Seminars 2024

17.01.2024 [online] Comparison of methods for detecting guanine quadruplexes

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Speaker: Dmitry Konovalov, research intern

The report presented a comparison of the effectiveness of the main experimental and theoretical methods for detecting quadruplexes. Their similarities, differences, main advantages and disadvantages are described.

21.02.2024 [online] Analysis of differential expression in various samples

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Speaker: Artem Voitetsky, trainee researcher

The report presented an analysis of differential expression in different samples. RNA and small RNA samples were compared separately. The analysis examined the dependence of differential gene expression depending on the presence or absence of the ADAR and PRKRA genes. Thus, it is planned to find out how these two genes influence what. Additionally, the effect of interferon on the samples was studied.

20.03.2024 [online] Analysis of breast cancer snRNA-seq data: from primary tumor to metastases

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Speaker: Anastasia Mikhailova, trainee researcher

Single cell sequencing (scRNA-seq) technology is an important tool for investigating cellular heterogeneity. This method provides the ability to analyze unique gene expression profiles and other intracellular parameters, which, in turn, allows the study of intracellular processes, such as tumor heterogeneity and their interaction with surrounding tissues.

17.04.2024 [online] Experiments on Z-DNA prediction by trained machine learning models

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Speaker: Beknazarov Nazar, research intern

The study and prediction of Z-DNA regions in various organisms has become relevant. The report presents experiments on predicting Z-DNA using machine learning models trained on experimental markings and analysis of the resulting predictions, followed by comparison of the conclusions obtained on different organisms.

15.05.2024 [online] Creating a Joint Track for Z-Flipon Prediction

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Speaker: Nazar Beknazarov, trainee researcher

To accomplish this task, approaches developed for other tasks, such as quadruplex prediction, were considered. At the saminar, approaches that can be successful in this task were discussed, the results obtained were tested on current experimental data, and the best options were selected. The results will be published.

29.05.2024 [online] Regulation of cell death pathways in cancer samples by ADAR and PRKRA

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Speaker: Artem Voitetsky, research intern

In this research project, we aimed to study the effect of ADAR and PRKRA gene knockout, as well as the effect of interferon on the transcriptome. These genes play important roles in RNA regulation and interferon response, making them promising targets for therapeutic interventions. ADAR was found to have a significant effect on RNA editing, and knockout of ADAR and PRKRA resulted in changes in the expression of their associated genes. A particularly strong link was found between the study results and lung cancer.

03.06.2024 [online] Study of signaling pathways for suppressing the immune response

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Speaker: Anastasia Mikhailova, trainee researcher

The study performed a systematic analysis of single-cell profiles of primary breast cancer tumors and their bone marrow metastases. Key patterns of interaction between tumor cells and their microenvironment have been identified. Particular attention was paid to the MIF and MDK signaling pathways, which play an important role in the metastasis process by modulating the immune response and promoting the growth and survival of cancer cells. These results indicate the promise of these signaling pathways as targets for therapeutic intervention in metastatic breast cancer.

24.06.2024 [online] Quadruplexes in promoter-enhancer interactions

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Speaker: Dmitry Konovalov, research intern

The report presented a description of the interaction model of quadruplexes within a promoter-enhancer pair. The model assumes stacking of quadruplexes to stabilize the promoter-enhancer loop. The results of testing the model were presented, and the results of a statistical analysis of experimental data on the colocalization of quadruplexes were presented.

02.07.2024 [online] Non-canonical quadruplexes

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Speaker: Dmitry Konovalov, trainee researcher

Previously, it was believed that quadruplexes correspond to a pattern of four guanine repeats separated by short (1-7) loops. More and more experimental data indicate the existence of quadruplexes that deviate from this pattern: quadruplexes with loops and mismatches. The report presented the sequences and patterns of non-canonical quadruplexes observed experimentally.

