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Raitoharju E, Rajić S, Marttila S. Non-coding 886 ( nc886/ vtRNA2-1), the epigenetic odd duck - implications for future studies. Epigenetics 2024; 19:2332819. [PMID: 38525792 DOI: 10.1080/15592294.2024.2332819] [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: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 03/26/2024] Open
Abstract
Non-coding 886 (nc886, vtRNA2-1) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability and consequences of the methylation pattern, as well as the nature and function of the nc886 RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced nc886 RNA(s) has been redefined multiple times, and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the nc886 locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Herein, we aim to summarize the existing literature regarding nc886, discuss how the characteristics of nc886 give rise to contradictory results, as well as to reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the distribution of the nc886 methylation pattern is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.
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Affiliation(s)
- Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
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2
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Chang WJ, Baker MS, Laritsky E, Gunasekara CJ, Maduranga U, Galliou JC, McFadden JW, Waltemyer JR, Berggren-Thomas B, Tate BN, Zhang H, Rosen BD, Van Tassell CP, Liu GE, Coarfa C, Ren YA, Waterland RA. Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. Genome Biol 2024; 25:185. [PMID: 39004763 PMCID: PMC11247883 DOI: 10.1186/s13059-024-03307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in blood provide information on epigenetic regulation throughout the body. Moreover, establishment of DNA methylation at human CoRSIVs is labile to periconceptional influences such as nutrition. Here, we analyze publicly available whole-genome bisulfite sequencing data on multiple tissues of each of two Holstein cows to determine whether CoRSIVs exist in cattle. RESULTS Focusing on genomic blocks with ≥ 5 CpGs and a systemic interindividual variation index of at least 20, our approach identifies 217 cattle CoRSIVs, a subset of which we independently validate by bisulfite pyrosequencing. Similar to human CoRSIVs, those in cattle are strongly associated with genetic variation. Also as in humans, we show that establishment of DNA methylation at cattle CoRSIVs is particularly sensitive to early embryonic environment, in the context of embryo culture during assisted reproduction. CONCLUSIONS Our data indicate that CoRSIVs exist in cattle, as in humans, suggesting these systemic epigenetic variants may be common to mammals in general. To the extent that individual epigenetic variation at cattle CoRSIVs affects phenotypic outcomes, assessment of CoRSIV methylation at birth may become an important tool for optimizing agriculturally important traits. Moreover, adjusting embryo culture conditions during assisted reproduction may provide opportunities to tailor agricultural outcomes by engineering CoRSIV methylation profiles.
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Affiliation(s)
- Wen-Jou Chang
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Maria S Baker
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Eleonora Laritsky
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Chathura J Gunasekara
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Uditha Maduranga
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Justine C Galliou
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Joseph W McFadden
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | | | | | - Brianna N Tate
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Hanxue Zhang
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States
| | - Yi Athena Ren
- Department of Animal Science, Cornell University, Ithaca, NY, United States.
| | - Robert A Waterland
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States.
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, United States.
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3
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Hjort L, Bredgaard SS, Manitta E, Marques I, Sørensen AE, Martino D, Grunnet LG, Kelstrup L, Houshmand-Oeregaard A, Clausen TD, Mathiesen ER, Olsen SF, Saffery R, Barrès R, Damm P, Vaag AA, Dalgaard LT. Epigenetics of the non-coding RNA nc886 across blood, adipose tissue and skeletal muscle in offspring exposed to diabetes in pregnancy. Clin Epigenetics 2024; 16:61. [PMID: 38715048 PMCID: PMC11077860 DOI: 10.1186/s13148-024-01673-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/20/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Diabetes in pregnancy is associated with increased risk of long-term metabolic disease in the offspring, potentially mediated by in utero epigenetic variation. Previously, we identified multiple differentially methylated single CpG sites in offspring of women with gestational diabetes mellitus (GDM), but whether stretches of differentially methylated regions (DMRs) can also be identified in adolescent GDM offspring is unknown. Here, we investigate which DNA regions in adolescent offspring are differentially methylated in blood by exposure to diabetes in pregnancy. The secondary aim was to characterize the RNA expression of the identified DMR, which contained the nc886 non-coding RNA. METHODS To identify DMRs, we employed the bump hunter method in samples from young (9-16 yr, n = 92) offspring of women with GDM (O-GDM) and control offspring (n = 94). Validation by pyrosequencing was performed in an adult offspring cohort (age 28-33 years) consisting of O-GDM (n = 82), offspring exposed to maternal type 1 diabetes (O-T1D, n = 67) and control offspring (O-BP, n = 57). RNA-expression was measured using RT-qPCR in subcutaneous adipose tissue and skeletal muscle. RESULTS One significant DMR represented by 10 CpGs with a bimodal methylation pattern was identified, located in the nc886/VTRNA2-1 non-coding RNA gene. Low methylation status across all CpGs of the nc886 in the young offspring was associated with maternal GDM. While low methylation degree in adult offspring in blood, adipose tissue, and skeletal muscle was not associated with maternal GDM, adipose tissue nc886 expression was increased in O-GDM compared to O-BP, but not in O-T1D. In addition, adipose tissue nc886 expression levels were positively associated with maternal pre-pregnancy BMI (p = 0.006), but not with the offspring's own adiposity. CONCLUSIONS Our results highlight that nc886 is a metastable epiallele, whose methylation in young offspring is negatively correlated with maternal obesity and GDM status. The physiological effect of nc886 may be more important in adipose tissue than in skeletal muscle. Further research should aim to investigate how nc886 regulation in adipose tissue by exposure to GDM may contribute to development of metabolic disease.
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Affiliation(s)
- Line Hjort
- Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark.
| | | | - Eleonora Manitta
- Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Irene Marques
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
| | | | - David Martino
- Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, Australia
| | - Louise Groth Grunnet
- Clinical Research, Steno Diabetes Center Copenhagen, Herlev Hospital, Herlev, Denmark
| | - Louise Kelstrup
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Gynecology and Obstetrics, Herlev Hospital, Herlev, Denmark
| | - Azadeh Houshmand-Oeregaard
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Novo Nordisk A/S, Bagsværd, Denmark
| | - Tine Dalsgaard Clausen
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Reinhardt Mathiesen
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | | | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Damm
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Allan Arthur Vaag
- Clinical Research, Steno Diabetes Center Copenhagen, Herlev Hospital, Herlev, Denmark
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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Avila-Bonilla RG, Martínez-Montero JP. Crosstalk between vault RNAs and innate immunity. Mol Biol Rep 2024; 51:387. [PMID: 38443657 PMCID: PMC10914904 DOI: 10.1007/s11033-024-09305-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
PURPOSE Vault (vt) RNAs are noncoding (nc) RNAs transcribed by RNA polymerase III (RNA Pol III) with 5'-triphosphate (5'-PPP) termini that play significant roles and are recognized by innate immune sensors, including retinoic acid-inducible protein 1 (RIG-I). In addition, vtRNAs adopt secondary structures that can be targets of interferon-inducible protein kinase R (PKR) and the oligoadenylate synthetase (OAS)/RNase L system, both of which are important for activating antiviral defenses. However, changes in the expression of vtRNAs have been associated with pathological processes that activate proinflammatory pathways, which influence cellular events such as differentiation, aging, autophagy, apoptosis, and drug resistance in cancer cells. RESULTS In this review, we summarized the biology of vtRNAs and focused on their interactions with the innate immune system. These findings provide insights into the diverse roles of vtRNAs and their correlation with various cellular processes to improve our understanding of their biological functions.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Departamento de Genética y Biología Molecular, Av. IPN 2508, 07360, Mexico City, Mexico.
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5
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Mattijssen S, Kerkhofs K, Stephen J, Yang A, Han CG, Tadafumi Y, Iben JR, Mishra S, Sakhawala RM, Ranjan A, Gowda M, Gahl WA, Gu S, Malicdan MC, Maraia RJ. A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.577363. [PMID: 38410490 PMCID: PMC10896340 DOI: 10.1101/2024.02.05.577363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3'-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>G and patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3'-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.
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Affiliation(s)
- Sandy Mattijssen
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kyra Kerkhofs
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Joshi Stephen
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Acong Yang
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - Chen G. Han
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yokoyama Tadafumi
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - James R. Iben
- Molecular Genetics Core, NICHD, NIH, Bethesda, MD 20892, USA
| | - Saurabh Mishra
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rima M. Sakhawala
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Amitabh Ranjan
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mamatha Gowda
- Department of Obstetrics & Gynaecology, Jawaharlal Institute of Post-Graduate Medical Education and Research, Puducherry, India
| | - William A. Gahl
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Shuo Gu
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - May C. Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Richard J. Maraia
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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6
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van Dongen J, Hubers N, Boomsma DI. New insights into the (epi)genetics of twinning. Hum Reprod 2024; 39:35-42. [PMID: 38052159 PMCID: PMC10767898 DOI: 10.1093/humrep/dead131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 05/24/2023] [Indexed: 12/07/2023] Open
Abstract
Spontaneous dizygotic (DZ) twins, i.e. twins conceived without the use of ARTs, run in families and their prevalence varies widely around the globe. In contrast, monozygotic (MZ) twins occur at a constant rate across time and geographical regions and, with some rare exceptions, do not cluster in families. The leading hypothesis for MZ twins, which arise when a zygote splits during preimplantation stages of development, is random occurrence. We have found the first series of genes underlying the liability of being the mother of DZ twins and have shown that being an MZ twin is strongly associated with a stable DNA methylation signature in child and adult somatic tissues. Because identical twins keep this molecular signature across the lifespan, this discovery opens up completely new possibilities for the retrospective diagnosis of whether a person is an MZ twin whose co-twin may have vanished in the early stages of pregnancy. Here, we summarize the gene finding results for mothers of DZ twins based on genetic association studies followed by meta-analysis, and further present the striking epigenetic results for MZ twins.
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Affiliation(s)
- Jenny van Dongen
- Netherlands Twin Register, Department of Biological Psychology, Amsterdam Reproduction and Development Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Nikki Hubers
- Netherlands Twin Register, Department of Biological Psychology, Amsterdam Reproduction and Development Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, Amsterdam Reproduction and Development Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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7
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Derakhshan M, Kessler NJ, Hellenthal G, Silver MJ. Metastable epialleles in humans. Trends Genet 2024; 40:52-68. [PMID: 38000919 DOI: 10.1016/j.tig.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 11/26/2023]
Abstract
First identified in isogenic mice, metastable epialleles (MEs) are loci where the extent of DNA methylation (DNAm) is variable between individuals but correlates across tissues derived from different germ layers within a given individual. This property, termed systemic interindividual variation (SIV), is attributed to stochastic methylation establishment before germ layer differentiation. Evidence suggests that some putative human MEs are sensitive to environmental exposures in early development. In this review we introduce key concepts pertaining to human MEs, describe methods used to identify MEs in humans, and review their genomic features. We also highlight studies linking DNAm at putative human MEs to early environmental exposures and postnatal (including disease) phenotypes.
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Affiliation(s)
- Maria Derakhshan
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Noah J Kessler
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | | | - Matt J Silver
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia.
