1
|
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: 49] [Impact Index Per Article: 49.0] [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.
Collapse
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.
| |
Collapse
|
2
|
Dos Santos Oliveira NC, Serpeloni F, Gonçalves de Assis S. The interplay between DNA methylation and cardiac autonomic system functioning: a systematic review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023; 33:54-70. [PMID: 34753378 DOI: 10.1080/09603123.2021.2000590] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Epigenetic marks, particularly DNA methylation (DNAm), are emerging as an important biological marker of susceptibility to cardiac autonomic dysfunction. This review summarizes recent discoveries about the association between DNAm and cardiac autonomic activity. A systematic literature search was performed through the Embase, Web of Science, Cochrane Library, Pubmed, PsycINFO, and Pilots databases. Twenty-two studies met inclusion criteria, of which 18 were human studies including a total of 2,686 participants. DNAm differences in multiple genes, such as NR3C1, TLR2, GPR133, EPO, PHGDH, OXTR, and SLC7A11, linked environmental stressors to physiological responses. For instance, exposure to psychosocial stressors increased NR3C1 methylation, which was associated with both decreased blood pressure and increased parasympathetic activity. Additionally, GPR133 played a potential role in cardiac autonomic dysfunction in an occupational setting, affecting the heart rate's deceleration capacity in welders. This review's findings suggest that DNAm is involved in cardiac autonomic regulation under different stress-mediated responses.
Collapse
Affiliation(s)
- Nayara Cristina Dos Santos Oliveira
- National Institute of Woman, Child, and Adolescence Health Fernandes Figueira, PPGSCM/IFF/FIOCRUZ, Rio de Janeiro, Brazil
- Department of Violence and Health Studies Jorge Careli, National School of Public Health, Rio de Janeiro, Brazil
| | - Fernanda Serpeloni
- Department of Violence and Health Studies Jorge Careli, National School of Public Health, Rio de Janeiro, Brazil
| | - Simone Gonçalves de Assis
- National Institute of Woman, Child, and Adolescence Health Fernandes Figueira, PPGSCM/IFF/FIOCRUZ, Rio de Janeiro, Brazil
- Department of Violence and Health Studies Jorge Careli, National School of Public Health, Rio de Janeiro, Brazil
- Neurology Post-Gradate Program, Federal University of State of Rio de Janeiro, Unirio, Rio de Janeiro, Brazil
| |
Collapse
|
3
|
Andrawus M, Sharvit L, Atzmon G. Epigenetics and Pregnancy: Conditional Snapshot or Rolling Event. Int J Mol Sci 2022; 23:ijms232012698. [PMID: 36293556 PMCID: PMC9603966 DOI: 10.3390/ijms232012698] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Epigenetics modification such as DNA methylation can affect maternal health during the gestation period. Furthermore, pregnancy can drive a range of physiological and molecular changes that have the potential to contribute to pathological conditions. Pregnancy-related risk factors include multiple environmental, behavioral, and hereditary factors that can impact maternal DNA methylation with long-lasting consequences. Identification of the epigenetic patterns linked to poor pregnancy outcomes is crucial since changes in DNA methylation patterns can have long-term effects. In this review, we provide an overview of the epigenetic changes that influence pregnancy-related molecular programming such as gestational diabetes, immune response, and pre-eclampsia, in an effort to close the gap in current understanding regarding interactions between the environment, the genetics of the fetus, and the pregnant woman.
