1
|
Hong SH, Yu X, Zhu Y, Chen Y. Liver epigenomic signature associated with chronic oxidative stress in a mouse model of glutathione deficiency. Chem Biol Interact 2024; 398:111093. [PMID: 38830566 DOI: 10.1016/j.cbi.2024.111093] [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: 04/20/2024] [Revised: 05/17/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
Abstract
Oxidative stress is intimately involved in the pathogenesis of fatty liver disease (FLD). A major factor contributing to oxidative stress is the depletion of the ubiquitous antioxidant glutathione (GSH). Unexpectedly, chronic GSH deficiency renders glutamate-cysteine ligase modifier subunit (Gclm)-null mice protected from fatty liver injuries. Epigenetic regulation serves as an important cellular mechanism in modulating gene expression and disease outcome in FLD, although it is not well understood how systemic redox imbalance modifies the liver epigenome. In the current study, utilizing the Gclm-null mouse model, we aimed to elucidate redox-associated epigenomic changes and their implications in liver stress response. We performed high-throughput array-based DNA methylation profiling (MeDIP array) in 22,327 gene promoter regions (from -1300 bp to +500 bp of the Transcription Start Sites) in the liver and peripheral blood cells. Results from the MeDIP array demonstrate that, although global methylation enrichment in gene promoters did not change, low GSH resulted in prevalent demethylation at the individual promoter level. Such an effect likely attributed to a declined availability of the methyl donor S-adenosyl methionine (SAM) in Gclm-null liver. Functional enrichment analysis of liver target genes is suggestive of a potential role of epigenetic mechanisms in promoting cellular survival and lipid homeostasis in Gclm-null liver. In comparison with the liver tissue, MeDIP array in peripheral blood cells revealed a panel of 19 gene promoters that are candidate circulating biomarkers for hepatic epigenomic changes associated with chronic GSH deficiency. Collectively, our results provided new insights into the in vivo interplay between liver redox state and DNA methylation status. The current study laid the groundwork for future epigenetic/epigenomic investigations in experimental settings or human populations under conditions of liver oxidative stress induced by environmental or dietary challenges.
Collapse
Affiliation(s)
- Seong Hwi Hong
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Xiaoqing Yu
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Yong Zhu
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Ying Chen
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, 06510, USA.
| |
Collapse
|
2
|
Li Q, Wang W, Duan F, Wang Y, Chen S, Shi K, Xia Y, Li X, Gao Y, Liu G. DNMT3B Alleviates Liver Steatosis Induced by Chronic Low-grade LPS via Inhibiting CIDEA Expression. Cell Mol Gastroenterol Hepatol 2023; 17:59-77. [PMID: 37703946 PMCID: PMC10665944 DOI: 10.1016/j.jcmgh.2023.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND & AIMS Nonalcoholic fatty liver disease is the most prevalent chronic liver disease and threats to human health. Gut dysbiosis caused by lipopolysaccharide (LPS) leakage has been strongly related to nonalcoholic fatty liver disease progression, although the underlying mechanisms remain unclear. METHODS Previous studies have shown that low-grade LPS administration to mice on a standard, low-fat chow diet is sufficient to induce symptoms of fatty liver. This study confirmed these findings and supported LPS as a lipid metabolism regulator in the liver. RESULTS Mechanically, LPS induced dysregulated lipid metabolism by inhibiting the expression of DNA methyltransferases 3B (DNMT3B). Genetic overexpression of DNMT3B alleviated LPS-induced lipid accumulation, whereas its knockdown increased steatosis in mice and human hepatocytes. LPS-induced lower expression of DNMT3B led to hypomethylation in promoter region of CIDEA, resulting in increased binding of SREBP-1c to its promoter and activated CIDEA expression. Hepatic interference of CIDEA reversed the effect of LPS on lipogenesis. These effects were independent of a high-fat diet or high fatty acid action. CONCLUSIONS Overall, these findings sustain the conclusion that LPS is a lipogenic factor and could be involved in hepatic steatosis progression.
Collapse
Affiliation(s)
- Qiang Li
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China; Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Anhui, China.
| | - Wenjing Wang
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China
| | - Feifan Duan
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China
| | - Yaju Wang
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China
| | - Shuya Chen
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China
| | - Kangyun Shi
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China
| | - Yinyin Xia
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China
| | - Xinyu Li
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China
| | - Yu Gao
- Department of Cell Biology, School of Life Science, Bengbu Medical College, Anhui, China; Bengbu Medical College Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, Bengbu Medical College, Bengbu, China
| | - Guoquan Liu
- Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Anhui, China; Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical College, Anhui, China.
| |
Collapse
|
3
|
Lavoro A, Falzone L, Tomasello B, Conti GN, Libra M, Candido S. In silico analysis of the solute carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity. Front Pharmacol 2023; 14:1191262. [PMID: 37397501 PMCID: PMC10308049 DOI: 10.3389/fphar.2023.1191262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction: The oncogenic transformation is driven by genetic and epigenetic alterations influencing cancer cell fate. These alterations also result in metabolic reprogramming by modulating the expression of membrane Solute Carrier (SLC) transporters involved in biomolecules trafficking. SLCs act as tumor suppressors or promoters influencing cancer methylome, tumor growth, immune-escape, and chemoresistance. Methods: This in silico study aimed to identify the deregulated SLCs in various tumor types compared to normal tissues by analyzing the TCGA Target GTEx dataset. Furthermore, the relationship between SLCs expression and the most relevant tumor features was tackled along with their genetic regulation mediated by DNA methylation. Results: We identified 62 differentially expressed SLCs, including the downregulated SLC25A27 and SLC17A7, as well as the upregulated SLC27A2 and SLC12A8. Notably, SLC4A4 and SLC7A11 expression was associated with favorable and unfavorable outcome, respectively. Moreover, SLC6A14, SLC34A2, and SLC1A2 were linked to tumor immune responsiveness. Interestingly, SLC24A5 and SLC45A2 positively correlated with anti-MEK and anti-RAF sensitivity. The expression of relevant SLCs was correlated with hypo- and hyper-methylation of promoter and body region, showing an established DNA methylation pattern. Noteworthy, the positive association of cg06690548 (SLC7A11) methylation with cancer outcome suggests the independent predictive role of DNA methylation at a single nucleotide resolution. Discussion: Although our in silico overview revealed a wide heterogeneity depending on different SLCs functions and tumor types, we identified key SLCs and pointed out the role of DNA methylation as regulatory mechanism of their expression. Overall, these findings deserve further studies to identify novel cancer biomarkers and promising therapeutic targets.
Collapse
Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori “Fondazione G. Pascale”, Naples, Italy
| | - Barbara Tomasello
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Giuseppe Nicolò Conti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy
| |
Collapse
|
4
|
Tryndyak VP, Willett RA, Nagumalli SK, Li D, Avigan MI, Beland FA, Rusyn I, Pogribny IP. Effect of an obesogenic high-fat and high-sucrose diet on hepatic gene expression signatures in male Collaborative Cross mice. Am J Physiol Gastrointest Liver Physiol 2023; 324:G232-G243. [PMID: 36625475 PMCID: PMC10191133 DOI: 10.1152/ajpgi.00225.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/12/2022] [Accepted: 01/01/2023] [Indexed: 01/11/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD), the most prevalent chronic liver disease, is characterized by substantial variations in case-level severity. In this study, we used a genetically diverse Collaborative Cross (CC) mouse population model to analyze the global transcriptome and clarify the molecular mechanisms involved in hepatic fat accumulation that determine the level and severity of NAFLD. Twenty-four strains of male CC mice were maintained on a high-fat/high-sucrose (HF/HS) diet for 12 wk, and their hepatic gene expression profiles were determined by next-generation RNA sequencing. We found that the development of the nonalcoholic fatty liver (NAFL) phenotype in CC mice coincided with significant changes in the expression of hepatic genes at the population level, evidenced by the presence of 724 differentially expressed genes involved in lipid and carbohydrate metabolism, cell morphology, vitamin and mineral metabolism, energy production, and DNA replication, recombination, and repair. Importantly, expression of 68 of these genes strongly correlated with the extent of hepatic lipid accumulation in the overall population of HF/HS diet-fed male CC mice. Results of partial least squares (PLS) modeling showed that these derived hepatic gene expression signatures help to identify the individual mouse strains that are highly susceptible to the development of NAFLD induced by an HF/HS diet. These findings imply that gene expression profiling, combined with a PLS modeling approach, may be a useful tool to predict NAFLD severity in genetically diverse patient populations.NEW & NOTEWORTHY Feeding male Collaborative Cross mice an obesogenic diet allows modeling NAFLD at the population level. The development of NAFLD coincided with significant hepatic transcriptomic changes in this model. Genes (724) were differentially expressed and expression of 68 genes strongly correlated with the extent of hepatic lipid accumulation. Partial least squares modeling showed that derived hepatic gene expression signatures may help to identify individual mouse strains that are highly susceptible to the development of NAFLD.
Collapse
Affiliation(s)
- Volodymyr P Tryndyak
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| | - Rose A Willett
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| | - Suresh K Nagumalli
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| | - Dan Li
- Division of Bioinformatics and Biostatistics, Food and Drug Agency-National Center for Toxicological Research, Jefferson, Arkansas
| | - Mark I Avigan
- Office of Pharmacovigilance and Epidemiology, Food and Drug Administration-Center for Drug Evaluation and Research, Silver Spring, Maryland
| | - Frederick A Beland
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| | - Ivan Rusyn
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas
| | - Igor P Pogribny
- Division of Biochemical Toxicology, Food and Drug Administration-National Center for Toxicological Research, Jefferson, Arkansas
| |
Collapse
|
5
|
Zeng Z, Chen J, Sun L, Zeng F, Wu S. A biomarker-responsive nanoprobe for detecting hepatic ischemia-reperfusion injury via optoacoustic/NIR-II fluorescence imaging. Chem Commun (Camb) 2023; 59:571-574. [PMID: 36537537 DOI: 10.1039/d2cc06031k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A nanoprobe for detecting hepatic ischemia-reperfusion injury has been developed. Apparent optoacoustic and NIR-II fluorescent signals are given out upon the nanoprobe's response to the in situ biomarker H2O2 in the liver in the case of ischemia-reperfusion injury.
Collapse
Affiliation(s)
- Zhuo Zeng
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, College of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Junjie Chen
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, College of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Lihe Sun
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, College of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Fang Zeng
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, College of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Shuizhu Wu
- State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, College of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| |
Collapse
|
6
|
Hong X, Miao K, Cao W, Lv J, Yu C, Huang T, Sun D, Liao C, Pang Y, Pang Z, Yu M, Wang H, Wu X, Liu Y, Gao W, Li L. Association Between DNA Methylation and Blood Pressure: A 5-Year Longitudinal Twin Study. Hypertension 2023; 80:169-181. [PMID: 36345830 DOI: 10.1161/hypertensionaha.122.19953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Previous EWASs (Epigenome-Wide Association Studies) have reported hundreds of blood pressure (BP) associated 5'-cytosine-phosphate-guanine-3' (CpG) sites. However, their results were inconsistent. Longitudinal observations on the temporal relationship between DNA methylation and BP are lacking. METHODS A candidate CpG site association study for BP was conducted on 1072 twins in the Chinese National Twin Registry. PubMed and EMBASE were searched for candidate CpG sites. Cross-lagged models were used to assess the temporal relationship between BP and DNA methylation in 308 twins who completed 2 surveys in 2013 and 2018. Then, the significant cross-lagged associations were validated by adopting the Inference About Causation From Examination of Familial Confounding approach. Finally, to evaluate the cumulative effects of DNA methylation on the progression of hypertension, we established methylation risk scores based on BP-associated CpG sites and performed Markov multistate models. RESULTS 16 and 20 CpG sites were validated to be associated with systolic BP and diastolic BP, respectively. In the cross-lagged analysis, we detected that methylation of 2 CpG sites could predict subsequent systolic BP, and systolic BP predicted methylation at another 3 CpG sites. For diastolic BP, methylation at 3 CpG sites had significant cross-lagged effects for predicting diastolic BP levels, while the prediction from the opposite direction was observed at one site. Among these, 3 associations were validated in the Inference About Causation From Examination of Familial Confounding analysis. Using the Markov multistate model, we observed that methylation risk scores were associated with the development of hypertension. CONCLUSIONS Our findings suggest the significance of DNA methylation in the development of hypertension.
Collapse
Affiliation(s)
- Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Ke Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, China (Z.P.)
| | - Min Yu
- Zhejiang Center for Disease Control and Prevention, Hangzhou, China (M.Y.)