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8
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Kadalayil L, Alam MZ, White CH, Ghantous A, Walton E, Gruzieva O, Merid SK, Kumar A, Roy RP, Solomon O, Huen K, Eskenazi B, Rzehak P, Grote V, Langhendries JP, Verduci E, Ferre N, Gruszfeld D, Gao L, Guan W, Zeng X, Schisterman EF, Dou JF, Bakulski KM, Feinberg JI, Soomro MH, Pesce G, Baiz N, Isaevska E, Plusquin M, Vafeiadi M, Roumeliotaki T, Langie SAS, Standaert A, Allard C, Perron P, Bouchard L, van Meel ER, Felix JF, Jaddoe VWV, Yousefi PD, Ramlau-Hansen CH, Relton CL, Tobi EW, Starling AP, Yang IV, Llambrich M, Santorelli G, Lepeule J, Salas LA, Bustamante M, Ewart SL, Zhang H, Karmaus W, Röder S, Zenclussen AC, Jin J, Nystad W, Page CM, Magnus M, Jima DD, Hoyo C, Maguire RL, Kvist T, Czamara D, Räikkönen K, Gong T, Ullemar V, Rifas-Shiman SL, Oken E, Almqvist C, Karlsson R, Lahti J, Murphy SK, Håberg SE, London S, Herberth G, Arshad H, Sunyer J, Grazuleviciene R, Dabelea D, Steegers-Theunissen RPM, Nohr EA, Sørensen TIA, Duijts L, Hivert MF, Nelen V, Popovic M, Kogevinas M, Nawrot TS, Herceg Z, Annesi-Maesano I, Fallin MD, Yeung E, Breton CV, Koletzko B, Holland N, Wiemels JL, Melén E, Sharp GC, Silver MJ, Rezwan FI, Holloway JW. Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude. Clin Epigenetics 2023; 15:148. [PMID: 37697338 PMCID: PMC10496224 DOI: 10.1186/s13148-023-01542-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/27/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Seasonal variations in environmental exposures at birth or during gestation are associated with numerous adult traits and health outcomes later in life. Whether DNA methylation (DNAm) plays a role in the molecular mechanisms underlying the associations between birth season and lifelong phenotypes remains unclear. METHODS We carried out epigenome-wide meta-analyses within the Pregnancy And Childhood Epigenetic Consortium to identify associations of DNAm with birth season, both at differentially methylated probes (DMPs) and regions (DMRs). Associations were examined at two time points: at birth (21 cohorts, N = 9358) and in children aged 1-11 years (12 cohorts, N = 3610). We conducted meta-analyses to assess the impact of latitude on birth season-specific associations at both time points. RESULTS We identified associations between birth season and DNAm (False Discovery Rate-adjusted p values < 0.05) at two CpGs at birth (winter-born) and four in the childhood (summer-born) analyses when compared to children born in autumn. Furthermore, we identified twenty-six differentially methylated regions (DMR) at birth (winter-born: 8, spring-born: 15, summer-born: 3) and thirty-two in childhood (winter-born: 12, spring and summer: 10 each) meta-analyses with few overlapping DMRs between the birth seasons or the two time points. The DMRs were associated with genes of known functions in tumorigenesis, psychiatric/neurological disorders, inflammation, or immunity, amongst others. Latitude-stratified meta-analyses [higher (≥ 50°N), lower (< 50°N, northern hemisphere only)] revealed differences in associations between birth season and DNAm by birth latitude. DMR analysis implicated genes with previously reported links to schizophrenia (LAX1), skin disorders (PSORS1C, LTB4R), and airway inflammation including asthma (LTB4R), present only at birth in the higher latitudes (≥ 50°N). CONCLUSIONS In this large epigenome-wide meta-analysis study, we provide evidence for (i) associations between DNAm and season of birth that are unique for the seasons of the year (temporal effect) and (ii) latitude-dependent variations in the seasonal associations (spatial effect). DNAm could play a role in the molecular mechanisms underlying the effect of birth season on adult health outcomes.
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Affiliation(s)
- Latha Kadalayil
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Md Zahangir Alam
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Cory Haley White
- Merck Exploratory Science Center in Cambridge MA, Merck Research Laboratories, Cambridge, MA, 02141, USA
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Esther Walton
- Department of Psychology, University of Bath, Bath, UK
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Simon Kebede Merid
- Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Ashish Kumar
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Ritu P Roy
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, CA, 94143, USA
- Computational Biology and Informatics Core, University of California, San Francisco, CA, 94143, USA
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | | | - Elvira Verduci
- Department of Pediatrics, Vittore Buzzi Children Hospital, University of Milan, Milan, Italy
| | - Natalia Ferre
- Pediatric Nutrition and Human Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Darek Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, MMC 303, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
| | | | - Enrique F Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA, 19104, USA
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities Johns Hopkins University, Baltimore, MD, USA
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris Cedex 12, France
- Department of Community Medicine and Public Health, SMBB Medical University, Larkana, Pakistan
| | - Giancarlo Pesce
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris Cedex 12, France
| | - Nour Baiz
- Institut Desbrest de Santé Publique (IDESP), INSERM and Montpellier University, Montpellier, France
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, CPO Piemonte, Italy
| | - Michelle Plusquin
- Center for Environmental Sciences, University of Hasselt, 3590, Diepenbeek, Belgium
| | - Marina Vafeiadi
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Theano Roumeliotaki
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Sabine A S Langie
- Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Limburg, The Netherlands
| | - Arnout Standaert
- Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Canada
| | - Patrice Perron
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Universite de Sherbrooke, Sherbrooke, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-Saint-Jean - Hôpital de Chicoutimi, Chicoutimi, Canada
| | - Evelien R van Meel
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Anne P Starling
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Maria Llambrich
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | - Johanna Lepeule
- Institute for Advanced Biosciences, University Grenoble-Alpes, INSERM, CNRS, Grenoble, France
| | - Lucas A Salas
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA
| | - Mariona Bustamante
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Stefan Röder
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ana Claudia Zenclussen
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jianping Jin
- 2530 Meridian Pkwy, Suite 200, Durham, NC 27713, USA
| | - Wenche Nystad
- Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Section for Statistics and Data Science, Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Maria Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Obstetrics and Gynaecology, Duke University Medical Center, Durham, NC, USA
| | - Tuomas Kvist
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804, Munich, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Tong Gong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sheryl L Rifas-Shiman
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Susan K Murphy
- Department of Obstetrics and Gynaecology, Duke University Medical Center, Durham, NC, USA
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, NC, 27709, USA
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- NIHR Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, UK
| | - Jordi Sunyer
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Regina Grazuleviciene
- Department of Environmental Science, Vytautas Magnus University, 44248, Kaunas, Lithuania
| | - Dana Dabelea
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Régine P M Steegers-Theunissen
- Periconceptional Epidemiology, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Ellen A Nohr
- Department of Clinical Research, Odense Universitetshospital, Odense, Denmark
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Neonatology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Vera Nelen
- Provincial Institute for Hygiene, Antwerp, Belgium
| | - Maja Popovic
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, CPO Piemonte, Italy
| | | | - Tim S Nawrot
- Center for Environmental Sciences, University of Hasselt, 3590, Diepenbeek, Belgium
- Department of Public Health and Primary Care, Leuven University, Louvain, Belgium
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Isabella Annesi-Maesano
- Institut Desbrest de Santé Publique (IDESP), INSERM and Montpellier University, Montpellier, France
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities Johns Hopkins University, Baltimore, MD, USA
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, USA
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Nina Holland
- Children's Environmental Health Laboratory, CERCH, Berkeley Public Health, University of California, 2121 Berkeley Way #5216, Berkeley, CA, 94720, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Psychology, University of Exeter, Exeter, UK
| | - Matt J Silver
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
- NIHR Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, UK.
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9
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Belesova K, Gasparrini A, Wilkinson P, Sié A, Sauerborn R. Child Survival and Annual Crop Yield Reductions in Rural Burkina Faso: Critical Windows of Vulnerability Around Early-Life Development. Am J Epidemiol 2023; 192:1116-1127. [PMID: 37116074 PMCID: PMC10326605 DOI: 10.1093/aje/kwad068] [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: 11/14/2021] [Revised: 10/02/2022] [Accepted: 03/21/2023] [Indexed: 04/30/2023] Open
Abstract
Populations that are reliant on subsistence farming are particularly vulnerable to climatic effects on crop yields. However, empirical evidence on the role of the timing of exposure to crop yield deficits in early-life development is limited. We examined the relationship between child survival and annual crop yield reductions at different stages of early-life development in a subsistence farming population in Burkina Faso. Using shared frailty Cox proportional hazards models adjusting for confounders, we analyzed 57,288 children under 5 years of age followed by the Nouna Health and Demographic Surveillance System (1994-2016) in relation to provincial food-crop yield levels experienced in 5 nonoverlapping time windows (12 months before conception, gestation, birth-age 5.9 months, ages 6.0 months-1.9 years, and ages 2.0-4.9 years) and their aggregates (birth-1.9 years, first 1,000 days from conception, and birth-4.9 years). Of the nonoverlapping windows, point estimates were largest for child survival related to food-crop yields for the time window of 6.0 months-1.9 years: The adjusted mortality hazard ratio was 1.10 (95% confidence interval: 1.03, 1.19) for a 90th-to-10th percentile yield reduction. These findings suggest that child survival in this setting is particularly vulnerable to cereal-crop yield reductions during the period of nonexclusive breastfeeding.
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Affiliation(s)
- Kristine Belesova
- Correspondence to Dr. Kristine Belesova, Department of Department of Primary Care and Public Health, Faculty of Medicine, Imperial College London, Reynolds Building, St. Dunstan's Road, London W6 8RP, United Kingdom (e-mail: )
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10
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Sainty R, Silver MJ, Prentice AM, Monk D. The influence of early environment and micronutrient availability on developmental epigenetic programming: lessons from the placenta. Front Cell Dev Biol 2023; 11:1212199. [PMID: 37484911 PMCID: PMC10358779 DOI: 10.3389/fcell.2023.1212199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. Somatic DNA methylation patterns that can persist throughout life are established shortly after fertilisation when the majority of epigenetic marks, including DNA methylation, are erased from the pre-implantation embryo. Therefore, the period around conception is potentially critical for influencing DNA methylation, including methylation at imprinted alleles and metastable epialleles (MEs), loci where methylation varies between individuals but is correlated across tissues. Exposures before and during conception can affect pregnancy outcomes and health throughout life. Retrospective studies of the survivors of famines, such as those exposed to the Dutch Hunger Winter of 1944-45, have linked exposures around conception to later disease outcomes, some of which correlate with DNA methylation changes at certain genes. Animal models have shown more directly that DNA methylation can be affected by dietary supplements that act as cofactors in one-carbon metabolism, and in humans, methylation at birth has been associated with peri-conceptional micronutrient supplementation. However, directly showing a role of micronutrients in shaping the epigenome has proven difficult. Recently, the placenta, a tissue with a unique hypomethylated methylome, has been shown to possess great inter-individual variability, which we highlight as a promising target tissue for studying MEs and mixed environmental exposures. The placenta has a critical role shaping the health of the fetus. Placenta-associated pregnancy complications, such as preeclampsia and intrauterine growth restriction, are all associated with aberrant patterns of DNA methylation and expression which are only now being linked to disease risk later in life.
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Affiliation(s)
- Rebecca Sainty
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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11
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Ma X, Xiao L, Wen SJ, Yu T, Sharma S, Chung HK, Warner B, Mallard CG, Rao JN, Gorospe M, Wang J. Small noncoding vault RNA2-1 disrupts gut epithelial barrier function via interaction with HuR. EMBO Rep 2023; 24:e54925. [PMID: 36440604 PMCID: PMC9900329 DOI: 10.15252/embr.202254925] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022] Open
Abstract
Vault RNAs (vtRNAs) are small noncoding RNAs and highly expressed in many eukaryotes. Here, we identified vtRNA2-1 as a novel regulator of the intestinal barrier via interaction with RNA-binding protein HuR. Intestinal mucosal tissues from patients with inflammatory bowel diseases and from mice with colitis or sepsis express increased levels of vtRNAs relative to controls. Ectopically expressed vtRNA2-1 decreases the levels of intercellular junction (IJ) proteins claudin 1, occludin, and E-cadherin and causes intestinal epithelial barrier dysfunction in vitro, whereas vtRNA2-1 silencing promotes barrier function. Increased vtRNA2-1 also decreases IJs in intestinal organoid, inhibits epithelial renewal, and causes Paneth cell defects ex vivo. Elevating the levels of tissue vtRNA2-1 in the intestinal mucosa increases the vulnerability of the gut barrier to septic stress in mice. vtRNA2-1 interacts with HuR and prevents HuR binding to claudin 1 and occludin mRNAs, thus decreasing their translation. These results indicate that vtRNA2-1 impairs intestinal barrier function by repressing HuR-facilitated translation of claudin 1 and occludin.
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Affiliation(s)
- Xiang‐Xue Ma
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
- Present address:
Department of Gastroenterology, Xiyuan HospitalChina Academy of Chinese Medical SciencesBeijingChina
| | - Lan Xiao
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Susan J Wen
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Ting‐Xi Yu
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Shweta Sharma
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Hee K Chung
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Bridgette Warner
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Caroline G Mallard
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Jaladanki N Rao
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
- Baltimore Veterans Affairs Medical CenterBaltimoreMDUSA
| | - Myriam Gorospe
- Laboratory of Genetics and GenomicsNational Institute on Aging‐IRP, NIHBaltimoreMDUSA
| | - Jian‐Ying Wang
- Cell Biology Group, Department of SurgeryUniversity of Maryland School of MedicineBaltimoreMDUSA
- Laboratory of Genetics and GenomicsNational Institute on Aging‐IRP, NIHBaltimoreMDUSA
- Department of PathologyUniversity of Maryland School of MedicineBaltimoreMDUSA
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12
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Colwell ML, Townsel C, Petroff RL, Goodrich JM, Dolinoy DC. Epigenetics and the Exposome: DNA Methylation as a Proxy for Health Impacts of Prenatal Environmental Exposures. EXPOSOME 2023; 3:osad001. [PMID: 37333730 PMCID: PMC10275510 DOI: 10.1093/exposome/osad001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The accumulation of every day exposures can impact health across the life course, but our understanding of such exposures is impeded by our ability to delineate the relationship between an individual's early life exposome and later life health effects. Measuring the exposome is challenging. Exposure assessed at a given time point captures a snapshot of the exposome but does not represent the full spectrum of exposures across the life course. In addition, the assessment of early life exposures and their effects is often further challenged by lack of relevant samples and the time gap between exposures and related health outcomes in later life. Epigenetics, specifically DNA methylation, has the potential to overcome these barriers as environmental epigenetic perturbances can be retained through time. In this review, we describe how DNA methylation can be framed in the world of the exposome. We offer three compelling examples of common environmental exposures, including cigarette smoke, the endocrine active compound bisphenol A (BPA), and the metal lead (Pb), to illustrate the application of DNA methylation as a proxy to measure the exposome. We discuss areas for future explorations and current limitations of this approach. Epigenetic profiling is a promising and rapidly developing tool and field of study, offering us a unique and powerful way to assess the early life exposome and its effects across different life stages.