Collapse
|
4
|
Qi H, Song S, Wang P. ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells. Database (Oxford) 2022; 2022:6562126. [PMID: 35363305 PMCID: PMC9216548 DOI: 10.1093/database/baac020] [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: 08/02/2021] [Revised: 01/09/2022] [Accepted: 03/18/2022] [Indexed: 11/23/2022]
Abstract
Differential DNA methylation is a feature of numerous physiological and pathological processes. However, the extent to which single-base cytosine methylation modifies cellular responses to various stimuli has not been well characterized. In this study, we carried out a systematic analysis of methylome data derived from human blood and immune cells and constructed the ImmuMethy database. ImmuMethy allows interrogation of DNA methylation plasticity (MPL) at the single cytosine level. MPL, which refers to the variability of DNA methylation, is quantitatively measured in multiple ways, such as quartiles and standard deviations. ImmuMethy comprises over 36 000 samples from the Human Methylation450 and MethylationEPIC BeadChips platforms and provides multiple applications, such as an overview of methylation status and plasticity, differential methylation analysis, identification of methylation markers and sample stratification. An analysis of all datasets revealed that DNA methylation is generally stable, with minimal changes in beta values. This further supports the characteristics of DNA methylation homeostasis. Based on the beta value distribution, we identified three types of methylation sites: methylation tendency sites, unmethylation tendency sites and dual tendency or nonbiased methylation sites. These sites represent different methylation tendentiousness of DNA methylation across samples. The occurrence of multiple methylation tendencies in a site means split methylation, which generally corresponds to high MPL. Inverted methylation tendencies from methylation tendency sites to unmethylation tendency sites, or vice versa, represent strong differential methylation in response to conditions. All these sites can be identified in ImmuMethy, making it a useful tool for omics-based data-driven knowledge discovery. Database URL: http://immudb.bjmu.edu.cn/immumethy/
Collapse
Affiliation(s)
- Huiying Qi
- Department of Health Informatics and Management, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing 100191, China
| | - Shibin Song
- Information Technology Center, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing 100191, China
| | - Pingzhang Wang
- Department of Immunology, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing 100191, China
- Peking University Center for Human Disease Genomics, No. 38 Xueyuan Road, Beijing 100191, China
| |
Collapse
|
5
|
Winchester P, Nilsson E, Beck D, Skinner MK. Preterm birth buccal cell epigenetic biomarkers to facilitate preventative medicine. Sci Rep 2022; 12:3361. [PMID: 35232984 PMCID: PMC8888575 DOI: 10.1038/s41598-022-07262-9] [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: 11/13/2021] [Accepted: 02/11/2022] [Indexed: 11/09/2022] Open
Abstract
Preterm birth is the major cause of newborn and infant mortality affecting nearly one in every ten live births. The current study was designed to develop an epigenetic biomarker for susceptibility of preterm birth using buccal cells from the mother, father, and child (triads). An epigenome-wide association study (EWAS) was used to identify differential DNA methylation regions (DMRs) using a comparison of control term birth versus preterm birth triads. Epigenetic DMR associations with preterm birth were identified for both the mother and father that were distinct and suggest potential epigenetic contributions from both parents. The mother (165 DMRs) and female child (136 DMRs) at p < 1e-04 had the highest number of DMRs and were highly similar suggesting potential epigenetic inheritance of the epimutations. The male child had negligible DMR associations. The DMR associated genes for each group involve previously identified preterm birth associated genes. Observations identify a potential paternal germline contribution for preterm birth and identify the potential epigenetic inheritance of preterm birth susceptibility for the female child later in life. Although expanded clinical trials and preconception trials are required to optimize the potential epigenetic biomarkers, such epigenetic biomarkers may allow preventative medicine strategies to reduce the incidence of preterm birth.