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, China (H.W.)
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, China (X.W.)
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, China (Y.L.)
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| |
Collapse
|
7
|
Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to understand cellular responses to environmental influences in diseases. PLoS Genet 2023; 19:e1010567. [PMID: 36656803 PMCID: PMC9851565 DOI: 10.1371/journal.pgen.1010567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.
Collapse
Affiliation(s)
- Julia J. Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York, United States of America
| | - Srilakshmi Raj
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David A. Knowles
- New York Genome Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - John M. Greally
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| |
Collapse
|
8
|
Szukiewicz D, Trojanowski S, Kociszewska A, Szewczyk G. Modulation of the Inflammatory Response in Polycystic Ovary Syndrome (PCOS)-Searching for Epigenetic Factors. Int J Mol Sci 2022; 23:ijms232314663. [PMID: 36498989 PMCID: PMC9736994 DOI: 10.3390/ijms232314663] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine disorder in women of reproductive age. Despite its incidence, the syndrome is poorly understood and remains underdiagnosed, and female patients are diagnosed with a delay. The heterogenous nature of this complex disorder results from the combined occurrence of genetic, environmental, endocrine, and behavioral factors. Primary clinical manifestations of PCOS are derived from the excess of androgens (anovulation, polycystic ovary morphology, lack of or scanty, irregular menstrual periods, acne and hirsutism), whereas the secondary manifestations include multiple metabolic, cardiovascular, and psychological disorders. Dietary and lifestyle factors play important roles in the development and course of PCOS, which suggests strong epigenetic and environmental influences. Many studies have shown a strong association between PCOS and chronic, low-grade inflammation both in the ovarian tissue and throughout the body. In the vast majority of PCOS patients, elevated values of inflammatory markers or their gene markers have been reported. Development of the vicious cycle of the chronic inflammatory state in PCOS is additionally stimulated by hyperinsulinemia and obesity. Changes in DNA methylation, histone acetylation and noncoding RNA levels are presented in this review in the context of oxidative stress, reactive oxygen species, and inflammatory signaling in PCOS. Epigenetic modulation of androgenic activity in response to inflammatory signaling is also discussed.
Collapse
Affiliation(s)
- Dariusz Szukiewicz
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
- Correspondence:
| | - Seweryn Trojanowski
- Chair and Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 03-242 Warsaw, Poland
| | - Anna Kociszewska
- Chair and Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 03-242 Warsaw, Poland
| | - Grzegorz Szewczyk
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
| |
Collapse
|
9
|
Moylan CA, Mavis AM, Jima D, Maguire R, Bashir M, Hyun J, Cabezas MN, Parish A, Niedzwiecki D, Diehl AM, Murphy SK, Abdelmalek MF, Hoyo C. Alterations in DNA methylation associate with fatty liver and metabolic abnormalities in a multi-ethnic cohort of pre-teenage children. Epigenetics 2022; 17:1446-1461. [PMID: 35188871 PMCID: PMC9586600 DOI: 10.1080/15592294.2022.2039850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Non-Alcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver disease in children. Epigenetic alterations, such as through DNA methylation (DNAm), may link adverse childhood exposures and fatty liver and provide non-invasive methods for identifying children at high risk for NAFLD and associated metabolic dysfunction. We investigated the association between differential DNAm and liver fat content (LFC) and liver injury in pre-adolescent children. Leveraging data from the Newborn Epigenetics Study (NEST), we enrolled 90 mother-child dyads and used linear regression to identify CpG sites and differentially methylated regions (DMRs) in peripheral blood associated with LFC and alanine aminotransferase (ALT) levels in 7-12yo children. DNAm was measured using Infinium HumanMethylationEPIC BeadChips (Illumina). LFC and fibrosis were quantified by magnetic resonance imaging proton density fat fraction and elastography. Median LFC was 1.4% (range, 0.3-13.4%) and MRE was 2.5 kPa (range, 1.5-3.6kPa). Three children had LFC ≥ 5%, while six (7.6%) met our definition of NAFLD (LFC ≥ 3.7%). All children with NAFLD were obese and five were Black. LFC was associated with 88 DMRs and 106 CpGs (FDR<5%). The top two CpGs, cg25474373 and cg07264203, mapped to or near RFTN2 and PRICKLE2 genes. These two CpG sites were also significantly associated with a NAFLD diagnosis. As higher LFC associates with an adverse cardiometabolic profile already in childhood, altered DNAm may identify these children early in disease course for targeted intervention. Larger, longitudinal studies are needed to validate these findings and determine mechanistic relevance.
Collapse
Affiliation(s)
- Cynthia A. Moylan
- Department of Medicine, Duke University Medical Center, Durham, NC, United States,Contact Cynthia A. Moylan 905 South LaSalle Street, Division of Gastroenterology, Duke University Medical Center, Durham27710NC, United States
| | - Alisha M. Mavis
- Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Dereje Jima
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Rachel Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Mustafa Bashir
- Department of Radiology, Center of Advanced Magnetic Resonance Development, Duke University Medical Center, Durham, NC, United States
| | - Jeongeun Hyun
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Melanie N. Cabezas
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Alice Parish
- Biostatistics and Bioinformatics, Duke University, Durham, NC, United States
| | - Donna Niedzwiecki
- Biostatistics and Bioinformatics, Duke University, Durham, NC, United States
| | - Anna Mae Diehl
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | | | - Manal F. Abdelmalek
- Department of Radiology, Center of Advanced Magnetic Resonance Development, Duke University Medical Center, Durham, NC, United States
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
10
|
Vachher M, Bansal S, Kumar B, Yadav S, Burman A. Deciphering the role of aberrant DNA methylation in NAFLD and NASH. Heliyon 2022; 8:e11119. [PMID: 36299516 PMCID: PMC9589178 DOI: 10.1016/j.heliyon.2022.e11119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/30/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
The global incidence of nonalcoholic fatty liver disease (NAFLD) is mounting incessantly, and it is emerging as the most frequent cause of chronic and end stage liver disorders. It is the starting point for a range of conditions from simple steatosis to more progressive nonalcoholic steatohepatitis (NASH) and associated hepatocellular carcinoma (HCC). Dysregulation of insulin secretion and dyslipidemia due to obesity and other lifestyle variables are the primary contributors to establishment of NAFLD. Onset and progression of NAFLD is orchestrated by an interplay of metabolic environment with genetic and epigenetic factors. An incompletely understood mechanism of NAFLD progression has greatly hampered the progress in identification of novel prognostic and therapeutic strategies. Emerging evidence suggests altered DNA methylation pattern as a key determinant of NAFLD pathogenesis. Environmental and lifestyle factors can manipulate DNA methylation patterns in a reversible manner, which manifests as changes in gene expression. In this review we attempt to highlight the importance of DNA methylation in establishment and progression of NAFLD. Development of novel diagnostic, prognostic and therapeutic strategies centered around DNA methylation signatures and modifiers has also been explored.
Collapse
|
11
|
Dragic D, Chang SL, Ennour-Idrissi K, Durocher F, Severi G, Diorio C. Association between alcohol consumption and DNA methylation in blood: a systematic review of observational studies. Epigenomics 2022; 14:793-810. [PMID: 35762294 DOI: 10.2217/epi-2022-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We systematically reviewed and evaluated current literature on alcohol consumption and DNA methylation (DNAm) at the genome-wide and probe-wise level in blood of adults. Materials & methods: Five databases (PubMed, Embase, Web of Science, CINAHL and PsycInfo) were searched until 20 December 2020. Studies assessing the effect of alcohol dependence on DNAm were not eligible. Results: 11 cross-sectional studies were included with 88 to 9643 participants. Overall, all studies had a risk of bias criteria unclear or unmet. Epigenome-wide association studies identified between 0 and 5458 differentially methylated positions, and 15 were observed in at least four studies. Conclusion: Potential methylation markers for alcohol consumption have been identified, but further validation in large cohorts is needed.
Collapse
Affiliation(s)
- Dzevka Dragic
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome & Heredity" team, Gustave Roussy, Villejuif, 94807, France
| | - Sue-Ling Chang
- Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada
| | - Kaoutar Ennour-Idrissi
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry & Pathology, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Francine Durocher
- Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Gianluca Severi
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome & Heredity" team, Gustave Roussy, Villejuif, 94807, France.,Department of Statistics, Computer Science & Applications "G. Parenti" (DISIA), University of Florence, Florence, 50134, Italy
| | - Caroline Diorio
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Deschênes-Fabia Center for Breast Diseases, Saint-Sacrement Hospital, Quebec, QC, G1S 4L8, Canada
| |
Collapse
|
12
|
Riccio S, Melone R, Vitulano C, Guida P, Maddaluno I, Guarino S, Marzuillo P, Miraglia del Giudice E, Di Sessa A. Advances in pediatric non-alcoholic fatty liver disease: From genetics to lipidomics. World J Clin Pediatr 2022; 11:221-238. [PMID: 35663007 PMCID: PMC9134151 DOI: 10.5409/wjcp.v11.i3.221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/05/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
As a result of the obesity epidemic, non-alcoholic fatty liver disease (NAFLD) represents a global medical concern in childhood with a closely related increased cardiometabolic risk. Knowledge on NAFLD pathophysiology has been largely expanded over the last decades. Besides the well-known key NAFLD genes (including the I148M variant of the PNPLA3 gene, the E167K allele of the TM6SF2, the GCKR gene, the MBOAT7-TMC4 rs641738 variant, and the rs72613567:TA variant in the HSD17B13 gene), an intriguing pathogenic role has also been demonstrated for the gut microbiota. More interestingly, evidence has added new factors involved in the “multiple hits” theory. In particular, omics determinants have been highlighted as potential innovative markers for NAFLD diagnosis and treatment. In fact, different branches of omics including metabolomics, lipidomics (in particular sphingolipids and ceramides), transcriptomics (including micro RNAs), epigenomics (such as DNA methylation), proteomics, and glycomics represent the most attractive pathogenic elements in NAFLD development, by providing insightful perspectives in this field. In this perspective, we aimed to provide a comprehensive overview of NAFLD pathophysiology in children, from the oldest pathogenic elements (including genetics) to the newest intriguing perspectives (such as omics branches).
Collapse
Affiliation(s)
- Simona Riccio
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Rosa Melone
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Caterina Vitulano
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Pierfrancesco Guida
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Ivan Maddaluno
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Stefano Guarino
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Pierluigi Marzuillo
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Emanuele Miraglia del Giudice
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| | - Anna Di Sessa
- Department of Woman, Child, General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples 80138, Italy
| |
Collapse
|
13
|
Pan X, Wu Y, Peng H, Cai X, Hu Z, Lin X, Peng XE. Genome-wide DNA methylation profiling in nonalcoholic fatty liver reveals predictive aberrant methylation in PRKCE and SEC14L3 promoters. Dig Liver Dis 2022; 54:521-528. [PMID: 34108094 DOI: 10.1016/j.dld.2021.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Optimal non-invasive biomarkers for diagnosis and treatment of nonalcoholic fatty liver disease (NAFLD) remain to be identified. AIMS To identify potential DNA methylation biomarkers for NAFLD. METHODS Genome-wide DNA methylation profiling was performed to identify differentially methylated CpG sites in peripheral blood leukocytes. Differentially methylated regions were validated using the MassCLEAVE assay. The expression levels of candidate genes were explored by Gene Expression Omnibus database. RESULTS The hypomethylation of PRKCE CpG 4.5 and CpG 18.19 was associated with nonalcoholic fatty liver (NAFL), the odds ratio (OR) and 95% confidence interval (CI) were 0.129 (0.026-0.639) and 0.231 (0.069-0.768). The methylation level of CpG 1.2 and average methylation level of SEC14L3 were correlated with NAFL, with OR (95% CI) being 0.283 (0.093-0.865) and 0.264 (0.087-0.799). PRKCE CpG 4.5 and cg17802464 of SEC14L3 were correlated with body mass index, waist circumference, total triglyceride, high-density lipoprotein cholesterol, alanine aminotransferase and aspartate aminotransferase. All selected datasets showed high expression levels of PRKCE and SEC14L3 in patients with NAFLD. CONCLUSIONS Our findings suggest that the hypomethylation of PRKCE and SEC14L3 promoters represent attractive biomarkers for NAFLD. Further studies are warranted to validate these biomarkers as molecular tools for diagnosis of NAFLD and therapeutic targets.