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Affiliation(s)
- Mathia L. Colwell
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Courtney Townsel
- Department of Obstetrics and Gynecology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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13
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Gunasekara CJ, MacKay H, Scott CA, Li S, Laritsky E, Baker MS, Grimm SL, Jun G, Li Y, Chen R, Wiemels JL, Coarfa C, Waterland RA. Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control. Genome Biol 2023; 24:2. [PMID: 36631879 PMCID: PMC9835319 DOI: 10.1186/s13059-022-02827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/01/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition. RESULTS We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of 188 donors in the NIH Gene-Tissue Expression (GTEx) program. At CoRSIVs, DNA methylation in peripheral blood correlates with methylation and gene expression in internal organs. We also discover unprecedented mQTL at these regions. Genetic influences on CoRSIV methylation are extremely strong (median R2=0.76), cumulatively comprising over 70-fold more human mQTL than detected in the most powerful previous study. Moreover, mQTL beta coefficients at CoRSIVs are highly skewed (i.e., the major allele predicts higher methylation). Both surprising findings are independently validated in a cohort of 47 non-GTEx individuals. Genomic regions flanking CoRSIVs show long-range enrichments for LINE-1 and LTR transposable elements; the skewed beta coefficients may therefore reflect evolutionary selection of genetic variants that promote their methylation and silencing. Analyses of GWAS summary statistics show that mQTL polymorphisms at CoRSIVs are associated with metabolic and other classes of disease. CONCLUSIONS A focus on systemic interindividual epigenetic variants, clearly enhanced in mQTL content, should likewise benefit studies attempting to link human epigenetic variation to the risk of disease.
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Affiliation(s)
- Chathura J. Gunasekara
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Harry MacKay
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - C. Anthony Scott
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Shaobo Li
- grid.42505.360000 0001 2156 6853Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Eleonora Laritsky
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Maria S. Baker
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Sandra L. Grimm
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Goo Jun
- grid.267308.80000 0000 9206 2401Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Yumei Li
- grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Rui Chen
- grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Joseph L. Wiemels
- grid.42505.360000 0001 2156 6853Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Cristian Coarfa
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX USA
| | - Robert A. Waterland
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
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14
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Krushkal J, Vural S, Jensen TL, Wright G, Zhao Y. Increased copy number of imprinted genes in the chromosomal region 20q11-q13.32 is associated with resistance to antitumor agents in cancer cell lines. Clin Epigenetics 2022; 14:161. [PMID: 36461044 PMCID: PMC9716673 DOI: 10.1186/s13148-022-01368-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Parent of origin-specific allelic expression of imprinted genes is epigenetically controlled. In cancer, imprinted genes undergo both genomic and epigenomic alterations, including frequent copy number changes. We investigated whether copy number loss or gain of imprinted genes in cancer cell lines is associated with response to chemotherapy treatment. RESULTS We analyzed 198 human imprinted genes including protein-coding genes and noncoding RNA genes using data from tumor cell lines from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We examined whether copy number of the imprinted genes in 35 different genome locations was associated with response to cancer drug treatment. We also analyzed associations of pretreatment expression and DNA methylation of imprinted genes with drug response. Higher copy number of BLCAP, GNAS, NNAT, GNAS-AS1, HM13, MIR296, MIR298, and PSIMCT-1 in the chromosomal region 20q11-q13.32 was associated with resistance to multiple antitumor agents. Increased expression of BLCAP and HM13 was also associated with drug resistance, whereas higher methylation of gene regions of BLCAP, NNAT, SGK2, and GNAS was associated with drug sensitivity. While expression and methylation of imprinted genes in several other chromosomal regions was also associated with drug response and many imprinted genes in different chromosomal locations showed a considerable copy number variation, only imprinted genes at 20q11-q13.32 had a consistent association of their copy number with drug response. Copy number values among the imprinted genes in the 20q11-q13.32 region were strongly correlated. They were also correlated with the copy number of cancer-related non-imprinted genes MYBL2, AURKA, and ZNF217 in that chromosomal region. Expression of genes at 20q11-q13.32 was associated with ex vivo drug response in primary tumor samples from the Beat AML 1.0 acute myeloid leukemia patient cohort. Association of the increased copy number of the 20q11-q13.32 region with drug resistance may be complex and could involve multiple genes. CONCLUSIONS Copy number of imprinted and non-imprinted genes in the chromosomal region 20q11-q13.32 was associated with cancer drug resistance. The genes in this chromosomal region may have a modulating effect on tumor response to chemotherapy.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD, 20850, USA.
| | - Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD, 20850, USA.,Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | | | - George Wright
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD, 20850, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD, 20850, USA
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15
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Marttila S, Tamminen H, Rajić S, Mishra PP, Lehtimäki T, Raitakari O, Kähönen M, Kananen L, Jylhävä J, Hägg S, Delerue T, Peters A, Waldenberger M, Kleber ME, März W, Luoto R, Raitanen J, Sillanpää E, Laakkonen EK, Heikkinen A, Ollikainen M, Raitoharju E. Methylation status of VTRNA2-1/ nc886 is stable across populations, monozygotic twin pairs and in majority of tissues. Epigenomics 2022; 14:1105-1124. [PMID: 36200237 DOI: 10.2217/epi-2022-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims & methods: The aim of this study was to characterize the methylation level of a polymorphically imprinted gene, VTRNA2-1/nc886, in human populations and somatic tissues.48 datasets, consisting of more than 30 tissues and >30,000 individuals, were used. Results: nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, whereas ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle. Conclusion: The nc886 imprint may be established in the oocyte, and, after implantation, the methylation status is stable, excluding a few specific tissues.
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Affiliation(s)
- Saara Marttila
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Gerontology Research Center, Tampere University, Tampere, 33014, Finland
| | - Hely Tamminen
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku & Turku University Hospital, Turku, 20014, Finland.,Research Centre of Applied & Preventive Cardiovascular Medicine, University of Turku, Turku, 20014, Finland.,Department of Clinical Physiology & Nuclear Medicine, Turku University Hospital, Turku, 20014, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
| | - Laura Kananen
- Faculty of Medicine & Health Technology, & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520,Finland.,Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Juulia Jylhävä
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Thomas Delerue
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,Competence Cluster for Nutrition & Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, 07743, Germany.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Augsburg, 86156, Germany.,Clinical Institute of Medical & Chemical Laboratory Diagnostics, Medical University of Graz, Graz, 8010, Austria
| | - Riitta Luoto
- The Social Insurance Institute of Finland (Kela), Helsinki, 00250, Finland.,The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland
| | - Jani Raitanen
- The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland.,Faculty of Social Sciences (Health Sciences), Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Elina Sillanpää
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland.,Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Eija K Laakkonen
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
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16
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Derakhshan M, Kessler NJ, Ishida M, Demetriou C, Brucato N, Moore G, Fall CHD, Chandak GR, Ricaut FX, Prentice A, Hellenthal G, Silver M. Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo. Nucleic Acids Res 2022; 50:6735-6752. [PMID: 35713545 PMCID: PMC9749461 DOI: 10.1093/nar/gkac503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs ('hvCpGs') with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
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Affiliation(s)
| | - Noah J Kessler
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK
| | - Miho Ishida
- UCL Great Ormond Street Institute of Child Health, UK
| | | | - Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton,
Southampton, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular
and Molecular Biology,Hyderabad, India
| | - Francois-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London,
Gower Street, London WC1E 6BT, UK
| | - Matt J Silver
- London School of Hygiene and Tropical Medicine, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
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17
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Fueyo R, Judd J, Feschotte C, Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nat Rev Mol Cell Biol 2022; 23:481-497. [PMID: 35228718 PMCID: PMC10470143 DOI: 10.1038/s41580-022-00457-y] [Citation(s) in RCA: 128] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
Abstract
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription machinery, which they use to express their own products and promote transposition. However, the regulatory sequences carried by TEs may affect host transcription long after the TEs have lost the ability to transpose. Recent advances in genome analysis and engineering have facilitated systematic interrogation of the regulatory activities of TEs. In this Review, we discuss diverse mechanisms by which TEs contribute to transcription regulation. Notably, TEs can donate enhancer and promoter sequences that influence the expression of host genes, modify 3D chromatin architecture and give rise to novel regulatory genes, including non-coding RNAs and transcription factors. We discuss how TEs spur regulatory evolution and facilitate the emergence of genetic novelties in mammalian physiology and development. By virtue of their repetitive and interspersed nature, TEs offer unique opportunities to dissect the effects of mutation and genomic context on the function and evolution of cis-regulatory elements. We argue that TE-centric studies hold the key to unlocking general principles of transcription regulation and evolution.
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Affiliation(s)
- Raquel Fueyo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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18
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Kostiniuk D, Tamminen H, Mishra PP, Marttila S, Raitoharju E. Methylation pattern of polymorphically imprinted nc886 is not conserved across mammalia. PLoS One 2022; 17:e0261481. [PMID: 35294436 PMCID: PMC8926257 DOI: 10.1371/journal.pone.0261481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/02/2022] [Indexed: 12/17/2022] Open
Abstract
Background In humans, the nc886 locus is a polymorphically imprinted metastable epiallele. Periconceptional conditions have an effect on the methylation status of nc886, and further, this methylation status is associated with health outcomes in later life, in line with the Developmental Origins of Health and Disease (DOHaD) hypothesis. Animal models would offer opportunities to study the associations between periconceptional conditions, nc886 methylation status and metabolic phenotypes further. Thus, we set out to investigate the methylation pattern of the nc886 locus in non-human mammals. Data We obtained DNA methylation data from the data repository GEO for mammals, whose nc886 gene included all three major parts of nc886 and had sequency similarity of over 80% with the human nc886. Our final sample set consisted of DNA methylation data from humans, chimpanzees, bonobos, gorillas, orangutangs, baboons, macaques, vervets, marmosets and guinea pigs. Results In human data sets the methylation pattern of nc886 locus followed the expected bimodal distribution, indicative of polymorphic imprinting. In great apes, we identified a unimodal DNA methylation pattern with 50% methylation level in all individuals and in all subspecies. In Old World monkeys, the between individual variation was greater and methylation on average was close to 60%. In guinea pigs the region around the nc886 homologue was non-methylated. Results obtained from the sequence comparison of the CTCF binding sites flanking the nc886 gene support the results on the DNA methylation data. Conclusions Our results indicate that unlike in humans, nc886 is not a polymorphically imprinted metastable epiallele in non-human primates or in guinea pigs, thus implying that animal models are not applicable for nc886 research. The obtained data suggests that the nc886 region may be classically imprinted in great apes, and potentially also in Old World monkeys, but not in guinea pigs.
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Affiliation(s)
- Daria Kostiniuk
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Hely Tamminen
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pashupati P. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere University Hospital, Tampere, Finland
- * E-mail:
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19
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Silver MJ, Saffari A, Kessler NJ, Chandak GR, Fall CHD, Issarapu P, Dedaniya A, Betts M, Moore SE, Routledge MN, Herceg Z, Cuenin C, Derakhshan M, James PT, Monk D, Prentice AM. Environmentally sensitive hotspots in the methylome of the early human embryo. eLife 2022; 11:e72031. [PMID: 35188105 PMCID: PMC8912923 DOI: 10.7554/elife.72031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/18/2022] [Indexed: 11/26/2022] Open
Abstract
In humans, DNA methylation marks inherited from gametes are largely erased following fertilisation, prior to construction of the embryonic methylome. Exploiting a natural experiment of seasonal variation including changes in diet and nutritional status in rural Gambia, we analysed three datasets covering two independent child cohorts and identified 259 CpGs showing consistent associations between season of conception (SoC) and DNA methylation. SoC effects were most apparent in early infancy, with evidence of attenuation by mid-childhood. SoC-associated CpGs were enriched for metastable epialleles, parent-of-origin-specific methylation and germline differentially methylated regions, supporting a periconceptional environmental influence. Many SoC-associated CpGs overlapped enhancers or sites of active transcription in H1 embryonic stem cells and fetal tissues. Half were influenced but not determined by measured genetic variants that were independent of SoC. Environmental 'hotspots' providing a record of environmental influence at periconception constitute a valuable resource for investigating epigenetic mechanisms linking early exposures to lifelong health and disease.
