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  1. Article ; Online: Identification of Potential Therapeutic Targets on the Level of DNA/mRNAs, Proteins and Metabolites: A Systematic Mapping Review of Scientific Texts' Fragments from Open Targets.

    Pogodin, Pavel V / Kiseleva, Olga I / Ilgisonis, Ekaterina V

    Current issues in molecular biology

    2023  Volume 45, Issue 4, Page(s) 3406–3418

    Abstract: Database records contain useful information, which is readily available, but, unfortunately, limited compared to the source (publications). Our study reviewed the text fragments supporting the association between the biological macromolecules and ... ...

    Abstract Database records contain useful information, which is readily available, but, unfortunately, limited compared to the source (publications). Our study reviewed the text fragments supporting the association between the biological macromolecules and diseases from Open Targets to map them on the biological level of study (DNA/RNA, proteins, metabolites). We screened records using a dictionary containing terms related to the selected levels of study, reviewed 600 hits manually and used machine learning to classify 31,260 text fragments. Our results indicate that association studies between diseases and macromolecules conducted on the level of DNA and RNA prevail, followed by the studies on the level of proteins and metabolites. We conclude that there is a clear need to translate the knowledge from the DNA/RNA level to the evidence on the level of proteins and metabolites. Since genes and their transcripts rarely act in the cell by themselves, more direct evidence may be of greater value for basic and applied research.
    Language English
    Publishing date 2023-04-13
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2000024-8
    ISSN 1467-3045 ; 1467-3037
    ISSN (online) 1467-3045
    ISSN 1467-3037
    DOI 10.3390/cimb45040223
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The Curious Case of the HepG2 Cell Line: 40 Years of Expertise.

    Arzumanian, Viktoriia A / Kiseleva, Olga I / Poverennaya, Ekaterina V

    International journal of molecular sciences

    2021  Volume 22, Issue 23

    Abstract: Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require ... ...

    Abstract Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
    MeSH term(s) Biomedical Research ; Hep G2 Cells ; Hepatocytes ; Humans ; Liver Neoplasms/genetics ; Liver Neoplasms/pathology ; Metabolome ; Proteins/genetics ; Proteins/metabolism
    Chemical Substances Proteins
    Language English
    Publishing date 2021-12-04
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms222313135
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Estimating Total Quantitative Protein Content in

    Dolgalev, Georgii V / Safonov, Taras A / Arzumanian, Viktoriia A / Kiseleva, Olga I / Poverennaya, Ekaterina V

    International journal of molecular sciences

    2023  Volume 24, Issue 3

    Abstract: The continuous improvement of proteomic techniques, most notably mass spectrometry, has generated quantified proteomes of many organisms with unprecedented depth and accuracy. However, there is still a significant discrepancy in the reported numbers of ... ...

    Abstract The continuous improvement of proteomic techniques, most notably mass spectrometry, has generated quantified proteomes of many organisms with unprecedented depth and accuracy. However, there is still a significant discrepancy in the reported numbers of total protein molecules per specific cell type. In this article, we explore the results of proteomic studies of
    MeSH term(s) Humans ; Escherichia coli/metabolism ; Saccharomyces cerevisiae/metabolism ; Proteome/metabolism ; Proteomics/methods ; HeLa Cells ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances Proteome ; Saccharomyces cerevisiae Proteins
    Language English
    Publishing date 2023-01-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24032081
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Evolution of Protein Functional Annotation: Text Mining Study.

    Ilgisonis, Ekaterina V / Pogodin, Pavel V / Kiseleva, Olga I / Tarbeeva, Svetlana N / Ponomarenko, Elena A

    Journal of personalized medicine

    2022  Volume 12, Issue 3

    Abstract: Within the Human Proteome Project initiative framework for creating functional annotations of uPE1 proteins, the neXt-CP50 Challenge was launched in 2018. In analogy with the missing-protein challenge, each command deciphers the functional features of ... ...

    Abstract Within the Human Proteome Project initiative framework for creating functional annotations of uPE1 proteins, the neXt-CP50 Challenge was launched in 2018. In analogy with the missing-protein challenge, each command deciphers the functional features of the proteins in the chromosome-centric mode. However, the neXt-CP50 Challenge is more complicated than the missing-protein challenge: the approaches and methods for solving the problem are clear, but neither the concept of protein function nor specific experimental and/or bioinformatics protocols have been standardized to address it. We proposed using a retrospective analysis of the key HPP repository, the neXtProt database, to identify the most frequently used experimental and bioinformatic methods for analyzing protein functions, and the dynamics of accumulation of functional annotations. It has been shown that the dynamics of the increase in the number of proteins with known functions are greater than the progress made in the experimental confirmation of the existence of questionable proteins in the framework of the missing-protein challenge. At the same time, the functional annotation is based on the guilty-by-association postulate, according to which, based on large-scale experiments on API-MS and Y2H, proteins with unknown functions are most likely mapped through "handshakes" to biochemical processes.
    Language English
    Publishing date 2022-03-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm12030479
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications.

