Specific TT virus sequences and chimeric TT virus host cell DNA molecules for use in diagnosis, prevention and treatment of cancer and autoimmunity

Abstract

Described are single-stranded new sequences of TT viruses, rearranged TTV sequences and hybrid molecules of a specific TT virus sequence and host cell DNA that are capable of replicating autonomously for use in diagnosis, prevention and treatment of diseases like cancer and autoimmunity. In addition, it relates to the use of such molecules as gene vectors and artificial chromosomes.

1 . An isolated TT virus polynucleic acid comprising
 (a) a nucleotide sequence consisting of SEQ ID NOS: 1-4;   (b) a nucleotide sequence which shows 70% identity to a nucleotide sequence of (a) and is capable of replicating autonomously;   (c) a fragment of a nucleotide sequence of (a) or (b) which is capable of replicating autonomously;   (d) a nucleotide sequence which is the complement of the nucleotide sequence of (a), (b), or (c); or   (e) a nucleotide sequence which is redundant as a result of the degeneracy of the genetic code compared to any of the above-given nucleotide sequences.   
     
     
         2 . The TT virus polynucleic acid of  claim 1  comprising
 (a) a nucleotide sequence consisting of SEQ ID NOS: 1-4; 
 (b) a nucleotide sequence which shows 70% identity to a nucleotide sequence of (a) and is capable of replicating autonomously; 
 (c) a fragment of a nucleotide sequence of (a) or (b) which is capable of replicating autonomously; 
 (d) a nucleotide sequence which is the complement of a nucleotide sequence of (a), (b), or (c); or 
 (e) a nucleotide sequence which is redundant as a result of the degeneracy of the genetic code compared to any of the above-given nucleotide sequences. 
 
     
     
         3 . The TT virus polynucleic acid of  claim 1  which is present as a single- or double-stranded extrachromosomal episome. 
     
     
         4 . The TT virus polynucleic acid of  claim 1  which is a single-stranded DNA. 
     
     
         5 . The TT virus polynucleic acid of  claim 4  which is linked to a host cell DNA. 
     
     
         6 . The TT virus polynucleic acid of  claim 5  having at least one of the following properties:
 (a) growth-stimulation; 
 (b) oncogene function; 
 (c) tumor suppressor gene-like function; or 
 (d) stimulation of autoimmune reactions. 
 
     
     
         7 . The TT virus polynucleic acid of  claim 1  comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 5-7, 13, 18-19, 26-27, 28-29 and 30-31. 
     
     
         8 . An oligonucleotide primer comprising part of a polynucleic acid according to  claim 1 , with said primer being able to act as primer for specifically sequencing or specifically amplifying said polynucleic acid. 
     
     
         9 . The oligonucleotide primer of  claim 8  having a nucleotide sequence selected from the group consisting of SEQ ID NOS: 20-25. 
     
     
         10 . An oligonucleotide probe comprising part of a polynucleic acid according to  claim 1 , wherein said probe can specifically hybridize to said polynucleic acid. 
     
     
         11 . The oligonucleotide probe of  claim 10  having a nucleotide sequence selected from the group consisting of SEQ ID NOS: 13, 18 and 19. 
     
     
         12 . The oligonucleotide probe of  claim 10 , which is detectably labelled or attached to a solid support. 
     
     
         13 . The oligonucleotide primer of  claim 8  having a length of at least 13 bases. 
     
     
         14 . An expression vector comprising a TT virus polynucleic acid of  claim 1  operably linked to prokaryotic, eukaryotic or viral transcription and translation control elements. 
     
     
         15 . An artificial chromosome comprising the expression vector of  claim 14 . 
     
     
         16 . A host cell transformed with an expression vector according to  claim 14 . 
     
     
         17 . A polypeptide being encoded by a TT virus polynucleic acid of  claim 1 . 
     
     
         18 . An antibody or fragment thereof specifically binding to a polypeptide of  claim 17 . 
     
     
         19 . The antibody or fragment thereof of  claim 18 , wherein said antibody or fragment is detectably labelled. 
     
     
         20 . A diagnostic kit for use in determining the presence of a TT virus polynucleic acid of  claim 1 , said kit comprising
 an oligonucleotide primer comprising part of said polynucleic acids, with said primer being able to act as a primer for specifically sequencing or specifically amplifying said polynucleic acid; or   an oligonucleotide probe comprising part of said polynucleic acid, wherein said probe can specifically hybridize to said polynucleic acid.   
     
     
         21 - 34 . (canceled) 
     
     
         35 . A diagnostic kit for use in determining the presence of a TT virus polypeptide, said kit comprising
 an antibody or fragment thereof specifically binding to a polypeptide being encoded by a TT virus polynucleic acid of  claim 1 .   
     
