TARGET GENES FOR CANCER THERAPY

The invention provides new gene targets for cancer chemotherapy, their use in assays for identifying new small molecule cancer chemotherapeutic agents, methods for inhibiting cancer cell growth comprising contacting a cell with a gene expression blocking agent that inhibits the expression of such genes and methods for therapeutic treatment of cancer in a mammal, comprising administering to the mammal such a gene expression blocking agent. A preferred gene target is coatomer protein zeta-1 subunit (COPZ1).

1-10. (canceled)

11. A method for selectively killing tumor cells comprising selectively inhibiting expression or function of coatomer protein zeta-1 subunit (COPZ1) gene or its encoded CopI-ζ1 protein, respectively.

12. The method according to claim 11, wherein the expression of COPZ1 is inhibited by an agent selected from an siRNA, an antisense oligonucleotide, and a ribozyme, wherein the agent selectively targets mRNA encoding CopI-ζ1 protein.

13. The method according to claim 11, wherein the expression of COPZ1 is inhibited by a small molecule that selectively inhibits COPZ1 expression.

14. The method according to claim 11, wherein the function of CopI-ζ1 protein is inhibited by a small molecule that inhibits CopI-ζ1 protein.

15. A method for treating an individual having cancer, comprising selectively inhibiting in the individual expression or function of COPZ1 gene or its encoded CopI-ζ1 protein respectively.

16. The method according to claim 15, wherein the expression of COPZ1 is inhibited by an agent selected from an siRNA, an antisense oligonucleotide, and a ribozyme, wherein the agent selectively targets mRNA encoding CopI-ζ1 protein.

17. The method according to claim 15, wherein the expression of COPZ1 is inhibited by a small molecule that selectively inhibits COPZ1 expression.

18. The method according to claim 15, wherein the function of CopI-ζ1 protein is inhibited by a small molecule that inhibits CopI-ζ1 protein.

19. (canceled)

20. A method for identifying a selective small molecule inhibitor of cancer cell growth comprising:

(a) culturing a mammalian cell comprising a recombinant DNA construct comprising a first reporter gene operatively associated with a COPZ1 promoter and a second reporter gene operatively associated with a COPZ2 promoter in the presence of a test compound;

(b) culturing the mammalian cell in the absence of the test compound;

(c) assaying the cells from (a) and (b) for the expression or activity of the first reporter gene and the second reporter gene, or their encoded proteins; and

(d) identifying the test compound as a selective small molecule inhibitor of cancer cell growth if the expression or activity of the first reporter gene or its encoded protein is inhibited to a greater extent than the expression or activity of the second reporter gene or its encoded protein in cells cultured as in (a), but not in cells cultured as in (b).

21-23. (canceled)

24. A method for identifying a selective small molecule inhibitor of cancer cell growth comprising:

(a) providing purified CopI-ζ1 protein and purified CopI-γ protein in the presence of a test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ1 protein and the purified CopI-γ protein;

(b) providing purified CopI-ζ1 protein and purified CopI-γ protein in the absence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ1 protein and the purified CopI-γ protein;

(c) providing purified CopI-ζ2 protein and purified CopI-γ protein in the presence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ2 protein and the purified CopI-γ protein;

(d) providing purified CopI-ζ2 protein and purified CopI-γ protein in the absence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ2 protein and the purified CopI-γ protein;

(e) assaying the magnitude of the interaction between purified CopI-ζ1 protein and purified CopI-ζ protein in steps (a) and (b);

(f) assaying the magnitude of the interaction between purified CopI-ζ2 protein and purified CopI-γ protein in steps (c) and (d); and

(g) identifying the test compound as a selective inhibitor of CopI-ζ1 protein if the magnitude of the interaction is lesser in step (a) than in step (c), but the magnitude of the interaction in step (b) is not lesser than the magnitude of the interaction in step (d).

