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Saucedo-Cuevas L, Ma MPQ, Le AH, Akin N, Pham TD, Ho TM, Pita G, Gonzalez-Neira A, De Vos M, Smitz J, Anckaert E, Vuong LN. Epigenetic variation in neonatal tissues in infants conceived using capacitation-in vitro maturation vs. in vitro fertilization. Fertil Steril 2024; 121:506-518. [PMID: 38052376 DOI: 10.1016/j.fertnstert.2023.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023]
Abstract
OBJECTIVE To investigate alterations of the global DNA methylation profile in placenta, cord blood, and neonatal buccal smears in infants conceived using in vitro maturation (IVM) with a prematuration step (capacitation-IVM [CAPA-IVM]) vs. in vitro fertilization (IVF). DESIGN Analysis of data from the offspring of participants in a randomized controlled trial. SETTING Private clinic. PATIENTS Forty-six women with polycystic ovary syndrome and/or high antral follicle count and their offspring (58 newborns). INTERVENTION(S) Women with polycystic ovary syndrome and/or a high antral follicle count participating in the clinical trial were randomized to undergo CAPA-IVM or conventional IVF. MAIN OUTCOME MEASURE(S) At delivery, biological samples including cord blood, placental tissue, and a neonatal buccal smear were collected. Genome-wide DNA methylation was determined using the Illumina Infinium MethylationEPIC BeadChip. Variability in methylation was also considered, and mean variances for the two treatment categories were compared. RESULTS In neonatal buccal smears, there were no significant differences between the CAPA-IVM and conventional IVF groups on the basis of the CpG probe after linear regression analysis using a significant cut-off of false-discovery rate <0.05 and |Δβ|≥0.05. In cord blood, only one CpG site showed a significant gain of methylation in the CAPA-IVM group. In the placenta, CAPA-IVM was significantly associated with changes in methylation at five CpG sites. Significantly more variable DNA methylation was found in five probes in the placenta, 54 in cord blood, and two in buccal smears after IVM of oocytes. In cord blood samples, 20 CpG sites had more variable methylation in the conventional IVF vs. IVM group. Isolated CpG sites showing differences in methylation in cord blood were not associated with changes in gene expression of the overlapping genes. CONCLUSION(S) Capacitation-IVM appeared to be associated with only a small amount of epigenetic variation in cord blood, placental tissue, and neonate buccal smears. CLINICAL TRIAL REGISTRATION NUMBER NCT03405701 (www. CLINICALTRIALS gov).
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Affiliation(s)
- Laura Saucedo-Cuevas
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Mai P Q Ma
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam; HOPE Research Center, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Anh H Le
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam; HOPE Research Center, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Nazli Akin
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Toan D Pham
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam; HOPE Research Center, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Tuong M Ho
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam; HOPE Research Center, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Anna Gonzalez-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Michel De Vos
- Centre for Reproductive Medicine, Universitair Ziekenhuis Brussel, Brussels, Belgium; Department of Obstetrics, Gynecology, Perinatology, and Reproductology, Institute of Professional Education, Sechenov University, Moscow, Russia
| | - Johan Smitz
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Ellen Anckaert
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Lan N Vuong
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam.
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2
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Jiang H, Awuti G, Guo X. Construction of an Immunophenoscore-Related Signature for Evaluating Prognosis and Immunotherapy Sensitivity in Ovarian Cancer. ACS OMEGA 2023; 8:33017-33031. [PMID: 37720747 PMCID: PMC10500650 DOI: 10.1021/acsomega.3c04856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023]
Abstract
Ovarian cancer (OC) is the deadliest gynecological malignancy in the world, and immunotherapy is emerging as a promising treatment. Immunophenoscore (IPS) is a robust biomarker distinguishing sensitive responders from immunotherapy. In this study, we aimed to construct a prognostic model for predicting overall survival (OS) and identifying patients who would benefit from immunotherapy. First, we combined The Cancer Genome Atlas (TCGA) and The Cancer Immune Atlas (TCIA) data sets and incorporated 229 OC samples into a training cohort. The validation cohort included 240 OC samples from the Gene Expression Omnibus (GEO) cohort. The training cohort was divided into high- and low-IPS subgroups to obtain differentially expressed genes (DEGs). DEGs with OS were identified by Univariate Cox regression analysis. The least absolute shrinkage and selection operator (LASSO) Cox regression was used to construct the prognostic model. Then, immune and mutation analyses were performed to explore the relationship between the model and the tumor microenvironment (TME) and tumor mutation burden (TMB). Eighty-three DEGs were obtained between the high-and low-IPS subgroups, where 17 DEGs were associated with OS. The five essential genes were selected to establish the prognostic model, which showed high accuracy for predicting OS and could be an independent survival indicator. OC samples that were divided by risk scores showed distinguished immune status, TME, TMB, immunotherapy response, and chemotherapy sensitivity. Similar results were validated in the GEO cohort. We developed an immunophenoscore-related signature associated with the TME to predict OS and response to immunotherapy in OC.
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Affiliation(s)
- Haonan Jiang
- Shanghai
Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal
Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity
and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Guzhanuer Awuti
- Shanghai
Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal
Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity
and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xiaoqing Guo
- Department
of Gynecological Oncology, Shanghai First Maternity and Infant Hospital,
School of Medicine, Tongji University, Shanghai 200092, China
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3
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Fiorentino V, Pizzimenti C, Franchina M, Rossi ED, Tralongo P, Carlino A, Larocca LM, Martini M, Fadda G, Pierconti F. Bladder Epicheck Test: A Novel Tool to Support Urothelial Carcinoma Diagnosis in Urine Samples. Int J Mol Sci 2023; 24:12489. [PMID: 37569864 PMCID: PMC10420163 DOI: 10.3390/ijms241512489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Bladder cancer and upper urothelial tract carcinoma are common diseases with a high risk of recurrence, thus necessitating follow-up after initial treatment. The management of non-muscle invasive bladder carcinoma (NMIBC) after transurethral resection involves surveillance, intravesical therapy, and cytology with cystoscopy. Urinary cytology, cystoscopy, and radiological evaluation of the upper urinary tract are recommended during follow-up in the international urological guidelines. Cystoscopy is the standard examination for the first assessment and follow-up of NMIBC, and urine cytology is a widely used urinary test with high sensitivity for high-grade urothelial carcinoma (HGUC) and carcinoma in situ (CIS). In recent years, various urinary assays, including DNA methylation markers, have been used to detect bladder tumors. Among these, the Bladder EpiCheck test is one of the most widely used and is based on analysis of the methylation profile of urothelial cells to detect bladder neoplasms. This review assesses the importance of methylation analysis and the Bladder EpiCheck test as urinary biomarkers for diagnosing urothelial carcinomas in patients in follow-up for NMIBC, helping cytology and cystoscopy in doubtful cases. A combined approach of cytology and methylation analysis is suggested not only to diagnose HGUC, but also to predict clinical and histological recurrences.