    Arzumanian, Viktoriia A / Dolgalev, Georgii V / Kurbatov, Ilya Y / Kiseleva, Olga I / Poverennaya, Ekaterina V

    International journal of molecular sciences

    2022  Volume 23, Issue 22

    Abstract: The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally ...

    Abstract The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
    MeSH term(s) RNA Processing, Post-Transcriptional ; RNA/metabolism ; Nucleotides
    Chemical Substances RNA (63231-63-0) ; Nucleotides
    Language English
    Publishing date 2022-11-10
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms232213851
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The Expectation and Reality of the HepG2 Core Metabolic Profile.

    Kiseleva, Olga I / Kurbatov, Ilya Y / Arzumanian, Viktoriia A / Ilgisonis, Ekaterina V / Zakharov, Svyatoslav V / Poverennaya, Ekaterina V

    Metabolites

    2023  Volume 13, Issue 8

    Abstract: To represent the composition of small molecules circulating in HepG2 cells and the formation of the "core" of characteristic metabolites that often attract researchers' attention, we conducted a meta-analysis of 56 datasets obtained through metabolomic ... ...

    Abstract To represent the composition of small molecules circulating in HepG2 cells and the formation of the "core" of characteristic metabolites that often attract researchers' attention, we conducted a meta-analysis of 56 datasets obtained through metabolomic profiling via mass spectrometry and NMR. We highlighted the 288 most commonly studied compounds of diverse chemical nature and analyzed metabolic processes involving these small molecules. Building a complete map of the metabolome of a cell, which encompasses the diversity of possible impacts on it, is a severe challenge for the scientific community, which is faced not only with natural limitations of experimental technologies, but also with the absence of transparent and widely accepted standards for processing and presenting the obtained metabolomic data. Formulating our research design, we aimed to reveal metabolites crucial to the Hepg2 cell line, regardless of all chemical and/or physical impact factors. Unfortunately, the existing paradigm of data policy leads to a streetlight effect. When analyzing and reporting only target metabolites of interest, the community ignores the changes in the metabolomic landscape that hide many molecular secrets.
    Language English
    Publishing date 2023-08-03
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo13080908
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Multiomics Picture of Obesity in Young Adults.

    Kiseleva, Olga I / Pyatnitskiy, Mikhail A / Arzumanian, Viktoriia A / Kurbatov, Ilya Y / Ilinsky, Valery V / Ilgisonis, Ekaterina V / Plotnikova, Oksana A / Sharafetdinov, Khaider K / Tutelyan, Victor A / Nikityuk, Dmitry B / Ponomarenko, Elena A / Poverennaya, Ekaterina V

    Biology

    2024  Volume 13, Issue 4

    Abstract: Obesity is a socially significant disease that is characterized by a disproportionate accumulation of fat. It is also associated with chronic inflammation, cancer, diabetes, and other comorbidities. Investigating biomarkers and pathological processes ... ...

    Abstract Obesity is a socially significant disease that is characterized by a disproportionate accumulation of fat. It is also associated with chronic inflammation, cancer, diabetes, and other comorbidities. Investigating biomarkers and pathological processes linked to obesity is especially vital for young individuals, given their increased potential for lifestyle modifications. By comparing the genetic, proteomic, and metabolomic profiles of individuals categorized as underweight, normal, overweight, and obese, we aimed to determine which omics layer most accurately reflects the phenotypic changes in an organism that result from obesity. We profiled blood plasma samples by employing three omics methodologies. The untargeted GC×GC-MS metabolomics approach identified 313 metabolites. To augment the metabolomic dataset, we integrated a label-free HPLC-MS/MS proteomics method, leading to the identification of 708 proteins. The genomic layer encompassed the genotyping of 647,250 SNPs. Utilizing omics data, we trained sparse Partial Least Squares models to predict body mass index. Molecular features exhibiting frequently non-zero coefficients were selected as potential biomarkers, and we further explored enriched biological pathways. Proteomics was the most effective in single-omics analyses, with a median absolute error (MAE) of 5.44 ± 0.31 kg/m
    Language English
    Publishing date 2024-04-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology13040272
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Exploring Dynamic Metabolome of the HepG2 Cell Line: Rise and Fall.