28.08.2024 [онлайн] Chemokine-mediated immunosuppression mechanisms in the tumor microenvironment

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Speaker: Anastasia Mikhailova, trainee researcher

The report presented the results of a study of immunosuppressive chemokines such as MIF, CCL2, and CCL3 and their role in creating a tumor-friendly microenvironment. Analysis of primary breast tumor samples and bone marrow metastases showed that these chemokines are actively involved in suppressing the antitumor immune response. They promote the polarization of macrophages into a proinflammatory phenotype that supports tumor growth, and inhibit the activation and proliferation of T cells and other immune cells. Thus, immunosuppressive chemokines create a tumor-friendly environment, promoting its progression and metastasis.

11.09.2024 [онлайн] Assessing the influence of major regulatory genes in various tissues on tissue-specific genes

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Speaker: Artem Bashkatov, expert.

The report presented the results of the analysis of the assessment of the intersections of the transcription factor markings of major regulatory genes (MRGs) and tissue-specific genes that were isolated after obtaining full-genome predictions by the DeepG4 model. Based on the results, a block of graphs was presented comparing the obtained data on the intersection of MRGs with the distributions of random hits of the corresponding genes in nervous tissue, liver and muscle tissue. Several genes were identified that showed statistically significant enrichment (MYOD1, HNF1A, HNF1B) and depletion (NEUROD1) relative to a random sample. These results require further study.

25.09.2024 [онлайн] The Role of Immunostimulatory Chemokines in Antitumor Immunity

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Speaker: Anastasia Mikhailova, trainee researcher

The report presented the results of a study on the role of immunostimulatory chemokines, such as CXCR9, CXCR10, CXCR11, and CXCL9, in activating the antitumor immune response. Immunostimulatory chemokines promote the recruitment and activation of various immune cells, such as T cells, NK cells, and dendritic cells, into the tumor microenvironment. In addition, they can stimulate the proliferation and differentiation of these cells, enhancing the antitumor immune response. Particular attention was paid to CXCL9, the expression of which in an aggressive form of breast cancer significantly improves the prognosis of the disease.

02.10.2024 [online] Distribution of Non-Canonical Quadruplexes in the Genome

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Speaker: Dmitry Konovalov, trainee researcher

The report examined the distribution of quadruplexes in the genome. It covered both canonical and non-canonical quadruplexes, and also discussed the relationship of quadruplexes with transposons and the problems associated with experimental validation of quadruplex formation in repeats using high-throughput sequencing-based methods.

23.10.2024 [online] Analysis of the intersection of genes with changes in expression in samples with ADAR and PRKRA knockout

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Speaker: Voitetsky Artem, trainee researcher

The report presented an analysis of changes in gene expression upon knockout of the ADAR and PRKRA genes. The study showed that a significant number of genes significantly change their expression levels when these genes are knocked out. An intersection table of significantly altered genes between different experimental conditions was compiled.

The analysis revealed that genes that changed expression when one of the genes under study were knocked out often also changed expression when another gene was knocked out. However, cases of opposite changes in expression turned out to be extremely rare. The highest agreement (about 60%) was observed between the Mock and IFN conditions, which was explained by knockout of the same gene. There was also a 20-40% overlap in gene expression changes between ADAR and PRKRA knockouts.

The results showed that knocking out one gene led to a decrease in the expression levels of many other genes, and knocking out another gene often had a similar effect. This observation supports the hypothesis that the ADAR and PRKRA genes are involved in the same immune response mechanism. It is interesting to note that among genes with decreased expression, the percentage of matches is close to 40%, while among genes with increased expression it is just over 20%.

06.11.2024 [online] Analysis of gene expression during knockout of ADAR and PRKRA and subsequent treatment with interferon

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Speaker: Voitetsky Artem, trainee researcher

The report presented a comparison of gene expression levels between interferon-treated and untreated knockout samples. The analysis showed the opposite situation compared to previous results: most significantly changed genes showed increased expression levels.

This observation suggests that the most common response to interferon in the setting of ADAR or PRKRA gene knockout is an increase in the expression of other genes.

Combining the results of both differential expression studies, it was concluded that knockout of the ADAR and PRKRA genes results in suppression of the expression of a significant number of genes, while interferon treatment causes an increase in expression.