Compositions and Methods for Therapy and Diagnosis of Cancer

Abstract

The present invention is directed to siRNA molecules which specifically target and cause RNAi-induced degradation of mRNA from TPTE genes, so that the protein product of the TPTE gene is not produced or is produced in reduced amounts. The siRNA compounds and compositions of the invention are useful for treating diseases which require inhibition of TPTE expression for their treatment, in particular cancer pathologies. The present invention also includes methods which make possible to assess and/or prognose the metastatic behaviour of a cancer disease and/or the occurrence of a relapse of cancer.

1 . A siRNA comprising a sense RNA strand and an antisense RNA strand, wherein the sense and antisense RNA strands form an RNA duplex, and wherein the sense RNA strand comprises a nucleotide sequence substantially identical to a target sequence of about 19 to about 25 contiguous nucleotides in TPTE mRNA. 
     
     
         2 . The siRNA of  claim 1 , which is isolated. 
     
     
         3 . The siRNA of  claim 1 , wherein said TPTE mRNA comprises a nucleic acid sequence which is selected from the group consisting of:
 (a) a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 7, a part or derivative thereof,   (b) a nucleic acid sequence which hybridizes with the nucleic acid sequence of (a) under stringent conditions,   (c) a nucleic acid sequence which is degenerate with respect to the nucleic acid of (a) or (b),   (d) a nucleic acid sequence which is complementary to the nucleic acid sequence of (a), (b) or (c), and   (e) a nucleic acid sequence which encodes an amino acid sequence selected from the group consisting of SEQ ID NOs: 8, 9, 10, 11, 12, 13, and 14, a part or derivative thereof.   
     
     
         4 . The siRNA of  claim 1 , wherein said siRNA molecule is assembled from two nucleic acid fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of said siRNA molecule. 
     
     
         5 . The siRNA of  claim 1 , wherein the sense and antisense RNA strands forming the RNA duplex are covalently linked by a single-stranded hairpin. 
     
     
         6 . The siRNA of  claim 1 , wherein the siRNA further comprises non-nucleotide material. 
     
     
         7 . The siRNA of  claim 1 , wherein the sense and antisense RNA strands are stabilized against nuclease degradation. 
     
     
         8 . The siRNA of  claim 1 , further comprising a 3′-overhang. 
     
     
         9 . The siRNA of  claim 8 , wherein the 3′-overhang comprises from 1 to about 6 nucleotides. 
     
     
         10 . The siRNA of  claim 8 , wherein the 3′-overhang comprises about 2 nucleotides. 
     
     
         11 . The siRNA of  claim 8 , wherein the sense RNA strand comprises a first 3′-overhang, and the antisense RNA strand comprises a second 3′-overhang. 
     
     
         12 . The siRNA of  claim 11 , wherein the first and second 3′-overhangs independently comprise from 1 to about 6 nucleotides. 
     
     
         13 . The siRNA of  claim 12 , wherein the first 3′-overhang comprises a dinucleotide and the second 3′-overhang comprises a dinucleotide. 
     
     
         14 . The siRNA of  claim 13 , where the dinucleotide is dideoxythymidylic acid or diuridylic acid. 
     
     
         15 . The siRNA of  claim 8 , wherein the 3′-overhang is stabilized against nuclease degradation. 
     
     
         16 . The siRNA of  claim 1 , wherein said target sequence has a nucleic acid sequence selected from the group consisting of nucleotide positions 3-21 of SEQ ID NO: 15, nucleotide positions 3-21 of SEQ ID NO: 18, nucleotide positions 3-21 of SEQ ID NO: 21, nucleotide positions 3-21 of SEQ ID NO: 24, nucleotide positions 3-21 of SEQ ID NO: 27, nucleotide positions 3-21 of SEQ ID NO: 30, and nucleotide positions 3-21 of SEQ ID NO: 33. 
     
     
         17 . The siRNA of  claim 1 , wherein said sense RNA strand has the sequence of SEQ ID NO: 16 and the antisense RNA strand has the sequence of SEQ ID NO: 17. 
     
     
         18 . The siRNA of  claim 1 , wherein said sense RNA strand has the sequence of SEQ ID NO: 19 and the antisense RNA strand has the sequence of SEQ ID NO: 20. 
     
     
         19 . The siRNA of  claim 16 , wherein said sense RNA strand has the sequence of SEQ ID NO: 22 and the antisense RNA strand has the sequence of SEQ ID NO: 23. 
     
     
         20 . The siRNA of  claim 1 , wherein said sense RNA strand has the sequence of SEQ ID NO: 25 and the antisense RNA strand has the sequence of SEQ ID NO: 26. 
     
