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For: Azimi Z, Isa MR, Khan J, Wang SM, Ismail Z. Association of zinc level with DNA methylation and its consequences: A systematic review. Heliyon 2022;8:e10815. [PMID: 36203899 PMCID: PMC9530842 DOI: 10.1016/j.heliyon.2022.e10815] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022] Open

For:	Azimi Z, Isa MR, Khan J, Wang SM, Ismail Z. Association of zinc level with DNA methylation and its consequences: A systematic review. Heliyon 2022;8:e10815. [PMID: 36203899 PMCID: PMC9530842 DOI: 10.1016/j.heliyon.2022.e10815] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022] Open

Number

Cited by Other Article(s)

dos Santos PVBE, Brasil ADA, Milone LTV, Chalfun G, Saide SCADO, Salú MDS, de Oliveira MBG, Robaina JR, Lima-Setta F, Rodrigues-Santos G, de Magalhães-Barbosa MC, da Cunha AJLA, Prata-Barbosa A. Impact of prematurity on LINE-1 promoter methylation. Epigenomics 2024;16:1253-1264. [PMID: 39297700 PMCID: PMC11486321 DOI: 10.1080/17501911.2024.2397329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 08/20/2024] [Indexed: 10/12/2024] Open

Affiliation(s)

Paulo Victor Barbosa Eleutério dos Santos Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil Martagão Gesteira Institute of Childcare & Pediatrics (IPPMG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
Aline de Araújo Brasil Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil
Leo Travassos Vieira Milone Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil Institute of Genetics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
Georgia Chalfun Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil Department of Neonatology, Maternity School, Federal University of Rio de Janeiro (UFRJ), RJ, Brazil
Stephanie Cristina Alves de Oliveira Saide Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil Institute of Genetics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
Margarida dos Santos Salú Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil
Mariana Barros Genuíno de Oliveira Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil
Jaqueline Rodrigues Robaina Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil
Fernanda Lima-Setta Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil
Gustavo Rodrigues-Santos Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil
Maria Clara de Magalhães-Barbosa Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil
Antônio José Ledo Alves da Cunha Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil Martagão Gesteira Institute of Childcare & Pediatrics (IPPMG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
Arnaldo Prata-Barbosa Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, Brazil Martagão Gesteira Institute of Childcare & Pediatrics (IPPMG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil

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Shi W, Fang J, Ren H, Sun P, Liu J, Deng F, Zhang S, Wang Q, Wang J, Tong S, Tang S, Shi X. Association between exposure to chemical mixtures and epigenetic ageing biomarkers: Modifying effects of thyroid hormones and physical activity. JOURNAL OF HAZARDOUS MATERIALS 2024;469:134009. [PMID: 38492399 DOI: 10.1016/j.jhazmat.2024.134009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/23/2024] [Accepted: 03/09/2024] [Indexed: 03/18/2024]

Affiliation(s)

Wanying Shi Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China; China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
Jianlong Fang China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
Huimin Ren China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China; Department of Toxicology, School of Public Health, China Medical University, Shenyang, Liaoning 110122, China
Peijie Sun China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China; Department of Toxicology, School of Public Health, China Medical University, Shenyang, Liaoning 110122, China
Juan Liu China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
Fuchang Deng China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
Shuyi Zhang China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
Qiong Wang China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
Jiaonan Wang China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
Shilu Tong China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China; School of Public Health and Social Work, Queensland University of Technology, Brisbane 4001, Australia
Song Tang China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
Xiaoming Shi China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.

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Sfakianoudis K, Zikopoulos A, Grigoriadis S, Seretis N, Maziotis E, Anifandis G, Xystra P, Kostoulas C, Giougli U, Pantos K, Simopoulou M, Georgiou I. The Role of One-Carbon Metabolism and Methyl Donors in Medically Assisted Reproduction: A Narrative Review of the Literature. Int J Mol Sci 2024;25:4977. [PMID: 38732193 PMCID: PMC11084717 DOI: 10.3390/ijms25094977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open

Affiliation(s)

Konstantinos Sfakianoudis Centre for Human Reproduction, Genesis Athens Clinic, 14-16, Papanikoli, 15232 Athens, Greece; (K.S.); (K.P.)
Athanasios Zikopoulos Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.) Obstetrics and Gynecology, Royal Cornwall Hospital, Treliske, Truro TR1 3LJ, UK
Sokratis Grigoriadis Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
Nikolaos Seretis Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
Evangelos Maziotis Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
George Anifandis Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41222 Larisa, Greece;
Paraskevi Xystra Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
Charilaos Kostoulas Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
Urania Giougli Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
Konstantinos Pantos Centre for Human Reproduction, Genesis Athens Clinic, 14-16, Papanikoli, 15232 Athens, Greece; (K.S.); (K.P.)
Mara Simopoulou Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
Ioannis Georgiou Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)

