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Chen J, Ruan X, Sun Y, Lu S, Hu S, Yuan S, Li X. Multi-omic insight into the molecular networks of mitochondrial dysfunction in the pathogenesis of inflammatory bowel disease. EBioMedicine 2024; 99:104934. [PMID: 38103512 PMCID: PMC10765009 DOI: 10.1016/j.ebiom.2023.104934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Mitochondrial dysfunction has been linked to the development of inflammatory bowel disease (IBD), but the genetic pathophysiology was not fully elucidated. We employed Mendelian randomization and colocalization analyses to investigate the associations between mitochondrial-related genes and IBD via integrating multi-omics. METHODS Summary-level data of mitochondrial gene methylation, expression and protein abundance levels were obtained from corresponding methylation, expression and protein quantitative trait loci studies, respectively. We obtained genetic associations with IBD and its two subtypes from the Inflammatory Bowel Disease Genetics Consortium (discovery), the UK Biobank (replication), and the FinnGen study (replication). We performed summary-data-based Mendelian randomization analysis to assess the associations of mitochondrial gene-related molecular features with IBD. Colocalization analysis was further conducted to assess whether the identified signal pairs shared a causal genetic variant. FINDINGS After integrating the multi-omics data between mQTL-eQTL and eQTL-pQTL, we identified two mitochondrial genes, i.e., PARK7 and ACADM, with tier 1 evidence for their associations with IBD and ulcerative colitis (UC). PDK1 and FISI genes were associated with UC risk with tier 2 and tier 3 evidence, respectively. The methylation of cg05467918 in ACADM was associated with lower expression of ACADM, which fits with the positive effect of cg05467918 methylation on UC risk. Consistently, the inverse associations between gene methylation and gene expression were also observed in PARK7 (cg10385390) and PDK1 (cg17679246), which were corroborated with the protective role in UC. At circulating protein level, genetically predicted higher levels of PARK7 (OR 0.36, 95% CI 0.25-0.52) and HINT1 (OR 0.47, 95% CI 0.30-0.74) were inversely associated with IBD risk; genetically predicted higher level of HINT1 was associated with a decreased risk of Crohn's disease (CD) (OR 0.26, 95% CI 0.14-0.49) and a higher level of ACADM (OR 0.67, 95% CI 0.55-0.83), PDK1 (OR 0.63, 95% CI 0.49-0.81), FIS1 (OR 0.63, 95% CI 0.47-0.83) was associated with a decreased risk of UC. INTERPRETATION We found that the mitochondrial PARK7 gene was putatively associated with IBD risk, and mitochondrial FIS1, PDK1, and ACADM genes were associated with UC risk with evidence from multi-omics levels. This study identified mitochondrial genes in relation to IBD, which may enhance the understanding of the pathogenic mechanisms of IBD development. FUNDING XL is supported by the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province (LR22H260001) and Healthy Zhejiang One Million People Cohort (K-20230085).
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Affiliation(s)
- Jie Chen
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xixian Ruan
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yuhao Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Shiyuan Lu
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Shixian Hu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Xue Li
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Odimba U, Senthilselvan A, Farrell J, Gao Z. Sex-Specific Genetic Determinants of Asthma-COPD Phenotype and COPD in Middle-Aged and Older Canadian Adults: An Analysis of CLSA Data. COPD 2023; 20:233-247. [PMID: 37466093 DOI: 10.1080/15412555.2023.2229906] [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: 02/17/2023] [Revised: 05/22/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023]
Abstract
The etiology of sex differences in the risk of asthma-COPD phenotype and COPD is still not completely understood. Genetic and environmental risk factors are commonly believed to play an important role. This study aims to identify sex-specific genetic markers associated with asthma-COPD phenotype and COPD using the Canadian Longitudinal Study on Aging (CLSA) Baseline Comprehensive and Genomic data. There were a total of 1,415 COPD cases. Out of them, 504 asthma-COPD phenotype cases were identified. 20,524 participants without a diagnosis of asthma and COPD served as controls. We performed genome-wide SNP-by-sex interaction analysis. SNPs with an interaction p-value < 10-5 were included in a sex-stratified multivariable logistic regression for asthma-COPD phenotype and COPD outcomes. 18 and 28 SNPs had a significant interaction term p-value < 10-5 with sex in the regression analyses of asthma-COPD phenotype and COPD outcomes, respectively. Sex-stratified multivariable analysis of asthma-COPD phenotype showed that 7 SNPs in/near SMYD3, FHIT, ZNF608, RIMBP2, ZNF133, BPIFB1, and S100B loci were significant in males. Sex-stratified multivariable analysis of COPD showed that 8 SNPs in/near MAGI1, COX18, OSTC, ELOVL5, C7orf72 FGF14, and NKAIN4 were significant in males, and 4 SNPs in/near genes CAMTA1, SATB2, PDE10A, and LINC00908 were significant in females. An SNP in the ZPBP gene was associated with COPD in both males and females. Identification of sex-specific loci associated with asthma-COPD phenotype and COPD may offer valuable evidence toward a better understanding of the sex-specific differences in the pathophysiology of the diseases.
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Affiliation(s)
- Ugochukwu Odimba
- Clinical Epidemiology Unit, Division of Community Health and Humanities, Faculty of Medicine, Memorial University, St. John's, Canada
| | | | - Jamie Farrell
- Clinical Epidemiology Unit, Division of Community Health and Humanities, Faculty of Medicine, Memorial University, St. John's, Canada
- Faculty of Medicine, Health Sciences Centre (Respirology Department), Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Zhiwei Gao
- Clinical Epidemiology Unit, Division of Community Health and Humanities, Faculty of Medicine, Memorial University, St. John's, Canada
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3
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Martino DJ, Bui DS, Li S, Idrose S, Perret J, Lowe AJ, Lodge CJ, Bowatte G, Moodley Y, Thomas PS, Zosky G, Hansbro PM, Holloway JW, Svanes C, Faner R, Walters EH, Dharmage SC. Genetic and Epigenetic Associations with Pre-Chronic Obstructive Pulmonary Disease Lung Function Trajectories. Am J Respir Crit Care Med 2023; 208:1135-1137. [PMID: 37610423 DOI: 10.1164/rccm.202306-1025le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/23/2023] [Indexed: 08/24/2023] Open
Affiliation(s)
- David J Martino
- Wal-yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, West Perth, Western Australia, Australia
| | - Dinh S Bui
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shuai Li
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Sabrina Idrose
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer Perret
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Adrian J Lowe
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Caroline J Lodge
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Gayan Bowatte
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yuben Moodley
- Department of Respiratory Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Paul S Thomas
- Respiratory Medicine, Prince of Wales Hospital and Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Graeme Zosky
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, New South Wales, Australia
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Cecilie Svanes
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | - Rosa Faner
- Immunology Unit, Biomedicine Department, University of Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomediques August Pi i Sunyer-Fundació Clinic Recerca, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Eugene H Walters
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia; and
- School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Shaymali C Dharmage
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
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Chen H, Luo H, Tian T, Li S, Jiang Y. Integrated Analyses of Single-Cell Transcriptome and Mendelian Randomization Reveal the Protective Role of Resistin in Sepsis Survival in Intensive Care Unit. Int J Mol Sci 2023; 24:14982. [PMID: 37834432 PMCID: PMC10573869 DOI: 10.3390/ijms241914982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
The high morbidity and mortality rates associated with sepsis highlight the challenges of finding specific remedies for this condition in the intensive care unit (ICU). This study aimed to explore the differentially expressed genes (DEGs) specific to cell types in sepsis and investigate the role of resistin in the survival of sepsis patients through Mendelian randomization (MR) analyses. We used single-cell and bulk transcriptome data to identify cell type-specific DEGs between sepsis and healthy controls. MR analyses were then conducted to investigate the causal relationships between resistin (one of the identified DEGs) levels and the survival of sepsis patients. Additionally, we utilized meQTL (methylation quantitative trait loci) to identify cytosine-phosphate-guanine (CpG) sites that may directly affect sepsis. We identified 560 cell type-specific DEGs between sepsis and healthy controls. Notably, we observed the upregulation of resistin levels in macrophages during sepsis. In bulk transcriptome, RETN is also upregulated in sepsis samples compared with healthy controls. MR analyses revealed a negative association existed between the expression of resistin, at both gene and protein levels, and the mortality or severity of sepsis patients in ICU. Moreover, there were no associations observed between resistin levels and death or organ failure due to other causes. We also identified three methylation CpG sites, located in RETN or its promoter region-cg06633066, cg22322184, and cg02346997-that directly affected both resistin protein levels and sepsis death in the ICU. Our findings suggest that resistin may provide feasible protection for sepsis patients, particularly those with severe cases, without serious side effects. Therefore, resistin could be a potential drug candidate for sepsis treatment. Additionally, we identified two CpG sites, cg06633066 and cg22322184, that were associated with RETN protein levels and sepsis death, providing novel insights into the underlying mechanisms of sepsis.
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Affiliation(s)
| | | | | | | | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; (H.C.); (H.L.); (T.T.); (S.L.)
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5
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Han R, Huang J, Zeng N, Xie F, Wang Y, Wang Y, Fan J. Systematic analyses of GWAS summary statistics from UK Biobank identified novel susceptibility loci and genes for upper gastrointestinal diseases. J Hum Genet 2023; 68:599-606. [PMID: 37198407 DOI: 10.1038/s10038-023-01151-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/24/2023] [Accepted: 04/10/2023] [Indexed: 05/19/2023]
Abstract
In recent decades, upper gastrointestinal (GI) diseases have been highly prevalent worldwide. Although genome-wide association studies (GWASs) have identified thousands of susceptibility loci, only a few of them were conducted for chronic upper GI disorders, and most of them were underpowered and with small sample sizes. Additionally, for the known loci, only a tiny fraction of heritability can be explained and the underlying mechanisms and related genes remain unclear. In this study, we conducted a multi-trait analysis by the MTAG software and a two-stage transcriptome-wide association study (TWAS) with UTMOST and FUSION for seven upper GI diseases (oesophagitis, gastro-oesophageal reflux disease, other diseases of oesophagus, gastric ulcer, duodenal ulcer, gastritis and duodenitis and other diseases of stomach and duodenum) based on summary GWAS statistics from UK Biobank. In the MTAG analysis, we identified 7 loci associated with these upper GI diseases, including 3 novel ones at 4p12 (rs10029980), 12q13.13 (rs4759317) and 18p11.32 (rs4797954). In the TWAS analysis, we revealed 5 susceptibility genes in known loci and identified 12 novel potential susceptibility genes, including HOXC9 at 12q13.13. Further functional annotations and colocalization analysis indicated that rs4759317 (A>G) driven the association for GWAS signals and expression quantitative trait loci (eQTL) simultaneously at 12q13.13. The identified variant acted by decreasing the expression of HOXC9 to affect the risk of gastro-oesophageal reflux disease. This study provided insights into the genetic nature of upper GI diseases.
