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Ramirez CA, Becker-Hapak M, Singhal K, Russler-Germain DA, Frenkel F, Barnell EK, McClain ED, Desai S, Schappe T, Onyeador OC, Kudryashova O, Belousov V, Bagaev A, Ocheredko E, Kiwala S, Hundal J, Skidmore ZL, Watkins MP, Mooney TB, Walker JR, Krysiak K, Gomez F, Fronick CC, Fulton RS, Schreiber RD, Mehta-Shah N, Cashen AF, Kahl BS, Ataullakhanov R, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Neoantigen landscape supports feasibility of personalized cancer vaccine for follicular lymphoma. Blood Adv 2024; 8:4035-4049. [PMID: 38713894 PMCID: PMC11339042 DOI: 10.1182/bloodadvances.2022007792] [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: 04/07/2022] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024] Open
Abstract
ABSTRACT Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that "polyvalent" vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by the alignment of B-cell receptor (BCR) CDR3 regions from RNA-seq data, grouping at the protein level, and comparison with the BCR repertoire from healthy individuals using RNA-seq data. An average of 52 somatic mutations per patient (range, 2-172) were identified, and ≥2 (median, 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all 4 patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field. This trial was registered at www.ClinicalTrials.gov as #NCT03121677.
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Affiliation(s)
- Cody A. Ramirez
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | | | - Kartik Singhal
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - David A. Russler-Germain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | - Erica K. Barnell
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Ethan D. McClain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Sweta Desai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy Schappe
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | | | | | | | | | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Zachary L. Skidmore
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Marcus P. Watkins
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Thomas B. Mooney
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Jason R. Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Kilannin Krysiak
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Felicia Gomez
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Catrina C. Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert D. Schreiber
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Neha Mehta-Shah
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Amanda F. Cashen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Brad S. Kahl
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | - Nancy L. Bartlett
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Obi L. Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Todd A. Fehniger
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
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Chen L, Ma J, Xu W, Shen F, Yang Z, Sonne C, Dietz R, Li L, Jie X, Li L, Yan G, Zhang X. Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet-driven adaptive evolution. Evol Appl 2024; 17:e13731. [PMID: 38894980 PMCID: PMC11183199 DOI: 10.1111/eva.13731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Epigenetic regulation plays an important role in the evolution of species adaptations, yet little information is available on the epigenetic mechanisms underlying the adaptive evolution of bamboo-eating in both giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To investigate the potential contribution of epigenetic to the adaptive evolution of bamboo-eating in giant and red pandas, we performed hepatic comparative transcriptome and methylome analyses between bamboo-eating pandas and carnivorous polar bears (Ursus maritimus). We found that genes involved in carbohydrate, lipid, amino acid, and protein metabolism showed significant differences in methylation and expression levels between the two panda species and polar bears. Clustering analysis of gene expression revealed that giant pandas did not form a sister group with the more closely related polar bears, suggesting that the expression pattern of genes in livers of giant pandas and red pandas have evolved convergently driven by their similar diets. Compared to polar bears, some key genes involved in carbohydrate metabolism and biological oxidation and cholesterol synthesis showed hypomethylation and higher expression in giant and red pandas, while genes involved in fat digestion and absorption, fatty acid metabolism, lysine degradation, resistance to lipid peroxidation and detoxification showed hypermethylation and low expression. Our study elucidates the special nutrient utilization mechanism of giant pandas and red pandas and provides some insights into the molecular mechanism of their adaptive evolution of bamboo feeding. This has important implications for the breeding and conservation of giant pandas and red pandas.
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Affiliation(s)
- Lei Chen
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Jinnan Ma
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- College of Continuing EducationYunnan Normal UniversityKunmingChina
| | - Wencai Xu
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Fujun Shen
- Sichuan Key Laboratory for Conservation Biology of Endangered WildlifeChengdu Research Base of Giant Panda BreedingChengduChina
| | | | - Christian Sonne
- Arctic Research Centre, Faculty of Science and Technology, Department of EcoscienceAarhus UniversityRoskildeDenmark
| | - Rune Dietz
- Arctic Research Centre, Faculty of Science and Technology, Department of EcoscienceAarhus UniversityRoskildeDenmark
| | - Linzhu Li
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Xiaodie Jie
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Lu Li
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Guoqiang Yan
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Xiuyue Zhang
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life SciencesSichuan UniversityChengduChina
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3
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Feng J, Zhu Z, Zhou R, Liu H, Hu Z, Wu F, Wang H, Yue J, Zhou T, Yang L, Wu F. Differential methylation patterns from clusters associated with glucose metabolism: evidence from a Shanghai twin study. Epigenomics 2024; 16:445-459. [PMID: 38410918 DOI: 10.2217/epi-2023-0449] [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] [Indexed: 02/28/2024] Open
Abstract
Aim: To assess the associations between genome-wide DNA methylation (DNAm) and glucose metabolism among a Chinese population, in particular the multisite correlation. Materials & methods: Epigenome-wide associations with fasting plasma glucose (FPG) and hemoglobin A1c (HbA1c) were analyzed among 100 Shanghai monozygotic (MZ) twin pairs using the Infinium HumanMethylationEPIC v2.0 BeadChip. We conducted a Pearson's correlation test, hierarchical cluster and pairwise analysis to examine the differential methylation patterns from clusters. Results: Cg01358804 (TXNIP) was identified as the most significant site associated with FPG and HbA1c. Two clusters with hypermethylated and hypomethylated patterns were observed for both FPG and HbA1c. Conclusion: Differential methylation patterns from clusters may provide new clues for epigenetic changes and biological mechanisms in glucose metabolism.
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Affiliation(s)
- Jingyuan Feng
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Zhenni Zhu
- Division of Health Risk Factors Monitoring & Control, Shanghai Municipal Center for Disease Control & Prevention, 200336, Shanghai, China
| | - Rongfei Zhou
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Hongwei Liu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Zihan Hu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Fei Wu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Huiting Wang
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Junhong Yue
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Tong Zhou
- Shanghai Precision Medicine Co. Ltd, Shanghai, 201406, China
| | - Li Yang
- Shanghai Precision Medicine Co. Ltd, Shanghai, 201406, China
| | - Fan Wu
- School of Public Health, Fudan University, Shanghai, 200032, China
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4
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Xiao D, Fang L, Liu Z, He Y, Ying J, Qin H, Lu A, Shi M, Li T, Zhang B, Guan J, Wang C, Abu-Amer Y, Shen J. DNA methylation-mediated Rbpjk suppression protects against fracture nonunion caused by systemic inflammation. J Clin Invest 2023; 134:e168558. [PMID: 38051594 PMCID: PMC10849763 DOI: 10.1172/jci168558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
Challenging skeletal repairs are frequently seen in patients experiencing systemic inflammation. To tackle the complexity and heterogeneity of the skeletal repair process, we performed single-cell RNA sequencing and revealed that progenitor cells were one of the major lineages responsive to elevated inflammation and this response adversely affected progenitor differentiation by upregulation of Rbpjk in fracture nonunion. We then validated the interplay between inflammation (via constitutive activation of Ikk2, Ikk2ca) and Rbpjk specifically in progenitors by using genetic animal models. Focusing on epigenetic regulation, we identified Rbpjk as a direct target of Dnmt3b. Mechanistically, inflammation decreased Dnmt3b expression in progenitor cells, consequently leading to Rbpjk upregulation via hypomethylation within its promoter region. We also showed that Dnmt3b loss-of-function mice phenotypically recapitulated the fracture repair defects observed in Ikk2ca-transgenic mice, whereas Dnmt3b-transgenic mice alleviated fracture repair defects induced by Ikk2ca. Moreover, Rbpjk ablation restored fracture repair in both Ikk2ca mice and Dnmt3b loss-of-function mice. Altogether, this work elucidates a common mechanism involving a NF-κB/Dnmt3b/Rbpjk axis within the context of inflamed bone regeneration. Building on this mechanistic insight, we applied local treatment with epigenetically modified progenitor cells in a previously established mouse model of inflammation-mediated fracture nonunion and showed a functional restoration of bone regeneration under inflammatory conditions through an increase in progenitor differentiation potential.
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Affiliation(s)
- Ding Xiao
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
- The Second Xiangya Hospital, Central South University, Changsha, China
| | - Liang Fang
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Zhongting Liu
- Department of Mechanical Engineering & Materials Sciences, School of Engineering and
| | - Yonghua He
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Jun Ying
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Haocheng Qin
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
- The Second Xiangya Hospital, Central South University, Changsha, China
| | - Aiwu Lu
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Meng Shi
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Tiandao Li
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University, St. Louis, Missouri, USA
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University, St. Louis, Missouri, USA
| | - Jianjun Guan
- Department of Mechanical Engineering & Materials Sciences, School of Engineering and
| | - Cuicui Wang
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University, St. Louis, Missouri, USA
| | - Yousef Abu-Amer
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
- Shriners Hospital for Children, St. Louis, Missouri, USA
| | - Jie Shen
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, Missouri, USA
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5
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Strulovici-Barel Y, Rostami MR, Kaner RJ, Mezey JG, Crystal RG. Serial Sampling of the Small Airway Epithelium to Identify Persistent Smoking-dysregulated Genes. Am J Respir Crit Care Med 2023; 208:780-790. [PMID: 37531632 PMCID: PMC10563181 DOI: 10.1164/rccm.202204-0786oc] [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: 04/25/2022] [Accepted: 08/02/2023] [Indexed: 08/04/2023] Open
Abstract
Rationale: The small airway epithelium (beyond the sixth generation), the initiation site of smoking-induced airway disorders, is highly sensitive to the stress of smoking. Because of variations over time in smoking habits, the small airway epithelium transcriptome is dynamic, fluctuating not only among smokers but also within each smoker. Objectives: To perform accurate assessment of the smoking-related dysregulation of the human small airway epithelium despite the variation of smoking within the same individual and of the effects of smoking cessation on the dysregulated transcriptome. Methods: We conducted serial sampling of the same smokers and nonsmoker control subjects over time to identify persistent smoking dysregulation of the biology of the small airway epithelium over 1 year. We conducted serial sampling of smokers who quit smoking, before and after smoking cessation, to assess the effect of smoking cessation on the smoking-dysregulated genes. Measurements and Main Results: Repeated measures ANOVA of the small airway epithelium transcriptome sampled four times in the same individuals over 1 year enabled the identification of 475 persistent smoking-dysregulated genes. Most genes were normalized after 12 months of smoking cessation; however, 53 (11%) genes, including CYP1B1, PIR, ME1, and TRIM16, remained persistently abnormally expressed. Dysregulated pathways enriched with the nonreversible genes included xenobiotic metabolism signaling, bupropion degradation, and nicotine degradation. Conclusions: Analysis of repetitive sampling of the same individuals identified persistent smoking-induced dysregulation of the small airway epithelium transcriptome and the effect of smoking cessation. These results help identify targets for the development of therapies that can be applicable to smoking-related airway diseases.