Collapse
Affiliation(s)
- Paul Winchester
- Department of Pediatrics, St. Franciscan Hospital, School of Medicine, Indiana University, Indianapolis, IN, 46202-5201, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
| |
Collapse
|
6
|
Yamazaki J, Toyomaki H, Nakayama SMM, Yabe J, Muzandu K, Jelinek J, Yokoyama S, Ikenaka Y, Takiguchi M, Ishizuka M. Genome-wide DNA methylation analysis of dogs with high lead exposure living near a lead mining area in Kabwe, Zambia. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117229. [PMID: 33975213 DOI: 10.1016/j.envpol.2021.117229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Lead (Pb) is a heavy metal that has been proven to be toxic to both animals and humans. Genom-wide DNA methylation in domestic dogs exposed to high levels of Pb in Kabwe, Zambia was analyzed in this study. Using next-generation sequencing on samples from 20 domestic dogs (mean blood Pb concentration: 43.6 μg/dL and 7.2 μg/dL in the high and low exposure groups), a digital restriction enzyme analysis of methylation was performed to identify the genomic locations of differentially methylated CpG sites. A validation study on an additional 20 dogs followed (blood Pb concentration: 4.9-29.7 μg/dL). The cluster analysis resolved two broad clusters indicating high and low Pb exposure. The study identified 827 (1.2%) CpG sites with differences in methylation (101 CpG sites were hypermethylated in the low exposure group and 726 were hypermethylated in the high exposure group). The sites corresponded to 26 genes with differentially methylated CpG sites at their promoter regions, including the NGF gene. The methylation of four CpG sites was validated using bisulfite pyrosequencing. The results indicate that aberrant hypermethylation is prevalent in dogs exposed to Pb. The altered DNA methylation of the genes identified in this study contributes to a greater understanding of the epigenetic changes caused by Pb exposure and highlights novel biomarker discoveries across species.
Collapse
Affiliation(s)
- Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan; One Health Research Center, Hokkaido University, Japan
| | - Haruya Toyomaki
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Japan
| | - Shouta M M Nakayama
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Japan.
| | - John Yabe
- School of Veterinary Medicine, The University of Zambia, P.O. Box 32379, Lusaka, Zambia; Dept of Pathobiology, Faculty of Agriculture & Natural Resources, School of Veterinary Medicine, University of Namibia, Windhoek, Namibia
| | - Kaampwe Muzandu
- School of Veterinary Medicine, The University of Zambia, P.O. Box 32379, Lusaka, Zambia
| | | | - Shoko Yokoyama
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan
| | - Yoshinori Ikenaka
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan; Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Japan; One Health Research Center, Hokkaido University, Japan; Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mitsuyoshi Takiguchi
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan
| | - Mayumi Ishizuka
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Japan
| |
Collapse
|
7
|
Zhang YH, Li Z, Zeng T, Chen L, Li H, Gamarra M, Mansour RF, Escorcia-Gutierrez J, Huang T, Cai YD. Investigating gene methylation signatures for fetal intolerance prediction. PLoS One 2021; 16:e0250032. [PMID: 33886611 PMCID: PMC8062050 DOI: 10.1371/journal.pone.0250032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Pregnancy is a complicated and long procedure during one or more offspring development inside a woman. A short period of oxygen shortage after birth is quite normal for most babies and does not threaten their health. However, if babies have to suffer from a long period of oxygen shortage, then this condition is an indication of pathological fetal intolerance, which probably causes their death. The identification of the pathological fetal intolerance from the physical oxygen shortage is one of the important clinical problems in obstetrics for a long time. The clinical syndromes typically manifest five symptoms that indicate that the baby may suffer from fetal intolerance. At present, liquid biopsy combined with high-throughput sequencing or mass spectrum techniques provides a quick approach to detect real-time alteration in the peripheral blood at multiple levels with the rapid development of molecule sequencing technologies. Gene methylation is functionally correlated with gene expression; thus, the combination of gene methylation and expression information would help in screening out the key regulators for the pathogenesis of fetal intolerance. We combined gene methylation and expression features together and screened out the optimal features, including gene expression or methylation signatures, for fetal intolerance prediction for the first time. In addition, we applied various computational methods to construct a comprehensive computational pipeline to identify the potential biomarkers for fetal intolerance dependent on the liquid biopsy samples. We set up qualitative and quantitative computational models for the prediction for fetal intolerance during pregnancy. Moreover, we provided a new prospective for the detailed pathological mechanism of fetal intolerance. This work can provide a solid foundation for further experimental research and contribute to the application of liquid biopsy in antenatal care.
