Matvey Mikhailovich Murashko

Background: Identification of immunogenic neoantigens remains one of the major computational bottlenecks limiting the development of effective personalized cancer vaccines. Although various computational methods have been proposed for neoantigen discovery, there is little independent evidence regarding which approaches most effectively prioritize vaccine candidates using experimentally validated datasets. We focused on an independent multi-cohort benchmark of widely used neoantigen discovery pipelines and neoantigen scoring tools using publicly available datasets with experimentally validated immunogenic peptide–Major Histocompatibility complexes (MHC). Methods: In order to evaluate computational strategies used for selection of candidate vaccine peptides, five end-to-end neoantigen prediction pipelines and seven neoantigen scoring and prioritization tools were independently benchmarked using experimentally validated neoantigen datasets. End-to-end pipelines were evaluated on the TESLA cohort using raw WES and RNA-seq data from five patients, while individual prediction tools were additionally assessed on the TESLA, NCI, and HiTIDE validation cohorts comprising experimentally verified immunogenic and non-immunogenic peptide–MHC complexes. Results: NeoHunter achieved the highest overall recovery of experimentally validated neoantigens among the evaluated pipelines, while the scoring and prioritization tools NetMHCpan, MixMHCpred, and MHCFlurry generally showed the strongest ranking performance, although their relative performance varied substantially between datasets and patients. Precision–recall, average precision, and top K analyses demonstrated that no single predictor consistently dominated across cohorts and revealed a clear trade-off between candidate list size, precision, and recovery of validated neoantigens. Analysis of clinically relevant candidate selection thresholds demonstrated that restricting vaccine design to only the highest-ranked peptides substantially reduces sensitivity, whereas broader candidate selection improves recovery at the expense of increased experimental burden. Conclusions: These findings provide practical recommendations for computational selection of vaccine targets and highlight current limitations that must be addressed to improve the success of personalized neoantigen-based vaccines.

SLAMF1 encodes CD150, an immunoregulatory receptor involved in lymphocyte activation, T–B-cell interactions, and humoral immune responses. The SLAMF1 promoter polymorphism rs2295613(G>A) was previously associated with systemic lupus erythematosus (SLE) susceptibility in a Chinese case–control cohort. Here, we investigated the regulatory activity of rs2295613 in the transformed B-cell lines Raji and MP1 and in primary human CD19⁺ B cells. The rs2295613(A)-containing reporter showed higher promoter activity than the rs2295613(G)-containing reporter in all three cellular systems. Bioinformatic analysis predicted that the G to A substitution strengthens a pre-existing MYC-compatible motif. Substitutions disrupting the motif-containing region attenuated the rs2295613(A)-associated increase in reporter activity and reduced enrichment of the promoter fragment in anti-c-MYC DNA pull-down assays. Partial siRNA-mediated reduction in MYC mRNA also decreased the activity of the rs2295613(A)-containing reporter in Raji cells. Together, these findings identify rs2295613 as a functional SLAMF1 promoter variant in B-cell reporter systems and support a contribution of c-MYC-associated regulation to the enhanced activity of the rs2295613(A)-containing promoter.

Chromosomal rearrangements that lead to the formation of oncogenic gene fusions, such as EML4-ALK, are thought to arise from incorrect repair of double-strand breaks in DNA. However, the mechanisms and factors driving rearrangement formation remain poorly understood, and analysis of these processes is limited by detection methods that are labor-intensive, low-throughput, and not readily quantitative at single-cell resolution. Here, we developed a genetically encoded ALK reporter based on A549 lung adenocarcinoma cells, created by inserting an ALK-P2A-mCherry cassette into the endogenous ALK locus, so that induced EML4-ALK fusion activated mCherry fluorescence. Reporter activation yielded a readily quantifiable mCherry-positive subpopulation that could be measured and enriched by flow cytometry and correlated with EML4-ALK levels. Using this platform, we combined CRISPR-mediated rearrangement induction with knockdown of DNA repair factors using RNA interference. Of the factors involved in base excision repair, homologous recombination-related pathways and canonical non-homologous end joining, knockdown of the APEX1 gene encoding apurinic endonuclease 1 (APE1) selectively increased EML4-ALK levels both in the reporter cell line and in parental A549 cells. Together, this work provides a sensitive, single-cell A549-based ALK reporter platform and a framework for future studies aimed at identifying cellular and environmental factors that modulate oncogenic EML4-ALK rearrangement formation.

The MPC 1 gene is involved in the transport of pyruvate into mitochondria, playing an important role in metabolic processes. Recently, it has been reported that higher MPC 1 expression correlates with an increased number of immune cells in human cervical and lung cancers, indicating an enhanced antitumor immune response. Reduced MPC 1 levels in gastric tumors are associated with a more severe disease course. Correlational analysis of the MPC 1 gene in human lung, hippocampus and frontal cortex tissue samples based on data from the GTEx database revealed associations of this gene with schizophrenia, non-small cell lung cancer, and immune diseases. Our experiments showed that the mRNA level of the MPC 1 gene in the non-small cell lung cancer cell line A549 increases 5-fold under the influence of the schizophrenia neuroleptic thioridazine. The observed elevation of MPC 1 level may cause tumor infiltration by immune cells, complementing the previously reported data indicating the ability of thioridazine to slow cell growth, induce apoptosis and reduce the ability of cells to migrate.