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Affiliation(s)
- Vincenzo Fiorentino
- Department of Human Pathology of the Adult and Developmental Age “G. Barresi”, University of Messina, 98125 Messina, Italy; (M.F.); (G.F.)
| | - Cristina Pizzimenti
- PhD Programme in Translational Molecular Medicine and Surgery, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98125 Messina, Italy;
| | - Mariausilia Franchina
- Department of Human Pathology of the Adult and Developmental Age “G. Barresi”, University of Messina, 98125 Messina, Italy; (M.F.); (G.F.)
| | - Esther Diana Rossi
- Department of Women, Children and Public Health Sciences, Catholic University of the Sacred Heart, Agostino Gemelli IRCCS University Hospital Foundation, 00168 Rome, Italy; (E.D.R.); (P.T.); (A.C.); (F.P.)
| | - Pietro Tralongo
- Department of Women, Children and Public Health Sciences, Catholic University of the Sacred Heart, Agostino Gemelli IRCCS University Hospital Foundation, 00168 Rome, Italy; (E.D.R.); (P.T.); (A.C.); (F.P.)
| | - Angela Carlino
- Department of Women, Children and Public Health Sciences, Catholic University of the Sacred Heart, Agostino Gemelli IRCCS University Hospital Foundation, 00168 Rome, Italy; (E.D.R.); (P.T.); (A.C.); (F.P.)
| | - Luigi Maria Larocca
- Department of Medicine and Surgery, Saint Camillus International University of Health and Medical Sciences (UniCamillus), 00131 Rome, Italy;
| | - Maurizio Martini
- Department of Human Pathology of the Adult and Developmental Age “G. Barresi”, University of Messina, 98125 Messina, Italy; (M.F.); (G.F.)
| | - Guido Fadda
- Department of Human Pathology of the Adult and Developmental Age “G. Barresi”, University of Messina, 98125 Messina, Italy; (M.F.); (G.F.)
| | - Francesco Pierconti
- Department of Women, Children and Public Health Sciences, Catholic University of the Sacred Heart, Agostino Gemelli IRCCS University Hospital Foundation, 00168 Rome, Italy; (E.D.R.); (P.T.); (A.C.); (F.P.)
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Shabalala S, Ghai M, Okpeku M. Analysis of Y-STR diversity and DNA methylation variation among Black and Indian males from KwaZulu-Natal, South Africa. Forensic Sci Int 2023; 348:111682. [PMID: 37094501 DOI: 10.1016/j.forsciint.2023.111682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023]
Abstract
Y-chromosome short tandem repeats (Y-STRs) are essential in understanding genetic structure and diversity of human populations and, most importantly, in identification of male perpetrators in criminal investigations. DNA methylation differences have been reported in human populations and methylation pattern at the CpG sites found within or flanking the Y-STR sites could also aid in human identification. Studies based on DNA methylation (DNAm) at Y-STRs are currently limited. The current study aimed to analyze the Y-STR diversity in South African Black and Indian individuals living in KwaZulu-Natal, Durban, South Africa, with the Yfiler™ Plus Kit and to analyze DNAm patterns in Y-STR markers CpG sites. DNA from 247 stored saliva samples were isolated and quantified. Across the 27 Y-STR loci in the Yfiler™ Plus Kit, 253 alleles were observed in 113 South African Black and Indian males, 112 unique haplotypes were observed, and one haplotype appeared twice (two Black individuals). No statistically significant differences were observed in the genetic diversity between the two population groups (Fst = 0.028, p-value ≥ 0.05). The kit showed a high discrimination capacity (DC) of 0.9912 and an overall haplotype diversity (HD) = 0.9995 among the sampled population groups. DYS438 and DYS448 markers displayed 2 and 3 CpG sites, respectively. Based on the two-tailed Fisher's Exact test, there were no statistically significant differences in the DNAm levels at DYS438 CpGs of Black and Indian males (p > 0.05). The Yfiler™ Plus Kit can be considered highly discriminatory among South African Black and Indian males. Studies on the South African population using Yfiler™ Plus Kit are scarce. Hence, accumulating Y-STR data on the diverse South African population will enhance the representation of South Africa in STR databases. Knowing which Y-STR markers are significantly informative for South Africa is essential for developing Y-STR kits better suited for the different ethnic groups. And to the best of our knowledge, DNA methylation analysis in Y-STR for different ethnic groups has never been done before. Complementing Y-STR data with methylation knowledge could provide population-specific information for forensic identification.
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Affiliation(s)
- Sthabile Shabalala
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban 4000, South Africa
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban 4000, South Africa.
| | - Moses Okpeku
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban 4000, South Africa
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5
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Chan MHM, Merrill SM, Konwar C, Kobor MS. An integrative framework and recommendations for the study of DNA methylation in the context of race and ethnicity. DISCOVER SOCIAL SCIENCE AND HEALTH 2023; 3:9. [PMID: 37122633 PMCID: PMC10118232 DOI: 10.1007/s44155-023-00039-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023]
Abstract
Human social epigenomics research is critical to elucidate the intersection of social and genetic influences underlying racial and ethnic differences in health and development. However, this field faces major challenges in both methodology and interpretation with regard to disentangling confounded social and biological aspects of race and ethnicity. To address these challenges, we discuss how these constructs have been approached in the past and how to move forward in studying DNA methylation (DNAm), one of the best-characterized epigenetic marks in humans, in a responsible and appropriately nuanced manner. We highlight self-reported racial and ethnic identity as the primary measure in this field, and discuss its implications in DNAm research. Racial and ethnic identity reflects the biological embedding of an individual's sociocultural experience and environmental exposures in combination with the underlying genetic architecture of the human population (i.e., genetic ancestry). Our integrative framework demonstrates how to examine DNAm in the context of race and ethnicity, while considering both intrinsic factors-including genetic ancestry-and extrinsic factors-including structural and sociocultural environment and developmental niches-when focusing on early-life experience. We reviewed DNAm research in relation to health disparities given its relevance to race and ethnicity as social constructs. Here, we provide recommendations for the study of DNAm addressing racial and ethnic differences, such as explicitly acknowledging the self-reported nature of racial and ethnic identity, empirically examining the effects of genetic variants and accounting for genetic ancestry, and investigating race-related and culturally regulated environmental exposures and experiences. Supplementary Information The online version contains supplementary material available at 10.1007/s44155-023-00039-z.