25. The method according to claim 24, wherein the purified CopI-ζ1 protein or the purified CopI-γ protein are labeled with a fluorophore suitable for fluorescence resonance energy transfer (FRET), the CopI-ζ2 protein or the purified CopI-γ protein are labeled with a fluorophore suitable for FRET, and the magnitude of the interactions are assayed by FRET.

26-27. (canceled)

1. Field of the Invention

The invention relates to the discovery of new targets for cancer chemotherapy and to the discovery of new small molecule cancer chemotherapeutics effective against such targets.

2. Summary of the Related Art

There has been much interest in the identification of genes that are essential for cancer cell growth. Such genes can be used as targets for the treatment of cancer. One approach to identifying such genes utilizes expression selection of Transdominant Genetic Inhibitors (TGIs) that inhibit the growth of carcinoma cells in vitro. TGIs are represented by Genetic Suppressor Elements (GSEs) and small hairpin RNA (shRNA) templates. GSEs are biologically active cDNA fragments that interfere with the function of the gene from which they are derived. GSEs may encode antisense RNA molecules that inhibit gene expression or peptides that interfere with the function of the target protein as dominant inhibitors (Holzmayer et al., 1992; Roninson et al., 1995). shRNA templates are small (19-21 bp) cDNA fragments, cloned into an expression vector in the form of inverted repeats and giving rise upon transcription to shRNAs, which are processed by cellular enzymes into double-stranded RNA duplexes, short interfering RNA (siRNA) that cause degradation of their cDNA target via RNA interference (RNAi) (Boutros and Ahringer, 2008). General strategies for the isolation of biologically active TGIs involves the use of expression libraries that express GSEs or shRNAs derived from either a single gene, or several genes, or all the genes expressed in a cell. These libraries are then introduced into recipient cells, followed by selection for the desired phenotype and the recovery of biologically active GSEs, which should be enriched in the selected cells.

Genes that are required for the growth of the recipient cells are expected to give rise to TGIs that would inhibit cell proliferation. Such TGIs can be isolated through negative selection techniques, such as bromodeoxyuridine (BrdU) suicide selection (Stetten et al., 1977). The applicability of this approach to the isolation of growth-inhibitory GSEs was demonstrated by Pestov and Lau (Pestov and Lau, 1994) and Primiano et al. (Primiano et al., 2003). Pestov et al. used an isopropyl-β-thio-galactoside (IPTG)-inducible plasmid expression vector to isolate cytostatic GSEs from a mixture of 19 cDNA clones of murine genes associated with the G₀/G₁transition, using the BrdU suicide selection protocol. Through this approach, Pestov and Lau found that three of the genes in their mixture gave rise to growth-inhibitory GSEs. Primiano et al. (2003) used a GSE library derived from normalized (reduced-redundance) cDNA of human MCF7 breast carcinoma cells and cloned into an IPTG-inducible retroviral vector to isolate GSEs that allow MDA-MB-231 human breast carcinoma cells to survive BrdU suicide selection. That study yielded biologically active GSEs from 57 human genes, potential targets for breast cancer therapy.

There remains a need for the identification of new gene targets for cancer therapy.

The invention relates to the discovery of new gene targets for cancer chemotherapy and to the discovery of new small molecule cancer chemotherapeutics effective against such targets. The invention provides new gene targets for cancer chemotherapy, their use in assays for identifying new small molecule cancer chemotherapeutic agents, methods for inhibiting cancer cell growth comprising contacting a cell with a gene expression blocking agent that inhibits the expression of such genes and methods for therapeutic treatment of cancer in a mammal, comprising administering to the mammal such a gene expression blocking agent.