Collapse
Affiliation(s)
- Yu-Hang Zhang
- School of Life Sciences, Shanghai University, Shanghai, China
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Margarita Gamarra
- Department of Computational Science and Electronic, Universidad de la Costa, CUC, Barranquilla, Colombia
| | - Romany F. Mansour
- Department of Mathematics, Faculty of Science, New Valley University, El-Kharga, Egypt
| | - José Escorcia-Gutierrez
- Electronic and Telecommunicacions Program, Universidad Autónoma del Caribe, Barranquilla, Colombia
- * E-mail: (JEG); (TH); (YDC)
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
| |
Collapse
|
8
|
Payne JL, Osborne LM, Cox O, Kelly J, Meilman S, Jones I, Grenier W, Clark K, Ross E, McGinn R, Wadhwa PD, Entringer S, Dunlop AL, Knight AK, Smith AK, Buss C, Kaminsky ZA. DNA methylation biomarkers prospectively predict both antenatal and postpartum depression. Psychiatry Res 2020; 285:112711. [PMID: 31843207 PMCID: PMC7702696 DOI: 10.1016/j.psychres.2019.112711] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022]
Abstract
We sought to replicate and expand upon previous work demonstrating antenatal TTC9B and HP1BP3 gene DNA methylation is prospectively predictive of postpartum depression (PPD) with ~80% accuracy. In a preterm birth study from Emory, Illumina MethylEPIC microarray derived 1st but not 3rd trimester biomarker models predicted 3rd trimester Edinburgh Postnatal Depression Scale (EPDS) scores ≥ 13 with an AUC=0.8 (95% CI: 0.63-0.8). Bisulfite pyrosequencing derived biomarker methylation was generated using bisulfite pyrosequencing across all trimesters in a pregnancy cohort at UC Irvine and in 3rd trimester from an independent Johns Hopkins pregnancy cohort. A support vector machine model incorporating 3rd trimester EPDS scores, TTC9B, and HP1BP3 methylation status predicted 4 week to 6 week postpartum EPDS ≥ 13 from 3rd trimester blood in the UC Irvine cohort (AUC=0.78, 95% CI: 0.64-0.78) and from the Johns Hopkins cohort (AUC=0.84, 95% CI: 0.72-0.97), both independent of previous psychiatric diagnosis. Technical replicate predictions in a subset of the Johns Hopkins cohort exhibited strong cross experiment correlation. This study confirms the PPD prediction model has the potential to be developed into a clinical tool enabling the identification of pregnant women at future risk of PPD who may benefit from clinical intervention.
Collapse
Affiliation(s)
- Jennifer L. Payne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lauren M. Osborne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olivia Cox
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John Kelly
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Samantha Meilman
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ilenna Jones
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Winston Grenier
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen Clark
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Evelyn Ross
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel McGinn
- The Royal’s Institute of Mental Health Research, University of Ottawa, 1145 Carling Avenue, Rm, 6458 Ottawa, Ontario, Canada
| | - Pathik D. Wadhwa
- Department of Psychiatry & Human Behavior, UC Irvine Genetic Epidemiology Research Institute, University of California, Irvine, CA, USA
| | - Sonja Entringer
- Development, Health and Disease Research Program, University of California, Irvine, CA, USA,Medical Psychology Department, Charité University Medicine Berlin, Berlin, Germany
| | - Anne L. Dunlop
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA
| | - Anna K. Knight
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA
| | - Alicia K. Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA
| | - Claudia Buss
- Development, Health and Disease Research Program, University of California, Irvine, CA, USA,Medical Psychology Department, Charité University Medicine Berlin, Berlin, Germany
| | - Zachary A. Kaminsky
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA,The Royal’s Institute of Mental Health Research, University of Ottawa, 1145 Carling Avenue, Rm, 6458 Ottawa, Ontario, Canada,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada,Corresponding author at: The Royal Ottawa Mental Health Center, Institute of Mental Health Research, University of Ottawa, 1145 Carling Avenue, Rm 6458, Ottawa Ontario Canada. (Z.A. Kaminsky)
| |
Collapse
|
9
|