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Affiliation(s)
- Meingold Hiu-ming Chan
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Chaini Konwar
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
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6
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Szalanczy AM, Goff E, Seshie O, Deal A, Grzybowski M, Klotz J, Chuang Key CC, Geurts AM, Solberg Woods LC. Keratinocyte-associated protein 3 plays a role in body weight and adiposity with differential effects in males and females. Front Genet 2022; 13:942574. [PMID: 36212147 PMCID: PMC9535360 DOI: 10.3389/fgene.2022.942574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Despite the obesity crisis in the United States, the underlying genetics are poorly understood. Our lab previously identified Keratinocyte-associated protein 3, Krtcap3, as a candidate gene for adiposity through a genome-wide association study in outbred rats, where increased liver expression of Krtcap3 correlated with decreased fat mass. Here we seek to confirm that Krtcap3 expression affects adiposity traits. To do so, we developed an in vivo whole-body Krtcap3 knock-out (KO) rat model. Wild-type (WT) and KO rats were placed onto a high-fat (HFD) or low-fat diet (LFD) at 6 weeks of age and were maintained on diet for 13 weeks, followed by assessments of metabolic health. We hypothesized that Krtcap3-KO rats will have increased adiposity and a worsened metabolic phenotype relative to WT. We found that KO male and female rats have significantly increased body weight versus WT, with the largest effect in females on a HFD. KO females also ate more and had greater adiposity, but were more insulin sensitive than WT regardless of diet condition. Although KO males weighed more than WT under both diet conditions, there were no differences in eating behavior or fat mass. Interestingly, KO males on a HFD were more insulin resistant than WT. This study confirms that Krtcap3 plays a role in body weight regulation and demonstrates genotype- and sex-specific effects on food intake, adiposity, and insulin sensitivity. Future studies will seek to better understand these sex differences, the role of diet, and establish a mechanism for Krtcap3 in obesity.
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Affiliation(s)
- Alexandria M. Szalanczy
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Emily Goff
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Osborne Seshie
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Aaron Deal
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Michael Grzybowski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jason Klotz
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Chia-Chi Chuang Key
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Aron M. Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Leah C. Solberg Woods
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
- *Correspondence: Leah C. Solberg Woods,
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7
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Meloni M, Moll T, Issaka A, Kuzawa CW. A biosocial return to race? A cautionary view for the postgenomic era. Am J Hum Biol 2022; 34:e23742. [PMID: 35275433 PMCID: PMC9286859 DOI: 10.1002/ajhb.23742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/20/2022] [Indexed: 12/21/2022] Open
Abstract
Recent studies demonstrating epigenetic and developmental sensitivity to early environments, as exemplified by fields like the Developmental Origins of Health and Disease (DOHaD) and environmental epigenetics, are bringing new data and models to bear on debates about race, genetics, and society. Here, we first survey the historical prominence of models of environmental determinism in early formulations of racial thinking to illustrate how notions of direct environmental effects on bodies have been used to naturalize racial hierarchy and inequalities in the past. Next, we conduct a scoping review of postgenomic work in environmental epigenetics and DOHaD that looks at the role of race/ethnicity in human health (2000–2021). Although there is substantial heterogeneity in how race is conceptualized and interpreted across studies, we observe practices that may unwittingly encourage typological thinking, including: using DNA methylation as a novel marker of racial classification; neglect of variation and reversibility within supposedly homogenous racial groups; and a tendency to label and reify whole groups as pathologized or impaired. Even in the very different politico‐economic and epistemic context of contemporary postgenomic science, these trends echo deeply held beliefs in Western thinking which claimed that different environments shape different bodies and then used this logic to argue for essential differences between Europeans and non‐Europeans. We conclude with a series of suggestions on interpreting and reporting findings in these fields that we feel will help researchers harness this work to benefit disadvantaged groups while avoiding the inadvertent dissemination of new and old forms of stigma or prejudice.
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Affiliation(s)
- Maurizio Meloni
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Victoria, Australia
| | - Tessa Moll
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Victoria, Australia.,Department School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Cape Town, South Africa
| | - Ayuba Issaka
- School of Health and Social Development, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Victoria, Australia
| | - Christopher W Kuzawa
- Department of Anthropology and Institute for Policy Research, Northwestern University, Evanston, Illinois, USA
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8
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Epigenomic Modifications in Modern and Ancient Genomes. Genes (Basel) 2022; 13:genes13020178. [PMID: 35205223 PMCID: PMC8872240 DOI: 10.3390/genes13020178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/26/2022] Open
Abstract
Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.
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Methylmercury and Polycyclic Aromatic Hydrocarbons in Mediterranean Seafood: A Molecular Anthropological Perspective. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112311179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Eating seafood has numerous health benefits; however, it constitutes one of the main sources of exposure to several harmful environmental pollutants, both of anthropogenic and natural origin. Among these, methylmercury and polycyclic aromatic hydrocarbons give rise to concerns related to their possible effects on human biology. In the present review, we summarize the results of epidemiological investigations on the genetic component of individual susceptibility to methylmercury and polycyclic aromatic hydrocarbons exposure in humans, and on the effects that these two pollutants have on human epigenetic profiles (DNA methylation). Then, we provide evidence that Mediterranean coastal communities represent an informative case study to investigate the potential impact of methylmercury and polycyclic aromatic hydrocarbons on the human genome and epigenome, since they are characterized by a traditionally high local seafood consumption, and given the characteristics that render the Mediterranean Sea particularly polluted. Finally, we discuss the challenges of a molecular anthropological approach to this topic.
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10
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Becker J, Böhme P, Reckert A, Eickhoff SB, Koop BE, Blum J, Gündüz T, Takayama M, Wagner W, Ritz-Timme S. Evidence for differences in DNA methylation between Germans and Japanese. Int J Legal Med 2021; 136:405-413. [PMID: 34739581 PMCID: PMC8847189 DOI: 10.1007/s00414-021-02736-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
As a contribution to the discussion about the possible effects of ethnicity/ancestry on age estimation based on DNA methylation (DNAm) patterns, we directly compared age-associated DNAm in German and Japanese donors in one laboratory under identical conditions. DNAm was analyzed by pyrosequencing for 22 CpG sites (CpGs) in the genes PDE4C, RPA2, ELOVL2, DDO, and EDARADD in buccal mucosa samples from German and Japanese donors (N = 368 and N = 89, respectively). Twenty of these CpGs revealed a very high correlation with age and were subsequently tested for differences between German and Japanese donors aged between 10 and 65 years (N = 287 and N = 83, respectively). ANCOVA was performed by testing the Japanese samples against age- and sex-matched German subsamples (N = 83 each; extracted 500 times from the German total sample). The median p values suggest a strong evidence for significant differences (p < 0.05) at least for two CpGs (EDARADD, CpG 2, and PDE4C, CpG 2) and no differences for 11 CpGs (p > 0.3). Age prediction models based on DNAm data from all 20 CpGs from German training data did not reveal relevant differences between the Japanese test samples and German subsamples. Obviously, the high number of included “robust CpGs” prevented relevant effects of differences in DNAm at two CpGs. Nevertheless, the presented data demonstrates the need for further research regarding the impact of confounding factors on DNAm in the context of ethnicity/ancestry to ensure a high quality of age estimation. One approach may be the search for “robust” CpG markers—which requires the targeted investigation of different populations, at best by collaborative research with coordinated research strategies.