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Affiliation(s)
- Renfang Han
- Health Management Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Junxiang Huang
- Health Management Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Nimei Zeng
- Health Management Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Fangfei Xie
- Health Management Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yi Wang
- Health Management Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yun Wang
- Health Management Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| | - Jingyi Fan
- Health Management Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
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6
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Role of cellular senescence in inflammatory lung diseases. Cytokine Growth Factor Rev 2023; 70:26-40. [PMID: 36797117 DOI: 10.1016/j.cytogfr.2023.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
Cellular senescence, a characteristic sign of aging, classically refers to permanent cell proliferation arrest and is a vital contributor to the pathogenesis of cancer and age-related illnesses. A lot of imperative scientific research has shown that senescent cell aggregation and the release of senescence-associated secretory phenotype (SASP) components can cause lung inflammatory diseases as well. In this study, the most recent scientific progress on cellular senescence and phenotypes was reviewed, including their impact on lung inflammation and the contributions of these findings to understanding the underlying mechanisms and clinical relevance of cell and developmental biology. Within a dozen pro-senescent stimuli, the irreparable DNA damage, oxidative stress, and telomere erosion are all crucial in the long-term accumulation of senescent cells, resulting in sustained inflammatory stress activation in the respiratory system. An emerging role for cellular senescence in inflammatory lung diseases was proposed in this review, followed by the identification of the main ambiguities, thus further understanding this event and the potential to control cellular senescence and pro-inflammatory response activation. In addition, novel therapeutic strategies for the modulation of cellular senescence that might help to attenuate inflammatory lung conditions and improve disease outcomes were also presented in this research.
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7
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He BF, Wu YX, Hu WP, Hua JL, Han Y, Zhang J. ROS induced the Rab26 promoter hypermethylation to promote cigarette smoking-induced airway epithelial inflammation of COPD through activation of MAPK signaling. Free Radic Biol Med 2023; 195:359-370. [PMID: 36610560 DOI: 10.1016/j.freeradbiomed.2023.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Cigarette smoking (CS) exposure-induced airway inflammatory responses drive the occurrence and development of emphysema and chronic obstructive pulmonary disease (COPD). However, its precise mechanisms have not been fully elucidated. In this study, we explore the role of Rab26 in CS exposure modulating the inflammatory response of airway epithelium and the novel mechanism of CS exposure regulation Rab26. These data showed that CS exposure and H2O2 (a type of ROS) suppressed the expression of Rab26 and increased the expression of DNMT3b in vivo and in vitro. GEO data analysis found the level of Rab26 was decreased in the lung tissue of COPD patients. CSE-induced ROS promoted DNA methylation of the Rab26 promoter and inhibited its promoter activity by elevating the DNMT3b level. Antioxidants N-Acetyl-l-cysteine (NAC), 5-Aza-2'-deoxycytidine (5-AZA) (DNA methylation inhibitor) and DNMT3B siRNA alleviated CSE's inhibitory effect on Rab26 expression in vitro. Importantly, NAC alleviated the improved expression of Rab26 and reduced DNMT3B expression, in the airway of smoking exposure as well as attenuated the inflammatory response in vivo. Overexpression of Rab26 attenuated CSE-induced production of inflammatory mediators through part inactivation of p38 and JNK MAPK. On the contrary, silencing Rab26 enhanced p38 and JNK activation and aggravated inflammatory response. These findings suggest that ROS-mediated Rab26 promoter hypermethylation is a critical step in cigarette smoking-induced airway epithelial inflammatory response. Restoring Rab26 in the airway epithelium might be a potential strategy for treating airway inflammation and COPD.
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Affiliation(s)
- Bin-Feng He
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yi-Xing Wu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei-Ping Hu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jian-Lan Hua
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yaoping Han
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Gunasekara CJ, MacKay H, Scott CA, Li S, Laritsky E, Baker MS, Grimm SL, Jun G, Li Y, Chen R, Wiemels JL, Coarfa C, Waterland RA. Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control. Genome Biol 2023; 24:2. [PMID: 36631879 PMCID: PMC9835319 DOI: 10.1186/s13059-022-02827-3] [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: 08/04/2022] [Accepted: 12/01/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition. RESULTS We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of 188 donors in the NIH Gene-Tissue Expression (GTEx) program. At CoRSIVs, DNA methylation in peripheral blood correlates with methylation and gene expression in internal organs. We also discover unprecedented mQTL at these regions. Genetic influences on CoRSIV methylation are extremely strong (median R2=0.76), cumulatively comprising over 70-fold more human mQTL than detected in the most powerful previous study. Moreover, mQTL beta coefficients at CoRSIVs are highly skewed (i.e., the major allele predicts higher methylation). Both surprising findings are independently validated in a cohort of 47 non-GTEx individuals. Genomic regions flanking CoRSIVs show long-range enrichments for LINE-1 and LTR transposable elements; the skewed beta coefficients may therefore reflect evolutionary selection of genetic variants that promote their methylation and silencing. Analyses of GWAS summary statistics show that mQTL polymorphisms at CoRSIVs are associated with metabolic and other classes of disease. CONCLUSIONS A focus on systemic interindividual epigenetic variants, clearly enhanced in mQTL content, should likewise benefit studies attempting to link human epigenetic variation to the risk of disease.
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Affiliation(s)
- Chathura J. Gunasekara
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Harry MacKay
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - C. Anthony Scott
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Shaobo Li
- grid.42505.360000 0001 2156 6853Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Eleonora Laritsky
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Maria S. Baker
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Sandra L. Grimm
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Goo Jun
- grid.267308.80000 0000 9206 2401Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Yumei Li
- grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Rui Chen
- grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Joseph L. Wiemels
- grid.42505.360000 0001 2156 6853Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Cristian Coarfa
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX USA
| | - Robert A. Waterland
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
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Oliva M, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS, Pierce BL. DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. Nat Genet 2023; 55:112-122. [PMID: 36510025 PMCID: PMC10249665 DOI: 10.1038/s41588-022-01248-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/26/2022] [Indexed: 12/14/2022]
Abstract
Studies of DNA methylation (DNAm) in solid human tissues are relatively scarce; tissue-specific characterization of DNAm is needed to understand its role in gene regulation and its relevance to complex traits. We generated array-based DNAm profiles for 987 human samples from the Genotype-Tissue Expression (GTEx) project, representing 9 tissue types and 424 subjects. We characterized methylome and transcriptome correlations (eQTMs), genetic regulation in cis (mQTLs and eQTLs) across tissues and e/mQTLs links to complex traits. We identified mQTLs for 286,152 CpG sites, many of which (>5%) show tissue specificity, and mQTL colocalizations with 2,254 distinct GWAS hits across 83 traits. For 91% of these loci, a candidate gene link was identified by integration of functional maps, including eQTMs, and/or eQTL colocalization, but only 33% of loci involved an eQTL and mQTL present in the same tissue type. With this DNAm-focused integrative analysis, we contribute to the understanding of molecular regulatory mechanisms in human tissues and their impact on complex traits.
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Affiliation(s)
- Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yihao Lu
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Meytal Chernoff
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA.
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10
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Borie R, Cardwell J, Konigsberg IR, Moore CM, Zhang W, Sasse SK, Gally F, Dobrinskikh E, Walts A, Powers J, Brancato J, Rojas M, Wolters PJ, Brown KK, Blackwell TS, Nakanishi T, Richards JB, Gerber AN, Fingerlin TE, Sachs N, Pulit SL, Zappala Z, Schwartz DA, Yang IV. Colocalization of Gene Expression and DNA Methylation with Genetic Risk Variants Supports Functional Roles of MUC5B and DSP in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2022; 206:1259-1270. [PMID: 35816432 PMCID: PMC9746850 DOI: 10.1164/rccm.202110-2308oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Common genetic variants have been associated with idiopathic pulmonary fibrosis (IPF). Objectives: To determine functional relevance of the 10 IPF-associated common genetic variants we previously identified. Methods: We performed expression quantitative trait loci (eQTL) and methylation quantitative trait loci (mQTL) mapping, followed by co-localization of eQTL and mQTL with genetic association signals and functional validation by luciferase reporter assays. Illumina multi-ethnic genotyping arrays, mRNA sequencing, and Illumina 850k methylation arrays were performed on lung tissue of participants with IPF (234 RNA and 345 DNA samples) and non-diseased controls (188 RNA and 202 DNA samples). Measurements and Main Results: Focusing on genetic variants within 10 IPF-associated genetic loci, we identified 27 eQTLs in controls and 24 eQTLs in cases (false-discovery-rate-adjusted P < 0.05). Among these signals, we identified associations of lead variants rs35705950 with expression of MUC5B and rs2076295 with expression of DSP in both cases and controls. mQTL analysis identified CpGs in gene bodies of MUC5B (cg17589883) and DSP (cg08964675) associated with the lead variants in these two loci. We also demonstrated strong co-localization of eQTL/mQTL and genetic signal in MUC5B (rs35705950) and DSP (rs2076295). Functional validation of the mQTL in MUC5B using luciferase reporter assays demonstrates that the CpG resides within a putative internal repressor element. Conclusions: We have established a relationship of the common IPF genetic risk variants rs35705950 and rs2076295 with respective changes in MUC5B and DSP expression and methylation. These results provide additional evidence that both MUC5B and DSP are involved in the etiology of IPF.
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Affiliation(s)
| | | | | | - Camille M. Moore
- Department of Biostatistics and Bioinformatics and
- Center for Genes, Environment, and Health
| | | | | | - Fabienne Gally
- Department of Medicine
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | | | | | | | | | - Mauricio Rojas
- Department of Internal Medicine, Ohio State College of Medicine, The Ohio State University, Columbus, Ohio
| | - Paul J. Wolters
- Department of Medicine, University of California, San Francisco, California
| | | | - Timothy S. Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tomoko Nakanishi
- Department of Human Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Canada
| | - J. Brent Richards
- Department of Human Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Canada
| | - Anthony N. Gerber
- Department of Medicine
- Department of Medicine, and
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | - Tasha E. Fingerlin
- Department of Biostatistics and Bioinformatics and
- Center for Genes, Environment, and Health
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | - Norman Sachs
- Cell Biology, Vertex Pharmaceuticals, San Diego, California; and
| | - Sara L. Pulit
- Computational Genomics, Vertex Pharmaceuticals, Boston, Massachusetts
| | - Zachary Zappala
- Computational Genomics, Vertex Pharmaceuticals, Boston, Massachusetts
| | - David A. Schwartz
- Department of Medicine
- Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus; Aurora, Colorado
| | - Ivana V. Yang
- Department of Medicine
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado
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11
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Feng Y, Liu T, Xu S, Ren Y, Ge Y, Yin L, Pu Y, Liang G. The role of N6-methyladenosine methylation in environmental exposure-induced health damage. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69153-69175. [PMID: 35951238 DOI: 10.1007/s11356-022-22093-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
The health risks caused by environmental pollution have long been of substantial concern. With the development of epigenetics, a large number of studies have demonstrated that N6-methyladenosine (m6A) modification is involved in the regulation of various important life activities associated with various diseases. Recent studies have revealed that m6A plays a key role in health damage caused by environmental exposure by regulating post-transcriptional gene expression. Therefore, our study outlined the effects of environmental pollutant exposure on m6A methylation and its regulator levels. Moreover, we found that m6A methylation modifications were involved in the development of various health damages by regulating important life activities in vivo, such as reactive oxygen species imbalance, apoptosis, epithelial-mesenchymal transition (EMT), and inflammatory processes. More importantly, we delved into the regulatory mechanisms of m6A methylation dysregulation in environmental pollution-induced diseases. Finally, by examining the published literature, we found that methyltransferase-like protein 3 (METTL3) and fat mass- and obesity-associated protein (FTO) were potentially used as biomarkers of health damage induced by particulate matter exposure and heavy metal exposure, respectively. The current studies on regulators of METTL3 and FTO were more promising to bring new perspectives for the treatment of environmental health-related diseases.
