Biology subjects

Tonevitsky, A.

Publications and source records attributed to Tonevitsky, A..

7 recordsLinked to original sources

bioRxiv2025

Single-cell sequencing of trophoblasts in preeclampsia and chemical hypoxia in BeWo b30 cells reveals EBI3, COL17A1, miR-27a-5p, and miR-193b-5p as hypoxia-response markers

BackgroundPreeclampsia (PE) complicates 2-8% of pregnancies and is marked by placental hypoxia and HIF-pathway activation, especially in early-onset PE (eoPE). Integrating patient tissue analyses with experimental models may reveal common molecular markers of trophoblast hypoxic response. MethodsWe analyzed scRNA-seq data from 10 eoPE, 7 late-onset PE (loPE), and corresponding control placentas, identifying villous cytotrophoblast (VCT), syncytiotrophoblast (SCT), and extravillous trophoblast (EVT) subpopulations. BeWo b30 cells were treated for 24 h with CoCl2 (300 {micro}M) or an oxyquinoline derivative (OD, 5 {micro}M) to induce hypoxia. RNA and small RNA sequencing quantified mRNA and microRNA changes. PROGENy inferred pathway activities. ResultsSingle-cell analysis revealed highest hypoxia pathway activation in eoPE, with EVT showing maximum activity among trophoblast populations. Nine genes were upregulated across all trophoblast types in eoPE: EBI3, CST6, FN1, RFK, COL17A1, LDHA, PKP2, RPS4Y1, and RPS26. In vitro, OD induced more specific hypoxia responses than CoCl2, with 1,284 versus 3,032 differentially expressed genes respectively. Critically, EBI3, FN1, and COL17A1 showed concordant upregulation in both placental tissue and OD-treated cells, while CoCl2 treatment produced opposite expression patterns. MicroRNA analysis identified hsa-miR-27a-5p and hsa-miR-193b-5p as consistently elevated in both experimental conditions and previously reported in PE placental vesicles. We also identified isoforms of hsa-miR-9-5p and hsa-miR-92b-3p as hypoxia-associated in trophoblast. ConclusionsEBI3, COL17A1, hsa-miR-27a-5p, and hsa-miR-193b-5p emerge as trophoblast hypoxia markers in PE. Oxyquinoline derivatives offer a more physiologically relevant in vitro hypoxia model than CoCl2. This integrated approach advances understanding of PE pathophysiology and suggests candidate therapeutic targets.

developmental biology↗

bioRxiv2023

miRNA binding pressure channels evolution of SARS-CoV-2 genomes

In somatic cells, microRNAs (miRNAs) bind to the genomes of RNA viruses and influence their translation and replication. Here we demonstrate that a significant number of miRNA binding sites locate in the NSP4 region of the SARS-CoV-2 genome, and the intestinal human miRNAs exert evolutionary pressure on this region. Notably, in infected cells, NSP4 promotes the formation of double-membrane vesicles, which serve as the scaffolds for replication-transcriptional complexes and protect viral RNA from intracellular destruction. In three years of selection, the loss of many miRNA binding sites, in particular, those within the NSP4, has shaped the SARS-CoV-2 genomes to promote the descendants of the BA.2 variants as the dominant strains and define current momentum of the pandemics.

evolutionary biology↗

bioRxiv2022

Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules

The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide after N211 deletion, L212I substitution and EPE 212-214 insertion. The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.

immunology↗

bioRxiv2021

ExhauFS: exhaustive search-based feature selection for classification and survival regression

MotivationFeature selection is one of the main techniques used to prevent overfitting in machine learning applications. The most straightforward approach for feature selection is exhaustive search: one can go over all possible feature combinations and pick up the model with the highest accuracy. This method together with its optimizations were actively used in biomedical research, however, publicly available implementation is missing. ResultsWe present ExhauFS - the user-friendly command-line implementation of the exhaustive search approach for classification and survival regression. Aside from tool description, we included three application examples in the manuscript to comprehensively review the implemented functionality. First, we executed ExhauFS on a toy cervical cancer dataset to illustrate basic concepts. Then, a multi-cohort microarray and RNA-seq breast cancer datasets were used to construct gene signatures for 5-year recurrence classification. Finally, Cox survival regression models were used to fit isomiR signatures for overall survival prediction for patients with colorectal cancer. AvailabilitySource codes and documentation of ExhauFS are available on GitHub: https://github.com/s-a-nersisyan/ExhauFS. Contactsnersisyan@hse.ru

bioinformatics↗

bioRxiv2021

T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations

Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which can help the virus to evade either CD8 or CD4 T-cell responses. We developed T-cell COVID-19 Atlas (T-CoV, https://t-cov.hse.ru) - the comprehensive web portal, which allows one to analyze how SARS-CoV-2 mutations alter the presentation of viral peptides by HLA molecules. The data are presented for common virus variants and the most frequent HLA class I and class II alleles. Binding affinities of HLA molecules and viral peptides were assessed with accurate in silico methods. The obtained results highlight the importance of taking HLA alleles diversity into account: mutation-mediated alterations in HLA-peptide interactions were highly dependent on HLA alleles. For example, we found that the essential number of peptides tightly bound to HLA-B*07:02 in the reference Wuhan variant ceased to be tight binders for the Indian (Delta) and the UK (Alpha) variants. In summary, we believe that T-CoV will help researchers and clinicians to predict the susceptibility of individuals with different HLA genotypes to infection with variants of SARS-CoV-2 and/or forecast its severity.

bioinformatics↗

bioRxiv2020

The potential role of miR-21-3p in coronavirus-host interplay

ABSTRACTHost miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses by several possible mechanisms including direct binding the viral RNA. Identification of human miRNAs involved in coronavirus-host interplay is becoming important due to the ongoing COVID-19 pandemic. In this work we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. In order to uncover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV. Further bioinformatic analysis of binding sites revealed high conservativity of miR-21-3p binding regions within RNAs of human coronaviruses and their strains.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2019

Dissection of demethylation and toxicity induced gene expression changes after decitabine treatment.

The DNA methyltransferase inhibitor decitabine (DAC) is a widely used drug for both fundamental epigenetics studies and anti-cancer therapy. Besides DNA demethylation, DAC also induces cell toxicity associated with DNA damage. The dual-mode of DAC action on cells provides a significant hurdle to study genes which expression is regulated by CpG methylation. In this work, we performed the analysis of global DNA methylation levels in cultured cancer cells after treatment with increasing doses of DAC and have found the U-shaped curve of the de-methylation efficacy induced by the drug. Specifically, high doses of DAC induced significantly lower DNA hypomethylation as compared to hundred-fold less concentrated doses. At the same time, the impact of DAC on cell viability was dose-dependent. These findings allowed dissecting the demethylation and the cell toxicity impact of DAC on gene expression in subsequent mRNA-seq experiments. Surprisingly, the number of genes that were upregulated due to DNA hypomethylation was comparable to the number of genes induced by DAC toxicity. Furthermore, we show that high DAC concentrations induce downregulation of housekeeping genes which are most widely used for RT-qPCR normalization (including GAPDH, actin and tubulin). The latter suggests that genes unaffected by DAC treatment would manifest themselves as upregulated when their expression is normalized on a downregulated housekeeping reference. Finally, we show that expression of most human oncogenes and tumor-suppressor genes remains unaffected after DAC treatment, and only a few of them were upregulated due to DNA hypomethylation. Our work stresses the importance of closely studying the correlation of the degree of DNA demethylation induced by varying doses of DAC with changes in gene expression levels to avoid erroneous conclusions regarding epigenetic silencing of a gene.

molecular biology↗