidney, lymph node, pancreas, small intestine, blood cells, colon, stomach, breast, endometrium, prostate, testicle, ovary, skin, head and neck, esophagus, bone marrow, blood or other tissue.

In many contexts, it is not necessary that the tumor cell be killed or induced to undergo normal cell death or "apoptosis." Rather, to accomplish a meaningful treatment, all that is required is that the tumor growth be slowed to some degree. It may be that the tumor growth is completely blocked, however, or that some tumor regression is achieved. Clinical terminology such as "remission" and "reduction of tumor" burden also are contemplated given their normal usage.

A. Formulations and Routes for Administration to Patients

Where clinical applications are contemplated, it will be necessary to prepare pharmaceutical compositions in a form appropriate for the intended application. Generally, this will entail preparing compositions that are essentially free of pyrogens, as well as other impurities that could be harmful to humans or animals. One will generally desire to employ appropriate salts and buffers to render delivery vectors stable and allow for uptake by target cells. Buffers also will be employed when recombinant cells are introduced into a patient. Aqueous compositions of the present invention comprise an effective amount of the vector to cells, dissolved or dispersed in a pharmaceutically acceptable carrier or aqueous medium. Such compositions also are referred to as inocula. The phrase "pharmaceutically or pharmacologically acceptable" refers to molecular entities and compositions that do not produce adverse, allergic, or other untoward reactions when administered to an animal or a human. As used herein, "pharmaceutically acceptable carrier" includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the vectors or cells of the present invention, its use in therapeutic compositions is contemplated. Supplementary active ingredients also can be incorporated into the compositions.

The active compositions of the present invention may include classic pharmaceutical preparations. Administration of these compositions according to the present invention will be via any common route so long as the target tissue is available via that route. This includes oral, nasal, buccal, rectal, vaginal or topical. Alternatively, administration may be by intradermal, subcutaneous, intramuscular, intraperitoneal or intravenous injection. Such compositions would normally be administered as pharmaceutically acceptable compositions, described supra. Of particular interest is direct intratumoral administration, perfusion of a tumor, or administration local or regional to a tumor, for example, in the local or regional vasculature or lymphatic system, or in a resected tumor bed (e.g., post-operative catheter). For practically any tumor, systemic delivery also is contemplated. This will prove especially important for attacking microscopic or metastatic cancer. In a different embodiment, ex vivo gene therapy is contemplated. This approach is particularly suited, although not limited, to treatment of bone marrow associated cancers. In an ex vivo embodiment, cells from the patient are removed and maintained outside the body for at least some period of time. During this period, a therapy is delivered, after which the cells are reintroduced into the patient; hopefully, any tumor cells in the sample have been killed.

Autologous bone marrow transplant (ABMT) is an example of ex vivo gene therapy. Basically, the notion behind ABMT is that the patient will serve as his or her own bone marrow donor. Thus, a normally lethal dose of irradiation or chemotherapeutic may be delivered to the patient to kill tumor cells, and the bone marrow repopulated with the patients own cells that have been maintained (and perhaps expanded) ex vivo. Because, bone marrow often is contaminated with tumor cells, it is desirable to purge the bone marrow of these cells.

Compounds or substances of the invention may also be administered as free base or pharmacologically acceptable salts which can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.

The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial or antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile- filtered solution thereof.

As used herein, "pharmaceutically acceptable carrier" includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.

For oral administration the polynucleotides of the present invention may be incorporated with excipients and used in the form of non-ingestible mouthwashes and dentifrices. A mouthwash may be prepared incorporating the active ingredient in the required amount in an appropriate solvent, such as a sodium borate solution (Dobell's Solution). Alternatively, the active ingredient may be incorporated into an antiseptic wash containing sodium borate, glycerin and potassium bicarbonate. The active ingredient may also be dispersed in dentifrices, including: gels, pastes, powders and slurries. The active ingredient may be added in a therapeutically effective amount to a paste dentifrice that may include water, binders, abrasives, flavoring agents, foaming agents, and humectants. The compositions of the present invention may be formulated in a neutral or salt form. Pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.

Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms such as injectable solutions, drug release capsules and the like. For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage could be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, "Remington's Pharmaceutical Sciences" 15th Edition, pages 1035-1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. Moreover, for human administration, preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biologies standards.

B. Delivery of Inhibitory Nucleic Acids

Any of a variety of methods may be employed to deliver inhibitory nucleic acids to cells and/or to enhance delivery. 1. Transfection Reagents

In some embodiments of the invention, one or more transfection reagents may be used to enhance intracellular delivery of a nucleic acid. A number of transfection reagents have been developed to enhance delivery of large DNA molecules (typically several hundred to thousands of base pairs in length), which differ significantly in terms of structure from small RNA species such as short RNAi agents and tRNAs. Nevertheless, certain of these transfection reagents mediate intracellular delivery of short RNAi agents and/or tRNAs.

A transfection reagent may contain one or more naturally occurring, synthetic, and/or derivatized lipids. Cationic and/or neutral lipids or mixtures thereof may be used. Many cationic lipids are amphiphilic molecules containing a positively charged polar headgroup linked (e.g., via an anchor) to a hydrophobic domain often comprising two alkyl chains. Structural variations include the length and degree of unsaturation of the alkyl chains (Elouhabi and Ruysschaert, 2005; Heyes et al, 2005). Cationic lipids include, for example, dimyristyl oxypropyl-3-dimethylhydroxy ethylamrnonium bromide (DMRIE), dilauryl oxypropyl-3- dimethylhydroxy ethylammonium bromide (DLRIE), N-[I -(2,3 -dioleoyloxyl) propal]-n,n,n- trimethylammonium sulfate (DOTAP), dioleoylphosphatidylethanolamine (DOPE), dipalmitoylethylphosphatidylcholine (DPEPC), dioleoylphosphatidylcholine (DOPC),, lipopolylysine, didoceyl methylammonium bromide (DDAB), 2,3-dioleoyloxy-N-[2- (sperminecarboxamidoet- N-di-methyl-1-propanaminium trifluoroacetate (DOSPA), cetyltrimethylammonium bromide (CTAB), beta.-[N,(N',Nl-dimethylaminoethane)- carbamoyl] cholesterol (DC-Cholesterol, also known as DC-Choi), (-alanyl cholesterol, N41-(2,3- dioleoyloxy)propyll-N, N, N-trimethylammonium chloride (DOTMA), N¹- cholesteryloxycarbonyl-3,7-diazanonane-l,9-diamine (CDAN), dipalmitoylphosphatidylethanolamine- 5-carboxyspermylamide (DPPES), dicaproylphosphatidylethanolamine (DCPE), 4-dimethylaminopyridine (DMAP), dimyristoylphosphatidylethanolamine (DMPE), dioleoylethylphosphocholine (DOEPC), dioctadecylamidoglycyl spermidine (DOGS), and N-[l-(2,3-dioleoyloxy)propyl]-N-[l - (2- hydroxyethyl) ]-N,N-dimethylammonium iodide (DOHME). Some representative cationic lipids include, but are not limited to, phosphatidylethanolamine, phospatidylcholine, glycero-3- ethylphosphatidyl- choline and fatty acyl esters thereof, di- and trimethyl ammonium propane, di- and tri-ethylarnmonium propane and fatty acyl esters thereof, e.g., N41-(2,3- dioleoyloxy)propyll-N,N-,N-trimethylammonium chloride (DOTMA).

A number of proprietary transfection reagents, most of which comprise one or more lipids, are available commercially from suppliers such as Invitrogen (Carlsbad, CA), Quiagen (Valencia, CA), Promega (Madison, WI), etc., may be used. Examples include Lipofectin®, Lipofec_tamine^® Lipofectamine 2000^®, Optifect^®, Cytofectin^®, Transfec_tace^® Transfectam®, Cytofectin^®, Oligofectamine^®, Effectene^®, etc. Other transfection reagents have been developed or optimized for delivery of siRNA to mammalian cells. Examples include, but are not limited to, XtremeGENE siRNA Transfection Reagent (Roche Applied Science), silMPORTER™ siRNA Transfection Reagent (Upstate), BLOCK-iT^Tm Technology (Invitrogen), RNAiFect Reagent (QIAGEN), GeneEraser™ siRNA Transfection Reagent (Stratagene), RiboJuice™ siRNA Transfection Reagent (Novagen), EXPRESS-si Delivery Kit (Genospectra, Inc.), HiPerFect Transfection Reagent (QIAGEN), siPORT™ siPORT^Tm lipid, siPORT™ amine (all from Ambion), DharmaFECT^Tm (Dharmacon), etc.

Cationic polymers may be used as transfection reagents in the present invention. Exemplary cationic polymers include polyethylenimine (PEI), polylysine (PLL), polyarginine (PLA), polyvinylpyrrolidone (PVP), chitosan, protamine, polyphosphates, polyphosphoesters (see U.S. Pub. No. 2002/0045263), poly(N- isopropylacrylamide), etc. Some of these polymers comprise primary amine groups, imine groups, guanidine groups, and/or imidazole groups. Some examples include poly(3-amino ester) (PAE) polymers (such as those described in U.S. Pub. No. 2002/0131951, which are hereby incorporated by reference). The cationic polymer may be linear or branched. Blends, copolymers, and modified cationic polymers can be used. In certain embodiments of the invention, a cationic polymer having a molecular weight of at least about 25 kD is used. In one embodiment, deacylated PEI is used. For example, residual N-acyl moieties can be removed from commercially available PEI, or PEI can be synthesized, e.g., by acid-catalyzed hydrolysis of poly(2-ethyl-2-oxazoline), to yield the pure polycations (Thomas et al, 2005). Dendrimers may be used as transfection reagents in the present invention. Dendrimers are polymers that are synthesized as approximately spherical structures typically ranging from 1 to about 20 nanometers in diameter having a center from which chains extend in a tree-like, branching morphology. Molecular weight and the number of terminal groups increase exponentially as a function of generation (the number of layers) of the polymer. Different types of dendrimers can be synthesized based on different core structures. Dendrimers suitable for use with the present invention include, but are not limited to, polyamidoamine (PAMAM), polypropylamine (POPAM), polyethylenimine, iptycene, aliphatic poly(ether), and/or aromatic polyether dendrimers (see U.S. Pat. No. 6,471,968 and Derfus et al. (2004); and Boas and Ueegaard (2004), all of which are hereby incorporated by reference).

Polysaccharides such as natural and synthetic cyclodextrins and derivatives and modified forms thereof are of use in certain embodiments of the invention (see, e.g., U.S. Pub. No. 2003/0157030 and Singh et al. (2002), which are hereby incorporated by reference).

In certain embodiments of the invention, the transfection reagent forms a complex with one or more nucleic acids. Typically the complex will contain a plurality of RNA molecules of one or more sequences. Components of the complex are physical associated. The physical association is mediated, for example, by non- covalent interactions such as electrostatic interactions, hydrophobic or hydrophilic interactions, hydrogen bonds, etc., rather than covalent interactions or high affinity specific binding interactions.

Standard transfection protocols can be used to deliver the nucleic acids to cells. Typically the cells are contacted with the transfection reagent, nanoparticles, and RNA (e.g., as a complex) for time periods ranging from minutes to hours. Protocols can be varied to optimize uptake.

2. Electroporation

In particular embodiments of the invention, an electric field is applied to effect intracellular delivery of nucleic acid. This procedure has long been known in the art

(Somiari et al, 2002; Nikoloff, 1995). While not wishing to be bound by any theory, the mechanism may involve temporary disruption of the cell membrane, allowing foreign bodies to enter, followed by resealing of the membrane. In the present invention electroporation is used to enhance the uptake of nucleic acids by cells. Standard electroporation protocols known in the art can be used. Parameters such as electric field strength, voltage, capacitance, duration and number of electric pulse(s), cell number of concentration, and the composition of the solution in which the cells are maintained during or after electroporation can be optimized for the delivery of nucleic acids of any particular size, shape, and composition and/or to achieve desired levels of cell viability. The methods of the invention are not limited to parameters that have been successfully used to enhance cell transfection in the art. Exemplary parameter ranges include, e.g., charging voltages of 100-500 volts and pulse lengths of 0.5-20 ms. 3. Microinjection

In other embodiments of the invention, cells are microinjected with a composition comprising a nucleic acid. An automated microinjection apparatus can be used (see, e.g., U.S. Pat. No. 5,976,826, which is hereby incorporated by reference).

4. Translocation Peptides In additional embodiments of the invention, the transfection reagent comprises a translocation peptide. The translocation peptide can be any of a variety of protein domains that are capable of inducing or enhancing translocation of an associated moiety into a eukaryotic cell, e.g., a mammalian cell. For example, presence of these domains within a larger protein enhances transport of the larger protein into cells. These domains are sometimes referred to as protein transduction domains (PTDs) or cell penetrating peptides (CPPs). Translocation peptides include peptides derived from various viruses, DNA binding segments of leucine zipper proteins, synthetic arginine-rich peptides, etc. (see, e.g., Langel, 2002). Exemplary translocation peptides that may be used in accordance with the present invention include, but are not limited to, the TAT49-57 peptide, referred to herein as "TAT peptide" from the HIV-I protein (Wadia et al, 2004; Won et al, 2005); longer peptides that comprise the TAT peptide; and a peptide from the Antennapedia protein that is known for this use. hi some embodiments, translocation-enhancing moieties of use include peptide- like molecules known as peptoid molecular transporters (U.S. Pat. Nos. 6,306,933 and 6,759,387, which are hereby incorporated by reference). Certain of these molecules contain contiguous, highly basic subunits, particularly subunits containing guanidyl or amidinyl moieties.