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Affiliation(s)
- Yanlu Feng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Tong Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Siyi Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yiyi Ren
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yiling Ge
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China.
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12
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Yuan J, Wang T, Wang L, Li P, Shen H, Mo Y, Zhang Q, Ni C. Transcriptome-wide association study identifies PSMB9 as a susceptibility gene for coal workers' pneumoconiosis. ENVIRONMENTAL TOXICOLOGY 2022; 37:2103-2114. [PMID: 35506645 DOI: 10.1002/tox.23554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 06/14/2023]
Abstract
Coal workers' pneumoconiosis (CWP) is a type of typical occupational lung disease caused by prolonged inhalation of coal mine dust. The individuals' different genetic background may underlie their different susceptibility to develop pneumoconiosis, even under the same exposure level. This study aimed to identify susceptibility genes associated with CWP. Based on our previous genome-wide association study (GWAS, 202 CWP cases vs. 198 controls) and gene expression data obtained by analyzing human lungs and whole blood from the Genotype-Tissue Expression (GTEx) Portal, a transcriptome-wide association study (TWAS) was applied to identify CWP risk-related genes. Luciferase report gene assay, qRT-PCR, Western blot, immunofluorescence assay, and TUNEL assay were conducted to explore the potential role of the candidate gene in CWP. Proteasome 20S subunit beta 9 (PSMB9) was identified as a strong risk-related gene of CWP in both lungs and whole blood (Lungs: PTWAS = 4.22 × 10-4 ; Whole blood: PTWAS = 2.11 × 10-4 ). Single nucleotide polymorphisms (SNPs) rs2071480 and rs1351383, which locate in the promoter region and the first intron of the PSMB9 gene, were in high linkage disequilibrium (LD, r2 = 0.98) with the best GWAS SNP rs4713600 (G>T, OR = 0.55, 95% CI: 0.42-0.74, P = 6.86 × 10-5 ). Both rs2071480 and rs1351383 significantly enhanced the transcriptional activity of PSMB9. Functional experiments revealed that silica exposure remarkably reduced the PSMB9 expression and caused cell apoptosis, while overexpression of PSMB9 markedly abolished silica-induced cell apoptosis. We here identified PSMB9 as a novel susceptibility gene for CWP and provided important insights into the further exploration of the CWP pathogenesis.
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Affiliation(s)
- Jiali Yuan
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Pathology, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Lijuan Wang
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ping Li
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yiqun Mo
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, Louisville, Kentucky, USA
| | - Qunwei Zhang
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, Louisville, Kentucky, USA
| | - Chunhui Ni
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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13
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Association of childhood BMI trajectory with post-adolescent and adult lung function is mediated by pre-adolescent DNA methylation. Respir Res 2022; 23:194. [PMID: 35906571 PMCID: PMC9335987 DOI: 10.1186/s12931-022-02089-4] [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: 12/09/2021] [Accepted: 06/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background Body mass index (BMI) has been shown to be associated with lung function. Recent findings showed that DNA methylation (DNAm) variation is likely to be a consequence of changes in BMI. However, whether DNAm mediates the association of BMI with lung function is unknown. We examined the mediating role of DNAm on the association of pre-adolescent BMI trajectories with post-adolescent and adulthood lung function (forced expiratory volume (FEV1), forced vital capacity (FVC), and FEV1/FVC). Methods Analyses were undertaken in the Isle of Wight birth cohort (IOWBC). Group-based trajectory modelling was applied to infer latent BMI trajectories from age 1 to 10 years. An R package, ttscreening, was applied to identify CpGs at 10 years potentially associated with BMI trajectories for each sex. Linear regressions were implemented to further screen CpGs for their association with lung function at 18 years. Path analysis, stratified by sex, was applied to each screened CpG to assess its role of mediation. Internal validation was applied to further examine the mediation consistency of the detected CpGs based on lung function at 26 years. Mendelian randomization (MR-base) was used to test possible causal effects of the identified CpGs. Results Two BMI trajectories (high vs. low) were identified. Of the 442,475 CpG sites, 18 CpGs in males and 33 in females passed screening. Eight CpGs in males and 16 CpGs in females (none overlapping) were identified as mediators. For subjects with high BMI trajectory, high DNAm at all CpGs in males were associated with decreased lung function, while 8 CpGs in females were associated with increased lung function at 18 years. At 26 years, 6 CpGs in males and 14 CpGs in females showed the same direction of indirect effects as those at 18 years. DNAm at CpGs cg19088553 (GRIK2) and cg00612625 (HPSE2) showed a potential causal effect on FEV1. Conclusions The effects of BMI trajectory in early childhood on post-adolescence lung function were likely to be mediated by pre-adolescence DNAm in both males and females, but such mediation effects were likely to diminish over time. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02089-4.
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14
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Kaner RJ. Premature Aging of the Airway Epithelium in Chronic Obstructive Pulmonary Disease in People Living with HIV. Am J Respir Crit Care Med 2022; 206:131-132. [PMID: 35579631 PMCID: PMC9887417 DOI: 10.1164/rccm.202204-0743ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Robert J. Kaner
- Department of Medicine,Department of Genetic MedicineWeill Cornell MedicineNew York, New York
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15
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Lyu C, Huang M, Liu N, Chen Z, Lupo PJ, Tycko B, Witte JS, Hobbs CA, Li M. Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci. Bioinformatics 2022; 38:3853-3862. [PMID: 35781319 PMCID: PMC9364381 DOI: 10.1093/bioinformatics/btac443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION CpG sites within the same genomic region often share similar methylation patterns and tend to be co-regulated by multiple genetic variants that may interact with one another. RESULTS We propose a multi-trait methylation random field (multi-MRF) method to evaluate the joint association between a set of CpG sites and a set of genetic variants. The proposed method has several advantages. First, it is a multi-trait method that allows flexible correlation structures between neighboring CpG sites (e.g. distance-based correlation). Second, it is also a multi-locus method that integrates the effect of multiple common and rare genetic variants. Third, it models the methylation traits with a beta distribution to characterize their bimodal and interval properties. Through simulations, we demonstrated that the proposed method had improved power over some existing methods under various disease scenarios. We further illustrated the proposed method via an application to a study of congenital heart defects (CHDs) with 83 cardiac tissue samples. Our results suggested that gene BACE2, a methylation quantitative trait locus (QTL) candidate, colocalized with expression QTLs in artery tibial and harbored genetic variants with nominal significant associations in two genome-wide association studies of CHD. AVAILABILITY AND IMPLEMENTATION https://github.com/chenlyu2656/Multi-MRF. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chen Lyu
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN 47405, USA,Department of Population Health, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manyan Huang
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Nianjun Liu
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Zhongxue Chen
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Philip J Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA,Department of Biomedical Data Sciences, Stanford University, Stanford, CA 94305, USA
| | - Charlotte A Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ming Li
- To whom correspondence should be addressed.
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16
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Christenson SA, Smith BM, Bafadhel M, Putcha N. Chronic obstructive pulmonary disease. Lancet 2022; 399:2227-2242. [PMID: 35533707 DOI: 10.1016/s0140-6736(22)00470-6] [Citation(s) in RCA: 190] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/16/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a major cause of morbidity, mortality, and health-care use worldwide. COPD is caused by exposure to inhaled noxious particles, notably tobacco smoke and pollutants. However, the broad range of factors that increase the risk of development and progression of COPD throughout the life course are increasingly being recognised. Innovations in omics and imaging techniques have provided greater insight into disease pathobiology, which might result in advances in COPD prevention, diagnosis, and treatment. Although few novel treatments have been approved for COPD in the past 5 years, advances have been made in targeting existing therapies to specific subpopulations using new biomarker-based strategies. Additionally, COVID-19 has undeniably affected individuals with COPD, who are not only at higher risk for severe disease manifestations than healthy individuals but also negatively affected by interruptions in health-care delivery and social isolation. This Seminar reviews COPD with an emphasis on recent advances in epidemiology, pathophysiology, imaging, diagnosis, and treatment.
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Affiliation(s)
- Stephanie A Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin M Smith
- Department of Medicine, Columbia University Medical Center, New York, NY, USA; Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Mona Bafadhel
- School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Department of Respiratory Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nirupama Putcha
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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17
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Cho MH, Hobbs BD, Silverman EK. Genetics of chronic obstructive pulmonary disease: understanding the pathobiology and heterogeneity of a complex disorder. THE LANCET. RESPIRATORY MEDICINE 2022; 10:485-496. [PMID: 35427534 DOI: 10.1016/s2213-2600(21)00510-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/20/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a deadly and highly morbid disease. Susceptibility to and heterogeneity of COPD are incompletely explained by environmental factors such as cigarette smoking. Family-based and population-based studies have shown that a substantial proportion of COPD risk is related to genetic variation. Genetic association studies have identified hundreds of genetic variants that affect risk for COPD, decreased lung function, and other COPD-related traits. These genetic variants are associated with other pulmonary and non-pulmonary traits, demonstrate a genetic basis for at least part of COPD heterogeneity, have a substantial effect on COPD risk in aggregate, implicate early-life events in COPD pathogenesis, and often involve genes not previously suspected to have a role in COPD. Additional progress will require larger genetic studies with more ancestral diversity, improved profiling of rare variants, and better statistical methods. Through integration of genetic data with other omics data and comprehensive COPD phenotypes, as well as functional description of causal mechanisms for genetic risk variants, COPD genetics will continue to inform novel approaches to understanding the pathobiology of COPD and developing new strategies for management and treatment.
