СТРУКТУРНО-ФУНКЦИОНАЛЬНЫЙ АНАЛИЗ ОПУХОЛЕВЫХ ГЕНОМОВ И РАЗРАБОТКА ТЕСТ-СИСТЕМ ДЛЯ РАННЕЙ ДИАГНОСТИКИ, ПРОГНОЗА ТЕЧЕНИЯ И ОПТИМИЗАЦИИ ТЕРАПИИ ЗЛОКАЧЕСТВЕННЫХ НОВООБРАЗОВАНИЙ

The article discusses results of the structural and functional analysis of molecular genetic abnormalities in various malignant tumors. Investigations have discovered more than 20 new markers for sporadic breast cancer. Several of them formed the test system, allowing the diagnosis with a specificity of 100%. Appearance of TMPRSS2/ERG4 chimeric gene is a frequent tumor-specific event, its expression is correlated with more aggressive forms of prostate cancer, may serve as a molecular marker for tumor cells and androgen assessment of tumor response to hormonal therapy. The effective systems for the early diagnosis of cervix and endometrium cancer were developed as well. Mutations in the VHL, deletions of chromosome 3 and methylation of several genes can predict the course and selection of effective therapy of clear cell kidney cancer. a number of molecular markers were identified for early diagnosis and prognosis of recurrence of bladder cancer. For diagnosis, prognosis and treatment of brain tumors we developed an effective complex system of markers. Protocol of molecular genetics investigation reveals the cause of the disease by more than 90% of patients with retinoblastoma. In order to study abnormal methylation in tumor genomes an innovative technology AFLOAT has been developed that allows to efficiently identify new markers with diagnostic value. Test systems of molecular genetic and epigenetic markers for early diagnosis and prognosis as well as for cancer therapy optimization have shown to be effective, have been approved for use in clinical practice and are being introduced into practical healthcare.Рассматриваются результаты структурно-функционального анализа молекулярно-генетических нарушений при различных злокачественных опухолях. Исследования позволили обнаружить более 20 новых маркеров для спорадического рака молочной железы, из которых сформированы тест-системы, позволяющие проводить диагностику со специфичностью 100%. Образование химерного гена TMPRSS2/ERG4 является частым опухоль-специфическим событием, его экспрессия коррелирует с более агрессивными формами рака предстательной железы может служить молекулярным маркером  андрогенчувствительности опухолевых клеток и оценки ответа опухоли на гормональную терапию. Разработаны эффективные системы для ранней диагностики рака шейки матки и эндометрия. Мутации гена VHL, делеции хромосомы 3 и метилирование ряда генов позволяет прогнозировать течение и подбор эффективной терапии светлоклеточного рака почки. Для ранней диагностики, прогноза течения и рецидивирования рака мочевого пузыря определен целый ряд молекулярных маркеров. Для диагностики, прогноза и лечения опухолей мозга разработана эффективная комплексная система маркеров. Протокол молекулярно-генетического  исследования позволяет обнаружить причину заболевания более чем у 90% пациентов с ретинобластомой.  Для исследования аномального метилирования в опухолевых геномах разработана инновационная технология AFLOAT, позволяющая эффективно выявлять новые маркеры, имеющие диагностическое значение. Тест-системы молекулярно-генетических и эпигенетических маркеров для ранней диагностики, прогноза течения и оптимизации терапии злокачественных новообразований показали свою эффективность, получили разрешение на использование в клинической практике и в настоящее время активно внедряются в практическое здравоохранение.