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Affiliation(s)
| | | | - Robert J. Kaner
- Department of Genetic Medicine and
- Department of Medicine, Weill Cornell Medical College, New York, New York; and
| | - Jason G. Mezey
- Department of Genetic Medicine and
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York
| | - Ronald G. Crystal
- Department of Genetic Medicine and
- Department of Medicine, Weill Cornell Medical College, New York, New York; and
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6
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Rodger EJ, Gimenez G, Ajithkumar P, Stockwell PA, Almomani S, Bowden SA, Leichter AL, Ahn A, Pattison S, McCall JL, Schmeier S, Frizelle FA, Eccles MR, Purcell RV, Chatterjee A. An epigenetic signature of advanced colorectal cancer metastasis. iScience 2023; 26:106986. [PMID: 37378317 PMCID: PMC10291510 DOI: 10.1016/j.isci.2023.106986] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/12/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of morbidity and mortality worldwide. The majority of CRC deaths are caused by tumor metastasis, even following treatment. There is strong evidence for epigenetic changes, such as DNA methylation, accompanying CRC metastasis and poorer patient survival. Earlier detection and a better understanding of molecular drivers for CRC metastasis are of critical clinical importance. Here, we identify a signature of advanced CRC metastasis by performing whole genome-scale DNA methylation and full transcriptome analyses of paired primary cancers and liver metastases from CRC patients. We observed striking methylation differences between primary and metastatic pairs. A subset of loci showed coordinated methylation-expression changes, suggesting these are potentially epigenetic drivers that control the expression of critical genes in the metastatic cascade. The identification of CRC epigenomic markers of metastasis has the potential to enable better outcome prediction and lead to the discovery of new therapeutic targets.
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Affiliation(s)
- Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | | | - Peter A. Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Suzan Almomani
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Sarah A. Bowden
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Anna L. Leichter
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Antonio Ahn
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Sharon Pattison
- Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - John L. McCall
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | | | - Frank A. Frizelle
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Rachel V. Purcell
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Honorary Professor, School of Health Sciences and Technology, UPES University, India
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7
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McAllan L, Baranasic D, Villicaña S, Brown S, Zhang W, Lehne B, Adamo M, Jenkinson A, Elkalaawy M, Mohammadi B, Hashemi M, Fernandes N, Lambie N, Williams R, Christiansen C, Yang Y, Zudina L, Lagou V, Tan S, Castillo-Fernandez J, King JWD, Soong R, Elliott P, Scott J, Prokopenko I, Cebola I, Loh M, Lenhard B, Batterham RL, Bell JT, Chambers JC, Kooner JS, Scott WR. Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes. Nat Commun 2023; 14:2784. [PMID: 37188674 PMCID: PMC10185556 DOI: 10.1038/s41467-023-38439-z] [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: 10/13/2021] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P < 1 × 10-7). We connect obesity-associated methylation variations to transcriptomic changes at >500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions.
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Affiliation(s)
- Liam McAllan
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Scarlett Brown
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Marco Adamo
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Andrew Jenkinson
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Mohamed Elkalaawy
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Borzoueh Mohammadi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Majid Hashemi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Nadia Fernandes
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nathalie Lambie
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Richard Williams
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - Youwen Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- School of Cardiovascular and Metabolic Medicine and Sciences, James Black Centre, King's College London British Heart Foundation Centre of Excellence, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Liudmila Zudina
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
| | - Vasiliki Lagou
- Department of Microbiology and Immunology, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Sili Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - James W D King
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Institute for Health Research Biomedical Research Centre, Imperial College London, London, UK
| | - James Scott
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Inga Prokopenko
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Marie Loh
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Rachel L Batterham
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
- Centre for Obesity Research, Rayne Institute, Department of Medicine, University College, London, WC1E 6JJ, UK
- National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, W1T 7DN, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - William R Scott
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK.
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK.
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8
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Mao W, Miller CM, Nair VD, Ge Y, Amper MAS, Cappuccio A, George M, Goforth CW, Guevara K, Marjanovic N, Nudelman G, Pincas H, Ramos I, Sealfon RSG, Soares‐Schanoski A, Vangeti S, Vasoya M, Weir DL, Zaslavsky E, Kim‐Schulze S, Gnjatic S, Merad M, Letizia AG, Troyanskaya OG, Sealfon SC, Chikina M. A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation. Mol Syst Biol 2023; 19:e11361. [PMID: 36919946 PMCID: PMC10167476 DOI: 10.15252/msb.202211361] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
DNA methylation comprises a cumulative record of lifetime exposures superimposed on genetically determined markers. Little is known about methylation dynamics in humans following an acute perturbation, such as infection. We characterized the temporal trajectory of blood epigenetic remodeling in 133 participants in a prospective study of young adults before, during, and after asymptomatic and mildly symptomatic SARS-CoV-2 infection. The differential methylation caused by asymptomatic or mildly symptomatic infections was indistinguishable. While differential gene expression largely returned to baseline levels after the virus became undetectable, some differentially methylated sites persisted for months of follow-up, with a pattern resembling autoimmune or inflammatory disease. We leveraged these responses to construct methylation-based machine learning models that distinguished samples from pre-, during-, and postinfection time periods, and quantitatively predicted the time since infection. The clinical trajectory in the young adults and in a diverse cohort with more severe outcomes was predicted by the similarity of methylation before or early after SARS-CoV-2 infection to the model-defined postinfection state. Unlike the phenomenon of trained immunity, the postacute SARS-CoV-2 epigenetic landscape we identify is antiprotective.
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Affiliation(s)
- Weiguang Mao
- Department of Computational and Systems Biology, School of MedicineUniversity of PittsburghPAPittsburghUSA
- Present address:
Center for Computational BiologyFlatiron Institute, Simons FoundationNew YorkNYUSA
| | - Clare M Miller
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Venugopalan D Nair
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Yongchao Ge
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Mary Anne S Amper
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Antonio Cappuccio
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | | | | | - Kristy Guevara
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Nada Marjanovic
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - German Nudelman
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Hanna Pincas
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Irene Ramos
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Rachel S G Sealfon
- Center for Computational Biology, Flatiron InstituteSimons FoundationNYNew YorkUSA
| | - Alessandra Soares‐Schanoski
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Present address:
Ragon Institute of MGH, MIT, and HarvardCambridgeMAUSA
| | - Sindhu Vangeti
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Mital Vasoya
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Dawn L Weir
- Naval Medical Research CenterMDSilver SpringUSA
| | - Elena Zaslavsky
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Seunghee Kim‐Schulze
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Sacha Gnjatic
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | | | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron InstituteSimons FoundationNYNew YorkUSA
- Department of Computer SciencePrinceton UniversityNJPrincetonUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityNJPrincetonUSA
| | - Stuart C Sealfon
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Maria Chikina
- Department of Computational and Systems Biology, School of MedicineUniversity of PittsburghPAPittsburghUSA
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9
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Poganik JR, Zhang B, Baht GS, Tyshkovskiy A, Deik A, Kerepesi C, Yim SH, Lu AT, Haghani A, Gong T, Hedman AM, Andolf E, Pershagen G, Almqvist C, Clish CB, Horvath S, White JP, Gladyshev VN. Biological age is increased by stress and restored upon recovery. Cell Metab 2023; 35:807-820.e5. [PMID: 37086720 PMCID: PMC11055493 DOI: 10.1016/j.cmet.2023.03.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/22/2022] [Accepted: 03/20/2023] [Indexed: 04/24/2023]
Abstract
Aging is classically conceptualized as an ever-increasing trajectory of damage accumulation and loss of function, leading to increases in morbidity and mortality. However, recent in vitro studies have raised the possibility of age reversal. Here, we report that biological age is fluid and exhibits rapid changes in both directions. At epigenetic, transcriptomic, and metabolomic levels, we find that the biological age of young mice is increased by heterochronic parabiosis and restored following surgical detachment. We also identify transient changes in biological age during major surgery, pregnancy, and severe COVID-19 in humans and/or mice. Together, these data show that biological age undergoes a rapid increase in response to diverse forms of stress, which is reversed following recovery from stress. Our study uncovers a new layer of aging dynamics that should be considered in future studies. The elevation of biological age by stress may be a quantifiable and actionable target for future interventions.
