From identification of genomic polymorphism to diagnostic and prognostic markers of human epithelial tumors

The review considers the results obtained by several groups in the fields of identification of polymorphic loci in the human genome, localization and analysis of genes associated with epithelial tumors of various origins, and generation of molecular markers of socially important oncological diseases. In the first two cases, work was initiated and supported by the Russian program Human Genome. To find new polymorphic loci in the human genome, di-, tri-, and tetranucleotide repeats were searched for in an ordered cosmid library of chromosome 13, NotI and cosmid clones of chromosome 3, and in brain EST. In total, nine polymorphisms and almost 200 STS were identified. Markers of NotI clones of chromosome 3 were associated with particular genes. Polymorphic loci NL1-024, NL2-007, and EST04896 were employed in analysis of deletions from chromosome 3p in tumor DNA. Deletion mapping of 3p in epithelial tumors of five types revealed six critical regions containing potential tumor suppressor genes. Of these, two were in the distal region of chromosome 3p and four, in region 3p21.3. A significant correlation was observed for the frequency of allelic deletions and the stage and the grade of tumors (P < 0.05). On the strength of these findings, genes of region 3p were associated with both tumor development and progression, and proposed as prognostic markers. Regions LUCA and AP20 (3p21.3) showed a high (90%) frequency of aberrations, including homozygous deletions in almost 20% cases. The peak of allelic deletions from region D3S2409-D3S3667 (600 kb) was statistically valid (P = 10(-3)). Regions AP20 and D3S2409-D3S3667 (3p21.3) were for the first time associated with tumorigenesis. Clusters of tumor suppressor genes were identified in regions LUCA, AP20, and D3S2409-D3S3667. Methylation of RASSF1A and RARbeta2 (3p) was associated with early carcinogenesis, and that of SEMA3B, with tumor progression. These findings are useful for early diagnostics and post-surgery prognosis of tumors.