Collapse
Affiliation(s)
- Xinting Pan
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, PR China
| | - Yunli Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, PR China
| | - Hewei Peng
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China
| | - Xiaoling Cai
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China
| | - Zhijian Hu
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China
| | - Xu Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, PR China
| | - Xian-E Peng
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, PR China.
| |
Collapse
|
14
|
Lohoff FW, Clarke TK, Kaminsky ZA, Walker RM, Bermingham ML, Jung J, Morris SW, Rosoff D, Campbell A, Barbu M, Charlet K, Adams M, Lee J, Howard DM, O'Connell EM, Whalley H, Porteous DJ, McIntosh AM, Evans KL. Epigenome-wide association study of alcohol consumption in N = 8161 individuals and relevance to alcohol use disorder pathophysiology: identification of the cystine/glutamate transporter SLC7A11 as a top target. Mol Psychiatry 2022; 27:1754-1764. [PMID: 34857913 PMCID: PMC9095480 DOI: 10.1038/s41380-021-01378-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/22/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022]
Abstract
Alcohol misuse is common in many societies worldwide and is associated with extensive morbidity and mortality, often leading to alcohol use disorders (AUD) and alcohol-related end-organ damage. The underlying mechanisms contributing to the development of AUD are largely unknown; however, growing evidence suggests that alcohol consumption is strongly associated with alterations in DNA methylation. Identification of alcohol-associated methylomic variation might provide novel insights into pathophysiology and novel treatment targets for AUD. Here we performed the largest single-cohort epigenome-wide association study (EWAS) of alcohol consumption to date (N = 8161) and cross-validated findings in AUD populations with relevant endophenotypes, as well as alcohol-related animal models. Results showed 2504 CpGs significantly associated with alcohol consumption (Bonferroni p value < 6.8 × 10-8) with the five leading probes located in SLC7A11 (p = 7.75 × 10-108), JDP2 (p = 1.44 × 10-56), GAS5 (p = 2.71 × 10-47), TRA2B (p = 3.54 × 10-42), and SLC43A1 (p = 1.18 × 10-40). Genes annotated to associated CpG sites are implicated in liver and brain function, the cellular response to alcohol and alcohol-associated diseases, including hypertension and Alzheimer's disease. Two-sample Mendelian randomization confirmed the causal relationship of consumption on AUD risk (inverse variance weighted (IVW) p = 5.37 × 10-09). A methylation-based predictor of alcohol consumption was able to discriminate AUD cases in two independent cohorts (p = 6.32 × 10-38 and p = 5.41 × 10-14). The top EWAS probe cg06690548, located in the cystine/glutamate transporter SLC7A11, was replicated in an independent cohort of AUD and control participants (N = 615) and showed strong hypomethylation in AUD (p < 10-17). Decreased CpG methylation at this probe was consistently associated with clinical measures including increased heavy drinking days (p < 10-4), increased liver function enzymes (GGT (p = 1.03 × 10-21), ALT (p = 1.29 × 10-6), and AST (p = 1.97 × 10-8)) in individuals with AUD. Postmortem brain analyses documented increased SLC7A11 expression in the frontal cortex of individuals with AUD and animal models showed marked increased expression in liver, suggesting a mechanism by which alcohol leads to hypomethylation-induced overexpression of SLC7A11. Taken together, our EWAS discovery sample and subsequent validation of the top probe in AUD suggest a strong role of abnormal glutamate signaling mediated by methylomic variation in SLC7A11. Our data are intriguing given the prominent role of glutamate signaling in brain and liver and might provide an important target for therapeutic intervention.
Collapse
Affiliation(s)
- Falk W Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA.
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Zachary A Kaminsky
- Royal's Institute of Mental Health Research, University of Ottawa, Ottawa, ON, Canada
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mairead L Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel Rosoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Miruna Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Katrin Charlet
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Mark Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Jisoo Lee
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - David M Howard
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Emma M O'Connell
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Heather Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
15
|
Ko YK, Kim H, Lee Y, Lee YS, Gim JA. DNA Methylation Patterns According to Fatty Liver Index and Longitudinal Changes from the Korean Genome and Epidemiology Study (KoGES). Curr Issues Mol Biol 2022; 44:1149-1168. [PMID: 35723298 PMCID: PMC8947460 DOI: 10.3390/cimb44030075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
The role of differentially methylated regions (DMRs) in nonalcoholic fatty liver disease (NAFLD) is unclear. This study aimed to identify the role of DMR in NAFLD development and progression using the Korean Genome and Epidemiology Study (KoGES) cohort. We used laboratory evaluations and Illumina Methylation 450 k DNA methylation microarray data from KoGES. The correlation between fatty liver index (FLI) and genomic CpG sites was analyzed in 322 subjects. Longitudinal changes over 8 years were confirmed in 33 subjects. To identify CpG sites and genes related to FLI, we obtained enrichment terms for 6765 genes. DMRs were identified for both high (n = 128) and low (n = 194) groups on the basis of FLI 30 in 142 men and 180 women. To confirm longitudinal changes in 33 subjects, the ratio of follow-up and baseline investigation values was obtained. Correlations and group comparisons were performed for the 8 year change values. PITPNM3, RXFP3, and THRB were hypermethylated in the increased FLI groups, whereas SLC9A2 and FOXI3 were hypermethylated in the decreased FLI groups. DMRs describing NAFLD were determined, and functions related to inflammation were identified. Factors related to longitudinal changes are suggested, and blood circulation-related functions appear to be important in the management of NAFLD.
Collapse
Affiliation(s)
- Young Kyung Ko
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul 08308, Korea;
| | - Hayeon Kim
- Department of Pathology, Korea University College of Medicine, Seoul 08308, Korea;
| | - Yoonseok Lee
- Department of Internal Medicine, Korea University College of Medicine, Seoul 08308, Korea;
| | - Young-Sun Lee
- Department of Internal Medicine, Korea University College of Medicine, Seoul 08308, Korea;
- Correspondence: (Y.-S.L.); (J.-A.G.); Tel.: +82-2-2626-3013 (Y.-S.L.); +82-2-2626-2362 (J.-A.G.)
| | - Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea
- Correspondence: (Y.-S.L.); (J.-A.G.); Tel.: +82-2-2626-3013 (Y.-S.L.); +82-2-2626-2362 (J.-A.G.)
| |
Collapse
|
16
|
Rodríguez-Sanabria JS, Escutia-Gutiérrez R, Rosas-Campos R, Armendáriz-Borunda JS, Sandoval-Rodríguez A. An Update in Epigenetics in Metabolic-Associated Fatty Liver Disease. Front Med (Lausanne) 2022; 8:770504. [PMID: 35087844 PMCID: PMC8787199 DOI: 10.3389/fmed.2021.770504] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD) is characterized by hepatic steatosis accompanied by one of three features: overweight or obesity, T2DM, or lean or normal weight with evidence of metabolic dysregulation. It is distinguished by excessive fat accumulation in hepatocytes, and a decrease in the liver's ability to oxidize fats, the accumulation of ectopic fat, and the activation of proinflammatory pathways. Chronic damage will keep this pathophysiologic cycle active causing progression from hepatic steatosis to cirrhosis and eventually, hepatocarcinoma. Epigenetics affecting gene expression without altering DNA sequence allows us to study MAFLD pathophysiology from a different perspective, in which DNA methylation processes, histone modifications, and miRNAs expression have been closely associated with MAFLD progression. However, these considerations also faced us with the circumstance that modifying those epigenetics patterns might lead to MAFLD regression. Currently, epigenetics is an area of great interest because it could provide new insights in therapeutic targets and non-invasive biomarkers. This review comprises an update on the role of epigenetic patterns, as well as innovative therapeutic targets and biomarkers in MAFLD.
Collapse
Affiliation(s)
- J Samael Rodríguez-Sanabria
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Rebeca Escutia-Gutiérrez
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Rebeca Rosas-Campos
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Juan S Armendáriz-Borunda
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico.,School of Medicine and Health Sciences, Tecnologico de Monterrey, Campus Guadalajara, Zapopan, Mexico
| | - Ana Sandoval-Rodríguez
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| |
Collapse
|
17
|
Plasma S-Adenosylmethionine Is Associated with Lung Injury in COVID-19. DISEASE MARKERS 2021; 2021:7686374. [PMID: 34956420 PMCID: PMC8702356 DOI: 10.1155/2021/7686374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/25/2021] [Accepted: 11/26/2021] [Indexed: 12/14/2022]
Abstract
Objective S-Adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) are indicators of global transmethylation and may play an important role as markers of severity of COVID-19. Methods The levels of plasma SAM and SAH were determined in patients admitted with COVID-19 (n = 56, mean age = 61). Lung injury was identified by computed tomography (CT) in accordance with the CT0-4 classification. Results SAM was found to be a potential marker of lung damage risk in COVID-19 patients (SAM > 80 nM; CT3,4 vs. CT 0-2: relative ratio (RR) was 3.0; p = 0.0029). SAM/SAH > 6.0 was also found to be a marker of lung injury (CT2-4 vs. CT0,1: RR = 3.47, p = 0.0004). There was a negative association between SAM and glutathione level (ρ = −0.343, p = 0.011). Interleukin-6 (IL-6) levels were associated with SAM (ρ = 0.44, p = 0.01) and SAH (ρ = 0.534, p = 0.001) levels. Conclusions A high SAM level and high methylation index are associated with the risk of lung injury in patients with COVID-19. The association of SAM with IL-6 and glutathione indicates an important role of transmethylation in the development of cytokine imbalance and oxidative stress in patients with COVID-19.
Collapse
|
18
|
Tin A, Schlosser P, Matias-Garcia PR, Thio CHL, Joehanes R, Liu H, Yu Z, Weihs A, Hoppmann A, Grundner-Culemann F, Min JL, Kuhns VLH, Adeyemo AA, Agyemang C, Ärnlöv J, Aziz NA, Baccarelli A, Bochud M, Brenner H, Bressler J, Breteler MMB, Carmeli C, Chaker L, Coresh J, Corre T, Correa A, Cox SR, Delgado GE, Eckardt KU, Ekici AB, Endlich K, Floyd JS, Fraszczyk E, Gao X, Gào X, Gelber AC, Ghanbari M, Ghasemi S, Gieger C, Greenland P, Grove ML, Harris SE, Hemani G, Henneman P, Herder C, Horvath S, Hou L, Hurme MA, Hwang SJ, Kardia SLR, Kasela S, Kleber ME, Koenig W, Kooner JS, Kronenberg F, Kühnel B, Ladd-Acosta C, Lehtimäki T, Lind L, Liu D, Lloyd-Jones DM, Lorkowski S, Lu AT, Marioni RE, März W, McCartney DL, Meeks KAC, Milani L, Mishra PP, Nauck M, Nowak C, Peters A, Prokisch H, Psaty BM, Raitakari OT, Ratliff SM, Reiner AP, Schöttker B, Schwartz J, Sedaghat S, Smith JA, Sotoodehnia N, Stocker HR, Stringhini S, Sundström J, Swenson BR, van Meurs JBJ, van Vliet-Ostaptchouk JV, Venema A, Völker U, Winkelmann J, Wolffenbuttel BHR, Zhao W, Zheng Y, Loh M, Snieder H, Waldenberger M, Levy D, Akilesh S, Woodward OM, Susztak K, Teumer A, Köttgen A. Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus. Nat Commun 2021; 12:7173. [PMID: 34887389 PMCID: PMC8660809 DOI: 10.1038/s41467-021-27198-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Elevated serum urate levels, a complex trait and major risk factor for incident gout, are correlated with cardiometabolic traits via incompletely understood mechanisms. DNA methylation in whole blood captures genetic and environmental influences and is assessed in transethnic meta-analysis of epigenome-wide association studies (EWAS) of serum urate (discovery, n = 12,474, replication, n = 5522). The 100 replicated, epigenome-wide significant (p < 1.1E-7) CpGs explain 11.6% of the serum urate variance. At SLC2A9, the serum urate locus with the largest effect in genome-wide association studies (GWAS), five CpGs are associated with SLC2A9 gene expression. Four CpGs at SLC2A9 have significant causal effects on serum urate levels and/or gout, and two of these partly mediate the effects of urate-associated GWAS variants. In other genes, including SLC7A11 and PHGDH, 17 urate-associated CpGs are associated with conditions defining metabolic syndrome, suggesting that these CpGs may represent a blood DNA methylation signature of cardiometabolic risk factors. This study demonstrates that EWAS can provide new insights into GWAS loci and the correlation of serum urate with other complex traits.