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Affiliation(s)
- J Becker
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany.
| | - P Böhme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - A Reckert
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - S B Eickhoff
- Institute for Systems Neuroscience, University Hospital Düsseldorf, 40225, Düsseldorf, Germany.,Institute of Neuroscience and Medicine, Brain and Behaviour, (INM-7), Research Centre Jülich, 52428, Jülich, Germany
| | - B E Koop
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - J Blum
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - T Gündüz
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - M Takayama
- Department of Forensic Medicine, Faculty of Medicine, Fukuoka University, Fukuoka, Japan.,Tokyo Medical Examiner's Office, Tokyo, Japan
| | - W Wagner
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - S Ritz-Timme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
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11
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Yang HC, Chen CW, Lin YT, Chu SK. Genetic ancestry plays a central role in population pharmacogenomics. Commun Biol 2021; 4:171. [PMID: 33547344 PMCID: PMC7864978 DOI: 10.1038/s42003-021-01681-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Recent studies have pointed out the essential role of genetic ancestry in population pharmacogenetics. In this study, we analyzed the whole-genome sequencing data from The 1000 Genomes Project (Phase 3) and the pharmacogenetic information from Drug Bank, PharmGKB, PharmaADME, and Biotransformation. Here we show that ancestry-informative markers are enriched in pharmacogenetic loci, suggesting that trans-ancestry differentiation must be carefully considered in population pharmacogenetics studies. Ancestry-informative pharmacogenetic loci are located in both protein-coding and non-protein-coding regions, illustrating that a whole-genome analysis is necessary for an unbiased examination over pharmacogenetic loci. Finally, those ancestry-informative pharmacogenetic loci that target multiple drugs are often a functional variant, which reflects their importance in biological functions and pathways. In summary, we develop an efficient algorithm for an ultrahigh-dimensional principal component analysis. We create genetic catalogs of ancestry-informative markers and genes. We explore pharmacogenetic patterns and establish a high-accuracy prediction panel of genetic ancestry. Moreover, we construct a genetic ancestry pharmacogenomic database Genetic Ancestry PhD (http://hcyang.stat.sinica.edu.tw/databases/genetic_ancestry_phd/). Hsin-Chou Yang et al. examine population structure in several genomic databases and identify that pharmacogenetic loci are enriched for markers of genetic ancestry. Their results suggest that genetic ancestry must be carefully considered in population pharmacogenetics studies.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan. .,Institute of Statistics, National Cheng Kung University, Tainan, Taiwan. .,Institute of Public Health, National Yang-Ming University, Taipei, Taiwan.
| | - Chia-Wei Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Shih-Kai Chu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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12
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Daca-Roszak P, Jaksik R, Paczkowska J, Witt M, Ziętkiewicz E. Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin. BMC Genomics 2020; 21:706. [PMID: 33045984 PMCID: PMC7549247 DOI: 10.1186/s12864-020-07092-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023] Open
Abstract
Background Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the methylation status of individual CpG sites. It has been demonstrated that a limited number of carefully selected differentially methylated sites may allow discrimination between main human populations. However, most of the few published results have been performed exclusively on B-lymphocyte cell lines. Results The goal of our study was to identify a set of CpG sites sufficient to discriminate between populations of European and Chinese ancestry based on the difference in the DNA methylation profile not only in cell lines but also in primary cell samples. The preliminary selection of CpG sites differentially methylated in these two populations (pop-CpGs) was based on the analysis of two groups of commercially available ethnically-specific B-lymphocyte cell lines, performed using Illumina Infinium Human Methylation 450 BeadChip Array. A subset of 10 pop-CpGs characterized by the best differentiating criteria (|Mdiff| > 1, q < 0.05; lack of the confounding genomic features), and 10 additional CpGs in their immediate vicinity, were further tested using pyrosequencing technology in both B-lymphocyte cell lines and in the primary samples of the peripheral blood representing two analyzed populations. To assess the population-discriminating potential of the selected set of CpGs (further referred to as “composite pop (CEU-CHB)-CpG marker”), three classification methods were applied. The predictive ability of the composite 8-site pop (CEU-CHB)-CpG marker was assessed using 10-fold cross-validation method on two independent sets of samples. Conclusions Our results showed that less than 10 pop-CpG sites may distinguish populations of European and Chinese ancestry; importantly, this small composite pop-CpG marker performs well in both lymphoblastoid cell lines and in non-homogenous blood samples regardless of a gender.
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Affiliation(s)
- Patrycja Daca-Roszak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland.
| | - Roman Jaksik
- Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland
| | - Julia Paczkowska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Michał Witt
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Ewa Ziętkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
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13
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Kougioumtsidou N, Vavoulidis E, Nasioutziki M, Symeonidou M, Pratilas GC, Mareti E, Petousis S, Chatzikyriakidou A, Grimbizis G, Theodoridis T, Miliaras D, Dinas K, Zepiridis L. DNA methylation patterns of RAR-β2 and RASSF1A gene promoters in FNAB samples from Greek population with benign or malignant breast lesions. Diagn Cytopathol 2020; 49:153-164. [PMID: 32530576 DOI: 10.1002/dc.24513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/27/2020] [Accepted: 05/19/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Promoter hypermethylation is common in Breast Cancer (BC) with studies mainly in histological specimens showing frequent methylation of tumor suppressor genes (TSGs) compared with normal tissues. The aim of this study was to estimate the frequency of promoter methylation of RAR-β2 and RASSF1A genes in breast FNAB material aiming to evaluate the methylation status of these two genes as biomarker for detecting BC in Greek population. METHODS FNAB material from 104 patients was collected for cytological evaluation and epigenetic analysis. DNA was extracted and subjected to bisulfite conversion. A methylation-specific PCR was carried out and the final products were separated with electrophoresis in 2% agarose gels. RESULTS From 104 samples, RASSF1A hypermethylation was observed in 78 (75%) and RAR-β2 hypermethylation in 64 (61.6%). 84% and 78% of the cases diagnosed with breast malignancy (n = 50) were methylated for RASSF1A and RAR-β2, respectively. Methylated RASSF1A and RAR-β2 were also detected in 88.3% and 76.5% in samples diagnosed as suspicious for malignancy (n = 17) and in 57.2% of samples diagnosed with atypia (n = 14). The Odds Ratio for breast malignancy was 4.545 in patients with RASSF1A hypermethylation and 9.167 in patients with RAR-β2 hypermethylation underlying their promoter's methylation positive correlation with breast malignancy. CONCLUSION To optimize the sensitivity and specificity of this epigenetic setting, more TSGs related to BC should be gradually imported in our evaluated methylation panel and be validated in a larger study sample with the aim that the obtained epigenetic profiles will provide clinicians with valuable tools for management of BC patients in Greece.
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Affiliation(s)
- Niki Kougioumtsidou
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Eleftherios Vavoulidis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Maria Nasioutziki
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Marianthi Symeonidou
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Georgios Chrysostomos Pratilas
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Mareti
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Stamatios Petousis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Anthoula Chatzikyriakidou
- Faculty of Medicine, Laboratory of Medical Biology-Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Gregorios Grimbizis
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Theodoros Theodoridis
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Dimosthenis Miliaras
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Dinas
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Leonidas Zepiridis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
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14
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Tkachev A, Stepanova V, Zhang L, Khrameeva E, Zubkov D, Giavalisco P, Khaitovich P. Differences in lipidome and metabolome organization of prefrontal cortex among human populations. Sci Rep 2019; 9:18348. [PMID: 31797944 PMCID: PMC6893025 DOI: 10.1038/s41598-019-53762-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Human populations, despite their overwhelming similarity, contain some distinct phenotypic, genetic, epigenetic, and gene expression features. In this study, we explore population differences at yet another level of molecular phenotype: the abundance of non-polar and polar low molecular weight compounds, lipids and metabolites in the prefrontal cortical region of the brain. We assessed the abundance of 1,670 lipids and 258 metabolites in 146 Han Chinese, 97 Western European, and 60 African American individuals of varying ages, covering most of the lifespan. The statistical analysis and logistic regression models both demonstrated extensive lipid and metabolic divergence of the Han Chinese individuals from the other two populations. This divergence was age-dependent, peaking in young adults, and involved metabolites and lipids clustering in specific metabolic pathways.