     
         36 . A diagnostic composition for the diagnosis of a predisposition or an early stage of cancer or an autoimmune disease said composition comprising
 an oligonucleotide primer comprising part of a TT virus polynucleic acid according to  claim 1 , with said primer being able to act as primer for specifically sequencing or specifically amplifying said polynucleic acid; or   an oligonucleotide probe comprising part of a polynucleic acid, wherein said probe can specifically hybridize to said polynucleic acid; or   an antibody or fragment thereof specifically binding to a polypeptide being encoded by said TT virus polynucleic acid.   
     
     
         37 . A method for the detection of a TTV polynucleic acid according to  claim 1  in a biological sample, comprising: (a) optionally extracting a polynucleic acid from said biological sample, (b) amplifying said polynucleic acid with at least one optionally labelled primer comprising part of said polynucleic acid, with said primer being able to act as primer for specifically sequencing or specifically amplifying said polynucleic acid and (c) detecting the amplified polynucleic acid. 
     
     
         38 . A method for the detection of a TTV polynucleic acid which is present as a single- or double-stranded extrachromosomal episome in a biological sample, comprising: (a) optionally extracting a polynucleic acid from said biological sample, (b) hybridizing the polynucleic acid as described above with at least one optionally labelled probe comprising part of a polynucleic acid according to  claim 1 , wherein said probe can specifically hybridize to said polynucleic acid and (c) detecting the hybridized polynucleic acid. 
     
     
         39 . A method for detecting a polypeptide being encoded by a TT virus polynucleic acid of  claim 1  present in a biological sample, comprising: (a) contacting the biological sample for the presence of such polypeptide with an antibody against a polypeptide being encoded by said TT virus polynucleic acid, and (b) detecting the immunological complex formed between said antibody and said polypeptide. 
     
     
         40 . A method for detecting an antibody against a polypeptide being encoded by a TT virus polynucleic acid of  claim 1  present in a biological sample, comprising: (a) contacting the biological sample for the presence of said antibody with a polypeptide being encoded by said TT virus polynucleic acid, and (b) detecting the immunological complex formed between said antibody and said polypeptide. 
     
     
         41 . An antisense oligonucleotide reducing or inhibiting the expression of the TT virus polynucleic acid of  claim 1 . 
     
     
         42 . A pharmaceutical composition comprising the antibody of  claim 18  and a suitable pharmaceutical carrier. 
     
     
         43 . A pharmaceutical composition comprising the antisense oligonucleotide of  claim 41  and a suitable pharmaceutical carrier. 
     
     
         44 . A method of preventing or treating cancer or an autoimmune disease or early stages thereof comprising administering to a subject with such disorder a therapeutically effective amount of the antibody or fragment of  claim 18 . 
     
     
         45 . A method of preventing or treating cancer or an autoimmune disease or early stages thereof comprising administering to a subject with such disorder a therapeutically effective amount of the antisense oligonucleotide of  claim 41 . 
     
     
         46 . The method according to  claim 44 , wherein said autoimmune disease is multiple sclerosis (MS), asthma, polyarthritis, juvenile diabetes, Lupus erythematodes, Colitis ulcerosa, or Crohn's disease; and wherein said cancer is breast cancer, colorectal cancer, pancreatic cancer, cervical cancer, Hodgkin's lymphoma, B-lymphoma, acute lymphocytic leukaemia, or Burkitt's lymphoma. 
     
     
         47 . A vaccine comprising a TT virus polynucleic acid of  claim 1 , or a polypeptide being encoded by said TT virus polynucleic acid. 
     
     
         48 . A method of immunizing a mammal against a TT virus infection wherein an effective amount of the vaccine of  claim 47  is administered to said mammal. 
     
     
         49 . A method for the generation of a database for determining the risk to develop cancer or an autoimmune disease, comprising the following steps
 (a) determining the nucleotide sequence of a host cell DNA linked to TT virus polynucleic acids according to  claim 5  and being present in episomal form, if present, in a sample from a patient suffering from at least one of said diseases; and   (b) compiling sequences determined in step (a) associated with said diseases in a database.   
     
     
         50 . A method for evaluating the risk to develop cancer or an autoimmune disease of a patient suspected of being at risk of developing such disease, comprising the following steps
 (a) determining the nucleotide sequence of a host cell DNA linked to TT virus polynucleic acids and being present in episomal form, in a sample from said patient; and   (b) comparing sequences determined in step (a) with the sequences compiled in the database generated to the method of  claim 49     
       wherein the absence of a host cell DNA linked to a TT virus polynucleic acid or the presence only of host cell DNA linked to a TT virus polynucleic acid not represented in said database indicates that the risk of developing such disease is decreased or absent.