Interleukin 10 (IL10) is a major anti-inflammatory cytokine that acts as a master regulator of the immune response. A single nucleotide polymorphism rs3024505(C/T), located downstream of the IL10 gene, is associated with several aggressive inflammatory diseases, including systemic lupus erythematosus, Sjögren’s syndrome, Crohn’s disease, and ulcerative colitis. In such autoimmune pathologies, IL10-producing B cells play a protective role by decreasing the level of inflammation and restoring immune homeostasis. This study demonstrates that rs3024505 is located within an enhancer that augments the activity of the IL10 promoter in a reporter system based on a human B cell line. The common rs3024505(C) variant creates a functional binding site for the transcription factor STAT3, whereas the risk allele rs3024505(T) disrupts STAT3 binding, thereby reducing the IL10 promoter activity. Our findings indicate that B cells from individuals carrying the minor rs3024505(T) allele may produce less IL10 due to the disrupted STAT3 binding site, contributing to the progression of inflammatory pathologies.

Chromosomal rearrangements leading to the relocation of proto-oncogenes into transcription-active regions are found in various types of tumors. In particular, the transfer of proto-oncogenes to the locus of heavy chains of immunoglobulins (IGH) is frequently observed in B-lymphomas. The increased expression of the MYC proto-oncogene due to IGH/MYC translocation is detected in approximately 85% of Burkitt lymphoma cases. The regulatory mechanisms affecting the oncogenes upon translocation include non-coding enhancer RNAs (eRNAs). We conducted a search for the eRNAs that may affect MYC transcription in the case of IGH/MYC translocation in Burkitt lymphoma, looking for potentially oncogenic eRNAs located at the IGH locus and predominantly expressed in B cells. Overexpression and knockdown of our primary candidate eRNA AL928768.3 led to the corresponding changes in the expression of MYC proto-oncogene in Burkitt lymphoma cells. Furthermore, we demonstrated that AL928768.3 knockdown decreased lymphoma cell proliferation and resistance to chemotherapy. Significant effects were observed only in cell lines bearing IGH/MYC abnormality but not in B-cell lines without this translocation nor primary B-cells. Our results indicate that AL928768.3 plays an important role in the development of Burkitt’s lymphoma and suggest it and similar, yet undiscovered eRNAs as potential tissue-specific targets for cancer treatment.

The flurry of publications devoted to the functions of long non-coding RNAs (lncRNAs) published in the last decade leaves no doubt about the exceptional importance of lncRNAs in various areas including tumor biology. Contribution of lncRNAs to the early stages of oncogenesis remains poorly understood. In this study we explored a new role for lncRNAs: stimulation of driver oncogenic mutations that result from specific chromosomal rearrangements. We demonstrated that lncRNA CASTL1 (ENSG00000269945) stimulates the formation of the CCDC6-RET inversion (RET/PTC1) in human thyroid cells subjected to radiation or chemical DNA damage. Facilitation of chromosomal rearrangement requires lncRNA to contain regions complementary to the introns of both CCDC6 and RET genes as deletion of these regions deprives CASTL1 of the ability to stimulate the gene fusion. We found that CASTL1 expression is elevated in tumors with CCDC6-RET fusion which is the most frequent rearrangement in papillary thyroid carcinoma. Our results open a new venue for the studies of early oncogenesis in various tumor types, especially those associated with physical or chemical DNA damage. Graphical

Alterations in the expression level of the MYC gene are often found in the cells of various malignant tumors. Overexpressed MYC has been shown to stimulate the main processes of oncogenesis: uncontrolled growth, unlimited cell divisions, avoidance of apoptosis and immune response, changes in cellular metabolism, genomic instability, metastasis, and angiogenesis. Thus, controlling the expression of MYC is considered as an approach for targeted cancer treatment. Since c-Myc is also a crucial regulator of many cellular processes in healthy cells, it is necessary to find ways for selective regulation of MYC expression in tumor cells. Many recent studies have demonstrated that non-coding RNAs play an important role in the regulation of the transcription and translation of this gene and some RNAs directly interact with the c-Myc protein, affecting its stability. In this review, we summarize current data on the regulation of MYC by various non-coding RNAs that can potentially be targeted in specific tumor types.

Incorrect reparation of DNA double-strand breaks (DSB) leading to chromosomal rearrangements is one of oncogenesis’s primary causes. Recently published data elucidate the key role of various types of RNA in DSB formation, recognition and repair. With growing interest in RNA biology, increasing RNAs are classified as crucial at the different stages of the main pathways of DSB repair in eukaryotic cells: nonhomologous end joining (NHEJ) and homology-directed repair (HDR). Gene mutations or variation in expression levels of such RNAs can lead to local DNA repair defects, increasing the chromosome aberration frequency. Moreover, it was demonstrated that some RNAs could stimulate long-range chromosomal rearrangements. In this review, we discuss recent evidence demonstrating the role of various RNAs in DSB formation and repair. We also consider how RNA may mediate certain chromosomal rearrangements in a sequence-specific manner.

Важной задачей здравоохранения является повышение числа успешных родов и проведение системных мероприятий, направленных на снижение факторов риска (ФР) у беременных и уже родивших женщин. Цель данной работы заключается в построении статистической модели для оценки и прогноза ФР на ближайшие 5 лет. Применив метод линейной регрессии и методы анализа временных рядов, удалось с высоким уровнем значимости определить наличие трендов в динамике заболеваний, построить прогноз с доверительными интервалами для таких заболеваний, как варикозная болезнь, заболевания мочевыделительной системы и системы органов дыхания, а также рассмотреть осложнения, связанные непосредственно с повышенным показателем индекса массы тела. По полученным данным был сделан вывод о необходимости разработки системы мониторинга, которая будет учитывать положительную динамику роста данных...