Collapse
Affiliation(s)
- Adrienne Tin
- Department of Medicine, University of Mississippi Medical Center, Jackson, 39216, MS, USA.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Pascal Schlosser
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Roby Joehanes
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hongbo Liu
- Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
| | - Zhi Yu
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Antoine Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Agyemang
- Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society (NVS), Family Medicine and Primary Care Unit, Karolinska Institutet, Huddinge, Sweden
- School of Health and Social Studies, Dalarna University, Falun, Sweden
| | - Nasir A Aziz
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Andrea Baccarelli
- Laboratory of Environmental Precision Health, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Hermann Brenner
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Bressler
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030, TX, USA
| | - Monique M B Breteler
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Cristian Carmeli
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Population Health Laboratory, University of Fribourg, Fribourg, Switzerland
| | - Layal Chaker
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tanguy Corre
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, 39216, MS, USA
| | - Simon R Cox
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University of Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-UniversitätErlangen-Nürnberg, 91054, Erlangen, Germany
| | - Karlhans Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - James S Floyd
- Department of Medicine, University of Washington, Seattle, 98101, WA, USA
- Department of Epidemiology, University of Washington, Seattle, 98101, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, 98101, WA, USA
| | - Eliza Fraszczyk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xu Gao
- Laboratory of Environmental Precision Health, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China
| | - Xīn Gào
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
| | - Allan C Gelber
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sahar Ghasemi
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Megan L Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030, TX, USA
| | - Sarah E Harris
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Munich-Neuherberg, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
- Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, CA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mikko A Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, MA, USA
- Division of Intramural Research, Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Silva Kasela
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Jaspal S Kooner
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Dan Liu
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
- Synlab Academy, SYNLAB Holding Deutschland GmbH, Mannheim and Augsburg, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christoph Nowak
- Department of Neurobiology, Care Sciences and Society (NVS), Family Medicine and Primary Care Unit, Karolinska Institutet, Huddinge, Sweden
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Ludwig-Maximilians Universität München, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Computational Health, Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Bruce M Psaty
- Department of Medicine, University of Washington, Seattle, 98101, WA, USA
- Department of Epidemiology, University of Washington, Seattle, 98101, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, 98101, WA, USA
- Department of Health Services, University of Washington, Seattle, 98101, WA, USA
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Scott M Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, 98101, WA, USA
| | - Ben Schöttker
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sanaz Sedaghat
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, 98101, WA, USA
| | - Hannah R Stocker
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Silvia Stringhini
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Johan Sundström
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
| | - Brenton R Swenson
- Cardiovascular Health Research Unit, University of Washington, Seattle, 98101, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jana V van Vliet-Ostaptchouk
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - Uwe Völker
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Chair Neurogenetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Bruce H R Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Munich Heart Alliance, Munich, Germany
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Owen M Woodward
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Katalin Susztak
- Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
| | - Alexander Teumer
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
19
|
Wu N, Yuan F, Yue S, Jiang F, Ren D, Liu L, Bi Y, Guo Z, Ji L, Han K, Yang X, Feng M, Su K, Yang F, Wu X, Lu Q, Li X, Wang R, Liu B, Le S, Shi Y, He G. Effect of exercise and diet intervention in NAFLD and NASH via GAB2 methylation. Cell Biosci 2021; 11:189. [PMID: 34736535 PMCID: PMC8569968 DOI: 10.1186/s13578-021-00701-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is a disorder that extends from simple hepatic steatosis to nonalcoholic steatohepatitis (NASH), which is effectively alleviated by lifestyle intervention. Nevertheless, DNA methylation mechanism underling the effect of environmental factors on NAFLD and NASH is still obscure. The aim of this study was to investigate the effect of exercise and diet intervention in NAFLD and NASH via DNA methylation of GAB2. METHODS Methylation of genomic DNA in human NAFLD was quantified using Infinium Methylation EPIC BeadChip assay after exercise (Ex), low carbohydrate diet (LCD) and exercise plus low carbohydrate diet (ELCD) intervention. The output Idat files were processed using ChAMP package. False discovery rate on genome-wide analysis of DNA methylation (q < 0.05), and cytosine-guanine dinucleotides (CpGs) which are located in promoters were used for subsequent analysis (|Δβ|≥ 0.1). K-means clustering was used to cluster differentially methylated genes according to 3D genome information from Human embryonic stem cell. To quantify DNA methylation and mRNA expression of GRB2 associated binding protein 2 (GAB2) in NASH mice after Ex, low fat diet (LFD) and exercise plus low fat diet (ELFD), MassARRAY EpiTYPER and quantitative reverse transcription polymerase chain reaction were used. RESULTS Both LCD and ELCD intervention on human NAFLD can induce same DNA methylation alterations at critical genes in blood, e.g., GAB2, which was also validated in liver and adipose of NASH mice after LFD and ELFD intervention. Moreover, methylation of CpG units (i.e., CpG_10.11.12) inversely correlated with mRNA expression GAB2 in adipose tissue of NASH mice after ELFD intervention. CONCLUSIONS We highlighted the susceptibility of DNA methylation in GAB2 to ELFD intervention, through which exercise and diet can protect against the progression of NAFLD and NASH on the genome level, and demonstrated that the DNA methylation variation in blood could mirror epigenetic signatures in target tissues of important biological function, i.e., liver and adipose tissue. Trial registration International Standard Randomized Controlled Trial Number Register (ISRCTN 42622771).
Collapse
Affiliation(s)
- Na Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yuan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Siran Yue
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fengyan Jiang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Decheng Ren
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Liangjie Liu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Bi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenming Guo
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Ji
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Mofan Feng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Su
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Ruirui Wang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Baocheng Liu
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shenglong Le
- Exercise Translational Medicine Center, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China. .,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China. .,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
20
|
Goodrich JM, Calkins MM, Caban-Martinez AJ, Stueckle T, Grant C, Calafat AM, Nematollahi A, Jung AM, Graber JM, Jenkins T, Slitt AL, Dewald A, Botelho JC, Beitel S, Littau S, Gulotta J, Wallentine D, Hughes J, Popp C, Burgess JL. Per- and polyfluoroalkyl substances, epigenetic age and DNA methylation: a cross-sectional study of firefighters. Epigenomics 2021; 13:1619-1636. [PMID: 34670402 PMCID: PMC8549684 DOI: 10.2217/epi-2021-0225] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/27/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Per- and polyfluoroalkyl substances (PFASs) are persistent chemicals that firefighters encounter. Epigenetic modifications, including DNA methylation, could serve as PFASs toxicity biomarkers. Methods: With a sample size of 197 firefighters, we quantified the serum concentrations of nine PFASs, blood leukocyte DNA methylation and epigenetic age indicators via the EPIC array. We examined the associations between PFASs with epigenetic age, site- and region-specific DNA methylation, adjusting for confounders. Results: Perfluorohexane sulfonate, perfluorooctanoate (PFOA) and the sum of branched isomers of perfluorooctane sulfonate (Sm-PFOS) were associated with accelerated epigenetic age. Branched PFOA, linear PFOS, perfluorononanoate, perfluorodecanoate and perfluoroundecanoate were associated with differentially methylated loci and regions. Conclusion: PFASs concentrations are associated with accelerated epigenetic age and locus-specific DNA methylation. The implications for PFASs toxicity merit further investigation.
Collapse
Affiliation(s)
- Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Miriam M Calkins
- National Institute for Occupational Safety & Health, Centers for Disease Control & Prevention, Cincinnati, OH 45226, USA
| | - Alberto J Caban-Martinez
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Todd Stueckle
- National Institute for Occupational Safety & Health, Centers for Disease Control & Prevention, Morgantown, WV 26505, USA
| | - Casey Grant
- Fire Protection Research Foundation, Quincy, MA 02169, USA
| | - Antonia M Calafat
- National Center for Environmental Health, Centers for Disease Control & Prevention, Atlanta, GA 30341, USA
| | - Amy Nematollahi
- Department of Community, Environment & Policy, University of Arizona Mel & Enid Zuckerman College of Public Health, Tucson, AZ 85724, USA
| | - Alesia M Jung
- Department of Epidemiology & Biostatistics, University of Arizona Mel & Enid Zuckerman College of Public Health, Tucson, AZ 85724, USA
| | - Judith M Graber
- Department of Biostatistics & Epidemiology, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Timothy Jenkins
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Angela L Slitt
- Department of Biomedical Sciences, University of Rhode Island College of Pharmacy, Kingston, RI 02881, USA
| | - Alisa Dewald
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Julianne Cook Botelho
- National Center for Environmental Health, Centers for Disease Control & Prevention, Atlanta, GA 30341, USA
| | - Shawn Beitel
- Department of Community, Environment & Policy, University of Arizona Mel & Enid Zuckerman College of Public Health, Tucson, AZ 85724, USA
| | - Sally Littau
- Department of Community, Environment & Policy, University of Arizona Mel & Enid Zuckerman College of Public Health, Tucson, AZ 85724, USA
| | | | | | - Jeff Hughes
- Orange County Fire Authority, Irvine, CA 92602, USA
| | | | - Jefferey L Burgess
- Department of Community, Environment & Policy, University of Arizona Mel & Enid Zuckerman College of Public Health, Tucson, AZ 85724, USA
| |
Collapse
|
21
|
Suhre K, Zaghlool S. Connecting the epigenome, metabolome and proteome for a deeper understanding of disease. J Intern Med 2021; 290:527-548. [PMID: 33904619 DOI: 10.1111/joim.13306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Epigenome-wide association studies (EWAS) identify genes that are dysregulated by the studied clinical endpoints, thereby indicating potential new diagnostic biomarkers, drug targets and therapy options. Combining EWAS with deep molecular phenotyping, such as approaches enabled by metabolomics and proteomics, allows further probing of the underlying disease-associated pathways. For instance, methylation of the TXNIP gene is associated robustly with prevalent type 2 diabetes and further with metabolites that are short-term markers of glycaemic control. These associations reflect TXNIP's function as a glucose uptake regulator by interaction with the major glucose transporter GLUT1 and suggest that TXNIP methylation can be used as a read-out for the organism's exposure to glucose stress. Another case is the association between DNA methylation of the AHRR and F2RL3 genes with smoking and a protein that is involved in the reprogramming of the bronchial epithelium. These examples show that associations between DNA methylation and intermediate molecular traits can open new windows into how the body copes with physiological challenges. This knowledge, if carefully interpreted, may indicate novel therapy options and, together with monitoring of the methylation state of specific methylation sites, may in the future allow the early diagnosis of impending disease. It is essential for medical practitioners to recognize the potential that this field holds in translating basic research findings to clinical practice. In this review, we present recent advances in the field of EWAS with metabolomics and proteomics and discuss both the potential and the challenges of translating epigenetic associations, with deep molecular phenotypes, to biomedical applications.
Collapse
Affiliation(s)
- K Suhre
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
| | - S Zaghlool
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
| |
Collapse
|
22
|
Xu T, Wang L, Jia P, Song X, Zhao Z. An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change. Biomedicines 2021; 9:biomedicines9060657. [PMID: 34201256 PMCID: PMC8227141 DOI: 10.3390/biomedicines9060657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/15/2021] [Accepted: 05/25/2021] [Indexed: 01/27/2023] Open
Abstract
Recently, accumulating evidence has supported that circular RNA (circRNA) plays important roles in tumorigenesis by regulating gene expression at transcriptional and post-transcriptional levels. Expression of circRNAs can be epigenetically silenced by DNA methylation; however, the underlying regulatory mechanisms of circRNAs by DNA methylation remains largely unknown. We explored this regulation in hepatocellular carcinoma (HCC) using genome-wide DNA methylation and RNA sequencing data of the primary tumor and matched adjacent normal tissues from 20 HCC patients. Our pipeline identified 1012 upregulated and 747 downregulated circRNAs (collectively referred to as differentially expressed circRNAs, or DE circRNAs) from HCC RNA-seq data. Among them, 329 DE circRNAs covered differentially methylated sites (adjusted p-value < 0.05, |ΔM| > 0.5) in circRNAs’ interior and/or flanking regions. Interestingly, the corresponding parental genes of 46 upregulated and 31 downregulated circRNAs did not show significant expression change in the HCC tumor versus normal samples. Importantly, 34 of the 77 DE circRNAs (44.2%) had significant correlation with DNA methylation change in HCC (Spearman’s rank-order correlation, p-value < 0.05), suggesting that aberrant DNA methylation might regulate circular RNA expression in HCC. Our study revealed genome-wide differential circRNA expression in HCC. The significant correlation with DNA methylation change suggested that epigenetic regulation might act on both mRNA and circRNA expression. The specific regulation in HCC and general view in other cancer or disease requires further investigation.