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Affiliation(s)
- Jesse R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gurpreet S Baht
- Department of Orthopaedic Surgery, Duke University, Durham, NC 27701, USA; Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 01241, USA
| | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI), Eötvös Loránd Research Network, Budapest, 1111, Hungary
| | - Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Altos Labs, San Diego, CA, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Altos Labs, San Diego, CA, USA
| | - Tong Gong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anna M Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ellika Andolf
- Department of Clinical Sciences, Division of Obstetrics and Gynaecology, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 01241, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Altos Labs, San Diego, CA, USA; Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James P White
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27701, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 01241, USA.
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10
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Gim JA. Integrative Approaches of DNA Methylation Patterns According to Age, Sex and Longitudinal Changes. Curr Genomics 2023; 23:385-399. [PMID: 37920553 PMCID: PMC10173416 DOI: 10.2174/1389202924666221207100513] [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: 07/22/2022] [Revised: 10/04/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
Background In humans, age-related DNA methylation has been studied in blood, tissues, buccal swabs, and fibroblasts, and changes in DNA methylation patterns according to age and sex have been detected. To date, approximately 137,000 samples have been analyzed from 14,000 studies, and the information has been uploaded to the NCBI GEO database. Methods A correlation between age and methylation level and longitudinal changes in methylation levels was revealed in both sexes. Here, 20 public datasets derived from whole blood were analyzed using the Illumina BeadChip. Batch effects with respect to the time differences were correlated. The overall change in the pattern was provided as the inverse of the coefficient of variation (COV). Results Of the 20 datasets, nine were from a longitudinal study. All data had age and sex as common variables. Comprehensive details of age-, sex-, and longitudinal change-based DNA methylation levels in the whole blood sample were elucidated in this study. ELOVL2 and FHL2 showed the maximum correlation between age and DNA methylation. The methylation patterns of genes related to mental health differed according to age. Age-correlated genes have been associated with malformations (anteverted nostril, craniofacial abnormalities, and depressed nasal bridge) and drug addiction (drug habituation and smoking). Conclusion Based on 20 public DNA methylation datasets, methylation levels according to age and longitudinal changes by sex were identified and visualized using an integrated approach. The results highlight the molecular mechanisms underlying the association of sex and biological age with changes in DNA methylation, and the importance of optimal genomic information management.
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Affiliation(s)
- Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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11
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Ma J, Zhang L, Shen F, Geng Y, Huang Y, Wu H, Fan Z, Hou R, Song Z, Yue B, Zhang X. Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation. BMC Genomics 2023; 24:23. [PMID: 36647013 PMCID: PMC9843897 DOI: 10.1186/s12864-023-09111-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND It is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species. RESULTS The clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn't exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region. CONCLUSIONS Our results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.
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Affiliation(s)
- Jinnan Ma
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.410739.80000 0001 0723 6903College of Continuing Education, Yunnan Normal University, Kunming, 650092 China
| | - Liang Zhang
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Fujun Shen
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Yang Geng
- grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Wolong, 623006 Sichuan China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, Wolong, 623006 Sichuan China
| | - Zhenxin Fan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Rong Hou
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Zhaobin Song
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Bisong Yue
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Xiuyue Zhang
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
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12
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Genome-Wide DNA Methylation Profile Indicates Potential Epigenetic Regulation of Aging in the Rhesus Macaque Thymus. Int J Mol Sci 2022; 23:ijms232314984. [PMID: 36499310 PMCID: PMC9738698 DOI: 10.3390/ijms232314984] [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: 10/21/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
We analyzed whole-genome bisulfite sequencing (WGBS) and RNA sequencing data of two young (1 year old) and two adult (9 years old) rhesus macaques (Macaca mulatta) to characterize the genomic DNA methylation profile of the thymus and explore the molecular mechanism of age-related changes in the thymus. Combining the two-omics data, we identified correlations between DNA methylation and gene expression and found that DNA methylation played an essential role in the functional changes of the aging thymus, especially in immunity and coagulation. The hypomethylation levels of C3 and C5AR2 and the hypermethylation level of C7 may lead to the high expressions of these genes in adult rhesus macaque thymuses, thus activating the classical complement pathway and the alternative pathway and enhancing their innate immune function. Adult thymuses had an enhanced coagulation pathway, which may have resulted from the hypomethylation and upregulated expressions of seven coagulation-promoting factor genes (F13A1, CLEC4D, CLEC4E, FCN3, PDGFRA, FGF2 and FGF7) and the hypomethylation and low expression of CPB2 to inhibit the degradation of blood clots. Furthermore, the functional decline in differentiation, activation and maturation of T cells in adult thymuses was also closely related to the changes in methylation levels and gene expression levels of T cell development genes (CD3G, GAD2, ADAMDEC1 and LCK) and the thymogenic hormone gene TMPO. A comparison of the age-related methylated genes among four mammal species revealed that most of the epigenetic clocks were species-specific. Furthermore, based on the genomic landscape of allele-specific DNA methylation, we identified several age-related clustered sequence-dependent allele-specific DNA methylated (cS-ASM) genes. Overall, these DNA methylation patterns may also help to assist with understanding the mechanisms of the aging thymus with the epigenome.
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13
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Peterson JA, Meng L, Rani A, Sinha P, Johnson AJ, Huo Z, Foster TC, Fillingim RB, Cruz-Almeida Y. Epigenetic aging, knee pain and physical performance in community-dwelling middle-to-older age adults. Exp Gerontol 2022; 166:111861. [PMID: 35640781 PMCID: PMC9887947 DOI: 10.1016/j.exger.2022.111861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/10/2022] [Accepted: 05/26/2022] [Indexed: 02/02/2023]
Abstract
Knee pain is a leading cause of disability in the aging population and may indirectly accelerate biological aging processes. Chronological aging increases the risk of developing of knee pain and knee pain reduces physical function; however, limited data exist on how epigenetic aging, a known hallmark of biological aging shown to predict health span and mortality, may influence this relationship. The purpose of this study was to examine whether decreased physical performance associated with knee pain is mediated by markers of epigenetic aging. Participants (57.91 ± 8.04 years) with low impact knee pain (n = 95), high impact knee pain (n = 53) and pain-free controls (n = 26) completed self-reported pain, a blood draw and a short physical performance battery (SPPB) that included balance, walking, and sit to stand tasks. We employed an epigenetic clock previously associated with knee pain and shown to predict overall mortality risk (DNAmGrimAge). Bootstrapped-mediation analyses were used to determine associations of DNAmGrimAge and SPPB between pain groups. Those with high impact and low impact pain had a biologically older epigenetic age (5.14y ± 5.66 and 1.32y ± 5.41, respectively). However, while there were direct effects of pain on overall physical performance, these were not explained by epigenetic aging. Epigenetic aging only mediated the effect of pain on balance performance. Future work is needed to examine pain's impact on biological aging processes including epigenetic aging and its ultimate effect on physical function measures known to predict health span and mortality.
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Affiliation(s)
- Jessica A Peterson
- Pain Research & Intervention Center of Excellence, University of Florida, Gainesville, FL, United States of America; Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, United States of America
| | - Lingsong Meng
- Department of Biostatistics, University of Florida, Gainesville, FL, United States of America
| | - Asha Rani
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States of America
| | - Puja Sinha
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States of America
| | - Alisa J Johnson
- Pain Research & Intervention Center of Excellence, University of Florida, Gainesville, FL, United States of America; Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, United States of America
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL, United States of America
| | - Thomas C Foster
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States of America; Genetics and Genomics Program, University of Florida, Gainesville, FL, United States of America
| | - Roger B Fillingim
- Pain Research & Intervention Center of Excellence, University of Florida, Gainesville, FL, United States of America; Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, United States of America
| | - Yenisel Cruz-Almeida
- Pain Research & Intervention Center of Excellence, University of Florida, Gainesville, FL, United States of America; Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, United States of America; Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States of America.
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14
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Pang APS, Higgins-Chen AT, Comite F, Raica I, Arboleda C, Went H, Mendez T, Schotsaert M, Dwaraka V, Smith R, Levine ME, Ndhlovu LC, Corley MJ. Longitudinal Study of DNA Methylation and Epigenetic Clocks Prior to and Following Test-Confirmed COVID-19 and mRNA Vaccination. Front Genet 2022; 13:819749. [PMID: 35719387 PMCID: PMC9203887 DOI: 10.3389/fgene.2022.819749] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/25/2022] [Indexed: 01/01/2023] Open
Abstract
The host epigenetic landscape rapidly changes during SARS-CoV-2 infection, and evidence suggest that severe COVID-19 is associated with durable scars to the epigenome. Specifically, aberrant DNA methylation changes in immune cells and alterations to epigenetic clocks in blood relate to severe COVID-19. However, a longitudinal assessment of DNA methylation states and epigenetic clocks in blood from healthy individuals prior to and following test-confirmed non-hospitalized COVID-19 has not been performed. Moreover, the impact of mRNA COVID-19 vaccines upon the host epigenome remains understudied. Here, we first examined DNA methylation states in the blood of 21 participants prior to and following test-confirmed COVID-19 diagnosis at a median time frame of 8.35 weeks; 756 CpGs were identified as differentially methylated following COVID-19 diagnosis in blood at an FDR adjusted p-value < 0.05. These CpGs were enriched in the gene body, and the northern and southern shelf regions of genes involved in metabolic pathways. Integrative analysis revealed overlap among genes identified in transcriptional SARS-CoV-2 infection datasets. Principal component-based epigenetic clock estimates of PhenoAge and GrimAge significantly increased in people over 50 following infection by an average of 2.1 and 0.84 years. In contrast, PCPhenoAge significantly decreased in people fewer than 50 following infection by an average of 2.06 years. This observed divergence in epigenetic clocks following COVID-19 was related to age and immune cell-type compositional changes in CD4+ T cells, B cells, granulocytes, plasmablasts, exhausted T cells, and naïve T cells. Complementary longitudinal epigenetic clock analyses of 36 participants prior to and following Pfizer and Moderna mRNA-based COVID-19 vaccination revealed that vaccination significantly reduced principal component-based Horvath epigenetic clock estimates in people over 50 by an average of 3.91 years for those who received Moderna. This reduction in epigenetic clock estimates was significantly related to chronological age and immune cell-type compositional changes in B cells and plasmablasts pre- and post-vaccination. These findings suggest the potential utility of epigenetic clocks as a biomarker of COVID-19 vaccine responses. Future research will need to unravel the significance and durability of short-term changes in epigenetic age related to COVID-19 exposure and mRNA vaccination.