In a first aspect, the invention provides a method for identifying a small molecule anti-cancer compound, the method comprising (a) culturing a mammalian cell in the presence of a test compound; (b) culturing the mammalian cell in the absence of the test compound; (c) assaying the cells from (a) and (b) for the expression or activity of a nucleic acid or its encoded protein selected from the group of nucleic acids identified in Table 1; and (d) identifying the test compound as an anti-cancer compound if the expression or activity of the nucleic acid or its encoded protein is greater in cells cultured as in (b) than in cells cultured as in (a). In certain preferred embodiments, the nucleic acid is selected from the nucleic acids identified in Tables 2, 4, 5 and 6. In particularly preferred embodiments, the nucleic acid is selected from the nucleic acids identified in Tables 2 and 6.

More generally, in a second aspect, the method provides the use, in an assay for identifying a cancer chemotherapeutic small molecule compound, of a recombinant nucleic acid comprising a nucleic acid selected from the nucleic acids identified in Tables 2 and 6.

In a third aspect, the invention provides a method for inhibiting cancer cell growth, comprising inhibiting the expression of a nucleic acid selected from the nucleic acids identified in Tables 2 and 6.

In a fourth aspect, the invention provides a method for therapeutically treating a mammal having cancer, comprising administering to the mammal a gene expression blocking agent that inhibits the expression of a nucleic acid selected from the nucleic acids identified in Tables 2 and 6.

In a fifth aspect, the invention provides a method for selectively inhibiting the growth of cancer cells comprising selectively inhibiting expression or function of coatomer protein zeta-1 subunit gene (COPZ1) or its encoded CopI-ζ1 protein, respectively.

In a sixth aspect, the invention provides a method for identifying a selective small molecule inhibitor or peptide inhibitor of COPZ1 expression comprising: (a) culturing a mammalian cell comprising a recombinant DNA construct comprising a first reporter gene operatively associated with a COPZ1 promoter and a second reporter gene operatively associated with a COPZ2 promoter in the presence of a test compound; (b) culturing the mammalian cell in the absence of the test compound; (c) assaying the cells from (a) and (b) for the expression or activity of the first reporter gene and the second reporter gene, or their encoded proteins; and (d) identifying the test compound as a selective small molecule inhibitor of COPZ1 expression if the expression or activity of the first reporter gene or its encoded protein is inhibited to a greater extent than the expression or activity of the second reporter gene or its encoded protein in cells cultured as in (a), but not in cells cultured as in (b).

In a seventh aspect, the invention provides a method for identifying a selective small molecule inhibitor or peptide inhibitor of CopI-ζ1 protein comprising: (a) providing purified CopI-ζ1 protein and purified CopI-ζ1 protein in the presence of a test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ1 protein and the purified CopI-γ protein; (b) providing purified CopI-ζ2 protein and purified CopI-γ protein in the absence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ1 protein and the purified CopI-γ protein; (c) providing purified CopI-ζ2 protein and purified CopI-ζ1 protein in the presence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ2 protein and the purified CopI-γ protein; (d) providing purified CopI-ζ2 protein and purified CopI-γ protein in the absence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ2 protein and the purified CopI-γ protein; (e) assaying the magnitude of the interaction between purified CopI-ζ1 protein and purified CopI-γ protein in steps (a) and (b); (0 assaying the magnitude of the interaction between purified CopI-ζ2 protein and purified CopI-γ protein in steps (c) and (d); and (g) identifying the test compound as a selective inhibitor of CopI-ζ1 protein if the magnitude of the interaction is lesser in step (a) than in step (c), but the magnitude of the interaction in step (b) is not lesser than the magnitude of the interaction in step (d).

In an eighth aspect, the invention provides a method for identifying a selective small molecule inhibitor or peptide inhibitor of cancer cell growth, the method comprising providing a computer model in the form of three-dimensional structural coordinates of CopI-ζ1 protein, providing three dimensional structural coordinates of a candidate compound, using a docking program to compare the three dimensional structural coordinates of the CopI-ζ1 protein with the three dimensional structural coordinates of the compound and calculate an energy-minimized conformation of the candidate compound in the CopI-ζ1 protein, and evaluating an interaction between the candidate compound and the CopI-ζ1 protein to determine binding affinity of the compound for the CopI-ζ1 protein, wherein the candidate compound is identified as a compound that selectively inhibits cancer cell growth if it has a binding affinity for the CopI-ζ1 protein site of at least 10 μM.