Collapse
Affiliation(s)
- Tianyi Xu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (T.X.); (P.J.)
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - LiPing Wang
- Department of Biobank, Clinical Medical College, Yangzhou University, Yangzhou 225001, China;
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (T.X.); (P.J.)
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
- Correspondence: (X.S.); (Z.Z.)
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (T.X.); (P.J.)
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Correspondence: (X.S.); (Z.Z.)
| |
Collapse
|
23
|
Karabegović I, Portilla-Fernandez E, Li Y, Ma J, Maas SCE, Sun D, Hu EA, Kühnel B, Zhang Y, Ambatipudi S, Fiorito G, Huang J, Castillo-Fernandez JE, Wiggins KL, de Klein N, Grioni S, Swenson BR, Polidoro S, Treur JL, Cuenin C, Tsai PC, Costeira R, Chajes V, Braun K, Verweij N, Kretschmer A, Franke L, van Meurs JBJ, Uitterlinden AG, de Knegt RJ, Ikram MA, Dehghan A, Peters A, Schöttker B, Gharib SA, Sotoodehnia N, Bell JT, Elliott P, Vineis P, Relton C, Herceg Z, Brenner H, Waldenberger M, Rebholz CM, Voortman T, Pan Q, Fornage M, Levy D, Kayser M, Ghanbari M. Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption. Nat Commun 2021; 12:2830. [PMID: 33990564 PMCID: PMC8121846 DOI: 10.1038/s41467-021-22752-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 03/26/2021] [Indexed: 02/03/2023] Open
Abstract
Coffee and tea are extensively consumed beverages worldwide which have received considerable attention regarding health. Intake of these beverages is consistently linked to, among others, reduced risk of diabetes and liver diseases; however, the mechanisms of action remain elusive. Epigenetics is suggested as a mechanism mediating the effects of dietary and lifestyle factors on disease onset. Here we report the results from epigenome-wide association studies (EWAS) on coffee and tea consumption in 15,789 participants of European and African-American ancestries from 15 cohorts. EWAS meta-analysis of coffee consumption reveals 11 CpGs surpassing the epigenome-wide significance threshold (P-value <1.1×10-7), which annotated to the AHRR, F2RL3, FLJ43663, HDAC4, GFI1 and PHGDH genes. Among them, cg14476101 is significantly associated with expression of the PHGDH and risk of fatty liver disease. Knockdown of PHGDH expression in liver cells shows a correlation with expression levels of genes associated with circulating lipids, suggesting a role of PHGDH in hepatic-lipid metabolism. EWAS meta-analysis on tea consumption reveals no significant association, only two CpGs annotated to CACNA1A and PRDM16 genes show suggestive association (P-value <5.0×10-6). These findings indicate that coffee-associated changes in DNA methylation levels may explain the mechanism of action of coffee consumption in conferring risk of diseases.
Collapse
Affiliation(s)
- Irma Karabegović
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Genetic Identification, Erasmus University Medical Center, Rotterdam, the Netherlands
- Epidemiology and Microbial Genomics, National Health Laboratory, Dudelange, Luxembourg
| | | | - Yang Li
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jiantao Ma
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland and the Framingham Heart Study, Framingham, MA, USA
| | - Silvana C E Maas
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Genetic Identification, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Daokun Sun
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Emily A Hu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Srikant Ambatipudi
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, Cedex 08, France
| | - Giovanni Fiorito
- Laboratory of Biostatistics, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
| | - Jian Huang
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
- UK Dementia Research Institute at Imperial College London, London, UK
- Imperial College NIHR Biomedical Research Centre, London, UK
| | - Juan E Castillo-Fernandez
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, CHRU, Seattle, WA, USA
| | - Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sara Grioni
- Epidemiology and Prevention Unit, IRCCS National Cancer Institute Foundation, Milan, Italy
| | - Brenton R Swenson
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, CHRU, Seattle, WA, USA
| | - Silvia Polidoro
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
- Italian Institute for Genomic Medicine (IIGM, former HuGeF), c/o IRCCS Candiolo, Candiolo, Italy
| | - Jorien L Treur
- Department of Psychiatry, Amsterdam UMC, Amsterdam, the Netherlands
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, Cedex 08, France
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Veronique Chajes
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Kim Braun
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Niek Verweij
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Genomics plc, Park End St, Oxford, UK
| | - Anja Kretschmer
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert J de Knegt
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Abbas Dehghan
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
- UK Dementia Research Institute at Imperial College London, London, UK
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sina A Gharib
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, CHRU, Seattle, WA, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Paul Elliott
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
- UK Dementia Research Institute at Imperial College London, London, UK
- Imperial College NIHR Biomedical Research Centre, London, UK
- Health Data Research UK-London, London, UK
| | - Paolo Vineis
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, Cedex 08, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Casey M Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland and the Framingham Heart Study, Framingham, MA, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.
- Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
24
|
Zhang X, Asllanaj E, Amiri M, Portilla-Fernandez E, Bramer WM, Nano J, Voortman T, Pan Q, Ghanbari M. Deciphering the role of epigenetic modifications in fatty liver disease: A systematic review. Eur J Clin Invest 2021; 51:e13479. [PMID: 33350463 PMCID: PMC8243926 DOI: 10.1111/eci.13479] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fatty liver disease (FLD), primarily nonalcoholic fatty liver disease (NAFLD), is the most common liver disorder that affects a quarter of the global population. NAFLD is a spectrum of disease ranging from simple steatosis to nonalcoholic steatohepatitis, which is associated with increased risk of developing liver cancer. Given that the pathogenic mechanisms of fatty liver remain largely elusive, it is important to further investigate potential underlying mechanisms including epigenetic modifications. Here, we performed a systematic review of human epigenetic studies on FLD presence. METHODS Five bibliographic databases were screened until 28 August 2020. We included cross-sectional, case-control and cohort studies in humans that examined the association of epigenetic modifications including global, candidate or epigenome-wide methylation of DNA, noncoding RNAs and histone modifications with FLD. RESULTS In total 36 articles, based on 33 unique studies, consisting of 12 112 participants met the inclusion criteria. Among these, two recent epigenome-wide association studies conducted among large population-based cohorts have reported the association between cg06690548 (SLC7A11) and FLD. Moreover, several studies have demonstrated the association between microRNAs (miRNAs) and FLD, in which miR-122, miR-34a and miR-192 were recognized as the most relevant miRNAs as biomarkers for FLD. We did not find any studies examining histone modifications in relation to FLD. CONCLUSIONS Cumulative evidence suggests a link between epigenetic mechanisms, specifically DNA methylation and miRNAs, and FLD. Further efforts should investigate the molecular pathways by which these epigenetic markers may regulate FLD and also the potential role of histone modifications in FLD.
Collapse
Affiliation(s)
- Xiaofang Zhang
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eralda Asllanaj
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands.,Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Masoud Amiri
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eliana Portilla-Fernandez
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wichor M Bramer
- Medical Library, Erasmus MC, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jana Nano
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Diabetes Center, München-Neuherberg, Germany
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| |
Collapse
|
25
|
Gomez-Alonso MDC, Kretschmer A, Wilson R, Pfeiffer L, Karhunen V, Seppälä I, Zhang W, Mittelstraß K, Wahl S, Matias-Garcia PR, Prokisch H, Horn S, Meitinger T, Serrano-Garcia LR, Sebert S, Raitakari O, Loh M, Rathmann W, Müller-Nurasyid M, Herder C, Roden M, Hurme M, Jarvelin MR, Ala-Korpela M, Kooner JS, Peters A, Lehtimäki T, Chambers JC, Gieger C, Kettunen J, Waldenberger M. DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures. Clin Epigenetics 2021; 13:7. [PMID: 33413638 PMCID: PMC7789600 DOI: 10.1186/s13148-020-00957-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The discovery of robust and trans-ethnically replicated DNA methylation markers of metabolic phenotypes, has hinted at a potential role of epigenetic mechanisms in lipid metabolism. However, DNA methylation and the lipid compositions and lipid concentrations of lipoprotein sizes have been scarcely studied. Here, we present an epigenome-wide association study (EWAS) (N = 5414 total) of mostly lipid-related metabolic measures, including a fine profiling of lipoproteins. As lipoproteins are the main players in the different stages of lipid metabolism, examination of epigenetic markers of detailed lipoprotein features might improve the diagnosis, prognosis, and treatment of metabolic disturbances. RESULTS We conducted an EWAS of leukocyte DNA methylation and 226 metabolic measurements determined by nuclear magnetic resonance spectroscopy in the population-based KORA F4 study (N = 1662) and replicated the results in the LOLIPOP, NFBC1966, and YFS cohorts (N = 3752). Follow-up analyses in the discovery cohort included investigations into gene transcripts, metabolic-measure ratios for pathway analysis, and disease endpoints. We identified 161 associations (p value < 4.7 × 10-10), covering 16 CpG sites at 11 loci and 57 metabolic measures. Identified metabolic measures were primarily medium and small lipoproteins, and fatty acids. For apolipoprotein B-containing lipoproteins, the associations mainly involved triglyceride composition and concentrations of cholesterol esters, triglycerides, free cholesterol, and phospholipids. All associations for HDL lipoproteins involved triglyceride measures only. Associated metabolic measure ratios, proxies of enzymatic activity, highlight amino acid, glucose, and lipid pathways as being potentially epigenetically implicated. Five CpG sites in four genes were associated with differential expression of transcripts in blood or adipose tissue. CpG sites in ABCG1 and PHGDH showed associations with metabolic measures, gene transcription, and metabolic measure ratios and were additionally linked to obesity or previous myocardial infarction, extending previously reported observations. CONCLUSION Our study provides evidence of a link between DNA methylation and the lipid compositions and lipid concentrations of different lipoprotein size subclasses, thus offering in-depth insights into well-known associations of DNA methylation with total serum lipids. The results support detailed profiling of lipid metabolism to improve the molecular understanding of dyslipidemia and related disease mechanisms.
Collapse
Affiliation(s)
- Monica Del C Gomez-Alonso
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Anja Kretschmer
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Liliane Pfeiffer
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Pirkanmaa Hospital District, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, Middlesex, UK
| | - Kirstin Mittelstraß
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Pamela R Matias-Garcia
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany
| | - Sacha Horn
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Luis R Serrano-Garcia
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Turku, Turku University Hospital, Turku, Finland
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Wolfgang Rathmann
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55101, Mainz, Germany
| | - Christian Herder
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Roden
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mikko Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
- UKMRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Mika Ala-Korpela
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, Middlesex, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Pirkanmaa Hospital District, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, Middlesex, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Kettunen
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany.
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.
| |
Collapse
|
26
|
Ferreira-Gonzalez S, Rodrigo-Torres D, Gadd VL, Forbes SJ. Cellular Senescence in Liver Disease and Regeneration. Semin Liver Dis 2021; 41:50-66. [PMID: 33764485 DOI: 10.1055/s-0040-1722262] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Cellular senescence is an irreversible cell cycle arrest implemented by the cell as a result of stressful insults. Characterized by phenotypic alterations, including secretome changes and genomic instability, senescence is capable of exerting both detrimental and beneficial processes. Accumulating evidence has shown that cellular senescence plays a relevant role in the occurrence and development of liver disease, as a mechanism to contain damage and promote regeneration, but also characterizing the onset and correlating with the extent of damage. The evidence of senescent mechanisms acting on the cell populations of the liver will be described including the role of markers to detect cellular senescence. Overall, this review intends to summarize the role of senescence in liver homeostasis, injury, disease, and regeneration.
Collapse
Affiliation(s)
| | - Daniel Rodrigo-Torres
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Victoria L Gadd
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stuart J Forbes
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
27
|
Maude H, Sanchez-Cabanillas C, Cebola I. Epigenetics of Hepatic Insulin Resistance. Front Endocrinol (Lausanne) 2021; 12:681356. [PMID: 34046015 PMCID: PMC8147868 DOI: 10.3389/fendo.2021.681356] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/20/2021] [Indexed: 01/14/2023] Open
Abstract
Insulin resistance (IR) is largely recognized as a unifying feature that underlies metabolic dysfunction. Both lifestyle and genetic factors contribute to IR. Work from recent years has demonstrated that the epigenome may constitute an interface where different signals may converge to promote IR gene expression programs. Here, we review the current knowledge of the role of epigenetics in hepatic IR, focusing on the roles of DNA methylation and histone post-translational modifications. We discuss the broad epigenetic changes observed in the insulin resistant liver and its associated pathophysiological states and leverage on the wealth of 'omics' studies performed to discuss efforts in pinpointing specific loci that are disrupted by these changes. We envision that future studies, with increased genomic resolution and larger cohorts, will further the identification of biomarkers of early onset hepatic IR and assist the development of targeted interventions. Furthermore, there is growing evidence to suggest that persistent epigenetic marks may be acquired over prolonged exposure to disease or deleterious exposures, highlighting the need for preventative medicine and long-term lifestyle adjustments to avoid irreversible or long-term alterations in gene expression.
