Isoforms of gata6 and nkx2-1 as markers for diagnosis and therapy of cancer and as targets for anti-cancer therapy

Abstract

The present invention relates to a method of assessing whether a subject suffers from cancer or is prone to suffering from cancer, in particular lung cancer, comprising the measurement of the amounts of specific isoforms of GATA6 and/or NKX2-1 in a sample of said subject. Furthermore, the present invention relates to a composition for use in medicine comprising (an) inhibitor(s) of specific isoforms of GATA6 and/or NKX2-1. Additionally, the present invention relates to a kit for use in a method of assessing whether a subject suffers from cancer or is prone to suffering from cancer, in particular lung cancer.

1 . A method of assessing whether a subject suffers from cancer or is prone to suffering from cancer, said method comprising the steps of
 a) measuring in a sample of said subject the amount of specific transcription factor isoforms wherein said specific transcription isoforms are
 i) the GATA6 Em isoform comprising the nucleic acid sequence of SEQ ID No: 1 or the GATA6 Em isoform comprising a nucleic acid sequence with up to 55 additions, deletions or substitutions of SEQ ID NO: 1; 
 and 
 ii) the NKX2-1 Em isoform comprising the nucleic acid sequence of SEQ ID No: 2 or the NKX2-1 Em isoform comprising a nucleic acid sequence with up to 39 additions, deletions or substitutions of SEQ ID NO: 2; 
   b) comparing the amount of said specific transcription factor Em isoforms with the amount of said specific transcription factor Em isoforms in a control sample; and   c) assessing that said subject suffers from cancer or is prone to suffering from cancer if the amount of said two specific transcription factor Em isoforms in said sample from said subject is increased in comparison to the amount of said specific transcription factor Em isoforms in the control sample.   
     
     
         2 . The method according to  claim 1 , wherein the amount of said specific transcription factor isoform(s) is measured via a polymerase chain reaction-based method, an in situ hybridization-based method, or a microarray. 
     
     
         3 . The method according to  claim 2 , wherein the amount of said specific transcription factor isoform(s) is measured via a polymerase chain reaction-based method and wherein said polymerase chain reaction-based method is a quantitative reverse transcriptase polymerase chain reaction. 
     
     
         4 . The method according to  claim 3 , wherein the step of measuring in a sample of said subject the amount of a specific transcription factor comprises the contacting of the sample with primers, wherein said primers can be used for amplifying at least one of the specific transcription factor isoforms. 
     
     
         5 . The method according to  claim 4 , wherein said primers are selected from the group of primers having a nucleic acid sequence as set forth in SEQ ID NOs 9 to 40. 
     
     
         6 . The method according to any one of  claims 1  to  5 , wherein said step a) further comprises measuring in a sample of said subject the amount of one or two further specific transcription factor isoform(s) selected from the group of specific transcription factor isoforms consisting of
 i) the FOXA2 Em isoform comprising the nucleic acid sequence of SEQ ID No: 3 or the FOXA2 Em isoform comprising nucleic acid sequence with up to 68 additions, deletions or substitutions of SEQ ID NO: 3; and 
 ii) the ID2 Em isoform comprising the nucleic acid sequence of SEQ ID No: 4 or the ID2 Em isoform comprising nucleic acid sequence with up to 34 additions, deletions or substitutions of SEQ ID NO: 4;
 and wherein for assessing that said subject suffers from cancer or is prone to suffering from cancer the amount of all analyzed specific transcription factor Em isoforms has to be increased in comparison to the amount of the analyzed specific transcription factor Em isoforms in the control sample. 
 
 
     
     
         7 . The method according to any one of  claims 1  to  6 , wherein for assessing that said subject suffers from cancer or is prone to suffering from cancer the amount of said analyzed specific transcription factor Em isoform(s) has to be increased by at least 1.3-fold in comparison to the amount of the analyzed specific transcription factor Em isoform(s) in the control sample. 
     
     
         8 . The method according to any of  claims 1  to  7 , wherein the amount of said specific transcription factor isoform(s) is measured on the polypeptide level. 
     
     
         9 . The method according to  claim 8 , wherein the amount of said specific transcription factor isoform(s) is measured by an ELISA, a gel- or blot-based method, mass spectrometry, flow cytometry or FACS. 
     
     
         10 . The method according to any one of  claims 1  to  9 , wherein said cancer is a lung cancer. 
     
     
         11 . The method according to  claim 10 , wherein said lung cancer is an adenocarcinoma or a bronchoalveolar carcinoma. 
     
     
         12 . The method according to any one of  claims 1  to  11 , wherein said sample comprises tumor cells. 
     
