Multiple-tumor aberrant growth genes

Abstract

The invention relates to the multi-tumor aberrant growth gene having the nucleotide sequence of any one of the strands of any one of the members of the High Mobility Group protein genes or LIM protein genes, including modified versions and derivatives thereof. The gene and its derivatives may be used in various diagnostic and therapeutic applications.

1 . Multi-tumor Aberrant Growth (MAG) gene having the nucleotide sequence of any one of the strands of any one of the members of the High Mobility Group protein genes or LIM protein genes, including modified versions thereof.  
     
     
         2 . Multi-tumor Aberrant Growth (MAG) gene as claimed in  claim 1  having essentially the nucleotide sequence of the HMGI-C gene as depicted in FIG. 7, or the complementary strand thereof, including modified or elongated versions of both strands.  
     
     
         3 . Multi-tumor Aberrant Growth (MAG) gene as claimed in  claim 1  having essentially the nucleotide sequence of the LPP gene as depicted in FIG. 5, or the complementary strand thereof, including modified or elongated versions of both strands.  
     
     
         4 . Multi-tumor Aberrant Growth (MAG) gene as claimed in  claim 1 ,  2  or  3  for use as a starting point for designing suitable expression-modulating compounds or techniques for the treatment of non-physiological proliferation phenomena in human or animal.  
     
     
         5 . Multi-tumor Aberrant Growth (MAG) gene as claimed in  claim 1 ,  2  or  3  for use as a starting point for designing suitable nucleotide probes for (clinically/medically) diagnosing cells having a non-physiological proliferative capacity as compared to wildtype cells.  
     
     
         6 . Protein encoded by the Multi-tumor Aberrant Growth (MAG) gene as claimed in  claim 1 ,  2  or  3  for use as a starting point for preparing suitable antibodies for (clinically/medically) diagnosing cells having a non-physiological proliferative capacity as compared to wildtype cells.  
     
     
         7 . Derivatives of the MAG gene as claimed in  claim 1 ,  2  or  3  or of its immediate vicinity for use in diagnosis and the preparation of therapeutical compositions, wherein the derivatives are selected from the group consisting of sense and anti-sense cDNA or fragments thereof, transcripts of the gene or practically usable fragments thereof, antisense RNA, fragments of the gene or its complementary strand, proteins encoded by the gene or fragments thereof, antibodies directed to the gene, the cDNA, the transcript, the protein or the fragments thereof, as well as antibody fragments.  
     
     
         8 . In situ diagnostic method for diagnosing cells having a non-physiological proliferative capacity, comprising at least some of the following steps: 
 a) designing a set of nucleotide probes based on the information obtainable from the nucleotide sequence of the MAG gene as claimed in  claim 1  or  2 , wherein one of the probes is hybridisable to a region of the aberrant gene substantially mapping at the same locus as a corresponding region of the wildtype gene and the other probe is hybridisable to a region of the aberrant gene mapping at a different locus than a corresponding region of the wildtype gene;    b) incubating one or more interphase or metaphase chromosomes or cells having a non-physiological proliferative capacity, with the probe under hybridising conditions; and    c) visualising the hybridisation between the probe and the gene.    
     
     
         9 . Method of diagnosing cells having a non-physiological proliferative capacity, comprising at least some of the following steps: 
 a) taking a biopsy of the cells to be diagnosed;    b) isolating a suitable MAG gene-related macromolecule therefrom;    c) analysing the macromolecule thus obtained by comparison with a wildtype reference molecule preferably from the same individual.    
     
     
         10 . Method as claimed in  claim 9 , comprising at least some of the following steps: 
 a) taking a biopsy of the cells to be diagnosed;    b) extracting total RNA thereof;    c) preparing at least one first strand cDNA of the mRNA species in the total RNA extract, which cDNA comprises a suitable tail;    d) performing a PCR and/or RT-PCR using a MAG gene specific primer and a tail-specific and/or partner-specific/nested primer in order to amplify MAG gene specific cDNA's;    e) separating the PCR products on a gel to obtain a pattern of bands;    f) evaluating the presence of aberrant bands by comparison to wildtype bands, preferably originating from the same individual.    
     
     
         11 . Method as claimed in  claim 9 , comprising at least some of the following steps: 
 a) taking a biopsy of the cells to be diagnosed;    b) isolating total protein therefrom;    c) separating the total protein on a gel to obtain essentially individual bands and optionally trnasferring the bands to a Western blot;    d) hybridising the bands thus obtained with antibodies directed against a part of the protein encoded by the remaining part of the MAG gene and against a part of the protein encoded by the substitution part of the MAG gene;    e) visualising the antigen-antibody reactions and establishing the presence of aberrant bands by comparison with bands from wildtype proteins, preferably originating from the same individual.    
     
     
         12 . Method as claimed in  claim 9 , comprising at least some of the following steps: 
 a) taking a biopsy of the cells to be diagnosed;    b) isolating total DNA therefrom;    c) digesting the DNA with one or more so-called “rare cutter” restriction enzymes;    d) separating the digest thus prepared on a gel to obtain a separation pattern;    e) optionally transfering the separation pattern to a Southern blot;    f) hybridising the separation pattern in the gel or on the blot with one or more informative probes under hybridising conditions;    g) visualising the hybridisations and establishing the presence of aberrant bands by comparison to wildtype bands, preferably originating from the same individual.    
     
     
         13 . Method as claimed in  claim 9 , comprising at least some of the following steps: 
 a) taking a biopsy of the cells to be diagnosed;    b) extracting mRNA therefrom;    c) establishing the presence or the (relative) quantity of mRNA derived from the MAG gene; and    d) comparing the result of step c) with the result of a similar experiment with wildtype cells, preferably originating from the same individual.    
     
