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 a lung cell sample or a breath condensate from a subject, said method comprising the steps of
 a) measuring in the lung cell sample or breath condensate of said subject the amount of specific embryonic and adult transcription factor isoforms by performing detection assay to specifically detect said specific embryonic and adult transcription factor isoforms, wherein said specific embryonic and adult 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 capable of hybridizing a primer pair having SEQ ID NO: 9 and SEQ ID NO: 11 or a primer pair having SEQ ID NO: 10 and SEQ ID NO: 12; and 
 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 and capable of hybridizing a primer pair having SEQ ID NO: 13 and SEQ ID NO: 15 or a primer pair having SEQ ID NO: 14 and SEQ ID NO: 16; 
 and/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 and capable of hybridizing a primer pair having SEQ ID NO: 17 and SEQ ID NO: 19 or a primer pair having SEQ ID NO: 18 and SEQ ID NO: 20; and 
 the NKX2-1 Ad isoform comprising the nucleic acid sequence of SEQ ID NO: 6 or the NKX2-1 Ad isoform comprising a nucleic acid sequence with up to 55 additions, deletions or substitutions of SEQ ID NO: 6 and capable of hybridizing a primer pair having SEQ ID NO: 21 and SEQ ID NO: 23 or a primer pair having SEQ ID NO: 22 and SEQ ID NO: 24; 
   b) comparing the amount of said specific embryonic and adult transcription factor isoforms to provide a ratio of the specific embryonic and adult transcription factor isoforms in the lung cell sample or breath condensate; and   c) assessing that said subject suffers from cancer or is prone to suffering from cancer if the ratio is higher than 0.5 when the transcription factor is GATA 6 and higher than 0.3 when the transcription factor is NKX2-1.   
     
     
         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. 
     
     
         4 . The method according to  claim 3 , wherein the step of measuring in a lung cell sample or a breath condensate 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  claim 1 , wherein
 said step a) further comprises measuring in the lung cell sample or the breath condensate 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 a nucleic acid sequence with up to 68 additions, deletions or substitutions of SEQ ID NO: 3 and capable of hybridizing a primer pair having SEQ ID NO: 25 and SEQ ID NO: 27 or a primer pair having SEQ ID NO: 26 and SEQ ID NO: 28; 
 and 
 ii) the ID2 Em isoform comprising the nucleic acid sequence of SEQ ID No: 4 or the ID2 Em isoform comprising a nucleic acid sequence with up to 34 additions, deletions or substitutions of SEQ ID NO: 4 and capable of hybridizing a primer pair having SEQ ID NO: 33 and SEQ ID NO: 35 or by a primer pair having SEQ ID NO: 34 and SEQ ID NO: 36. 
   
     
     
         7 . (canceled) 
     
     
         8 . The method according to  claim 1 , 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  claim 1 , 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  claim 1 , wherein said lung cell sample comprises tumor cells. 
     
     
         13 . The method according to  claim 1 , wherein said lung cell sample is a blood sample, a bronchoalveolar lavage fluid sample, a mucus sample or a phlegm sample. 
     
     
         14 . (canceled) 
     
     
         15 . The method according to  claim 1 , 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 subject, said method comprising
 a) assessing a lung cell sample or a breath condensate from the subject according to the method of  claim 1 ; and   b) administering to said subject 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 isoform specific siRNA 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 and capable of hybridizing a primer pair having SEQ ID NO: 9 and SEQ ID NO: 11 or a primer pair having SEQ ID NO: 10 and SEQ ID NO: 12; 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 and capable of hybridizing a primer pair having SEQ ID NO: 17 and SEQ ID NO: 19 or a primer pair having SEQ ID NO: 18 and SEQ ID NO: 20.   
     
     
         19 . The method of treating a subject according to  claim 17 , wherein said subject is a subject suffering from lung cancer. 
     
     
         20 . The method of treating a subject according to  claim 19 , wherein said lung cancer is a lung adenocarcinoma or a bronchoalveolar carcinoma. 
     
     
         21 .- 27 . (canceled) 
     
     
         28 . The method according to  claim 5 , wherein said primers comprise primers having a nucleic acid sequence as set forth in:
 (i) SEQ ID NO: 10 and SEQ ID NO: 12;   (ii) SEQ ID NO: 14 and SEQ ID NO: 16;   (iii) SEQ ID NO: 18 and SEQ ID NO: 20; or   (iv) SEQ ID NO: 22 and SEQ ID NO: 24.   
     
     
         29 . The method according to  claim 3 , wherein said polymerase chain reaction-based method is a quantitative reverse transcriptase polymerase chain reaction. 
     
     
         30 . The method according to  claim 1 , wherein the measuring is performed on the nucleic acid level by contacting the lung cell sample or the breath condensate with primers specific for said specific transcription isoforms; or wherein the measuring is performed on the polypeptide level by an ELISA, a gel- or blot-based method, mass spectrometry, flow cytometry or FACS. 
     
     
         31 . The method according to  claim 17 , wherein the lung cell sample or the breath condensate is a breath condensate from the subject. 
     
     
         32 . The method according to  claim 17 , wherein the lung cell sample is a blood sample, a bronchoalveolar lavage fluid sample, a mucus sample or a phlegm sample.