5. Endosome Escape Agents

In further embodiments of the invention, an endosome disrupting or fusogenic agent is administered to cells to enhance release of nucleic acids from the endosome.

Examples include fusogenic peptides, chloroquine, various viral components such as the N- terminal portion of the influenza virus HA protein (e.g., the HA2 peptide), adenoviral proteins or portions thereof, etc. (see, e.g., U.S. Pat. No. 6,274,322, which is hereby incorporated by reference). For example, in certain embodiments of the invention, the endosome disrupting agent is a peptide comprising the N-terminal 20 amino acids of the influenza HA protein. In some embodiments, the INF-7 peptide, which resembles the NH₂- terminal domain of the influenza virus hemagglutinin HA-2 submit, is used. In certain embodiments of the invention, an endosome escape agent or fusogenic peptide is conjugated to nucleic acid.

The membrane-lytic peptide mellitin may be used. In particular embodiments of the invention, an endosome disrupting agent is conjugated to a nucleic acid. In certain embodiments, a polypeptide having a first domain that serves as an endosome disrupting or fusogenic agent and a second domain that serves as a translocation peptide is employed. An agent that enhances release of endosomal contents or escape of an attached moiety from an internal cellular compartment such as an endosome may be referred to as an "endosomal escape agent."

6. Targeted Nucleic Acids In some embodiments, a nucleic acid comprises a targeting agent. A targeting agent is any agent that binds to a component present on or at the surface of a cell. Such a component is referred to as a "targeting agent." The targeting agent can be a polypeptide or portion thereof. The targeting agent can be a carbohydrate moiety. The targeting agent can be cell type specific, disease state specific, etc. For example, the targeting agent may be expressed in significant amounts mainly on one or a few cell types or in one or a few diseases. A cell type specific targeting agent for a particular cell type is expressed at levels at least 3 fold greater in that cell type than in a reference population of cells which may consist, for example, of a mixture containing cells from a plurality {e.g., 5-10 or more) of different tissues or organs in approximately equal amounts. In some embodiments, the cell type specific marker is present at levels at least 4-5 fold, between 5-10 fold, or more than 10-fold greater than its average expression in a reference population. Detection or measurement of a cell type specific targeting agent may make it possible to distinguish the cell type or types of interest from cells of many, most, or all other types.

Numerous targeting agent are known in the art. Typical targeting agent include cell surface proteins, e.g., receptors. Exemplary receptors include, but are not limited to, the transferrin receptor; LDL receptor; growth factor receptors such as epidermal growth factor receptor family members (e.g., EGFR, HER-2, HER-3, HER-4, HER-2/neu) or vascular endothelial growth factor receptors; cytokine receptors; cell adhesion molecules; integrins; selectins; CD molecules; etc. The marker can be a molecule that is present exclusively or in higher amounts on a malignant cell, e.g., a tumor antigen. For example, prostate-specific membrane antigen (PSMA) is expressed at the surface of prostate cancer cells. In certain embodiments of the invention the targeting agent is an endothelial cell marker. The targeting agent may be a polypeptide, peptide, nucleic acid, carbohydrate, glycoprotein, lipid, small molecule, etc. For example, the targeting agent may be a naturally occurring or synthetic ligand for a cell surface receptor, e.g., a growth factor, hormone, LDL, transferrin, etc. The targeting agent can be an antibody, which term is intended to include antibody fragments, single chain antibodies, etc. Synthetic binding proteins such as affibodies, etc., can be used. Peptide targeting agents can be identified, e.g., using procedures such as phage display. This widely used technique has been used to identify cell specific ligands for a variety of different cell types. In certain embodiments of the invention, the ligand is an aptamer that binds to a cell type specific marker. In general, an aptamer is an oligonucleotide (e.g., DNA or RNA or an analog thereof) that binds to a particular target, such as a polypeptide. Aptamers are typically derived from an in vitro evolution process such as SELEX, and methods for obtaining aptamers specific for a protein of interest are known in the art.

7. Plasmid and Viral Transformation

It is contemplated inhibitory nucleic acids may be provided to cells by contacting the cells with a vector that encodes or contains the inhibitory nucleic acid. In some embodiments of the invention, the vector is a plasmid, which is well known to those of skill in the art. Transfection or transformation of cells with a plasmid is well known to those of skill in the art. For example, it can be accomplished in vivo using lipid formulations, such as those discussed above. In other embodiments, the vector may be a viral vector. Viral vectors that can be used include, but are not limited to, adenovirus, adeno-associated virus, herpesvirus, lentivirus, retrovirus, and vaccinia virus. In specific embodiments, the viral vector is replication-deficient. In other embodiments, the viral vector is oncolytic. In this case, it is contemplated that about 10 to about 10¹ viral particles (cp) or plaque forming units (pfu) are administered to the patient either per administration (patient/administration) or per day (average daily dose). Such doses include about, at least about, or at most about 10⁹, 10¹⁰, 10¹¹, 10¹², or 10¹³ vp or pfu (or any range derivable therein), which may be the amount given per administration or per day or per treatment cycle. a. Adenoviral Infection

One method for delivery of inhibitory nucleic acid involves the use of an adenovirus expression vector. Although adenovirus vectors are known to have a low capacity for integration into genomic DNA, this feature is counterbalanced by the high efficiency of gene transfer afforded by these vectors. "Adenovirus expression vector" is meant to include those constructs containing adenovirus sequences sufficient to (a) support packaging of the construct and (b) to ultimately express a recombinant gene construct that has been cloned therein.

The vector comprises a genetically engineered form of adenovirus. Knowledge of the genetic organization or adenovirus, a 36 kb, linear, double-stranded DNA virus, allows substitution of large pieces of adenoviral DNA with foreign sequences up to 7 kb (Grunhaus and Horwitz, 1992). In contrast to retrovirus, the adenoviral infection of host cells does not result in chromosomal integration because adenoviral DNA can replicate in an episomal manner without potential genotoxicity. Also, adenoviruses are structurally stable, and no genome rearrangement has been detected after extensive amplification.

Adenovirus is particularly suitable for use as a gene transfer vector because of its mid-sized genome, ease of manipulation, high titer, wide target-cell range and high infectivity. Both ends of the viral genome contain 100-200 base pair inverted repeats (ITRs), which are cis elements necessary for viral DNA replication and packaging. The early (E) and late (L) regions of the genome contain different transcription units that are divided by the onset of viral DNA replication. The El region (ElA and ElB) encodes proteins responsible for the regulation of transcription of the viral genome and a few cellular genes. The expression of the E2 region (E2A and E2B) results in the synthesis of the proteins for viral DNA replication. These proteins are involved in DNA replication, late gene expression and host cell shut-off (Renan, 1990). The products of the late genes, including the majority of the viral capsid proteins, are expressed only after significant processing of a single primary transcript issued by the major late promoter (MLP). The MLP, (located at 16.8 m.u.) is particularly efficient during the late phase of infection, and all the mRNA's issued from this promoter possess a 5-tripartite leader (TPL) sequence which makes them some mRNA's for translation.

Generation and propagation of replication-deficient adenovirus vectors depend on a unique helper cell line, designated 293, which was transformed from human embryonic kidney cells by Ad5 DNA fragments and constitutively expresses El proteins (Graham et al., 1977). Since the E3 region is dispensable from the adenovirus genome (Jones and Shenk, 1978), the current adenovirus vectors, with the help of 293 cells, carry foreign DNA in either the El, the D3 or both regions (Graham and Prevec, 1991). In nature, adenovirus can package approximately 105% of the wild-type genome (Ghosh-Choudhury et al., 1987), providing capacity for about 2 extra kb of DNA. Combined with the approximately 5.5 kb of DNA that is replaceable in the El and E3 regions, the maximum capacity of the current adenovirus vector is under 7.5 kb, or about 15% of the total length of the vector. More than 80% of the adenovirus viral genome remains in the vector backbone. Helper cell lines may be derived from human cells such as human embryonic kidney cells, muscle cells, hematopoietic cells or other human embryonic mesenchymal or epithelial cells. Alternatively, the helper cells may be derived from the cells of other mammalian species that are permissive for human adenovirus. Such cells include, e.g., Vero cells or other monkey embryonic mesenchymal or epithelial cells. As stated above, the some helper cell line is 293.

Racher et al. (1995) have disclosed improved methods for culturing 293 cells and propagating adenovirus. In one format, natural cell aggregates are grown by inoculating individual cells into 1 liter siliconized spinner flasks (Techne, Cambridge, UK) containing 100-200 ml of medium. Following stirring at 40 rpm, the cell viability is estimated with trypan blue. In another format, Fibra-Cel microcarriers (Bibby Sterlin, Stone, UK) (5 g/1) is employed as follows. A cell inoculum, resuspended in 5 ml of medium, is added to the carrier (50 ml) in a 250 ml Erlenmeyer flask and left stationary, with occasional agitation, for 1 to 4 h. The medium is then replaced with 50 ml of fresh medium and shaking initiated. For virus production, cells are allowed to grow to about 80% confluence, after which time the medium is replaced (to 25% of the final volume) and adenovirus added at an MOI of 0.05. Cultures are left stationary overnight, following which the volume is increased to 100% and shaking commenced for another 72 h. The adenovirus vector may be replication defective, or at least conditionally defective, the nature of the adenovirus vector is not believed to be crucial to the successful practice of the invention. The adenovirus may be of any of the 42 different known serotypes or subgroups A-F. Adenovirus type 5 of subgroup C is the some starting material in order to obtain the conditional replication-defective adenovirus vector for use in the present invention. This is because Adenovirus type 5 is a human adenovirus about which a great deal of biochemical and genetic information is known, and it has historically been used for most constructions employing adenovirus as a vector. As stated above, the typical vector according to the present invention is replication defective and will not have an adenovirus El region. Thus, it will be most convenient to introduce the transforming construct at the position from which the El- coding sequences have been removed. However, the position of insertion of the construct within the adenovirus sequences is not critical to the invention. The polynucleotide encoding the gene of interest may also be inserted in lieu of the deleted E3 region in E3 replacement vectors as described by Karlsson et al (1986) or in the E4 region where a helper cell line or helper virus complements the E4 defect.

Adenovirus growth and manipulation is known to those of skill in the art, and exhibits broad host range in vitro and in vivo. This group of viruses can be obtained in high titers, e.g., 10⁹-10^u plaque-forming units per ml, and they are highly infective. The life cycle of adenovirus does not require integration into the host cell genome. The foreign genes delivered by adenovirus vectors are episomal and, therefore, have low genotoxicity to host cells. No side effects have been reported in studies of vaccination with wild-type adenovirus (Couch et al., 1963; Top et al., 1971), demonstrating their safety and therapeutic potential as in vivo gene transfer vectors.

Adenovirus vectors have been used in eukaryotic gene expression (Levrero et al, 1991; Gomez-Foix et al., 1992) and vaccine development (Grunhaus and Horwitz, 1992; Graham and Prevec, 1992). Animal studies have suggested that recombinant adenovirus could be used for gene therapy (Stratford-Perricaudet and Perricaudet, 1991; Stratford-Perricaudet et al, 1990; Rich et al, 1993). Studies in administering recombinant adenovirus to different tissues include trachea instillation (Rosenfeld et al, 1991; Rosenfeld et al, 1992), muscle injection (Ragot et al, 1993), peripheral intravenous injections (Herz and Gerard, 1993) and stereotactic inoculation into the brain (Le Gal La Salle et al, 1993). b. Retroviral Infection

The retroviruses are a group of single-stranded RNA viruses characterized by an ability to convert their RNA to double-stranded DNA in infected cells by a process of reverse- transcription (Coffin, 1990). The resulting DNA then stably integrates into cellular chromosomes as a provirus and directs synthesis of viral proteins. The integration results in the retention of the viral gene sequences in the recipient cell and its descendants. The retroviral genome contains three genes, gag, pol, and env that code for capsid proteins, polymerase enzyme, and envelope components, respectively. A sequence found upstream from the gag gene contains a signal for packaging of the genome into virions. Two long terminal repeat (LTR) sequences are present at the 5' and 3' ends of the viral genome. These contain strong promoter and enhancer sequences and are also required for integration in the host cell genome (Coffin, 1990).

In order to construct a retroviral vector, a nucleic acid encoding a gene of interest is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication-defective. In order to produce virions, a packaging cell line containing the gag, pol, and env genes but without the LTR and packaging components is constructed (Mann et al, 1983). When a recombinant plasmid containing a cDNA, together with the retroviral LTR and packaging sequences is introduced into this cell line (by calcium phosphate precipitation for example), the packaging sequence allows the RNA transcript of the recombinant plasmid to be packaged into viral particles, which are then secreted into the culture media (Nicolas and Rubinstein, 1988; Temin, 1986; Mann et al, 1983). The media containing the recombinant retroviruses is then collected, optionally concentrated, and used for gene transfer. Retroviral vectors are able to infect a broad variety of cell types. However, integration and stable expression require the division of host cells (Paskind et al., 1975).

Concern with the use of defective retrovirus vectors is the potential appearance of wild-type replication-competent virus in the packaging cells. This can result from recombination events in which the intact sequence from the recombinant virus inserts upstream from the gag, pol, env sequence integrated in the host cell genome. However, packaging cell lines are available that should greatly decrease the likelihood of recombination (Markowitz et al, 1988; Hersdorffer et al, 1990). c. AAV Infection

Adeno-associated virus (AAV) is an attractive vector system for use in the present invention as it has a high frequency of integration and it can infect nondividing cells, thus making it useful for delivery of genes into mammalian cells in tissue culture (Muzyczka, 1992). AAV has a broad host range for infectivity (Tratschin et al, 1984; Laughlin et al, 1986; Lebkowski et al, 1988; McLaughlin et al, 1988), which means it is applicable for use with the present invention. Details concerning the generation and use of rAAV vectors are described in U.S. Patent 5,139,941 and U.S. Patent 4,797,368, each incorporated herein by reference. Studies demonstrating the use of AAV in gene delivery include LaF ace et al.