     
         14 . Method as claimed in any one of the claims  8 - 13 , wherein the cells having a non-physiological proliferative capacity are selected from the group consisting of the mesenchymal tumors hamartomas (e.g. breast and lung), adipose tissue tumors (e.g. lipomas), pleomorphic salivary gland adenomas, uterine leiomyomas, angiomyxomas, fibroadenomas of the breast, polyps of the endometrium, atherosclerotic plaques, and other benign tumors as well as various malignant tumors, including but not limited to sarcomas (e.g. rhabdomyosarcoma, osteosarcoma) and carcinomas (e.g. of breast, lung, skin, thyroid), and haematological malignancies, like leukemias and lymphomas.  
     
     
         15 . Anti-sense molecules of a MAG gene as claimed in  claim 1 ,  2  or  3  for use in the treatment of diseases involving cells having a non-physiological proliferative capacity by modulating the expression of the gene.  
     
     
         16 . Expression modulators, such as inhibitors or enhancers, including ribozymes, of the MAG gene as claimed in  claim 1 ,  2  or  3  for use in the treatment of diseases involving cells having a non-physiological proliferative capacity.  
     
     
         17 . Antisense RNA molecules complementary to the mRNA molecules of the MAG gene and/or antibodies directed against the gene product of the MAG gene as claimed in  claim 1 ,  2  or  3  for use in the treatment of diseases involving cells having a non-physiological proliferative capacity.  
     
     
         18 . Diagnostic kit for performing the method as claimed in  claim 8 , comprising a suitable set of labeled nucleotide probes.  
     
     
         19 . Diagnostic kit for performing the method as claimed in  claim 10 , comprising a suitable set of labeled probes.  
     
     
         20 . Diagnostic kit for performing the method as claimed in  claim 11 , comprising a suitable set of labeled MAG gene specific and tail specific PCR primers.  
     
     
         21 . Diagnostic kit for performing the method as claimed in  claim 11 , comprising a suitable set of labeled probes, and suitable rare cutting restriction enzymes.  
     
     
         22 . Pharmaceutical composition for lowering the expression level of the MAG gene in cells having a non-physiological proliferative capacity, comprising one or more of the derivatives as claimed in  claim 7  and/or one or more expression modulators as claimed in  claim 16 .  
     
     
         23 . Pharmaceutical composition as claimed in  claim 22 , wherein the cells having a non-physiological proliferative capacity are selected from the group consisting of the mesenchymal tumors hamartomas (e.g. breast and lung), adipose tissue tumors (e.g. lipomas), pleomorphic salivary gland adenomas, uterine leiomyomas, angiomyxomas, fibroadenomas of the breast, polyps of the endometrium, atherosclerotic plaques, and other benign tumors as well as various malignant tumors, including but not limited to sarcomas (e.g. rhabdomyosarcoma, osteosarcoma) and carcinomas (e.g. of breast, lung, skin, thyroid), and haematological malignancies, like leukemias and lymphomas.  
     
     
         24 . Use of the derivatives as claimed in  claim 7  for the preparation of a diagnostic kit or a pharmaceutical composition for the diagnosis or treatment of diseases or disorders involving cells having a non-physiological proliferative capacity.  
     
     
         25 . Use of the expression modulators as claimed in  claim 16  for the preparation of a pharmaceutical composition for the treatment of diseases or disorders involving cells having a non-physiological proliferative capacity.  
     
     
         26 . Use as claimed in  claim 24  or  25 , wherein the cells having a non-physiological proliferative capacity are selected from the group consisting of the mesenchymal tumors hamartomas (e.g. breast and lung), adipose tissue tumors (e.g. lipomas), pleomorphic salivary gland adenomas, uterine leiomyomas, angiomyxomas, fibroadenomas of the breast, polyps of the endometrium, atherosclerotic plaques, and other benign tumors as well as various malignant tumors, including but not limited to sarcomas (e.g. rhabdomyosarcoma, osteosarcoma) and carcinomas (e.g. of breast, lung, skin, thyroid), and haematological malignancies, like leukemias and lymphomas.  
     
     
         27 . Method for isolating other MAG genes based on the existence of a fusion gene, fusion transcript or fusion protein in a tumor cell by using at least a part of a MAG gene for designing molecular tools (probes, primers etc.).  
     
     
         28 . MAG genes obtainable by the method of  claim 27 .  
     
     
         29 . MAG genes as claimed in  claim 28  for use in diagnostic or therapeutic methods.  
     
     
         30 . Animal model for the assessment of the utility of compounds or compositions in the treatment of diseases or disorders involving cells having a non-physiological proliferative capacity, which animal is a transgenic animal harbouring a MAG gene in its genome.  
     
     
         31 . Animal model as claimed in  claim 30 , wherein the MAG gene is an aberrant MAG gene, such as a fusion product of the remaining part of the gene and the substitution part of its translocation partner.  
     
     
         32 . Animal model as claimed in  claim 30 , wherein the MAG gene shows a non-physiological expression level.  
     
     
         33 . Animal model for the assessment of the utility of compounds or compositions in the treatment of diseases or disorders involving cells having a non-physiological proliferative capacity, which animal harbours a specific genetic aberration affecting a MAG gene as claimed in  claim 1 ,  2  or  3  in the genome of at least part of its cells, which aberration is induced via homologous recombination in embryonic stem cells.  
     
     
         34 . Animal model as claimed in any one of the claims  30 - 33 , which animal is a mammal, in particular a mouse, rat, dog, pig or higher primate, like chimpanzee.  
     
     
         35 . Poly- or oligonucleotide probes and primers as disclosed in the description and figures.