Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins
Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aber rant DNA methylation is a mediator of epigenetic changes that are closely a...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2023-01-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/3574 |
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| author | E. A. Antropova T. M. Khlebodarova P. S. Demenkov A. S. Venzel N. V. Ivanisenko A. D. Gavrilenko T. V. Ivanisenko A. V. Adamovskaya P. M. Revva I. N. Lavrik V. A. Ivanisenko |
| author_facet | E. A. Antropova T. M. Khlebodarova P. S. Demenkov A. S. Venzel N. V. Ivanisenko A. D. Gavrilenko T. V. Ivanisenko A. V. Adamovskaya P. M. Revva I. N. Lavrik V. A. Ivanisenko |
| author_sort | E. A. Antropova |
| collection | DOAJ |
| description | Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aber rant DNA methylation is a mediator of epigenetic changes that are closely associated with the HCC pathogenesis and considered a biomarker for its early diagnosis. The ANDSystem software package was used to reconstruct and evaluate the statistical significance of the pathways HCV could potentially use to regulate 32 hypermethylated genes in HCC, including both oncosuppressor and protumorigenic ones identified by genome-wide analysis of DNA methylation. The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. It has been shown that 8 out of 10 HCV proteins were involved in these pathways, the HCV NS3 protein being implicated in the largest number of regulatory pathways. NS3 was associated with the regulation of 5 tumor-suppressor genes, which may be the evidence of its central role in HCC pathogenesis. Analysis of the reconstructed pathways has demonstrated that following the transcription factor inhibition caused by binding to viral proteins, the expression of a number of oncosuppressors (WT1, MGMT, SOCS1, P53) was suppressed, while the expression of others (RASF1, RUNX3, WIF1, DAPK1) was activated. Thus, the performed gene-network reconstruction has shown that HCV proteins can influence not only the methylation status of oncosuppressor genes, but also their transcriptional regulation. The results obtained can be used in the search for pharmacological targets to develop new drugs against HCV-induced HCC. |
| format | Article |
| id | doaj-art-a780a4a984f145ff90b545ffa343b136 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-a780a4a984f145ff90b545ffa343b1362025-02-01T09:58:11ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592023-01-0126873374210.18699/VJGB-22-891311Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteinsE. A. Antropova0T. M. Khlebodarova1P. S. Demenkov2A. S. Venzel3N. V. Ivanisenko4A. D. Gavrilenko5T. V. Ivanisenko6A. V. Adamovskaya7P. M. Revva8I. N. Lavrik9V. A. Ivanisenko10Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of ScencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences; Novosibirsk State UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences; Kurchatov Genomic Center of ICG SB RASKurchatov Genomic Center of ICG SB RAS; Novosibirsk State UniversityKurchatov Genomic Center of ICG SB RAS; Novosibirsk State UniversityTranslational Inflammation Research, Medical Faculty, Otto von Guericke University MagdeburgInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences; Kurchatov Genomic Center of ICG SB RAS; Novosibirsk State UniversityHepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aber rant DNA methylation is a mediator of epigenetic changes that are closely associated with the HCC pathogenesis and considered a biomarker for its early diagnosis. The ANDSystem software package was used to reconstruct and evaluate the statistical significance of the pathways HCV could potentially use to regulate 32 hypermethylated genes in HCC, including both oncosuppressor and protumorigenic ones identified by genome-wide analysis of DNA methylation. The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. It has been shown that 8 out of 10 HCV proteins were involved in these pathways, the HCV NS3 protein being implicated in the largest number of regulatory pathways. NS3 was associated with the regulation of 5 tumor-suppressor genes, which may be the evidence of its central role in HCC pathogenesis. Analysis of the reconstructed pathways has demonstrated that following the transcription factor inhibition caused by binding to viral proteins, the expression of a number of oncosuppressors (WT1, MGMT, SOCS1, P53) was suppressed, while the expression of others (RASF1, RUNX3, WIF1, DAPK1) was activated. Thus, the performed gene-network reconstruction has shown that HCV proteins can influence not only the methylation status of oncosuppressor genes, but also their transcriptional regulation. The results obtained can be used in the search for pharmacological targets to develop new drugs against HCV-induced HCC.https://vavilov.elpub.ru/jour/article/view/3574hepatocellular carcinomahepatitis c virusexpression regulationmethylationregulatory pathwaysgene networksbioinformatics |
| spellingShingle | E. A. Antropova T. M. Khlebodarova P. S. Demenkov A. S. Venzel N. V. Ivanisenko A. D. Gavrilenko T. V. Ivanisenko A. V. Adamovskaya P. M. Revva I. N. Lavrik V. A. Ivanisenko Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins Вавиловский журнал генетики и селекции hepatocellular carcinoma hepatitis c virus expression regulation methylation regulatory pathways gene networks bioinformatics |
| title | Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins |
| title_full | Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins |
| title_fullStr | Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins |
| title_full_unstemmed | Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins |
| title_short | Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins |
| title_sort | computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by hcv proteins |
| topic | hepatocellular carcinoma hepatitis c virus expression regulation methylation regulatory pathways gene networks bioinformatics |
| url | https://vavilov.elpub.ru/jour/article/view/3574 |
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