In a ninth aspect, the invention provides a method for determining whether a cancer in an individual is responsive to treatment by selectively inhibiting expression or function of COPZ1 or CopI-ζ1 protein, respectively, comprising obtaining cancer cells from the individual, assaying the expression of COPZ2 and/or mIR-152 in the cancer cells, and determining that the cancer in an individual is responsive to treatment by selectively inhibiting expression or function of COPZ1 or CopI-ζ1 protein, respectively, if the expression of COPZ2 and/or mIR-152 in the cancer cells is lower than in normal cells.

The invention relates to the discovery of new gene targets for cancer chemotherapy and to the discovery of new small molecule cancer chemotherapeutics effective against such targets. The invention provides new gene targets for cancer chemotherapy, their use in assays for identifying new small molecule cancer chemotherapeutic agents, methods for inhibiting cancer cell growth comprising contacting a cell with a gene expression blocking agent that inhibits the expression of such genes and methods for therapeutic treatment of cancer in a mammal, comprising administering to the mammal such a gene expression blocking agent.

The references cited herein reflect the level of knowledge in the art and are hereby incorporated by reference in their entirety. Any conflicts between the teachings of the cited references and the present specification shall be resolved in favor of the latter.

The present inventors have used both GSE and shRNA libraries constructed in tetracycline/doxycline-inducible lentiviral vectors, to select for growth-inhibitory TGIs in several types of human tumor cells, using BrdU suicide selection. As described below, this approach has enabled the inventors to select TGIs that are enriched through BrdU suicide selection. Subsequent testing of synthetic siRNAs against a set of genes enriched by this selection confirmed that the majority of these genes are required for cell growth. Some of the selected TGIs are derived from known oncogenes or known positive regulators of cell growth. Other TGIs are derived from known genes that had not been previously implicated in cell growth regulation. Genes that give rise to the isolated TGIs are identified as positive growth regulators of tumor cells. Such genes may therefore be considered as targets for the development of new anticancer drugs.

In a first aspect, the invention provides a method for identifying a small molecule anti-cancer compound, the method comprising (a) culturing a mammalian cell in the presence of a test compound; (b) culturing the mammalian cell in the absence of the test compound; (c) assaying the cells from (a) and (b) for the expression or activity of a nucleic acid or its encoded protein selected from the group of nucleic acids identified in Table 1; and (d) identifying the test compound as an anti-cancer compound if the expression or activity of the nucleic acid or its encoded protein is greater in cells cultured as in (b) than in cells cultured as in (a). In certain preferred embodiments, the nucleic acid is selected from the nucleic acids identified in Tables 2, 4, 5 and 6. In particularly preferred embodiments, the nucleic acid is selected from the nucleic acids identified in Tables 2 and 6. In some embodiments the expression or activity of more than one nucleic acid or its encoded protein from the tables is assayed in step (c).

More generally, in a second aspect, the method provides the use, in an assay for identifying a cancer chemotherapeutic small molecule compound, of a recombinant nucleic acid comprising a nucleic acid selected from the nucleic acids identified in Tables 2 and 6. For purposes of this aspect of the invention, “a recombinant nucleic acid comprising a nucleic acid selected from” is intended to mean the selected nucleic acid covalently linked to other nucleic acid elements that do not occur in the normal chromosomal locus of the gene. Such other nucleic acid elements may include gene expression elements, such as heterologous promoters and/or enhancers, selectable markers, reporter genes and the like. Preferably, the other nucleic acid elements allow the selected nucleic acid to be expressed in mammalian cells. Such recombinant nucleic acids may frequently be incorporated into a chromosome of the mammalian cell.

