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Ye Z, Dite GS, Nguyen TL, MacInnis RJ, Schmidt DF, Makalic E, Al-Qershi OM, Nguyen-Dumont T, Goudey B, Stone J, Dowty JG, Giles GG, Southey MC, Hopper JL, Li S. Genetic and Environmental Causes of Variation in an Automated Breast Cancer Risk Factor Based on Mammographic Textures. Cancer Epidemiol Biomarkers Prev 2024; 33:306-313. [PMID: 38059829 DOI: 10.1158/1055-9965.epi-23-1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/24/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Cirrus is an automated risk predictor for breast cancer that comprises texture-based mammographic features and is mostly independent of mammographic density. We investigated genetic and environmental variance of variation in Cirrus. METHODS We measured Cirrus for 3,195 breast cancer-free participants, including 527 pairs of monozygotic (MZ) twins, 271 pairs of dizygotic (DZ) twins, and 1,599 siblings of twins. Multivariate normal models were used to estimate the variance and familial correlations of age-adjusted Cirrus as a function of age. The classic twin model was expanded to allow the shared environment effects to differ by zygosity. The SNP-based heritability was estimated for a subset of 2,356 participants. RESULTS There was no evidence that the variance or familial correlations depended on age. The familial correlations were 0.52 (SE, 0.03) for MZ pairs and 0.16(SE, 0.03) for DZ and non-twin sister pairs combined. Shared environmental factors specific to MZ pairs accounted for 20% of the variance. Additive genetic factors accounted for 32% (SE = 5%) of the variance, consistent with the SNP-based heritability of 36% (SE = 16%). CONCLUSION Cirrus is substantially familial due to genetic factors and an influence of shared environmental factors that was evident for MZ twin pairs only. The latter could be due to nongenetic factors operating in utero or in early life that are shared by MZ twins. IMPACT Early-life factors, shared more by MZ pairs than DZ/non-twin sister pairs, could play a role in the variation in Cirrus, consistent with early life being recognized as a critical window of vulnerability to breast carcinogens.
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Affiliation(s)
- Zhoufeng Ye
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Genetic Technologies Limited, Fitzroy, Victoria, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Daniel F Schmidt
- Department of Data Science and AI, Faculty of IT, Monash University, Melbourne, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Osamah M Al-Qershi
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Tu Nguyen-Dumont
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Benjamin Goudey
- ARC Training Centre in Cognitive Computing for Medical Technologies, University of Melbourne, Carlton, Victoria, Australia
- The Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Jennifer Stone
- Genetic Epidemiology Group, School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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2
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Hopper JL, Dowty JG, Nguyen TL, Li S, Dite GS, MacInnis RJ, Makalic E, Schmidt DF, Bui M, Stone J, Sung J, Jenkins MA, Giles GG, Southey MC, Mathews JD. Variance of age-specific log incidence decomposition (VALID): a unifying model of measured and unmeasured genetic and non-genetic risks. Int J Epidemiol 2023; 52:1557-1568. [PMID: 37349888 PMCID: PMC10655167 DOI: 10.1093/ije/dyad086] [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: 07/11/2022] [Accepted: 06/16/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND The extent to which known and unknown factors explain how much people of the same age differ in disease risk is fundamental to epidemiology. Risk factors can be correlated in relatives, so familial aspects of risk (genetic and non-genetic) must be considered. DEVELOPMENT We present a unifying model (VALID) for variance in risk, with risk defined as log(incidence) or logit(cumulative incidence). Consider a normally distributed risk score with incidence increasing exponentially as the risk increases. VALID's building block is variance in risk, Δ2, where Δ = log(OPERA) is the difference in mean between cases and controls and OPERA is the odds ratio per standard deviation. A risk score correlated r between a pair of relatives generates a familial odds ratio of exp(rΔ2). Familial risk ratios, therefore, can be converted into variance components of risk, extending Fisher's classic decomposition of familial variation to binary traits. Under VALID, there is a natural upper limit to variance in risk caused by genetic factors, determined by the familial odds ratio for genetically identical twin pairs, but not to variation caused by non-genetic factors. APPLICATION For female breast cancer, VALID quantified how much variance in risk is explained-at different ages-by known and unknown major genes and polygenes, non-genomic risk factors correlated in relatives, and known individual-specific factors. CONCLUSION VALID has shown that, while substantial genetic risk factors have been discovered, much is unknown about genetic and familial aspects of breast cancer risk especially for young women, and little is known about individual-specific variance in risk.
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Affiliation(s)
- John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Genetic Technologies Ltd., Fitzroy, VIC, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer Stone
- School of Population and Global Health, University of Western Australia, Perth, WA, Australia
| | - Joohon Sung
- Division of Genome and Health Big Data, Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - John D Mathews
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
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3
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Gull N, Arshad F, Naikoo GA, Hassan IU, Pedram MZ, Ahmad A, Aljabali AAA, Mishra V, Satija S, Charbe N, Negi P, Goyal R, Serrano-Aroca Á, Al Zoubi MS, El-Tanani M, Tambuwala MM. Recent Advances in Anticancer Activity of Novel Plant Extracts and Compounds from Curcuma longa in Hepatocellular Carcinoma. J Gastrointest Cancer 2023; 54:368-390. [PMID: 35285010 PMCID: PMC8918363 DOI: 10.1007/s12029-022-00809-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE Among all forms of cancers, hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. There are several treatment options for HCC ranging from loco-regional therapy to surgical treatment. Yet, there is high morbidity and mortality. Recent research focus has shifted towards more effective and less toxic cancer treatment options. Curcumin, the active ingredient in the Curcuma longa plant, has gained widespread attention in recent years because of its multifunctional properties as an antioxidant, anti-inflammatory, antimicrobial, and anticancer agent. METHODS A systematic search of PubMed, Embase and Google Scholar was performed for studies reporting incidence of HCC, risk factors associated with cirrhosis and experimental use of curcumin as an anti-cancer agent. RESULTS This review exclusively encompasses the anti-cancer properties of curcumin in HCC globally and it's postulated molecular targets of curcumin when used against liver cancers. CONCLUSIONS This review is concluded by presenting the current challenges and future perspectives of novel plant extracts derived from C. longa and the treatment options against cancers.
