Method of diagnosing neoplasms

Abstract

The present invention relates generally to a nucleic acid molecule, the RNA and protein expression profiles of which are indicative of the onset, predisposition to the onset and/or progression of a large intestine neoplasm. More particularly, the present invention is directed to a nucleic acid molecule, the expression profiles of which are indicative of the onset and/or progression of a colorectal neoplasm, such as an adenoma or an adenocarcinoma. The expression profiles of the present invention are useful in a range of applications including, but not limited to, those relating to the diagnosis and/or monitoring of colorectal neoplasms, such as colorectal adenomas and adenocarcinomas. Accordingly, in a related aspect the present invention is directed to a method of screening a subject for the onset, predisposition to the onset and/or progression of a large intestine neoplasm by screening for modulation in the expression profile of said nucleic acid molecule markers.

1 . A method of screening for the onset or predisposition to the onset of a large intestine neoplasm, or monitoring the progress of a neoplasm, in an individual, said method comprising: (i) measuring the level of expression of hCG — 1815491 in a biological sample from said individual wherein a higher level of expression of hCG — 1815491 or variant thereof relative to control levels is indicative of a neoplastic large intestine cell or a cell predisposed to the onset of a neoplastic state; or (ii) measuring the level of expression of a gene comprising a sequence of nucleotides as set forth in SEQ ID NO:1 or a sequence having at least 90% similarity to SEQ ID NO:1 across the length of the gene, or variant of SEQ ID NO:1, in a biological sample from said individual wherein a higher level of expression of said gene or variant thereof relative to control levels is indicative of a neoplastic large intestine cell or a cell predisposed to the onset of a neoplastic state. 
     
     
         2 . (canceled) 
     
     
         3 . The method according to  claim 1  said method comprising measuring the level of expression of one or more mRNA transcripts, which transcripts comprise an RNA sequence selected from:
 (i) an RNA sequence characterized by the sequence of one of:
 SEQ ID NO:21, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:21; 
 SEQ ID NO:22, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:22; 
 SEQ ID NO:23, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:23; 
 SEQ ID NO:24, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:24; 
 SEQ ID NO:25, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:25; 
 SEQ ID NO:26, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:26; 
 SEQ ID NO:27, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:27; 
 SEQ ID NO:28, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:28; 
 SEQ ID NO:29, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:29; 
 SEQ ID NO:30, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:30; or 
 SEQ ID NO:31, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:31 
 
 (ii) an RNA sequence characterized by the sequence of one of:
 SEQ ID NO:21, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:21; 
 SEQ ID NO:24, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:24; 
 SEQ ID NO:27, or a sequence having at least 90% similarity length of the sequence, or variant of SEQ ID NO:27; 
 SEQ ID NO:22, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:22; 
 SEQ ID NO:23, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:23; 
 SEQ ID NO:30, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:30; 
 SEQ ID NO:31, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:31; 
 SEQ ID NO:25, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:25. 
 
 (iii) an RNA sequence characterized by the sequence of one of:
 SEQ ID NO:21, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:21; 
 SEQ ID NO:24, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:24; 
 SEQ ID NO:27, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:27; 
 SEQ ID NO:22, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:22. 
 
 
     
     
         4 . (canceled) 
     
     
         5 . (canceled) 
     
