Compositions and methods for the diagnosis and treatment of ovarian cancers that are associated with reduced smarca4 gene expression or protein function

Abstract

Provided are compositions and methods for the identification and treatment of ovarian cancers, such as small cell ovarian cancers, in particular small cell carcinoma of the ovary, hypercalcemic type (SCCOHT), which ovarian cancers are characterized by reduced SMARCA4 gene expression and/or protein function and, as a consequence, are sensitive to growth and/or survival inhibition by one or more compounds that restore SMARCA4 gene expression and/or protein function.

1 . A method for the diagnosis of small cell carcinoma of the ovary hypercalcemic type (SCCOHT), said method comprising detecting in a biological sample from a subject one or more mutations in a SMARCA4 gene and/or a regulatory sequence associated with the SMARCA4 gene, each of which mutations is known, predicted, or demonstrated to reduce or eliminate at least one of SMARCA4 gene expression, SMARCA4 protein level, and SMARCA4 protein function. 
     
     
         2 . The method of  claim 1  wherein at least one of said mutations in said SMARCA4 gene is a germline mutation or a somatic mutation. 
     
     
         3 . (canceled) 
     
     
         4 . The method of  claim 1  wherein each allele of the SMARCA4 gene and/or associated regulatory sequence comprises one or more mutations, each of which mutations is known, predicted, or demonstrated to reduce or eliminate at least one of SMARCA4 gene expression, SMARCA4 protein level, and SMARCA4 protein function. 
     
     
         5 . The method of  claim 1  where each of said mutations in said SMARCA4 gene is selected from the group consisting of an insertion mutation, a deletion mutation, a frame shift mutation, a splice site mutation, a nonsense mutation, and a missense mutation. 
     
     
         6 . The method of  claim 1  wherein at least one of said mutations in said SMARCA4 gene is upstream of the region of said SMARCA4 gene that encodes a HAS domain. 
     
     
         7 . The method of  claim 1  wherein at least one of said mutations in said SMARCA4 gene is (i) upstream of a region of said SMARCA4 gene that encodes a BRK domain; or (ii) within a region of said SMARCA4 gene that encodes a SNF2_N domain; or (iii) is upstream of or within a region of said SMARCA4 gene that encodes a Helicase Domain; or (iv) is upstream of or within a region of said SMARCA4 gene that encodes a SnAC Domain; or (v) is upstream of or within the region of said SMARCA4 gene that encodes a Bromo Domain or a combination of two or more of the foregoing. 
     
     
         8 . (canceled) 
     
     
         9 . (canceled) 
     
     
         10 . (canceled) 
     
     
         11 . (canceled) 
     
     
         12 . A method for inhibiting the growth of a cancer cell exhibiting reduced or undetectable: (i) SMARCA4 protein level; (ii) SMARCA4 protein function, or (iii) both SMARCA4 protein levels and function, said method comprising contacting said cancer cell with one or more compounds that can restore one or more of SMARCA4 gene expression, SMARCA4 protein level, and/or SMARCA4 protein function, wherein said one or more compounds slows or stops the growth of said cancer cell. 
     
     
         13 . The method of  claim 12  wherein said cancer cell is an ovarian cancer cell. 
     
     
         14 . The method of  claim 13  wherein said ovarian cancer cell is a small cell carcinoma of the ovary hypercalcemic type (SCCOHT). 
     
     
         15 . The method of  claim 12  wherein said compound is selected from the group consisting of a small molecule, a polynucleotide, and a polypeptide. 
     
     
         16 . A method for treating a patient afflicted with a cancer that is associated with a cell exhibiting reduced or undetectable SMARCA4 protein levels and/or protein function, said method comprising contacting said cancer cell with one or more compounds that can restore one or more of SMARCA4 gene expression, SMARCA4 protein level, and/or SMARCA4 protein function, wherein said one or more compounds slows or stops the growth of said cancer cell. 
     
     
         17 . The method of  claim 16  wherein said cancer cell is an ovarian cancer cell. 
     
     
         18 . The method of  claim 17  wherein said ovarian cancer cell is a small cell carcinoma of the ovary hypercalcemic type (SCCOHT). 
     
     
         19 . The method of  claim 16  wherein said compound is selected from the group consisting of a small molecule, a polynucleotide, and a polypeptide. 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . (canceled) 
     
     
         24 . (canceled) 
     
     
         25 . A diagnostic kit for identifying a cancer cell or for detecting in a patient a cancer cell that exhibits reduced SMARCA4 gene expression, reduced SMARCA4 protein function, and/or reduced SMARCA4 protein level, which diagnostic kit contains one or more reagents that can be used alone or in combination to: (a) detect a mutation in a SMARCA4 gene and/or mRNA; (b) detect a reduction in SMARCA4 mRNA level; (c) detect a reduction in SMARCA4 protein level; and/or (d) detect a reduction in SMARCA4 protein functionality, wherein said kit also contains positive and negative controls for said identification or detection. 
     
     
         26 . The diagnostic kit of  claim 25  wherein said mutation in said SMARCA4 gene and/or mRNA is selected from the group consisting of an insertion mutation, a deletion mutation, a frame shift mutation, a splice site mutation, a nonsense mutation, and a missense mutation. 
     