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Affiliation(s)
- Anna Tkachev
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia.,Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per. 19/1, 127051, Moscow, Russia
| | - Vita Stepanova
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia.,Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per. 19/1, 127051, Moscow, Russia
| | - Lei Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, 200031, Shanghai, China
| | | | - Dmitry Zubkov
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
| | - Patrick Giavalisco
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9B, 50931, Cologne, Germany.
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia. .,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, 200031, Shanghai, China. .,Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
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15
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Kader F, Ghai M, Olaniran AO. Characterization of DNA methylation-based markers for human body fluid identification in forensics: a critical review. Int J Legal Med 2019; 134:1-20. [PMID: 31713682 DOI: 10.1007/s00414-019-02181-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]
Abstract
Body fluid identification in crime scene investigations aids in reconstruction of crime scenes. Several studies have identified and reported differentially methylated sites (DMSs) and regions (DMRs) which differ between forensically relevant tissues (tDMRs) and body fluids. Diverse factors affect methylation patterns such as the environment, diets, lifestyle, disease, ethnicity, genetic variation, amongst others. Thus, it is important to analyse the stability of markers employed for forensic identification. Furthermore, even though epigenetic modifications are described as stable and heritable, epigenetic inheritance of potential markers for body fluid identification needs to be assessed in the long term. Here, we discuss the current status of reported DNA methylation-based markers and their verification studies. Such thorough investigation is crucial to develop a stable panel of DNA methylation-based markers for accurate body fluid identification.
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Affiliation(s)
- Farzeen Kader
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa.
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa
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16
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Abstract
Risk of disease is multifactorial and can be shaped by socio-economic, demographic, cultural, environmental and genetic factors. Our understanding of the genetic determinants of disease risk has greatly advanced with the advent of genome-wide association studies (GWAS), which detect associations between genetic variants and complex traits or diseases by comparing populations of cases and controls. However, much of this discovery has occurred through GWAS of individuals of European ancestry, with limited representation of other populations, including from Africa, The Americas, Asia and Oceania. Population demography, genetic drift and adaptation to environments over thousands of years have led globally to the diversification of populations. This global genomic diversity can provide new opportunities for discovery and translation into therapies, as well as a better understanding of population disease risk. Large-scale multi-ethnic and representative biobanks and population health resources provide unprecedented opportunities to understand the genetic determinants of disease on a global scale.
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17
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Jaacks LM, Vandevijvere S, Pan A, McGowan CJ, Wallace C, Imamura F, Mozaffarian D, Swinburn B, Ezzati M. The obesity transition: stages of the global epidemic. Lancet Diabetes Endocrinol 2019; 7:231-240. [PMID: 30704950 PMCID: PMC7360432 DOI: 10.1016/s2213-8587(19)30026-9] [Citation(s) in RCA: 571] [Impact Index Per Article: 114.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
Abstract
The global prevalence of obesity has increased substantially over the past 40 years, from less than 1% in 1975, to 6-8% in 2016, among girls and boys, and from 3% to 11% among men and from 6% to 15% among women over the same time period. Our aim was to consolidate the evidence on the epidemiology of obesity into a conceptual model of the so-called obesity transition. We used illustrative examples from the 30 most populous countries, representing 77·5% of the world's population to propose a four stage model. Stage 1 of the obesity transition is characterised by a higher prevalence of obesity in women than in men, in those with higher socioeconomic status than in those with lower socioeconomic status, and in adults than in children. Many countries in south Asia and sub-Saharan Africa are presently in this stage. In countries in stage 2 of the transition, there has been a large increase in the prevalence among adults, a smaller increase among children, and a narrowing of the gap between sexes and in socioeconomic differences among women. Many Latin American and Middle Eastern countries are presently at this stage. High-income east Asian countries are also at this stage, albeit with a much lower prevalence of obesity. In stage 3 of the transition, the prevalence of obesity among those with lower socioeconomic status surpasses that of those with higher socioeconomic status, and plateaus in prevalence can be observed in women with high socioeconomic status and in children. Most European countries are presently at this stage. There are too few signs of countries entering into the proposed fourth stage of the transition, during which obesity prevalence declines, to establish demographic patterns. This conceptual model is intended to provide guidance to researchers and policy makers in identifying the current stage of the obesity transition in a population, anticipating subpopulations that will develop obesity in the future, and enacting proactive measures to attenuate the transition, taking into consideration local contextual factors.
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Affiliation(s)
- Lindsay M Jaacks
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, USA.
| | | | - An Pan
- Department of Epidemiology and Biostatistics, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Craig J McGowan
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Chelsea Wallace
- School of Population Health, The University of Auckland, Auckland, New Zealand
| | - Fumiaki Imamura
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Dariush Mozaffarian
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Boyd Swinburn
- School of Population Health, The University of Auckland, Auckland, New Zealand; Global Obesity Centre, Deakin University, Melbourne, VIC, Australia
| | - Majid Ezzati
- School of Public Health, MRC-PHE Centre for Environment and Health, and WHO Collaborating Centre on NCD Surveillance and Epidemiology, Imperial College London, London, UK
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18
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Loss of SMYD1 Results in Perinatal Lethality via Selective Defects within Myotonic Muscle Descendants. Diseases 2018; 7:diseases7010001. [PMID: 30577454 PMCID: PMC6473627 DOI: 10.3390/diseases7010001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 12/11/2022] Open
Abstract
SET and MYND Domain 1 (SMYD1) is a cardiac and skeletal muscle-specific, histone methyl transferase that is critical for both embryonic and adult heart development and function in both mice and men. We report here that skeletal muscle-specific, myogenin (myoG)-Cre-mediated conditional knockout (CKO) of Smyd1 results in perinatal death. As early as embryonic day 12.5, Smyd1 CKOs exhibit multiple skeletal muscle defects in proliferation, morphology, and gene expression. However, all myotonic descendants are not afflicted equally. Trunk muscles are virtually ablated with excessive accumulation of brown adipose tissue (BAT), forelimb muscles are disorganized and improperly differentiated, but other muscles, such as the masseter, are normal. While expression of major myogenic regulators went unscathed, adaptive and innate immune transcription factors critical for BAT development/physiology were downregulated. Whereas classical mitochondrial BAT accumulation went unscathed following loss of SMYD1, key transcription factors, including PRDM16, UCP-1, and CIDE-a that control skeletal muscle vs. adipose fate, were downregulated. Finally, in rare adults that survive perinatal lethality, SMYD1 controls specification of some, but not all, skeletal muscle fiber-types.