(1988); Zhou et al (1993); Flotte et al (1993); and Walsh et al (1994). Recombinant AAV vectors have been used successfully for in vitro and in vivo transduction of marker genes (Kaplitt et al, 1994; Lebkowski et al, 1988; Samulski et al, 1989; Shelling and Smith, 1994; Yoder et al, 1994; Zhou et al, 1994; Hermonat and Muzyczka, 1984; Tratschin et al, 1985; McLaughlin et al, 1988) and genes involved in human diseases (Flotte et al, 1992; Ohi et al, 1990; Walsh et al, 1994; Wei et al, 1994). Recently, an AAV vector has been approved for phase I human trials for the treatment of cystic fibrosis.

AAV is a dependent parvovirus in that it requires coinfection with another virus (either adenovirus or a member of the herpes virus family) to undergo a productive infection in cultured cells (Muzyczka, 1992). In the absence of coinfection with helper virus, the wild-type AAV genome integrates through its ends into human chromosome 19 where it resides in a latent state as a provirus (Kotin et al, 1990; Samulski et al, 1991). rAAV, however, is not restricted to chromosome 19 for integration unless the AAV Rep protein is also expressed (Shelling and Smith, 1994). When a cell carrying an AAV provirus is superinfected with a helper virus, the AAV genome is "rescued" from the chromosome or from a recombinant plasmid, and a normal productive infection is established (Samulski et al, 1989; McLaughlin et al, 1988; Kotin et al, 1990; Muzyczka, 1992). Typically, recombinant AAV (rAAV) virus is made by cotransfecting a plasmid containing the gene of interest flanked by the two AAV terminal repeats (McLaughlin et al, 1988; Samulski et al, 1989; each incorporated herein by reference) and an expression plasmid containing the wild-type AAV coding sequences without the terminal repeats, for example pIM45 (McCarty et al, 1991; incorporated herein by reference). The cells are also infected or transfected with adenovirus or plasmids carrying the adenovirus genes required for AAV helper function. rAAV virus stocks made in such fashion are contaminated with adenovirus which must be physically separated from the rAAV particles (for example, by cesium chloride density centrifugation). Alternatively, adenovirus vectors containing the AAV coding regions or cell lines containing the AAV coding regions and some or all of the adenovirus helper genes could be used (Yang et al, 1994a; Clark et al, 1995). Cell lines carrying the rAAV DNA as an integrated pro virus can also be used (Flotte et al, 1995). d. Other Viral Vectors

Other viral vectors may be employed as constructs in the present invention. Vectors derived from viruses such as vaccinia virus (Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al, 1988) and herpesviruses may be employed. They offer several attractive features for various mammalian cells (Friedmann, 1989; Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al, 1988; Horwich et al, 1990).

A molecularly cloned strain of Venezuelan equine encephalitis (VEE) virus has been genetically refined as a replication competent vaccine vector for the expression of heterologous viral proteins (Davis et al, 1996). Studies have demonstrated that VEE infection stimulates potent CTL responses and has been suggested that VEE may be an extremely useful vector for immunizations (Caley et al, 1997). It is contemplated in the present invention, that VEE virus may be useful in targeting dendritic cells.

With the recent recognition of defective hepatitis B viruses, new insight was gained into the structure-function relationship of different viral sequences. In vitro studies showed that the virus could retain the ability for helper-dependent packaging and reverse transcription despite the deletion of up to 80% of its genome (Horwich et al, 1990). This suggested that large portions of the genome could be replaced with foreign genetic material. Chang et al (1991) recently introduced the chloramphenicol acetyltransferase (CAT) gene into duck hepatitis B virus genome in the place of the polymerase, surface, and pre-surface coding sequences. It was cotransfected with wild-type virus into an avian hepatoma cell line. Culture media containing high titers of the recombinant virus were used to infect primary duckling hepatocytes. Stable CAT gene expression was detected for at least 24 days after transfection (Chang et al. , 1991).

In still further embodiments of the present invention, the nucleic acid encoding a MDA-7 to be delivered is housed within an infective virus that has been engineered to express a specific binding ligand. Alternatively, the nucleic acid encoding the MDA-7 polypeptide to be delivered is housed within an infective virus that has been engineered to express an immunogen. The virus particle will thus bind specifically to the cognate receptors of the target cell and deliver the contents to the cell. A novel approach designed to allow specific targeting of retrovirus vectors was recently developed based on the chemical modification of a retrovirus by the chemical addition of lactose residues to the viral envelope. This modification can permit the specific infection of hepatocytes via sialoglycoprotein receptors.

For example, to targeting of recombinant retroviruses was designed in which biotinylated antibodies against a retroviral envelope protein and against a specific cell receptor were used. The antibodies were coupled via the biotin components by using streptavidin (Roux et al, 1989). Using antibodies against major histocompatibility complex class I and class II antigens, they demonstrated the infection of a variety of human cells that bore those surface antigens with an ecotropic virus in vitro (Roux et al, 1989).

8. Non- Viral Delivery

In addition to viral delivery of the inhibitory nucleic acid, the following are additional methods of recombinant gene delivery to a given host cell and are thus considered in the present invention. a. Lipid Mediated Transformation

In a further embodiment of the invention, the nucleic acid may be entrapped in a liposome or lipid formulation. Liposomes are vesicular structures characterized by a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh and Bachhawat, 1991). Also contemplated is a gene construct complexed with Lipofectamine (Gibco BRL).

Lipid-mediated nucleic acid delivery and expression of foreign DNA in vitro has been very successful (Nicolau and Sene, 1982; Fraley et al, 1979; Nicolau et al, 1987). Wong et al (1980) demonstrated the feasibility of lipid-mediated delivery and expression of foreign DNA in cultured chick embryo, HeLa and hepatoma cells.

Lipid based non-viral formulations provide an alternative to adenoviral gene therapies. Although many cell culture studies have documented lipid based non-viral gene transfer, systemic gene delivery via lipid based formulations has been limited. A major limitation of non- viral lipid based gene delivery is the toxicity of the cationic lipids that comprise the non-viral delivery vehicle. The in vivo toxicity of liposomes partially explains the discrepancy between in vitro and in vivo gene transfer results. Another factor contributing to this contradictory data is the difference in lipid vehicle stability in the presence and absence of serum proteins. The interaction between lipid vehicles and serum proteins has a dramatic impact on the stability characteristics of lipid vehicles (Yang and Huang, 1997). Cationic lipids attract and bind negatively charged serum proteins. Lipid vehicles associated with serum proteins are either dissolved or taken up by macrophages leading to their removal from circulation. Current in vivo lipid delivery methods use subcutaneous, intradermal, intratumoral, or intracranial injection to avoid the toxicity and stability problems associated with cationic lipids in the circulation. The interaction of lipid vehicles and plasma proteins is responsible for the disparity between the efficiency of in vitro (Feigner et al, 1987) and in vivo gene transfer (Zhu et al, 1993; Philip et al, 1993; Solodin et al, 1995; Liu et al, 1995; Thierry et al, 1995; Tsukamoto et al, 1995; Aksentijevich et al, 1996).

Recent advances in lipid formulations have improved the efficiency of gene transfer in vivo (Smyth-Templeton et al, 1997; WO 98/07408). A novel lipid formulation composed of an equimolar ratio of l,2-bis(oleoyloxy)-3-(trimethyl ammonio)propane (DOTAP) and cholesterol significantly enhances systemic in vivo gene transfer, approximately 150-fold. The DOTAP: cholesterol lipid formulation is said to form a unique structure termed a "sandwich liposome". This formulation is reported to "sandwich" DNA between an invaginated bi-layer or 'vase' structure. Beneficial characteristics of these lipid structures include a positive colloidal stabilization by cholesterol, two dimensional DNA packing and increased serum stability.

The production of lipid formulations often is accomplished by sonication or serial extrusion of liposomal mixtures after (I) reverse phase evaporation (II) dehydration-rehydration (III) detergent dialysis and (IV) thin film hydration. Once manufactured, lipid structures can be used to encapsulate compounds that are toxic (chemotherapeutics) or labile (nucleic acids) when in circulation. Lipid encapsulation has resulted in a lower toxicity and a longer serum half-life for such compounds (Gabizon et ai, 1990). Numerous disease treatments are using lipid based gene transfer strategies to enhance conventional or establish novel therapies, in particular immune therapies.

In certain embodiments of the invention, the lipid vehicle may be complexed with a hemagglutinating virus (HVJ). This has been shown to facilitate fusion with the cell membrane and promote cell entry of lipid-encapsulated DNA (Kaneda et al, 1989). In other embodiments, the lipid vehicle may be complexed or employed in conjunction with nuclear non-histone chromosomal proteins (HMG-I) (Kato et al., 1991). In yet further embodiments, the lipid vehicle may be complexed or employed in conjunction with both HVJ and HMG-I .

C. Combined Therapy with Immunotherapy, Traditional Chemo- or

Radiotherapy

One goal of current cancer research is to find ways to improve the efficacy of chemo- and radiotherapy, such as by combining traditional therapies with other anticancer treatments. For example, the herpes simplex-thymidine kinase (HS-tk) gene, when delivered to brain tumors by a retroviral vector system, successfully induced susceptibility to the antiviral agent gancyclovir (Culver et al, 1992). In the context of the present invention, it is contemplated that DNMT3B therapy could be used similarly in conjunction with chemotherapy, radiotherapy, immunotherapy, or other therapeutic intervention. To kill cells, inhibit cell growth, inhibit metastasis, inhibit angiogenesis or otherwise reverse or reduce the malignant phenotype of tumor cells, using the methods and compositions of the present invention, one would generally contact a "target" cell with an inhibitor according to the present invention and at least one other agent. These compositions would be provided in a combined amount effective to kill or inhibit proliferation of the cell. This process may involve contacting the cells with an inhibitor according to the present invention and the other agent(s) or treatment(s) at the same time. This may be achieved by contacting the cell with a single composition or pharmacological formulation that includes both modalities, or by contacting the cell with two distinct compositions or formulations, at the same time, wherein one composition includes an inhibitor according to the present invention and the other includes the secondary agent/therapy.

Alternatively, the inhibitor therapy treatment may precede or follow the other agent/treatment by intervals ranging from minutes to weeks. In embodiments where the other agent and the inhibitor are applied separately to the cell, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the agent/therapy and the inhibitor would still be able to exert an advantageously combined effect on the cell. In such instances, it is contemplated that one would contact the cell with both modalities within about 12-24 hours of each other and, more preferably, within about 6-12 hours of each other, with a delay time of only about 12 hours being most preferred. In some situations, it may be desirable to extend the time period for treatment significantly, however, where several days (2,

3, 4, 5, 6 or 7) to several weeks (1, 2, 3, 4, 5, 6, 7 or 8) lapse between the respective administrations.

It also is conceivable that more than one administration of either the inhibitor of DNMT3B or the other agent will be desired. Various combinations may be employed, where an inhibitor according to the present invention is "A" and the other agent is "B," as exemplified below.

A/B/A B/A/B B/B/A A/A/B B/A/A A/B/B B/B/B/A B/B/A/B

A/A/B/B A/B/A/B A/B/B/A B/B/A/A B/A/B/A B/A/A/B B/B/B/A A/A/A/B B/A/A/A A/B/A/A AJ AJB/ A A/B/B/B B/A/B/B

B/B/A/B

Other combinations are contemplated. Again, to achieve cell killing, both agents/therapies are delivered to a cell in a combined amount effective to kill the cell. 1. Chemotherapy

A wide variety of chemotherapeutic agents may be used in accordance with the present invention. The term "chemotherapy" refers to the use of drugs to treat cancer. A "chemotherapeutic agent" is used to connote a compound or composition that is administered in the treatment of cancer. These agents or drugs are categorized by their mode of activity within a cell, for example, whether and at what stage they affect the cell cycle. Alternatively, an agent may be characterized based on its ability to directly cross-link DNA, to intercalate into DNA, or to induce chromosomal and mitotic aberrations by affecting nucleic acid synthesis. Most chemotherapeutic agents fall into the following categories: alkylating agents, antimetabolites, antitumor antibiotics, mitotic inhibitors, and nitrosoureas.

i. Alkylating agents

Alkylating agents are drugs that directly interact with genomic DNA to prevent the cancer cell from proliferating. This category of chemotherapeutic drugs represents agents that affect all phases of the cell cycle, that is, they are not phase- specific. Alkylating agents can be implemented to treat chronic leukemia, non- Hodgkin's lymphoma, Hodgkin's disease, multiple myeloma, and particular cancers of the breast, lung, and ovary. They include: busulfan, chlorambucil, cisplatin, cyclophosphamide (cytoxan), dacarbazine, ifosfamide, mechlorethamine (mustargen), and melphalan.

a. Busulfan

Busulfan (also known as myleran) is a bifunctional alkylating agent. Busulfan is known chemically as 1 ,4-butanediol dimethanesulfonate.

Busulfan is not a structural analog of the nitrogen mustards. Busulfan is available in tablet form for oral administration. Each scored tablet contains 2 mg busulfan and the inactive ingredients magnesium stearate and sodium chloride.