     
         13 . The method according to any one of  claims 1  to  12 , wherein said sample is a breath condensate sample, a blood sample, a bronchoalveolar lavage fluid sample, a mucus sample or a phlegm sample. 
     
     
         14 . The method according to any one of  claims 1  to  12 , wherein said sample is a breath condensate sample. 
     
     
         15 . The method according to any one of  claims 1  to  14 , wherein said subject is a human subject. 
     
     
         16 . The method of  claim 15 , wherein said human subject is a subject having an increased risk for developing cancer. 
     
     
         17 . A method of treating a patient, said method comprising
 a) selecting a cancer patient according to the method of any of  claims 1  to  16     b) administering to said cancer patient an effective amount of an anti-cancer agent and/or radiation therapy.   
     
     
         18 . The method of treating a patient according to  claim 17 , wherein said anti-cancer agent is an inhibitor of
 i) the GATA6 Em isoform comprising the nucleic acid sequence of SEQ ID No: 1 or the GATA6 Em isoform nucleic acid sequence with up to 55 additions, deletions or substitutions of SEQ ID NO: 1; or   ii) the NKX2-1 Em isoform comprising the nucleic acid sequence of SEQ ID No: 2 or the NKX2-1 Em isoform comprising a nucleic acid sequence with up to 39 additions, deletions or substitutions of SEQ ID NO: 2.   
     
     
         19 . The method of treating a patient according to  claim 17  or  18 , wherein said cancer patient is a patient suffering from lung cancer. 
     
     
         20 . The method of treating a patient according to  claim 19 , wherein said lung cancer is a lung adenocarcinoma or a bronchoalveolar carcinoma. 
     
     
         21 . A kit for use in any of the methods according to  claims 1  to  20  comprising reagents for measuring in a sample specifically the amount of two transcription factor isoforms selected from the group of specific transcription factor isoforms consisting of
 i) the GATA6 Em isoform comprising the nucleic acid sequence of SEQ ID No: 1 or the GATA6 Em isoform comprising a nucleic acid sequence with up to 55 additions, deletions or substitutions of SEQ ID NO: 1; and 
 ii) the NKX2-1 Em isoform comprising the nucleic acid sequence of SEQ ID No: 2 or the NKX2-1 Em isoform comprising a nucleic acid sequence with up to 39 additions, deletions or substitutions of SEQ ID NO: 2. 
 
     
     
         22 . The kit according to  claim 21  further comprising reagents for measuring in a sample specifically the amount of one or two transcription factor isoforms selected from the group of specific transcription factor isoforms consisting of
 iii) the FOXA2 Em isoform comprising the nucleic acid sequence of SEQ ID No: 3 or the FOXA2 Em isoform comprising nucleic acid sequence with up to 68 additions, deletions or substitutions of SEQ ID NO: 3; and 
 iv) the ID2 Ern isoform comprising the nucleic acid sequence of SEQ ID No: 4 or the ID2 Em isoform comprising nucleic acid sequence with up to 34 additions, deletions or substitutions of SEQ ID NO: 4. 
 
     
     
         23 . The kit according to  claim 21  or  22 , further comprising reagents for measuring in a sample specifically the amount of one or several further transcription factor isoform(s) selected from the group of specific transcription factor isoforms consisting of
 i) the GATA6 Ad isoform comprising the nucleic acid sequence of SEQ ID No: 5 or the GATA6 Ad isoform comprising a nucleic acid sequence with up to 55 additions, deletions or substitutions of SEQ ID NO: 5; 
 ii) the NKX2-1 Ad isoform comprising the nucleic acid sequence of SEQ ID No: 2 or the NKX2-1 Ad isoform comprising the nucleic acid sequence with up to 38 additions, deletions or substitutions of SEQ ID NO: 6; 
 iii) the FOXA2 Ad isoform comprising the nucleic acid sequence of SEQ ID No: 7 or FOXA2 Ad isoform comprising the nucleic acid sequence with up to 74 additions, deletions or substitutions of SEQ ID NO: 3; and 
 iv) the ID2 Ad isoform consisting of the nucleic acid sequence of SEQ ID No: 8 or ID2 Ad isoform consisting of nucleic acid sequence with up to 30 additions, deletions or substitutions of SEQ ID NO: 8; 
 
     
     
         24 . The kit of any one of  claims 21  to  23 , wherein said sample is breath condensate sample or a blood sample. 
     
     
         25 . The kit of any one of  claims 21  to  23 , wherein said sample is a breath condensate sample. 
     
     
         26 . The kit of any one of  claims 21  to  25 , wherein said sample is a sample from a human subject. 
     
     
         27 . The kit of  claim 26 , wherein the kit comprises one or several primers selected from the group of primers comprising the nucleic acid sequence of SEQ IDs 9 to 40.