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Affiliation(s)
- Alina P. S. Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Albert T. Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
- VA Connecticut Healthcare System, West Haven, CT, United States
| | - Florence Comite
- Comite Center for Precision Medicine & Health, New York, NY, United States
- Lenox Hill Hospital/Northwell, New York, NY, United States
| | - Ioana Raica
- Comite Center for Precision Medicine & Health, New York, NY, United States
| | | | | | | | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Ryan Smith
- TruDiagnostic, Lexington, KY, United States
| | - Morgan E. Levine
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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15
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Ma J, Zhang L, Huang Y, Shen F, Wu H, Yang Z, Hou R, Song Z, Yue B, Zhang X. Epigenomic profiling indicates a role for DNA methylation in the postnatal liver and pancreas development of giant pandas. Genomics 2022; 114:110342. [PMID: 35306168 DOI: 10.1016/j.ygeno.2022.110342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 02/14/2022] [Accepted: 03/13/2022] [Indexed: 01/14/2023]
Abstract
Giant pandas are unique within Carnivora with a strict bamboo diet. Here, the epigenomic profiles of giant panda liver and pancreas tissues collected from three important feeding stages were investigated using BS-seq. Few differences in DNA methylation profiles were exhibited between no feeding and suckling groups in both tissues. However, we observed a tendency toward a global loss of DNA methylation in the gene-body and promoter region of metabolism-related genes from newborn to adult. Correlation analysis revealed a significant negative correlation between the changes in methylation levels within gene promoters and gene expression. The majority of genes related to nutrition metabolism had lost DNA methylation with increased mRNA expression in adult giant pandas. The few galactose metabolism and unsaturated fatty acid metabolism related genes that were hypomethylated and highly-expressed at early stages of giant panda development may meet the nutritional requirement of this species' highly altricial neonates.
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Affiliation(s)
- Jinnan Ma
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, 98 Tongjiang Road, Dujiangyan, Chengdu, Sichuan 611800, China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, 98 Tongjiang Road, Dujiangyan, Chengdu, Sichuan 611800, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Zhaobin Song
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China.
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16
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Galow AM, Peleg S. How to Slow down the Ticking Clock: Age-Associated Epigenetic Alterations and Related Interventions to Extend Life Span. Cells 2022; 11:468. [PMID: 35159278 PMCID: PMC8915189 DOI: 10.3390/cells11030468] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic alterations pose one major hallmark of organismal aging. Here, we provide an overview on recent findings describing the epigenetic changes that arise during aging and in related maladies such as neurodegeneration and cancer. Specifically, we focus on alterations of histone modifications and DNA methylation and illustrate the link with metabolic pathways. Age-related epigenetic, transcriptional and metabolic deregulations are highly interconnected, which renders dissociating cause and effect complicated. However, growing amounts of evidence support the notion that aging is not only accompanied by epigenetic alterations, but also at least in part induced by those. DNA methylation clocks emerged as a tool to objectively determine biological aging and turned out as a valuable source in search of factors positively and negatively impacting human life span. Moreover, specific epigenetic signatures can be used as biomarkers for age-associated disorders or even as targets for therapeutic approaches, as will be covered in this review. Finally, we summarize recent potential intervention strategies that target epigenetic mechanisms to extend healthy life span and provide an outlook on future developments in the field of longevity research.
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Affiliation(s)
- Anne-Marie Galow
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Shahaf Peleg
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
- Institute of Neuroregeneration and Neurorehabilitation of Qingdao University, Qingdao 266071, China
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17
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Roberts ML, Kotchen TA, Pan X, Li Y, Yang C, Liu P, Wang T, Laud PW, Chelius TH, Munyura Y, Mattson DL, Liu Y, Cowley AW, Kidambi S, Liang M. Unique Associations of DNA Methylation Regions With 24-Hour Blood Pressure Phenotypes in Blacks. Hypertension 2022; 79:761-772. [PMID: 34994206 PMCID: PMC8917053 DOI: 10.1161/hypertensionaha.121.18584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Epigenetic marks (eg, DNA methylation) may capture the effect of gene-environment interactions. DNA methylation is involved in blood pressure (BP) regulation and hypertension development; however, no studies have evaluated its relationship with 24-hour BP phenotypes (daytime, nighttime, and 24-hour average BPs). METHODS We examined the association of whole blood DNA methylation with 24-hour BP phenotypes and clinic BPs in a discovery cohort of 281 Blacks using reduced representation bisulfite sequencing. We developed a deep and region-specific methylation sequencing method, Bisulfite ULtrapLEx Targeted Sequencing and utilized it to validate our findings in a separate validation cohort (n=117). RESULTS Analysis of 38 215 DNA methylation regions (MRs), derived from 1 549 368 CpG sites across the genome, identified up to 72 regions that were significantly associated with 24-hour BP phenotypes. No MR was significantly associated with clinic BP. Two to 3 MRs were significantly associated with various 24-hour BP phenotypes after adjustment for age, sex, and body mass index. Together, these MRs explained up to 16.5% of the variance of 24-hour average BP, while age, sex, and BMI explained up to 11.0% of the variance. Analysis of one of the MRs in an independent cohort using Bisulfite ULtrapLEx Targeted Sequencing confirmed its association with 24-hour average BP phenotype. CONCLUSIONS We identified several MRs that explain a substantial portion of variances in 24-hour BP phenotypes, which might be excellent markers of cumulative effect of factors influencing 24-hour BP levels. The Bisulfite ULtrapLEx Targeted Sequencing workflow has potential to be suitable for clinical testing and population screenings on a large scale.
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Affiliation(s)
- Michelle L Roberts
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee. (M.L.R., X.P., Y.L., C.Y., P.L., F.L.M., A.W.C., M.L.)
| | - Theodore A Kotchen
- Department of Medicine, Medical College of Wisconsin, Milwaukee. (T.A.K., Y.M., S.K.)
| | - Xiaoqing Pan
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee. (M.L.R., X.P., Y.L., C.Y., P.L., F.L.M., A.W.C., M.L.).,Department of Mathematics, Shanghai Normal University, China (X.P.)
| | - Yingchuan Li
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee. (M.L.R., X.P., Y.L., C.Y., P.L., F.L.M., A.W.C., M.L.).,Department of Critical Care Medicine, Shanghai JiaoTong University affiliated the Sixth People's Hospital, China (Y.L.)
| | - Chun Yang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee. (M.L.R., X.P., Y.L., C.Y., P.L., F.L.M., A.W.C., M.L.)
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee. (M.L.R., X.P., Y.L., C.Y., P.L., F.L.M., A.W.C., M.L.).,The Sir Run Run Shaw Hospital, Institute of Translational Medicine, Zhejiang University, China (P.L.)
| | | | - Purushottam W Laud
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee. (P.W.L.)
| | - Thomas H Chelius
- Division of Epidemiology, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee. (T.H.C.)
| | - Yannick Munyura
- Department of Medicine, Medical College of Wisconsin, Milwaukee. (T.A.K., Y.M., S.K.)
| | - David L Mattson
- Department of Physiology, Medical College of Georgia, Augusta (D.L.M.)
| | | | - Allen W Cowley
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee. (M.L.R., X.P., Y.L., C.Y., P.L., F.L.M., A.W.C., M.L.)
| | - Srividya Kidambi
- Department of Medicine, Medical College of Wisconsin, Milwaukee. (T.A.K., Y.M., S.K.)
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee. (M.L.R., X.P., Y.L., C.Y., P.L., F.L.M., A.W.C., M.L.)
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18
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Zeng Q, Zhao M, Wang F, Li Y, Li H, Zheng J, Chen X, Zhao X, Ji L, Gao X, Liu C, Wang Y, Cheng S, Xu J, Pan B, Sun J, Li Y, Li D, He Y, Zheng L. Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study. Front Endocrinol (Lausanne) 2022; 13:906310. [PMID: 35832425 PMCID: PMC9271784 DOI: 10.3389/fendo.2022.906310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
Emerging evidence is examining the precise role of intestinal microbiota in the pathogenesis of type 2 diabetes. The aim of this study was to investigate the association of intestinal microbiota and microbiota-generated metabolites with glucose metabolism systematically in a large cross-sectional study in China. 1160 subjects were divided into three groups based on their glucose level: normal glucose group (n=504), prediabetes group (n=394), and diabetes group (n=262). Plasma concentrations of TMAO, choline, betaine, and carnitine were measured. Intestinal microbiota was measured in a subgroup of 161 controls, 144 prediabetes and 56 diabetes by using metagenomics sequencing. We identified that plasma choline [Per SD of log-transformed change: odds ratio 1.36 (95 confidence interval 1.16, 1.58)] was positively, while betaine [0.77 (0.66, 0.89)] was negatively associated with diabetes, independently of TMAO. Individuals with diabetes could be accurately distinguished from controls by integrating data on choline, and certain microbiota species, as well as traditional risk factors (AUC=0.971). KOs associated with the carbohydrate metabolism pathway were enhanced in individuals with high choline level. The functional shift in the carbohydrate metabolism pathway in high choline group was driven by species Ruminococcus lactaris, Coprococcus catus and Prevotella copri. We demonstrated the potential ability for classifying diabetic population by choline and specific species, and provided a novel insight of choline metabolism linking the microbiota to impaired glucose metabolism and diabetes.