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Affiliation(s)
- Michael H Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
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18
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Eriksson Ström J, Kebede Merid S, Pourazar J, Blomberg A, Lindberg A, Ringh MV, Hagemann-Jensen M, Ekström TJ, Behndig AF, Melén E. COPD is Associated with Epigenome-wide Differential Methylation in BAL Lung Cells. Am J Respir Cell Mol Biol 2022; 66:638-647. [PMID: 35286818 PMCID: PMC9163645 DOI: 10.1165/rcmb.2021-0403oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
DNA methylation patterns in chronic pulmonary obstructive disease (COPD) might offer new insights into disease pathogenesis. To assess methylation profiles in the main COPD target organ, we performed an epigenome-wide association study on bronchoalveolar lavage (BAL) cells. Bronchoscopies were performed in 18 COPD subjects and 15 controls (ex- and current smokers). DNA methylation was measured with Illumina MethylationEPIC BeadChip covering >850,000 CpGs. Differentially methylated positions (DMPs) were examined for 1) enrichment in pathways and functional gene relationships using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology; 2) accelerated aging using Horvath's epigenetic clock; 3) correlation with gene expression; and 4) co-localization with genetic variation. We found 1,155 Bonferroni significant (P < 6.74 × 10-8) DMPs associated with COPD, many with large effect sizes. Functional analysis identified biologically plausible pathways and gene relationships, including enrichment for transcription factor activity. Strong correlation was found between COPD and chronological age, but not with accelerated epigenetic aging. For 79 unique DMPs, DNA methylation correlated significantly with gene expression in BAL cells. Thirty-nine percent of DMPs were co-localized with COPD-associated SNPs. To the best of our knowledge, this is the first EWAS of COPD on BAL cells, and our analyses revealed many differential methylation sites. Integration with mRNA data showed a strong functional readout for relevant genes, identifying sites where DNA methylation might directly impact expression. Almost half of DMPs were co-located with SNPs identified in previous GWAS of COPD, suggesting joint genetic and epigenetic pathways related to disease.
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Affiliation(s)
- Jonas Eriksson Ström
- Department of Public Health and Clinical Medicine, Division of Medicine/Respiratory Medicine, Umeå University, Umeå, Sweden;
| | - Simon Kebede Merid
- Karolinska Institutet, 27106, Institute of Environmental Medicine, Stockholm, Sweden
| | - Jamshid Pourazar
- Umeå Universitet Medicinska fakulteten, 59588, Dept. of Public Health and Clinical Medicine, Umeå, Sweden
| | - Anders Blomberg
- Umea University, 8075, Dept. of Public Health and Clinical Medicine, Umea, Sweden
| | - Anne Lindberg
- Umeå Universitet, 8075, Department of Public Health and Clinical Medicine, Section of Medicine, Umea, Sweden
| | - Mikael V Ringh
- Karolinska Institutet, 27106, Department of Clinical Neuroscience and Center for Molecular Medicine, Stockholm, Sweden
| | | | - Tomas J Ekström
- Karolinska Institutet, 27106, Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Stockholm, Sweden
| | - Annelie F Behndig
- Department of Public Health and Clinical Medicine, Division of Medicine/Respiratory Medicine, Umeå University, Umeå, Sweden
| | - Erik Melén
- Karolinska Institutet Department of Clinical Science and Education Sodersjukhuset, 411435, Karolinska Institutet, Stockholm, Sweden
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19
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Sauler M, McDonough JE, Adams TS, Kothapalli N, Barnthaler T, Werder RB, Schupp JC, Nouws J, Robertson MJ, Coarfa C, Yang T, Chioccioli M, Omote N, Cosme C, Poli S, Ayaub EA, Chu SG, Jensen KH, Gomez JL, Britto CJ, Raredon MSB, Niklason LE, Wilson AA, Timshel PN, Kaminski N, Rosas IO. Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nat Commun 2022; 13:494. [PMID: 35078977 PMCID: PMC8789871 DOI: 10.1038/s41467-022-28062-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 12/14/2021] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide, however our understanding of cell specific mechanisms underlying COPD pathobiology remains incomplete. Here, we analyze single-cell RNA sequencing profiles of explanted lung tissue from subjects with advanced COPD or control lungs, and we validate findings using single-cell RNA sequencing of lungs from mice exposed to 10 months of cigarette smoke, RNA sequencing of isolated human alveolar epithelial cells, functional in vitro models, and in situ hybridization and immunostaining of human lung tissue samples. We identify a subpopulation of alveolar epithelial type II cells with transcriptional evidence for aberrant cellular metabolism and reduced cellular stress tolerance in COPD. Using transcriptomic network analyses, we predict capillary endothelial cells are inflamed in COPD, particularly through increased CXCL-motif chemokine signaling. Finally, we detect a high-metallothionein expressing macrophage subpopulation enriched in advanced COPD. Collectively, these findings highlight cell-specific mechanisms involved in the pathobiology of advanced COPD.
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Affiliation(s)
- Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
| | - John E McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
| | - Taylor S Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Neeharika Kothapalli
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Thomas Barnthaler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Jonas C Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Jessica Nouws
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Matthew J Robertson
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Tao Yang
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Maurizio Chioccioli
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Norihito Omote
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Carlos Cosme
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Department of Internal Medicine, Mount Sinai Medical Center, Miami, FL, USA
| | - Ehab A Ayaub
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah G Chu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jose L Gomez
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Clemente J Britto
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Micha Sam B Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | | | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ivan O Rosas
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
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20
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Scherer M, Gasparoni G, Rahmouni S, Shashkova T, Arnoux M, Louis E, Nostaeva A, Avalos D, Dermitzakis ET, Aulchenko YS, Lengauer T, Lyons PA, Georges M, Walter J. Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR. Epigenetics Chromatin 2021; 14:44. [PMID: 34530905 PMCID: PMC8444396 DOI: 10.1186/s13072-021-00415-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/02/2021] [Indexed: 12/18/2022] Open
Abstract
Background Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for determining methylation quantitative trait loci (methQTL), but also for discriminating general from cell type-specific effects. Results Here, we present a two-step computational framework MAGAR (https://bioconductor.org/packages/MAGAR), which fully supports the identification of methQTLs from matched genotyping and DNA methylation data, and additionally allows for illuminating cell type-specific methQTL effects. In a pilot analysis, we apply MAGAR on data in four tissues (ileum, rectum, T cells, B cells) from healthy individuals and demonstrate the discrimination of common from cell type-specific methQTLs. We experimentally validate both types of methQTLs in an independent data set comprising additional cell types and tissues. Finally, we validate selected methQTLs located in the PON1, ZNF155, and NRG2 genes by ultra-deep local sequencing. In line with previous reports, we find cell type-specific methQTLs to be preferentially located in enhancer elements. Conclusions Our analysis demonstrates that a systematic analysis of methQTLs provides important new insights on the influences of genetic variants to cell type-specific epigenomic variation. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00415-6.
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Affiliation(s)
- Michael Scherer
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.,Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Saarbrücken, Germany.,Department of Bioinformatics and Genomics, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Gilles Gasparoni
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Souad Rahmouni
- Unit of Animal Genomics, GIGA-Institute & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Tatiana Shashkova
- Kurchatov Genomics Center of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Research and Training Center on Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Marion Arnoux
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Edouard Louis
- Department of Gastroenterology, Liège University Hospital, CHU Liège, Liège, Belgium
| | | | - Diana Avalos
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Yurii S Aulchenko
- Kurchatov Genomics Center of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,Moscow Institute of Physics and Technology (State University), Moscow, Russia.,PolyKnomics BV, 's-Hertogenbosch, The Netherlands
| | - Thomas Lengauer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Paul A Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Michel Georges
- Unit of Animal Genomics, GIGA-Institute & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.
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21
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Li J, Tang F, Si S, Wang B, Xue F. Integration analysis of GWAS and expression quantitative trait loci to identify candidate genes and pathways for clozapine-related neutropaenia. Br J Clin Pharmacol 2021; 88:1904-1912. [PMID: 34409637 DOI: 10.1111/bcp.15043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022] Open
Abstract
AIMS Little is known about the genetic basis of clozapine-related neutropaenia. This study aims to explore candidate genes and pathways involved in clozapine-related neutropaenia. METHODS This study conducted a two-stage integrative analysis of the summary statistics from the genome-wide association study (GWAS, n = 552) of the lowest absolute neutrophil count (ANC) during clozapine treatment and the summary data of the expressed quantitative trait locus (eQTL). First, we use the probabilistic Mendelian randomization (PMR-Egger) to identify genes whose expression is causally related to ANC, and then use Bayesian co-localization analysis to investigate whether there are shared causal variants between them [posterior probability for hypotheses 4 (PP.H4) > 0.80]. Finally, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted to explore the pathways that may be associated with ANC during clozapine treatment. RESULTS PMR-Egger analysis identified 146 genes that may be causally associated with ANC after Bonferroni correction (P-value < 3.25e-6). Bayesian co-localization analysis identified six further genes whose gene expression shared common variants with ANC, including NT5E (PP.H4 = 0.96), GLDC (PP.H4 = 0.82), NUDT17 (PP.H4 = 0.88), MSH4 (PP.H4 = 0.88), PTER (PP.H4 = 0.89) and SERPINB6 (PP.H4 = 0.83). Enrichment analysis identified 52 GO terms and seven pathways associated with ANC, such as NAD metabolic process, drug catabolic process and glyoxylate and dicarboxylate metabolism. CONCLUSION This study identified multiple candidate genes and pathways that may be involved in clozapine-related neutropaenia, providing novel clues for the mechanism of clozapine-related neutropaenia.
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Affiliation(s)
- Jiqing Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,Healthcare Big Data Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Fang Tang
- Center for Big Data Research in Health and Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China.,Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shucheng Si
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,Healthcare Big Data Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Bojie Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,Healthcare Big Data Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,Healthcare Big Data Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
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22
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Huo X, Jin S, Wang Y, Ma L. DNA methylation in chronic obstructive pulmonary disease. Epigenomics 2021; 13:1145-1155. [PMID: 34142873 DOI: 10.2217/epi-2021-0111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), a complex disease with polygenetic tendency, is one of the most important health problems in the world. Recently, in the study of the pathogenesis of the COPD, epigenetic changes caused by environmental factors, such as DNA methylation, started to attract more attention than genetic factors. In this review, we discuss the main features of DNA methylation, such as DNA methyltransferases and the methylation sites that modulate the DNA methylation level, and their roles in COPD progression. Finally, to promote new ideas for the prevention and treatment of COPD, we focus on the potential of DNA methylation as a COPD therapeutic target.
