vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJGB-23-10vavilov-3634Research ArticleЭПИГЕНЕТИКА И РЕГУЛЯЦИЯ АКТИВНОСТИ ГЕНОВEPIGENETICS AND GENE REGULATIONИзменение профиля метилирования ДНК в ткани печени при прогрессировании HCV-индуцированного фиброза до гепатоцеллюлярной карциномыChanges in DNA methylation profile in liver tissue during progression of HCV-induced fibrosis to hepatocellular carcinomahttps://orcid.org/0000-0002-9527-7015ГончароваИ. А.GoncharovaI. A.

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Tomsk

irina.goncharova@medgenetics.ruhttps://orcid.org/0000-0001-6568-6339ЗарубинА. А.ZarubinA. A.

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Tomsk

https://orcid.org/0000-0001-6133-8986БабушкинаН. П.BabushkinaN. P.

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https://orcid.org/0000-0003-1498-6934КоролеваЮ. А.KorolevaI. A.

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Tomsk

https://orcid.org/0000-0002-0673-4094НазаренкоМ. С.NazarenkoM. S.

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Tomsk

Научно-исследовательский институт медицинской генетики, Томский национальный исследовательский медицинский центр Российской академии наукРоссияResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of SciencesRussian Federation2023070320232717282Copyright © Гончарова И.А., Зарубин А.А., Бабушкина Н.П., Королева Ю.А., Назаренко М.С., 20232023Гончарова И.А., Зарубин А.А., Бабушкина Н.П., Королева Ю.А., Назаренко М.С.Goncharova I.A., Zarubin A.A., Babushkina N.P., Koroleva I.A., Nazarenko M.S.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3634

С использованием данных GSE73003 и GSE37988, представленных в базе данных GEODataSets (https://www.ncbi.nlm.nih.gov/), проведен сравнительный анализ уровня метилирования 27 578 CpG-сайтов между парными образцами опухолевой и окружающей опухоль тканями печени различной степени поражения (фиброз, цирроз) у больных HCV-индуцированной гепатоцеллюлярной карциномой (ГЦК), а также между опухолевой и нормальной тканью у больного ГЦК невирусной этиологии. Выявлено значительно меньшее число дифференциально метилированных сайтов между нормальной тканью печени и ГЦК невирусной этиологии, а также между ГЦК и фиброзом (32 и 40), чем между ГЦК и циррозом (2450 и 2304 соответственно по данным GSE73003 и GSE37988). По мере прогрессирования патологического изменения окружающей опухоль ткани уменьшается соотношение количества гипер-/гипометилированных дифференциально метилированных сайтов в опухоли. Так, в опухолевой ткани по сравнению с нормальной/фиброзом/циррозом печени гиперметилированы 75/62.5/47.7 % (GSE73003) и 16 % (GSE37988) CpG-сайтов соответственно. Стойкое гиперметилирование генов ZNF154 и ZNF540, а также гипометилирование CCL20 зарегистрировано в опухолевой ткани относительно как фиброза, так и цирроза печени. Белковые продукты генов EDG4, CCL20, GPR109A и GRM8, CpG-сайты которых характеризуются изменением уровня метилирования ДНК в опухоли на фоне цирроза и фиброза, принадлежат к категории «передачи сигналов рецепторов, связанных с G-белком». Однако изменение уровня метилирования «драйверных» для онкопатологии генов (АРС, CDKN2B, GSTP1, ELF4, TERT, WT1) регистрируется в опухолевой ткани на фоне цирроза печени, но не фиброза. Среди гиперметилированных в опухолевой ткани генов на фоне цирроза печени наиболее представленными биологическими путями являются процессы развития, передачи межклеточных сигналов, регуляции транскрипции, связывания с белками Wnt-пути. Гены, гипометилированные в опухолевой ткани печени на фоне ее цирротического поражения, относятся к передаче обонятельных сигналов, нейроактивному взаимодействию лиганда с рецептором, кератинизации, иммунному ответу, ингибированию сериновых протеаз и метаболизму цинка. Гиперметилированные в опухоли гены локализуются в локусе 7р15.2 в регионе кластера HOXA, а гипометилированные CpG-сайты занимают протяженные области генома в кластерах генов обонятельных рецепторов (11p15.4), кератина и кератин-ассоциированных белков (12q13.13, 17q21.2 и 21q22.11), комплекса эпидермальной дифференцировки (1q21.3), а также функционирования иммунной системы – локусы 9p21.3 (кластер IFNA, IFNB1, IFNW1) и 19q13.41–19q13.42 (кластеры KLK, SIGLEC, LILR, KIR). Среди генов фиброгенеза или репарации ДНК cg14143055 (ADAMDEC1) локализован в регионе связывания транскрипционных факторов семейства HOX, а cg05921699 (CD79A), cg06196379 (TREM1) и cg10990993 (MLH1) расположены в области связывания транскрипционных факторов семейства белков ZNF. Таким образом, профиль метилирования ДНК в печени при HCV-индуцированной ГЦК является уникальным и различается в зависимости от степени поражения окружающей ткани – фиброз или цирроз.