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19
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Giuliani C, Biggs D, Nguyen TT, Marasco E, De Fanti S, Garagnani P, Le Phan MT, Nguyen VN, Luiselli D, Romeo G. First evidence of association between past environmental exposure to dioxin and DNA methylation of CYP1A1 and IGF2 genes in present day Vietnamese population. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:976-985. [PMID: 30373043 DOI: 10.1016/j.envpol.2018.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 06/08/2023]
Abstract
During the Vietnam War, the United States military sprayed over 74 million litres of Agent Orange (AO) to destroy forest cover as a counterinsurgency tactic in Vietnam, Laos and Cambodia. The main ingredient was contaminated by 2,3,7,8-tetrachlorodibenzo-paradioxin (TCDD). DNA methylation (DNAm) differences are potential biomarker of environmental toxicants exposure. The aim of this study was to perform a preliminary investigation of the DNAm levels from peripheral blood of the present-day Vietnamese population, including individuals whose parents, according to historical data, were exposed to AO/TCDD during the war. 94 individuals from heavily sprayed areas (cases) and 94 individuals from non-sprayed areas (controls) were studied, and historical data on alleged exposure of parents collected. 94 cases were analysed considering those whose father/parents participated in the war (N = 29) and considering the place of residence of both parents (64 living in sprayed areas versus 30 in non-contaminated areas). DNAm levels in CYP1A1 and IGF2 genes were measured (MALDI-TOF technology). The analyses showed that: 1) one CpG site in the CYP1A1 and one in the IGF2 gene showed significant differences in DNAm levels between cases and controls; 2) the CYP1A1 region resulted to be hypomethylated (in 9 out of 16 sites/units; p-val<0.01) in 29 individuals whose father/parents participated in the war in the spray zones; 3) we showed that the place of residence of both parents influenced methylation levels of the CYP1A1 and IGF2 genes (p-val<0.05). In conclusion this study indicates that past environmental exposure to dioxin (AO/TCDD) shapes the DNAm profile of CYP1A1 and that the place of living for parents in former spray zones influences DNAm of CYP1A1 and IGF2 genes. These results open the way to new applications of DNAm as potential biomarker(s) of past human exposure to dioxin.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy; School of Anthropology and Museum Ethnography, University of Oxford, UK.
| | - David Biggs
- Department of History and School of Public Policy, University of California, Riverside, USA
| | | | - Elena Marasco
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Sara De Fanti
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy; Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86 Stockholm, Sweden
| | | | | | - Donata Luiselli
- Department for the Cultural Heritage (DBC), Campus of Ravenna, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- Medical Genetics Unit, S. Orsola Hospital, University of Bologna, Italy and European School of Genetic Medicine, Italy
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20
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Tungekar A, Mandarthi S, Mandaviya PR, Gadekar VP, Tantry A, Kotian S, Reddy J, Prabha D, Bhat S, Sahay S, Mascarenhas R, Badkillaya RR, Nagasampige MK, Yelnadu M, Pawar H, Hebbar P, Kashyap MK. ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. Sci Rep 2018. [PMID: 30143675 DOI: 10.1038/s41598-018-30579-3,] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Esophageal cancer (EC) is the eighth most aggressive malignancy and its treatment remains a challenge due to the lack of biomarkers that can facilitate early detection. EC is identified in two major histological forms namely - Adenocarcinoma (EAC) and Squamous cell carcinoma (ESCC), each showing differences in the incidence among populations that are geographically separated. Hence the detection of potential drug target and biomarkers demands a population-centric understanding of the molecular and cellular mechanisms of EC. To provide an adequate impetus to the biomarker discovery for ESCC, which is the most prevalent esophageal cancer worldwide, here we have developed ESCC ATLAS, a manually curated database that integrates genetic, epigenetic, transcriptomic, and proteomic ESCC-related genes from the published literature. It consists of 3475 genes associated to molecular signatures such as, altered transcription (2600), altered translation (560), contain copy number variation/structural variations (233), SNPs (102), altered DNA methylation (82), Histone modifications (16) and miRNA based regulation (261). We provide a user-friendly web interface ( http://www.esccatlas.org , freely accessible for academic, non-profit users) that facilitates the exploration and the analysis of genes among different populations. We anticipate it to be a valuable resource for the population specific investigation and biomarker discovery for ESCC.
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Affiliation(s)
- Asna Tungekar
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Sumana Mandarthi
- Mbiomics, Manipal, Karnataka, India.,Department of Biochemistry, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Pooja Rajendra Mandaviya
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Veerendra P Gadekar
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.,Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria
| | - Ananthajith Tantry
- Mbiomics, Manipal, Karnataka, India.,Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
| | - Sowmya Kotian
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Jyotshna Reddy
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Sushma Bhat
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Roshan Mascarenhas
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.,Newcastle University Medicine Malaysia, Johor Bahru, 79200, Malaysia
| | - Raghavendra Rao Badkillaya
- Mbiomics, Manipal, Karnataka, India.,Department of Biotechnology, Alva's college, Moodubidre, Karnataka, India
| | - Manoj Kumar Nagasampige
- Mbiomics, Manipal, Karnataka, India.,Department of Biotechnology, Sikkim Manipal University, Gangtok, Sikkim, 737102, India
| | - Mohan Yelnadu
- Mbiomics, Manipal, Karnataka, India.,Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India.,Infosys Technologies Ltd, Bangalore, Karnataka, India.,Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Harsh Pawar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Prashantha Hebbar
- Mbiomics, Manipal, Karnataka, India. .,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.
| | - Manoj Kumar Kashyap
- Mbiomics, Manipal, Karnataka, India. .,Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India. .,School of Life and Allied Health Sciences, Glocal University, Saharanpur, Uttar Pradesh, 247001, India. .,Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria.
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21
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Tungekar A, Mandarthi S, Mandaviya PR, Gadekar VP, Tantry A, Kotian S, Reddy J, Prabha D, Bhat S, Sahay S, Mascarenhas R, Badkillaya RR, Nagasampige MK, Yelnadu M, Pawar H, Hebbar P, Kashyap MK. ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. Sci Rep 2018; 8:12715. [PMID: 30143675 PMCID: PMC6109081 DOI: 10.1038/s41598-018-30579-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
Esophageal cancer (EC) is the eighth most aggressive malignancy and its treatment remains a challenge due to the lack of biomarkers that can facilitate early detection. EC is identified in two major histological forms namely - Adenocarcinoma (EAC) and Squamous cell carcinoma (ESCC), each showing differences in the incidence among populations that are geographically separated. Hence the detection of potential drug target and biomarkers demands a population-centric understanding of the molecular and cellular mechanisms of EC. To provide an adequate impetus to the biomarker discovery for ESCC, which is the most prevalent esophageal cancer worldwide, here we have developed ESCC ATLAS, a manually curated database that integrates genetic, epigenetic, transcriptomic, and proteomic ESCC-related genes from the published literature. It consists of 3475 genes associated to molecular signatures such as, altered transcription (2600), altered translation (560), contain copy number variation/structural variations (233), SNPs (102), altered DNA methylation (82), Histone modifications (16) and miRNA based regulation (261). We provide a user-friendly web interface ( http://www.esccatlas.org , freely accessible for academic, non-profit users) that facilitates the exploration and the analysis of genes among different populations. We anticipate it to be a valuable resource for the population specific investigation and biomarker discovery for ESCC.
