ncRNA AND USES THEREOF

Abstract

The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to ncRNAs as diagnostic markers and clinical targets for prostate, lung, breast and pancreatic cancer.

1 - 19 . (canceled) 
     
     
         20 . A method of detecting non-coding RNAs (ncRNA) in a subject comprising (a) obtaining a sample from a subject suspected of having prostate cancer, wherein the sample comprises ncRNA; (b) processing the sample to isolate or enrich the sample for ncRNA or cells containing ncRNA; and (c) detecting the level of expression of one or more ncRNAs in said sample by sequencing, nucleic acid hybridization or nucleic acid amplification, wherein said one or more ncRNAs is selected from the group consisting of one or more PCATs and SChLAP-1. 
     
     
         21 . The method of  claim 20 , wherein the one or more PCATs is selected from the group consisting of PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, or PCAT121. 
     
     
         22 . The method of  claim 20 , wherein the sample is selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions and prostate cells. 
     
     
         23 . The method of  claim 20 , wherein the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification. 
     
     
         24 . The method of  claim 20 , wherein said cancer is selected from the group consisting of localized prostate cancer and metastatic prostate cancer. 
     
     
         25 . A method of diagnosing and treating prostate cancer in a subject, said method comprising: (a) obtaining a sample from a subject, wherein the sample comprises non-coding RNAs (ncRNA)); (b) processing the sample to isolate or enrich the sample for ncRNA or cells containing ncRNA; (c) detecting the level of expression of one or more ncRNAs in said sample by sequencing, nucleic acid hybridization or nucleic acid amplification, wherein said one or more ncRNAs is selected from the group consisting of one or more PCATs and SChLAP-1; (d) diagnosing the subject with prostate cancer when an increased level of expression of said one or more ncRNAs in said sample relative to the level in normal prostate cells is detected; and (e) administering an effective amount of a PARP inhibitor or radiation to the diagnosed subject. 
     
     
         26 . The method of  claim 25 , wherein the PARP inhibitor is olaparib or ABT-888. 
     
     
         27 . The method of  claim 25 , wherein the one or more PCATs is selected from the group consisting of PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, or PCAT121. 
     
     
         28 . The method of  claim 25 , wherein the sample is selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions and prostate cells. 
     
     
         29 . The method of  claim 25 , wherein the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification. 
     
     
         30 . The method of  claim 25 , wherein said cancer is selected from the group consisting of localized prostate cancer and metastatic prostate cancer. 
     
     
         31 . A method of diagnosing prostate cancer in a subject, said method comprising: (a) obtaining a sample from a subject, wherein the sample comprises non-coding RNAs (ncRNA)); (b) processing the sample to isolate or enrich the sample for ncRNA or cells containing ncRNA; (c) detecting the level of expression of one or more ncRNAs in said sample by sequencing, nucleic acid hybridization or nucleic acid amplification, wherein said one or more ncRNAs is selected from the group consisting of one or more PCATs and SChLAP-1; and (d) diagnosing the subject with prostate cancer when an increased level of expression of said one or more ncRNAs in said sample relative to the level in normal prostate cells is detected. 
     
     
         32 . The method of  claim 31 , wherein the one or more PCATs is selected from the group consisting of PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, or PCAT121. 
     
     
         33 . The method of  claim 31 , wherein the sample is selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions and prostate cells. 
     
     
         34 . The method of  claim 31 , wherein the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification. 
     
     
         35 . The method of  claim 31 , wherein said cancer is selected from the group consisting of localized prostate cancer and metastatic prostate cancer. 
     
     
         36 . A method comprising: (a) obtaining a sample from a subject, wherein the sample comprises non-coding RNAs (ncRNA); (b) processing the sample to isolate or enrich the sample for ncRNA or cells containing ncRNA; (c) detecting the level of expression of one or more ncRNAs in said sample by sequencing, nucleic acid hybridization or nucleic acid amplification, wherein said one or more ncRNAs is selected from the group consisting of one or more PCATs and SChLAP-1; and (d) administering an effective amount of a PARP inhibitor or radiation to the subject based on the level of expression of one or more ncRNAs in said sample. 
     
     
         37 . The method of  claim 36 , wherein the one or more PCATs is selected from the group consisting of PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, or PCAT121. 
     
     
         38 . The method of  claim 36 , wherein the sample is selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions and prostate cells. 
     
     
         39 . The method of  claim 36 , wherein the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification. 
     
     
         40 . The method of  claim 36 , wherein said cancer is selected from the group consisting of localized prostate cancer and metastatic prostate cancer.