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Affiliation(s)
- XinXin Huo
- School of Public Health, Lanzhou University, Lanzhou, China
| | - SiHui Jin
- School of Public Health, Lanzhou University, Lanzhou, China
| | - YiGe Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Li Ma
- School of Public Health, Lanzhou University, Lanzhou, China
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23
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Yang Y, Yuan L, Yang M, Du X, Qin L, Wang L, Zhou K, Wu M, He R, Feng J, Xiang Y, Qu X, Liu H, Qin X, Liu C. Aberrant Methylation of Aging-Related Genes in Asthma. Front Mol Biosci 2021; 8:655285. [PMID: 34136532 PMCID: PMC8203316 DOI: 10.3389/fmolb.2021.655285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Background: Asthma is a complex pulmonary inflammatory disease which is common among older adults. Aging-related alterations have also been found in structural cells and immune cells of asthma patients. Nonetheless, the underlying mechanism by which differenced aging-related gene contributes to asthma pathology remains unclear. Of note, DNA methylation (DNAm) has been proven to play a critical mechanism for age-related gene expression changes. However, the methylation changes of aging-related genes in asthma patients are still obscure. Methods: First, changes in DNAm and gene expression were detected with multiple targeted bisulfite enrichment sequencing (MethTarget) and qPCR in peripheral blood of 51 healthy controls (HCs) and 55 asthmatic patients. Second, the correlation between the DNAm levels of specific altered CpG sites and the pulmonary function indicators of asthma patients was evaluated. Last, the receiver operator characteristic (ROC) curve and principal component analysis (PCA) were used to identify the feasibility of the candidate CpG sites as biomarkers for asthma. Results: Compared with HCs, there was a differential mRNA expression for nine aging-related genes in peripheral blood of asthma patients. Besides, the methylation levels of the nine aging-related genes were also altered in asthma patients, and a total of 68 CpG sites were associated with the severity of asthma. Notably, 9 of the 68 CpG sites were significantly associated with pulmonary function parameters. Moreover, ROC curve and PCA analysis showed that the candidate differential methylation sites (DMSs) can be used as potential biomarkers for asthma. Conclusions: In summary, this study confirmed the differentially expressed mRNA and aberrant DNAm level of aging-related genes in asthma patients. DMSs are associated with the clinical evaluation indicators of asthma, which indicate the involvement of aging-related genes in the pathogenesis of asthma and provide some new possible biomarkers for asthma.
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Affiliation(s)
- Yu Yang
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China.,Basic and Clinical Research Laboratory of Major Respiratory Diseases, Central South University, Changsha, China
| | - Lin Yuan
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Ming Yang
- Centre for Asthma and Respiratory Disease, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle and Hunter Medical Research Institute, Callaghan, NSW, Australia
| | - Xizi Du
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Ling Qin
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Basic and Clinical Research Laboratory of Major Respiratory Diseases, Central South University, Changsha, China
| | - Leyuan Wang
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Kai Zhou
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Mengping Wu
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Ruoxi He
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Basic and Clinical Research Laboratory of Major Respiratory Diseases, Central South University, Changsha, China
| | - Juntao Feng
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Basic and Clinical Research Laboratory of Major Respiratory Diseases, Central South University, Changsha, China
| | - Yang Xiang
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Xiangping Qu
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Huijun Liu
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Xiaoqun Qin
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Chi Liu
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China.,Research Center of China-Africa Infectious Diseases, Xiangya School of Medicine Central South University, Changsha, China
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24
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Villicaña S, Bell JT. Genetic impacts on DNA methylation: research findings and future perspectives. Genome Biol 2021; 22:127. [PMID: 33931130 PMCID: PMC8086086 DOI: 10.1186/s13059-021-02347-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple recent studies highlight that genetic variants can have strong impacts on a significant proportion of the human DNA methylome. Methylation quantitative trait loci, or meQTLs, allow for the exploration of biological mechanisms that underlie complex human phenotypes, with potential insights for human disease onset and progression. In this review, we summarize recent milestones in characterizing the human genetic basis of DNA methylation variation over the last decade, including heritability findings and genome-wide identification of meQTLs. We also discuss challenges in this field and future areas of research geared to generate insights into molecular processes underlying human complex traits.
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Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
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25
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Zhu M, Fan J, Zhang C, Xu J, Yin R, Zhang E, Wang Y, Ji M, Sun Q, Dai J, Jin G, Chen L, Xu L, Hu Z, Ma H, Shen H. A cross-tissue transcriptome-wide association study identifies novel susceptibility genes for lung cancer in Chinese populations. Hum Mol Genet 2021; 30:1666-1676. [PMID: 33909040 DOI: 10.1093/hmg/ddab119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 01/04/2023] Open
Abstract
Although dozens of susceptibility loci have been identified for lung cancer in genome-wide association studies (GWASs), the susceptibility genes and underlying mechanisms remain unclear. In this study, we conducted a cross-tissue transcriptome-wide association study (TWAS) with UTMOST based on summary statistics from 13 327 lung cancer cases and 13 328 controls and the genetic-expression matrix over 44 human tissues in the Genotype-Tissue Expression (GTEx) project. After further evaluating the associations in each tissue, we revealed 6 susceptibility genes in known loci and identified 12 novel ones. Among those, five novel genes, including DCAF16 (Pcross-tissue = 2.57 × 10-5, PLung = 2.89 × 10-5), CBL (Pcross-tissue = 5.08 × 10-7, PLung = 1.82 × 10-4), ATR (Pcross-tissue = 1.45 × 10-5, PLung = 9.68 × 10-5), GYPE (Pcross-tissue = 1.45 × 10-5, PLung = 2.17 × 10-3) and PARD3 (Pcross-tissue = 5.79 × 10-6, PLung = 4.05 × 10-3), were significantly associated with the risk of lung cancer in both cross-tissue and lung tissue models. Further colocalization analysis indicated that rs7667864 (C > A) and rs2298650 (G > T) drove the GWAS association signals at 4p15.31-32 (OR = 1.09, 95%CI: 1.04-1.12, PGWAS = 5.54 × 10-5) and 11q23.3 (OR = 1.08, 95%CI: 1.04-1.13, PGWAS = 5.55 × 10-5), as well as the expression of DCAF16 (βGTEx = 0.24, PGTEx = 9.81 × 10-15; βNJLCC = 0.29, PNJLCC = 3.84 × 10-8) and CBL (βGTEx = -0.17, PGTEx = 2.82 × 10-8; βNJLCC = -0.32, PNJLCC = 2.61 × 10-7) in lung tissue. Functional annotations and phenotype assays supported the carcinogenic effect of these novel susceptibility genes in lung carcinogenesis.
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Affiliation(s)
- Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China
| | - Jingyi Fan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chang Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology, School of Public Health, Southeast University, Nanjing 210009, China
| | - Jing Xu
- Department of Thoracic Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yuzhuo Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China
| | - Mengmeng Ji
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qi Sun
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Liang Chen
- Department of Thoracic Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
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26
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Yao C, Joehanes R, Wilson R, Tanaka T, Ferrucci L, Kretschmer A, Prokisch H, Schramm K, Gieger C, Peters A, Waldenberger M, Marzi C, Herder C, Levy D. Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases. Clin Epigenetics 2021; 13:60. [PMID: 33752734 PMCID: PMC7986283 DOI: 10.1186/s13148-021-01041-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/28/2021] [Indexed: 11/28/2022] Open
Abstract
Background DNA methylation is a key epigenetic modification that can directly affect gene regulation. DNA methylation is highly influenced by environmental factors such as cigarette smoking, which is causally related to chronic obstructive pulmonary disease (COPD) and lung cancer. To date, there have been few large-scale, combined analyses of DNA methylation and gene expression and their interrelations with lung diseases. Results We performed an epigenome-wide association study of whole blood gene expression in ~ 6000 individuals from four cohorts. We discovered and replicated numerous CpGs associated with the expression of cis genes within 500 kb of each CpG, with 148 to 1,741 cis CpG-transcript pairs identified across cohorts. We found that the closer a CpG resided to a transcription start site, the larger its effect size, and that 36% of cis CpG-transcript pairs share the same causal genetic variant. Mendelian randomization analyses revealed that hypomethylation and lower expression of CHRNA5, which encodes a smoking-related nicotinic receptor, are causally linked to increased risk of COPD and lung cancer. This putatively causal relationship was further validated in lung tissue data. Conclusions Our results provide a large and comprehensive association study of whole blood DNA methylation with gene expression. Expression platform differences rather than population differences are critical to the replication of cis CpG-transcript pairs. The low reproducibility of trans CpG-transcript pairs suggests that DNA methylation regulates nearby rather than remote gene expression. The putatively causal roles of methylation and expression of CHRNA5 in relation to COPD and lung cancer provide evidence for a mechanistic link between patterns of smoking-related epigenetic variation and lung diseases, and highlight potential therapeutic targets for lung diseases and smoking cessation. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01041-5.
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Affiliation(s)
- Chen Yao
- The Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Roby Joehanes
- The Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Rory Wilson
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany
| | - Toshiko Tanaka
- Longitudinal Study Section, National Institute On Aging, Baltimore, MD, USA
| | - Luigi Ferrucci
- Longitudinal Study Section, National Institute On Aging, Baltimore, MD, USA
| | - Anja Kretschmer
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Technical University Munich, München, Germany.,Institute for Neurogenomics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Katharina Schramm
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, 81377, Munich, Germany.,Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University (LMU) Munich, 81377, Munich, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany
| | - Annette Peters
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Bavaria, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Carola Marzi
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, German Research Center for Environmental Health, Neuherberg, Germany
| | - 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 (DZD), Partner Düsseldorf, Germany.,Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Levy
- The Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA. .,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA.
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27
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Xia H, Wu Y, Zhao J, Li W, Lu L, Ma H, Cheng C, Sun J, Xiang Q, Bian T, Liu Q. The aberrant cross-talk of epithelium-macrophages via METTL3-regulated extracellular vesicle miR-93 in smoking-induced emphysema. Cell Biol Toxicol 2021; 38:167-183. [PMID: 33660100 DOI: 10.1007/s10565-021-09585-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/01/2021] [Indexed: 01/20/2023]
Abstract
Cigarette smoke (CS), a complex chemical indoor air pollutant, induces degradation of elastin, resulting in emphysema. Aberrant cross-talk between macrophages and bronchial epithelial cells is essential for the degradation of elastin that contributes to emphysema, in which extracellular vesicles (EVs) play a critical role. The formation of N6-methyladenosine (m6A) is a modification in miRNA processing, but its role in the development of emphysema remains unclear. Here, we established that production of excess mature microRNA-93 (miR-93) in bronchial epithelial cells via enhanced m6A modification was mediated by overexpressed methyltransferase-like 3 (METTL3) induced by CS. Mature miR-93 was transferred from bronchial epithelial cells into macrophages by EVs. In macrophages, miR-93 activated the JNK pathway by targeting dual-specificity phosphatase 2 (DUSP2), which elevated the levels of matrix metalloproteinase 9 (MMP9) and matrix metalloproteinase 12 (MMP12) and induced elastin degradation, leading to emphysema. These results demonstrate that METTL3-mediated formation of EV miR-93, facilitated by m6A, is implicated in the aberrant cross-talk of epithelium-macrophages, indicating that this process is involved in the smoking-related emphysema. EV miR-93 may use as a novel risk biomarker for CS-induced emphysema.