Collapse
Affiliation(s)
| | | | - Inês Cebola
- *Correspondence: Hannah Maude, ; Inês Cebola,
| |
Collapse
|
28
|
Shu C, Zhang X, Aouizerat BE, Xu K. Comparison of methylation capture sequencing and Infinium MethylationEPIC array in peripheral blood mononuclear cells. Epigenetics Chromatin 2020; 13:51. [PMID: 33228774 PMCID: PMC7684759 DOI: 10.1186/s13072-020-00372-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/02/2020] [Indexed: 11/11/2022] Open
Abstract
Background Epigenome-wide association studies (EWAS) have been widely applied to identify methylation CpG sites associated with human disease. To date, the Infinium MethylationEPIC array (EPIC) is commonly used for high-throughput DNA methylation profiling. However, the EPIC array covers only 30% of the human methylome. Methylation Capture bisulfite sequencing (MC-seq) captures target regions of methylome and has advantages of extensive coverage in the methylome at an affordable price. Methods Epigenome-wide DNA methylation in four peripheral blood mononuclear cell samples was profiled by using SureSelectXT Methyl-Seq for MC-seq and EPIC platforms separately. CpG site-based reproducibility of MC-seq was assessed with DNA sample inputs ranging in quantity of high (> 1000 ng), medium (300–1000 ng), and low (150 ng–300 ng). To compare the performance of MC-seq and the EPIC arrays, we conducted a Pearson correlation and methylation value difference at each CpG site that was detected by both MC-seq and EPIC. We compared the percentage and counts in each CpG island and gene annotation between MC-seq and the EPIC array. Results After quality control, an average of 3,708,550 CpG sites per sample were detected by MC-seq with DNA quantity > 1000 ng. Reproducibility of DNA methylation in MC-seq-detected CpG sites was high among samples with high, medium, and low DNA inputs (r > 0.96). The EPIC array captured an average of 846,464 CpG sites per sample. Compared with the EPIC array, MC-seq detected more CpGs in coding regions and CpG islands. Among the 472,540 CpG sites captured by both platforms, methylation of a majority of CpG sites was highly correlated in the same sample (r: 0.98–0.99). However, methylation for a small proportion of CpGs (N = 235) differed significantly between the two platforms, with differences in beta values of greater than 0.5. Conclusions Our results show that MC-seq is an efficient and reliable platform for methylome profiling with a broader coverage of the methylome than the array-based platform. Although methylation measurements in majority of CpGs are highly correlated, a number of CpG sites show large discrepancy between the two platforms, which warrants further investigation and needs cautious interpretation.
Collapse
Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06516, USA.,Connecticut Veteran Healthcare System, West Haven, CT, 06515, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06516, USA.,Connecticut Veteran Healthcare System, West Haven, CT, 06515, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University, New York, 10010, USA.,Department of Oral and Maxillofacial Surgery, College of Dentistry, Yale School of Medicine, New York University, New York, 10010, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06516, USA. .,Connecticut Veteran Healthcare System, West Haven, CT, 06515, USA.
| |
Collapse
|
29
|
Hyun J, Jung Y. DNA Methylation in Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2020; 21:ijms21218138. [PMID: 33143364 PMCID: PMC7662478 DOI: 10.3390/ijms21218138] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a widespread hepatic disorder in the United States and other Westernized countries. Nonalcoholic steatohepatitis (NASH), an advanced stage of NAFLD, can progress to end-stage liver disease, including cirrhosis and liver cancer. Poor understanding of mechanisms underlying NAFLD progression from simple steatosis to NASH has limited the development of effective therapies and biomarkers. An accumulating body of studies has suggested the importance of DNA methylation, which plays pivotal roles in NAFLD pathogenesis. DNA methylation signatures that can affect gene expression are influenced by environmental and lifestyle experiences such as diet, obesity, and physical activity and are reversible. Hence, DNA methylation signatures and modifiers in NAFLD may provide the basis for developing biomarkers indicating the onset and progression of NAFLD and therapeutics for NAFLD. Herein, we review an update on the recent findings in DNA methylation signatures and their roles in the pathogenesis of NAFLD and broaden people’s perspectives on potential DNA methylation-related treatments and biomarkers for NAFLD.
Collapse
Affiliation(s)
- Jeongeun Hyun
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea;
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
- Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Korea
- Cell and Matter Institute, Dankook University, Cheonan 31116, Korea
| | - Youngmi Jung
- Department of Integrated Biological Science, Pusan National University, Pusan 46241, Korea
- Department of Biological Sciences, Pusan National University, Pusan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2262
| |
Collapse
|
30
|
Shu C, Justice AC, Zhang X, Marconi VC, Hancock DB, Johnson EO, Xu K. DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population. Epigenetics 2020; 16:741-753. [PMID: 33092459 PMCID: PMC8216205 DOI: 10.1080/15592294.2020.1824097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. Methods: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. Results: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. Conclusions: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. Abbreviations: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
Collapse
Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Vincent C Marconi
- Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| |
Collapse
|
31
|
Prospects of Genetics and Epigenetics of Alcohol Use Disorder. CURRENT ADDICTION REPORTS 2020. [DOI: 10.1007/s40429-020-00331-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
Purpose of Review
In this study, we illustrate recent findings regarding the genetics and epigenetics of alcohol use disorder (AUD). We further outline the future direction of genetic and epigenetic research in AUD.
Recent Findings
Recent genome- and epigenome-wide studies allow new insight into genetic and epigenetic variation associated with AUD. The largest EWAS of AUD so far/to date found evidence for altered glucocorticoid receptor regulation. Longitudinal studies provide insight into the dynamics of the disease. Analyses of postmortem brain tissue reveal the impact of chronic alcohol consumption on DNA methylation in the brain.
Summary
Genetic and environmental factors—mediated via epigenetic mechanisms—play an important role in AUD. Although knowledge of the biological underpinnings of AUD is still limited, ongoing research will ultimately lead to the development of biomarkers for disease classification, course of disease, and treatment response to support personalized medicine in the future.
Collapse
|
32
|
Ikram MA, Brusselle G, Ghanbari M, Goedegebure A, Ikram MK, Kavousi M, Kieboom BCT, Klaver CCW, de Knegt RJ, Luik AI, Nijsten TEC, Peeters RP, van Rooij FJA, Stricker BH, Uitterlinden AG, Vernooij MW, Voortman T. Objectives, design and main findings until 2020 from the Rotterdam Study. Eur J Epidemiol 2020; 35:483-517. [PMID: 32367290 PMCID: PMC7250962 DOI: 10.1007/s10654-020-00640-5] [Citation(s) in RCA: 277] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/23/2020] [Indexed: 12/19/2022]
Abstract
The Rotterdam Study is an ongoing prospective cohort study that started in 1990 in the city of Rotterdam, The Netherlands. The study aims to unravel etiology, preclinical course, natural history and potential targets for intervention for chronic diseases in mid-life and late-life. The study focuses on cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. Since 2016, the cohort is being expanded by persons aged 40 years and over. The findings of the Rotterdam Study have been presented in over 1700 research articles and reports. This article provides an update on the rationale and design of the study. It also presents a summary of the major findings from the preceding 3 years and outlines developments for the coming period.
Collapse
Affiliation(s)
- M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Guy Brusselle
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - André Goedegebure
- Department of Otorhinolaryngology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M Kamran Ikram
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Brenda C T Kieboom
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert J de Knegt
- Department of Gastroenterology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemarie I Luik
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Tamar E C Nijsten
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank J A van Rooij
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| |
Collapse
|
33
|
Mens MMJ, Maas SCE, Klap J, Weverling GJ, Klatser P, Brakenhoff JPJ, van Meurs JBJ, Uitterlinden AG, Ikram MA, Kavousi M, Ghanbari M. Multi-Omics Analysis Reveals MicroRNAs Associated With Cardiometabolic Traits. Front Genet 2020; 11:110. [PMID: 32174972 PMCID: PMC7056871 DOI: 10.3389/fgene.2020.00110] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/30/2020] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNA molecules that regulate gene expression. Extensive research has explored the role of miRNAs in the risk for type 2 diabetes (T2D) and coronary heart disease (CHD) using single-omics data, but much less by leveraging population-based omics data. Here we aimed to conduct a multi-omics analysis to identify miRNAs associated with cardiometabolic risk factors and diseases. First, we used publicly available summary statistics from large-scale genome-wide association studies to find genetic variants in miRNA-related sequences associated with various cardiometabolic traits, including lipid and obesity-related traits, glycemic indices, blood pressure, and disease prevalence of T2D and CHD. Then, we used DNA methylation and miRNA expression data from participants of the Rotterdam Study to further investigate the link between associated miRNAs and cardiometabolic traits. After correcting for multiple testing, 180 genetic variants annotated to 67 independent miRNAs were associated with the studied traits. Alterations in DNA methylation levels of CpG sites annotated to 38 of these miRNAs were associated with the same trait(s). Moreover, we found that plasma expression levels of 8 of the 67 identified miRNAs were also associated with the same trait. Integrating the results of different omics data showed miR-10b-5p, miR-148a-3p, miR-125b-5p, and miR-100-5p to be strongly linked to lipid traits. Collectively, our multi-omics analysis revealed multiple miRNAs that could be considered as potential biomarkers for early diagnosis and progression of cardiometabolic diseases.
Collapse
Affiliation(s)
- Michelle M J Mens
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Silvana C E Maas
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jaco Klap
- World Without Disease Accelerator, Data Sciences & Prevention Biomarkers, Johnson & Johnson, Leiden, Netherlands
| | - Gerrit Jan Weverling
- World Without Disease Accelerator, Data Sciences & Prevention Biomarkers, Johnson & Johnson, Leiden, Netherlands
| | - Paul Klatser
- World Without Disease Accelerator, Data Sciences & Prevention Biomarkers, Johnson & Johnson, Leiden, Netherlands
| | - Just P J Brakenhoff
- World Without Disease Accelerator, Data Sciences & Prevention Biomarkers, Johnson & Johnson, Leiden, Netherlands
| | - Joyce B J van Meurs
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| |
Collapse
|
34
|
Cabré N, Luciano-Mateo F, Baiges-Gayà G, Fernández-Arroyo S, Rodríguez-Tomàs E, Hernández-Aguilera A, París M, Sabench F, Del Castillo D, López-Miranda J, Menéndez JA, Camps J, Joven J. Plasma metabolic alterations in patients with severe obesity and non-alcoholic steatohepatitis. Aliment Pharmacol Ther 2020; 51:374-387. [PMID: 31825539 DOI: 10.1111/apt.15606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/05/2019] [Accepted: 11/16/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Obesity can influence hepatic mitochondrial function, and cause non-alcoholic steatohepatitis (NASH). Diagnosis and follow-up rely on invasive liver biopsy so blood-based markers are urgently required. AIM To investigate whether values of circulating metabolites from energy and one-carbon (1-C) metabolism may: (a) reflect hepatic mitochondrial flexibility failure and (b) act as NASH biomarkers. METHODS Patients with severe obesity undergoing bariatric surgery (n = 270) were investigated using quantitative targeted plasma metabolomics. Comparisons were with non-obese controls without liver disease (n = 50). Obese patients with NASH (n = 53) and without NASH (n = 130) representing extreme groups of liver disease were assessed to test the diagnostic ability of the measured circulating metabolites. Paired liver biopsy and plasma samples from NASH patients were available 1 year post-surgery and were evaluated to monitor metabolomic changes with liver damage resolution. RESULTS We identified correlations between human liver metabolism and obesity. High-plasma α-ketoglutarate (α-KG) and lactate concentrations in NASH patients indicating citric acid cycle replenishment via glutaminolysis might also be a crucial point in NASH onset. Plasma measurements of α-KG, β-hydroxybutyrate, pyruvate and oxaloacetate reduced the uncertainty in clinical diagnosis of NASH [area under receiver operating characteristic curve (AUC) of 0.826] and predicted NASH resolution without ambiguity (AUC of 0.999). CONCLUSION Changes in plasma mitochondrial metabolites appear to be associated with NASH. These metabolic responses may be dynamically remodelled following resolution of liver damage through massive weight loss.