In a third aspect, the invention provides a method for inhibiting cancer cell growth, comprising inhibiting the expression of a nucleic acid selected from the nucleic acids identified in Tables 2 and 6. In preferred embodiments of this aspect of the invention, such inhibition of expression of the nucleic acid is achieved by contacting the cell with a gene expression blocking agent. For purposes of the invention, “a gene expression blocking agent” is an agent that prevents an RNA transcribed from the nucleic acid from carrying out its normal cellular function, such function being either regulatory, or being translated into a functional protein. Such prevention may be either steric, e.g., by the agent simply binding to the RNA, or may be through the destruction of the bound RNA by cellular enzymes. Representative gene expression blocking agents include, without limitation, antisense oligonucleotides, ribozymes, short interfering RNAs (siRNA), short hairpin RNAs (shRNA), microRNAs (miRNA) and the like.

In a fourth aspect, the invention provides a method for therapeutically treating a mammal having cancer, comprising administering to the mammal a gene expression blocking agent that inhibits the expression of a nucleic acid selected from the nucleic acids identified in Tables 2 and 6. Such gene expression blocking agent is administered in a therapeutically effective amount. A therapeutically effective amount is an amount sufficient to reduce or ameliorate signs and symptoms of the cancer, such as cell proliferation or metastasis.

The inventors have surprisingly discovered that COPZ1 knockdown selectively kills tumor cells relative to normal cells and the mechanism of this selectivity, which warrants the development of COPZ1-targeting drugs. Such drugs should inhibit the expression or function of COPZ1 but not COPZ2, since the inhibition of both COPZ1 and COPZ2 kills not only tumor but also normal cells. There are several approaches to selective inhibition of COPZ1 preferentially to COPZ2.

In a fifth aspect, the invention provides a method for selectively inhibiting the growth of cancer cells comprising selectively inhibiting expression or function of coatomer protein zeta-1 subunit gene (COPZ1) or its encoded CopI-ζ1 protein, respectively. “Selective inhibition of cancer cell growth” means killing or inhibiting the growth of cancer cells without killing or inhibiting the growth of normal cells.

In some embodiments, the expression of COPZ1 is inhibited by an agent selected from an siRNA, an antisense oligonucleotide, and a ribozyme, wherein the agent selectively targets mRNA encoding CopI-ζ1 protein. siRNAs and their chemically modified variants are being actively developed for therapeutic applications (Ashihara et al., 2010; Vaishnaw et al., 2010). Related approaches targeting RNA sequences that distinguish COPZ1 from COPZ2 include the use of antisense oligonucleotides (Bennett and Swayze, 2010) and ribozymes (Freelove and Zheng, 2002; Asif-Ullah et al., 2007). In some embodiments, the expression of COPZ1 is inhibited by a small molecule that selectively inhibits COPZ1 expression. The terms “selectively targets” and selectively inhibits” mean that expression of the COPZ1 gene is inhibited, but expression of the COPZ2 gene is not inhibited.

In some embodiments, the function of CopI-ζ1 protein is inhibited by a small molecule or peptide that selectively inhibits CopI-ζ1 protein. The term “selectively inhibits CopI-ζ1 protein” means that the small molecule prevents CopI-ζ1 protein from forming CopI-ζ1 protein/CopI-γ protein dimers, to a greater extent than it prevents CopI-ζ2 protein from forming CopI-ζ2 protein/CopI-γ protein dimers.

The term “small molecule” means a molecule having a molecular weight of less than about 1500 daltons. The greater extent includes at least 10-fold, at least 20-fold, at least 50-fold and at least 100-fold. A “peptide” is an oligomer of from about 3 to about 50 naturally occurring or modified amino acids, and thus also includes peptidomimetics. Such peptides may be further modified, e.g., by pegylation.