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Affiliation(s)
- Haibo Xia
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.,China International Cooperation Center for Environment and Human Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Yan Wu
- Department of Respiratory and Critical Care Medicine, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, Jiangsu, People's Republic of China
| | - Jing Zhao
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.,China International Cooperation Center for Environment and Human Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Wenqi Li
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.,China International Cooperation Center for Environment and Human Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Lu Lu
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.,China International Cooperation Center for Environment and Human Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Huimin Ma
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.,China International Cooperation Center for Environment and Human Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Cheng Cheng
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.,China International Cooperation Center for Environment and Human Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Jing Sun
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.,China International Cooperation Center for Environment and Human Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Quanyong Xiang
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Tao Bian
- Department of Respiratory and Critical Care Medicine, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, Jiangsu, People's Republic of China.
| | - Qizhan Liu
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China. .,China International Cooperation Center for Environment and Human Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, People's Republic of China.
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DNA methylation perturbations may link altered development and aging in the lung. Aging (Albany NY) 2021; 13:1742-1764. [PMID: 33468710 PMCID: PMC7880367 DOI: 10.18632/aging.202544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
Fetal perturbations in DNA methylation during lung development may reveal insights into the enduring impacts on adult lung health and disease during aging that have not been explored altogether before. We studied the association between genome-wide DNA-methylation and post-conception age in fetal-lung (n=78, 42 exposed to in-utero-smoke (IUS)) tissue and chronological age in adult-lung tissue (n=160, 114 with Chronic Obstructive Pulmonary Disease) using multi-variate linear regression models with covariate adjustment and tested for effect modification by phenotypes. Overlapping age-associations were evaluated for functional and tissue-specific enrichment using the Genotype-Tissue-Expression (GTEx) project. We identified 244 age-associated differentially methylated positions and 878 regions overlapping between fetal and adult-lung tissues. Hyper-methylated CpGs (96%) were enriched in transcription factor activity (FDR adjusted P=2x10-33) and implicated in developmental processes including embryonic organ morphogenesis, neurogenesis and growth delay. Hypo-methylated CpGs (2%) were enriched in oxido-reductase activity and VEGFA-VEGFR2 Signaling. Twenty-one age-by-sex and eleven age-by-pack-years interactions were statistically significant (FDR<0.05) in adult-lung tissue. DNA methylation in transcription factors during development in fetal lung recapitulates in adult-lung tissue with aging. These findings reveal molecular mechanisms and pathways that may link disrupted development in early-life and age-associated lung diseases.
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Abstract
Chronic obstructive pulmonary disease (COPD) has been traditionally considered a self-inflicted disease caused by tobacco smoking. Current available evidence, however, indicates that the pathogenesis of COPD needs to consider the dynamic and cumulative nature of a series of environment (including smoking plus other exposures)-host interactions that eventually determine lung development, maintenance, repair, and aging. By doing so, these factors modulate the trajectory of lung function of the individual through life and the odds of developing COPD through different routes, which likely represent different forms of the disease that require different preventive and therapeutic strategies.
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Affiliation(s)
- Alvar Agusti
- Respiratory Institute, Hospital Clinic, Villarroel 170, Barcelona 08036, Spain; University of Barcelona, Barcelona, Spain; Institut d'Investigacio August Pi I Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red (CIBER) Enfermedades Respiratorias, Instituto de Salud Carlos III, Spain.
| | - Rosa Faner
- Institut d'Investigacio August Pi I Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red (CIBER) Enfermedades Respiratorias, Instituto de Salud Carlos III, Spain
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30
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DNA Methylation in Chronic Obstructive Pulmonary Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:83-98. [PMID: 32949392 DOI: 10.1007/978-981-15-4494-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a lung disease affected by both genetic and environmental factors. Therefore, the role of epigenetics in the pathogenesis of COPD has attracted much attention. As one of the three epigenetic mechanisms, DNA methylation has been extensively studied in COPD. The present review aims at overviewing the effect of DNA methylation on etiology, pathogenesis, pathophysiological changes, and complications of COPD. The clarification of aberrant methylation of target genes, which play important roles in the initiation and progression of COPD, will provide new disease-specific biomarker and targets for early diagnosis and therapy.
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31
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Agustí A, Vogelmeier C, Faner R. COPD 2020: changes and challenges. Am J Physiol Lung Cell Mol Physiol 2020; 319:L879-L883. [PMID: 32964724 DOI: 10.1152/ajplung.00429.2020] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Alvar Agustí
- Respiratory Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain.,CIBER Enfermedades Respiratorias, Barcelona, Spain.,Chair of the Board of Directors, Global Initiative for Chronic Obstructive Lung Disease (GOLD), Fontana, Wisconsin
| | - Claus Vogelmeier
- Department of Medicine, Pulmonary and Critical Care Medicine, University of Marburg, Member of the German Center for Lung Research (DZL), Marburg, Germany.,Chair of the Science Committee, Global Initiative for Chronic Obstructive Lung Disease (GOLD), Fontana, Wisconsin
| | - Rosa Faner
- CIBER Enfermedades Respiratorias, Barcelona, Spain
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32
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Morrow JD, Make B, Regan E, Han M, Hersh CP, Tal-Singer R, Quackenbush J, Choi AMK, Silverman EK, DeMeo DL. DNA Methylation Is Predictive of Mortality in Current and Former Smokers. Am J Respir Crit Care Med 2020; 201:1099-1109. [PMID: 31995399 DOI: 10.1164/rccm.201902-0439oc] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rationale: Smoking results in at least a decade lower life expectancy. Mortality among current smokers is two to three times as high as never smokers. DNA methylation is an epigenetic modification of the human genome that has been associated with both cigarette smoking and mortality.Objectives: We sought to identify DNA methylation marks in blood that are predictive of mortality in a subset of the COPDGene (Genetic Epidemiology of COPD) study, representing 101 deaths among 667 current and former smokers.Methods: We assayed genome-wide DNA methylation in non-Hispanic white smokers with and without chronic obstructive pulmonary disease (COPD) using blood samples from the COPDGene enrollment visit. We tested whether DNA methylation was associated with mortality in models adjusted for COPD status, age, sex, current smoking status, and pack-years of cigarette smoking. Replication was performed in a subset of 231 individuals from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) study.Measurements and Main Results: We identified seven CpG sites associated with mortality (false discovery rate < 20%) that replicated in the ECLIPSE cohort (P < 0.05). None of these marks were associated with longitudinal lung function decline in survivors, smoking history, or current smoking status. However, differential methylation of two replicated PIK3CD (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta) sites were associated with lung function at enrollment (P < 0.05). We also observed associations between DNA methylation and gene expression for the PIK3CD sites.Conclusions: This study is the first to identify variable DNA methylation associated with all-cause mortality in smokers with and without COPD. Evaluating predictive epigenomic marks of smokers in peripheral blood may allow for targeted risk stratification and aid in delivery of future tailored therapeutic interventions.
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Affiliation(s)
| | - Barry Make
- National Jewish Health, Denver, Colorado
| | | | - MeiLan Han
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Craig P Hersh
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; and
| | - Augustine M K Choi
- Department of Medicine, NewYork-Presbyterian/Weill Cornell Medical Center, New York, New York
| | - Edwin K Silverman
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Dawn L DeMeo
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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33
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Swarr D, Putcha N, Zacharias W. "PIK"ing Out New Epigenetic Markers in Lung Disease. Am J Respir Crit Care Med 2020; 201:1029-1030. [PMID: 32109362 PMCID: PMC7193860 DOI: 10.1164/rccm.202002-0295ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Daniel Swarr
- Cincinnati Children's HospitalUniversity of Cincinnati School of MedicineCincinnati, Ohioand
| | - Nirupama Putcha
- Division of Pulmonary and Critical Care MedicineJohns Hopkins University School of MedicineBaltimore, Maryland
| | - William Zacharias
- Cincinnati Children's HospitalUniversity of Cincinnati School of MedicineCincinnati, Ohioand
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34
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He LX, Tang ZH, Huang QS, Li WH. DNA Methylation: A Potential Biomarker of Chronic Obstructive Pulmonary Disease. Front Cell Dev Biol 2020; 8:585. [PMID: 32733890 PMCID: PMC7358425 DOI: 10.3389/fcell.2020.00585] [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: 05/08/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a serious public health concern worldwide. By 2040, 4.41 million people are estimated to expire annually due to COPD. However, till date, it has remained difficult to alter the activity or progress of the disease through treatment. In order to address this issue, the best way would be to find biomarkers and new therapeutic targets for COPD. DNA methylation (DNAm) may be a potential biomarker for disease prevention, diagnosis, and prognosis, and its reversibility further makes it a potential drug design target in COPD. In this review, we aimed to explore the role of DNAm as biomarkers and disease mediators in different tissue samples from patients with COPD.
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Affiliation(s)
- Lin-Xi He
- School of Basic Medicine Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhao-Hui Tang
- School of Basic Medicine Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qing-Song Huang
- Department of Respiratory, Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wei-Hong Li
- School of Basic Medicine Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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35
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Tessema M, Tassew DD, Yingling CM, Do K, Picchi MA, Wu G, Petersen H, Randell S, Lin Y, Belinsky SA, Tesfaigzi Y. Identification of novel epigenetic abnormalities as sputum biomarkers for lung cancer risk among smokers and COPD patients. Lung Cancer 2020; 146:189-196. [PMID: 32559455 DOI: 10.1016/j.lungcan.2020.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Smoking is a common risk factor for chronic obstructive pulmonary disease (COPD) and lung cancer. Although COPD patients have higher risk of lung cancer compared to non-COPD smokers, the molecular links between these diseases are not well-defined. This study aims to identify genes that are downregulated by cigarette smoke and commonly repressed in COPD and lung cancer. MATERIALS AND METHODS Primary human airway epithelial cells (HAEC) were exposed to cigarette-smoke-extract (CSE) for 10-weeks and significantly suppressed genes were identified by transcriptome array. Epigenetic abnormalities of these genes in lung adenocarcinoma (LUAD) from patients with or without COPD were determined using genome-wide and gene-specific assays and by in vitro treatment of cell lines with trichostatin-A or 5-aza-2-deoxycytidine. RESULTS The ten most commonly downregulated genes following chronic CSE exposure of HAEC and show promoter hypermethylation in LUAD were selected. Among these, expression of CCNA1, SNCA, and ZNF549 was significantly reduced in lung tissues from COPD compared with non-COPD cases while expression of CCNA1 and SNCA was further downregulated in tumors with COPD. The promoter regions of all three genes were hypermethylated in LUAD but not normal or COPD lungs. The reduced expression and aberrant promoter hypermethylation of these genes in LUAD were independently validated using data from the Cancer Genome Atlas project. Importantly, SNCA and ZNF549 methylation detected in sputum DNA from LUAD (52% and 38%) cases were more prevalent compared to cancer-free smokers (26% and 15%), respectively (p < 0.02). CONCLUSIONS Our data show that suppression of CCNA1, SNCA, and ZNF549 in lung cancer and COPD occurs with or without promoter hypermethylation, respectively. Detecting methylation of these and previously identified genes in sputum of cancer-free smokers may serve as non-invasive biomarkers for early detection of lung cancer among high risk smokers including COPD patients.