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Affiliation(s)
- Asna Tungekar
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Sumana Mandarthi
- Mbiomics, Manipal, Karnataka, India
- Department of Biochemistry, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Pooja Rajendra Mandaviya
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Veerendra P Gadekar
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria
| | - Ananthajith Tantry
- Mbiomics, Manipal, Karnataka, India
- Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
| | - Sowmya Kotian
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Jyotshna Reddy
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Sushma Bhat
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Roshan Mascarenhas
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
- Newcastle University Medicine Malaysia, Johor Bahru, 79200, Malaysia
| | - Raghavendra Rao Badkillaya
- Mbiomics, Manipal, Karnataka, India
- Department of Biotechnology, Alva's college, Moodubidre, Karnataka, India
| | - Manoj Kumar Nagasampige
- Mbiomics, Manipal, Karnataka, India
- Department of Biotechnology, Sikkim Manipal University, Gangtok, Sikkim, 737102, India
| | - Mohan Yelnadu
- Mbiomics, Manipal, Karnataka, India
- Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
- Infosys Technologies Ltd, Bangalore, Karnataka, India
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Harsh Pawar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Prashantha Hebbar
- Mbiomics, Manipal, Karnataka, India.
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.
| | - Manoj Kumar Kashyap
- Mbiomics, Manipal, Karnataka, India.
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India.
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, Uttar Pradesh, 247001, India.
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria.
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22
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Banerjee N, Polushina T, Bettella F, Giddaluru S, Steen VM, Andreassen OA, Le Hellard S. Recently evolved human-specific methylated regions are enriched in schizophrenia signals. BMC Evol Biol 2018; 18:63. [PMID: 29747567 PMCID: PMC5946405 DOI: 10.1186/s12862-018-1177-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 04/11/2018] [Indexed: 01/10/2023] Open
Abstract
Background One explanation for the persistence of schizophrenia despite the reduced fertility of patients is that it is a by-product of recent human evolution. This hypothesis is supported by evidence suggesting that recently-evolved genomic regions in humans are involved in the genetic risk for schizophrenia. Using summary statistics from genome-wide association studies (GWAS) of schizophrenia and 11 other phenotypes, we tested for enrichment of association with GWAS traits in regions that have undergone methylation changes in the human lineage compared to Neanderthals and Denisovans, i.e. human-specific differentially methylated regions (DMRs). We used analytical tools that evaluate polygenic enrichment of a subset of genomic variants against all variants. Results Schizophrenia was the only trait in which DMR SNPs showed clear enrichment of association that passed the genome-wide significance threshold. The enrichment was not observed for Neanderthal or Denisovan DMRs. The enrichment seen in human DMRs is comparable to that for genomic regions tagged by Neanderthal Selective Sweep markers, and stronger than that for Human Accelerated Regions. The enrichment survives multiple testing performed through permutation (n = 10,000) and bootstrapping (n = 5000) in INRICH (p < 0.01). Some enrichment of association with height was observed at the gene level. Conclusions Regions where DNA methylation modifications have changed during recent human evolution show enrichment of association with schizophrenia and possibly with height. Our study further supports the hypothesis that genetic variants conferring risk of schizophrenia co-occur in genomic regions that have changed as the human species evolved. Since methylation is an epigenetic mark, potentially mediated by environmental changes, our results also suggest that interaction with the environment might have contributed to that association. Electronic supplementary material The online version of this article (10.1186/s12862-018-1177-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Niladri Banerjee
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tatiana Polushina
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Francesco Bettella
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Sudheer Giddaluru
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Vidar M Steen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ole A Andreassen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Stephanie Le Hellard
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway. .,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway. .,Department of Clinical Medicine, Laboratory Building, Haukeland University Hospital, N-5021, Bergen, Norway.
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23
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Barcelona de Mendoza V, Huang Y, Crusto CA, Sun YV, Taylor JY. Perceived Racial Discrimination and DNA Methylation Among African American Women in the InterGEN Study. Biol Res Nurs 2018; 20:145-152. [PMID: 29258399 PMCID: PMC5741522 DOI: 10.1177/1099800417748759] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Experiences of racial discrimination have been associated with poor health outcomes. Little is known, however, about how perceived racial discrimination influences DNA methylation (DNAm) among African Americans (AAs). We examined the association of experiences of discrimination with DNAm among AA women in the Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN) study. METHODS The InterGEN study examines the effects of genetic and psychological factors on blood pressure among AA women and their children. Measures include the Major Life Discrimination (MLD) and the Race-Related Events (RES) scales. In the present analysis, we examined discrimination and DNAm at baseline in the InterGEN study. The 850K EPIC Illumina BeadChip was used for evaluating DNAm in this epigenome-wide association study (EWAS). RESULTS One hundred and fifty-two women contributed data for the RES-EWAS analysis and 147 for the MLD-EWAS analysis. Most were 30-39 years old, nonsmokers, had some college education, and had incomes CONCLUSION We observed significant epigenetic associations between disease-associated genes (e.g., schizophrenia, bipolar disorder, and asthma) and perceived discrimination as measured by the MLD Scale. Future health disparities research should include epigenetics in high-risk populations to elucidate functional consequences induced by the psychosocial environment.
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Affiliation(s)
| | - Yunfeng Huang
- 2 Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Cindy A Crusto
- 3 Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Yan V Sun
- 2 Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
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24
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De Nys S, Duca RC, Nawrot T, Hoet P, Van Meerbeek B, Van Landuyt KL, Godderis L. Temporal variability of global DNA methylation and hydroxymethylation in buccal cells of healthy adults: Association with air pollution. ENVIRONMENT INTERNATIONAL 2018; 111:301-308. [PMID: 29217223 DOI: 10.1016/j.envint.2017.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/11/2017] [Accepted: 11/02/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Epigenetic changes, such as DNA methylation, are observed in response to environmental exposure and in the development of several chronic diseases. Consequently, DNA methylation alterations might serve as indicators of early effects. In this context, the aim of this study was to assess the temporal variability of global DNA methylation and hydroxymethylation levels in buccal cells from healthy adult volunteers. METHODS Global DNA methylation (%5mdC) and hydroxymethylation (%5hmdC) levels in human buccal cells, collected from 26 healthy adults at different time points, were quantified by UPLC-MS/MS. Associations between %5mdC and %5hmdC, respectively, and short-term exposure (1-7days) to air pollutants PM2.5 and PM10 were tested with mixed-effects models including various covariates. RESULTS/DISCUSSION Dynamic short-term changes in DNA methylation and hydroxymethylation levels in buccal cells were observed, which were inversely associated with exposure to PM2.5 and PM10. An IQR increase in PM2.5 over a 7-day moving average period was significantly associated with a decrease of -1.47% (-1.74%, -1.20%) and -0.043% (-0.054%, -0.032%) in %5mdC and %5hmdC, respectively. Likewise, for PM10, a decrease of -1.42% (-1.70, -1.13) and -0.040% (-0.051%, -0.028%) was observed. CONCLUSION Global DNA methylation and hydroxymethylatation varied over a time period of three weeks. The observed temporal variability was associated with exposure to ambient PM2.5 and PM10 levels. This should be taken into account when interpreting epigenetic alterations in buccal cells.