In this study we compared methylation levels of 27,578 CpG sites between paired samples of the tumor and surrounding liver tissues with various degrees of damage (fibrosis, cirrhosis) in HCV-induced hepatocellular carcinoma (HCC) patients, as well as between tumor and normal tissue in non-viral HCC patients, using GSE73003 and GSE37988 data from GEODataSets (https://www.ncbi.nlm.nih.gov/). A significantly lower number of differentially methylated sites (DMS) were found between HCC of non-viral etiology and normal liver tissue, as well as between HCC and fibrosis (32 and 40), than between HCC and cirrhosis (2450 and 2304, respectively, according to GSE73003 and GSE37988 datasets). As the pathological changes in the tissue surrounding the tumor progress, the ratio of hyper-/ hypomethylated DMSs in the tumor decreases. Thus, in tumor tissues compared with normal/fibrosis/cirrhosis of the liver, 75/62.5/47.7 % (GSE73003) and 16 % (GSE37988) of CpG sites are hypermethylated, respectively. Persistent hypermethylation of the ZNF154 and ZNF540 genes, as well as CCL20 hypomethylation, were registered in tumor tissue in relation to both liver fibrosis and liver cirrhosis. Protein products of the EDG4, CCL20, GPR109A, and GRM8 genes, whose CpG sites are characterized by changes in DNA methylation level in tumor tissue in the setting of cirrhosis and fibrosis, belong to “Signaling by G-protein-coupled receptors (GPCRs)” category. However, changes in the methylation level of the “driver” genes for oncopathology (АРС, CDKN2B, GSTP1, ELF4, TERT, WT1) are registered in tumor tissue in the setting of liver cirrhosis but not fibrosis. Among the genes hypermethylated in tumor tissue in the setting of liver cirrhosis, the most represented biological pathways are developmental processes, cell-cell signaling, transcription regulation, Wnt-protein binding. Genes hypomethylated in liver tumor tissue in the setting of liver cirrhosis are related to olfactory signal transduction, neuroactive ligand-receptor interaction, keratinization, immune response, inhibition of serine proteases, and zinc metabolism. The genes hypermethylated in the tumor are located at the 7p15.2 locus in the HOXA cluster region, and the hypomethylated CpG sites occupy extended regions of the genome in the gene clusters of olfactory receptors (11p15.4), keratin and keratin-associated proteins (12q13.13, 17q21.2, and 21q22.11), epidermal differentiation complex (1q21.3), and immune system function loci 9p21.3 (IFNA, IFNB1, IFNW1 cluster) and 19q13.41–19q13.42 (KLK, SIGLEC, LILR, KIR clusters). Among the genes of fibrogenesis or DNA repair, cg14143055 (ADAMDEC1) is located in the binding region of the HOX gene family transcription factors (TFs), while cg05921699 (CD79A), cg06196379 (TREM1) and cg10990993 (MLH1) are located in the binding region of the ZNF protein family transcription factor (TF). Thus, the DNA methylation profile in the liver in HCV-induced HCC is unique and differs depending on the degree of surrounding tissue lesion – liver fibrosis or liver cirrhosis.

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The authors declare that there are no conflicts of interest present.