     
         6 . A method of screening for the onset or predisposition to the onset of a large intestine neoplasm in an individual, said method comprising measuring the level of expression of an RNA transcript, which transcript comprises one or more exon segments selected from:
 (i) an exon segment defined by SEQ ID NO:2, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:2;   (ii) an exon segment defined by SEQ ID NO:3, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:3   (iii) an exon segment defined by SEQ ID NO:4, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:4;   (iv) an exon segment defined by SEQ ID NO:5, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:5;   (v) an exon segment defined by SEQ ID NO:6, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:6;   (vi) an exon segment defined by SEQ ID NO:7, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:7;   (vii) an exon segment defined by SEQ ID NO:8, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:8;   (viii) an exon segment defined by SEQ ID NO:9, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:9;   (ix) an exon segment defined by SEQ ID NO:10, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:10;   (x) an exon segment defined by SEQ ID NO:11, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:11;   (xi) an exon segment defined by SEQ ID NO:12, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:12   (xii) an exon segment defined by SEQ ID NO:13, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:13   (xiii) an exon segment defined by SEQ ID NO:14, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:14   (xiv) an exon segment defined by SEQ ID NO:15, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:15   (xv) an exon segment defined by SEQ ID NO:16, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:16   (xvi) an exon segment defined by SEQ ID NO:17, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:17   (xvii) an exon segment defined by SEQ ID NO:18, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:18   (xviii) an exon segment defined by SEQ ID NO:19, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:19; or   (xix) an exon segment defined by SEQ ID NO:20, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:20   
       in a biological sample from said individual wherein a higher level of said RNA transcript or variant thereof relative to control levels is indicative of a neoplastic large intestine cell or a cell predisposed to the onset of a neoplastic state. 
     
     
         7 . The method according to  claim 6  wherein said transcript comprises one or more exon segments selected from:
 (i) an exon segment defined by SEQ ID NO:3, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:3 
 (ii) an exon segment defined by SEQ ID NO:4, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:4; 
 (iii) an exon segment defined by SEQ ID NO:5, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:5; 
 (iv) an exon segment defined by SEQ ID NO:6, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:6; 
 (v) an exon segment defined by SEQ ID NO:7, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:7; 
 (vi) an exon segment defined by SEQ ID NO:8, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:8; 
 (vii) an exon segment defined by SEQ ID NO:9, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:9; or 
 (viii) an exon segment defined by SEQ ID NO:10, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:10; 
 (ix) an exon segment defined by SEQ ID NO:11, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:11; 
 (x) an exon segment defined by SEQ ID NO:12, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:12; 
 (xi) an exon segment defined by SEQ ID NO:13, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:13; 
 (xii) an exon segment defined by SEQ ID NO:14, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:14; 
 (xiii) an exon segment defined by SEQ ID NO:15, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:15; 
 (xiv) an exon segment defined by SEQ ID NO:18, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:18; 
 (xv) an exon segment defined by SEQ ID NO:19, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:19 
 
     
     
         8 . The method according to  claim 7  wherein said transcript is selected from:
 (i) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:12, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:12; 
 (ii) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:14, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:14; 
 (iii) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:3 and SEQ ID NO:6, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:3 and SEQ ID NO:6; 
 (iv) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:11, SEQ ID NO:12 and SEQ ID NO:18, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:11, SEQ ID NO:12 and SEQ ID NO:18; 
 (v) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:4 and SEQ ID NO:7, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:4 and SEQ ID NO:7; 
 (vi) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:13, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:13; 
 (vii) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:6 and SEQ ID NO:8, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:6 and SEQ ID NO:8; 
 (viii) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:19 and SEQ ID NO:18, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:19 and SEQ ID NO:18; 
 (ix) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:15 and SEQ ID NO:18, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:15 and SEQ ID NO:18; 
 (x) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:6 and SEQ ID NO:9, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:6 and SEQ ID NO:9; or 
 (xi) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:12, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:12. 
 
     
     
         9 . The method according to  claim 6  wherein said transcript comprises one or more exon segments selected from:
 (i) an exon segment defined by SEQ ID NO:5, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:5; 
 (ii) an exon segment defined by SEQ ID NO:6, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:6; 
 (iii) an exon segment defined by SEQ ID NO:8, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:8; 
 (iv) an exon segment defined by SEQ ID NO:10, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:10; 
 (v) an exon segment defined by SEQ ID NO:11, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:11; 
 (vi) an exon segment defined by SEQ ID NO: 12, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:12; 
 (vii) an exon segment defined by SEQ ID NO:14, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO: 14; or    
 (viii) an exon segment defined by SEQ ID NO:18, or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:18. 
 