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Affiliation(s)
- Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Ayden Saffari
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Noah J Kessler
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Gririraj R Chandak
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Caroline HD Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General HospitalSouthamptonUnited Kingdom
| | - Prachand Issarapu
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Akshay Dedaniya
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Modupeh Betts
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
- Department of Women and Children's Health, King's College LondonLondonUnited Kingdom
| | - Michael N Routledge
- School of Medicine, University of LeedsLeedsUnited Kingdom
- School of Food and Biological Engineering, Jiangsu UniversityZhenjiangChina
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Maria Derakhshan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Philip T James
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - David Monk
- Biomedical Research Centre, University of East AngliaNorwichUnited Kingdom
- Bellvitge Institute for Biomedical ResearchBarcelonaSpain
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
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20
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Jedynak P, Tost J, Calafat AM, Bourova-Flin E, Busato F, Forhan A, Heude B, Jakobi M, Rousseaux S, Schwartz J, Slama R, Vaiman D, Philippat C, Lepeule J. Pregnancy exposure to synthetic phenols and placental DNA methylation - An epigenome-wide association study in male infants from the EDEN cohort. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118024. [PMID: 34523531 PMCID: PMC8590835 DOI: 10.1016/j.envpol.2021.118024] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 05/14/2023]
Abstract
In utero exposure to environmental chemicals, such as synthetic phenols, may alter DNA methylation in different tissues, including placenta - a critical organ for fetal development. We studied associations between prenatal urinary biomarker concentrations of synthetic phenols and placental DNA methylation. Our study involved 202 mother-son pairs from the French EDEN cohort. Nine phenols were measured in spot urine samples collected between 22 and 29 gestational weeks. We performed DNA methylation analysis of the fetal side of placental tissues using the IlluminaHM450 BeadChips. We evaluated methylation changes of individual CpGs in an adjusted epigenome-wide association study (EWAS) and identified differentially methylated regions (DMRs). We performed mediation analysis to test whether placental tissue heterogeneity mediated the association between urinary phenol concentrations and DNA methylation. We identified 46 significant DMRs (≥5 CpGs) associated with triclosan (37 DMRs), 2,4-dichlorophenol (3), benzophenone-3 (3), methyl- (2) and propylparaben (1). All but 2 DMRs were positively associated with phenol concentrations. Out of the 46 identified DMRs, 7 (6 for triclosan) encompassed imprinted genes (APC, FOXG1, GNAS, GNASAS, MIR886, PEG10, SGCE), which represented a significant enrichment. Other identified DMRs encompassed genes encoding proteins responsible for cell signaling, transmembrane transport, cell adhesion, inflammatory, apoptotic and immunological response, genes encoding transcription factors, histones, tumor suppressors, genes involved in tumorigenesis and several cancer risk biomarkers. Mediation analysis suggested that placental cell heterogeneity may partly explain these associations. This is the first study describing the genome-wide modifications of placental DNA methylation associated with pregnancy exposure to synthetic phenols or their precursors. Our results suggest that cell heterogeneity might mediate the effects of triclosan exposure on placental DNA methylation. Additionally, the enrichment of imprinted genes within the DMRs suggests mechanisms by which certain exposures, mainly to triclosan, could affect fetal development.
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Affiliation(s)
- Paulina Jedynak
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Antonia M Calafat
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ekaterina Bourova-Flin
- University Grenoble Alpes, Inserm, CNRS, EpiMed Group, Institute for Advanced Biosciences, Grenoble, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Anne Forhan
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004, Paris, France
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004, Paris, France
| | - Milan Jakobi
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Sophie Rousseaux
- University Grenoble Alpes, Inserm, CNRS, EpiMed Group, Institute for Advanced Biosciences, Grenoble, France
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rémy Slama
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Vaiman
- Genomics, Epigenetics and Physiopathology of Reproduction, Institut Cochin, U1016 Inserm - UMR 8104 CNRS - Paris-Descartes University, Paris, France
| | - Claire Philippat
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
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21
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Candler T, Kessler N, Gunasekara C, Ward K, James P, Laritsky E, Baker M, Dyer R, Elango R, Jeffries D, Waterland R, Moore S, Ludgate M, Prentice A, Silver M. DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children. SCIENCE ADVANCES 2021; 7:eabj1561. [PMID: 34739318 PMCID: PMC8570597 DOI: 10.1126/sciadv.abj1561] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/16/2021] [Indexed: 05/13/2023]
Abstract
PAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density. Furthermore, offspring PAX8 methylation was associated with periconceptional maternal nutrition, and methylation variability was influenced by genotype, suggesting that sensitivity to environmental exposures may be under partial genetic control. Together, our results demonstrate a possible link between early environment, PAX8 gene methylation and thyroid gland development and function, with potential implications for early embryonic programming of thyroid-related health and disease.
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Affiliation(s)
- Toby Candler
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Noah Kessler
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chathura Gunasekara
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kate Ward
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- MRC Lifecourse Epidemiology, University of Southampton, Southampton, UK
| | - Philip James
- Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Eleonora Laritsky
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria Baker
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Roger Dyer
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Rajavel Elango
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - David Jeffries
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Robert Waterland
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sophie Moore
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- Department of Women and Children’s Health, King’s College London, London, UK
| | - Marian Ludgate
- Thyroid Research Group, School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Matt Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
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22
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Fleming TP, Sun C, Denisenko O, Caetano L, Aljahdali A, Gould JM, Khurana P. Environmental Exposures around Conception: Developmental Pathways Leading to Lifetime Disease Risk. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:9380. [PMID: 34501969 PMCID: PMC8431664 DOI: 10.3390/ijerph18179380] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/11/2022]
Abstract
Environment around conception can influence the developmental programme with lasting effects on gestational and postnatal phenotype and with consequences for adult health and disease risk. Peri-conception exposure comprises a crucial part of the 'Developmental Origins of Health and Disease' (DOHaD) concept. In this review, we consider the effects of maternal undernutrition experienced during the peri-conception period in select human models and in a mouse experimental model of protein restriction. Human datasets indicate that macronutrient deprivation around conception affect the epigenome, with enduring effects on cardiometabolic and neurological health. The mouse model, comprising maternal low protein diet exclusively during the peri-conception period, has revealed a stepwise progression in altered developmental programming following induction through maternal metabolite deficiency. This progression includes differential effects in extra-embryonic and embryonic cell lineages and tissues, leading to maladaptation in the growth trajectory and increased chronic disease comorbidities. The timeline embraces an array of mechanisms across nutrient sensing and signalling, cellular, metabolic, epigenetic and physiological processes with a coordinating role for mTORC1 signalling proposed. Early embryos appear active participants in environmental sensing to optimise the developmental programme for survival but with the trade-off of later disease. Similar adverse health outcomes may derive from other peri-conception environmental experiences, including maternal overnutrition, micronutrient availability, pollutant exposure and assisted reproductive treatments (ART) and support the need for preconception health before pregnancy.
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Affiliation(s)
- Tom P. Fleming
- Biological Sciences, Southampton General Hospital, University of Southampton, Southampton SO16 6YD, UK; (L.C.); (A.A.); (P.K.)
| | - Congshan Sun
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
- Center for Genetic Muscle Disorders, Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Oleg Denisenko
- Department of Medicine, University of Washington, 850 Republican St., Rm 242, Seattle, WA 98109, USA;
| | - Laura Caetano
- Biological Sciences, Southampton General Hospital, University of Southampton, Southampton SO16 6YD, UK; (L.C.); (A.A.); (P.K.)
| | - Anan Aljahdali
- Biological Sciences, Southampton General Hospital, University of Southampton, Southampton SO16 6YD, UK; (L.C.); (A.A.); (P.K.)
- Department of Biological Sciences, Faculty of Science, Alfaisaliah campus, University of Jeddah, Jeddah 23442, Saudi Arabia
| | - Joanna M. Gould
- Clinical Neurosciences and Psychiatry, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | - Pooja Khurana
- Biological Sciences, Southampton General Hospital, University of Southampton, Southampton SO16 6YD, UK; (L.C.); (A.A.); (P.K.)
- Institute for Biogenesis Research, Research Corporation of the University of Hawaii, Manoa, Honolulu, HI 96822, USA
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23
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Oocyte age and preconceptual alcohol use are highly correlated with epigenetic imprinting of a noncoding RNA ( nc886). Proc Natl Acad Sci U S A 2021; 118:2026580118. [PMID: 33723081 PMCID: PMC8000112 DOI: 10.1073/pnas.2026580118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic imprinting occurs before fertilization, impacts every cell of the developing child, and may be sensitive to environmental perturbations. The noncoding RNA, nc886 (also called VTRNA2-1) is the only known example of the ∼100 human genes imprinted by DNA methylation, that shows polymorphic imprinting in the population. The nc886 gene is part of an ∼1.6-kb differentially methylated region (DMR) that is methylated in the oocyte and silenced on the maternal allele in about 75% of humans worldwide. Here, we show that the presence or absence of imprinting at the nc886 DMR in an individual is consistent across different tissues, confirming that the imprint is established before cellular differentiation and is maintained into adulthood. We investigated the relationships between the frequency of imprinting in newborns and maternal age, alcohol consumption and cigarette smoking before conception in more than 1,100 mother/child pairs from South Africa. The probability of imprinting in newborns was increased in older mothers and decreased in mothers who drank alcohol before conception. On the other hand, cigarette smoking had no apparent relationship with the frequency of imprinting. These data show an epigenetic change during oocyte maturation which is potentially subject to environmental influence. Much focus has been placed on avoiding alcohol consumption during pregnancy, but our data suggest that drinking before conception may affect the epigenome of the newborn.
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24
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Gunasekara CJ, Hannon E, MacKay H, Coarfa C, McQuillin A, Clair DS, Mill J, Waterland RA. A machine learning case-control classifier for schizophrenia based on DNA methylation in blood. Transl Psychiatry 2021; 11:412. [PMID: 34341337 PMCID: PMC8329061 DOI: 10.1038/s41398-021-01496-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/07/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
Epigenetic dysregulation is thought to contribute to the etiology of schizophrenia (SZ), but the cell type-specificity of DNA methylation makes population-based epigenetic studies of SZ challenging. To train an SZ case-control classifier based on DNA methylation in blood, therefore, we focused on human genomic regions of systemic interindividual epigenetic variation (CoRSIVs), a subset of which are represented on the Illumina Human Methylation 450K (HM450) array. HM450 DNA methylation data on whole blood of 414 SZ cases and 433 non-psychiatric controls were used as training data for a classification algorithm with built-in feature selection, sparse partial least squares discriminate analysis (SPLS-DA); application of SPLS-DA to HM450 data has not been previously reported. Using the first two SPLS-DA dimensions we calculated a "risk distance" to identify individuals with the highest probability of SZ. The model was then evaluated on an independent HM450 data set on 353 SZ cases and 322 non-psychiatric controls. Our CoRSIV-based model classified 303 individuals as cases with a positive predictive value (PPV) of 80%, far surpassing the performance of a model based on polygenic risk score (PRS). Importantly, risk distance (based on CoRSIV methylation) was not associated with medication use, arguing against reverse causality. Risk distance and PRS were positively correlated (Pearson r = 0.28, P = 1.28 × 10-12), and mediational analysis suggested that genetic effects on SZ are partially mediated by altered methylation at CoRSIVs. Our results indicate two innate dimensions of SZ risk: one based on genetic, and the other on systemic epigenetic variants.
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Affiliation(s)
- Chathura J. Gunasekara
- grid.39382.330000 0001 2160 926XUSDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Eilis Hannon
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Harry MacKay
- grid.39382.330000 0001 2160 926XUSDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Cristian Coarfa
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Andrew McQuillin
- grid.83440.3b0000000121901201Division of Psychiatry, Faculty of Brain Sciences, University College London, London, UK
| | - David St. Clair
- grid.7107.10000 0004 1936 7291The Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jonathan Mill
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Robert A. Waterland
- grid.39382.330000 0001 2160 926XUSDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
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25
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Marttila S, Viiri LE, Mishra PP, Kühnel B, Matias-Garcia PR, Lyytikäinen LP, Ceder T, Mononen N, Rathmann W, Winkelmann J, Peters A, Kähönen M, Hutri-Kähönen N, Juonala M, Aalto-Setälä K, Raitakari O, Lehtimäki T, Waldenberger M, Raitoharju E. Methylation status of nc886 epiallele reflects periconceptional conditions and is associated with glucose metabolism through nc886 RNAs. Clin Epigenetics 2021; 13:143. [PMID: 34294131 PMCID: PMC8296652 DOI: 10.1186/s13148-021-01132-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-coding RNA 886 (nc886) is coded from a maternally inherited metastable epiallele. We set out to investigate the determinants and dynamics of the methylation pattern at the nc886 epiallele and how this methylation status associates with nc886 RNA expression. Furthermore, we investigated the associations between the nc886 methylation status or the levels of nc886 RNAs and metabolic traits in the YFS and KORA cohorts. The association between nc886 epiallele methylation and RNA expression was also validated in induced pluripotent stem cell (iPSC) lines. RESULTS We confirm that the methylation status of the nc886 epiallele is mostly binomial, with individuals displaying either a non- or hemi-methylated status, but we also describe intermediately and close to fully methylated individuals. We show that an individual's methylation status is associated with the mother's age and socioeconomic status, but not with the individual's own genetics. Once established, the methylation status of the nc886 epiallele remains stable for at least 25 years. This methylation status is strongly associated with the levels of nc886 non-coding RNAs in serum, blood, and iPSC lines. In addition, nc886 methylation status associates with glucose and insulin levels during adolescence but not with the indicators of glucose metabolism or the incidence of type 2 diabetes in adulthood. However, the nc886-3p RNA levels also associate with glucose metabolism in adulthood. CONCLUSIONS These results indicate that nc886 metastable epiallele methylation is tuned by the periconceptional conditions and it associates with glucose metabolism through the expression of the ncRNAs coded in the epiallele region.