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Affiliation(s)
- Qiang Zeng
- Health Management Institute, the Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Mingming Zhao
- China National Clinical Research Center for Neurological Diseases, Tiantan Hospital, Advanced Innovation Center for Human Brain Protection, The Capital Medical University, Beijing, China
- The Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides of Ministry of Health, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Fei Wang
- Health Management Institute, the Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yanping Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, China
| | - Huimin Li
- National Human Genetic Resources Center, Beijing, China, National Research Institute for Family Planning, Beijing, China
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianqiong Zheng
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, The Third Affiliated Hospital of Shanghai University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, China
| | - Xianyang Chen
- Bao Feng Key Laboratory of Genetics and Metabolism, Zhongyuan Biotechnology Holdings Group, Beijing, China
- Zhong Guan Cun Biological and Medical Big Data Center, Zhong Guan Cun Medical Engineering & Health Industry Base, Beijing, China
| | - Xiaolan Zhao
- Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Liang Ji
- The Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides of Ministry of Health, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Xiangyang Gao
- Health Management Institute, the Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Changjie Liu
- The Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides of Ministry of Health, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Yu Wang
- Health Management Center, The 910th Hospital of People's Liberation Army, Quanzhou, China
| | - Si Cheng
- China National Clinical Research Center for Neurological Diseases, Tiantan Hospital, Advanced Innovation Center for Human Brain Protection, The Capital Medical University, Beijing, China
| | - Jie Xu
- China National Clinical Research Center for Neurological Diseases, Tiantan Hospital, Advanced Innovation Center for Human Brain Protection, The Capital Medical University, Beijing, China
| | - Bing Pan
- The Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides of Ministry of Health, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Jing Sun
- Health Management Center, The China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yongli Li
- Department of Health Management, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Dongfang Li
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, Guangdong, China
- Institute of Statistics, NanKai University, Tianjin, China
| | - Yuan He
- National Human Genetic Resources Center, Beijing, China, National Research Institute for Family Planning, Beijing, China
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- *Correspondence: Yuan He, ; Lemin Zheng,
| | - Lemin Zheng
- China National Clinical Research Center for Neurological Diseases, Tiantan Hospital, Advanced Innovation Center for Human Brain Protection, The Capital Medical University, Beijing, China
- The Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides of Ministry of Health, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
- *Correspondence: Yuan He, ; Lemin Zheng,
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19
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Gao P, Snyder M. Exposome-wide Association Study for Metabolic Syndrome. Front Genet 2021; 12:783930. [PMID: 34950191 PMCID: PMC8688998 DOI: 10.3389/fgene.2021.783930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
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20
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Wen G, Zhou T, Gu W. The potential of using blood circular RNA as liquid biopsy biomarker for human diseases. Protein Cell 2021; 12:911-946. [PMID: 33131025 PMCID: PMC8674396 DOI: 10.1007/s13238-020-00799-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a novel class of single-stranded RNAs with a closed loop structure. The majority of circRNAs are formed by a back-splicing process in pre-mRNA splicing. Their expression is dynamically regulated and shows spatiotemporal patterns among cell types, tissues and developmental stages. CircRNAs have important biological functions in many physiological processes, and their aberrant expression is implicated in many human diseases. Due to their high stability, circRNAs are becoming promising biomarkers in many human diseases, such as cardiovascular diseases, autoimmune diseases and human cancers. In this review, we focus on the translational potential of using human blood circRNAs as liquid biopsy biomarkers for human diseases. We highlight their abundant expression, essential biological functions and significant correlations to human diseases in various components of peripheral blood, including whole blood, blood cells and extracellular vesicles. In addition, we summarize the current knowledge of blood circRNA biomarkers for disease diagnosis or prognosis.
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Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China.
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21
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Metwally AA, Mehta P, Johnson BS, Nagarjuna A, Snyder MP. COVID-19-Induced New-Onset Diabetes: Trends and Technologies. Diabetes 2021; 70:2733-2744. [PMID: 34686519 PMCID: PMC8660988 DOI: 10.2337/dbi21-0029] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/23/2021] [Indexed: 01/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) global pandemic continues to spread worldwide with approximately 216 million confirmed cases and 4.49 million deaths to date. Intensive efforts are ongoing to combat this disease by suppressing viral transmission, understanding its pathogenesis, developing vaccination strategies, and identifying effective therapeutic targets. Individuals with preexisting diabetes also show higher incidence of COVID-19 illness and poorer prognosis upon infection. Likewise, an increased frequency of diabetes onset and diabetes complications has been reported in patients following COVID-19 diagnosis. COVID-19 may elevate the risk of hyperglycemia and other complications in patients with and without prior diabetes history. It is unclear whether the virus induces type 1 or type 2 diabetes or instead causes a novel atypical form of diabetes. Moreover, it remains unknown if recovering COVID-19 patients exhibit a higher risk of developing new-onset diabetes or its complications going forward. The aim of this review is to summarize what is currently known about the epidemiology and mechanisms of this bidirectional relationship between COVID-19 and diabetes. We highlight major challenges that hinder the study of COVID-19-induced new-onset of diabetes and propose a potential framework for overcoming these obstacles. We also review state-of-the-art wearables and microsampling technologies that can further study diabetes management and progression in new-onset diabetes cases. We conclude by outlining current research initiatives investigating the bidirectional relationship between COVID-19 and diabetes, some with emphasis on wearable technology.
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Affiliation(s)
- Ahmed A Metwally
- Department of Genetics, Stanford University, Stanford, CA
- Illumina Artificial Intelligence Laboratory, Illumina Inc., San Diego, CA
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
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22
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Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health. Cell Syst 2021; 13:241-255.e7. [PMID: 34856119 DOI: 10.1016/j.cels.2021.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 09/15/2021] [Accepted: 11/09/2021] [Indexed: 01/04/2023]
Abstract
We explored opportunities for personalized and predictive health care by collecting serial clinical measurements, health surveys, genomics, proteomics, autoantibodies, metabolomics, and gut microbiome data from 96 individuals who participated in a data-driven health coaching program over a 16-month period with continuous digital monitoring of activity and sleep. We generated a resource of >20,000 biological samples from this study and a compendium of >53 million primary data points for 558,032 distinct features. Multiomics factor analysis revealed distinct and independent molecular factors linked to obesity, diabetes, liver function, cardiovascular disease, inflammation, immunity, exercise, diet, and hormonal effects. For example, ethinyl estradiol, a common oral contraceptive, produced characteristic molecular and physiological effects, including increased levels of inflammation and impact on thyroid, cortisol levels, and pulse, that were distinct from other sources of variability observed in our study. In total, this work illustrates the value of combining deep molecular and digital monitoring of human health. A record of this paper's transparent peer review process is included in the supplemental information.
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23
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Silva R, Moran B, Baird AM, O'Rourke CJ, Finn SP, McDermott R, Watson W, Gallagher WM, Brennan DJ, Perry AS. Longitudinal analysis of individual cfDNA methylome patterns in metastatic prostate cancer. Clin Epigenetics 2021; 13:168. [PMID: 34454584 PMCID: PMC8403420 DOI: 10.1186/s13148-021-01155-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/17/2021] [Indexed: 01/27/2023] Open
Abstract
Background Disease progression and therapeutic resistance are hallmarks of advanced stage prostate cancer (PCa), which remains a major cause of cancer-related mortality around the world. Longitudinal studies, coupled with the use of liquid biopsies, offer a potentially new and minimally invasive platform to study the dynamics of tumour progression. Our aim was to investigate the dynamics of personal DNA methylomic profiles of metastatic PCa (mPCa) patients, during disease progression and therapy administration. Results Forty-eight plasma samples from 9 mPCa patients were collected, longitudinally, over 13–21 months. After circulating cell-free DNA (cfDNA) isolation, DNA methylation was profiled using the Infinium MethylationEPIC BeadChip. The top 5% most variable probes across time, within each individual, were utilised to study dynamic methylation patterns during disease progression and therapeutic response. Statistical testing was carried out to identify differentially methylated genes (DMGs) in cfDNA, which were subsequently validated in two independent mPCa (cfDNA and FFPE tissue) cohorts. Individual cfDNA global methylation patterns were temporally stable throughout the disease course. However, a proportion of CpG sites presented a dynamic temporal pattern that was consistent with clinical events, including different therapies, and were prominently associated with genes linked to immune response pathways. Additionally, study of the tumour fraction of cfDNA identified > 2000 DMGs with dynamic methylation patterns. Conclusions Longitudinal assessment of cfDNA methylation in mPCa patients unveiled dynamic patterns associated with disease progression and therapy administration, thus highlighting the potential of using liquid biopsies to study PCa evolution at a methylomic level. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01155-w.
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Affiliation(s)
- Romina Silva
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,School of Biology and Environmental Science, Science West, O'Brien Science Centre, University College Dublin, Dublin, Ireland
| | - Bruce Moran
- Department of Pathology, St. Vincent's University Hospital, Dublin, Ireland
| | - Anne-Marie Baird
- Department of Clinical Medicine, Trinity College, Dublin, Ireland
| | - Colm J O'Rourke
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stephen P Finn
- Department of Clinical Medicine, Trinity College, Dublin, Ireland.,Department of Histopathology, St James's Hospital, Dublin, Ireland
| | - Ray McDermott
- Cancer Trials Ireland, Dublin, Ireland.,Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| | - William Watson
- School of Medicine, University College Dublin, Dublin, Ireland
| | - William M Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Donal J Brennan
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland
| | - Antoinette S Perry
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland. .,School of Biology and Environmental Science, Science West, O'Brien Science Centre, University College Dublin, Dublin, Ireland.