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Affiliation(s)
- Nighat Gull
- School of Sciences, Maulana Azad National Urdu University, 32, Hyderabad, TS, India
| | - Fareeha Arshad
- Department of Biochemistry, Aligarh Muslim University, U.P., India
| | - Gowhar A Naikoo
- Department of Mathematics and Sciences, College of Arts and Applied Sciences, Dhofar University, Salalah, Sultanate of Oman.
| | - Israr Ul Hassan
- College of Engineering, Dhofar University, Salalah, Sultanate of Oman
| | - Mona Zamani Pedram
- Faculty of Mechanical Engineering-Energy Division, K. N. Toosi University of Technology, P.O. Box: 19395-1999, No. 15-19, Pardis St., Mollasadra Ave., Vanak Sq., Tehran, 1999 143344, Iran
| | - Arif Ahmad
- School of Sciences, Maulana Azad National Urdu University, 32, Hyderabad, TS, India
| | - Alaa A A Aljabali
- Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid, 21163, Jordan
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Saurabh Satija
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Nitin Charbe
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M University, Kingsville, TX, 78363, USA
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology & Management Sciences, Solan, 173229, India
| | - Rohit Goyal
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology & Management Sciences, Solan, 173229, India
| | - Ángel Serrano-Aroca
- Biomaterials & Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia, San Vicente Mártir, 46001, Valencia, Spain
| | - Mazhar S Al Zoubi
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | - Mohamed El-Tanani
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
| | - Murtaza M Tambuwala
- School of Pharmacy & Pharmaceutical Sciences, Ulster University, Northern Ireland, Coleraine, BT52 1SA, County Londonderry, UK.
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Xu R, Li S, Wu Y, Yue X, Wong EM, Southey MC, Hopper JL, Abramson MJ, Li S, Guo Y. Wildfire-related PM 2.5 and DNA methylation: An Australian twin and family study. ENVIRONMENT INTERNATIONAL 2023; 171:107704. [PMID: 36542997 DOI: 10.1016/j.envint.2022.107704] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/24/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Wildfire-related fine particulate matter (PM2.5) has many adverse health impacts, but its impacts on human epigenome are unknown. We aimed to evaluate the associations between long-term exposure to wildfire-related PM2.5 and blood DNA methylation, and whether the associations differ from those with non-wildfire-related PM2.5. METHODS We studied 479 Australian women comprising 132 twin pairs and 215 of their sisters. Blood-derived DNA methylation was measured using the HumanMethylation450 BeadChip array. Data on 3-year (year of blood collection and previous two years) average wildfire-related and non-wildfire-related PM2.5 at 0.01°×0.01° spatial resolution were created by combining information from satellite observations, chemical transport models, and ground-based observations. Exposure data were linked to each participant's home address, assuming the address did not change during the exposure window. For DNA methylation of each cytosine-guanine dinucleotide (CpG), and for global DNA methylation represented by the average of all measured CpGs or CpGs in repetitive elements, we evaluated their associations with wildfire- or non-wildfire-related PM2.5 using a within-sibship analysis controlling for factors shared between siblings and other important covariates. Differentially methylated regions (DMRs) were defined by comb-p and DMRcate. RESULTS The 3-year average wildfire-related PM2.5 (range: 0.3 to 7.6 µg/m3, mean: 1.6 µg/m3) was negatively, but not significantly (p-values greater than 0.05) associated with all seven global DNA methylation measures. There were 26 CpGs and 33 DMRs associated with wildfire-related PM2.5 (Bonferroni adjusted p-value < 0.05) mapped to 47 genes enriched for pathways related to inflammatory regulation and platelet activation. These genes have been related to many human diseases or phenotypes e.g., cancer, mental disorders, diabetes, obesity, asthma, blood pressure. These CpGs, DMRs and enriched pathways did not overlap with the 1 CpG and 7 DMRs associated with non-wildfire-related PM2.5. CONCLUSIONS Long-term exposure to wildfire-related PM2.5 was associated with various blood DNA methylation signatures in Australian women, and these were distinct from those associated with non-wildfire-related PM2.5.
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Affiliation(s)
- Rongbin Xu
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Shanshan Li
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Yao Wu
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Xu Yue
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia; Cancer Epidemiology Division, Cancer Council Victoria, VIC 3004, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael J Abramson
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Shuai Li
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Yuming Guo
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia.
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5
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Auvinen P, Vehviläinen J, Marjonen H, Modhukur V, Sokka J, Wallén E, Rämö K, Ahola L, Salumets A, Otonkoski T, Skottman H, Ollikainen M, Trokovic R, Kahila H, Kaminen-Ahola N. Chromatin modifier developmental pluripotency associated factor 4 (DPPA4) is a candidate gene for alcohol-induced developmental disorders. BMC Med 2022; 20:495. [PMID: 36581877 PMCID: PMC9801659 DOI: 10.1186/s12916-022-02699-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Prenatal alcohol exposure (PAE) affects embryonic development, causing a variable fetal alcohol spectrum disorder (FASD) phenotype with neuronal disorders and birth defects. We hypothesize that early alcohol-induced epigenetic changes disrupt the accurate developmental programming of embryo and consequently cause the complex phenotype of developmental disorders. To explore the etiology of FASD, we collected unique biological samples of 80 severely alcohol-exposed and 100 control newborns at birth. METHODS We performed genome-wide DNA methylation (DNAm) and gene expression analyses of placentas by using microarrays (EPIC, Illumina) and mRNA sequencing, respectively. To test the manifestation of observed PAE-associated DNAm changes in embryonic tissues as well as potential biomarkers for PAE, we examined if the changes can be detected also in white blood cells or buccal epithelial cells of the same newborns by EpiTYPER. To explore the early effects of alcohol on extraembryonic placental tissue, we selected 27 newborns whose mothers had consumed alcohol up to gestational week 7 at maximum to the separate analyses. Furthermore, to explore the effects of early alcohol exposure on embryonic cells, human embryonic stem cells (hESCs) as well as hESCs during differentiation into endodermal, mesodermal, and ectodermal cells were exposed to alcohol in vitro. RESULTS DPPA4, FOXP2, and TACR3 with significantly decreased DNAm were discovered-particularly the regulatory region of DPPA4 in the early alcohol-exposed placentas. When hESCs were exposed to alcohol in vitro, significantly altered regulation of DPPA2, a closely linked heterodimer of DPPA4, was observed. While the regulatory region of DPPA4 was unmethylated in both control and alcohol-exposed hESCs, alcohol-induced decreased DNAm similar to placenta was seen in in vitro differentiated mesodermal and ectodermal cells. Furthermore, common genes with alcohol-associated DNAm changes in placenta and hESCs were linked exclusively to the neurodevelopmental pathways in the enrichment analysis, which emphasizes the value of placental tissue when analyzing the effects of prenatal environment on human development. CONCLUSIONS Our study shows the effects of early alcohol exposure on human embryonic and extraembryonic cells, introduces candidate genes for alcohol-induced developmental disorders, and reveals potential biomarkers for prenatal alcohol exposure.
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Affiliation(s)
- P Auvinen
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - J Vehviläinen
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - H Marjonen
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - V Modhukur
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia.,Competence Centre on Health Technologies, 50411, Tartu, Estonia
| | - J Sokka
- Research Programs Unit, Stem cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - E Wallén
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - K Rämö
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - L Ahola
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - A Salumets
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia.,Competence Centre on Health Technologies, 50411, Tartu, Estonia.,Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, S-171 76, Stockholm, Sweden
| | - T Otonkoski
- Research Programs Unit, Stem cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland.,Children's Hospital, Helsinki University Central Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - H Skottman
- Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - M Ollikainen
- Institute for Molecular Medicine, Finland, FIMM, HiLIFE, University of Helsinki, 00290, Helsinki, Finland
| | - R Trokovic
- Research Programs Unit, Stem cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - H Kahila
- Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - N Kaminen-Ahola
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland.