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Grants
- 755320 Horizon 2020 (Taxinomisis)
- WA 4081/1-1 German Research Foundation
- BB/S020845/1 Biotechnology and Biological Sciences Research Council
- 134309, 126925, 121584, 124282, 129378, 117787, 41071 Academy of Finland
- 286284 and 322098 Academy of Finland
- 01EA1902A Joint Programming Initiative A healthy diet for a healthy life (DIMENSION)
- 848146 Horizon 2020 (To_Aition)
- 9X047, 9S054, and 9AB059 Tampere University Hospital Medical Funds
- 742927 European Research Council (MULTIEPIGEN)
- 285902, 330809 and 338395 academy of finland
- X51001 Tampere University Hospital Medical Funds
- the Social Insurance Institution of Finland
- Kuopio, Tampere, and Turku University Hospital Medical Funds
- Juho Vainion Säätiö
- Paavo Nurmen Säätiö
- Sydäntutkimussäätiö
- Suomen Kulttuurirahasto
- Tampereen Tuberkuloosisäätiö
- Emil Aaltosen Säätiö
- Yrjö Jahnssonin Säätiö
- Signe ja Ane Gyllenbergin Säätiö
- Diabetesliitto
- the Tampere University Hospital Supporting Foundation
- the Finnish Society of Clinical Chemistry
- Foundation of Clinical Chemistry
- Laboratoriolääketieteen edistämissäätiö sr.
- Orionin Tutkimussäätiö
- the Paulo Foundation
- Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München
- German Federal Ministry of Education and Research
- State of Bavaria
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Affiliation(s)
- Saara Marttila
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland.
- Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Leena E Viiri
- Heart Group, Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Tiina Ceder
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research At Heinrich Heine University, Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Neurogenetics and Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Annette Peters
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Tampere University, Tampere, Finland
| | - Markus Juonala
- Division of Medicine, Department of Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Katriina Aalto-Setälä
- Heart Group, Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Heart Hospital, Tampere University Hospital, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Turku, Turku University Hospital, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Emma Raitoharju
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland.
- Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland.
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26
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Marttila S, Viiri LE, Mishra PP, Kühnel B, Matias-Garcia PR, Lyytikäinen LP, Ceder T, Mononen N, Rathmann W, Winkelmann J, Peters A, Kähönen M, Hutri-Kähönen N, Juonala M, Aalto-Setälä K, Raitakari O, Lehtimäki T, Waldenberger M, Raitoharju E. Methylation status of nc886 epiallele reflects periconceptional conditions and is associated with glucose metabolism through nc886 RNAs. Clin Epigenetics 2021. [PMID: 34294131 DOI: 10.1186/s13148‐021‐01132‐3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Non-coding RNA 886 (nc886) is coded from a maternally inherited metastable epiallele. We set out to investigate the determinants and dynamics of the methylation pattern at the nc886 epiallele and how this methylation status associates with nc886 RNA expression. Furthermore, we investigated the associations between the nc886 methylation status or the levels of nc886 RNAs and metabolic traits in the YFS and KORA cohorts. The association between nc886 epiallele methylation and RNA expression was also validated in induced pluripotent stem cell (iPSC) lines. RESULTS We confirm that the methylation status of the nc886 epiallele is mostly binomial, with individuals displaying either a non- or hemi-methylated status, but we also describe intermediately and close to fully methylated individuals. We show that an individual's methylation status is associated with the mother's age and socioeconomic status, but not with the individual's own genetics. Once established, the methylation status of the nc886 epiallele remains stable for at least 25 years. This methylation status is strongly associated with the levels of nc886 non-coding RNAs in serum, blood, and iPSC lines. In addition, nc886 methylation status associates with glucose and insulin levels during adolescence but not with the indicators of glucose metabolism or the incidence of type 2 diabetes in adulthood. However, the nc886-3p RNA levels also associate with glucose metabolism in adulthood. CONCLUSIONS These results indicate that nc886 metastable epiallele methylation is tuned by the periconceptional conditions and it associates with glucose metabolism through the expression of the ncRNAs coded in the epiallele region.
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Affiliation(s)
- Saara Marttila
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland. .,Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Leena E Viiri
- Heart Group, Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Tiina Ceder
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany.,Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research At Heinrich Heine University, Düsseldorf, Germany.,Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Department of Neurogenetics and Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Annette Peters
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Tampere University, Tampere, Finland
| | - Markus Juonala
- Division of Medicine, Department of Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Katriina Aalto-Setälä
- Heart Group, Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Heart Hospital, Tampere University Hospital, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Department of Clinical Physiology and Nuclear Medicine, University of Turku, Turku University Hospital, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Emma Raitoharju
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland. .,Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland.
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27
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You YA, Kwon EJ, Hwang HS, Choi SJ, Choi SK, Kim YJ. Elevated methylation of the vault RNA2-1 promoter in maternal blood is associated with preterm birth. BMC Genomics 2021; 22:528. [PMID: 34246240 PMCID: PMC8272312 DOI: 10.1186/s12864-021-07865-y] [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: 03/10/2020] [Accepted: 06/30/2021] [Indexed: 11/23/2022] Open
Abstract
Background Preterm birth, defined as parturition before 37 completed weeks of gestation, is associated with an increased risk of neonatal complications and death, as well as poor health and disease later in life. Epigenetics could contribute to the mechanism underlying preterm birth. Results Genome-wide DNA methylation analysis of whole blood cells from 10 women (5 term and 5 preterm deliveries) was performed using an Illumina Infinium HumanMethylation450 BeadChips array. We identified 1,581 differentially methylated CpG sites in promoter regions between term and preterm birth. Although the differences were not significant after correcting for multiple tests, seven CpGs on the genomically imprinted vault RNA2-1 (VTRNA2-1; also known as non-coding RNA, nc886 or miR-886) showed the largest differences (range: 26–39 %). Pyrosequencing verification was performed with blood samples from pregnant women recruited additionally (39 term and 43 preterm deliveries). In total, 28 (34.1 %) samples showed hypomethylation of the VTRNA2-1 promoter (< 13 % methylation), while 54 (65.9 %) samples showed elevated methylation levels between 30 and 60 %. Elevated methylation of VTRNA2-1 promoter was associated with an increased risk of preterm birth after adjusting for maternal age, season of delivery, parity and white blood cell count. The mRNA expression of VTRNA2-1 was 0.51-fold lower in women with preterm deliveries (n = 20) compared with women with term deliveries (n = 20). Conclusions VTRNA2-1 is a noncoding transcript to environmentally responsive epialleles. Our results suggest that elevated methylation of the VTRNA2-1 promoter may result in increased risk of PTB caused by the pro-inflammatory cytokines. Further studies are needed to confirm the association of VTRNA2-1 methylation with preterm birth in a large population, and to elucidate the underlying mechanism. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07865-y.
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Affiliation(s)
- Young-Ah You
- Department of Obstetrics and Gynecology, Ewha Medical Research Institute, Ewha Womans University Medical School, 07985, Seoul, Korea
| | - Eun Jin Kwon
- Graduate Program in System Health Science and Engineering, Ewha Womans University, 03760, Seoul, Korea
| | - Han-Sung Hwang
- Department of Obstetrics and Gynecology, Research Institute of Medical Science, Konkuk University School of Medicine, 143-729, Seoul, Korea
| | - Suk-Joo Choi
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 135-710, Seoul, Korea
| | - Sae Kyung Choi
- College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, 137-040, Seoul, Korea
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, Ewha Medical Research Institute, Ewha Womans University Medical School, 07985, Seoul, Korea. .,Graduate Program in System Health Science and Engineering, Ewha Womans University, 03760, Seoul, Korea. .,Department of Obstetrics and Gynecology, Ewha Womans University Mok Dong Hospital, 158-051, Seoul, South Korea.
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28
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Rodriguez N, Martinez-Pinteño A, Blázquez A, Ortiz AE, Moreno E, Gassó P, Lafuente A, Lazaro L, Mas S. Integrative DNA Methylation and Gene Expression Analysis of Cognitive Behavioral Therapy Response in Children and Adolescents with Obsessive-Compulsive Disorder; a Pilot Study. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:757-766. [PMID: 34234515 PMCID: PMC8254600 DOI: 10.2147/pgpm.s313015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/05/2021] [Indexed: 11/28/2022]
Abstract
Purpose Here, we propose an integrative analysis of genome-wide methylation and gene expression to provide new insight into the biological mechanisms of Cognitive behavioral therapy (CBT) in pediatric obsessive-compulsive disorder (OCD). Patients and Methods Twelve children and adolescents with OCD receiving CBT for the first time were classified as responders or non-responders after eight weeks of CBT. Differentially methylated positions (DMPs) and gene co-expression modules were identified using specific R software packages. Correlations between the DMPs and gene co-expression modules were investigated. Results Two genes were enriched with significant DMPs (Δβ > ± 0.2, FDR-adjusted p-value < 0.05): PIWIL1 and MIR886. The yellowgreen module of co-expressed genes was associated with CBT response (FDR-adjusted p-value = 0.0003). Significant correlations were observed between the yellowgreen module and the CpGs in PIWIL1 and MIR886 (p < 0.008). Patients showing hypermethylation in these CpGs presented an upregulation in the genes in the yellowgreen module. Conclusion Taken together, the preliminary results of this systems-level approach, despite the study limitations, provide evidence that the epigenetic regulation of ncRNAs could be a predictor of CBT response. Limitations The sample size limited the statistical power, and given that the study was hypothesis-driven, our results should be seen as preliminary.
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Affiliation(s)
- Natalia Rodriguez
- Department of Basic Clinical Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain
| | - Albert Martinez-Pinteño
- Department of Basic Clinical Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain
| | - Ana Blázquez
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Ana Encarnación Ortiz
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Elena Moreno
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Patricia Gassó
- Department of Basic Clinical Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Amalia Lafuente
- Department of Basic Clinical Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,G04 Group, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Carlos III Health Institute, Madrid, Spain
| | - Luisa Lazaro
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,G04 Group, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Carlos III Health Institute, Madrid, Spain.,Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Sergi Mas
- Department of Basic Clinical Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,G04 Group, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Carlos III Health Institute, Madrid, Spain
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Kalbermatter C, Fernandez Trigo N, Christensen S, Ganal-Vonarburg SC. Maternal Microbiota, Early Life Colonization and Breast Milk Drive Immune Development in the Newborn. Front Immunol 2021; 12:683022. [PMID: 34054875 PMCID: PMC8158941 DOI: 10.3389/fimmu.2021.683022] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
The innate immune system is the oldest protection strategy that is conserved across all organisms. Although having an unspecific action, it is the first and fastest defense mechanism against pathogens. Development of predominantly the adaptive immune system takes place after birth. However, some key components of the innate immune system evolve during the prenatal period of life, which endows the newborn with the ability to mount an immune response against pathogenic invaders directly after birth. Undoubtedly, the crosstalk between maternal immune cells, antibodies, dietary antigens, and microbial metabolites originating from the maternal microbiota are the key players in preparing the neonate’s immunity to the outer world. Birth represents the biggest substantial environmental change in life, where the newborn leaves the protective amniotic sac and is exposed for the first time to a countless variety of microbes. Colonization of all body surfaces commences, including skin, lung, and gastrointestinal tract, leading to the establishment of the commensal microbiota and the maturation of the newborn immune system, and hence lifelong health. Pregnancy, birth, and the consumption of breast milk shape the immune development in coordination with maternal and newborn microbiota. Discrepancies in these fine-tuned microbiota interactions during each developmental stage can have long-term effects on disease susceptibility, such as metabolic syndrome, childhood asthma, or autoimmune type 1 diabetes. In this review, we will give an overview of the recent studies by discussing the multifaceted emergence of the newborn innate immune development in line with the importance of maternal and early life microbiota exposure and breast milk intake.