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24
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Liang X, Justice AC, So-Armah K, Krystal JH, Sinha R, Xu K. DNA methylation signature on phosphatidylethanol, not on self-reported alcohol consumption, predicts hazardous alcohol consumption in two distinct populations. Mol Psychiatry 2021; 26:2238-2253. [PMID: 32034291 PMCID: PMC8440221 DOI: 10.1038/s41380-020-0668-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/20/2019] [Accepted: 01/28/2020] [Indexed: 12/28/2022]
Abstract
The process of diagnosing hazardous alcohol drinking (HAD) is based on self-reported data and is thereby vulnerable to bias. There has been an interest in developing epigenetic biomarkers for HAD that might complement clinical assessment. Because alcohol consumption has been previously linked to DNA methylation (DNAm), we aimed to select DNAm signatures in blood to predict HAD from two demographically and clinically distinct populations (Ntotal = 1,549). We first separately conducted an epigenome-wide association study (EWAS) for phosphatidylethanol (PEth), an objective measure of alcohol consumption, and for self-reported alcohol consumption in Cohort 1. We identified 83 PEth-associated CpGs, including 23 CpGs previously associated with alcohol consumption or alcohol use disorder. In contrast, no CpG reached epigenome-wide significance on self-reported alcohol consumption. Using a machine learning approach, two CpG subsets from EWAS on PEth and on self-reported alcohol consumption from Cohort 1 were separately tested for the prediction of HAD in Cohort 2. We found that a subset of 143 CpGs selected from the EWAS on PEth showed an excellent prediction of HAD with the area under the receiver operating characteristic curve (AUC) of 89.4% in training set and 73.9% in validation set of Cohort 2. However, CpGs preselected from the EWAS on self-reported alcohol consumption showed a poor prediction of HAD with AUC 75.2% in training set and 57.6% in validation set. Our results demonstrate that an objective measure for alcohol consumption is a more informative phenotype than self-reported data for revealing epigenetic mechanisms. The PEth-associated DNAm signature in blood could serve as a robust biomarker for alcohol consumption.
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Affiliation(s)
- Xiaoyu Liang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- VA Connecticut Healthcare System, West Haven, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Kaku So-Armah
- Boston University School of Medicine, Boston, MA, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Rajita Sinha
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
- Stress Center, Yale School of Medicine, New Haven, CT, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.
- VA Connecticut Healthcare System, West Haven, CT, USA.
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25
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Zheng M, Xiao S, Guo T, Rao L, Li L, Zhang Z, Huang L. DNA methylomic homogeneity and heterogeneity in muscles and testes throughout pig adulthood. Aging (Albany NY) 2020; 12:25412-25431. [PMID: 33231562 PMCID: PMC7803572 DOI: 10.18632/aging.104143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/09/2020] [Indexed: 01/24/2023]
Abstract
DNA methylome pattern is significantly different among tissues, ages, breeds, and genders. We assessed 20 methylome and transcriptome data in longissimus dorsi (LD) or testicles from Bamaxiang (BMX) and Large White pigs (LW) by deep sequencing technology. We identified ~55.7M CpGs and 5.30M, 0.20M, 1.20M, and 0.16M differential CpGs (P<0.01) between tissues, ages, breeds, and genders, respectively. Interestingly, 7.54% of differentially methylated regions (DMRs) are co-localized with promoters, which potentially regulate gene expression. RNA-seq analysis revealed that 23.42% CpGs are significantly correlated with gene expression (mean |r|=0.58, P<0.01), most of which are enriched in tissue-specific functions. Specially, we also found that the methylation levels in promoters of 655 genes were strongly associated with their expression levels (mean |r|=0.66, P<0.01). In addition, differentially methylated CpGs (DMCpGs) between breeds in HOXC gene cluster imply important regulatory roles in myocytes hypertrophy and intermuscular fat (IMF) deposition. Dramatically, higher similarity of methylation pattern was observed within pedigree than across pedigrees, which indicates the existence of heritable methylation regions. In summary, a part of CpGs in promoter can change its methylation pattern and play a marked regulatory function in different physiological or natural environments.
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Affiliation(s)
- Min Zheng
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tianfu Guo
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lin Rao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Longyun Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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26
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Shu C, Justice AC, Zhang X, Marconi VC, Hancock DB, Johnson EO, Xu K. DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population. Epigenetics 2020; 16:741-753. [PMID: 33092459 PMCID: PMC8216205 DOI: 10.1080/15592294.2020.1824097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. Methods: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. Results: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. Conclusions: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. Abbreviations: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Vincent C Marconi
- Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
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27
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Longitudinal assessment of clonal mosaicism in human hematopoiesis via mitochondrial mutation tracking. Blood Adv 2020; 3:4161-4165. [PMID: 31841597 DOI: 10.1182/bloodadvances.2019001196] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Our ability to track cellular dynamics in humans over time in vivo has been limited. Here, we demonstrate how somatic mutations in mitochondrial DNA (mtDNA) can be used to longitudinally track the dynamic output of hematopoietic stem and progenitor cells in humans. Over the course of 3 years of blood sampling in a single individual, our analyses reveal somatic mtDNA sequence variation and evolution reminiscent of models of hematopoiesis established by genetic labeling approaches. Furthermore, we observe fluctuations in mutation heteroplasmy, coinciding with specific clinical events, such as infections, and further identify lineage-specific somatic mtDNA mutations in longitudinally sampled circulating blood cell subsets in individuals with leukemia. Collectively, these observations indicate the significant potential of using tracking of somatic mtDNA sequence variation as a broadly applicable approach to systematically assess hematopoietic clonal dynamics in human health and disease.
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28
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Yin Q, Yang X, Li L, Xu T, Zhou W, Gu W, Ma F, Yang R. The Association Between Breast Cancer and Blood-Based Methylation of S100P and HYAL2 in the Chinese Population. Front Genet 2020; 11:977. [PMID: 33005177 PMCID: PMC7485126 DOI: 10.3389/fgene.2020.00977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 02/05/2023] Open
Abstract
Previous work has shown that DNA methylation in peripheral blood may be associated with malignancy; however, these studies have mainly been conducted within Caucasian populations. Here, we investigated the association between blood-based methylation of S100 calcium-binding protein P gene (S100P) and hyaluronoglucosaminidase 2 gene (HYAL2) and breast cancer (BC) via mass spectrometry in two independent case-control studies of the Chinese population with a total of 351 BC cases and 427 cancer-free female controls. In Study I, in which subjects had an average of 45 years, hypomethylation of S100P showed a protective effect for women ≤45 years (six out of nine CpG sites, p < 0.05) but not for women >45 years. In contrast, hypomethylation of HAYL2 was not correlated with BC in women ≤45 years but was a risk factor for women >45 years (three out of four CpG sites, p < 0.05). We proposed an age-dependent correlation between BC and methylation of S100P and HYAL2 and performed further validation in Study II with older subjects (average age = 52.5 years), where hypomethylation of both S100P and HYAL2 was a risk factor for BC (p < 0.05 for 10 CpG sites) as reported in Caucasians who develop BC around 55 years old. Together with the observation that Chinese cancer-free females having variant basal methylation levels comparing to Caucasians, we assumed that blood-based methylation might be modified by ethnic background, hormone status, and lifestyle. Here, we highlighted that the epigenetic biomarkers warrant validations when its application in variant ethnic groups is considered.
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Affiliation(s)
- Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaoqin Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wenjie Zhou
- Chengdu Shang Jin Nan Fu Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
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Abstract
The primary aim of the Guangzhou Twin Eye Study (GTES) is to explore the impact that genes and environmental influences have on common eye diseases. Since 2006, approximately 1300 pairs of twins, aged 7-15 years, were enrolled at baseline. Progressive phenotypes, such as cycloplegic refraction, axial length, height and weight, have been collected annually. Nonprogressive phenotypes such as parental refraction, corneal thickness, fundus photo, intraocular pressure and DNA were collected once at baseline. We are collaborating with fellow international twin researchers and psychologists to further explore links with general medical conditions. In this article, we review the history, major findings and future research directions for the GTES.
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30
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Wall J, Xie H, Wang X. Interaction of Sleep and Cortical Structural Maintenance From an Individual Person Microlongitudinal Perspective and Implications for Precision Medicine Research. Front Neurosci 2020; 14:769. [PMID: 32848551 PMCID: PMC7411006 DOI: 10.3389/fnins.2020.00769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022] Open
Abstract
Sleep and maintenance of brain structure are essential for the continuity of a person's cognitive/mental health. Interestingly, whether normal structural maintenance of the brain and sleep continuously interact in some way over day-week-month times has never been assessed at an individual-person level. This study used unconventional microlongitudinal sampling, structural magnetic resonance imaging, and n-of-1 analyses to assess normal interactions between fluctuations in the structural maintenance of cerebral cortical thickness and sleep duration for day, week, and multi-week intervals over a 6-month period in a healthy adult man. Correlation and time series analyses provided indications of "if-then," i.e., "if" this preceded "then" this followed, sleep-to-thickness maintenance and thickness maintenance-to-sleep bidirectional inverse interactions. Inverse interaction patterns were characterized by concepts of graded influences across nights, bilaterally positive relationships, continuity across successive weeks, and longer delayed/prolonged effects in the thickness maintenance-to-sleep than sleep-to-thickness maintenance direction. These interactions are proposed to involve normal circadian/allostatic/homeostatic mechanisms that continuously influence, and are influenced by, cortical substrate remodeling/turnover and sleep/wake cycle. Understanding interactions of individual person "-omics" is becoming a central interest in precision medicine research. The present n-of-1 findings contribute to this interest and have implications for precision medicine research use of a person's cortical structural and sleep "-omics" to optimize the continuous maintenance of that individual's cortical structure, sleep, and cognitive/mental health.