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Pietrzak S, Marciniak W, Derkacz R, Matuszczak M, Kiljańczyk A, Baszuk P, Bryśkiewicz M, Sikorski A, Gronwald J, Słojewski M, Cybulski C, Gołąb A, Huzarski T, Dębniak T, Lener MR, Jakubowska A, Kluz T, Scott RJ, Lubiński J. Correlation between Selenium and Zinc Levels and Survival among Prostate Cancer Patients. Nutrients 2024;16:527. [PMID: 38398851 PMCID: PMC10891521 DOI: 10.3390/nu16040527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open

Affiliation(s)

Sandra Pietrzak Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.)
Wojciech Marciniak Read-Gene, Grzepnica, ul. Alabastrowa 8, 72-003 Dobra, Poland; (W.M.); (R.D.)
Róża Derkacz Read-Gene, Grzepnica, ul. Alabastrowa 8, 72-003 Dobra, Poland; (W.M.); (R.D.)
Milena Matuszczak Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.)
Adam Kiljańczyk Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.)
Piotr Baszuk Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.) Read-Gene, Grzepnica, ul. Alabastrowa 8, 72-003 Dobra, Poland; (W.M.); (R.D.)
Marta Bryśkiewicz Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.)
Andrzej Sikorski Department of Urology and Urological Oncology, Pomeranian Medical University in Szczecin, al. Powstańców Wielkopolskich 72, 71-899 Szczecin, Poland; (A.S.); (M.S.); (A.G.)
Jacek Gronwald Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.) Read-Gene, Grzepnica, ul. Alabastrowa 8, 72-003 Dobra, Poland; (W.M.); (R.D.)
Marcin Słojewski Department of Urology and Urological Oncology, Pomeranian Medical University in Szczecin, al. Powstańców Wielkopolskich 72, 71-899 Szczecin, Poland; (A.S.); (M.S.); (A.G.)
Cezary Cybulski Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.) Read-Gene, Grzepnica, ul. Alabastrowa 8, 72-003 Dobra, Poland; (W.M.); (R.D.)
Adam Gołąb Department of Urology and Urological Oncology, Pomeranian Medical University in Szczecin, al. Powstańców Wielkopolskich 72, 71-899 Szczecin, Poland; (A.S.); (M.S.); (A.G.)
Tomasz Huzarski Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.) Read-Gene, Grzepnica, ul. Alabastrowa 8, 72-003 Dobra, Poland; (W.M.); (R.D.) Department of Clinical Genetics and Pathology, University of Zielona Góra, ul. Zyty 28, 65-046 Zielona Góra, Poland
Tadeusz Dębniak Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.)
Marcin R. Lener Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.)
Anna Jakubowska Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.)
Tomasz Kluz Department of Gynecology, Gynecology Oncology and Obstetrics, Fryderyk Chopin University Hospital No. 1, 35-055 Rzeszow, Poland; Institute of Medical Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
Rodney J. Scott Priority Research Centre for Cancer Research, Innovation and Translation, Hunter Medical Research Institute, New Lambton, NSW 2305, Australia; School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia Division of Molecular Medicine, Pathology North, John Hunter Hospital, New Lambton, NSW 2305, Australia
Jan Lubiński Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, ul. Unii Lubelskiej 1, 71-252 Szczecin, Poland; (S.P.); (M.M.); (A.K.); (P.B.); (M.B.); (J.G.); (C.C.); (T.H.); (T.D.); (M.R.L.); (A.J.) Read-Gene, Grzepnica, ul. Alabastrowa 8, 72-003 Dobra, Poland; (W.M.); (R.D.)