     
     
         10 . The method according to  claim 7  wherein said transcript is selected from:
 (i) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:12, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:12; 
 (ii) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:14, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:10 and SEQ ID NO:14; 
 (iii) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:18 and SEQ ID NO:24, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:18 and SEQ ID NO:24; or 
 (iv) an RNA transcript which comprises each of the exon segments defined by SEQ ID NO:6 and SEQ ID NO:8, or a sequence having at least 90% similarity across the length of these sequences, or variants of SEQ ID NO:6 and SEQ ID NO:8. 
 
     
     
         11 . The method according to  claims 1  or  6  wherein the exon segments of said transcripts are spliced such that they are joined. 
     
     
         12 . A method of screening for the onset or predisposition to the onset of a large intestine neoplasm in an individual, said method comprising measuring the level of expression of one or more RNA transcripts, which transcripts comprise an RNA sequence characterised by the sequence of one of:
 (i) SEQ ID NO:21 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:21;   (ii) SEQ ID NO:24 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:24;   (iii) SEQ ID NO:25 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:25;   (iv) SEQ ID NO:26 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:26;   (v) SEQ ID NO:27 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:27;   (vi) SEQ ID NO:29 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:29;   (vii) SEQ ID NO:30 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:30; or   (viii) SEQ ID NO:31 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:31;   
       in a biological sample from said individual wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to background levels is indicative of a neoplastic cell or a cell predisposed to the onset of a neoplastic state. 
     
     
         13 . The method according to  claim 12  wherein said transcripts comprise an RNA sequence characterised by the sequence of one of:
 (i) SEQ ID NO:21 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:21; 
 (ii) SEQ ID NO:22 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:22; 
 (iii) SEQ ID NO:23 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:23; 
 (iv) SEQ ID NO:24 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:24; or 
 (v) SEQ ID NO:27 or a sequence having at least 90% similarity across the length of the sequence, or variant of SEQ ID NO:27; 
 
       in a biological sample from said individual wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to background levels is indicative of a neoplastic cell or a cell predisposed to the onset of a neoplastic state. 
     
     
         14 . The method according to  claim 13  wherein said RNA sequences are characterised by the sequence of either SEQ ID NO:21 or SEQ ID NO:22. 
     
     
         15 . The method according to any one of  claims 1 ,  6  or  12  wherein said level of expression is mRNA expression. 
     
     
         16 . The method according to any one of  claims 1 ,  6  or  12  wherein said at least 90% similarity is 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. 
     
     
         17 . The method according to any one of  claims 1 ,  6  or  12  wherein said level of expression is assessed by analysing RNA expression or protein expression. 
     
     
         18 . (canceled) 
     
     
         19 . The method according to any one of  claims 1 ,  6  or  12  wherein said control level is a non-neoplastic level. 
     
     
         20 . The method according to any one of  claims 1 ,  6  or  12  wherein said neoplastic cell is an adenoma or adenocarcinoma. 
     
     
         21 . The method according to  claim 20  wherein said cell is a colorectal cell. 
     
     
         22 . The method according to any one of  claims 1 ,  6  or  12  wherein said individual is a human. 
     
     
         23 . A molecular array, which array comprises:
 (i) nucleic acid molecules comprising a nucleotide sequence corresponding to any one or more of the hCG — 1815491 sequences described in  claims 1  or  6  or a sequence exhibiting at least 90% identity thereto or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or   (ii) nucleic acid molecules comprising a nucleotide sequence capable of hybridising to any one or more of the sequences of (i) under medium stringency conditions or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or   (iii) nucleic acid probes or oligonucleotides comprising a nucleotide sequence capable of hybridising to any one or more of the sequences of (i) under medium stringency conditions or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or   (iv) probes capable of binding to any one or more of the proteins encoded by the nucleic acid molecules of (i) or a derivative, fragment or homologue thereof   
       wherein the level of expression of said marker genes of (i) or proteins of (iv) is indicative of the neoplastic state of a cell or cellular subpopulation derived from the large intestine. 
     
     
         24 . A diagnostic kit for assaying biological samples comprising an agent for detecting one or more neoplastic markers as defined in  claim 1  or  6  and reagents useful for facilitating the detection of said agent.