Collapse
Affiliation(s)
- Noemí Cabré
- Department of Medicine and Surgery, Universitat Rovira i Virgili, Reus, Spain.,Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Fedra Luciano-Mateo
- Department of Medicine and Surgery, Universitat Rovira i Virgili, Reus, Spain.,Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Gerard Baiges-Gayà
- Department of Medicine and Surgery, Universitat Rovira i Virgili, Reus, Spain.,Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Salvador Fernández-Arroyo
- Department of Medicine and Surgery, Universitat Rovira i Virgili, Reus, Spain.,Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Elisabet Rodríguez-Tomàs
- Department of Medicine and Surgery, Universitat Rovira i Virgili, Reus, Spain.,Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Anna Hernández-Aguilera
- Department of Medicine and Surgery, Universitat Rovira i Virgili, Reus, Spain.,Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Marta París
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Fàtima Sabench
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Daniel Del Castillo
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - José López-Miranda
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | - Javier A Menéndez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jordi Camps
- Department of Medicine and Surgery, Universitat Rovira i Virgili, Reus, Spain.,Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Jorge Joven
- Department of Medicine and Surgery, Universitat Rovira i Virgili, Reus, Spain.,Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain.,The Campus of International Excellence Southern Catalonia, Tarragona, Spain
| |
Collapse
|
35
|
Papatheodoridi AM, Chrysavgis L, Koutsilieris M, Chatzigeorgiou A. The Role of Senescence in the Development of Nonalcoholic Fatty Liver Disease and Progression to Nonalcoholic Steatohepatitis. Hepatology 2020; 71:363-374. [PMID: 31230380 DOI: 10.1002/hep.30834] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/17/2019] [Indexed: 12/17/2022]
Abstract
In recent years, cellular senescence has generated a lot of interest among researchers because of its involvement in both the normal aging process and common human diseases. During senescence, cells undergo alterations that include telomere shortening, nuclear area enlargement, and genomic and mitochondrial DNA damage, leading to irreversible cell cycle arrest, and secretion of proinflammatory cytokines. Evidence suggests that the complex process of senescence is involved in the development of a plethora of chronic diseases including metabolic and inflammatory disorders and tumorigenesis. Recently, several human and animal studies have emphasized the involvement of senescence in the pathogenesis and development of liver steatosis including the progression to nonalcoholic steatohepatitis (NASH) as characterized by the additional emergence of inflammation, hepatocyte ballooning, and liver fibrosis. The development of nonalcoholic fatty liver disease (NAFLD) and its progression to NASH are commonly accompanied by several pathophysiological events including metabolic dysregulation and inflammatory phenomena occurring within the liver that may contribute to or derive from cellular senescence, implying that the latter may be both a stimulus and a consequence of the disease. Conclusion: In this review, we summarize the current literature on the impact of cellular senescence in NAFLD/NASH and discuss the effectiveness and safety of novel senolytic drugs and therapeutic options available to delay or treat the disease. Finally, we identify the open questions and issues to be addressed in the near future.
Collapse
Affiliation(s)
| | - Lampros Chrysavgis
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Michael Koutsilieris
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Antonios Chatzigeorgiou
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| |
Collapse
|
36
|
Xu K, Montalvo‐Ortiz JL, Zhang X, Southwick SM, Krystal JH, Pietrzak RH, Gelernter J. Epigenome‐Wide
DNA
Methylation Association Analysis Identified Novel Loci in Peripheral Cells for Alcohol Consumption Among European American Male Veterans. Alcohol Clin Exp Res 2019; 43:2111-2121. [PMID: 31386212 DOI: 10.1111/acer.14168] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/25/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Ke Xu
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
| | - Janitza L. Montalvo‐Ortiz
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
| | - Xinyu Zhang
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
| | - Steven M. Southwick
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
- Clinical Neurosciences Division U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder West Haven Connecticut
| | - John H. Krystal
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
- Clinical Neurosciences Division U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder West Haven Connecticut
| | - Robert H. Pietrzak
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
- Clinical Neurosciences Division U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder West Haven Connecticut
| | - Joel Gelernter
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
- Clinical Neurosciences Division U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder West Haven Connecticut
| |
Collapse
|
37
|
DNA Hydroxymethylation at the Interface of the Environment and Nonalcoholic Fatty Liver Disease. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16152791. [PMID: 31387232 PMCID: PMC6695744 DOI: 10.3390/ijerph16152791] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 12/25/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is one of the most prevalent forms of chronic liver disorders among adults, children, and adolescents, and a growing epidemic, worldwide. Notwithstanding the known susceptibility factors for NAFLD, i.e., obesity and metabolic syndrome, the exact cause(s) of this disease and the underlying mechanisms of its initiation and progression are not fully elucidated. NAFLD is a multi-faceted disease with metabolic, genetic, epigenetic, and environmental determinants. Accumulating evidence shows that exposure to environmental toxicants contributes to the development of NAFLD by promoting mitochondrial dysfunction and generating reactive oxygen species in the liver. Imbalances in the redox state of the cells are known to cause alterations in the patterns of 5-hydroxymethylcytosine (5hmC), the oxidative product of 5-methylcytosine (5mC), thereby influencing gene regulation. The 5hmC-mediated deregulation of genes involved in hepatic metabolism is an emerging area of research in NAFLD. This review summarizes our current knowledge on the interactive role of xenobiotic exposure and DNA hydroxymethylation in the pathogenesis of fatty liver disease. Increasing the mechanistic knowledge of NAFLD initiation and progression is crucial for the development of new and effective strategies for prevention and treatment of this disease.
Collapse
|
38
|
Epigenetics and Inflammatory Markers: A Systematic Review of the Current Evidence. Int J Inflam 2019; 2019:6273680. [PMID: 31205673 PMCID: PMC6530203 DOI: 10.1155/2019/6273680] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/07/2019] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms have been suggested to play a role in the genetic regulation of pathways related to inflammation. Therefore, we aimed to systematically review studies investigating the association between DNA methylation and histone modifications with circulatory inflammation markers in blood. Five bibliographic databases were screened until 21 November of 2017. We included studies conducted on humans that examined the association between epigenetic marks (DNA methylation and/or histone modifications) and a comprehensive list of inflammatory markers. Of the 3,759 identified references, 24 articles were included, involving, 17,399 individuals. There was suggestive evidence for global hypomethylation but better-quality studies in the future have to confirm this. Epigenome-wide association studies (EWAS) (n=7) reported most of the identified differentially methylated genes to be hypomethylated in inflammatory processes. Candidate genes studies reported 18 differentially methylated genes related to several circulatory inflammation markers. There was no overlap in the methylated sites investigated in candidate gene studies and EWAS, except for TMEM49, which was found to be hypomethylated with higher inflammatory markers in both types of studies. The relation between histone modifications and inflammatory markers was assessed by one study only. This review supports an association between epigenetic marks and inflammation, suggesting hypomethylation of the genome. Important gaps in the quality of studies were reported such as inadequate sample size, lack of adjustment for relevant confounders, and failure to replicate the findings. While most of the studies have been focused on C-reactive protein, further efforts should investigate other inflammatory markers.
Collapse
|
39
|
Ma J, Nano J, Ding J, Zheng Y, Hennein R, Liu C, Speliotes EK, Huan T, Song C, Mendelson MM, Joehanes R, Long MT, Liang L, Smith JA, Reynolds LM, Ghanbari M, Muka T, van Meurs JBJ, Alferink LJM, Franco OH, Dehghan A, Ratliff S, Zhao W, Bielak L, Kardia SLR, Peyser PA, Ning H, VanWagner LB, Lloyd-Jones DM, Carr JJ, Greenland P, Lichtenstein AH, Hu FB, Liu Y, Hou L, Darwish Murad S, Levy D. A Peripheral Blood DNA Methylation Signature of Hepatic Fat Reveals a Potential Causal Pathway for Nonalcoholic Fatty Liver Disease. Diabetes 2019; 68:1073-1083. [PMID: 30936141 PMCID: PMC6477898 DOI: 10.2337/db18-1193] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/14/2019] [Indexed: 02/07/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a risk factor for type 2 diabetes (T2D). We aimed to identify the peripheral blood DNA methylation signature of hepatic fat. We conducted epigenome-wide association studies of hepatic fat in 3,400 European ancestry (EA) participants and in 401 Hispanic ancestry and 724 African ancestry participants from four population-based cohort studies. Hepatic fat was measured using computed tomography or ultrasound imaging and DNA methylation was assessed at >400,000 cytosine-guanine dinucleotides (CpGs) in whole blood or CD14+ monocytes using a commercial array. We identified 22 CpGs associated with hepatic fat in EA participants at a false discovery rate <0.05 (corresponding P = 6.9 × 10-6) with replication at Bonferroni-corrected P < 8.6 × 10-4 Mendelian randomization analyses supported the association of hypomethylation of cg08309687 (LINC00649) with NAFLD (P = 2.5 × 10-4). Hypomethylation of the same CpG was also associated with risk for new-onset T2D (P = 0.005). Our study demonstrates that a peripheral blood-derived DNA methylation signature is robustly associated with hepatic fat accumulation. The hepatic fat-associated CpGs may represent attractive biomarkers for T2D. Future studies are warranted to explore mechanisms and to examine DNA methylation signatures of NAFLD across racial/ethnic groups.
Collapse
Affiliation(s)
- Jiantao Ma
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, and Framingham Heart Study, Framingham, MA
- Nutrition Data Science, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA
| | - Jana Nano
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Epidemiology, Neuherberg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Jingzhong Ding
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Rachel Hennein
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, and Framingham Heart Study, Framingham, MA
| | - Chunyu Liu
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, and Framingham Heart Study, Framingham, MA
- Department of Biostatistics, Boston University, Boston, MA
| | | | - Tianxiao Huan
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, and Framingham Heart Study, Framingham, MA
| | - Ci Song
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, and Framingham Heart Study, Framingham, MA
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael M Mendelson
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, and Framingham Heart Study, Framingham, MA
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, and Framingham Heart Study, Framingham, MA
| | - Michelle T Long
- Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Lindsay M Reynolds
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Taulant Muka
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Joyce B J van Meurs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Louise J M Alferink
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, U.K
| | - Scott Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Lawrence Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hongyan Ning
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Lisa B VanWagner
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
- Division of Gastroenterology and Hepatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - John Jeffrey Carr
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Alice H Lichtenstein
- Cardiovascular Nutrition Laboratory, USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Sarwa Darwish Murad
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, and Framingham Heart Study, Framingham, MA
| |
Collapse
|
40
|
Grau-Perez M, Agha G, Pang Y, Bermudez JD, Tellez-Plaza M. Mendelian Randomization and the Environmental Epigenetics of Health: a Systematic Review. Curr Environ Health Rep 2019; 6:38-51. [DOI: 10.1007/s40572-019-0226-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
41
|
Mordaunt CE, Kieffer DA, Shibata NM, Członkowska A, Litwin T, Weiss KH, Zhu Y, Bowlus CL, Sarkar S, Cooper S, Wan YJY, Ali MR, LaSalle JM, Medici V. Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers. Epigenetics Chromatin 2019; 12:10. [PMID: 30709419 PMCID: PMC6357467 DOI: 10.1186/s13072-019-0255-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/21/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Wilson disease (WD) is an autosomal recessive disease caused by mutations in ATP7B encoding a copper transporter. Consequent copper accumulation results in a variable WD clinical phenotype involving hepatic, neurologic, and psychiatric symptoms, without clear genotype-phenotype correlations. The goal of this study was to analyze alterations in DNA methylation at the whole-genome level in liver and blood from patients with WD to investigate epigenomic alterations associated with WD diagnosis and phenotype. We used whole-genome bisulfite sequencing (WGBS) to examine distinct cohorts of WD subjects to determine whether DNA methylation could differentiate patients from healthy subjects and subjects with other liver diseases and distinguish between different WD phenotypes. RESULTS WGBS analyses in liver identified 969 hypermethylated and 871 hypomethylated differentially methylated regions (DMRs) specifically identifying patients with WD, including 18 regions with genome-wide significance. WD-specific liver DMRs were associated with genes enriched for functions in folate and lipid metabolism and acute inflammatory response and could differentiate early from advanced fibrosis in WD patients. Functional annotation revealed that WD-hypermethylated liver DMRs were enriched in liver-specific enhancers, flanking active liver promoters, and binding sites of liver developmental transcription factors, including Hepatocyte Nuclear Factor 4 alpha (HNF4A), Retinoid X Receptor alpha (RXRA), Forkhead Box A1 (FOXA1), and FOXA2. DMRs associated with WD progression were also identified, including 15 with genome-wide significance. However, WD DMRs in liver were not related to large-scale changes in proportions of liver cell types. DMRs detected in blood differentiated WD patients from healthy and disease control subjects, and distinguished between patients with hepatic and neurologic WD manifestations. WD phenotype DMRs corresponded to genes enriched for functions in mental deterioration, abnormal B cell physiology, and as members of the polycomb repressive complex 1 (PRC1). 44 DMRs associated with WD phenotype tested in a small validation cohort had a predictive value of 0.9. CONCLUSIONS We identified a disease-mechanism relevant epigenomic signature of WD that reveals new insights into potential biomarkers and treatments for this complex monogenic disease.
