Methods for determining the biological effect and/or activity of r pharmaceutical compositions based on their effect on the methylation status of the DNA

Abstract

This invention is related to methods, systems and computer program products for determining the biological effect and/or activity of drugs, chemical substances and/or pharmaceutical compositions using their effect on DNA methylation as a marker for their biological effect(s). The invention is further related to the use of the inventive methods, systems and computer program products in obtaining new biologically active compounds for new and effective medicaments and treatment strategies of, in particular, human diseases.

1 . A method for screening at least one pharmaceutical composition for a biological effect and/or activity in the treatment of a disease, comprising the steps of:
 (a) obtaining a biological sample A containing DNA, said biological sample A being from at least one of an individual, a tissue, a cell or another biological material containing DNA, wherein said biological sample A was exposed to said at least one pharmaceutical composition;   (b) obtaining a biological sample B containing DNA, said biological sample B being from at least of an individual, a tissue, a cell or another biological material containing DNA, wherein said biological sample B was not exposed to said at least one pharmaceutical composition;   (c) selecting sites which are relevant for the expression of gene(s) known to be related with said disease;   (d) analysing the level of cytosine methylation at said selected sites of the DNA contained in the samples A and B;   (e) selecting those said sites which are differentially methylated between the DNA in samples A and B, whereby a disease specific knowledge base is generated; and   (f) concluding from the said knowledge base on the biological effect and/or activity of said at least one pharmaceutical composition in the treatment of said disease.   
     
     
         2 . A method according to  claim 1 , characterised in that the biological sample comprises a eukaryotic and/or prokaryotic cell line, a biopsy sample, blood, sputum, faeces urine, cerebral liquid, tissue embedded in paraffin, tissue derived from eyes, intestine, brain, heart, prostate, kidney, lung, breast or liver, histological samples or a combination thereof. 
     
     
         3 . A method according to  claim 1 , characterised in that said biological samples A and B are derived from biological material of healthy individuals. 
     
     
         4 . A method according to  claim 1 , characterised in that said biological sample A is derived from biological material of healthy individuals and said biological sample B is derived from biological material of disease individuals. 
     
     
         5 . A method according to  claim 1 , characterised in that said biological sample A is derived from biological material of disease individuals and said biological sample B is derived from biological material of healthy individuals. 
     
     
         6 . A method according to  claim 1 , characterised in that the biological samples A and B are derived from the identical individual, tissue, cell or other biological material. 
     
     
         7 . A method according to  claim 6 , characterised in that the biological samples A and B are derived from samples taken at, during and/or after the onset of a treatment with said pharmaceutical composition. 
     
     
         8 . A method according to  claim 1 , further comprising the step of isolating DNA from the said samples before analysing the level of cytosine methylation at said chosen sites in said isolated DNA. 
     
     
         9 . A method according to  claim 8 , characterised in that the isolation of said DNA contained in said biological sample comprises isolating subcellular compartments, organelles, macromolecular structures and multiprotein complexes, partial or complete preparation of the DNA and/or mRNA, reverse transcription or partial digestion of the material with an enzyme selected from proteases, RNAses and/or DNAses or combination thereof. 
     
     
         10 . A method according to  claim 1 , characterised in that the methylation sites are located in methylation relevant regions of the DNA selected from the group comprising complete genes, promoters, introns, first exons, and enhancers. 
     
     
         11 . A method according to  claim 1 , characterised in that the level of at least 100 cytosine methylation sites are analysed in parallel. 
     
     
         12 . A method according to  claim 1 , characterised in that steps (a) to (e) are repeated. 
     
     
         13 . A method according to  claim 1 , characterised in that steps (c) to (e) are repeated. 
     
     
         14 . A method according to  claim 1 , characterised in that at least part of the method is performed on a computer having implemented thereon program code means for performing the method according to  claim 1 .