Busulfan is indicated for the palliative treatment of chronic myelogenous (myeloid, myelocytic, granulocytic) leukemia. Although not curative, busulfan reduces the total granulocyte mass, relieves symptoms of the disease, and improves the clinical state of the patient. Approximately 90% of adults with previously untreated chronic myelogenous leukemia will obtain hematologic remission with regression or stabilization of organomegaly following the use of busulfan. It has been shown to be superior to splenic irradiation with respect to survival times and maintenance of hemoglobin levels, and to be equivalent to irradiation at controlling splenomegaly.

b. Chlorambucil

Chlorambucil (also known as leukeran) is a bifunctional alkylating agent of the nitrogen mustard type that has been found active against selected human neoplastic diseases. Chlorambucil is known chemically as 4-[bis(2-chlorethyl)amino] benzenebutanoic acid. Chlorambucil is available in tablet form for oral administration. It is rapidly and completely absorbed from the gastrointestinal tract. After single oral doses of 0.6-1.2 mg/kg, peak plasma chlorambucil levels are reached within one hour and the terminal half-life of the parent drug is estimated at 1.5 hours. 0.1 to 0.2 mg/kg/day or 3 to 6 mg/m²/day or alternatively 0.4 mg/kg may be used for antineoplastic treatment. Treatment regimes are well know to those of skill in the art and can be found in the "Physicians Desk Reference" and in "Remington's Pharmaceutical Sciences" referenced herein.

Chlorambucil is indicated in the treatment of chronic lymphatic (lymphocytic) leukemia, malignant lymphomas including lymphosarcoma, giant follicular lymphoma and Hodgkin's disease. It is not curative in any of these disorders but may produce clinically useful palliation. Thus, it can be used in combination with troglitazone in the treatment of cancer.

c. Cisplatin Cisplatin has been widely used to treat cancers such as metastatic testicular or ovarian carcinoma, advanced bladder cancer, head or neck cancer, cervical cancer, lung cancer or other tumors. Cisplatin can be used alone or in combination with other agents, with efficacious doses used in clinical applications of 15-20 mg/m for 5 days every three weeks for a total of three courses. Exemplary doses may be 0.50 mg/m , 1.0 mg/m², 1.50 mg/m², 1.75 mg/m², 2.0 mg/m², 3.0 mg/m² , 4.0 mg/m², 5.0 mg/m² , 10 mg/m². Of course, all of these dosages are exemplary, and any dosage in-between these points is also expected to be of use in the invention.

Cisplatin is not absorbed orally and must therefore be delivered via injection intravenously, subcutaneously, intratumorally or intraperitoneally. d. Cyclophosphamide

Cyclophosphamide is 2H-l,3,2-Oxazaphosphorin-2-amine, iV,7V-bis(2- chloroethyl)tetrahydro-, 2-oxide, monohydrate; termed Cytoxan available from Mead Johnson; and Neosar available from Adria. Cyclophosphamide is prepared by condensing 3-amino-l-propanol with vV,iV-bis(2-chlorethyl) phosphoramidic dichloride [(C1CH₂CH₂)₂N~POC1₂] in dioxane solution under the catalytic influence of triethylamine. The condensation is double, involving both the hydroxyl and the amino groups, thus effecting the cyclization. Unlike other β-chloroethylamino alkylators, it does not cyclize readily to the active ethyleneimonium form until activated by hepatic enzymes. Thus, the substance is stable in the gastrointestinal tract, tolerated well and effective by the oral and parental routes and does not cause local vesication, necrosis, phlebitis or even pain.

Suitable doses for adults include, orally, 1 to 5 mg/kg/day (usually in combination), depending upon gastrointestinal tolerance; or 1 to 2 mg/kg/day; intravenously, initially 40 to 50 mg/kg in divided doses over a period of 2 to 5 days or 10 to 15 mg/kg every 7 to 10 days or 3 to 5 mg/kg twice a week or 1.5 to 3 mg/kg/day . A dose 250 mg/kg/day may be administered as an antineoplastic. Because of gastrointestinal adverse effects, the intravenous route is preferred for loading. During maintenance, a leukocyte count of 3000 to 4000/mm³ usually is desired. The drug also sometimes is administered intramuscularly, by infiltration or into body cavities. It is available in dosage forms for injection of 100, 200 and 500 mg, and tablets of 25 and 50 mg the skilled artisan is referred to "Remington's Pharmaceutical Sciences" 15th Edition, chapter 61, incorporate herein as a reference, for details on doses for administration.

e. Melphalan

Melphalan, also known as alkeran, L-phenylalanine mustard, phenylalanine mustard, L-PAM, or L-sarcolysin, is a phenylalanine derivative of nitrogen mustard. Melphalan is a bifunctional alkylating agent which is active against selective human neoplastic diseases. It is known chemically as 4-[bis(2-chloroethyl)amino]-L- phenylalanine.

Melphalan is the active L-isomer of the compound and was first synthesized in 1953 by Bergel and Stock; the D-isomer, known as medphalan, is less active against certain animal tumors, and the dose needed to produce effects on chromosomes is larger than that required with the L-isomer. The racemic (DL-) form is known as merphalan or sarcolysin. Melphalan is insoluble in water and has a pKai of -2.1. Melphalan is available in tablet form for oral administration and has been used to treat multiple myeloma.

Available evidence suggests that about one third to one half of the patients with multiple myeloma show a favorable response to oral administration of the drug.

Melphalan has been used in the treatment of epithelial ovarian carcinoma. One commonly employed regimen for the treatment of ovarian carcinoma has been to administer melphalan at a dose of 0.2 mg/kg daily for five days as a single course. Courses are repeated every four to five weeks depending upon hematologic tolerance (Smith and Rutledge, 1975; Young et al, 1978). Alternatively the dose of melphalan used could be as low as 0.05 mg/kg/day or as high as 3 mg/kg/day or any dose in between these doses or above these doses. Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject

ii. Antimetabolites Antimetabolites disrupt DNA and RNA synthesis. Unlike alkylating agents, they specifically influence the cell cycle during S phase. They have been used to combat chronic leukemias in addition to tumors of breast, ovary and the gastrointestinal tract. Antimetabolites include 5-fluorouracil (5-FU), cytarabine (Ara- C), fludarabine, gemcitabine, and methotrexate. 5-Fluorouracil (5-FU) has the chemical name of 5-fluoro-2,4(lH,3H)- pyrimidinedione. Its mechanism of action is thought to be by blocking the methylation reaction of deoxyuridylic acid to thymidylic acid. Thus, 5-FU interferes with the syntheisis of deoxyribonucleic acid (DNA) and to a lesser extent inhibits the formation of ribonucleic acid (RNA). Since DNA and RNA are essential for cell division and proliferation, it is thought that the effect of 5-FU is to create a thymidine deficiency leading to cell death. Thus, the effect of 5-FU is found in cells that rapidly divide, a characteristic of metastatic cancers. iii. Antitumor Antibiotics

Antitumor antibiotics have both antimicrobial and cytotoxic activity. These drugs also interfere with DNA by chemically inhibiting enzymes and mitosis or altering cellular membranes. These agents are not phase specific so they work in all phases of the cell cycle. Thus, they are widely used for a variety of cancers. Examples of antitumor antibiotics include bleomycin, dactinomycin, daunorubicin, doxorubicin

(adriamycin), and idarubicin, some of which are discussed in more detail below.

Widely used in clinical setting for the treatment of neoplasms these compounds are administered through bolus injections intravenously at doses ranging from 25-75 mg/m² at 21 day intervals for adriamycin, to 35-100 mg/m² for etoposide intravenously or orally.

a. Doxorubicin

Doxorubicin hydrochloride, 5,12-Naphthacenedione, (8s-czV)-10-[(3-ammo- 2,3,6-trideoxy-a-L-lyxo-hexopyranosyl)oxy]-7,8,9, 10-tetrahydro-6,8, 11 -trihydroxy-8- (hydroxyacetyl)- 1 -methoxy-hydrochloride (hydroxydaunorubicin hydrochloride, adriamycin) is used in a wide antineoplastic spectrum. It binds to DNA and inhibits nucleic acid synthesis, inhibits mitosis and promotes chromosomal aberrations.

Administered alone, it is the drug of first choice for the treatment of thyroid adenoma and primary hepatocellular carcinoma. It is a component of 31 first-choice combinations for the treatment of ovarian, endometrial and breast tumors, bronchogenic oat-cell carcinoma, non-small cell lung carcinoma, gastric adenocarcinoma, retinoblastoma, neuroblastoma, mycosis fungoides, pancreatic carcinoma, prostatic carcinoma, bladder carcinoma, myeloma, diffuse histiocytic lymphoma, Wilms' tumor, Hodgkin's disease, adrenal tumors, osteogenic sarcoma soft tissue sarcoma, Ewing's sarcoma, rhabdomyosarcoma and acute lymphocytic leukemia. It is an alternative drug for the treatment of islet cell, cervical, testicular and adrenocortical cancers. It is also an immunosuppressant.

Doxorubicin is absorbed poorly and must be administered intravenously. The pharmacokinetics are multicompartmental. Distribution phases have half-lives of 12 minutes and 3.3 hr. The elimination half-life is about 30 hr. Forty to 50% is secreted into the bile. Most of the remainder is metabolized in the liver, partly to an active metabolite (doxorubicinol), but a few percent is excreted into the urine. In the presence of liver impairment, the dose should be reduced. Appropriate doses are, intravenous, adult, 60 to 75 mg/m 2 at 21 -day intervals or 25 to 30 mg/m² on each of 2 or 3 successive days repeated at 3- or 4-wk intervals or 20 mg/m² once a week. The lowest dose should be used in elderly patients, when there is prior bone-marrow depression caused by prior chemotherapy or neoplastic marrow invasion, or when the drug is combined with other myelopoietic suppressant drugs. The dose should be reduced by 50% if the serum bilirubin lies between 1.2 and 3 mg/dL and by 75% if above 3 mg/dL. The lifetime total dose should not exceed 550 mg/m² in patients with normal heart function and 400 mg/m² in persons having received mediastinal irradiation. Alternatively, 30 mg/m on each of 3 consecutive days, repeated every 4 wk. Exemplary doses may be 10 mg/m², 20 mg/m², 30 mg/m², 50 mg/m², 100 mg/m², 150 mg/m², 175 mg/m², 200 mg/m², 225 mg/m², 250 mg/m², 275 mg/m², 300 mg/m², 350 mg/m², 400 mg/m², 425 mg/m², 450 mg/m², 475 mg/m², 500 mg/m². Of course, all of these dosages are exemplary, and any dosage in- between these points is also expected to be of use in the invention.

b. Daunorubicin

Daunorubicin hydrochloride, 5,12-Naphthacenedione, (8S-cw)-8-acetyl-10- [(3-amino-2,3,6-trideoxy-a-L-lyxo-hexanopyr anosyl)oxy]-7, 8,9,10-tetrahydro-6,8,l l- trihydroxy-10-methoxy-, hydrochloride; also termed cerubidine and available from Wyeth. Daunorubicin intercalates into DNA, blocks DNA-directed RNA polymerase and inhibits DNA synthesis. It can prevent cell division in doses that do not interfere with nucleic acid synthesis.

In combination with other drugs it is included in the first-choice chemotherapy of acute myelocytic leukemia in adults (for induction of remission), acute lymphocytic leukemia and the acute phase of chronic myelocytic leukemia. Oral absorption is poor, and it must be given intravenously. The half-life of distribution is 45 minutes and of elimination, about 19 hr. The half-life of its active metabolite, daunorubicinol, is about 27 hr. Daunorubicin is metabolized mostly in the liver and also secreted into the bile (ca 40%). Dosage must be reduced in liver or renal insufficiencies.

Suitable doses are (base equivalent), intravenous adult, younger than 60 yr. 45 mg/m /day (30 mg/m for patients older than 60 yr.) for 1, 2 or 3 days every 3 or 4 wk or 0.8 mg/kg/day for 3 to 6 days every 3 or 4 wk; no more than 550 mg/m² should be given in a lifetime, except only 450 mg/m² if there has been chest irradiation; children, 25 mg/m once a week unless the age is less than 2 yr. or the body surface less than 0.5 m, in which case the weight-based adult schedule is used. It is available in injectable dosage forms (base equivalent) 20 mg (as the base equivalent to 21.4 mg of the hydrochloride). Exemplary doses may be 10 mg/m², 20 mg/m², 30 mg/m², 50 mg/m², 100 mg/m², 150 mg/m², 175 mg/m², 200 mg/m², 225 mg/m², 250 mg/m², 275 mg/m², 300 mg/m², 350 mg/m², 400 mg/m², 425 mg/m², 450 mg/m², 475 mg/m², 500 mg/m . Of course, all of these dosages are exemplary, and any dosage in-between these points is also expected to be of use in the invention.

c. Mitomycin

Mitomycin (also known as mutaniycin and/or mitomycin-C) is an antibiotic isolated from the broth of Streptomyces caespitosus which has been shown to have antitumor activity. The compound is heat stable, has a high melting point, and is freely soluble in organic solvents. Mitomycin selectively inhibits the synthesis of DNA. The guanine and cytosine content correlates with the degree of mitomycin-induced cross-linking. At high concentrations of the drug, cellular RNA and protein synthesis are also suppressed.