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Affiliation(s)
- Mathewos Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA.
| | - Dereje D Tassew
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA; Currently, Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Christin M Yingling
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Kieu Do
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Hans Petersen
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Scott Randell
- Department of Cell and Molecular Physiology, The University of North Carolina, Chapel Hill, NC, USA
| | - Yong Lin
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Yohannes Tesfaigzi
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA; Currently, Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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36
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Wallace C. Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses. PLoS Genet 2020; 16:e1008720. [PMID: 32310995 PMCID: PMC7192519 DOI: 10.1371/journal.pgen.1008720] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/30/2020] [Accepted: 03/17/2020] [Indexed: 01/03/2023] Open
Abstract
Horizontal integration of summary statistics from different GWAS traits can be used to evaluate evidence for their shared genetic causality. One popular method to do this is a Bayesian method, coloc, which is attractive in requiring only GWAS summary statistics and no linkage disequilibrium estimates and is now being used routinely to perform thousands of comparisons between traits. Here we show that while most users do not adjust default software values, misspecification of prior parameters can substantially alter posterior inference. We suggest data driven methods to derive sensible prior values, and demonstrate how sensitivity analysis can be used to assess robustness of posterior inference. The flexibility of coloc comes at the expense of an unrealistic assumption of a single causal variant per trait. This assumption can be relaxed by stepwise conditioning, but this requires external software and an LD matrix aligned to study alleles. We have now implemented conditioning within coloc, and propose a new alternative method, masking, that does not require LD and approximates conditioning when causal variants are independent. Importantly, masking can be used in combination with conditioning where allelically aligned LD estimates are available for only a single trait. We have implemented these developments in a new version of coloc which we hope will enable more informed choice of priors and overcome the restriction of the single causal variant assumptions in coloc analysis.
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Affiliation(s)
- Chris Wallace
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, and MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
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37
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Jamieson E, Korologou-Linden R, Wootton RE, Guyatt AL, Battram T, Burrows K, Gaunt TR, Tobin MD, Munafò M, Davey Smith G, Tilling K, Relton C, Richardson TG, Richmond RC. Smoking, DNA Methylation, and Lung Function: a Mendelian Randomization Analysis to Investigate Causal Pathways. Am J Hum Genet 2020; 106:315-326. [PMID: 32084330 PMCID: PMC7058834 DOI: 10.1016/j.ajhg.2020.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022] Open
Abstract
Whether smoking-associated DNA methylation has a causal effect on lung function has not been thoroughly evaluated. We first investigated the causal effects of 474 smoking-associated CpGs on forced expiratory volume in 1 s (FEV1) in UK Biobank (n = 321,047) by using two-sample Mendelian randomization (MR) and then replicated this investigation in the SpiroMeta Consortium (n = 79,055). Second, we used two-step MR to investigate whether DNA methylation mediates the effect of smoking on FEV1. Lastly, we evaluated the presence of horizontal pleiotropy and assessed whether there is any evidence for shared causal genetic variants between lung function, DNA methylation, and gene expression by using a multiple-trait colocalization ("moloc") framework. We found evidence of a possible causal effect for DNA methylation on FEV1 at 18 CpGs (p < 1.2 × 10-4). Replication analysis supported a causal effect at three CpGs (cg21201401 [LIME1 and ZGPAT], cg19758448 [PGAP3], and cg12616487 [EML3 and AHNAK] [p < 0.0028]). DNA methylation did not clearly mediate the effect of smoking on FEV1, although DNA methylation at some sites might influence lung function via effects on smoking. By using "moloc", we found evidence of shared causal variants between lung function, gene expression, and DNA methylation. These findings highlight potential therapeutic targets for improving lung function and possibly smoking cessation, although larger, tissue-specific datasets are required to confirm these results.
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Affiliation(s)
- Emily Jamieson
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Roxanna Korologou-Linden
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Robyn E Wootton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; School of Psychological Science, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol National Health Service Foundation Trust and University of Bristol, Bristol, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Thomas Battram
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Kimberley Burrows
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Tom R Gaunt
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol National Health Service Foundation Trust and University of Bristol, Bristol, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Marcus Munafò
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; School of Psychological Science, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol National Health Service Foundation Trust and University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol National Health Service Foundation Trust and University of Bristol, Bristol, UK
| | - Kate Tilling
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Tom G Richardson
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
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38
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Beetch M, Harandi-Zadeh S, Shen K, Lubecka K, Kitts DD, O'Hagan HM, Stefanska B. Dietary antioxidants remodel DNA methylation patterns in chronic disease. Br J Pharmacol 2019; 177:1382-1408. [PMID: 31626338 DOI: 10.1111/bph.14888] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic diseases account for over 60% of all deaths worldwide according to the World Health Organization reports. Majority of cases are triggered by environmental exposures that lead to aberrant changes in the epigenome, specifically, the DNA methylation patterns. These changes result in altered expression of gene networks and activity of signalling pathways. Dietary antioxidants, including catechins, flavonoids, anthocyanins, stilbenes and carotenoids, demonstrate benefits in the prevention and/or support of therapy in chronic diseases. This review provides a comprehensive discussion of potential epigenetic mechanisms of antioxidant compounds in reversing altered patterns of DNA methylation in chronic disease. Antioxidants remodel the DNA methylation patterns through multiple mechanisms, including regulation of epigenetic enzymes and chromatin remodelling complexes. These effects can further contribute to antioxidant properties of the compounds. On the other hand, decrease in oxidative stress itself can impact DNA methylation delivering additional link between antioxidant mechanisms and epigenetic effects of the compounds. LINKED ARTICLES: This article is part of a themed section on The Pharmacology of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.6/issuetoc.
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Affiliation(s)
- Megan Beetch
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Sadaf Harandi-Zadeh
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Kate Shen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Katarzyna Lubecka
- Department of Biomedical Chemistry, Medical University of Lodz, Lodz, Poland
| | - David D Kitts
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Heather M O'Hagan
- Cell, Molecular and Cancer Biology, Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, USA
| | - Barbara Stefanska
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
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Corley J, Cox SR, Harris SE, Hernandez MV, Maniega SM, Bastin ME, Wardlaw JM, Starr JM, Marioni RE, Deary IJ. Epigenetic signatures of smoking associate with cognitive function, brain structure, and mental and physical health outcomes in the Lothian Birth Cohort 1936. Transl Psychiatry 2019; 9:248. [PMID: 31591380 PMCID: PMC6779733 DOI: 10.1038/s41398-019-0576-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/29/2019] [Indexed: 12/18/2022] Open
Abstract
Recent advances in genome-wide DNA methylation (DNAm) profiling for smoking behaviour have given rise to a new, molecular biomarker of smoking exposure. It is unclear whether a smoking-associated DNAm (epigenetic) score has predictive value for ageing-related health outcomes which is independent of contributions from self-reported (phenotypic) smoking measures. Blood DNA methylation levels were measured in 895 adults aged 70 years in the Lothian Birth Cohort 1936 (LBC1936) study using the Illumina 450K assay. A DNA methylation score based on 230 CpGs was used as a proxy for smoking exposure. Associations between smoking variables and health outcomes at age 70 were modelled using general linear modelling (ANCOVA) and logistic regression. Additional analyses of smoking with brain MRI measures at age 73 (n = 532) were performed. Smoking-DNAm scores were positively associated with self-reported smoking status (P < 0.001, eta-squared ɳ2 = 0.63) and smoking pack years (r = 0.69, P < 0.001). Higher smoking DNAm scores were associated with variables related to poorer cognitive function, structural brain integrity, physical health, and psychosocial health. Compared with phenotypic smoking, the methylation marker provided stronger associations with all of the cognitive function scores, especially visuospatial ability (P < 0.001, partial eta-squared ɳp2 = 0.022) and processing speed (P < 0.001, ɳp2 = 0.030); inflammatory markers (all P < 0.001, ranges from ɳp2 = 0.021 to 0.030); dietary patterns (healthy diet (P < 0.001, ɳp2 = 0.052) and traditional diet (P < 0.001, ɳp2 = 0.032); stroke (P = 0.006, OR 1.48, 95% CI 1.12, 1.96); mortality (P < 0.001, OR 1.59, 95% CI 1.42, 1.79), and at age 73; with MRI volumetric measures (all P < 0.001, ranges from ɳp2 = 0.030 to 0.052). Additionally, education was the most important life-course predictor of lifetime smoking tested. Our results suggest that a smoking-associated methylation biomarker typically explains a greater proportion of the variance in some smoking-related morbidities in older adults, than phenotypic measures of smoking exposure, with some of the accounted-for variance being independent of phenotypic smoking status.
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Affiliation(s)
- Janie Corley
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
| | - Simon R Cox
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Maria Valdéz Hernandez
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Brain Research Imaging Centre, Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Susana Muñoz Maniega
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Brain Research Imaging Centre, Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Mark E Bastin
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Brain Research Imaging Centre, Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Joanna M Wardlaw
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Brain Research Imaging Centre, Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Royal Victoria Building, Western General Hospital, Porterfield Road, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
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40
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Affiliation(s)
- Alvar Agustí
- From the Respiratory Institute, Hospital Clinic, Institut d'Investigació Agustí Pi i Sunyer, and the University of Barcelona, Barcelona; and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid (A.A.); and the Center for Heart and Lung Innovation, University of British Columbia at St. Paul's Hospital, Vancouver, Canada (J.C.H.)
| | - James C Hogg
- From the Respiratory Institute, Hospital Clinic, Institut d'Investigació Agustí Pi i Sunyer, and the University of Barcelona, Barcelona; and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid (A.A.); and the Center for Heart and Lung Innovation, University of British Columbia at St. Paul's Hospital, Vancouver, Canada (J.C.H.)