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Kanarik M, Sakala K, Matrov D, Kaart T, Roy A, Ziegler GC, Veidebaum T, Lesch KP, Harro J. MAOA methylation is associated with impulsive and antisocial behaviour: dependence on allelic variation, family environment and diet. J Neural Transm (Vienna) 2024;131:59-71. [PMID: 37507512 DOI: 10.1007/s00702-023-02675-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]

Abstract

Congenital absence of monoamine oxidase A (MAO-A) activity predisposes to antisocial impulsive behaviour, and the MAOA uVNTR low-expressing genotype (MAOA-L) together with childhood maltreatment is associated with similar phenotypes in males. A possible explanation of how family environment may lead to such behaviour involves DNA methylation. We have assessed MAOA methylation and impulsive/antisocial behaviour in 121 males from the Estonian Children Personality Behaviour and Health Study. Of the 12 CpG sites measured, methylation levels at the locus designated CpG3 were significantly lower in subjects with antisocial behaviour involving police contact. CpG3 methylation was lower in subjects with alcohol use disorder by age 25, but only in MAOA-H genotype. No correlation between MAOA CpG3 methylation levels and adaptive impulsivity was found at age 15, but in MAOA-L genotype a positive correlation appeared by age 18. By age 25, this positive correlation was no longer observed in subjects with better family relationships but had increased further with experience of adversity within the family. MAOA CpG3 methylation had different developmental dynamics in relation to maladaptive impulsivity. At age 18, a positive correlation was observed in MAOA-L genotype with inferior family relationships and a negative correlation was found in MAOA-H with superior home environment; both of these associations had disappeared by age 25. CpG3 methylation was associated with dietary intake of several micronutrients, most notable was a negative correlation with the intake of zinc, but also with calcium, potassium and vitamin E; a positive correlation was found with intake of phosphorus. In conclusion, MAOA CpG3 methylation is related to both maladaptive and adaptive impulsivity in adolescence in MAOA-L males from adverse home environment. By young adulthood, this relationship with maladaptive impulsivity had disappeared but with adaptive impulsivity strengthened. Thus, MAOA CpG3 methylation may serve as a marker for adaptive developmental neuroplasticity in MAOA-L genotype. The mechanisms involved may include dietary factors.

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Boyer K, Domingo-Relloso A, Jiang E, Haack K, Goessler W, Zhang Y, Umans JG, Belsky DW, Cole SA, Navas-Acien A, Kupsco A. Metal mixtures and DNA methylation measures of biological aging in American Indian populations. ENVIRONMENT INTERNATIONAL 2023;178:108064. [PMID: 37364305 PMCID: PMC10617409 DOI: 10.1016/j.envint.2023.108064] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/18/2023] [Accepted: 06/22/2023] [Indexed: 06/28/2023]

Abstract

INTRODUCTION

Native American communities suffer disproportionately from elevated metal exposures and increased risk for cardiovascular diseases and diabetes. DNA methylation is a sensitive biomarker of aging-related processes and novel epigenetic-based "clocks" can be used to estimate accelerated biological aging that may underlie increased risk. Metals alter DNA methylation, yet little is known about their individual and combined impact on epigenetic age acceleration. Our objective was to investigate the associations of metals on several DNA methylation-based aging measures in the Strong Heart Study (SHS) cohort.

METHODS

Blood DNA methylation data from 2,301 SHS participants was used to calculate age acceleration of epigenetic clocks (PhenoAge, GrimAge, DunedinPACE, Hannum, Horvath). Urinary metals [arsenic (As), cadmium (Cd), tungsten (W), zinc (Zn), selenium (Se), molybdenum (Mo)] were creatinine-adjusted and categorized into quartiles. We examined associations of individual metals through linear regression models and used Bayesian Kernel Machine Regression (BKMR) for the impact of the total metal mixture on epigenetic age acceleration.

RESULTS

The mixture of nonessential metals (W, As, Cd) was associated with greater GrimAge acceleration and DunedinPACE, while the essential metal mixture (Se, Zn, Mo) was associated with lower epigenetic age acceleration. Cd was associated with increased epigenetic age acceleration across all clocks and BKMR analysis suggested nonlinear associations between Se and DunedinPACE, GrimAge, and PhenoAge acceleration. No interactions between individual metals were observed. The associations between Cd, Zn, and epigenetic age acceleration were greater in never smokers in comparison to current/former smokers.

CONCLUSION

Nonessential metals were positively associated with greater epigenetic age acceleration, with strongest associations observed between Cd and DunedinPACE and GrimAge acceleration. In contrast, essential metals were associated with lower epigenetic aging. Examining the influence of metal mixtures on epigenetic age acceleration can provide insight into metals and aging-related diseases.

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Goncharova IA, Zarubin AA, Babushkina NP, Koroleva IA, Nazarenko MS. Changes in DNA methylation profile in liver tissue during progression of HCV-induced fibrosis to hepatocellular carcinoma. Vavilovskii Zhurnal Genet Selektsii 2023;27:72-82. [PMID: 36923478 PMCID: PMC10009477 DOI: 10.18699/vjgb-23-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 03/11/2023] Open

Abstract

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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