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6
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Leake DW. Tracing Slow Phenoptosis to the Prenatal Stage in Social Vertebrates. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1512-1527. [PMID: 36717460 DOI: 10.1134/s0006297922120094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Vladimir Skulachev's coining of the term "phenoptosis" 25 years ago (Skulachev, V. P., Biochemistry (Moscow), 62, 1997) highlighted the theoretical possibility that aging is a programmed process to speed the exit of individuals posing some danger to their social group. While rapid "acute phenoptosis" might occur at any age (e.g., to prevent spread of deadly infections), "slow phenoptosis" is generally considered to occur later in life in the form of chronic age-related disorders. However, recent research indicates that risks for such chronic disorders can be greatly raised by early life adversity, especially during the prenatal stage. Much of this research uses indicators of biological aging, the speeding or slowing of natural physiological deterioration in response to environmental inputs, leading to divergence from chronological age. Studies using biological aging indicators commonly find it is accelerated not only in older individuals with chronic disorders, but also in very young individuals with health problems. This review will explain how accelerated biological aging equates to slow phenoptosis. Its occurrence even in the prenatal stage is theoretically supported by W. D. Hamilton's proposal that offsprings detecting they have dangerous mutations should then automatically speed their demise, in order to improve their inclusive fitness by giving their parents the chance to produce other fitter siblings.
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Affiliation(s)
- David W Leake
- University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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7
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Walhovd KB, Nyberg L, Lindenberger U, Amlien IK, Sørensen Ø, Wang Y, Mowinckel AM, Kievit RA, Ebmeier KP, Bartrés-Faz D, Kühn S, Boraxbekk CJ, Ghisletta P, Madsen KS, Baaré WFC, Zsoldos E, Magnussen F, Vidal-Piñeiro D, Penninx B, Fjell AM. Brain aging differs with cognitive ability regardless of education. Sci Rep 2022; 12:13886. [PMID: 35974034 PMCID: PMC9381768 DOI: 10.1038/s41598-022-17727-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
Higher general cognitive ability (GCA) is associated with lower risk of neurodegenerative disorders, but neural mechanisms are unknown. GCA could be associated with more cortical tissue, from young age, i.e. brain reserve, or less cortical atrophy in adulthood, i.e. brain maintenance. Controlling for education, we investigated the relative association of GCA with reserve and maintenance of cortical volume, -area and -thickness through the adult lifespan, using multiple longitudinal cognitively healthy brain imaging cohorts (n = 3327, 7002 MRI scans, baseline age 20-88 years, followed-up for up to 11 years). There were widespread positive relationships between GCA and cortical characteristics (level-level associations). In select regions, higher baseline GCA was associated with less atrophy over time (level-change associations). Relationships remained when controlling for polygenic scores for both GCA and education. Our findings suggest that higher GCA is associated with cortical volumes by both brain reserve and -maintenance mechanisms through the adult lifespan.
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Affiliation(s)
- Kristine B Walhovd
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway.
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway.
| | - Lars Nyberg
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
| | - Ulman Lindenberger
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
- Max Planck UCL Centre for Computational Psychiatry and Ageing Research, Berlin, Germany
- Max Planck UCL Centre for Computational Psychiatry and Ageing Research, London, UK
| | - Inge K Amlien
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway
| | - Øystein Sørensen
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway
| | - Yunpeng Wang
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway
| | - Athanasia M Mowinckel
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway
| | - Rogier A Kievit
- Cognitive Neuroscience Department, Donders Institute for Brain, Cognition and Behavior, The Netherlands, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - David Bartrés-Faz
- Department of Medicine, Faculty of Medicine and Health Sciences & Institute of Neurosciences, Universitat de Barcelona, and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Simone Kühn
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
- Clinic and Policlinic for Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carl-Johan Boraxbekk
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Department of Radiation Sciences, Diagnostic Radiology, Umeå University, Umeå, Sweden
- Institute of Sports Medicine Copenhagen (ISMC) and Department of Neurology, Copenhagen University Hospital Bispebjerg, Copenhagen, Denmark
- Institute for Clinical Medicine, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paolo Ghisletta
- Faculty of Psychology and Educational Sciences, University of Geneva, Geneva, Switzerland
- UniDistance Suisse, Brig, Switzerland
- Swiss National Centre of Competence in Research LIVES, University of Geneva, Geneva, Switzerland
| | - Kathrine Skak Madsen
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Radiography, Department of Technology, University College Copenhagen, Copenhagen, Denmark
| | - Willliam F C Baaré
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Enikő Zsoldos
- Department of Psychiatry, University of Oxford, Oxford, UK
- Welcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
| | - Fredrik Magnussen
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway
| | - Didac Vidal-Piñeiro
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway
| | - Brenda Penninx
- Amsterdam Neuroscience, Department of Psychiatry, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Anders M Fjell
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Blindern, POB1094, 0317, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
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8
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Laajala E, Halla-Aho V, Grönroos T, Kalim UU, Vähä-Mäkilä M, Nurmio M, Kallionpää H, Lietzén N, Mykkänen J, Rasool O, Toppari J, Orešič M, Knip M, Lund R, Lahesmaa R, Lähdesmäki H. Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples. Epigenetics 2022; 17:1608-1627. [PMID: 35246015 DOI: 10.1080/15592294.2022.2044127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn infants; whose umbilical cord blood samples were analysed with the reduced representation bisulphite sequencing (RRBS) method. A generalized linear mixed-effects model was fit for each high coverage CpG site, followed by spatial and multiple testing adjustment of P values to identify differentially methylated cytosines (DMCs) and regions (DMRs) associated with clinical variables, such as maternal age, mode of delivery, and birth weight. Type 1 error rate was then evaluated with a permutation analysis. We discovered a strong inflation of spatially adjusted P values through the permutation analysis, which we then applied for empirical type 1 error control. The inflation of P values was caused by a common method for spatial adjustment and DMR detection, implemented in tools comb-p and RADMeth. Based on empirically estimated significance thresholds, very little differential methylation was associated with any of the studied clinical variables, other than sex. With this analysis workflow, the sex-associated differentially methylated regions were highly reproducible across studies, technologies, and statistical models.