In some embodiments, the cancer cells are in the body of an individual. Thus, the invention provides a method for treating an individual having cancer, comprising selectively inhibiting in the individual expression or function of expression or function of COPZ1 gene or its encoded CopI-ζ1 protein, respectively. The method comprises administering to the individual any of the agents discussed above in an effective amount. The term “an effective amount” means an amount sufficient to inhibit cancer cell growth in vivo.

In a sixth aspect, the invention provides a method for identifying a selective small molecule inhibitor or peptide inhibitor of COPZ1 expression comprising: (a) culturing a mammalian cell comprising a recombinant DNA construct comprising a first reporter gene operatively associated with a COPZ1 promoter and a second reporter gene operatively associated with a COPZ2 promoter in the presence of a test compound; (b) culturing the mammalian cell in the absence of the test compound; (c) assaying the cells from (a) and (b) for the expression or activity of the first reporter gene and the second reporter gene, or their encoded proteins; and (d) identifying the test compound as a selective small molecule inhibitor of COPZ1 expression if the expression or activity of the first reporter gene or its encoded protein is inhibited to a greater extent than the expression or activity of the second reporter gene or its encoded protein in cells cultured as in (a), but not in cells cultured as in (b). The use of reporter gene/heterologous promoter systems to identify compounds that inhibit specific gene expression has been described previously, for example, in U.S. Pat. No. 7,235,403. A selective small molecule inhibitor of COPZ1 expression is a compound having a molecular weight of less than about 1500 daltons and which inhibits expression of the COPZ1 gene, but not the COPZ2 gene. A peptide is as described previously. A test compound can be a small molecule or a peptide. The term “inhibited to a greater extent” includes extents of at least 10-fold, at least 20-fold, at least 50-fold and at least 100-fold.

The selective small molecule inhibitors or peptide inhibitor of COPZ1 expression selectively inhibit cancer cell growth. Thus, this method is also a method for identifying a selective small molecule or peptide inhibitor of cancer cell growth. “Selective inhibition of cancer cell growth” means that the compound kills or inhibits the growth of cancer cells without killing or inhibiting the growth of normal cells.

In a seventh aspect, the invention provides a method for identifying a selective small molecule inhibitor or peptide inhibitor of CopI-ζ1 protein comprising: (a) providing purified CopI-ζ1 protein and purified CopI-γ protein in the presence of a test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ1 protein and the purified CopI-γ protein; (b) providing purified CopI-ζ1 protein and purified CopI-γ protein in the absence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ1 protein and the purified CopI-γ protein; (c) providing purified CopI-ζ2 protein and purified CopI-γ protein in the presence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ2 protein and the purified CopI-γ protein; (d) providing purified CopI-ζ2 protein and purified CopI-γ protein in the absence of the test compound to allow an interaction of an assayable magnitude between the purified CopI-ζ2 protein and the purified CopI-γ protein; (e) assaying the magnitude of the interaction between purified CopI-ζ1 protein and purified CopI-γ protein in steps (a) and (b); (f) assaying the magnitude of the interaction between purified CopI-ζ2 protein and purified CopI-γ protein in steps (c) and (d); and (g) identifying the test compound as a selective inhibitor of CopI-ζ1 protein if the magnitude of the interaction is lesser in step (a) than in step (c), but the magnitude of the interaction in step (b) is not lesser than the magnitude of the interaction in step (d).

An interaction between CopI-ζ1 protein and CopI-γ protein, or between CopI-ζ1 protein and CopI-γ protein, can involve either CopI-γ1 protein or CopI-γ2 protein. The interaction results in formation of an active coatomer protein complex.

In some embodiments, the purified CopI-ζ1 protein or the purified CopI-γ protein are labeled with a fluorophore suitable for fluorescence resonance energy transfer (FRET), the CopI-ζ2 protein or the purified CopI-γ protein are labeled with a fluorophore suitable for FRET, and the magnitude of the interactions are assayed by FRET. In some embodiments, the CopI-ζ1 protein and the CopI-ζ2 protein are labeled with a different fluorophore, thereby allowing the assays to take place simultaneously in the same vessel. The use of FRET to assay protein-protein interactions has been described, for example, in Boute et al., 2002; Degorce et al., 2009.