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Affiliation(s)
- Cristina Kalbermatter
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Nerea Fernandez Trigo
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sandro Christensen
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Stephanie C Ganal-Vonarburg
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
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Fort RS, Duhagon MA. Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. F1000Res 2021; 10:182. [PMID: 34354812 PMCID: PMC8287541 DOI: 10.12688/f1000research.28510.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNAs promoters are enriched in transcription factors related to viral infection. VtRNA2-1 is likely the most independently regulated homologue. VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA chromatin status cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.
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Affiliation(s)
- Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Montevideo, 11600, Uruguay
| | - María Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay
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VTRNA2-1: Genetic Variation, Heritable Methylation and Disease Association. Int J Mol Sci 2021; 22:ijms22052535. [PMID: 33802562 PMCID: PMC7961504 DOI: 10.3390/ijms22052535] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/28/2022] Open
Abstract
VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation and other factors such as age and adult lifestyle on blood DNA methylation in this region. We first sequenced the VTRNA2-1 gene region in multiple-case breast cancer families in which VTRNA2-1 methylation was identified as heritable and associated with breast cancer risk. Methylation quantitative trait loci (mQTL) were investigated using a prospective cohort study (4500 participants with genotyping and methylation data). The cis-mQTL analysis (334 variants ± 50 kb of the most heritable CpG site) identified 43 variants associated with VTRNA2-1 methylation (p < 1.5 × 10−4); however, these explained little of the methylation variation (R2 < 0.5% for each of these variants). No genetic variants elsewhere in the genome were found to strongly influence VTRNA2-1 methylation. SNP-based heritability estimates were consistent with the mQTL findings (h2 = 0, 95%CI: −0.14 to 0.14). We found no evidence that age, sex, country of birth, smoking, body mass index, alcohol consumption or diet influenced blood DNA methylation at VTRNA2-1. Genetic factors and adult lifestyle play a minimal role in explaining methylation variability at the heritable VTRNA2-1 cluster.
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Lin CH, Lee YS, Huang YY, Tsai CN. Methylation status of vault RNA 2-1 promoter is a predictor of glycemic response to glucagon-like peptide-1 analog therapy in type 2 diabetes mellitus. BMJ Open Diabetes Res Care 2021; 9:9/1/e001416. [PMID: 33674278 PMCID: PMC7938984 DOI: 10.1136/bmjdrc-2020-001416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 01/28/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Therapeutic efficiency of glucagon-like peptide-1 (GLP-1) analog is about 50%-70% in type 2 diabetes mellitus (T2DM). Discovery of potential genetic biomarkers for prediction of treatment efficiency of GLP-1 analog before therapy is still necessary. We assess whether DNA methylation was associated with glycemic response to GLP-1 analog therapy in patients with poorly controlled T2DM. RESEARCH DESIGN AND METHODS Genomic DNA was extracted from the peripheral blood of training (n=10) and validation (n=128) groups of patients with T2DM receiving GLP-1 analogs. DNA methylome was analyzed using Infinium Human Methylation EPIC Bead Chip in the training group. The candidate genes were examined using a pyrosequencing platform in the validation group. The association between DNA methylation status and glycemic response to GLP-1 was analyzed in these patients. RESULTS The most differential methylation region between those with a good (responsive) and poor (unresponsive) glycemic response to GLP-1 analog therapy was located on chromosome 5q31.1 (135415693 to 135416613), the promoter of VTRNA2-1 in the training group. The methylation status of the VTRNA2-1 promoter was examined in the validation group via pyrosequencing reaction, and the hypomethylation of VTRNA2-1 (<40% methylation) was significantly associated with poor glycemic response to GLP-1 treatment (OR 2.757, 95% CI 1.240 to 6.130, p=0.011). Since the VTRNA2-1 promoter region was previously reported maternal imprinting extended to the adjacent centromeric CCCTC-binding factor site that contained an A/C polymorphism (rs2346018), which was associated with methylation density of VTRNA2-1, this A/C polymorphism was also integrated to analyze association with glycemic response to GLP-1 analog therapy. In patients with the A allele of rs2346018 and hypomethylation (<40%) on the VTRNA2-1 promoter, the OR increased to 4.048 (95% CI 1.438 to 11.389, p=0.007). CONCLUSIONS The glycemic response to GLP-1 analog treatment is associated with the methylation status of the VTRNA2-1 promoter and polymorphism of rs2346018.
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Affiliation(s)
- Chia-Hung Lin
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yun-Shien Lee
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou Main Branch, Taoyuan, Taiwan
- Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan
| | - Yu-Yao Huang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Neu Tsai
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan
- Department of Surgery, New Taipei Municipal Tucheng Hospital, New Taipei City, Taiwan
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Elmer JL, Hay AD, Kessler NJ, Bertozzi TM, Ainscough EAC, Ferguson-Smith AC. Genomic properties of variably methylated retrotransposons in mouse. Mob DNA 2021; 12:6. [PMID: 33612119 PMCID: PMC7898769 DOI: 10.1186/s13100-021-00235-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. RESULTS Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. CONCLUSION Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
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Affiliation(s)
- Jessica L. Elmer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Amir D. Hay
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Noah J. Kessler
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Tessa M. Bertozzi
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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Lee YS, Bao X, Lee HH, Jang JJ, Saruuldalai E, Park G, Im WR, Park JL, Kim SY, Shin S, Jeon SH, Kang S, Lee HS, Lee JS, Zhang K, Park EJ, Kim IH, Lee YS. Nc886, a Novel Suppressor of the Type I Interferon Response Upon Pathogen Intrusion. Int J Mol Sci 2021; 22:ijms22042003. [PMID: 33670458 PMCID: PMC7922379 DOI: 10.3390/ijms22042003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 01/20/2023] Open
Abstract
Interferons (IFNs) are a crucial component in the innate immune response. Especially the IFN-β signaling operates in most cell types and plays a key role in the first line of defense upon pathogen intrusion. The induction of IFN-β should be tightly controlled, because its hyperactivation can lead to tissue damage or autoimmune diseases. Activation of the IFN-β promoter needs Interferon Regulatory Factor 3 (IRF3), together with Nuclear Factor kappa-light-chain-enhancer of activated B cells (NF-κB) and Activator Protein 1 (AP-1). Here we report that a human noncoding RNA, nc886, is a novel suppressor for the IFN-β signaling and inflammation. Upon treatment with several pathogen-associated molecular patterns and viruses, nc886 suppresses the activation of IRF3 and also inhibits NF-κB and AP-1 via inhibiting Protein Kinase R (PKR). These events lead to decreased expression of IFN-β and resultantly IFN-stimulated genes. nc886′s role might be to restrict the IFN-β signaling from hyperactivation. Since nc886 expression is regulated by epigenetic and environmental factors, nc886 might explain why innate immune responses to pathogens are variable depending on biological settings.
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Affiliation(s)
- Yeon-Su Lee
- Division of Clinical Cancer Research, Research Institute, National Cancer Center, Goyang 10408, Korea; (Y.-S.L.); (G.P.)
| | - Xiaoyong Bao
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA; (X.B.); (K.Z.)
| | - Hwi-Ho Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (H.-H.L.); (J.J.J.); (E.S.); (W.R.I.); (S.K.); (E.J.P.); (I.-H.K.)
| | - Jiyoung Joan Jang
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (H.-H.L.); (J.J.J.); (E.S.); (W.R.I.); (S.K.); (E.J.P.); (I.-H.K.)
| | - Enkhjin Saruuldalai
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (H.-H.L.); (J.J.J.); (E.S.); (W.R.I.); (S.K.); (E.J.P.); (I.-H.K.)
| | - Gaeul Park
- Division of Clinical Cancer Research, Research Institute, National Cancer Center, Goyang 10408, Korea; (Y.-S.L.); (G.P.)
| | - Wonkyun Ronny Im
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (H.-H.L.); (J.J.J.); (E.S.); (W.R.I.); (S.K.); (E.J.P.); (I.-H.K.)
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Korea; (S.S.); (S.H.J.)
| | - Jong-Lyul Park
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141, Korea; (J.-L.P.); (S.-Y.K.)
- Department of Functional Genomics, University of Science and Technology, Daejeon 34113, Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141, Korea; (J.-L.P.); (S.-Y.K.)
- Department of Functional Genomics, University of Science and Technology, Daejeon 34113, Korea
| | - Sooyong Shin
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Korea; (S.S.); (S.H.J.)
| | - Sung Ho Jeon
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Korea; (S.S.); (S.H.J.)
| | - Sangmin Kang
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (H.-H.L.); (J.J.J.); (E.S.); (W.R.I.); (S.K.); (E.J.P.); (I.-H.K.)
| | - Hyun-Sung Lee
- Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Ju-Seog Lee
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Ke Zhang
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA; (X.B.); (K.Z.)
| | - Eun Jung Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (H.-H.L.); (J.J.J.); (E.S.); (W.R.I.); (S.K.); (E.J.P.); (I.-H.K.)
| | - In-Hoo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (H.-H.L.); (J.J.J.); (E.S.); (W.R.I.); (S.K.); (E.J.P.); (I.-H.K.)
| | - Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (H.-H.L.); (J.J.J.); (E.S.); (W.R.I.); (S.K.); (E.J.P.); (I.-H.K.)
- Correspondence: ; Tel.: +82–31-920-2748; Fax: +82-31-920-2759
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Muskens IS, Li S, Jackson T, Elliot N, Hansen HM, Myint SS, Pandey P, Schraw JM, Roy R, Anguiano J, Goudevenou K, Siegmund KD, Lupo PJ, de Bruijn MFTR, Walsh KM, Vyas P, Ma X, Roy A, Roberts I, Wiemels JL, de Smith AJ. The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis. Nat Commun 2021; 12:821. [PMID: 33547282 PMCID: PMC7865055 DOI: 10.1038/s41467-021-21064-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Down syndrome is associated with genome-wide perturbation of gene expression, which may be mediated by epigenetic changes. We perform an epigenome-wide association study on neonatal bloodspots comparing 196 newborns with Down syndrome and 439 newborns without Down syndrome, adjusting for cell-type heterogeneity, which identifies 652 epigenome-wide significant CpGs (P < 7.67 × 10-8) and 1,052 differentially methylated regions. Differential methylation at promoter/enhancer regions correlates with gene expression changes in Down syndrome versus non-Down syndrome fetal liver hematopoietic stem/progenitor cells (P < 0.0001). The top two differentially methylated regions overlap RUNX1 and FLI1, both important regulators of megakaryopoiesis and hematopoietic development, with significant hypermethylation at promoter regions of these two genes. Excluding Down syndrome newborns harboring preleukemic GATA1 mutations (N = 30), identified by targeted sequencing, has minimal impact on the epigenome-wide association study results. Down syndrome has profound, genome-wide effects on DNA methylation in hematopoietic cells in early life, which may contribute to the high frequency of hematological problems, including leukemia, in children with Down syndrome.
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Affiliation(s)
- Ivo S Muskens
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Thomas Jackson
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Natalina Elliot
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Priyatama Pandey
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Jeremy M Schraw
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Ritu Roy
- Computational Biology and Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Joaquin Anguiano
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Katerina Goudevenou
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Kimberly D Siegmund
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Kyle M Walsh
- Department of Neurosurgery, Duke University, Durham, NC, USA
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Anindita Roy
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Irene Roberts
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA.
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Quilter CR, Harvey KM, Bauer J, Skinner BM, Gomez M, Shrivastava M, Doel AM, Drammeh S, Dunger DB, Moore SE, Ong KK, Prentice AM, Bernstein RM, Sargent CA, Affara NA. Identification of methylation changes associated with positive and negative growth deviance in Gambian infants using a targeted methyl sequencing approach of genomic DNA. FASEB Bioadv 2021; 3:205-230. [PMID: 33842847 PMCID: PMC8019263 DOI: 10.1096/fba.2020-00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/25/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Low birthweight and reduced height gain during infancy (stunting) may arise at least in part from adverse early life environments that trigger epigenetic reprogramming that may favor survival. We examined differential DNA methylation patterns using targeted methyl sequencing of regions regulating gene activity in groups of rural Gambian infants: (a) low and high birthweight (DNA from cord blood (n = 16 and n = 20, respectively), from placental trophoblast tissue (n = 21 and n = 20, respectively), and DNA from peripheral blood collected from infants at 12 months of age (n = 23 and n = 17, respectively)), and, (b) the top 10% showing rapid postnatal length gain (high, n = 20) and the bottom 10% showing slow postnatal length gain (low, n = 20) based on z score change between birth and 12 months of age (LAZ) (DNA from peripheral blood collected from infants at 12 months of age). Using BiSeq analysis to identify significant methylation marks, for birthweight, four differentially methylated regions (DMRs) were identified in trophoblast DNA, compared to 68 DMRs in cord blood DNA, and 54 DMRs in 12‐month peripheral blood DNA. Twenty‐five DMRs were observed to be associated with high and low length for age (LAZ) at 12 months. With the exception of five loci (associated with two different genes), there was no overlap between these groups of methylation marks. Of the 194 CpG methylation marks contained within DMRs, 106 were located to defined gene regulatory elements (promoters, CTCF‐binding sites, transcription factor‐binding sites, and enhancers), 58 to gene bodies (introns or exons), and 30 to intergenic DNA. Distinct methylation patterns associated with birthweight between comparison groups were observed in DNA collected at birth (at the end of intrauterine growth window) compared to those established by 12 months (near the infancy/childhood growth transition). The longitudinal differences in methylation patterns may arise from methylation adjustments, changes in cellular composition of blood or both that continue during the critical postnatal growth period, and in response to early nutritional and infectious environmental exposures with impacts on growth and longer‐term health outcomes.