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Affiliation(s)
- Essi Laajala
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland.,Department of Computer Science, Aalto University, Espoo, Finland
| | - Viivi Halla-Aho
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland
| | - Mari Vähä-Mäkilä
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Mirja Nurmio
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Henna Kallionpää
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Niina Lietzén
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Juha Mykkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland
| | - Jorma Toppari
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland.,Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland.,Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland.,School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
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9
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Li S, Ye Z, Mather KA, Nguyen TL, Dite GS, Armstrong NJ, Wong EM, Thalamuthu A, Giles GG, Craig JM, Saffery R, Southey MC, Tan Q, Sachdev PS, Hopper JL. Early life affects late-life health through determining DNA methylation across the lifespan: A twin study. EBioMedicine 2022; 77:103927. [PMID: 35301182 PMCID: PMC8927831 DOI: 10.1016/j.ebiom.2022.103927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/07/2022] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Background Previous findings for the genetic and environmental contributions to DNA methylation variation were for limited age ranges only. We investigated the lifespan contributions and their implications for human health for the first time. Methods 1,720 monozygotic twin (MZ) pairs and 1,107 dizygotic twin (DZ) pairs aged 0-92 years were included. Familial correlations (i.e., correlations between twins) for 353,681 methylation sites were estimated and modelled as a function of twin pair cohabitation history. Findings The methylome average familial correlation was around zero at birth (MZ pair: -0.01; DZ pair: -0.04), increased with the time of twins living together during childhood at rates of 0.16 (95%CI: 0.12-0.20) for MZ pairs and 0.13 (95%CI: 0.07-0.20) for DZ pairs per decade, and decreased with the time of living apart during adulthood at rates of 0.026 (95%CI: 0.019-0.033) for MZ pairs and 0.027 (95%CI: 0.011-0.043) for DZ pairs per decade. Neither the increasing nor decreasing rate differed by zygosity (both P>0.1), consistent with cohabitation environment shared by twins, rather than genetic factors, influencing the methylation familial correlation changes. Familial correlations for 6.6% (23,386/353,681) sites changed with twin pair cohabitation history. These sites were enriched for high heritability, proximal promoters, and epigenetic/genetic associations with various early-life factors and late-life health conditions. Interpretation Early life strongly influences DNA methylation variation across the lifespan, and the effects are stronger for heritable sites and sites biologically relevant to the regulation of gene expression. Early life could affect late-life health through influencing DNA methylation. Funding Victorian Cancer Agency, Cancer Australia, Cure Cancer Foundation.
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Affiliation(s)
- Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.
| | - Zhoufeng Ye
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing (CHeBA), Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Genetic Technologies Ltd, Fitzroy, Victoria, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Curtin University, Western Australia, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing (CHeBA), Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Jeffrey M Craig
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Faculty of Health, Deakin University, Waurn Ponds, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing (CHeBA), Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, New South Wales, Australia; Neuropsychiatric Institute, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
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10
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Mj S, N M, Jm C, Dj M, R S, Mc S, Dp B, J L, Nm K, Jl H, Kj S, S L. DNA methylation in childhood dental caries and hypomineralization. J Dent 2021; 117:103913. [PMID: 34875274 DOI: 10.1016/j.jdent.2021.103913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVES Epigenetic modulation of gene expression may be important in dental conditions, including dental caries and enamel hypomineralisation. The aims of this study were to assess associations between DNA methylation in cord blood leucocytes at birth, and caries experience and enamel hypomineralisation at six years of age. METHOD The study sample was from a birth cohort study of twins. Dental examinations at six years identified the presence/absence of (i) 'any caries' (untreated and treated caries), (ii) 'advanced caries' (untreated, advanced caries and/or past treatment) and (iii) hypomineralised second primary molars (HSPM). Genome-wide analysis of DNA methylation was performed on cord blood of 27 twin pairs (14 dizygotic and 13 monozygotic) using the Illumina Infinium MethylationEPIC BeadChip array. Differentially methylated CpGs (DMCpGs) and regions (DMRs) associated with each dental outcome were investigated, while accounting for the relatedness of twins. Results with a false discovery rate <0.05 were treated as statistically significant. RESULTS 19 children had 'any caries', 15 had 'advanced' caries, and 18 had HSPM. No DMCpGs were associated with 'any caries', 16 and 19 DMCpGs were associated with 'advanced caries' and HSPM, respectively. DMRs were identified in association with all three outcomes. Genes implicated by these analyses included PBX1, ACAT2, LTBP3 and DDR1 which have been linked with dental tissue development in genetic studies. CONCLUSION This exploratory study identified differential methylation in several genes at birth associated with dental caries and HSPM at six years. Further research may provide valuable insights into aetiology of dental disease and/or reveal novel molecular-based approaches for early risk stratification. CLINICAL SIGNIFICANCE Epigenetic differences at birth are likely to be associated with dental health at six years and may be valuable biomarkers of early influences on dental health.
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Affiliation(s)
- Silva Mj
- Inflammatory Origins, Murdoch Children's Research Institute, Melbourne, Australia; Melbourne Dental School, University of Melbourne, Melbourne, Australia; Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia.
| | - Mohandas N
- Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Craig Jm
- Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia; Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Manton Dj
- Melbourne Dental School, University of Melbourne, Melbourne, Australia; Centrum voor Tandheelkunde en Mondzorgkunde, UMCG, University of Groningen, Groningen, The Netherlands
| | - Saffery R
- Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Southey Mc
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Burgner Dp
- Inflammatory Origins, Murdoch Children's Research Institute, Melbourne, Australia; Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia; Department of Paediatrics, Monash University, Clayton, Australia
| | - Lucas J
- Melbourne Dental School, University of Melbourne, Melbourne, Australia
| | - Kilpatrick Nm
- Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia; Facial Sciences, Murdoch Children's Research Institute, Melbourne, Australia
| | - Hopper Jl
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Scurrah Kj
- Facial Sciences, Murdoch Children's Research Institute, Melbourne, Australia; Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Li S
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, United Kingdom
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11
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Tobi EW, Almqvist C, Hedman A, Andolf E, Holte J, Olofsson JI, Wramsby H, Wramsby M, Pershagen G, Heijmans BT, Iliadou AN. DNA methylation differences at birth after conception through ART. Hum Reprod 2021; 36:248-259. [PMID: 33227132 PMCID: PMC7801794 DOI: 10.1093/humrep/deaa253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/21/2020] [Indexed: 12/25/2022] Open
Abstract