In humans, mitomycin is rapidly cleared from the serum after intravenous administration. Time required to reduce the serum concentration by 50% after a 30 mg. bolus injection is 17 minutes. After injection of 30 mg, 20 mg, or 10 mg I.V., the maximal serum concentrations were 2.4 mg/ml, 1.7 mg/ml, and 0.52 mg/ml, respectively. Clearance is effected primarily by metabolism in the liver, but metabolism occurs in other tissues as well. The rate of clearance is inversely proportional to the maximal serum concentration because, it is thought, of saturation of the degradative pathways. Approximately 10% of a dose of mitomycin is excreted unchanged in the urine. Since metabolic pathways are saturated at relatively low doses, the percent of a dose excreted in urine increases with increasing dose. In children, excretion of intravenously administered mitomycin is similar. d. Actinomycin D

Actinomycin D (Dactinomycin) [50-76-0]; C₆₂H₈₆N₁₂Oi₆ (1255.43) is an antineoplastic drag that inhibits DNA-dependent RNA polymerase. It is a component of first-choice combinations for treatment of choriocarcinoma, embryonal rhabdomyosarcoma, testicular tumor and Wilms' tumor. Tumors that fail to respond to systemic treatment sometimes respond to local perfusion. Dactinomycin potentiates radiotherapy. It is a secondary (efferent) immunosuppressive.

Actinomycin D is used in combination with primary surgery, radiotherapy, and other drags, particularly vincristine and cyclophosphamide. Antineoplastic activity has also been noted in Ewing's tumor, Kaposi's sarcoma, and soft-tissue sarcomas. Dactinomycin can be effective in women with advanced cases of choriocarcinoma. It also produces consistent responses in combination with chlorambucil and methotrexate in patients with metastatic testicular carcinomas. A response may sometimes be observed in patients with Hodgkin's disease and non- Hodgkin's lymphomas. Dactinomycin has also been used to inhibit immunological responses, particularly the rejection of renal transplants.

Half of the dose is excreted intact into the bile and 10% into the urine; the half-life is about 36 hr. The drag does not pass the blood-brain barrier. Actinomycin D is supplied as a lyophilized powder (0/5 mg in each vial). The usual daily dose is 10 to 15 mg/kg; this is given intravenously for 5 days; if no manifestations of toxicity are encountered, additional courses may be given at intervals of 3 to 4 weeks. Daily injections of 100 to 400 mg have been given to children for 10 to 14 days; in other regimens, 3 to 6 mg/kg, for a total of 125 mg/kg, and weekly maintenance doses of 7.5 mg/kg have been used. Although it is safer to administer the drug into the tubing of an intravenous infusion, direct intravenous injections have been given, with the precaution of discarding the needle used to withdraw the drag from the vial in order to avoid subcutaneous reaction. Exemplary doses may be 100 mg/m , 150 mg/m , 175 mg/m², 200 mg/m², 225 mg/m², 250 mg/m², 275 mg/m², 300 mg/m², 350 mg/m², 400 mg/m , 425 mg/m , 450 mg/m , 475 mg/m , 500 mg/m . Of course, all of these dosages are exemplary, and any dosage in-between these points is also expected to be of use in the invention. e. Bleomycin

Bleomycin is a mixture of cytotoxic glycopeptide antibiotics isolated from a strain of Streptomyces verticillus. Although the exact mechanism of action of bleomycin is unknown, available evidence would seem to indicate that the main mode of action is the inhibition of DNA synthesis with some evidence of lesser inhibition of

RNA and protein synthesis.

In mice, high concentrations of bleomycin are found in the skin, lungs, kidneys, peritoneum, and lymphatics. Tumor cells of the skin and lungs have been found to have high concentrations of bleomycin in contrast to the low concentrations found in hematopoietic tissue. The low concentrations of bleomycin found in bone marrow may be related to high levels of bleomycin degradative enzymes found in that tissue.

In patients with a creatinine clearance of >35 ml per minute, the serum or plasma terminal elimination half-life of bleomycin is approximately 115 minutes. In patients with a creatinine clearance of <35 mL per minute, the plasma or serum terminal elimination half-life increases exponentially as the creatinine clearance decreases. In humans, 60% to 70% of an administered dose is recovered in the urine as active bleomycin. Bleomycin may be given by the intramuscular, intravenous, or subcutaneous routes. It is freely soluble in water. Bleomycin should be considered a palliative treatment. It has been shown to be useful in the management of the following neoplasms either as a single agent or in proven combinations with other approved chemotherapeutic agents in squamous cell carcinoma such as head and neck (including mouth, tongue, tonsil, nasopharynx, oropharynx, sinus, palate, lip, buccal mucosa, gingiva, epiglottis, larynx), skin, penis, cervix, and vulva. It has also been used in the treatment of lymphomas and testicular carcinoma.

Because of the possibility of an anaphylactoid reaction, lymphoma patients should be treated with two units or less for the first two doses. If no acute reaction occurs, then the regular dosage schedule may be followed. Improvement of Hodgkin's Disease and testicular tumors is prompt and noted within 2 weeks. If no improvement is seen by this time, improvement is unlikely. Squamous cell cancers respond more slowly, sometimes requiring as long as 3 weeks before any improvement is noted. iv. Mitotic Inhibitors

Mitotic inhibitors include plant alkaloids and other natural agents that can inhibit either protein synthesis required for cell division or mitosis. They operate during a specific phase during the cell cycle. Mitotic inhibitors comprise docetaxel, etoposide (VP 16), paclitaxel, taxol, taxotere, vinblastine, vincristine, and vinorelbine.

a. Etoposide (VP16)

VP 16 is also known as etoposide and is used primarily for treatment of testicular tumors, in combination with bleomycin and cisplatin, and in combination with cisplatin for small-cell carcinoma of the lung. It is also active against non- Hodgkin's lymphomas, acute non-lymphocytic leukemia, carcinoma of the breast, and Kaposi's sarcoma associated with acquired immunodeficiency syndrome (AIDS).

VP 16 is available as a solution (20 mg/ml) for intravenous administration and as 50-mg, liquid-filled capsules for oral use. For small-cell carcinoma of the lung, the intravenous dose (in combination therapy) can be as much as 100 mg/m² or as little as 2 mg/ m², and routinely 35 mg/m²/day for 4 days, to 50 mg/m²/day for 5 days have also been used. When given orally, the dose should be doubled. Hence the doses for small cell lung carcinoma may be as high as 200-250 mg/m². The intravenous dose for testicular cancer (in combination therapy) is 50 to 100 mg/m² daily for 5 days, or 100 mg/m² on alternate days, for three doses. Cycles of therapy are usually repeated every 3 to 4 weeks. The drug should be administered slowly during a 30- to 60- minute infusion in order to avoid hypotension and bronchospasm, which are probably due to the solvents used in the formulation.

b. Taxol

Taxol is an experimental antimitotic agent, isolated from the bark of the ash tree, Taxus brevifolia. It binds to tubulin (at a site distinct from that used by the vinca alkaloids) and promotes the assembly of microtubules. Taxol is currently being evaluated clinically; it has activity against malignant melanoma and carcinoma of the ovary. Maximal doses are 30 mg/m per day for 5 days or 210 to 250 mg/m given once every 3 weeks. Of course, all of these dosages are exemplary, and any dosage in- between these points is also expected to be of use in the invention. c. Vinblastine

Vinblastine is another example of a plant alkyloid that can be used in combination with DNM3B inhibitors for the treatment of cancer and precancer. When cells are incubated with vinblastine, dissolution of the microtubules occurs. Unpredictable absorption has been reported after oral administration of vinblastine. At the usual clinical doses the peak concentration of each drug in plasma is approximately 0.4 mM. Vinblastine bind to plasma proteins. It is extensively concentrated in platelets and to a lesser extent in leukocytes and erythrocytes.

After intravenous injection, vinblastine has a multiphasic pattern of clearance from the plasma; after distribution, drug disappears from plasma with half-lives of approximately 1 and 20 hours. Vinblastine is metabolized in the liver to biologically activate derivative desacetylvinblastine. Approximately 15% of an administered dose is detected intact in the urine, and about 10% is recovered in the feces after biliary excretion. Doses should be reduced in patients with hepatic dysfunction. At least a 50% reduction in dosage is indicated if the concentration of bilirubin in plasma is greater than 3 mg/dl (about 50 mM).

Vinblastine sulfate is available in preparations for injection. The drug is given intravenously; special precautions must be taken against subcutaneous extravasation, since this may cause painful irritation and ulceration. The drug should not be injected into an extremity with impaired circulation. After a single dose of 0.3 mg/kg of body weight, myelosuppression reaches its maximum in 7 to 10 days. If a moderate level of leukopenia (approximately 3000 cells/mm³) is not attained, the weekly dose may be increased gradually by increments of 0.05 mg/kg of body weight. In regimens designed to cure testicular cancer, vinblastine is used in doses of 0.3 mg/kg every 3 weeks irrespective of blood cell counts or toxicity.

The most important clinical use of vinblastine is with bleomycin and cisplatin in the curative therapy of metastatic testicular tumors. Beneficial responses have been reported in various lymphomas, particularly Hodgkin's disease, where significant improvement may be noted in 50 to 90% of cases. The effectiveness of vinblastine in a high proportion of lymphomas is not diminished when the disease is refractory to alkylating agents. It is also active in Kaposi's sarcoma, neuroblastoma, and Letterer- Siwe disease (histiocytosis X), as well as in carcinoma of the breast and choriocarcinoma in women. Doses of vinblastine will be determined by the clinician according to the individual patients need. 0.1 to 0.3 mg/kg can be administered or 1.5 to 2 mg/m² can also be administered. Alternatively, 0.1 mg/m , 0.12 mg/m , 0.14 mg/m , 0.15 mg/m , 0.2 mg/m², 0.25 mg/m², 0.5 mg/m², 1.0 mg/m², 1.2 mg/m², 1.4 mg/m², 1.5 mg/m², 2.0 mg/m , 2.5 mg/m , 5.0 mg/m , 6 mg/m , 8 mg/m , 9 mg/m , 10 mg/m , 20 mg/m , can be given. Of course, all of these dosages are exemplary, and any dosage in-between these points is also expected to be of use in the invention.

d. Vincristine Vincristine blocks mitosis and produces metaphase arrest. It seems likely that most of the biological activities of this drug can be explained by its ability to bind specifically to tubulin and to block the ability of protein to polymerize into microtubules. Through disruption of the microtubules of the mitotic apparatus, cell division is arrested in metaphase. The inability to segregate chromosomes correctly during mitosis presumably leads to cell death.

The relatively low toxicity of vincristine for normal marrow cells and epithelial cells make this agent unusual among anti-neoplastic drugs, and it is often included in combination with other myelosuppressive agents.

Unpredictable absorption has been reported after oral administration of vincristine. At the usual clinical doses the peak concentration of each drug in plasma is approximately 0.4 mM.

Vincristine bind to plasma proteins. It is extensively concentrated in platelets and to a lesser extent in leukocytes and erythrocytes.

Vincristine has a multiphasic pattern of clearance from the plasma; the terminal half-life is about 24 hours. The drug is metabolized in the liver, but no biologically active derivatives have been identified. Doses should be reduced in patients with hepatic dysfunction. At least a 50% reduction in dosage is indicated if the concentration of bilirubin in plasma is greater than 3 mg/dl (about 50 mM).

Vincristine sulfate is available as a solution (1 mg/ml) for intravenous injection. Vincristine used together with corticosteroids is presently the treatment of choice to induce remissions in childhood leukemia; the optimal dosages for these drugs appear to be vincristine, intravenously, 2 mg/m² of body-surface area, weekly, and prednisone, orally, 40 mg/m², daily. Adult patients with Hodgkin's disease or non-Hodgkin's lymphomas usually receive vincristine as a part of a complex protocol. When used in the mechlorethamine, prednisone, and procarbazine regimen (the so- called MOPP regimen), the recommended dose of vincristine is 1.4 mg/m². High doses of vincristine seem to be tolerated better by children with leukemia than by adults, who may experience sever neurological toxicity. Administration of the drug more frequently than every 7 days or at higher doses seems to increase the toxic manifestations without proportional improvement in the response rate. Precautions should also be used to avoid extravasation during intravenous administration of vincristine. Vincristine (and vinblastine) can be infused into the arterial blood supply of tumors in doses several times larger than those that can be administered intravenously with comparable toxicity.

Vincristine has been effective in Hodgkin's disease and other lymphomas. Although it appears to be somewhat less beneficial than vinblastine when used alone in Hodgkin's disease, when used with the MOPP regimen, it is the preferred treatment for the advanced stages (III and IV) of this disease. In non-Hodgkin's lymphomas, vincristine is an important agent, particularly when used with cyclophosphamide, bleomycin, doxorubicin, and prednisone. Vincristine is more useful than vinblastine in lymphocytic leukemia. Beneficial response have been reported in patients with a variety of other neoplasms, particularly Wilms' tumor, neuroblastoma, brain tumors, rhabdomyosarcoma, and carcinomas of the breast, bladder, and the male and female reproductive systems.

Doses of vincristine for use will be determined by the clinician according to the individual patients need. 0.01 to 0.03 mg/kg or 0.4 to 1.4 mg/m² can be administered or 1.5 to 2 mg/m² can also be administered. Alternatively 0.02 mg/m², 0.05 mg/m², 0.06 mg/m², 0.07 mg/m², 0.08 mg/m², 0.1 mg/m², 0.12 mg/m², 0.14 mg/m², 0.15 mg/m², 0.2 mg/m², 0.25 mg/m² can be given as a constant intravenous infusion. Of course, all of these dosages are exemplary, and any dosage in-between these points is also expected to be of use in the invention.

e. Camptothecin Camptothecin is an alkaloid derived from the Chinese tree Camptotheca acuminata Decne. Camptothecin and its derivatives are unique in their ability to inhibit DNA Topoisomerase by stabilizing a covalent reaction intermediate, termed "the cleavable complex," which ultimately causes tumor cell death. It is widely believed that camptothecin analogs exhibited remarkable anti-tumor and anti- leukemia activity. Application of camptothecin in clinic is limited due to serious side effects and poor water-solubility. At present, some camptothecin analogs (topotecan; irinotecan), either synthetic or semi-synthetic, have been applied to cancer therapy and have shown satisfactory clinical effects. The molecular formula for camptothecin is C₂₀Hi₆N₂O₄, with a molecular weight of 348.36. It is provided as a yellow powder, and may be solubilized to a clear yellow solution at 50 mg/ml in DMSO IN sodium hydroxide. It is stable for at least two years if stored at 2-8°X in a dry, airtight, light- resistant environment.

v. Nitrosureas

Nitrosureas, like alkylating agents, inhibit DNA repair proteins. They are used to treat non-Hodgkin's lymphomas, multiple myeloma, malignant melanoma, in addition to brain tumors. Examples include carmustine and lomustine.

a. Carmustine

Carmustine (sterile carmustine) is one of the nitrosoureas used in the treatment of certain neoplastic diseases. It is l,3bis (2-chloroethyl)-l -nitrosourea. It is lyophilized pale yellow flakes or congealed mass with a molecular weight of 214.06. It is highly soluble in alcohol and lipids, and poorly soluble in water. Carmustine is administered by intravenous infusion after reconstitution as recommended. Sterile carmustine is commonly available in 100 mg single dose vials of lyophilized material.

