Compositions, methods and kits for characterizing and screening for small cell ovarian carcinoma

Abstract

The present invention relates compositions, methods and kits for characterizing the type of and screening for the existence or predisposition for small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). The invention also relates to a method of treating a mammalian subject having SCCOHT or a predisposition for SCCOHT.

1 . A method of screening for the existence of or a predisposition for small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) in a mammalian subject, the method comprising:
 obtaining a sample from the subject;   screening the sample for an inactivation alteration in a SWI/SNF complex; and   determining that the subject has SCCOHT or a predisposition for SCCOHT if the SWI/SNF inactivation alteration is detected.   
     
     
         2 . The method of  claim 1 , further comprising
 screening a biological sample containing SCCOHT cells for an alteration in a SWI/SNF complex in vitro, wherein the alteration in the SWI/SNF complex results in inactivation of the SWI/SNF complex; and   classifying the SCCOHT as a SWI/SNF inactivation induced cancer upon detecting a germline or somatic inactivation alteration in the SWI/SNF complex in the SCCOHT cells.   
     
     
         3 . The method of  claim 1 , wherein gene members of the SWI/SNF complex comprise at least one gene selected from the group consisting of SMARCB1, SMRCA2, and SMARCA4. 
     
     
         4 . The method of  claim 1 , wherein the inactivation alteration is in the SWI/SNF complex is a mutation of a gene member of the SWI/SNF complex. 
     
     
         5 . The method of  claim 1 , wherein the mammalian subject is human and further comprising detecting a germline mutation of the wild-type SMARCA4 gene or its expression products in the subject. 
     
     
         6 . (canceled) 
     
     
         7 . The method of  claim 5 , wherein the germline mutation is an inactivating truncation mutation, a heterozygous nonsense mutation (c.T2935G) of the wild type SMARCA4 gene upstream of the helicase and bromodomains, resulting in a truncated SMARCA4 protein product with a protein alteration of p.R979*. 
     
     
         8 . (canceled) 
     
     
         9 . The method of  claim 7 , wherein the inactivating truncation mutation is a frameshift mutation in exon 4 (c.722-735del GGTCCCGGCCCGGCA) (SEQ ID NO: 1) of the wild-type SMARCA4 gene removing all essential SMARCA4 functional domains, resulting in a truncated SMARCA4 protein product with a predicted protein alteration of p.G241fs. 
     
     
         10 . The method of  claim 5 , wherein the expression product comprises a SMARCA4 mRNA, polypeptide or protein molecule. 
     
     
         11 . The method of  claim 5 , wherein the alteration of the wild-type SMARCA4 gene is detected by exome sequencing of the sample, the sample comprising peripheral blood DNA. 
     
     
         12 . The method of  claim 1 , comprising detecting a somatic alteration of the wild-type SMARCA4 gene or its expression product in the sample, wherein the alteration of the wild-type SMARCA4 gene is detected by sequencing of genomic DNA from a SCCOHT tumor and/or a SCCOHT cell line. 
     
     
         13 . (canceled) 
     
     
         14 . The method of  claim 12 , wherein the alteration of the wild-type SMARCA4 gene comprises a monoallelic or biallelic inactivating mutation in the wild-type SMARCA4 gene, and the monoallelic or biallelic inactivating mutation is either a truncation mutation of the wild-type SMARCA4 gene within its ATPase domain resulting in a truncated SMARCA4 protein product or a splice site mutation of the wild-type SMARCA4 gene resulting in a truncated SMARCA4 protein product. 
     
     
         15 - 16 . (canceled) 
     
     
         17 . The method of  claim 1 , further comprising detecting a somatic alteration of the wild-type SMARCB1 gene or its expression product in the sample and wherein the somatic alteration is a homozygous frameshift mutation, p.Asn34fs, resulting from the deletion of 14 base pairs in exon 2 of SMARCB1. 
     
     
         18 . (canceled) 
     
     
         19 . The method of  claim 1 , wherein the inactivation alteration comprises a mutation in the wild-type SMARCA4 gene and a mutation in the wild-type SMARCA2 gene. 
     
     
         20 . A therapeutic method for preventing and/or reducing the progression of SCCOHT in a subject having SCCOHT or having a predisposition to SCCOHT, the method comprising:
 (a) identifying a subject having SCCOHT or having a predisposition to SCCOHT comprising:
 (i) obtaining a sample from the subject; 
 (ii) detecting in the sample an inactivation mutation in a SWI/SNF complex, wherein the mutation inactivates the SMARCA4 gene and indicates a predisposition to SCCOHT; and 
 (iii) identifying the subject as having SCCOHT or having a predisposition for SCCOHT if the SWI/SNF inactivation alteration is detected in the sample; and 
   (b) treating the identified subject with an inhibitor of a target gene that is synthetic lethal with the SMARCA4 gene or with a SMARCA4 gene therapy, a SMARCA4 protein replacement therapy, and/or a SMARCA4 protein mimetic.   
     
     
         21 . (canceled) 
     
     
         22 . A composition for diagnosing the existence of or a predisposition for SCCOHT in a mammalian subject, the composition comprising:
 at least one oligonucleotide for specifically determining a presence or an absence of an inactivation alteration in at least one gene selected from the group consisting of SMARCB1, SMARCA2, and SMARCA4 of the SWI/SNF complex,   wherein the inactivation alteration in the SMARCA4 gene comprises a heterozygous nonsense mutation (c.T2935G) of the wild type SMARCA4 gene upstream of the helicase and bromodomains or a frameshift mutation in exon 4 (c.722-735del TCCCGGCCCGGCA) (SEQ ID NO: 1) of the wild type SMARCA4 gene removing all essential SMARCA4 functional domains.   
     
     
         23 . (canceled) 
     
     
         24 . The method of  claim 20 , wherein the target gene is selected from the group consisting of ARIDIA, SMARCA2, SMARCC1, SMARCD1, SMARCE1, BRD7, SMARCD2, and SMARCB1. 
     
     
         25 - 26 . (canceled) 
     
     
         27 . A method of treating SCCOHT in a subject in need thereof, the method comprising administering to the subject an effective amount of: (1) an epigenetic agent selected from the group consisting of: a modifier of acetylated histones, a DNA methylation inhibitor, a histone methyltransferase inhibitor, and a histone deacetylase (HDAC) inhibitor; (2) an fibroblast growth factor receptor (FGFR) inhibitor and/or a receptor tyrosine kinase (RTK) of the TYRO3/AXL/MerTK family (MERTK) inhibitor: or (3) both. 
     
     
         28 . The method of  claim 27 , wherein the epigenetic agent is an HDAC inhibitor selected from the group consisting of Romidepsin, Panobinostat, Belinostat, suberoylanilide hydroxamic acid (SAHA), and Entinostat. 
     
     
         29 - 30 . (canceled) 
     
     
         31 . The method of  claim 27 , wherein the FGFR inhibitor is ponatinib. 
     
     
         32 . The method of  claim 27 , wherein the FGFR inhibitor and/or MERTK inhibitor is an siRNA molecule.