STUDY QUESTION Is there a relation between ART and DNA methylation (DNAm) patterns in cord blood, including any differences between IVF and ICSI? SUMMARY ANSWER DNAm at 19 CpGs was associated with conception via ART, with no difference found between IVF and ICSI. WHAT IS KNOWN ALREADY Prior studies on either IVF or ICSI show conflicting outcomes, as both widespread effects on DNAm and highly localized associations have been reported. No study on both IVF and ICSI and genome-wide neonatal DNAm has been performed. STUDY DESIGN, SIZE, DURATION This was a cross-sectional study comprising 87 infants conceived with IVF or ICSI and 70 conceived following medically unassisted conception. The requirement for inclusion in the study was an understanding of the Swedish language and exclusion was the use of donor gametes. PARTICIPANTS/MATERIALS, SETTING, METHODS Participants were from the UppstART study, which was recruited from fertility and reproductive health clinics, and the Born into Life cohort, which is recruited from the larger LifeGene study. We measured DNAm from DNA extracted from cord blood collected at birth using a micro-array (450k array). Group differences in DNAm at individual CpG dinucleotides (CpGs) were determined using robust linear models and post-hoc Tukey’s tests. MAIN RESULTS AND THE ROLE OF CHANCE We found no association of ART conception with global methylation levels, imprinted loci and meta-stable epialleles. In contrast, we identify 19 CpGs at which DNAm was associated with being conceived via ART (effect estimates: 0.5–4.9%, PFDR < 0.05), but no difference was found between IVF and ICSI. The associated CpGs map to genes related to brain function/development or genes connected to the plethora of conditions linked to subfertility, but functional annotation did not point to any likely functional consequences. LIMITATIONS, REASONS FOR CAUTION We measured DNAm in cord blood and not at later ages or in other tissues. Given the number of tests performed, our study power is limited and the findings need to be replicated in an independent study. WIDER IMPLICATIONS OF THE FINDINGS We find that ART is associated with DNAm differences in cord blood when compared to non-ART samples, but these differences are limited in number and effect size and have unknown functional consequences in adult blood. We did not find indications of differences between IVF and ICSI. STUDY FUNDING/COMPETING INTEREST(S) E.W.T. was supported by a VENI grant from the Netherlands Organization for Scientific Research (91617128) and JPI-H2020 Joint Programming Initiative a Healthy Diet for a Healthy Life (JPI HDHL) under proposal number 655 (PREcisE Project) through ZonMw (529051023). Financial support was provided from the European Union’s Seventh Framework Program IDEAL (259679), the Swedish Research Council (K2011-69X-21871-01-6, 2011-3060, 2015-02434 and 2018-02640) and the Strategic Research Program in Epidemiology Young Scholar Awards, Karolinska Institute (to A.N.I.) and through the Swedish Initiative for Research on Microdata in the Social And Medical Sciences (SIMSAM) framework grant no 340-2013-5867, grants provided by the Stockholm County Council (ALF-projects), the Strategic Research Program in Epidemiology at Karolinska Institutet and the Swedish Heart-Lung Foundation and Danderyd University Hospital (Stockholm, Sweden). The funders had no role in study design, data collection, analysis, decision to publish or preparation of the manuscript. The authors declare no competing interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynaecology, University Medical Center Rotterdam, 3015 MC GE Rotterdam, The Netherlands.,Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden.,Pediatric Allergy and Pulmonology Unit, Astrid Lindgren Children's Hospital, Stockholm 171 76, Sweden
| | - Anna Hedman
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm 182 88, Sweden
| | - Ellika Andolf
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm 182 88, Sweden
| | - Jan Holte
- Carl von Linné Clinic, Uppsala, Sweden.,Department of Women's and Children's Health, Uppsala University, Uppsala 751 85, Sweden.,Center for Reproductive Biology in Uppsala, University of Agricultural Sciences and Uppsala University, Uppsala, Sweden
| | - Jan I Olofsson
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Håkan Wramsby
- S:t Görans Sjukhus, Livio Fertilitetscentrum Kungsholmen, Stockholm 112 81, Sweden
| | - Margaretha Wramsby
- Livio Fertilitetscentrum Gärdet Storängsvägen 10, Stockholm 115 42, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Anastasia N Iliadou
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden
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12
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Pubertal mammary gland development is a key determinant of adult mammographic density. Semin Cell Dev Biol 2020; 114:143-158. [PMID: 33309487 DOI: 10.1016/j.semcdb.2020.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/04/2023]
Abstract
Mammographic density refers to the radiological appearance of fibroglandular and adipose tissue on a mammogram of the breast. Women with relatively high mammographic density for their age and body mass index are at significantly higher risk for breast cancer. The association between mammographic density and breast cancer risk is well-established, however the molecular and cellular events that lead to the development of high mammographic density are yet to be elucidated. Puberty is a critical time for breast development, where endocrine and paracrine signalling drive development of the mammary gland epithelium, stroma, and adipose tissue. As the relative abundance of these cell types determines the radiological appearance of the adult breast, puberty should be considered as a key developmental stage in the establishment of mammographic density. Epidemiological studies have pointed to the significance of pubertal adipose tissue deposition, as well as timing of menarche and thelarche, on adult mammographic density and breast cancer risk. Activation of hypothalamic-pituitary axes during puberty combined with genetic and epigenetic molecular determinants, together with stromal fibroblasts, extracellular matrix, and immune signalling factors in the mammary gland, act in concert to drive breast development and the relative abundance of different cell types in the adult breast. Here, we discuss the key cellular and molecular mechanisms through which pubertal mammary gland development may affect adult mammographic density and cancer risk.
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13
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Li S, Nguyen TL, Wong EM, Dugué PA, Dite GS, Armstrong NJ, Craig JM, Mather KA, Sachdev PS, Saffery R, Sung J, Tan Q, Thalamuthu A, Milne RL, Giles GG, Southey MC, Hopper JL. Genetic and environmental causes of variation in epigenetic aging across the lifespan. Clin Epigenetics 2020; 12:158. [PMID: 33092643 PMCID: PMC7583207 DOI: 10.1186/s13148-020-00950-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/13/2020] [Indexed: 12/14/2022] Open
Abstract
Background DNA methylation-based biological age (DNAm age) is an important biomarker for adult health. Studies in specific age ranges have found widely varying results about its genetic and environmental causes of variation. However, these studies are not able to provide a comprehensive view of the causes of variation over the lifespan.
Results In order to investigate the genetic and environmental causes of DNAm age variation across the lifespan, we pooled genome-wide DNA methylation data for 4217 people aged 0–92 years from 1871 families. DNAm age was calculated using the Horvath epigenetic clock. We estimated familial correlations in DNAm age for monozygotic (MZ) twin, dizygotic (DZ) twin, sibling, parent–offspring, and spouse pairs by cohabitation status. Genetic and environmental variance components models were fitted and compared. We found that twin pair correlations were − 0.12 to 0.18 around birth, not different from zero (all P > 0.29). For all pairs of relatives, their correlations increased with time spent living together (all P < 0.02) at different rates (MZ > DZ and siblings > parent–offspring; P < 0.001) and decreased with time spent living apart (P = 0.02) at similar rates. These correlation patterns were best explained by cohabitation-dependent shared environmental factors, the effects of which were 1.41 (95% confidence interval [CI] 1.16 to 1.66) times greater for MZ pairs than for DZ and sibling pairs, and the latter were 2.03 (95% CI 1.13 to 9.47) times greater than for parent–offspring pairs. Genetic factors explained 13% (95% CI − 10 to 35%) of variation (P = 0.27). Similar results were found for another two epigenetic clocks, suggesting that our observations are robust to how DNAm age is measured. In addition, results for the other clocks were consistent with there also being a role for prenatal environmental factors in determining their variation. Conclusions Variation in DNAm age is mostly caused by environmental factors, including those shared to different extents by relatives while living together and whose effects persist into old age. The equal environment assumption of the classic twin study might not hold for epigenetic aging.