     
         27 . A method for establishing or excluding a diagnosis of small cell carcinoma of the ovary hypercalcemic type (SCCOHT) in a subject, said method comprising: determining whether a SMARCA4 nucleotide sequence from a cancer cell obtained from an ovarian tumor of said subject has a mutation as compared to a wild-type SMARCA4 nucleotide sequence, wherein:
 (a) if said mutation is associated with reduced SMARCA4 gene expression and/or reduced SMARCA4 protein functionality, the presence of said mutations is predictive of SCCOHT; or   (b) if said mutation is not associated with reduced SMARCA4 gene expression and/or reduced SMARCA4 protein functionality, the presence of said mutation is not predictive of SCCOHT; or   (c) if a mutation is absent in said SMARCA4 nucleotide sequence excludes SCCOHT from the diagnosis.   
     
     
         28 . The method of  claim 27  wherein said mutation in SMARCA4 nucleotide sequence includes a nonsense mutation, a missense mutation, a deletion, an insertion, a frameshift mutation, and/or a duplication mutation. 
     
     
         29 . The method of  claim 27  wherein the ascertaining step comprises comparing a SMARCA4 nucleotide sequence in said cancer cell with a SMARCA4 nucleotide sequence in said control wherein the presence of said mutation in the cancer cell SMARCA4 nucleotide sequence indicates SCCOHT; conversely, the absence of said mutation in the cancer cell SMARCA4 nucleotide sequence excludes SCCOHT. 
     
     
         30 . The method of  claim 27  wherein the ascertaining step comprises: comparing the level of a SMARCA4 gene expression in said cancer cell and to the level of expression in a SMARCA4 gene in said control; wherein a reduced level of SMARCA4 gene expression in said cancer cell as compared to said control indicates SCCOHT; and conversely, the absence of a reduced level of SMARCA4 gene expression in said cancer cell as compared to said control excludes SCCOHT. 
     
     
         31 . A method for detecting whether a cancer cell is involved in ovarian cancer, said method comprising: ascertaining a SMARCA4 protein level in said cancer cell in comparison to a SMARCA4 protein level in a non cancer cell, wherein a reduced level of SMARCA4 protein in said cancer cell as compared to said non-cancer cell indicates that is involved in ovarian cancer. 
     
     
         32 . A method for detecting whether a cancer cell is involved in ovarian cancer, said method comprising: detecting a carboxy-terminal truncation in a SMARCA4 protein in said cancer cell wherein the presence of said carboxy-terminal truncation in said SMARCA4 protein indicates that said cancer cell is involved in ovarian cancer. 
     
     
         33 . A method for detecting whether a cancer cell is involved in ovarian cancer, said method comprising: detecting levels of a SWI/SNF and/or a BAF protein-protein complex containing SMARCA4 in said cancer cell in comparison to a swi/snf and/or a baf protein-protein complexes containing SMARCA4 in a non cancer cell, wherein the presence of a reduced level of a SWI/SNF and/or a BAF protein-protein complex containing SMARCA4 in said cancer cell indicates that said cancer cell is involved in ovarian cancer. 
     
     
         34 . A method for detecting whether a cancer cell is involved in ovarian cancer, said method comprising: detecting levels of expression of one or more SMARCA4 downstream target genes in a cancer cell in comparison to a non-cancer cell, wherein said target gene is selected from the group consisting of CDH1, CDH3, EHF, RRAD, and ML-IAP, and wherein a reduced expression level of said SMARCA4 downstream target gene in said cancer cell indicates that said cancer cell is involved in ovarian cancer. 
     
     
         35 . A method for treating a patient previously diagnosed with ovarian cancer that is associated with ovarian cancer cell exhibiting reduced or undetectable SMARCA4 protein levels and/or protein function, said method comprising contacting said ovarian cancer cell with one or more compounds that can restore one or more of SMARCA4 gene expression, SMARCA4 protein level, and/or SMARCA4 protein function, wherein said one or more compounds slows or stops the growth of said ovarian cancer cell. 
     
     
         36 . A method for diagnosing and treating SCCOHT in a patient, said method comprising:
 detecting in a biological sample from a patient one or more mutations in a SMARCA4 gene and/or an associated regulatory sequence; and either
 (i) diagnosing the patient with SCCOHT when the presence of one or more mutations in a SMARCA4 gene and/or associated regulatory sequence is detected, each of which mutations is known, predicted, or demonstrated to reduce or eliminate at least one of SMARCA4 gene expression, SMARCA4 protein levels, and SMARCA4 protein function; and (ii) administering an effective amount of one or more compounds that can restore one or more of SMARCA4 gene expression, SMARCA4 protein level, and/or SMARCA4 protein function to the diagnosed patient; or 
 (ii) excluding diagnosis of SCCOHT when none of said mutations is known, predicted or demonstrated to reduce or eliminate at least one of SMARCA4 gene expression, SMARCA4 protein levels, and SMARCA4 protein function. 
   
     
     
         37 . A method for diagnosing a predisposition to developing SCCOHT, said method comprising: determining whether a SMARCA4 nucleotide sequence in a biological sample has a mutation as compared to a wild-type SMARCA4 nucleotide sequence, wherein
 if said mutation is present and associated with reduced SMARCA4 gene expression and/or reduced SMARCA4 protein functionality, the presence of said mutations is predictive of developing SCCOHT; or   if said mutation is present and not associated with reduced SMARCA4 gene expression and/or reduced SMARCA4 protein functionality, the presence of said mutation is not predictive of SCCOHT; or   if no mutation in said SMARCA4 nucleotide sequence is present then predisposition to developing SCCOHT is ruled out.