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Affiliation(s)
- John Wall
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Hong Xie
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Xin Wang
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
- Department of Psychiatry, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
- Department of Radiology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
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31
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Romanowska J, Haaland ØA, Jugessur A, Gjerdevik M, Xu Z, Taylor J, Wilcox AJ, Jonassen I, Lie RT, Gjessing HK. Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk. Clin Epigenetics 2020; 12:109. [PMID: 32678018 PMCID: PMC7367265 DOI: 10.1186/s13148-020-00881-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Current technology allows rapid assessment of DNA sequences and methylation levels at a single-site resolution for hundreds of thousands of sites in the human genome, in thousands of individuals simultaneously. This has led to an increase in epigenome-wide association studies (EWAS) of complex traits, particularly those that are poorly explained by previous genome-wide association studies (GWAS). However, the genome and epigenome are intertwined, e.g., DNA methylation is known to affect gene expression through, for example, genomic imprinting. There is thus a need to go beyond single-omics data analyses and develop interaction models that allow a meaningful combination of information from EWAS and GWAS. RESULTS We present two new methods for genetic association analyses that treat offspring DNA methylation levels as environmental exposure. Our approach searches for statistical interactions between SNP alleles and DNA methylation (G ×Me) and between parent-of-origin effects and DNA methylation (PoO ×Me), using case-parent triads or dyads. We use summarized methylation levels over nearby genomic region to ease biological interpretation. The methods were tested on a dataset of parent-offspring dyads, with EWAS data on the offspring. Our results showed that methylation levels around a SNP can significantly alter the estimated relative risk. Moreover, we show how a control dataset can identify false positives. CONCLUSIONS The new methods, G ×Me and PoO ×Me, integrate DNA methylation in the assessment of genetic relative risks and thus enable a more comprehensive biological interpretation of genome-wide scans. Moreover, our strategy of condensing DNA methylation levels within regions helps overcome specific disadvantages of using sparse chip-based measurements. The methods are implemented in the freely available R package Haplin ( https://cran.r-project.org/package=Haplin ), enabling fast scans of multi-omics datasets.
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Affiliation(s)
- Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway.
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway.
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway.
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, N-0473, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, N-0473, Norway
| | - Zongli Xu
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Jack Taylor
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Allen J Wilcox
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Inge Jonassen
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
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32
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Aref-Eshghi E, Biswas S, Chen C, Sadikovic B, Chakrabarti S. Glucose-induced, duration-dependent genome-wide DNA methylation changes in human endothelial cells. Am J Physiol Cell Physiol 2020; 319:C268-C276. [PMID: 32459505 DOI: 10.1152/ajpcell.00011.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation, a critical epigenetic mechanism, plays an important role in governing gene expressions during biological processes such as aging, which is well known to be accelerated in hyperglycemia (diabetes). In the present study, we investigated the effects of glucose on whole genome DNA methylation in small [human retinal microvascular endothelial cells (HRECs)] and large [human umbilical vein endothelial cells (HUVECs)] vessel endothelial cell (EC) lines exposed to basal or high glucose-containing media for variable lengths of time. Using the Infinium EPIC array, we obtained 773,133 CpG sites (probes) for analysis. Unsupervised clustering of the top 5% probes identified four distinct clusters within EC groups, with significant methylation differences attributed to EC types and the duration of cell culture rather than glucose stimuli alone. When comparing the ECs incubated for 2 days versus 7 days, hierarchical clustering analyses [methylation change >10% and false discovery rate (FDR) <0.05] identified 17,354 and 128 differentially methylated CpGs for HUVECs and HRECs, respectively. Predominant DNA hypermethylation was associated with the length of culture and was enriched for gene enhancer elements and regions surrounding CpG shores and shelves. We identified 88 differentially methylated regions (DMRs) for HUVECs and 8 DMRs for HRECs (all FDR <0.05). Pathway enrichment analyses of DMRs highlighted involvement of regulators of embryonic development (i.e., HOX genes) and cellular differentiation [transforming growth factor-β (TGF-β) family members]. Collectively, our findings suggest that DNA methylation is a complex process that involves tightly coordinated, cell-specific mechanisms. Such changes in methylation overlap genes critical for cellular differentiation and embryonic development.
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Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada
| | - Saumik Biswas
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Charlie Chen
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Subrata Chakrabarti
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
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33
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Yan Z, Zhou Z, Wu Q, Chen ZB, Koo EH, Zhong S. Presymptomatic Increase of an Extracellular RNA in Blood Plasma Associates with the Development of Alzheimer’s Disease. Curr Biol 2020; 30:1771-1782.e3. [DOI: 10.1016/j.cub.2020.02.084] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/18/2020] [Accepted: 02/26/2020] [Indexed: 12/12/2022]
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34
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Salameh Y, Bejaoui Y, El Hajj N. DNA Methylation Biomarkers in Aging and Age-Related Diseases. Front Genet 2020; 11:171. [PMID: 32211026 PMCID: PMC7076122 DOI: 10.3389/fgene.2020.00171] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Recent research efforts provided compelling evidence of genome-wide DNA methylation alterations in aging and age-related disease. It is currently well established that DNA methylation biomarkers can determine biological age of any tissue across the entire human lifespan, even during development. There is growing evidence suggesting epigenetic age acceleration to be strongly linked to common diseases or occurring in response to various environmental factors. DNA methylation based clocks are proposed as biomarkers of early disease risk as well as predictors of life expectancy and mortality. In this review, we will summarize key advances in epigenetic clocks and their potential application in precision health. We will also provide an overview of progresses in epigenetic biomarker discovery in Alzheimer's, type 2 diabetes, and cardiovascular disease. Furthermore, we will highlight the importance of prospective study designs to identify and confirm epigenetic biomarkers of disease.
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Affiliation(s)
| | | | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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35
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Delacrétaz A, Glatard A, Dubath C, Gholam-Rezaee M, Sanchez-Mut JV, Gräff J, von Gunten A, Conus P, Eap CB. Psychotropic drug-induced genetic-epigenetic modulation of CRTC1 gene is associated with early weight gain in a prospective study of psychiatric patients. Clin Epigenetics 2019; 11:198. [PMID: 31878957 PMCID: PMC6933694 DOI: 10.1186/s13148-019-0792-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/02/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Metabolic side effects induced by psychotropic drugs represent a major health issue in psychiatry. CREB-regulated transcription coactivator 1 (CRTC1) gene plays a major role in the regulation of energy homeostasis and epigenetic mechanisms may explain its association with obesity features previously described in psychiatric patients. This prospective study included 78 patients receiving psychotropic drugs that induce metabolic disturbances, with weight and other metabolic parameters monitored regularly. Methylation levels in 76 CRTC1 probes were assessed before and after 1 month of psychotropic treatment in blood samples. RESULTS Significant methylation changes were observed in three CRTC1 CpG sites (i.e., cg07015183, cg12034943, and cg 17006757) in patients with early and important weight gain (i.e., equal or higher than 5% after 1 month; FDR p value = 0.02). Multivariable models showed that methylation decrease in cg12034943 was more important in patients with early weight gain (≥ 5%) than in those who did not gain weight (p = 0.01). Further analyses combining genetic and methylation data showed that cg12034943 was significantly associated with early weight gain in patients carrying the G allele of rs4808844A>G (p = 0.03), a SNP associated with this methylation site (p = 0.03). CONCLUSIONS These findings give new insights on psychotropic-induced weight gain and underline the need of future larger prospective epigenetic studies to better understand the complex pathways involved in psychotropic-induced metabolic side effects.
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Affiliation(s)
- Aurélie Delacrétaz
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
| | - Anaïs Glatard
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
| | - Céline Dubath
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
| | - Mehdi Gholam-Rezaee
- Centre of Psychiatric Epidemiology and Psychopathology, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
| | - Jose Vicente Sanchez-Mut
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Armin von Gunten
- Service of Old Age Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
| | - Philippe Conus
- Service of General Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
| | - Chin B Eap
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland. .,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.
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36
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Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JPJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations. Genome Biol 2019; 20:249. [PMID: 31767039 PMCID: PMC6876109 DOI: 10.1186/s13059-019-1824-y] [Citation(s) in RCA: 455] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Stephan Beck
- Medical Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Trey Ideker
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA.
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.
- The Wellcome Trust Sanger Institute, Cambridge, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany.
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau.