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Affiliation(s)
- Siemon De Nys
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Radu-Corneliu Duca
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium
| | - Tim Nawrot
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium; Centre for Environmental Sciences, Hasselt University, Belgium
| | - Peter Hoet
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium
| | - Bart Van Meerbeek
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Kirsten L Van Landuyt
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Lode Godderis
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium; IDEWE, External Service for Prevention and Protection at Work, Heverlee, Belgium.
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25
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Ravaioli F, Bacalini MG, Franceschi C, Garagnani P. Age-Related Epigenetic Derangement upon Reprogramming and Differentiation of Cells from the Elderly. Genes (Basel) 2018; 9:genes9010039. [PMID: 29337900 PMCID: PMC5793190 DOI: 10.3390/genes9010039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/22/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023] Open
Abstract
Aging is a complex multi-layered phenomenon. The study of aging in humans is based on the use of biological material from hard-to-gather tissues and highly specific cohorts. The introduction of cell reprogramming techniques posed promising features for medical practice and basic research. Recently, a growing number of studies have been describing the generation of induced pluripotent stem cells (iPSCs) from old or centenarian biologic material. Nonetheless, Reprogramming techniques determine a profound remodelling on cell epigenetic architecture whose extent is still largely debated. Given that cell epigenetic profile changes with age, the study of cell-fate manipulation approaches on cells deriving from old donors or centenarians may provide new insights not only on regenerative features and physiology of these cells, but also on reprogramming-associated and age-related epigenetic derangement.
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Affiliation(s)
- Francesco Ravaioli
- Department of Specialty, Diagnostic and Experimental Medicine (DIMES), Via San Giacomo 12, 40126 Bologna, Italy.
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Via G. Petroni 26, 40126 Bologna, Italy.
| | - Maria G Bacalini
- IRCCS Institute of Neurological Sciences, Via Altura 1-8, 40139 Bologna, Italy.
| | - Claudio Franceschi
- IRCCS Institute of Neurological Sciences, Via Altura 1-8, 40139 Bologna, Italy.
| | - Paolo Garagnani
- Department of Specialty, Diagnostic and Experimental Medicine (DIMES), Via San Giacomo 12, 40126 Bologna, Italy.
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Via G. Petroni 26, 40126 Bologna, Italy.
- Karolinska Institute, Clinical Chemistry, Department of Laboratory Medicine (LABMED), H5, Huddinge University Hospital, 14186 Stockholm, Sweden.
- CNR Institute of Molecular Genetics, Unit of Bologna, 40136 Bologna, Italy.
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy.
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26
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Abstract
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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27
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Michopoulou E, Negre P, Nikita E, Kranioti EF. The auricular surface as age indicator in a modern Greek sample: A test of two qualitative methods. Forensic Sci Int 2017; 280:246.e1-246.e7. [PMID: 28965664 DOI: 10.1016/j.forsciint.2017.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 12/29/2022]
Abstract
The auricular surface is often found very well preserved, thus age-related changes in this anatomical area can be important for any set of human remains that require identification under different taphonomic conditions. This study tests the Buckberry and Chamberlain (2002) and Schmitt et al. (2005) methods in predicting the age of individuals in a documented sample from Crete, Greece. Both methods were used to record changes on the auricular surface in a mixed-sex sample of 74 individuals, directly as well as through photographs, by two independent observers. Cohen's kappa and intra class correlation coefficients (ICC) were used in order to assess inter-observer and intra-observer agreement. Results showed than none of the methods predicted age with sufficient accuracy, as high error rates were recorded. The Schmitt et al. (2005) method performed better, mainly because the age ranges it uses are broader. Scoring through photographs does not seem to introduce bias in predicting age, as demonstrated by the high intra-observer agreement rates. Inter-observer agreement was also high. The low intra- and inter-observer error rates suggest that the poor performance of both methods in the Cretan sample is not due to a lack of clarity in the description of the morphological changes recorded on the auricular surface; rather it should be attributed to a poor correlation between these changes and age at death in our material.
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Affiliation(s)
- Effrosyni Michopoulou
- Edinburgh Unit for Forensic Anthropology, School of History Classics and Archaeology, University of Edinburgh, 4 Teviot Place, EH8 9AG Edinburgh, UK
| | - Pierrick Negre
- Institut médico-légal, Centre Hospitalier Régional Universitaire, 191 Avenue du Doyen Gaston Giraud, 34295 Montpellier, Cedex 5, France
| | - Efthymia Nikita
- Science and Technology in Archaeology Research Center, The Cyprus Institute, Nicosia, Cyprus; Department of Archaeology, University of Sheffield, Sheffield, UK
| | - Elena F Kranioti
- Edinburgh Unit for Forensic Anthropology, School of History Classics and Archaeology, University of Edinburgh, 4 Teviot Place, EH8 9AG Edinburgh, UK; Forensic Pathology Division Crete, Hellenic Republic Ministry of Justice, Transparency and Human Rights, Heraklion, Crete, Greece.
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28
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Bacalini MG, D'Aquila P, Marasco E, Nardini C, Montesanto A, Franceschi C, Passarino G, Garagnani P, Bellizzi D. The methylation of nuclear and mitochondrial DNA in ageing phenotypes and longevity. Mech Ageing Dev 2017; 165:156-161. [PMID: 28115210 DOI: 10.1016/j.mad.2017.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/29/2016] [Accepted: 01/16/2017] [Indexed: 12/28/2022]
Abstract
An increasing body of data is progressively indicating that the comprehension of the epigenetic landscape, actively integrated with the genetic elements, is crucial to delineate the molecular basis of the inter-individual complexity of ageing process. Indeed, it has emerged that DNA methylation changes occur during ageing, consisting mainly in a progressive process of genome demethylation, in a hypermethylation of gene-specific CpG dinucleotides, as well as in an inter-individual divergence of the epigenome due to stochastic events and environmental exposures throughout life, namely as epigenetic drift. Additionally, it has also come to light an implication of the mitochondrial genome in the regulation of the intracellular epigenetic landscape, as demonstrated by the being itself object of epigenetic modifications. An overview of DNA methylation changes occurring during ageing process at both nuclear and mitochondrial level will be described in this review, also taking into account the recent and promising data available on the 5-hydroxymethylcytosine.
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Affiliation(s)
- Maria Giulia Bacalini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura 1/8, 40139 Bologna, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy
| | | | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura 1/8, 40139 Bologna, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; Applied Biomedical Research Center, S.Orsola-Malpighi Polyclinic, 40138 Bologna, Italy; Interdepartmental Center "L. Galvani", Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy.
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy.
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