    Kiseleva, Olga I / Kurbatov, Ilya Yu / Arzumanian, Viktoriia A / Ilgisonis, Ekaterina V / Vakhrushev, Igor V / Lupatov, Alexey Yu / Ponomarenko, Elena A / Poverennaya, Ekaterina V

    Cells

    2022  Volume 11, Issue 22

    Abstract: Both biological and technical variations can discredit the reliability of obtained data in omics studies. In this technical note, we investigated the effect of prolonged cultivation of the HepG2 hepatoma cell line on its metabolomic profile. Using the GC ...

    Abstract Both biological and technical variations can discredit the reliability of obtained data in omics studies. In this technical note, we investigated the effect of prolonged cultivation of the HepG2 hepatoma cell line on its metabolomic profile. Using the GC × GC-MS approach, we determined the degree of metabolic variability across HepG2 cells cultured in uniform conditions for 0, 5, 10, 15, and 20 days. Post-processing of obtained data revealed substantial changes in relative abundances of 110 metabolites among HepG2 samples under investigation. Our findings have implications for interpreting metabolomic results obtained from immortal cells, especially in longitudinal studies. There are still plenty of unanswered questions regarding metabolomics variability and many potential areas for future targeted and panoramic research. However, we suggest that the metabolome of cell lines is unstable and may undergo significant transformation over time, even if the culture conditions remain the same. Considering metabolomics variability on a relatively long-term basis, careful experimentation with particular attention to control samples is required to ensure reproducibility and relevance of the research results when testing both fundamentally and practically significant hypotheses.
    MeSH term(s) Humans ; Reproducibility of Results ; Hep G2 Cells ; Metabolome ; Metabolomics/methods ; Gas Chromatography-Mass Spectrometry/methods
    Language English
    Publishing date 2022-11-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells11223548
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Exploiting Multi-Omics Profiling and Systems Biology to Investigate Functions of TOMM34.

    Poverennaya, Ekaterina V / Pyatnitskiy, Mikhail A / Dolgalev, Georgii V / Arzumanian, Viktoria A / Kiseleva, Olga I / Kurbatov, Ilya Yu / Kurbatov, Leonid K / Vakhrushev, Igor V / Romashin, Daniil D / Kim, Yan S / Ponomarenko, Elena A

    Biology

    2023  Volume 12, Issue 2

    Abstract: Although modern biology is now in the post-genomic era with vastly increased access to high-quality data, the set of human genes with a known function remains far from complete. This is especially true for hundreds of mitochondria-associated genes, which ...

    Abstract Although modern biology is now in the post-genomic era with vastly increased access to high-quality data, the set of human genes with a known function remains far from complete. This is especially true for hundreds of mitochondria-associated genes, which are under-characterized and lack clear functional annotation. However, with the advent of multi-omics profiling methods coupled with systems biology algorithms, the cellular role of many such genes can be elucidated. Here, we report genes and pathways associated with
    Language English
    Publishing date 2023-01-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology12020198
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Workability of mRNA Sequencing for Predicting Protein Abundance.

    Ponomarenko, Elena A / Krasnov, George S / Kiseleva, Olga I / Kryukova, Polina A / Arzumanian, Viktoriia A / Dolgalev, Georgii V / Ilgisonis, Ekaterina V / Lisitsa, Andrey V / Poverennaya, Ekaterina V

    Genes

    2023  Volume 14, Issue 11

    Abstract: Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than proteomics methods, i.e., both mass spectrometry and immunochemical analysis. For this reason, most scientific studies are limited to assessing the level of mRNA content. ...

    Abstract Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than proteomics methods, i.e., both mass spectrometry and immunochemical analysis. For this reason, most scientific studies are limited to assessing the level of mRNA content. At the same time, protein content (and its post-translational status) largely determines the cell's state and behavior. Such a forced extrapolation of conclusions from the transcriptome to the proteome often seems unjustified. The ratios of "transcript-protein" pairs can vary by several orders of magnitude for different genes. As a rule, the correlation coefficient between transcriptome-proteome levels for different tissues does not exceed 0.3-0.5. Several characteristics determine the ratio between the content of mRNA and protein: among them, the rate of movement of the ribosome along the mRNA and the number of free ribosomes in the cell, the availability of tRNA, the secondary structure, and the localization of the transcript. The technical features of the experimental methods also significantly influence the levels of the transcript and protein of the corresponding gene on the outcome of the comparison. Given the above biological features and the performance of experimental and bioinformatic approaches, one may develop various models to predict proteomic profiles based on transcriptomic data. This review is devoted to the ability of RNA sequencing methods for protein abundance prediction.
    MeSH term(s) Proteome/genetics ; Proteomics/methods ; Gene Expression Profiling ; Transcriptome/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
    Chemical Substances Proteome ; RNA, Messenger
    Language English
    Publishing date 2023-11-11
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14112065
    Database MEDical Literature Analysis and Retrieval System OnLINE

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