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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Liu J, Carnero-Montoro E, van Dongen J, Lent S, Nedeljkovic I, Ligthart S, Tsai PC, Martin TC, Mandaviya PR, Jansen R, Peters MJ, Duijts L, Jaddoe VWV, Tiemeier H, Felix JF, Willemsen G, de Geus EJC, Chu AY, Levy D, Hwang SJ, Bressler J, Gondalia R, Salfati EL, Herder C, Hidalgo BA, Tanaka T, Moore AZ, Lemaitre RN, Jhun MA, Smith JA, Sotoodehnia N, Bandinelli S, Ferrucci L, Arnett DK, Grallert H, Assimes TL, Hou L, Baccarelli A, Whitsel EA, van Dijk KW, Amin N, Uitterlinden AG, Sijbrands EJG, Franco OH, Dehghan A, Spector TD, Dupuis J, Hivert MF, Rotter JI, Meigs JB, Pankow JS, van Meurs JBJ, Isaacs A, Boomsma DI, Bell JT, Demirkan A, van Duijn CM. An integrative cross-omics analysis of DNA methylation sites of glucose and insulin homeostasis. Nat Commun 2019; 10:2581. [PMID: 31197173 PMCID: PMC6565679 DOI: 10.1038/s41467-019-10487-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/09/2019] [Indexed: 02/07/2023] Open
Abstract
Despite existing reports on differential DNA methylation in type 2 diabetes (T2D) and obesity, our understanding of its functional relevance remains limited. Here we show the effect of differential methylation in the early phases of T2D pathology by a blood-based epigenome-wide association study of 4808 non-diabetic Europeans in the discovery phase and 11,750 individuals in the replication. We identify CpGs in LETM1, RBM20, IRS2, MAN2A2 and the 1q25.3 region associated with fasting insulin, and in FCRL6, SLAMF1, APOBEC3H and the 15q26.1 region with fasting glucose. In silico cross-omics analyses highlight the role of differential methylation in the crosstalk between the adaptive immune system and glucose homeostasis. The differential methylation explains at least 16.9% of the association between obesity and insulin. Our study sheds light on the biological interactions between genetic variants driving differential methylation and gene expression in the early pathogenesis of T2D.
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Affiliation(s)
- Jun Liu
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands. .,Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7FL, UK.
| | - Elena Carnero-Montoro
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18007, Spain.,Department of Twin Research and Genetic Epidemiology, King's College London, London, WC2R 2LS, UK
| | - Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health (APH) research institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1081BT, The Netherlands
| | - Samantha Lent
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Ivana Nedeljkovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Symen Ligthart
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, WC2R 2LS, UK.,Department of Biomedical Sciences, Chang Gung University, Taoyuan, 333, Taiwan.,Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, 333, Taiwan
| | - Tiphaine C Martin
- Department of Twin Research and Genetic Epidemiology, King's College London, London, WC2R 2LS, UK.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pooja R Mandaviya
- Department of Internal Medicine, Section of Pharmacology Vascular and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Rick Jansen
- Department of Psychiatry and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1081BT, The Netherlands
| | - Marjolein J Peters
- Department of Internal Medicine, Section of Pharmacology Vascular and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Liesbeth Duijts
- Division of Neonatology, Department of Pediatrics, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Division of Respiratory Medicine, Department of Pediatrics, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Department of Pediatrics, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Generation R Study Group, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - Janine F Felix
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Department of Pediatrics, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Generation R Study Group, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health (APH) research institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1081BT, The Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, Amsterdam Public Health (APH) research institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1081BT, The Netherlands
| | - Audrey Y Chu
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA.,The Framingham Heart Study, National Heart, Lung and Blood Institute, National Institutes of Health, Framingham, MA, 01702, USA
| | - Daniel Levy
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA.,The Framingham Heart Study, National Heart, Lung and Blood Institute, National Institutes of Health, Framingham, MA, 01702, USA
| | - Shih-Jen Hwang
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA.,The Framingham Heart Study, National Heart, Lung and Blood Institute, National Institutes of Health, Framingham, MA, 01702, USA
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Rahul Gondalia
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Elias L Salfati
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Christian Herder
- German Center for Diabetes Research (DZD), München-Neuherberg, 85764, Germany.,Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany.,Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Bertha A Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Ann Zenobia Moore
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Min A Jhun
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | | | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Donna K Arnett
- School of Public Health, University of Kentucky, Lexington, KY, 40536, USA
| | - Harald Grallert
- German Center for Diabetes Research (DZD), München-Neuherberg, 85764, Germany.,Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University Chicago, Evanston, IL, 60611, USA.,Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, NC, 27516, USA
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333ZA, The Netherlands.,Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, 2333ZA, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Department of Internal Medicine, Section of Pharmacology Vascular and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Eric J G Sijbrands
- Department of Internal Medicine, Section of Pharmacology Vascular and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, 3012, Switzerland
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,Department of Epidemiology and Biostatistics, Imperial College London, London, SW7 2AZ, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, WC2R 2LS, UK
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Marie-France Hivert
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, J1K0A5, Canada.,Diabetes Unit, Massachusetts General Hospital, Boston, MA, 02114, USA.,Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, 02215, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences and Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.,Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joyce B J van Meurs
- CARIM School for Cardiovascular Diseases, Maastricht Centre for Systems Biology (MaCSBio), and Departments of Biochemistry and Physiology, Maastricht University, Maastricht, 6211LK, The Netherlands
| | - Aaron Isaacs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands.,CARIM School for Cardiovascular Diseases, Maastricht Centre for Systems Biology (MaCSBio), and Departments of Biochemistry and Physiology, Maastricht University, Maastricht, 6211LK, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health (APH) research institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1081BT, The Netherlands
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, WC2R 2LS, UK
| | - Ayşe Demirkan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands. .,Department of Genetics, University Medical Center Groningen, Groningen, 9713GZ, The Netherlands. .,Section of Statistical Multi-Omics, Department of Experimental and Clinical Research, School of Bioscience and Medicine, Univeristy of Surrey, Guildford, GU2 7XH, UK.
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015GD, The Netherlands. .,Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7FL, UK. .,Leiden Academic Center for Drug Research, Leiden University, Leiden, 2311EZ, The Netherlands.
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O'Rourke CJ, Lafuente-Barquero J, Andersen JB. Epigenome Remodeling in Cholangiocarcinoma. Trends Cancer 2019; 5:335-350. [PMID: 31208696 DOI: 10.1016/j.trecan.2019.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 12/22/2022]
Abstract
Cholangiocarcinoma (CCA) comprises a heterogeneous collection of malignancies arising within the biliary tract, characterized by late diagnosis, innate chemoresistance, and abysmal prognosis. Sequencing data have uncovered recurrent mutations in diverse epigenetic regulators, implicating epigenetic destabilization at the root of these tumors. However, few studies have characterized biliary tumor epigenomes. In this Opinion article, we argue that an epigenome-oriented approach to CCA could establish diverse interconnections between many key aspects of research on this disease, including molecular heterogeneity, diverse cells of origin, and prominent tumor microenvironments. Moreover, we discuss plausible causes of epigenome dysregulation in biliary tumors, including genetic, epigenetic, metabolic, microenvironmental, and physiological factors. Lastly, we assess the translational potential of epigenomics in CCA to uncover robust biomarkers and therapeutic opportunities for this growing group of patients with limited treatment options.
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Affiliation(s)
- Colm J O'Rourke
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Juan Lafuente-Barquero
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark.
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39
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Zeeshan S, Xiong R, Liang BT, Ahmed Z. 100 Years of evolving gene-disease complexities and scientific debutants. Brief Bioinform 2019; 21:885-905. [PMID: 30972412 DOI: 10.1093/bib/bbz038] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/22/2022] Open
Abstract
It's been over 100 years since the word `gene' is around and progressively evolving in several scientific directions. Time-to-time technological advancements have heavily revolutionized the field of genomics, especially when it's about, e.g. triple code development, gene number proposition, genetic mapping, data banks, gene-disease maps, catalogs of human genes and genetic disorders, CRISPR/Cas9, big data and next generation sequencing, etc. In this manuscript, we present the progress of genomics from pea plant genetics to the human genome project and highlight the molecular, technical and computational developments. Studying genome and epigenome led to the fundamentals of development and progression of human diseases, which includes chromosomal, monogenic, multifactorial and mitochondrial diseases. World Health Organization has classified, standardized and maintained all human diseases, when many academic and commercial online systems are sharing information about genes and linking to associated diseases. To efficiently fathom the wealth of this biological data, there is a crucial need to generate appropriate gene annotation repositories and resources. Our focus has been how many gene-disease databases are available worldwide and which sources are authentic, timely updated and recommended for research and clinical purposes. In this manuscript, we have discussed and compared 43 such databases and bioinformatics applications, which enable users to connect, explore and, if possible, download gene-disease data.
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Affiliation(s)
- Saman Zeeshan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Ruoyun Xiong
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Bruce T Liang
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA.,Pat and Jim Calhoun Cardiology Center, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Zeeshan Ahmed
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
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40
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Li L, Fu K, Zhou W, Snyder M. Applying circulating tumor DNA methylation in the diagnosis of lung cancer. PRECISION CLINICAL MEDICINE 2019; 2:45-56. [PMID: 35694699 PMCID: PMC8985769 DOI: 10.1093/pcmedi/pbz003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/17/2019] [Accepted: 03/14/2019] [Indexed: 02/05/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Low dose computed tomography (LDCT) is commonly used for disease screening, with identified candidate cancerous regions further diagnosed using tissue biopsy. However, existing techniques are all invasive and unavoidably cause multiple complications. In contrast, liquid biopsy is a noninvasive, ideal surrogate for tissue biopsy that can identify circulating tumor DNA (ctDNA) containing tumorigenic signatures. It has been successfully implemented to assist treatment decisions and disease outcome prediction. ctDNA methylation, a type of lipid biopsy that profiles critical epigenetic alterations occurring during carcinogenesis, has gained increasing attention. Indeed, aberrant ctDNA methylation occurs at early stages in lung malignancy and therefore can be used as an alternative for the early diagnosis of lung cancer. In this review, we give a brief synopsis of the biological basis and detecting techniques of ctDNA methylation. We then summarize the latest progress in use of ctDNA methylation as a diagnosis biomarker. Lastly, we discuss the major issues that limit application of ctDNA methylation in the clinic, and propose possible solutions to enhance its usage.
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Affiliation(s)
- Lei Li
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, 37 Guoxuexiang, Chengdu, China
| | - Kai Fu
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
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41
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