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41
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Ortega VE. Picking the Right Fruit: Intersecting Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Discoveries with Epigenetics. Am J Respir Crit Care Med 2019; 197:1237-1239. [PMID: 29425467 DOI: 10.1164/rccm.201801-0084ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Victor E Ortega
- 1 Department of Internal Medicine and.,2 Center for Precision Medicine Wake Forest School of Medicine Winston-Salem, North Carolina
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42
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Labaki WW, Kimmig LM, Mutlu GM, Han MK, Bhatt SP. Update in Chronic Obstructive Pulmonary Disease 2018. Am J Respir Crit Care Med 2019; 199:1462-1470. [PMID: 30958976 PMCID: PMC6835078 DOI: 10.1164/rccm.201902-0374up] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/04/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Wassim W. Labaki
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lucas M. Kimmig
- Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, Illinois; and
| | - Gökhan M. Mutlu
- Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, Illinois; and
| | - MeiLan K. Han
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Surya P. Bhatt
- Division of Pulmonary, Allergy, and Critical Care Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
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43
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Rodiño-Janeiro BK, Pardo-Camacho C, Santos J, Martínez C. Mucosal RNA and protein expression as the next frontier in IBS: abnormal function despite morphologically intact small intestinal mucosa. Am J Physiol Gastrointest Liver Physiol 2019; 316:G701-G719. [PMID: 30767681 DOI: 10.1152/ajpgi.00186.2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Irritable bowel syndrome (IBS) is one of the commonest gastrointestinal disorders. Although long-time considered a pure functional disorder, intense research in past years has rendered a very complex and varied array of observations indicating the presence of structural and molecular abnormalities underlying characteristic motor and sensitive changes and clinical manifestations. Analysis of gene and protein expression in the intestinal mucosa has shed light on the molecular mechanisms implicated in IBS physiopathology. This analysis uncovers constitutive and inductive genetic and epigenetic marks in the small and large intestine that highlight the role of epithelial barrier, immune activation, and mucosal processing of foods and toxins and several new molecular pathways in the origin of IBS. The incorporation of innovative high-throughput techniques into IBS research is beginning to provide new insights into highly structured and interconnected molecular mechanisms modulating gene and protein expression at tissue level. Integration and correlation of these molecular mechanisms with clinical and environmental data applying systems biology/medicine and data mining tools emerge as crucial steps that will allow us to get meaningful and more definitive comprehension of IBS-detailed development and show the real mechanisms and causality of the disease and the way to identify more specific diagnostic biomarkers and effective treatments.
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Affiliation(s)
- Bruno Kotska Rodiño-Janeiro
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca , Barcelona , Spain.,Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina) , Barcelona , Spain
| | - Cristina Pardo-Camacho
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca , Barcelona , Spain.,Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina) , Barcelona , Spain
| | - Javier Santos
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca , Barcelona , Spain.,Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina) , Barcelona , Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas , Madrid , Spain
| | - Cristina Martínez
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca , Barcelona , Spain.,Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina) , Barcelona , Spain
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44
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Wang J, Zhao Y, Xu H, Ma J, Liang F, Zou Q, Lin F. Silencing NID2 by DNA Hypermethylation Promotes Lung Cancer. Pathol Oncol Res 2019; 26:801-811. [PMID: 30826972 DOI: 10.1007/s12253-019-00609-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/22/2019] [Indexed: 12/16/2022]
Abstract
To characterize the DNA methylation as well as exploring the relationship between NID2 methylation and the lung cancer development. Collecting chip data of 9 lung cancer samples and 11 adjacent normal samples from the Gene Expression Omnibus database. Tissues and cells NID2 gene methylation level was measured by methylation-specific PCR. NID2 mRNA level and protein level were validated by Real-Time PCR and Western blot separately. Functional study of lung cancer cells was performed with Cell Counting Kit-8 assay. Colony formation assay, transwell assay, wound healing assay and low cytometry were performed. Finally, NID2 tumorigenesis in vivo was tested in nude mice xenograft models. Microarray analysis outcome present NID2 hypermethylation status in lung cancer tissues. High methylation and low mRNA expression levels of NID2 were detected. After NID2 demethylation or overexpression in cancer cells, cell viability, proliferation, migration as well as invasion ability decreased. Nevertheless, a significant enhancement in apoptosis rate were observed. Overexpressing NID2 or demethylation in lung cancer cells inhibited the tumorigenesis of lung cancer in nude mice. The mRNA and protein level of NID2 in tumors obtained from nude mice xenograft were unanimous with the in vitro assays' outcome, which significantly decreased after overexpressing NID2 or demethylation. NID2 methylation reduces its expression level and promotes the development of lung cancer.
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Affiliation(s)
- Jianfeng Wang
- Department of Radiotherapy, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130031, China
| | - Yan Zhao
- Medical Examination Center, The Second Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Hongyan Xu
- Department of Oncology, Jilin Second People's Hospital, Jilin, 132011, Jilin, China
| | - Jun Ma
- Department of Radiotherapy, The Affiliated Hospital of Beihua University, Jilin, 132011, Jilin, China
| | - Feihai Liang
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, Guangxi, China
| | - Qingxu Zou
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, No. 126 freedom Avenue, Changchun, Jilin, 130031, China
| | - Fengwu Lin
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, No. 126 freedom Avenue, Changchun, Jilin, 130031, China.
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45
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Sakornsakolpat P, Prokopenko D, Lamontagne M, Reeve NF, Guyatt AL, Jackson VE, Shrine N, Qiao D, Bartz TM, Kim DK, Lee MK, Latourelle JC, Li X, Morrow JD, Obeidat M, Wyss AB, Bakke P, Barr RG, Beaty TH, Belinsky SA, Brusselle GG, Crapo JD, de Jong K, DeMeo DL, Fingerlin TE, Gharib SA, Gulsvik A, Hall IP, Hokanson JE, Kim WJ, Lomas DA, London SJ, Meyers DA, O'Connor GT, Rennard SI, Schwartz DA, Sliwinski P, Sparrow D, Strachan DP, Tal-Singer R, Tesfaigzi Y, Vestbo J, Vonk JM, Yim JJ, Zhou X, Bossé Y, Manichaikul A, Lahousse L, Silverman EK, Boezen HM, Wain LV, Tobin MD, Hobbs BD, Cho MH. Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations. Nat Genet 2019; 51:494-505. [PMID: 30804561 PMCID: PMC6546635 DOI: 10.1038/s41588-018-0342-2] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/20/2018] [Indexed: 11/09/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci associated with P < 5 × 10-8; 47 of these were previously described in association with either COPD or population-based measures of lung function. Of the remaining 35 new loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified functional enrichment of COPD risk loci in lung tissue, smooth muscle, and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups based on associations with quantitative imaging features and comorbidities. Our analyses provide further support for the genetic susceptibility and heterogeneity of COPD.
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Affiliation(s)
- Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Maxime Lamontagne
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Quebec, Canada
| | - Nicola F Reeve
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Victoria E Jackson
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Deog Kyeom Kim
- Seoul National University College of Medicine, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | - Jeanne C Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ma'en Obeidat
- University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - James D Crapo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado Denver, Aurora, CO, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ian P Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, UK
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - David A Lomas
- UCL Respiratory, University College London, London, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | | | - George T O'Connor
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Stephen I Rennard
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Clinical Discovery Unit, AstraZeneca, Cambridge, UK
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Denver, Aurora, CO, USA
- Department of Immunology, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Pawel Sliwinski
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - David Sparrow
- VA Boston Healthcare System and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St. George's University of London, London, UK
| | | | | | - Jørgen Vestbo
- School of Biological Sciences, University of Manchester, Manchester, UK
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Quebec, Canada
- Department of Molecular Medicine, Laval University, Québec, Québec, Canada
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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Selman M, Martinez FJ, Pardo A. Why Does an Aging Smoker’s Lung Develop Idiopathic Pulmonary Fibrosis and Not Chronic Obstructive Pulmonary Disease? Am J Respir Crit Care Med 2019; 199:279-285. [DOI: 10.1164/rccm.201806-1166pp] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias, Ismael Cosío Villegas, Mexico City, Mexico
| | - Fernando J. Martinez
- Weill Cornell Medicine, New York-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York
- Deputy Editor, AJRCCM; and
| | - Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
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47
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Beckmeyer-Borowko A, Imboden M, Rezwan FI, Wielscher M, Amaral AFS, Jeong A, Schaffner E, Auvinen J, Sebert S, Karhunen V, Bettschart R, Turk A, Pons M, Stolz D, Kronenberg F, Arathimos R, Sharp GC, Relton C, Henderson AJ, Jarvelin MR, Jarvis D, Holloway JW, Probst-Hensch NM. SERPINA1 methylation and lung function in tobacco-smoke exposed European children and adults: a meta-analysis of ALEC population-based cohorts. Respir Res 2018; 19:156. [PMID: 30134983 PMCID: PMC6103990 DOI: 10.1186/s12931-018-0850-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The pathophysiological role of SERPINA1 in respiratory health may be more strongly determined by the regulation of its expression than by common genetic variants. A family based study of predominantly smoking adults found methylation at two Cytosine-phosphate-Guanine sites (CpGs) in SERPINA1 gene to be associated with chronic obstructive pulmonary disease risk. The objective of this study was to confirm the association of lung function with SERPINA1 methylation in general population samples by testing a comprehensive set of CpGs in the SERPINA gene cluster. We considered lung function level and decline in adult smokers from three European population-based cohorts and lung function level and growth in tobacco-smoke exposed children from a birth cohort. METHODS DNA methylation using Illumina Infinium Human Methylation 450 k and EPIC beadchips and lung function were measured at two time points in 1076 SAPALDIA, ECRHS and NFBC adult cohort participants and 259 ALSPAC children. Associations of methylation at 119 CpG sites in the SERPINA gene cluster (PP4R4-SERPINA13P) with lung functions and circulating alpha-1-antitripsin (AAT) were assessed using multivariable cross-sectional and longitudinal regression models. RESULTS Methylation at cg08257009 in the SERPINA gene cluster, located 32 kb downstream of SERPINA1, not annotated to a gene, was associated with FEV1/FVC at the Bonferroni corrected level in adults, but not in children. None of the methylation signals in the SERPINA1 gene showed associations with lung function after correcting for multiple testing. CONCLUSIONS The results do not support a role of SERPINA1 gene methylation as determinant of lung function across the life course in the tobacco smoke exposed general population exposed.
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Affiliation(s)
- Anna Beckmeyer-Borowko
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG, London, UK
| | - Andre F. S. Amaral
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG, London, UK
- Population Health and Occupational Disease, NHLI, Imperial College London, London, UK
| | - Ayoung Jeong
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Emmanuel Schaffner
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Juha Auvinen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Oulunkaari Health Center, Ii, Finland
- Medical Research Center, University Hospital of Oulu, University of Oulu, Oulu, Finland
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department for Genomics of Common Diseases, School of Public Health, Imperial College London, London, UK
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | | | | | - Marco Pons
- Ospedale Regionale di Lugano-Sede Civico, Lugano, Switzerland
| | - Daiana Stolz
- Clinic of Pulmonary Medicine and Respiratory Cell Research, Basel, Switzerland
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Ryan Arathimos
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gemma C. Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, OYS, Kajaanintie 50, 90220 Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, Middlesex UB8 3PH UK
| | - Deborah Jarvis
- Population Health and Occupational Disease, NHLI, Imperial College London, London, UK
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nicole M. Probst-Hensch
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
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