     
         21 . The si RNA of  claim 1 , wherein said sense RNA strand has the sequence of SEQ ID NO: 28 and the antisense RNA strand has the sequence of SEQ ID NO: 29. 
     
     
         22 . The siRNA of  claim 1 , wherein said sense RNA strand has the sequence of SEQ ID NO: 31 and the antisense RNA strand has the sequence of SEQ ID NO: 32. 
     
     
         23 . The siRNA of  claim 1 , wherein said sense RNA strand has the sequence of SEQ ID NO: 34 and the antisense RNA strand has the sequence of SEQ ID NO: 35. 
     
     
         24 . An expression vector comprising nucleic acid sequences for expressing a sense RNA strand, an antisense RNA strand, or both of a siRNA according to  claim 1 . 
     
     
         25 . A recombinant viral vector comprising nucleic acid sequences for expressing a sense RNA strand, an antisense RNA strand, or both of a siRNA according to  claim 1 . 
     
     
         26 . A pharmaceutical composition comprising the siRNA of  claim 1 . 
     
     
         27 . The pharmaceutical composition of  claim 26 , which may be used for the treatment or prevention of cancer and/or cancer metastasis. 
     
     
         28 . The pharmaceutical composition of  claim 27 , wherein the cancer is a lung tumour, a breast tumour, a prostate tumour, a melanoma, a colon tumour, a gastric tumour, a pancreatic tumour, an ENT tumour, a renal cell carcinoma or a cervical carcinoma, a colon carcinoma or a mammary carcinoma. 
     
     
         29 . A method of inhibiting expression of TPTE, comprising administering to a subject an effective amount of a siRNA of  claim 1 , such that the TPTE mRNA is degraded. 
     
     
         30 . A method of treating cancer in a subject and/or inhibiting cancer metastasis in a subject, comprising administering to a subject an effective amount of an siRNA of  claim 1 . 
     
     
         31 . The method of  claim 30  wherein said cancer or cancer metastasis is characterized by expression or abnormal expression of
 (i) a nucleic acid which is selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 7, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c), and/or 
 
 (ii) a protein or peptide encoded by the nucleic acid under (i). 
 
     
     
         32 . The method of  claim 31 , wherein the nucleic acid under (i) comprises a nucleic acid sequence encoding a protein or peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 8, 9, 10, 11, 12, 13, and 14, a part or derivative thereof and/or the protein or peptide under (ii) comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 8, 9, 10, 11, 12, 13, and 14, a part or derivative thereof. 
     
     
         33 . The method of  claim 29 , wherein the siRNA, the expression vector, the recombinant viral vector and/or the pharmaceutical composition is administered in combination with radiation therapy, chemotherapy or surgery. 
     
     
         34 . The method of  claim 29 , wherein the subject is a human being. 
     
     
         35 . The method of  claim 29 , wherein the siRNA is expressed from a recombinant plasmid or a recombinant viral vector. 
     
     
         36 . The method of  claim 29 , wherein the siRNA is administered by an enteral administration route and/or a parenteral administration route. 
     
     
         37 . A method for diagnosing, monitoring and/or prognosing the metastatic behaviour of cancer and/or the presence of a relapse of cancer, which method comprises
 (i) detecting or determining the amount of a nucleic acid which is selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 7, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c), and/or 
   (ii) detecting or determining the amount of a protein or peptide encoded by the nucleic acid under (i) or of a part or derivative thereof, and/or   (iii) detecting or determining the amount of an antibody specific for the protein or peptide or the 20 part or derivative under (ii), and/or   (iv) detecting or determining the amount of a T lymphocyte specific for the protein or peptide or the part or derivative under (ii), optionally in a complex with a MHC molecule, in a biological sample isolated from a patient.   
     
     
         38 . The method of  claim 37 , wherein the nucleic acid under (i) comprises a nucleic acid sequence encoding a protein or peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 8, 9, 10, 11, 12, 13, and 14, a part or derivative thereof and/or the protein or peptide under (ii) comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 8, 9, 10, 11, 12, 13, and 14, a part or derivative thereof. 
     
     
         39 . The method of  claim 37 , wherein the presence of the nucleic acid, of the protein or peptide or part or derivative, of the antibody or of the T lymphocyte and/or an amount of the nucleic acid, of the protein or peptide or part or derivative, of the antibody or of the T lymphocyte which is increased compared to the amount in a subject without said cancer, without a risk for said cancer, without metastasis of said cancer, without a risk for metastasis of said cancer, without a relapse of said cancer, and/or without a risk for a relapse of said cancer is indicative for a metastatic behaviour of said cancer or a potential for a metastatic behaviour of said cancer and/or for a relapse of said cancer or a potential for a relapse of said cancer.