Collapse
Affiliation(s)
- Charles E Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Dorothy A Kieffer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
| | - Noreene M Shibata
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
| | - Anna Członkowska
- 2nd Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Tomasz Litwin
- 2nd Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Karl-Heinz Weiss
- Department of Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany
| | - Yihui Zhu
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Christopher L Bowlus
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
| | - Souvik Sarkar
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
| | - Stewart Cooper
- California Pacific Medical Center, San Francisco, CA, USA
| | - Yu-Jui Yvonne Wan
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, USA
| | - Mohamed R Ali
- Department of Surgery, University of California Davis, Sacramento, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Valentina Medici
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.
| |
Collapse
|
42
|
Zaghlool SB, Mook-Kanamori DO, Kader S, Stephan N, Halama A, Engelke R, Sarwath H, Al-Dous EK, Mohamoud YA, Roemisch-Margl W, Adamski J, Kastenmüller G, Friedrich N, Visconti A, Tsai PC, Spector T, Bell JT, Falchi M, Wahl A, Waldenberger M, Peters A, Gieger C, Pezer M, Lauc G, Graumann J, Malek JA, Suhre K. Deep molecular phenotypes link complex disorders and physiological insult to CpG methylation. Hum Mol Genet 2019; 27:1106-1121. [PMID: 29325019 PMCID: PMC5886112 DOI: 10.1093/hmg/ddy006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/02/2018] [Indexed: 01/12/2023] Open
Abstract
Epigenetic regulation of cellular function provides a mechanism for rapid organismal adaptation to changes in health, lifestyle and environment. Associations of cytosine-guanine di-nucleotide (CpG) methylation with clinical endpoints that overlap with metabolic phenotypes suggest a regulatory role for these CpG sites in the body's response to disease or environmental stress. We previously identified 20 CpG sites in an epigenome-wide association study (EWAS) with metabolomics that were also associated in recent EWASs with diabetes-, obesity-, and smoking-related endpoints. To elucidate the molecular pathways that connect these potentially regulatory CpG sites to the associated disease or lifestyle factors, we conducted a multi-omics association study including 2474 mass-spectrometry-based metabolites in plasma, urine and saliva, 225 NMR-based lipid and metabolite measures in blood, 1124 blood-circulating proteins using aptamer technology, 113 plasma protein N-glycans and 60 IgG-glyans, using 359 samples from the multi-ethnic Qatar Metabolomics Study on Diabetes (QMDiab). We report 138 multi-omics associations at these CpG sites, including diabetes biomarkers at the diabetes-associated TXNIP locus, and smoking-specific metabolites and proteins at multiple smoking-associated loci, including AHRR. Mendelian randomization suggests a causal effect of metabolite levels on methylation of obesity-associated CpG sites, i.e. of glycerophospholipid PC(O-36: 5), glycine and a very low-density lipoprotein (VLDL-A) on the methylation of the obesity-associated CpG loci DHCR24, MYO5C and CPT1A, respectively. Taken together, our study suggests that multi-omics-associated CpG methylation can provide functional read-outs for the underlying regulatory response mechanisms to disease or environmental insults.
Collapse
Affiliation(s)
- Shaza B Zaghlool
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar.,Computer Engineering Department, Virginia Tech, Blacksburg, VA 24061, USA
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Sara Kader
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Nisha Stephan
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Anna Halama
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Rudolf Engelke
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Hina Sarwath
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Eman K Al-Dous
- Genomics Core, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Yasmin A Mohamoud
- Genomics Core, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Werner Roemisch-Margl
- Institute of Bioinformatics and Systems Biology, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse, 85764 Neuherberg, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse, 85764 Neuherberg, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse, 85764 Neuherberg, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Alessia Visconti
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Pei-Chien Tsai
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Tim Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Mario Falchi
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Annika Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, D-85764 Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, D-85764 Neuherberg, Bavaria, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, D-85764 Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, D-85764 Neuherberg, Bavaria, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, D-85764 Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, D-85764 Neuherberg, Bavaria, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Bavaria, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, D-85764 Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, D-85764 Neuherberg, Bavaria, Germany
| | - Marija Pezer
- Glycoscience Research Laboratory, Genos Ltd, HR-10000, Zagreb, Croatia
| | - Gordan Lauc
- Glycoscience Research Laboratory, Genos Ltd, HR-10000, Zagreb, Croatia
| | - Johannes Graumann
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar.,Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, 61231 Bad Nauheim, Germany
| | - Joel A Malek
- Genomics Core, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, PO Box 24144, Doha, Qatar
| |
Collapse
|
43
|
Wu J, Zhang R, Shen F, Yang R, Zhou D, Cao H, Chen G, Pan Q, Fan J. Altered DNA Methylation Sites in Peripheral Blood Leukocytes from Patients with Simple Steatosis and Nonalcoholic Steatohepatitis (NASH). Med Sci Monit 2018; 24:6946-6967. [PMID: 30270343 PMCID: PMC6180948 DOI: 10.12659/msm.909747] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background The aim of this study was to identify DNA methylation sites in peripheral blood leukocytes from patients with histologically confirmed nonalcoholic fatty liver disease (NAFLD) that included simple hepatic steatosis and nonalcoholic steatohepatitis (NASH). Material/Methods DNA was isolated from peripheral blood leukocytes from patients with histologically diagnosed NAFLD (n=35), including simple hepatic steatosis (n=18) and NASH (n=17). Healthy controls included individuals without liver disease (n=30). DNA was hybridized, and DNA methylation was interrogated in an epigenome-wide association study (EWAS). DNA methylation levels (β-values) were correlated with serum lipid profiles, liver enzymes, and liver histology. Results Circulating blood leukocytes from 35 patients with NAFLD (simple steatosis and NASH) contained 65 CpG sites, which represented 60 genes that were differentially methylated when compared with healthy controls. In the simple hepatic steatosis group (n=18), 42 methylated CpG sites were found to be associated with increased levels of serum alanine aminotransferase (ALT), and 32 methylated CpG sites were associated with increased serum lipid profiles. In the NASH group (n=17), when compared with the simple hepatic steatosis group, methylated CpG sites showed significant correlations with the presence of lobular inflammation compared with hepatic steatosis and fibrosis. Six differentially methylated CpG sites were identified in the ACSL4, CRLS1, CTP1A, SIGIRR, SSBP1 and ZNF622 genes, which were associated with histologically confirmed simple hepatic steatosis and NASH. Conclusions The study identified some key methylated CpG sites from peripheral blood leukocytes, which might be used as serum biomarkers to stratify NAFLD patients into simple hepatic steatosis and NASH.
Collapse
Affiliation(s)
- Jiayu Wu
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Ruinan Zhang
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Feng Shen
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Ruixu Yang
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Da Zhou
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Haixia Cao
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Guangyu Chen
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Qin Pan
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Jiangao Fan
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland).,Shanghai Key Laboratory of Children's Digestion and Nutrition, Shanghai, China (mainland).,Shanghai Institute of Pediatrics, Shanghai, China (mainland)
| |
Collapse
|
44
|
Gutierrez Sanchez LH, Tomita K, Guo Q, Furuta K, Alhuwaish H, Hirsova P, Baheti S, Alver B, Hlady R, Robertson KD, Ibrahim SH. Perinatal Nutritional Reprogramming of the Epigenome Promotes Subsequent Development of Nonalcoholic Steatohepatitis. Hepatol Commun 2018; 2:1493-1512. [PMID: 30556038 PMCID: PMC6287484 DOI: 10.1002/hep4.1265] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/07/2018] [Indexed: 12/28/2022] Open
Abstract
With the epidemic of obesity, nonalcoholic fatty liver disease (NAFLD) has become the most common pediatric liver disease. The influence of a perinatal obesity‐inducing diet (OID) on the development and progression of NAFLD in offspring is important but incompletely studied. Hence, we fed breeding pairs of C57BL/6J mice during gestation and lactation (perinatally) either chow or an OID rich in fat, fructose, and cholesterol (FFC). The offspring were weaned to either chow or an FFC diet, generating four groups: perinatal (p)Chow‐Chow, pChow‐FFC, pFFC‐Chow, and pFFC‐FFC. Mice were sacrificed at 10 weeks of age. We examined the whole‐liver transcriptome by RNA sequencing (RNA‐seq) and whole‐liver genome methylation by reduced representation bisulfite sequencing (RRBS). Our results indicated that the pFFC‐FFC mice had a significant increase in hepatic steatosis, injury, inflammation, and fibrosis, as assessed histologically and biochemically. We identified 189 genes that were differentially expressed and methylated in the pFFC‐FFC mice versus the pChow‐FFC mice. Gene set enrichment analysis identified hepatic fibrosis/hepatic stellate cell activation as the top canonical pathway, suggesting that the differential DNA methylation events in the mice exposed to the FFC diet perinatally were associated with a profibrogenic transcriptome. To verify that this finding was consistent with perinatal nutritional reprogramming of the methylome, we exposed pFFC‐Chow mice to an FFC diet in adulthood. These mice developed significant hepatic steatosis, injury, inflammation, and more importantly fibrosis when compared to the appropriate controls. Conclusion: Perinatal exposure to an OID primes the immature liver for an accentuated fibrosing nonalcoholic steatohepatitis (NASH) phenotype, likely through nutritional reprogramming of the offspring methylome. These data have potential clinical implications for monitoring children of obese mothers and risk stratification of children with NAFLD.
Collapse
Affiliation(s)
| | - Kyoko Tomita
- Division of Gastroenterology and Hepatology Mayo Clinic Rochester MN
| | - Qianqian Guo
- Division of Gastroenterology and Hepatology Mayo Clinic Rochester MN
| | - Kunimaro Furuta
- Division of Gastroenterology and Hepatology Mayo Clinic Rochester MN
| | - Husam Alhuwaish
- Division of Gastroenterology and Hepatology Mayo Clinic Rochester MN
| | - Petra Hirsova
- Division of Gastroenterology and Hepatology Mayo Clinic Rochester MN.,Institute of Clinical Biochemistry and Diagnostics University Hospital Hradec Kralove Hradec Kralove Czech Republic
| | - Saurabh Baheti
- Division of Biomedical Statistics and Informatics Mayo Clinic Rochester MN
| | - Bonnie Alver
- Department of Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Rochester MN
| | - Ryan Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Rochester MN
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Rochester MN
| | - Samar H Ibrahim
- Division of Pediatric Gastroenterology and Hepatology Mayo Clinic Rochester MN.,Division of Gastroenterology and Hepatology Mayo Clinic Rochester MN
| |
Collapse
|
45
|
Ikram MA, Brusselle GGO, Murad SD, van Duijn CM, Franco OH, Goedegebure A, Klaver CCW, Nijsten TEC, Peeters RP, Stricker BH, Tiemeier H, Uitterlinden AG, Vernooij MW, Hofman A. The Rotterdam Study: 2018 update on objectives, design and main results. Eur J Epidemiol 2017; 32:807-850. [PMID: 29064009 PMCID: PMC5662692 DOI: 10.1007/s10654-017-0321-4] [Citation(s) in RCA: 329] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/06/2017] [Indexed: 02/07/2023]
Abstract
The Rotterdam Study is a prospective cohort study ongoing since 1990 in the city of Rotterdam in The Netherlands. The study targets cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. Since 2016, the cohort is being expanded by persons aged 40 years and over. The findings of the Rotterdam Study have been presented in over 1500 research articles and reports (see www.erasmus-epidemiology.nl/rotterdamstudy ). This article gives the rationale of the study and its design. It also presents a summary of the major findings and an update of the objectives and methods.
Collapse
Affiliation(s)
- M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Guy G O Brusselle
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Sarwa Darwish Murad
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Gastro-Enterology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - André Goedegebure
- Department of Otolaryngology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tamar E C Nijsten
- Department of Dermatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robin P Peeters
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| |
Collapse
|