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Affiliation(s)
- Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3051, Australia.,Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Precision Medicine, School of Clinical Sciences At Monash Health, Monash University, Clayton, VIC, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3051, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences At Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Pierre-Antoine Dugué
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3051, Australia.,Precision Medicine, School of Clinical Sciences At Monash Health, Monash University, Clayton, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3051, Australia
| | | | - Jeffrey M Craig
- Centre for Molecular and Medical Research, School of Medicine, Faculty of Health, Deakin University, Waurn Ponds, VIC, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.,Neuropsychiatric Institute, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.,Neuropsychiatric Institute, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Richard Saffery
- Murdoch Childrens Research Institute, Parkville, VIC, Australia
| | - Joohon Sung
- Institute of Health and Environment, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Korea
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3051, Australia.,Precision Medicine, School of Clinical Sciences At Monash Health, Monash University, Clayton, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3051, Australia.,Precision Medicine, School of Clinical Sciences At Monash Health, Monash University, Clayton, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences At Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3051, Australia.
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14
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Epigenetic Influences on Neurodevelopment at 11 Years of Age: Protocol for the Longitudinal Peri/Postnatal Epigenetic Twins Study at 11 Years of Age (PETS@11). Twin Res Hum Genet 2020; 22:446-453. [PMID: 32008589 DOI: 10.1017/thg.2019.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Neurodevelopment is sensitive to genetic and pre/postnatal environmental influences. These effects are likely mediated by epigenetic factors, yet current knowledge is limited. Longitudinal twin studies can delineate the link between genetic and environmental factors, epigenetic state at birth and neurodevelopment later in childhood. Building upon our study of the Peri/postnatal Epigenetic Twin Study (PETS) from gestation to 6 years of age, here we describe the PETS 11-year follow-up in which we will use neuroimaging and cognitive testing to examine the relationship between early-life environment, epigenetics and neurocognitive outcomes in mid-childhood. Using a within-pair twin model, the primary aims are to (1) identify early-life epigenetic correlates of neurocognitive outcomes; (2) determine the developmental stability of epigenetic effects and (3) identify modifiable environmental risk factors. Secondary aims are to identify factors influencing gut microbiota between 6 and 11 years of age to investigate links between gut microbiota and neurodevelopmental outcomes in mid-childhood. Approximately 210 twin pairs will undergo an assessment at 11 years of age. This includes a direct child cognitive assessment, multimodal magnetic resonance imaging, biological sampling, anthropometric measurements and a range of questionnaires on health and development, behavior, dietary habits and sleeping patterns. Data from complementary data sources, including the National Assessment Program - Literacy and Numeracy and the Australian Early Development Census, will also be sought. Following on from our previous focus on relationships between growth, cardiovascular health and oral health, this next phase of PETS will significantly advance our understanding of the environmental interactions that shape the developing brain.
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Cronjé HT, Elliott HR, Nienaber-Rousseau C, Pieters M. Leveraging the urban-rural divide for epigenetic research. Epigenomics 2020; 12:1071-1081. [PMID: 32657149 DOI: 10.2217/epi-2020-0049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Urbanization coincides with a complex change in environmental exposure and a rapid increase in noncommunicable diseases (NCDs). Epigenetics, including DNA methylation (DNAm), is thought to mediate part of the association between genetic/environmental exposure and NCDs. The urban-rural divide provides a unique opportunity to investigate the effect of the combined presence of multiple forms of environmental exposure on DNAm and the related increase in disease risk. This review evaluates the ability of three epidemiological study designs (migration, income-comparative and urban-rural designs) to investigate the role of DNAm in the association between urbanization and the rise in NCD prevalence. We also discuss the ability of each study design to address the gaps in the current literature, including the complex methylation-mediated risk attributable to the cluster of forms of exposure characterizing urban and rural living, while providing a platform for developing countries to leverage their demographic discrepancies in future research ventures.
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Affiliation(s)
- Héléne T Cronjé
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Cornelie Nienaber-Rousseau
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
| | - Marlien Pieters
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
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16
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Rizzo HE, Escaname EN, Alana NB, Lavender E, Gelfond J, Fernandez R, Hibbs MA, King JM, Carr NR, Blanco CL. Maternal diabetes and obesity influence the fetal epigenome in a largely Hispanic population. Clin Epigenetics 2020; 12:34. [PMID: 32075680 PMCID: PMC7031937 DOI: 10.1186/s13148-020-0824-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/05/2020] [Indexed: 01/12/2023] Open
Abstract
Background Obesity and diabetes mellitus are directly implicated in many adverse health consequences in adults as well as in the offspring of obese and diabetic mothers. Hispanic Americans are particularly at risk for obesity, diabetes, and end-stage renal disease. Maternal obesity and/or diabetes through prenatal programming may alter the fetal epigenome increasing the risk of metabolic disease in their offspring. The aims of this study were to determine if maternal obesity or diabetes mellitus during pregnancy results in a change in infant methylation of CpG islands adjacent to targeted genes specific for obesity or diabetes disease pathways in a largely Hispanic population. Methods Methylation levels in the cord blood of 69 newborns were determined using the Illumina Infinium MethylationEPIC BeadChip. Over 850,000 different probe sites were analyzed to determine whether maternal obesity and/or diabetes mellitus directly attributed to differential methylation; epigenome-wide and regional analyses were performed for significant CpG sites. Results Following quality control, agranular leukocyte samples from 69 newborns (23 normal term (NT), 14 diabetes (DM), 23 obese (OB), 9 DM/OB) were analyzed for over 850,000 different probe sites. Contrasts between the NT, DM, OB, and DM/OB were considered. After correction for multiple testing, 15 CpGs showed differential methylation from the NT, associated with 10 differentially methylated genes between the diabetic and non-diabetic subgroups, CCDC110, KALRN, PAG1, GNRH1, SLC2A9, CSRP2BP, HIVEP1, RALGDS, DHX37, and SCNN1D. The effects of diabetes were partly mediated by the altered methylation of HOOK2, LCE3C, and TMEM63B. The effects of obesity were partly mediated by the differential methylation of LTF and DUSP22. Conclusions The presented data highlights the associated altered methylation patterns potentially mediated by maternal diabetes and/or obesity. Larger studies are warranted to investigate the role of both the identified differentially methylated loci and the effects on newborn body composition and future health risk factors for metabolic disease. Additional future consideration should be targeted to the role of Hispanic inheritance. Potential future targeting of transgenerational propagation and developmental programming may reduce population obesity and diabetes risk.