Schaschl H, Wallner B. Population-specific, recent positive directional selection suggests adaptation of human male reproductive genes to different environmental conditions. BMC Evol Biol 2020; 20:27. [PMID: 32054438 PMCID: PMC7020506 DOI: 10.1186/s12862-019-1575-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/30/2019] [Indexed: 01/18/2023] Open
Abstract
Background Recent human transcriptomic analyses revealed a very large number of testis-enriched genes, many of which are involved in spermatogenesis. This comprehensive transcriptomic data lead us to the question whether positive selection was a decisive force influencing the evolution and variability of testis-enriched genes in humans. We used two methodological approaches to detect different levels of positive selection, namely episodic positive diversifying selection (i.e., past selection) in the human lineage within primate phylogeny, potentially driven by sperm competition, and recent positive directional selection in contemporary human populations, which would indicate adaptation to different environments. Results In the human lineage (after correction for multiple testing) we found that only the gene TULP2, for which no functional data are yet available, is subject to episodic positive diversifying selection. Using less stringent statistical criteria (uncorrected p-values), also the gene SPATA16, which has a pivotal role in male fertility and for which episodes of adaptive evolution have been suggested, also displays a putative signal of diversifying selection in the human branch. At the same time, we found evidence for recent positive directional selection acting on several human testis-enriched genes (MORC1, SLC9B1, ROPN1L, DMRT1, PLCZ1, RNF17, FAM71D and WBP2NL) that play important roles in human spermatogenesis and fertilization. Most of these genes are population-specifically under positive selection. Conclusion Episodic diversifying selection, possibly driven by sperm competition, was not an important force driving the evolution of testis-enriched genes in the human lineage. Population-specific, recent positive directional selection suggests an adaptation of male reproductive genes to different environmental conditions. Positive selection acts on eQTLS and sQTLs, indicating selective effects on important gene regulatory functions. In particular, the transcriptional diversity regulated by sQTLs in testis-enriched genes may be important for spermatocytes to respond to environmental and physiological stress.
Collapse
Affiliation(s)
- Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Bernard Wallner
- Department of Behavioural Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| |
Collapse
|
10
|
Park B, Khanam R, Vinayachandran V, Baqui AH, London SJ, Biswal S. Epigenetic biomarkers and preterm birth. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa005. [PMID: 32551139 PMCID: PMC7293830 DOI: 10.1093/eep/dvaa005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 05/06/2023]
Abstract
Preterm birth (PTB) is a major public health challenge, and novel, sensitive approaches to predict PTB are still evolving. Epigenomic markers are being explored as biomarkers of PTB because of their molecular stability compared to gene expression. This approach is also relatively new compared to gene-based diagnostics, which relies on mutations or single nucleotide polymorphisms. The fundamental principle of epigenome diagnostics is that epigenetic reprogramming in the target tissue (e.g. placental tissue) might be captured by more accessible surrogate tissue (e.g. blood) using biochemical epigenome assays on circulating DNA that incorporate methylation, histone modifications, nucleosome positioning, and/or chromatin accessibility. Epigenomic-based biomarkers may hold great potential for early identification of the majority of PTBs that are not associated with genetic variants or mutations. In this review, we discuss recent advances made in the development of epigenome assays focusing on its potential exploration for association and prediction of PTB. We also summarize population-level cohort studies conducted in the USA and globally that provide opportunities for genetic and epigenetic marker development for PTB. In addition, we summarize publicly available epigenome resources and published PTB studies. We particularly focus on ongoing genome-wide DNA methylation and epigenome-wide association studies. Finally, we review the limitations of current research, the importance of establishing a comprehensive biobank, and possible directions for future studies in identifying effective epigenome biomarkers to enhance health outcomes for pregnant women at risk of PTB and their infants.