Although it is generally agreed that carmustine alkylates DNA and RNA, it is not cross resistant with other alkylators. As with other nitrosoureas, it may also inhibit several key enzymatic processes by carbamoylation of amino acids in proteins. Carmustine is indicated as palliative therapy as a single agent or in established combination therapy with other approved chemotherapeutic agents in brain tumors such as glioblastoma, brainstem glioma, medullobladyoma, astrocytoma, ependymoma, and metastatic brain tumors. Also it has been used in combination with prednisone to treat multiple myeloma. Carmustine has proven useful, in the treatment of Hodgkin's Disease and in non-Hodgkin's lymphomas, as a secondary therapy in combination with other approved drugs in patients who relapse while being treated with primary therapy, or who fail to respond to primary therapy. The recommended dose of carmustine as a single agent in previously untreated patients is 150 to 200 mg/m² intravenously every 6 weeks. This may be given as a single dose or divided into daily injections such as 75 to 100 mg/m² on 2 successive days. When carmustine is used in combination with other myelosuppressive drugs or in patients in whom bone marrow reserve is depleted, the doses should be adjusted accordingly. Doses subsequent to the initial dose should be adjusted according to the hematologic response of the patient to the preceding dose. It is of course understood that other doses may be used in the present invention for example 10 mg/m , 20 mg/m², 30 mg/m² 40 mg/m² 50 mg/m² 60 mg/m² 70 mg/m² 80 mg/m² 90 mg/m² 100 mg/m² . The skilled artisan is directed to, "Remington's Pharmaceutical Sciences"

15th Edition, chapter 61. Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.

b. Lomustine

Lomustine is one of the nitrosoureas used in the treatment of certain neoplastic diseases. It is l-(2-chloro-ethyl)-3-cyclohexyl-l nitrosourea. It is a yellow powder with the empirical formula of CgHi₆ClN₃O₂ and a molecular weight of 233.71. Lomustine is soluble in 10% ethanol (0.05 mg per mL) and in absolute alcohol (70 mg per mL). Lomustine is relatively insoluble in water (<0.05 mg per mL). It is relatively unionized at a physiological pH. Inactive ingredients in lomustine capsules are magnesium stearate and mannitol.

Although it is generally agreed that lomustine alkylates DNA and RNA, it is not cross resistant with other alkylators. As with other nitrosoureas, it may also inhibit several key enzymatic processes by carbamoylation of amino acids in proteins.

Lomustine may be given orally. Following oral administration of radioactive lomustine at doses ranging from 30 mg/m to 100 mg/m , about half of the radioactivity given was excreted in the form of degradation products within 24 hours. The serum half-life of the metabolites ranges from 16 hours to 2 days. Tissue levels are comparable to plasma levels at 15 minutes after intravenous administration.

Lomustine has been shown to be useful as a single agent in addition to other treatment modalities, or in established combination therapy with other approved chemotherapeutic agents in both primary and metastatic brain tumors, in patients who have already received appropriate surgical and/or radiotherapeutic procedures. It has also proven effective in secondary therapy against Hodgkin's Disease in combination with other approved drugs in patients who relapse while being treated with primary therapy, or who fail to respond to primary therapy. The recommended dose of lomustine in adults and children as a single agent in previously untreated patients is 130 mg/m as a single oral dose every 6 weeks. In individuals with compromised bone marrow function, the dose should be reduced to 100 mg/m² every 6 weeks. When lomustine is used in combination with other myelosuppressive drugs, the doses should be adjusted accordingly. It is understood that other doses may be used for example, 20 mg/m² 30 mg/m², 40 mg/m², 50 mg/m², 60 mg/m², 70 mg/m², 80 mg/m², 90 mg/m², 100 mg/m², 120 mg/m² or any doses between these figures as determined by the clinician to be necessary for the individual being treated.

vi. Other Agents

Other agents that may be used include Avastin, Iressa, Erbitux, Velcade, and

Gleevec. In addition, growth factor inhibitors and small molecule kinase inhibitors have utility in the present invention as well. AU therapies described in Cancer:

Principles and Practice of Oncology (2001), are hereby incorporated by reference. The following additional therapies are encompassed, as well.

2. Immunotherapy

Immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells. The immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell. The antibody alone may serve as an effector of therapy or it may recruit other cells to actually effect cell killing. The antibody also may be conjugated to a drug or toxin

(chemotherapeutic, radionuclide, ricin A chain, cholera toxin, pertussis toxin, etc.) and serve merely as a targeting agent. Alternatively, the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target. Various effector cells include cytotoxic T cells and NK cells.

Immunotherapy, thus, could be used as part of a combined therapy, in conjunction with DNMT3B inhibitors. The general approach for combined therapy is discussed below. Generally, the tumor cell must bear some marker that is amenable to targeting, i.e., is not present on the majority of other cells. Many tumor markers exist and any of these may be suitable for targeting in the context of the present invention. Common tumor markers include carcino embryonic antigen, prostate specific antigen, urinary tumor associated antigen, fetal antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, PLAP, estrogen receptor, laminin receptor, erb B and pi 55.

Tumor Necrosis Factor is a glycoprotein that kills some kinds of cancer cells, activates cytokine production, activates macrophages and endothelial cells, promotes the production of collagen and collagenases, is an inflammatory mediator and also a mediator of septic shock, and promotes catabolism, fever and sleep. Some infectious agents cause tumor regression through the stimulation of TNF production. TNF can be quite toxic when used alone in effective doses, so that the optimal regimens probably will use it in lower doses in combination with other drugs. Its immunosuppressive actions are potentiated by gamma-interferon, so that the combination potentially is dangerous. A hybrid of TNF and interferon-α also has been found to possess anti-cancer activity.

3. Hormonal Therapy

Sex hormones can be used with the methods described herein in the treatment of cancer. While the methods described herein are not limited to the treatment of a specific cancer, this use of hormones has benefits with respect to cancers of the breast, prostate, and endometrial (lining of the uterus). Examples of these hormones are estrogens, anti-estrogens, progesterones, and androgens.

Corticosteroid hormones are useful in treating some types of cancer (lymphoma, leukemias, and multiple myeloma). Corticosteroid hormones can increase the effectiveness of other chemotherapy agents, and consequently, they are frequently used in combination treatments. Prednisone and dexamethasone are examples of corticosteroid hormones.

4. Radiotherapy

Radiotherapy, also called radiation therapy, is the treatment of cancer and other diseases with ionizing radiation. Ionizing radiation deposits energy that injures or destroys cells in the area being treated by damaging their genetic material, making it impossible for these cells to continue to grow. Although radiation damages both cancer cells and normal cells, the latter are able to repair themselves and function properly. Radiotherapy may be used to treat localized solid tumors, such as cancers of the skin, tongue, larynx, brain, breast, or cervix. It can also be used to treat leukemia and lymphoma (cancers of the blood-forming cells and lymphatic system, respectively).

Radiation therapy used according to the present invention may include, but is not limited to, the use of γ-rays, X-rays, and/or the directed delivery of radioisotopes to tumor cells. Other forms of DNA damaging factors are also contemplated such as microwaves and UV -irradiation. It is most likely that all of these factors effect a broad range of damage on DNA, on the precursors of DNA, on the replication and repair of DNA, and on the assembly and maintenance of chromosomes. Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens. Dosage ranges for radioisotopes vary widely, and depend on the half-life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells.

Radiotherapy may comprise the use of radiolabeled antibodies to deliver doses of radiation directly to the cancer site (radioimmuno therapy). Antibodies are highly specific proteins that are made by the body in response to the presence of antigens (substances recognized as foreign by the immune system). Some tumor cells contain specific antigens that trigger the production of tumor-specific antibodies. Large quantities of these antibodies can be made in the laboratory and attached to radioactive substances (a process known as radiolabeling). Once injected into the body, the antibodies actively seek out the cancer cells, which are destroyed by the cell-killing (cytotoxic) action of the radiation. This approach can minimize the risk of radiation damage to healthy cells.

Conformal radiotherapy uses the same radiotherapy machine, a linear accelerator, as the normal radiotherapy treatment but metal blocks are placed in the path of the x-ray beam to alter its shape to match that of the cancer. This ensures that a higher radiation dose is given to the tumor. Healthy surrounding cells and nearby structures receive a lower dose of radiation, so the possibility of side effects is reduced. A device called a multi-leaf collimator has been developed and can be used as an alternative to the metal blocks. The multi-leaf collimator consists of a number of metal sheets which are fixed to the linear accelerator. Each layer can be adjusted so that the radiotherapy beams can be shaped to the treatment area without the need for metal blocks. Precise positioning of the radiotherapy machine is very important for conformal radiotherapy treatment and a special scanning machine may be used to check the position of your internal organs at the beginning of each treatment.

High-resolution intensity modulated radiotherapy also uses a multi-leaf collimator. During this treatment the layers of the multi-leaf collimator are moved while the treatment is being given. This method is likely to achieve even more precise shaping of the treatment beams and allows the dose of radiotherapy to be constant over the whole treatment area.

Although research studies have shown that conformal radiotherapy and intensity modulated radiotherapy may reduce the side effects of radiotherapy treatment, it is possible that shaping the treatment area so precisely could stop microscopic cancer cells just outside the treatment area being destroyed. This means that the risk of the cancer coming back in the future may be higher with these specialized radiotherapy techniques. Stereotactic radiotherapy is used to treat brain tumors. This technique directs the radiotherapy from many different angles so that the dose going to the tumor is very high and the dose affecting surrounding healthy tissue is very low. Before treatment, several scans are analyzed by computers to ensure that the radiotherapy is precisely targeted, and the patient's head is held still in a specially made frame while receiving radiotherapy. Several doses are given.

Stereotactic radio-surgery (gamma knife) for brain tumors does not use a knife, but very precisely targeted beams of gamma radiotherapy from hundreds of different angles. Only one session of radiotherapy, taking about four to five hours, is needed. For this treatment a specially made metal frame is attached to the patient's head. Then several scans and x-rays are carried out to find the precise area where the treatment is needed. During the radiotherapy, the patient lies with their head in a large helmet, which has hundreds of holes in it to allow the radiotherapy beams through.

Scientists also are looking for ways to increase the effectiveness of radiation therapy. Two types of investigational drugs are being studied for their effect on cells undergoing radiation. Radiosensitizers make the tumor cells more likely to be damaged, and radioprotectors protect normal tissues from the effects of radiation. Hyperthermia, the use of heat, is also being studied for its effectiveness in sensitizing tissue to radiation. 5. Subsequent Surgery

Approximately 60% of persons with cancer will undergo surgery of some type, which includes preventative, diagnostic or staging, curative and palliative surgery. Curative surgery is a cancer treatment that may be used in conjunction with other therapies, such as the treatment of the present invention, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy and/or alternative therapies.

Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed. Tumor resection refers to physical removal of at least part of a tumor. In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically controlled surgery (Mohs' surgery). It is further contemplated that the present invention may be used in conjunction with removal of superficial cancers, precancers, or incidental amounts of normal tissue.

Upon excision of part of all of cancerous cells, tissue, or tumor, a cavity may be formed in the body. Treatment using a DNMT3B inhibitor may be accomplished by perfusion, direct injection or local application of the area with an additional anticancer therapy. Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. These treatments may be of varying dosages as well.

6. Gene Therapy

In another embodiment, the secondary treatment is a gene therapy. Delivery of a vector encoding a therapeutic gene in conjunction with an inhibitor of DNMT3B may be utilized. A variety of gene therapy agents are encompassed within this embodiment, some of which are described below.

i. Inducers of Cellular Proliferation The proteins that induce cellular proliferation further fall into various categories dependent on function. The commonality of all of these proteins is their ability to regulate cellular proliferation. For example, a form of PDGF, encoded by the sis oncogene, is a secreted growth factor. Oncogenes rarely arise from genes encoding growth factors, and at the present, Sis is the only known naturally-occurring oncogenic growth factor. In one embodiment of the present invention, it is contemplated that anti-sense mRNA directed to a particular inducer of cellular proliferation is used to prevent expression of the inducer of cellular proliferation.