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Affiliation(s)
- Claire R Quilter
- Department of Pathology University of Cambridge Cambridge UK.,Present address: East Midlands & East of England NHS Genomic Laboratory Hub, Genomics Laboratories Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Kerry M Harvey
- Department of Pathology University of Cambridge Cambridge UK
| | - Julien Bauer
- Department of Pathology University of Cambridge Cambridge UK
| | - Benjamin M Skinner
- Department of Pathology University of Cambridge Cambridge UK.,School of Life Sciences University of Essex Colchester UK
| | - Maria Gomez
- Department of Pathology University of Cambridge Cambridge UK.,Present address: Kennedy Institute of Rheumatology University of Oxford Oxford UK
| | - Manu Shrivastava
- Department of Pathology University of Cambridge Cambridge UK.,Present address: Oxford University Hospitals Oxford UK
| | - Andrew M Doel
- Department of Women and Children's Health King's College London London UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Saikou Drammeh
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - David B Dunger
- MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK
| | - Sophie E Moore
- Department of Women and Children's Health King's College London London UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Ken K Ong
- MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK.,Department of Paediatrics University of Cambridge School of Clinical Medicine Cambridge UK.,Institute of Metabolic Science Cambridge Biomedical Campus Cambridge Cambridge UK
| | - Andrew M Prentice
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Robin M Bernstein
- Growth and Development Lab Department of Anthropology University of Colorado Boulder CO USA.,Institute of Behavioural Science University of Colorado Boulder CO USA
| | | | - Nabeel A Affara
- Department of Pathology University of Cambridge Cambridge UK
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Peeters S, Declerck K, Thomas M, Boudin E, Beckers D, Chivu O, Heinrichs C, Devriendt K, de Zegher F, Van Hul W, Vanden Berghe W, De Schepper J, Rooman R, Mortier G. DNA Methylation Profiling and Genomic Analysis in 20 Children with Short Stature Who Were Born Small for Gestational Age. J Clin Endocrinol Metab 2020; 105:5873625. [PMID: 32685970 DOI: 10.1210/clinem/dgaa465] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/15/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE In a significant proportion of children born small for gestational age (SGA) with failure of catch-up growth, the etiology of short stature remains unclear after routine diagnostic workup. We wanted to investigate if extensive analysis of the (epi)genome can unravel the cause of growth failure in a significant portion of these children. PATIENTS AND METHODS Twenty SGA children treated with GH because of short stature were selected from the BELGROW database of the Belgian Society for Pediatric Endocrinology and Diabetology for exome sequencing, single-nucleotide polymorphism (SNP) array and genome-wide methylation analysis to identify the (epi)genetic cause. First-year response to GH was compared with the response of SGA patients in the KIGS database. RESULTS We identified (likely) pathogenic variants in 4 children (from 3 families) using exome sequencing and found pathogenic copy number variants in 2 probands using SNP array. In a child harboring a NSD1-containing microduplication, we identified a DNA methylation signature that is opposite to the genome-wide DNA methylation signature of Sotos syndrome. Moreover, we observed multilocus imprinting disturbances in 2 children in whom no other genomic alteration could be identified. Five of 6 children with a genetic diagnosis had an "above average" response to GH. CONCLUSIONS The study indicates that a more advanced approach with deep genotyping can unravel unexpected (epi)genomic alterations in SGA children with persistent growth failure. Most SGA children with a genetic diagnosis had a good response to GH treatment.
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Affiliation(s)
- Silke Peeters
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Muriel Thomas
- Belgian Society for Pediatric Endocrinology and Diabetology, Brussels, Belgium
| | - Eveline Boudin
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Dominique Beckers
- Unité d'Endocrinologie Pédiatrique, CHU Namur, Université catholique de Louvain, Yvoir, Belgium and Department of Pediatrics, University Hospital Leuven, Leuven, Belgium
| | - Olimpia Chivu
- Department of Pediatrics, Clinique de l'Espérance, Saint-Nicolas, Belgium
| | - Claudine Heinrichs
- Paediatric Endocrinology Unit, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Brussels, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University of Leuven and the University Hospital Leuven, Leuven, Belgium
| | - Francis de Zegher
- Department of Development & Regeneration, University of Leuven, Leuven, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jean De Schepper
- Department of Pediatrics, Vrije Universiteit Brussel, Universitair Ziekenhuis Brussel, Brussels, Belgium and Department of Pediatrics, Universitair Ziekenhuis Gent, Ghent, Belgium
| | | | - Geert Mortier
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
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Saffari A, Shrestha S, Issarapu P, Sajjadi S, Betts M, Sahariah SA, Tomar AS, James P, Dedaniya A, Yadav DK, Kumaran K, Prentice AM, Lillycrop KA, Fall CHD, Chandak GR, Silver MJ. Effect of maternal preconceptional and pregnancy micronutrient interventions on children's DNA methylation: Findings from the EMPHASIS study. Am J Clin Nutr 2020; 112:1099-1113. [PMID: 32889533 PMCID: PMC7528567 DOI: 10.1093/ajcn/nqaa193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Maternal nutrition in pregnancy has been linked to offspring health in early and later life, with changes to DNA methylation (DNAm) proposed as a mediating mechanism. OBJECTIVE We investigated intervention-associated DNAm changes in children whose mothers participated in 2 randomized controlled trials of micronutrient supplementation before and during pregnancy, as part of the EMPHASIS (Epigenetic Mechanisms linking Preconceptional nutrition and Health Assessed in India and sub-Saharan Africa) study (ISRCTN14266771). DESIGN We conducted epigenome-wide association studies with blood samples from Indian (n = 698) and Gambian (n = 293) children using the Illumina EPIC array and a targeted study of selected loci not on the array. The Indian micronutrient intervention was food based, whereas the Gambian intervention was a micronutrient tablet. RESULTS We identified 6 differentially methylated CpGs in Gambians [2.5-5.0% reduction in intervention group, all false discovery rate (FDR) <5%], the majority mapping to ESM1, which also represented a strong signal in regional analysis. One CpG passed FDR <5% in the Indian cohort, but overall effect sizes were small (<1%) and did not have the characteristics of a robust signature. We also found strong evidence for enrichment of metastable epialleles among subthreshold signals in the Gambian analysis. This supports the notion that multiple methylation loci are influenced by micronutrient supplementation in the early embryo. CONCLUSIONS Maternal preconceptional and pregnancy micronutrient supplementation may alter DNAm in children measured at 7-9 y. Multiple factors, including differences between the nature of the intervention, participants, and settings, are likely to have contributed to the lack of replication in the Indian cohort. Potential links to phenotypic outcomes will be explored in the next stage of the EMPHASIS study.
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Affiliation(s)
- Ayden Saffari
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
| | - Prachand Issarapu
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sara Sajjadi
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Modupeh Betts
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Ashutosh Singh Tomar
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Philip James
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Akshay Dedaniya
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Dilip K Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
- Department of Physiology, Boston University, School of Medicine, Boston, MA, USA
| | - Kalyanaraman Kumaran
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- CSI Holdsworth Memorial Hospital, Mysore, India
| | - Andrew M Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Matt J Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
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Leroy JL, Frongillo EA, Dewan P, Black MM, Waterland RA. Can Children Catch up from the Consequences of Undernourishment? Evidence from Child Linear Growth, Developmental Epigenetics, and Brain and Neurocognitive Development. Adv Nutr 2020; 11:1032-1041. [PMID: 32584399 PMCID: PMC7360439 DOI: 10.1093/advances/nmaa020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/04/2020] [Accepted: 02/12/2020] [Indexed: 11/13/2022] Open
Abstract
Recovery from nutritionally induced height deficits continues to garner attention. The current literature on catch-up growth, however, has 2 important limitations: wide-ranging definitions of catch-up growth are used, and it remains unclear whether children can recover from the broader consequences of undernutrition. We addressed these shortcomings by reviewing the literature on the criteria for catch-up in linear growth and on the potential to recover from undernutrition early in life in 3 domains: linear growth, developmental epigenetics, and child brain and neurocognitive development. Four criteria must be met to demonstrate catch-up growth in height: after a period in which a growth-inhibiting condition (criterion 1) causes a reduction in linear growth velocity (criterion 2), alleviation of the inhibiting condition (criterion 3) leads to higher-than-normal velocity (criterion 4). Accordingly, studies that are observational, do not use absolute height, or have no alleviation of an inhibiting condition cannot be used to establish catch-up growth. Adoption and foster care, which provide dramatic improvements in children's living conditions not typically attained in nutrition interventions, led to some (but incomplete) recovery in linear growth and brain and neurocognitive development. Maternal nutrition around the time of conception was shown to have long-term (potentially permanent) effects on DNA methylation in the offspring. Undernourishment early in life may thus have profound irreversible effects. Scientific, program, and policy efforts should focus on preventing maternal and child undernutrition rather than on correcting its consequences or attempting to prove they can be corrected.
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Affiliation(s)
- Jef L Leroy
- Poverty, Health, and Nutrition Division, International Food Policy Research Institute, Washington, DC, USA
| | - Edward A Frongillo
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, USA
| | - Pragya Dewan
- Poverty, Health, and Nutrition Division, International Food Policy Research Institute, Washington, DC, USA
| | - Maureen M Black
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
- RTI International, Research Triangle Park, NC, USA
| | - Robert A Waterland
- USDA/Agricultural Research Service Children's Nutrition Research Center, Departments of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
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40
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Periconceptional environment predicts leukocyte telomere length in a cross-sectional study of 7-9 year old rural Gambian children. Sci Rep 2020; 10:9675. [PMID: 32541825 PMCID: PMC7295801 DOI: 10.1038/s41598-020-66729-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022] Open
Abstract
Early life exposures are important predictors of adult disease risk. Although the underlying mechanisms are largely unknown, telomere maintenance may be involved. This study investigated the relationship between seasonal differences in parental exposures at time of conception and leukocyte telomere length (LTL) in their offspring. LTL was measured in two cohorts of children aged 2 yrs (N = 487) and 7–9 yrs (N = 218). The association between date of conception and LTL was examined using Fourier regression models, adjusted for age, sex, leukocyte cell composition, and other potential confounders. We observed an effect of season in the older children in all models [likelihood ratio test (LRT) χ²2 = 7.1, p = 0.03; fully adjusted model]. LTL was greatest in children conceived in September (in the rainy season), and smallest in those conceived in March (in the dry season), with an effect size (LTL peak–nadir) of 0.60 z-scores. No effect of season was evident in the younger children (LRT χ²2 = 0.87, p = 0.65). The different results obtained for the two cohorts may reflect a delayed effect of season of conception on postnatal telomere maintenance. Alternatively, they may be explained by unmeasured differences in early life exposures, or the increased telomere attrition rate during infancy.
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41
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DNA methylation at the crossroads of gene and environment interactions. Essays Biochem 2020; 63:717-726. [PMID: 31782496 PMCID: PMC6923319 DOI: 10.1042/ebc20190031] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an epigenetic mark involved in regulating genome function and is critical for normal development in mammals. It has been observed that the developmental environment can lead to permanent changes in gene expression and DNA methylation, at least at 'metastable epialleles'. These are defined as regions of the genome that show a variable epigenetic state that is established early in development and maintained through subsequent cell divisions. However, the majority of the known genome does not behave in this manner. Here, we use the developmental origins of adult disease hypothesis to understand environmental epigenomics. Some challenges to studying how DNA methylation is influenced by the environment include identifying DNA methylation changes associated with an environmental exposure in tissues with a complex cellular composition and at genomic regions for which DNA methylation is dynamically regulated in a cell-type specific manner. We also offer a perspective of how emerging technologies may be useful for dissecting the functional contribution of exposure-associated epigenetic changes and highlight recent evidence that suggests that genomic regions that are absent from genome assemblies may be unappreciated hotspots for environmental modulation of the epigenetic state.