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Affiliation(s)
- Heather E Rizzo
- Department of Biology, Trinity University, 1 Trinity Place, San Antonio, TX, 78212, USA
| | - Elia N Escaname
- Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, TX, USA.,University Health System, San Antonio, TX, USA
| | - Nicholas B Alana
- Department of Biology, Trinity University, 1 Trinity Place, San Antonio, TX, 78212, USA.,University Health System, San Antonio, TX, USA
| | - Elizabeth Lavender
- Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, TX, USA.,University Health System, San Antonio, TX, USA
| | | | | | - Matthew A Hibbs
- Department of Biology, Trinity University, 1 Trinity Place, San Antonio, TX, 78212, USA
| | - Jonathan M King
- Department of Biology, Trinity University, 1 Trinity Place, San Antonio, TX, 78212, USA.
| | - Nicholas R Carr
- Department of Neonatal Medicine, Brooke Army Medical Center, San Antonio, TX, USA
| | - Cynthia L Blanco
- Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, TX, USA.,University Health System, San Antonio, TX, USA
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17
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Abstract
AbstractTwins Research Australia (TRA) is a community of twins and researchers working on health research to benefit everyone, including twins. TRA leads multidisciplinary research through the application of twin and family study designs, with the aim of sustaining long-term twin research that, both now and in the future, gives back to the community. This article summarizes TRA’s recent achievements and future directions, including new methodologies addressing causation, linkage to health, economic and educational administrative datasets and to geospatial data to provide insight into health and disease. We also explain how TRA’s knowledge translation and exchange activities are key to communicating the impact of twin studies to twins and the wider community. Building researcher capability, providing registry resources and partnering with all key stakeholders, particularly the participants, are important for how TRA is advancing twin research to improve health outcomes for society. TRA provides researchers with open access to its vibrant volunteer membership of twins, higher order multiples (multiples) and families who are willing to consider participation in research. Established four decades ago, this resource facilitates and supports research across multiple stages and a breadth of health domains.
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18
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Saffari A, Arno M, Nasser E, Ronald A, Wong CCY, Schalkwyk LC, Mill J, Dudbridge F, Meaburn EL. RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation. Mol Autism 2019; 10:38. [PMID: 31719968 PMCID: PMC6839145 DOI: 10.1186/s13229-019-0285-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/01/2019] [Indexed: 11/13/2022] Open
Abstract
Background A gap exists in our mechanistic understanding of how genetic and environmental risk factors converge at the molecular level to result in the emergence of autism symptoms. We compared blood-based gene expression signatures in identical twins concordant and discordant for autism spectrum condition (ASC) to differentiate genetic and environmentally driven transcription differences, and establish convergent evidence for biological mechanisms involved in ASC. Methods Genome-wide gene expression data were generated using RNA-seq on whole blood samples taken from 16 pairs of monozygotic (MZ) twins and seven twin pair members (39 individuals in total), who had been assessed for ASC and autism traits at age 12. Differential expression (DE) analyses were performed between (a) affected and unaffected subjects (N = 36) and (b) within discordant ASC MZ twin pairs (total N = 11) to identify environmental-driven DE. Gene set enrichment and pathway testing was performed on DE gene lists. Finally, an integrative analysis using DNA methylation data aimed to identify genes with consistent evidence for altered regulation in cis. Results In the discordant twin analysis, three genes showed evidence for DE at FDR < 10%: IGHG4, EVI2A and SNORD15B. In the case-control analysis, four DE genes were identified at FDR < 10% including IGHG4, PRR13P5, DEPDC1B, and ZNF501. We find enrichment for DE of genes curated in the SFARI human gene database. Pathways showing evidence of enrichment included those related to immune cell signalling and immune response, transcriptional control and cell cycle/proliferation. Integrative methylomic and transcriptomic analysis identified a number of genes showing suggestive evidence for cis dysregulation. Limitations Identical twins stably discordant for ASC are rare, and as such the sample size was limited and constrained to the use of peripheral blood tissue for transcriptomic and methylomic profiling. Given these primary limitations, we focused on transcript-level analysis. Conclusions Using a cohort of ASC discordant and concordant MZ twins, we add to the growing body of transcriptomic-based evidence for an immune-based component in the molecular aetiology of ASC. Whilst the sample size was limited, the study demonstrates the utility of the discordant MZ twin design combined with multi-omics integration for maximising the potential to identify disease-associated molecular signals.
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Affiliation(s)
- Ayden Saffari
- 1Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
| | - Matt Arno
- 3Edinburgh Genomics, University of Edinburgh, Edinburgh, Scotland UK
- 4King's Genomics Centre, King's College London, London, UK
| | - Eric Nasser
- 4King's Genomics Centre, King's College London, London, UK
| | - Angelica Ronald
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
| | - Chloe C Y Wong
- 5Social Genetic and Developmental Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Jonathan Mill
- 7University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Frank Dudbridge
- 1Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- 8Department of Health Sciences, University of Leicester, Leicester, UK
| | - Emma L Meaburn
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
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19
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DNA methylation-based biological age, genome-wide average DNA methylation, and conventional breast cancer risk factors. Sci Rep 2019; 9:15055. [PMID: 31636290 PMCID: PMC6803691 DOI: 10.1038/s41598-019-51475-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
DNA methylation-based biological age (DNAm age), as well as genome-wide average DNA methylation, have been reported to predict breast cancer risk. We aimed to investigate the associations between these DNA methylation-based risk factors and 18 conventional breast cancer risk factors for disease-free women. A sample of 479 individuals from the Australian Mammographic Density Twins and Sisters was used for discovery, a sample of 3354 individuals from the Melbourne Collaborative Cohort Study was used for replication, and meta-analyses pooling results from the two studies were conducted. DNAm age based on three epigenetic clocks (Hannum, Horvath and Levine) and genome-wide average DNA methylation were calculated using the HumanMethylation 450 K BeadChip assay data. The DNAm age measures were positively associated with body mass index (BMI), smoking, alcohol drinking and age at menarche (all nominal P < 0.05). Genome-wide average DNA methylation was negatively associated with smoking and number of live births, and positively associated with age at first live birth (all nominal P < 0.05). The association of DNAm age with BMI was also evident in within-twin-pair analyses that control for familial factors. This study suggests that some lifestyle and hormonal risk factors are associated with these DNA methylation-based breast cancer risk factors, and the observed associations are unlikely to be due to familial confounding but are likely causal. DNA methylation-based risk factors could interplay with conventional risk factors in modifying breast cancer risk.
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20
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McCrory C, Fiorito G, McLoughlin S, Polidoro S, Cheallaigh CN, Bourke N, Karisola P, Alenius H, Vineis P, Layte R, Kenny RA. Epigenetic Clocks and Allostatic Load Reveal Potential Sex-Specific Drivers of Biological Aging. J Gerontol A Biol Sci Med Sci 2019; 75:495-503. [DOI: 10.1093/gerona/glz241] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Indexed: 12/31/2022] Open
Abstract
Abstract
Allostatic load (AL) and epigenetic clocks both attempt to characterize the accelerated aging of biological systems, but at present it is unclear whether these measures are complementary or distinct. This study examines the cross-sectional association of AL with epigenetic age acceleration (EAA) in a subsample of 490 community-dwelling older adults participating in The Irish Longitudinal study on Aging (TILDA). A battery of 14 biomarkers representing the activity of four different physiological systems: immunological, cardiovascular, metabolic, renal, was used to construct the AL score. DNA methylation age was computed according to the algorithms described by Horvath, Hannum, and Levine allowing for estimation of whether an individual is experiencing accelerated or decelerated aging. Horvath, Hannum, and Levine EAA correlated 0.05, 0.03, and 0.21 with AL, respectively. Disaggregation by sex revealed that AL was more strongly associated with EAA in men compared with women as assessed using Horvath’s clock. Metabolic dysregulation was a strong driver of EAA in men as assessed using Horvath and Levine’s clock, while metabolic and cardiovascular dysregulation were associated with EAA in women using Levine’s clock. Results indicate that AL and the epigenetic clocks are measuring different age-related variance and implicate sex-specific drivers of biological aging.