The proteins FMS, ErbA, ErbB and Neu are growth factor receptors. Mutations to these receptors result in loss of regulatable function. For example, a point mutation affecting the transmembrane domain of the Neu receptor protein results in the neu oncogene. The erbA oncogene is derived from the intracellular receptor for thyroid hormone. The modified oncogenic ErbA receptor is believed to compete with the endogenous thyroid hormone receptor, causing uncontrolled growth. The largest class of oncogenes includes the signal transducing proteins (e.g.,

Src, AbI and Ras). The protein Src is a cytoplasmic protein-tyrosine kinase, and the transformation of the gene encoding this protein from proto-oncogene to oncogene in some cases, results via mutations at tyrosine residue 527. In contrast, transformation of the gene encoding the GTP ase protein ras from proto-oncogene to oncogene, in one example, results from a valine to glycine mutation at amino acid 12 in the sequence, reducing Ras GTPase activity.

The proteins Jun, Fos and Myc are proteins that directly exert their effects on nuclear functions as transcription factors.

ii. Tumor Suppressors and Inhibitors of Cellular

Proliferation

The tumor suppressor oncogenes function to inhibit excessive cellular proliferation. The inactivation of these genes destroys their inhibitory activity, resulting in unregulated proliferation. The tumor suppressors Rb, pl6, MDA-7, PTEN and C-CAM are specifically contemplated.

Human p53 gene therapy has been described in the literature since the mid-

1990's. Roth et al. (1996) reported a retroviral-based therapy, and dayman et al.

(1998) described adenoviral delivery. U.S. Patents 6,017,524; 6,143,290; 6,410,010; and 6,511,847, and U.S. Patent Application No. 2002/0077313 each describe methods of treating patients with p53, and are hereby incorporated by reference.

One particular mode of administration that can be used in conjunction with surgery is treatment of an operative tumor bed. Thus, in either the primary gene therapy treatment, or in a subsequent treatment, one may perfuse the resected tumor bed with the vector during surgery, and following surgery, optionally by inserting a catheter into the surgery site.

Hi. Regulators of Programmed Cell Death Apoptosis, or programmed cell death, is an essential process for normal embryonic development, maintaining homeostasis in adult tissues, and suppressing carcinogenesis (Kerr et al, 1972). The Bcl-2 family of proteins and ICE-like proteases have been demonstrated to be important regulators and effectors of apoptosis in other systems. The Bcl-2 protein, discovered in association with follicular lymphoma, plays a prominent role in controlling apoptosis and enhancing cell survival in response to diverse apoptotic stimuli (Bakhshi et al, 1985; Cleary and Sklar, 1985; Cleary et al, 1986; Tsujimoto et al, 1985; Tsujimoto and Croce, 1986). The evolutionarily conserved Bcl-2 protein now is recognized to be a member of a family of related proteins, which can be categorized as death agonists or death antagonists.

Subsequent to its discovery, it was shown that Bcl-2 acts to suppress cell death triggered by a variety of stimuli. Also, it now is apparent that there is a family of Bcl-2 cell death regulatory proteins which share common structural and sequence homologies. These different family members have been shown to either possess similar functions to Bcl-2 {e.g., BCI_XL, BcIw, BcIs, McI-I, Al, BfI-I) or counteract Bcl-2 function and promote cell death {e.g., Bax, Bak, Bik, Bim, Bid, Bad, Harakiri).

IV. Examples

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention. Example 1 - Materials & Methods

Cell lines and primary acute leukemia cell samples. Hematopoietic cell lines were grown in RPMIl 640, 10 niM HEPES, 10% fetal bovine serum, and 100 units/mL penicillin/ 100 μg/mL Streptomycin. Adherent cell lines were grown in the recommended media. Viable primary acute leukemia cells were cryopreserved in liquid nitrogen after patients gave informed consent to participate in an IRB-approved research protocol.

Reverse-transcription, PCR amplification, and sequencing. Viable primary leukemia cells were isolated by Ficoll density centrifugation. Total RNA was isolated using STAT-60 (Tel-Test, Inc.) or Trizol (Invitrogen), and reverse transcription was performed using SuperScriptII (Invitrogen). PCR amplifications were performed using the Expand High Fidelity kit (Roche) using primers and temperatures listed in Table 4. PCR products were cloned by TA-cloning (Invitrogen), and sequencing was performed using universal or DNMT3B-specific primers and analyzed using an ABI 377 automated sequencer (Applied Biosystems) and DNAStar software.

Quantitative reverse transcription PCR of DNMT3B transcripts. RNA isolation and reverse transcription PCR were performed according to the protocols outlined by the Quantitative Genomics Core Laboratory at the University of Texas Health Science Center at Houston (research.uth.tmc.edu/corelabs/qgclassays.html). Amplification primers for both assays spanned intron-exon boundaries to ensure amplification of cDNA. Normalization was performed relative to 18S rRNA levels.

Construction of DNMT3B7 expression plasmid. To construct the DNMT3B7 expression plasmid, the DNMT3B7 cDNA was amplified from Raji cells, ligated into pcDNA3.1⁺ (Invitrogen), and sequenced. Stable Transfections in cultured cells. Transfections were performed using 2 μg of the desired plasmid and Effectamine (Qiagen). Stable transfectants were selected by adding 400 μg/mL G418 (Invitrogen) to the media 48 hours after transfection and picked after reculturing for three weeks.

Western blotting. Cytosolic protein extracts were made 48 hours after transfection by lysing cells in 5 mM PIPES, pH 8.0, 85 mM KCl, 0.5% NP-40, 1 :100 dilution protease inhibitors, followed by nuclear lysis in 50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 1% SDS. Protein extracts were separated by SDS-PAGE electrophoresis and transferred to nitrocellulose. The blot was incubated with a 1 :570 dilution of anti- DNMT3B antibody (T-16, sc-102B6, Santa Cruz Biotechnology) followed by a 1 :10,000 dilution of anti-goat IgG conjugated to horseradish peroxidase (Sigma) and was exposed using the Visualizer Western Blot Detection Kit (Upstate). Equal loading of the Western blots were confirmed using a 1:10,000 dilution of anti- GAPDH antibody (ab8245, AbCam).

Sodium bisulfite treatment and PCR amplification. Genomic DNA was treated with sodium bisulfite as previously described (Clark et al, 1994). PCR amplifications were performed using AmpliTaq Gold polymerase (Applied Biosystems), using the primers and temperatures given in Table 4, and cloned using TA-cloning (Invitrogen). The Student's t-test was used to compare methylation across clones, and the χ test was used to compare the methylation of individual CpG residues.

Microarray analysis. Cell lines were grown in identical conditions. Cells from at least five plates were combined and used to collect total RNA using STAT-60 (Tel-Test, Inc.) followed by RNeasy Mini column purification (Qiagen). In collaboration with the University of Chicago Functional Genomics Facility, each RNA sample was split into at least three samples. Each RNA sample was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies) to confirm an OD260/280 and OD260/230 ratio of >1.8 and an RNA concentration of >lμg/mL. Complementary RNA hybridization probes were hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays (Affymetrix, Inc.), washed, stained with streptavidin phycoerythrin in an Affymetrix Fluidics Station 450, and scanned using the Affymetrix GeneChip Scanner 3000, using standard protocols. Data were acquired, quantified, and analyzed using GCOS (Affymetrix) and DNA-Chip Analyzer 1.3 with default settings (Li & Wong, 2001). Thresholds for selecting significant genes were: a relative difference > 1.5 fold, absolute difference > 100 signal intensity, and statistical difference at P<0.05 (using Student t-test). Genes that met all three criteria simultaneously were considered significant.

Construction of DNMT3B RNAi expression plasmid. siRNA targets were found using various websites for RNAi design. The 94 bases of DNMT3B7 intron 10 that are retained in the DNMT3B7 transcript were entered into the Ambion website (www.ambion.com/techlib/misc/siRNA_finder.html), and the RNAi Central design tool (katahdin.cshl.org/homepage/siRNA/RNAi. cgi?type=siRNA) from the Greg Hannon Laboratory, Cold Spring Harbor Laboratories, to identify potential RNAi targets. The potential target sequences from both websites were checked for sequence specificity. The unique targets were entered into the siRNA hairpin oligonucleotide sequence designer program (bioinfo2.clontech.com/rnaidesigner/oligoDesigner.do) (Clontech), using the target hairpin loop sequence, and all three restriction enzyme sites. The resulting oligonucleotides, top and bottom strands, were ordered with 5' phosphates, annealed, and ligated into the pSIREN-RetroQ vector (Clontech, PT3737- 5) following the manufacturer's directions. The resulting clones were sequenced to confirm that the plasmids had the desired sequences, without mutations. A control ligation was also performed to produce a plasmid expressing a luciferase short hairpin RNA (shRNA) for use as a negative control.

Testing the RNAi expression plasmids. 293 cells stably-expressing DNMT3B7 were transfected with two plasmids (a green fluorescent protein (GFP)- expressing plasmid and an RNAi-expressing plasmid, expressing either one of the DNMT3B shRNAs or the luciferase shRNA) using the Effectamine reagent (Qiagen). After 48 hours, the cells were sorted for GFP expression, and 3X10 GFP-expressing cells were collected. Nuclear protein lysates were made and the proteins were separated on an SDS-PAGE gel. A Western blot for DNMT3B was performed as described above.

Example 2 - Results

Cancer cells express aberrant DNMT3B transcripts. To examine potential mechanisms for the abnormal patterns of DNA methylation in cancer cells, the inventors amplified the cDNAs encoding the three DNA methyltransferase enzymes from several cancer cell lines using a high-fidelity polymerase. Although amplicons derived from the DNMTl and DNMT3A cDNAs were wild-type in sequence (data not shown), PCR amplification of DNMT3B cDNA from exon 9 to exon 13 produced the two expected amplification products (Products A and B in FIG. IA) as well as an unexpected amplicon (Product C in FIG. IA). Sequence analysis demonstrated that this novel transcript contained an aberrant splicing event from exon 9 to the 3 ' end of intron 10, resulting in an insertion of 94 base pairs that is normally part of intron 10, located just 5' to exon 11. The inventors designated this transcript DNMT3B7 (Genbank accession number DQ321787; FIG. IB). To determine whether aberrant DNMT3B7 transcripts were expressed in cancer cell lines of diverse origins, the inventors expanded their screen to include 25 established cancer cell lines derived from hematopoietic malignancies (11 cell lines) as well as solid tumors (14 cell lines), and 30 primary acute leukemia samples (27 acute myeloid leukemia samples and 3 acute lymphoblastic leukemia samples) (Table 1 and FIG. 5). DNMT3B transcripts involving aberrant splicing events at the 5' end of the gene could be detected in all of the samples tested, except in HepG2 and Alexander cells, both of which are derived from hepatocellular carcinomas. Alexander cells are known to express DNMT3B4, which encodes a catalytically- inactive DNMT3B isoform (Saito et al., 2002). AU of the primary leukemia samples expressed a transcript containing aberrant splicing between exons 9 and 13 as originally observed, confirming that the expression of these novel mRNAs was not due to an artifact of in vitro culture. Notably, there was expression of at least one of the three wild-type DNMT3B transcripts in all of the tumor cell line-derived cDNAs as well as in all of the primary leukemia samples, in keeping with previous data that complete loss of DNMT3B activity is incompatible with viability (Li et al, 1992; Okano et α/., 1999).

Most of the aberrantly- spliced DNMT3B transcripts contain sequences that are normally intronic and lack various exons, and all of them encode truncated DNMT3B proteins containing novel amino acids but lacking the catalytic C-terminus. Table 3 lists the properties of each aberrant transcript. The inventors noted alternative splicing of several 5' exons, including exon 5 (Xu et al., 1999). The 5' half of each transcript could be amplified using a primer derived from exon IA (data not shown), suggesting that the promoter originally identified for DNMT3B is used to generate the aberrant transcripts (Yanagisawa et al, 2002).

To quantitate the levels of aberrant DNMT3B transcripts in cancer cells precisely, the inventors performed quantitative reverse transcription PCR (Q-RT- PCR) of DNMT3B transcripts. Two assays were designed: the first assay assessed the levels of aberrant DNMT3B transcripts containing intron 10 sequences by placing the forward primer in exon 9, and the reverse primer and Taqman probe within the retained intron sequence. The second assay assessed total DNMT3B transcript levels, by placing the forward primer in exon 12, and the reverse primer and Taqman probe within exon 13, since neither exon 12 nor exon 13 is subject to alternative splicing. Q-RT-PCR of eight normal human tissues (Clontech, Stratagene) demonstrated no detectable aberrant DNMT3B transcripts, whereas 2-5% of DNMT3B transcripts in cancer cell lines derived from both solid and hematopoietic tumors contained intron 10 sequences (Table T).

Cancer cells express truncated DNMT3B proteins. Although aberrant transcripts represent a minority of DNMT3B transcripts, the inventors next tested whether truncated DNMT3B proteins were detectable by Western blotting in protein extracts from cancer cells. All of the aberrant DNMT3B transcripts contain premature stop codons and are predicted to produce truncated DNMT3B proteins lacking the two strongest nuclear localization signals. Therefore, the inventors tested both cytoplasmic and nuclear protein extracts from SK-BR-3 cells (a breast cancer cell line) and HeLa cells (a cervical cancer cell line). The full-length DNMT3B (96kD) as well as the truncated DNMT3B7 (4OkD) protein were observed in the nuclear protein fractions by Western blot analysis using an N-terminal-specific anti- DNMT3B antibody (FIG. 2 A, upper panel). The signals were competed away with the respective antigenic peptides for each of the antibodies tested (FIG. 2A, middle panel), confirming that the observed signals were DNMT3B-derived species. Similar results were obtained with two other anti-DNMT3B antibodies as well as nuclear protein extracts from MD A-MB -231 and K562 cells (data not shown).