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42
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Ma H, Wang M, Zhou Y, Yang JJ, Wang LY, Yang RH, Wen MJ, Kong L. Noncoding RNA 886 alleviates tumor cellular immunological rejection in host C57BL/C mice. Cancer Med 2020; 9:5258-5271. [PMID: 32476259 PMCID: PMC7367629 DOI: 10.1002/cam4.3148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/08/2020] [Accepted: 05/04/2020] [Indexed: 12/16/2022] Open
Abstract
Non‐coding RNA 886 (nc886/VTRNA2‐1) is a Pol III transcript and an atypical imprinted gene. Its exact function as a negative regulator of protein kinase R establishes its connection with innate immunity. Studies have shown that nc886 silencing is closely associated with prostate cancer progression. Previous work has constructed a cell model of stable nc886 overexpression (“mimic” or “nc886+”) in PC‐3M‐1E8 cell lines (1E8), which are highly bone‐metastatic human prostate cancer cells with low expression of nc886, and cells expressing the mimic were validated to have lower invasive and metastatic abilities than cells expressing the scramble transcript in vitro and in vivo. In this study, we directly injected mimic or scramble cells into the left ventricle of C57BL/C mice, an immunocompetent animal model, to elucidate the immune mechanisms of tumor‐host interactions. Interestingly, we found that tumor cells induced the inflammation of many important organs due to xenogeneic antigen rejection; this inflammation was ultimately repaired by tissue fibrosis after 28 days, except for in the spleen. The reason is that mimic cells, as heterogeneous antigens, are mostly directly recognized by macrophages or T cells in blood, and few mimic cells enter the spleen compared with scramble cells. The induction of splenic macrophage polarization to M2 macrophages by scramble cells is a critical factor in maintaining chronic splenic inflammation. In addition, we recognize that nc886 broadly decreases the expression of some human leukocyte antigen molecules and antigen transporters. This evidence reveals the interesting role of nc886 in regulating tumor cell antigens.
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Affiliation(s)
- Hui Ma
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Miao Wang
- Department of Pathology, Beijing Friendship Hospital, The Second Clinical Medical College of Capital Medical University, Beijing, China
| | - Ying Zhou
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Jia-Jie Yang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Li-Yong Wang
- Core Facilities for Molecular Biology, Capital Medical University, Beijing, PR China
| | - Rong-Hui Yang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Min-Jie Wen
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Lu Kong
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
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Differential hypermethylation of the VTRNA2-1 promoter in hepatocellular carcinoma as a prognostic factor: Tumor marker prognostic study. Int J Surg 2020; 79:282-289. [PMID: 32417463 DOI: 10.1016/j.ijsu.2020.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/16/2020] [Accepted: 05/04/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Vault RNA 2-1 (VTRNA2-1, also called nc886) is a 108-nucleotide noncoding transcript that is epigenetically controlled via 18 CpG dinucleotide modifications of its promoter, and can exert either tumor suppressor or oncogenic functions depending on cell types of cancers. In hepatocellular carcinoma (HCC), the role of VTRNA2-1 in prognosis of patients remains unexplored. Here, we analysed the methylation status of the VTRNA2-1 promoter and its correlation with clinical parameters in patients with HCC. PATIENTS AND METHODS A total of 92 patients with HCC were enrolled, genomic DNA of tumor versus normal tissues were extracted and bisulfite modified. VTRNA2-1 promoter regions chr5: 135416381 (cg06536614), 135416388, 135416394 (cg26328633), and 135416398 (cg25340688) were PCR amplified and pyrosequenced. The methylation status of VTRNA2-1 in patients was further analysed with other clinical parameters via univariate and multivariate analysis. RESULTS The differential hypermethylation status (tumor- normal) of the VTRNA2-1 promoter in HCC correlated well with the presence of large tumor size (p = 0.001), pathological vascular invasion (p = 0.036), tumor recurrence (p = 0.007) and more advanced tumor stage (stage III AJCC) in patients (p = 0.03). In addition, the methylation of the VTRNA2-1 promoter increased in stage III HCC tumor compared with stage I & II tumor (64.7% versus 36.0%, p = 0.030). Furthermore, the differential hypermethylation status of the VTRNA2-1 promoter was an independent factor for patient outcome after partial hepatectomy using multivariate Cox regression analysis (p = 0.011, HR = 2.305). Using another public dataset (GSE89852), we found that the differential hypermethylation of the VTRNA2-1 promoter was also significantly associated with tumor recurrence. CONCLUSIONS Patients had unfavourable outcomes when the VTRNA2-1 promoter was differentially hypermethylated in tumor tissues compared to its adjacent normal tissues. These findings suggest that such patients should receive intensive follow-up care or possible adjuvant therapy after liver resection.
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Vukic M, Wu H, Daxinger L. Making headway towards understanding how epigenetic mechanisms contribute to early-life effects. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180126. [PMID: 30966890 DOI: 10.1098/rstb.2018.0126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It has become clear that in addition to the DNA sequence there is another layer of information, termed epigenetic modifications, that can influence phenotypes and traits. In particular, environmental epigenomics, which addresses the effect of the environment on the epigenome and human health, is becoming an area of great interest for many researchers working in different scientific fields. In this review, we will consider the current evidence that early-life environmental signals can have long-term effects on the epigenome. We will further evaluate how recent technological advances may enable us to unravel the molecular mechanisms underlying these phenomena, which will be crucial for understanding heritability in health and disease. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Centre , Einthovenweg 20, 2333 ZC Leiden , The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Centre , Einthovenweg 20, 2333 ZC Leiden , The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre , Einthovenweg 20, 2333 ZC Leiden , The Netherlands
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45
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Yang Y, Wu L, Shu XO, Cai Q, Shu X, Li B, Guo X, Ye F, Michailidou K, Bolla MK, Wang Q, Dennis J, Andrulis IL, Brenner H, Chenevix-Trench G, Campa D, Castelao JE, Gago-Dominguez M, Dörk T, Hollestelle A, Lophatananon A, Muir K, Neuhausen SL, Olsson H, Sandler DP, Simard J, Kraft P, Pharoah PDP, Easton DF, Zheng W, Long J. Genetically Predicted Levels of DNA Methylation Biomarkers and Breast Cancer Risk: Data From 228 951 Women of European Descent. J Natl Cancer Inst 2020; 112:295-304. [PMID: 31143935 PMCID: PMC7073907 DOI: 10.1093/jnci/djz109] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/08/2019] [Accepted: 05/22/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND DNA methylation plays a critical role in breast cancer development. Previous studies have identified DNA methylation marks in white blood cells as promising biomarkers for breast cancer. However, these studies were limited by low statistical power and potential biases. Using a new methodology, we investigated DNA methylation marks for their associations with breast cancer risk. METHODS Statistical models were built to predict levels of DNA methylation marks using genetic data and DNA methylation data from HumanMethylation450 BeadChip from the Framingham Heart Study (n = 1595). The prediction models were validated using data from the Women's Health Initiative (n = 883). We applied these models to genomewide association study (GWAS) data of 122 977 breast cancer patients and 105 974 controls to evaluate if the genetically predicted DNA methylation levels at CpG sites (CpGs) are associated with breast cancer risk. All statistical tests were two-sided. RESULTS Of the 62 938 CpG sites CpGs investigated, statistically significant associations with breast cancer risk were observed for 450 CpGs at a Bonferroni-corrected threshold of P less than 7.94 × 10-7, including 45 CpGs residing in 18 genomic regions, that have not previously been associated with breast cancer risk. Of the remaining 405 CpGs located within 500 kilobase flaking regions of 70 GWAS-identified breast cancer risk variants, the associations for 11 CpGs were independent of GWAS-identified variants. Integrative analyses of genetic, DNA methylation, and gene expression data found that 38 CpGs may affect breast cancer risk through regulating expression of 21 genes. CONCLUSION Our new methodology can identify novel DNA methylation biomarkers for breast cancer risk and can be applied to other diseases.
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Affiliation(s)
- Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Fei Ye
- Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Kyriaki Michailidou
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Irene L Andrulis
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research (HB) and German Cancer Consortium (HB), German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Biomedica Orense-Pontevedra-Vigo, Xerencia de Xestión Integrada de Vigo-SERGAS, Vigo, Spain
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago De Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, QC, Canada
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health (PK) and Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Paul D P Pharoah
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
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Vincenz C, Lovett JL, Wu W, Shedden K, Strassmann BI. Loss of Imprinting in Human Placentas Is Widespread, Coordinated, and Predicts Birth Phenotypes. Mol Biol Evol 2020; 37:429-441. [PMID: 31639821 PMCID: PMC6993844 DOI: 10.1093/molbev/msz226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Genomic imprinting leads to mono-allelic expression of genes based on parent of origin. Therian mammals and angiosperms evolved this mechanism in nutritive tissues, the placenta, and endosperm, where maternal and paternal genomes are in conflict with respect to resource allocation. We used RNA-seq to analyze allelic bias in the expression of 91 known imprinted genes in term human placentas from a prospective cohort study in Mali. A large fraction of the imprinted exons (39%) deviated from mono-allelic expression. Loss of imprinting (LOI) occurred in genes with either maternal or paternal expression bias, albeit more frequently in the former. We characterized LOI using binomial generalized linear mixed models. Variation in LOI was predominantly at the gene as opposed to the exon level, consistent with a single promoter driving the expression of most exons in a gene. Some genes were less prone to LOI than others, particularly lncRNA genes were rarely expressed from the repressed allele. Further, some individuals had more LOI than others and, within a person, the expression bias of maternally and paternally imprinted genes was correlated. We hypothesize that trans-acting maternal effect genes mediate correlated LOI and provide the mother with an additional lever to control fetal growth by extending her influence to LOI of the paternally imprinted genes. Limited evidence exists to support associations between LOI and offspring phenotypes. We show that birth length and placental weight were associated with allelic bias, making this the first comprehensive report of an association between LOI and a birth phenotype.
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Affiliation(s)
- Claudius Vincenz
- Research Center for Group Dynamics, Institute for Social Research, University of Michigan, Ann Arbor, MI
| | - Jennie L Lovett
- Department of Anthropology, University of Michigan, Ann Arbor, MI
| | - Weisheng Wu
- BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI
| | - Kerby Shedden
- Department of Statistics, University of Michigan, Ann Arbor, MI
| | - Beverly I Strassmann
- Research Center for Group Dynamics, Institute for Social Research, University of Michigan, Ann Arbor, MI
- Department of Anthropology, University of Michigan, Ann Arbor, MI
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47
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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: 16] [Impact Index Per Article: 4.0] [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.
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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
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Bertozzi TM, Ferguson-Smith AC. Metastable epialleles and their contribution to epigenetic inheritance in mammals. Semin Cell Dev Biol 2020; 97:93-105. [PMID: 31551132 DOI: 10.1016/j.semcdb.2019.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 02/02/2023]
Abstract
Many epigenetic differences between individuals are driven by genetic variation. Mammalian metastable epialleles are unusual in that they show variable DNA methylation states between genetically identical individuals. The occurrence of such states across generations has resulted in their consideration by many as strong evidence for epigenetic inheritance in mammals, with the classic Avy and AxinFu mouse models - each products of repeat element insertions - being the most widely accepted examples. Equally, there has been interest in exploring their use as epigenetic biosensors given their susceptibility to environmental compromise. Here we review the classic murine metastable epialleles as well as more recently identified candidates, with the aim of providing a more holistic understanding of their biology. We consider the extent to which epigenetic inheritance occurs at metastable epialleles and explore the limited mechanistic insights into the establishment of their variable epigenetic states. We discuss their environmental modulation and their potential relevance in genome regulation. In light of recent whole-genome screens for novel metastable epialleles, we point out the need to reassess their biological relevance in multi-generational studies and we highlight their value as a model to study repeat element silencing as well as the mechanisms and consequences of mammalian epigenetic stochasticity.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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49
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Perera BP, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC. The role of environmental exposures and the epigenome in health and disease. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:176-192. [PMID: 31177562 PMCID: PMC7252203 DOI: 10.1002/em.22311] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/02/2023]
Abstract
The genetic material of every organism exists within the context of regulatory networks that govern gene expression, collectively called the epigenome. Epigenetics has taken center stage in the study of diseases such as cancer and diabetes, but its integration into the field of environmental health is still emerging. As the Environmental Mutagenesis and Genomics Society (EMGS) celebrates its 50th Anniversary this year, we have come together to review and summarize the seminal advances in the field of environmental epigenomics. Specifically, we focus on the role epigenetics may play in multigenerational and transgenerational transmission of environmentally induced health effects. We also summarize state of the art techniques for evaluating the epigenome, environmental epigenetic analysis, and the emerging field of epigenome editing. Finally, we evaluate transposon epigenetics as they relate to environmental exposures and explore the role of noncoding RNA as biomarkers of environmental exposures. Although the field has advanced over the past several decades, including being recognized by EMGS with its own Special Interest Group, recently renamed Epigenomics, we are excited about the opportunities for environmental epigenetic science in the next 50 years. Environ. Mol. Mutagen. 61:176-192, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Bambarendage P.U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, St. Paul, Minnesota
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Correspondence to: Dana C. Dolinoy, Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan.
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50
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Affiliation(s)
- Chathura J Gunasekara
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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