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Affiliation(s)
- Cathal McCrory
- Department of Medical Gerontology, The Irish Longitudinal Study on Ageing, Trinity College Dublin, Ireland
- Department of Medical Gerontology, The Irish Longitudinal Study on Ageing, Trinity College Dublin, Ireland
| | - Giovanni Fiorito
- Laboratory of Biostatistics, Department of Biomedical Sciences, University of Sassari, Italy
| | - Sinead McLoughlin
- Department of Medical Gerontology, The Irish Longitudinal Study on Ageing, Trinity College Dublin, Ireland
| | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM, former HuGeF) Ireland
| | | | - Nollaig Bourke
- Department of Medical Gerontology, The Irish Longitudinal Study on Ageing, Trinity College Dublin, Ireland
| | - Piia Karisola
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Harri Alenius
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland
- Institute of Environmental Medicine (IMM), Karolinska Institutet, Stockholm, Sweden
| | - Paolo Vineis
- Italian Institute for Genomic Medicine (IIGM, former HuGeF) Ireland
- MRC Centre for Environment and Health, Imperial College London, UK
| | - Richard Layte
- Department of Sociology, Trinity College Dublin, Ireland
| | - Rose Anne Kenny
- Department of Medical Gerontology, The Irish Longitudinal Study on Ageing, Trinity College Dublin, Ireland
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21
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Assisted reproductive technologies are associated with limited epigenetic variation at birth that largely resolves by adulthood. Nat Commun 2019; 10:3922. [PMID: 31477727 PMCID: PMC6718382 DOI: 10.1038/s41467-019-11929-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022] Open
Abstract
More than 7 million individuals have been conceived by Assisted Reproductive Technologies (ART) and there is clear evidence that ART is associated with a range of adverse early life outcomes, including rare imprinting disorders. The periconception period and early embryogenesis are associated with widespread epigenetic remodeling, which can be influenced by ART, with effects on the developmental trajectory in utero, and potentially on health throughout life. Here we profile genome-wide DNA methylation in blood collected in the newborn period and in adulthood (age 22–35 years) from a unique longitudinal cohort of ART-conceived individuals, previously shown to have no differences in health outcomes in early adulthood compared with non-ART-conceived individuals. We show evidence for specific ART-associated variation in methylation around birth, most of which occurred independently of embryo culturing. Importantly, ART-associated epigenetic variation at birth largely resolves by adulthood with no direct evidence that it impacts on development and health. Use of Assisted Reproductive Technologies (ART) is increasing globally but their impact on long term health remains unclear. Here the authors show that ART-conceived individuals show variation in epigenetic profile at birth that largely resolves by adulthood, with no evidence of an impact on long term outcomes.
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22
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McCrory C, Fiorito G, Ni Cheallaigh C, Polidoro S, Karisola P, Alenius H, Layte R, Seeman T, Vineis P, Kenny RA. How does socio-economic position (SEP) get biologically embedded? A comparison of allostatic load and the epigenetic clock(s). Psychoneuroendocrinology 2019; 104:64-73. [PMID: 30818253 DOI: 10.1016/j.psyneuen.2019.02.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 01/07/2023]
Abstract
Individuals of lower socio-economic position (SEP) carry a heavier burden of disease and morbidity and live shorter lives on average compared with their more advantaged counterparts. This has sparked research interest in the processes and mechanisms via which social adversity gets biologically embedded. The present study directly compares the empirical worth of two candidate mechanisms: Allostatic Load (AL) and the Epigenetic Clock(s) for advancing our understanding of embodiment using a sub-sample of 490 individuals from the Irish Longitudinal Study (TILDA) who were explicitly selected for this purpose based on their inter-generational life course social class trajectory. A battery of 14 biomarkers representing the activity of 4 different physiological systems: Immunological, Cardiovascular, Metabolic, and Renal was used to construct the AL score. Biomarkers were dichotomised into high and low risk groups according to sex-specific quartiles of risk and summed to create a count ranging from 0-14. Three measures of epigenetic age acceleration were computed according to three sets of age-associated Cytosine-phosphate-Guanine (CpG) sites described by Horvath, Hannum and Levine. AL was strongly socially patterned across a number of measures of SEP, while the epigenetic clocks were not. AL partially mediated the association between measures of SEP and an objective measure of physiological functioning: performance on the Timed Up and Go (TUG test). We conclude that AL may represent the more promising candidate for understanding the pervasive link between SEP and health.
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Affiliation(s)
- Cathal McCrory
- The Irish Longitudinal Study on Ageing, Trinity College Dublin, Ireland.
| | - Giovanni Fiorito
- Italian Institute for Genomic Medicine (IIGM, former HuGeF), Italy
| | | | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM, former HuGeF), Italy
| | - Piia Karisola
- Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Harri Alenius
- Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland; Institute of Environmental Medicine (IMM), Karolinska Institutet, Stockholm, Sweden
| | - Richard Layte
- Department of Sociology, Trinity College Dublin, Ireland
| | | | - Paolo Vineis
- MRCPHE Centre for Environment and Health, Imperial College London, United Kingdom
| | - Rose Anne Kenny
- The Irish Longitudinal Study on Ageing, Trinity College Dublin, Ireland
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23
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Abstract
Research in the field of gerontology has traditionally focused on later life stages. There is increasing evidence, however, that both the rate of age-related functional decline and the later-life health status can be programmed during early development. The central role of epigenetic mechanisms (methylation of DNA, histone modifications and regulation by non-coding RNAs) in mediating these long-term effects has been elucidated. Both rate and direction of age-associated change of epigenetic patterns (“epigenetic drift”) were shown to be largely dependent on early-life environmental conditions. Inter-individual divergences in epigenetic profiles may arise following the stochastic errors in maintaining epigenetic marks, but they may also be adaptively mediated by specific environmental cues. Recent cohort studies indicate that ticking rate of epigenetic clock, estimated by a DNA methylation-based methods, may be developmentally adjusted, and that individual’s discrepancies among epigenetic and chronological age would be likely programmed early in development. In this Perspective article, recent findings suggesting the importance of early-life determinants for life-course dynamics of epigenetic drift are summarized and discussed.
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