To determine if low levels of a truncated DNMT3B protein could alter DNA methylation levels, the inventors isolated 293 cells (human embryonic kidney cells) that stably express DNMT3B7 (Table 2 and FIG. 2B, top panel). Although Q-RT- PCR indicated that 40-50% of DNMT3B transcripts within transfected cells encoded DNMT3B7 (Table 2), Western blot analysis demonstrated that the truncated protein represented a minority of DNMT3B protein within transfected cells (FIG. 2B, top panel), as the inventors observed in cancer cells. Therefore, DNMT3B7-expressing 293 cells could serve as a reasonable model of the relative amounts of full-length versus truncated DNMT3B proteins found in cancer cells. The inventors characterized the phenotype of two independently-derived clones expressing DNMT3B7 compared to vector-transfected cells. DNMT3B7-expressing 293 cells demonstrate gene expression changes that correspond with altered DNA methylation within some CpG islands. The inventors used microarray analysis to compare the gene expression changes found in DNMT3B7-expressing cells versus vector-transfected cells. Three independently- isolated RNA samples from DNMT3B7-expressing Line 1 and Line 2 cells were used as probes hybridized to Affymetrix GeneChip Human Genome Ul 33 Plus 2.0 oligonucleotide arrays. These samples were compared to four independently-isolated RNA samples from vector-transfected cells. The inventors searched for genes whose expression levels differed statistically between the two DNMT3B7-expressing lines and the vector-transfected cells, but not between the two DNMT3B7-expressing lines themselves. Fifty-one genes fulfilled these criteria (FIG. 3): 27 genes were underexpressed in the DNMT3B7-expressing cells, and 24 genes were overexpressed. Interestingly, more than half of the genes whose expression changed are located on chromosomes 1, 9, 16, and X, and 75% of the overexpressed genes are located on tho se chromo somes .

The inventors reasoned that at least some of the gene expression changes that they observed were likely to involve changes in DNA methylation of corresponding CpG islands. Genes whose expression decreased with DNMT3B7 expression would be expected to have increased CpG island/promoter methylation, whereas genes whose expression increased with DNMT3B7 expression would be expected to have less DNA methylation of their CpG islands/promoters. The inventors isolated genomic DNA from transfected cells and treated it with sodium bisulfite, which chemically converts unmethylated cytosine to uracil, but does not alter methylated cytosine. The inventors analyzed the DNA methylation state of particular CpG islands by PCR amplification and sequencing in vector-transfected versus DNMT3B7-expressing 293 cells. They observed changes in the DNA methylation state of the CpG islands/promoters of four genes whose expression was altered in DNMT3B7-expressing cells, in parallel to what is observed in cancer cells (FIGS. 4A- D). The E-cadherin (CDHl) gene is hypermethylated and transcriptionally repressed in gastric and breast cancers, myeloid malignancies, and other tumors (Aggerholm et al, 2006; Chan, 2006; Cowin et al, 2005). The inventors observed hypermethylation of the CDHl (E-cadherin) CpG island (FIG. 4A), corresponding to a 2.19-fold decrease in gene expression (FIG. 3). One CpG dinucleotide (#2, FIG. 4A) is contained within the known SpI binding site located closest to the gene's transcriptional start.

The X-linked MAGEA3 gene is hypomethylated and overexpressed in melanoma (Sigalotti et al, 2002), and the methylation status of the regulatory regions of SH2D1A, the X-linked lymphoproliferative disease gene, correlates with tissue- specific expression (Parolini et al, 2003). Hypomethylation of the CpG islands associated with the M AGE A3 and SH2D1A genes also correlated with increased expression, 2.54-fold and 3.05-fold, respectively (FIGS. 4B and 4D and FIG. 3). In addition, the inventors observed hypomethylation of the CpG island of PLP2, a gene located at XpI 1.2, which exhibited 2.85-fold increased expression in DNMT3B7- expressing cells (FIG. 4C and FIG. 3). Interestingly, most of the DNA methylation changes were located in the part of the CpG island just 5' to the transcriptional start site of the gene, but there was also some demethylation that extended well past the gene's translational start. The inventors confirmed that increased gene expression from the X chromosome occurred from the active X chromosome, rather than from reactivation of gene expression from the inactive X chromosomes, using an informative SNP in the X-linked MIDI gene in 293 cells (a T/C allele at position 10247528; SNP rsl6986145) (data not shown).

The inventors have tested each of the shRNAs in Table 3 for the ability to lower DNMT3B7 levels. They co-transfected 293 cells stably expressing DNMT3B7 with each of the RNAi constructs and a green fluorescent protein (GFP)-expressing plasmid (pLEGFP-Nl). After 48 hours, GFP -positive cells were sorted using flow- activated cell sorting (FACS) and were used to make nuclear protein extracts. Two of the shRNAs directed against non-overlapping portions of the retained 94 base pairs of intron sequence were able to lower DNMT3B7 levels to undetectable levels, and a third lowered DNMT3B7 levels by approximately 90%, without affecting levels of the full-length DNMT3B protein (FIG. 6). A fourth shRNA was ineffective in lowering DNMT3B7 levels (data not shown).

Growth of cancer cells slowed inhibited. Short hairpin RNA (shRNA) molecules were introduced into MD A-MB-231 cells, a well characterized breast cancer cell line, to lower DNMT3B7 levels specifically (FIG. 8A). Cells expressing the DNMT3B7 shRNA grew slower than control cells after eight cell passages, indicating a physiologic effect of lowering DNMT3B7 levels that is evident over time (FIG. 8B). Transgenic mice show altered DNA methylation. To test the hypothesis that truncated DNMT3B proteins can affect DNA methylation patterns in vivo, transgenic mice were constructed using a promoter/enhancer combination that was anticipated to direct tissue-specific expression of human DNMT3B7, the truncated DNMT3B protein most frequently observed in cancer cells. Transgenic mice were chosen because they most closely mimic what occurs in cancer cells: the expression of both wild-type and aberrant transcripts.

Eight founder animals were obtained, but the inventors were able to generate only two lines of mice (Lines A and C), since the majority of the founders were sterile. Surprisingly, DNMT3B7 transgene was expressed during embryonic development. In addition, both lines of transgenic mice displayed a remarkable phenotype of disrupted embryonic development, the extent of which depended on the number of copies of the transgene. In one line of transgenic mice, hemizygous transgenic animals were small compared to their wild-type littermates throughout the first 19 weeks of life, and homozygotes died around E8.5. In the other line (Line A), embryonic development was minimally disrupted in the hemizygous state, but homozygous embryos were severely runted and had craniofacial abnormalities, skeletal defects, and cardiac anomalies that are most likely responsible for their death within hours of birth. The phenotypes of the transgenic mice can be placed on a continuum with other genetically manipulated mice involving genes regulating DNA methylation. The most severe phenotypes in the homozygous transgenic animals (embryonic lethality, failure to undergo embryonic turning [in homozygous Line C embryos], and abnormal segmentation) were shared by the Dnmtl -/- mice ' and Dnmt3a -/- Dnmt3b -/- double knock-out mice ². Mice with small stature and craniofacial abnormalities were also observed, similar to what is observed in Dnmt3b -/- mice and those expressing mutations in the Dnmt3b catalytic domain. DNMT3B7 could interact with any of the Dnmts or the related protein, Dnmt3L. The fact that the Line C homozygous mice died earlier than the Dnmt3b -/- mice suggested that DNMT3B7 interrupts more than just Dnmt3b function.

Further analysis of the transgenic mice revealed that DNMT3B7 transgenic mice displayed alterations in DNA methyation that are dose-dependent and result in global hypomethylation and locus-specific differences in hypo- and hyper- methylation. Table 1. Expression of DNMT3B transcripts in cancer cell lines and primary acute leukemias

Expression of a particular transcript within each sample is indicated by an X. The PCR conditions used to analyze these samples could not distinguish among the DNMT3B2, DNMT3B3, and DNMT3B6 transcripts. The DNMT3B7, 12, and 13 transcripts are also indistinguishable by this analysis.

^* Other: DNMT3B4, 5, 8-11, or 14-30 [see Supplemetary Figure 1]. Table 2. Expression of DNMT3B transcripts containing intron 10 sequence

U = Undetectable

SD = Standard Deviation

Percentage (%) = Amount of intron 10 containing DNMT3B transcripts relative to total DNMT3B transcripts, determined by quantitative real-time reverse transcription PCR

The assay for intron 10-contaιnιng transcripts accurately measures > 180 molecules, and the assay for total DNMT3B transcripts accurately measures > 200 molecules

Table 3

Table 4

The sequences of the predicted truncated DNMT3B proteins, encoded by the aberrant DNMT3B7-DNMT3B30 transcripts

Table 5 - The sequences of the DNMT3B RNAi molecules tested

The sequences are given in lower and upper case letters to indicate distinct portions of the oligonucleotides. Lower case letters represent the portions of the oligonucleotides involved in ligation to the plasmid backbone. Upper case letters indicate the portions of the oligonucleotides that encode the short-hairpin RNAs.

10 * * * * * * * * * * * * * * * * * * * * *

AU of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations

15 may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such

20 similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims. REFERENCES

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Claims

CLAIMS:

1. A method of inhibiting a cancer cell comprising providing the cell with an nucleic acid that hybridizes to an intronic region of an aberrantly spliced DNA methyltransferase 3B (DNMT3B) transcript comprising a retained intron.

2. The method of claim 1, wherein inhibiting comprises inhibiting cancer cell growth, inhibiting cancer cell proliferation, inhibiting cancer cell survival, inhibiting cancer cell invasion, inhibiting cancer cell migration, restoring cancer cell growth control, or inducing cancer cell death.

3. The method of claim 1, wherein said cancer cell is a brain cancer cell, a head & neck cancer cell, a lung cancer cell, an esophageal cancer cell, a stomach cancer cell, a pancreatic cancer cell, a liver cancer cell, a colon cancer cell, a breast cancer cell, an ovarian cancer cell, a testicular cancer cell, a prostate cancer cell, a cervical cancer cell, a rectal cancer cell, a skin cancer cell, a leukemia cell, or a lymphoma cell.

4. The method of claim 1 , wherein the cell is provided with a vector that encodes a nucleic acid that hybridizes to the intronic region of a DNMT3B transcript.

5. The method of claim 4, wherein the vector is a plasmid or viral vector.

6. The method of claim 1, wherein the hybridizing nucleic acid is an antisense molecule.

7. The method of claim 1, wherein the hybridizing nucleic acid is an interfering nucleic acid molecule.

8. The method of claim 7, wherein said interfering nucleic acid molecule is a siRNA.

9. The method of claim 7, wherein said interfering nucleic acid molecule is a dsRNA.

10. The method of claim 7, wherein said interfering nucleic acid molecule is a shRNA.

11. The method of claim 1, wherein said DNMT3B transcript is DNMT3B7, DNMT3B8, DNMT3B9 or DNMT3B11-30.

12. The method of claim 1 , wherein said DNMT3B transcript is DNMT3B7.

13. The method of claim 1, further comprising contacting said cell with a second anti-cancer agent.

14. A method of altering methylation in a cancer cell comprising contacting said cell with an inhibitory nucleic acid that targets an intronic region of an aberrantly spliced DNMT3B transcript comprising a retained intron.

15. The method of claim 14, wherein the inhibitory nucleic acid is an interfering RNA.

16. The method of claim 14, wherein the overall methylation in the cancer cell is reduced.

17. The method of claim 14, wherein the the overall methylation in the cancer cell is increased.

18. A method of treating cancer in a subject comprising administering to a cancer cell in the subject a hybridizing nucleic acid that targets an intronic region of an aberrantly spliced DNMT3B transcript comprising a retained intron.

19. The method of claim 18, wherein inhibiting comprises inhibiting cancer cell growth, inhibiting cancer cell proliferation, inhibiting cancer cell survival, inhibiting cancer cell invasion, inhibiting cancer cell migration, restoring growth control of said cancer cell, or inducing cancer cell death.

20. The method of claim 18, wherein said cancer cell is a brain cancer cell, a head & neck cancer cell, a lung cancer cell, an esophageal cancer cell, a stomach cancer cell, a pancreatic cancer cell, a liver cancer cell, a colon cancer cell, a breast cancer cell, an ovarian cancer cell, a testicular cancer cell, a prostate cancer cell, a cervical cancer cell, a rectal cancer cell, a skin cancer cell, a leukemia cell, or a lymphoma cell.

21. The method of claim 18, wherein the hybridizing nucleic acid is an antisense molecule or an interfering nucleic acid.

22. The method of claim 18, wherein the DNMT3B transcript is DNMT3B7, DNMT3B8, DNMT3B9 or DNMT3B11-30.

23. The method of claim 18, wherein the DNMT3B transcript is DNMT3B7.

24. The method of claim 18, further comprising administering to said cell a second anti-cancer therapy.

25. The method of claim 24, wherein the second anti-cancer therapy is a chemotherapeutic.

26. The method of claim 24, wherein the second anti-cancer therapy is a radiotherapeutic.

27. The method of claim 24, wherein the second anti-cancer therapy is a hormone therapy or an immunotherapy.

28. The method of claim 24, wherein the second anti-cancer therapy is surgery.

29. An oligonucleotide consisting of 10 to 50 bases and comprising a segment of at least 10 bases of a DNMT3B intron or intron-exon boundary.

30. The oligonucleotide of claim 29, wherein the oligonucleotide is single- stranded.

31. The oligonucleotide of claim 29, wherein the oligonucleotide is double- stranded.

32. The oligonucleotide of claim 29, wherein the oligonucleotide comprises phosphodiester bases.

33. The oligonucleotide of claim 29, wherein the oligonucleotide is an antisense molecule.

34. The oligonucleotide of claim 29, wherein the oligonucleotide is an interfering nucleic acid.

35. The oligonucleotide of claim 29, wherein the oligonucleotide is a short hairpin RNA.