Abnormal hypermethylation of CpG dinucleotides in promoter regions of matrix metalloproteinases genes in breast cancer and its relation to epigenomic subtypes and HER2 overexpression

Matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) substantially contribute to the regulation of intercellular interactions and thereby play a role in maintaining the tissue structure and function. We examined methylation of a subset of 5'-cytosine-phosphate-guanine-3' (CpG) dinucleotides in promoter regions of the MMP2, MMP11, MMP14, MMP15, MMP16, MMP17, MMP21, MMP23B, MMP24, MMP25, MMP28, TIMP1, TIMP2, TIMP3, and TIMP4 genes by methylation-sensitive restriction enzyme digestion PCR. In our collection of 183 breast cancer samples, abnormal hypermethylation was observed for CpGs in MMP2, MMP23B, MMP24, MMP25, and MMP28 promoter regions. The non-methylated status of the examined CpGs in promoter regions of MMP2, MMP23B, MMP24, MMP25, and MMP28 in tumors was associated with low HER2 expression, while the group of samples with abnormal hypermethylation of at least two of these MMP genes was significantly enriched with HER2-positive tumors. Abnormal methylation of MMP24 and MMP25 was significantly associated with a CpG island hypermethylated breast cancer subtype discovered by genome-wide DNA bisulfite sequencing. Our results indicate that abnormal hypermethylation of at least several MMP genes promoters is a secondary event not directly functional in breast cancer (BC) pathogenesis. We suggest that it is elevated and/or ectopic expression, rather than methylation-driven silencing, that might link MMPs to tumorigenesis. © 2020 by the authors

Abnormal promoter DNA hypermethylation of the integrin, nidogen, and dystroglycan genes in breast cancer

Cell transmembrane receptors and extracellular matrix components play a pivotal role in regulating cell activity and providing for the concerted integration of cells in the tissue structures. We have assessed DNA methylation in the promoter regions of eight integrin genes, two nidogen genes, and the dystroglycan gene in normal breast tissues and breast carcinomas (BC). The protein products of these genes interact with the basement membrane proteins LAMA1, LAMA2, and LAMB1; abnormal hypermethylation of the LAMA1, LAMA2, and LAMB1 promoters in BC has been described in our previous publications. In the present study, the frequencies of abnormal promoter hypermethylation in BC were 13% for ITGA1, 31% for ITGA4, 4% for ITGA7, 39% for ITGA9, 38% for NID1, and 41% for NID2. ITGA2, ITGA3, ITGA6, ITGB1, and DAG1 promoters were nonmethylated in normal and BC samples. ITGA4, ITGA9, and NID1 promoter hypermethylation was associated with the HER2 positive tumors, and promoter hypermethylation of ITGA1, ITGA9, NID1 and NID2 was associated with a genome-wide CpG island hypermethylated BC subtype. Given that ITGA4 is not expressed in normal breast, one might suggest that its abnormal promoter hypermethylation in cancer is non-functional and is thus merely a passenger epimutation. Yet, this assumption is not supported by our finding that it is not associated with a hypermethylated BC subtype. ITGA4 acquires expression in a subset of breast carcinomas, and methylation of its promoter may be preventive against expression in some tumors. Strong association of abnormal ITGA4 hypermethylation with the HER2 positive tumors (p = 0.0025) suggests that simultaneous presence of both HER2 and integrin α4 receptors is not beneficial for tumor cells. This may imply HER2 and integrin α4 signaling pathways interactions that are yet to be discovered. © 2021, The Author(s)

Genome-wide methylotyping resolves breast cancer epigenetic heterogeneity and suggests novel therapeutic perspectives

Aim: To provide a breast cancer (BC) methylotype classification by genome-wide CpG islands bisulfite DNA sequencing. Materials & methods: XmaI-reduced representation bisulfite sequencing DNA methylation sequencing method was used to profile DNA methylation of 110 BC samples and 6 normal breast samples. Intrinsic DNA methylation BC subtypes were elicited by unsupervised hierarchical cluster analysis, and cluster-specific differentially methylated genes were identified. Results & conclusion: Overall, six distinct BC methylotypes were identified. BC cell lines constitute a separate group extremely highly methylated at the CpG islands. In turn, primary BC samples segregate into two major subtypes, highly and moderately methylated. Highly and moderately methylated superclusters, each incorporate three distinct epigenomic BC clusters with specific features, suggesting novel perspectives for personalized therapy. © 2019 Alexander Tanas et al