A “selective small molecule inhibitor or peptide inhibitor of CopI-ζ1 protein” is a molecule that prevents CopI-ζ1 protein from forming CopI-ζ1 protein/CopI-γ protein dimers, to a greater extent than it prevents CopI-ζ2 protein from forming CopI-ζ2 protein/CopI-γ protein dimers. The term “small molecule” means a molecule having a molecular weight of less than about 1500 daltons. A peptide is as described previously. The greater extent includes at least 10-fold, at least 20-fold, at least 50-fold and at least 100-fold.

The selective small molecule inhibitors or peptide inhibitors of CopI-ζ1 protein selectively inhibit cancer cell growth. Thus, this method is also a method for identifying a selective small molecule inhibitor or peptide inhibitor of cancer cell growth. “Selective inhibition of cancer cell growth” means that the compound kills or inhibits the growth of cancer cells without killing or inhibiting the growth of normal cells.

In an eighth aspect, the invention provides a method for identifying a selective small molecule inhibitor or peptide inhibitor of cancer cell growth, the method comprising providing a computer model in the form of three-dimensional structural coordinates of CopI-ζ1 protein, providing three dimensional structural coordinates of a candidate compound, using a docking program to compare the three dimensional structural coordinates of the CopI-ζ1 protein with the three dimensional structural coordinates of the compound and calculate an energy-minimized conformation of the candidate compound in the CopI-ζ1 protein, and evaluating an interaction between the candidate compound and the CopI-ζ1 protein to determine binding affinity of the compound for the CopI-ζ1 protein, wherein the candidate compound is identified as a compound that selectively inhibits cancer cell growth if it has a binding affinity for the CopI-ζ1 protein site of at least 10 μM. The solution structure of CopI-ζ1 protein has been described by Yu et al., 2009.

siRNAs or other RNA-targeting drugs, inhibitors of COPZ1 expression, and molecules identified in cell-free assays (such as FRET) or predicted by computer modeling to be selective inhibitors of CopI-ζ1 function can be further tested for the expected biological effects in tumor cells. These effects include inhibition of cell proliferation, induction of cell death, disruption of Golgi and inhibition of autophagy. COPZ1-specific inhibitors inducing such biological effects in tumor cells can be considered as therapeutic candidates for further development.

In a ninth aspect, the invention provides a method for determining whether a cancer in an individual is responsive to treatment by selectively inhibiting expression or function of COPZ1 or CopI-ζ1 protein, respectively, comprising, obtaining cancer cells from the individual, assaying the expression of COPZ2 and/or mIR-152 in the cancer cells, and determining that the cancer in an individual is responsive to treatment by selectively inhibiting expression or function of COPZ1 or CopI-ζ1 protein, respectively, if the expression of COPZ2 and/or mIR-152 in the cancer cells is lower than in normal cells. The expression level in normal cells may be measured from any normal cell, meaning a cell that is not neoplastically transformed. Alternatively, a standardized signal may be provided as a surrogate for normal cell expression. Such expression may be at least 10-fold greater, at least 20-fold greater, at least 50-fold greater or at least 100-fold greater.

In the methods for treatment according to of the invention, the gene expression blocking agent may be formulated with a physiologically acceptable carrier, excipient, or diluent. Such physiologically acceptable carriers, excipients and diluents are known in the art and include any agents that are not physiologically toxic and that do not interfere with the function of the gene expression blocking agent. Representative carriers, excipients and diluents include, without limitation, lipids, salts, hydrates, buffers and the like.

Administration of the gene expression blocking agents or formulations thereof may be by any suitable route, including, without limitation, parenteral, mucosal, transdermal and oral administration.