Epigenetic DNA diagnostics

SNP 5mC/T in AluSx repeat (Chr16: 75033884) in DNA samples from the human blood of 92donors was studied by GlaI and FatI-PCR assay. The work includes a) isolation of DNA from the blood cells, b) GlaI and FatI-PCR assay of DNA fragment Chr16: 75033860 – 75033957, c) determination of 5mC (Chr16: 75033884) and thymine (Chr16: 75033884) в in DNA preparations and d) comparative analysis of the obtained results. It was shown that in position (Chr16: 75033884) 53 donors (57,61%) have a heterozygote (5mC-T), 19 donors (20,65%) have homozygote (T-T) and 20 donors (21,74%) have homozygote (5mC-5mC). Thus, taking into account a diploid set of chromosomes in the blood cells, SNP 5mC/T is observed in 70 positions from 156 (49,46%). The results obtained have shown that cytosine in position Chr16: 75033884 in the most of the blood DNA is methylated in accordance with a literature data about a significant methylation of CG-dinucleotides in Alu-repeats

Methylation of ACGC site in position Chr11: 65647266 (according to GRCh38 PrimaryAssembly) in DNA preparations from blood cells of healthy donors and early stage breast cancers was studied with GlaI-PCR assay. The work includes a) preparation of light fraction of the blood cells, b) isolation of genomic DNA, c) determination of genomic DNA concentration by real-time PCR, d) determination of concentration of unmethylated ACGC site in position Chr11: 65647266 with GlaI-PCR assay and e) calculation of percent of DNA molecules with unmethylated ACGC site in position Chr11: 65647266. GLAD-PCR analysis showed that in more than 82% of donors, the level of ACGC methylation in the SIPA1 gene is 3% or less, while in approximately 70% of patients with breast cancer, the level of ACGC site methylation in SIPA1 gene is in the range of 3.2 to 6.4%. These data suggest that at early stages of breast cancer, demethylation of A(5mC)GC site in the SIPA1 gene at position 65647266 takes place in 2/3 of patients. The data of this work may be used for a development of PCR test-system for exclusion of diagnosis “early stage breast cancer”. GlaI-PCR assay doesn’t require special and expensive equipment. The study may be carried out in a standard PCR laboratory when a blood analysis is taken place.

DNA methylation in human genome is important for the cells specialization and functioning. An abnormal methylation of the regulation regions of some genes may cause the genes silencing and this phenomenon is often detected in cancer cells. Determination of differences of the genome-wide methylation in normal and tumor cells is useful for understanding the carcinogenesis process and for development of new methods of epigenetic diagnostics. The positions of methylated RCGY sites in the genomes of Raji, U-937 and L68 human cell lines have been determined using the previously developed method of massive parallel sequencing of Glal fragments. A comparison of the obtained data has revealed significant differences in methylation of CpG islands, putative regulatory regions and some repetitive DNA families between genomes of malignant and non-malignant cells. GO enrichment analysis of genes with highly methylated regulatory regions has shown the possible metabolic processes, which may be affected epigenetically in carcinogenesis. The new method allows to determine positions of many modified cytosine bases in the genomes and may be a simple alternative to the existing methods of genome-wide methylation analysis.