Collapse
Affiliation(s)
- Bongsoo Park
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Rasheda Khanam
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, International Center for Maternal and Newborn Health, Baltimore, MD 21205, USA
| | - Vinesh Vinayachandran
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Abdullah H Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, International Center for Maternal and Newborn Health, Baltimore, MD 21205, USA
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Shyam Biswal
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| |
Collapse
|
11
|
Kilaru V, Knight AK, Katrinli S, Cobb D, Lori A, Gillespie CF, Maihofer AX, Nievergelt CM, Dunlop AL, Conneely KN, Smith AK. Critical evaluation of copy number variant calling methods using DNA methylation. Genet Epidemiol 2019; 44:148-158. [PMID: 31737926 PMCID: PMC7028453 DOI: 10.1002/gepi.22269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/24/2019] [Accepted: 10/12/2019] [Indexed: 12/21/2022]
Abstract
Recent technological and methodological developments have enabled the use of array-based DNA methylation data to call copy number variants (CNVs). ChAMP, Conumee, and cnAnalysis450k are popular methods currently used to call CNVs using methylation data. However, so far, no studies have analyzed the reliability of these methods using real samples. Data from a cohort of individuals with genotype and DNA methylation data generated using the HumanMethylation450 and MethylationEPIC BeadChips were used to assess the consistency between the CNV calls generated by methylation and genotype data. We also took advantage of repeated measures of methylation data collected from the same individuals to compare the reliability of CNVs called by ChAMP, Conumee, and cnAnalysis450k for both the methylation arrays. ChAMP identified more CNVs than Conumee and cnAnalysis450k for both the arrays and, as a consequence, had a higher overlap (~62%) with the calls from the genotype data. However, all methods had relatively low reliability. For the MethylationEPIC array, Conumee had the highest reliability (57.6%), whereas for the HumanMethylation450 array, cnAnalysis450k had the highest reliability (43.0%). Overall, the MethylationEPIC array provided significant gains in reliability for CNV calling over the HumanMethylation450 array but not for overlap with CNVs called using genotype data.
Collapse
Affiliation(s)
- Varun Kilaru
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Anna K Knight
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Dawayland Cobb
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - Charles F Gillespie
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, San Diego, California
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, San Diego, California.,Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, California.,Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Anne L Dunlop
- Nell Hodgson Woodruff School of Nursing, Emory University School of Medicine, Atlanta, Georgia.,Department of Family and Preventive Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| |
Collapse
|
12
|
Pedersen SF, Counillon L. The SLC9A-C Mammalian Na +/H + Exchanger Family: Molecules, Mechanisms, and Physiology. Physiol Rev 2019; 99:2015-2113. [PMID: 31507243 DOI: 10.1152/physrev.00028.2018] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Na+/H+ exchangers play pivotal roles in the control of cell and tissue pH by mediating the electroneutral exchange of Na+ and H+ across cellular membranes. They belong to an ancient family of highly evolutionarily conserved proteins, and they play essential physiological roles in all phyla. In this review, we focus on the mammalian Na+/H+ exchangers (NHEs), the solute carrier (SLC) 9 family. This family of electroneutral transporters constitutes three branches: SLC9A, -B, and -C. Within these, each isoform exhibits distinct tissue expression profiles, regulation, and physiological roles. Some of these transporters are highly studied, with hundreds of original articles, and some are still only rudimentarily understood. In this review, we present and discuss the pioneering original work as well as the current state-of-the-art research on mammalian NHEs. We aim to provide the reader with a comprehensive view of core knowledge and recent insights into each family member, from gene organization over protein structure and regulation to physiological and pathophysiological roles. Particular attention is given to the integrated physiology of NHEs in the main organ systems. We provide several novel analyses and useful overviews, and we pinpoint main remaining enigmas, which we hope will inspire novel research on these highly versatile proteins.
Collapse
Affiliation(s)
- S F Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; and Université Côte d'Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, LP2M, France, and Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - L Counillon
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; and Université Côte d'Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, LP2M, France, and Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| |
Collapse
|