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Epigenome-Wide Exploratory Study of Monozygotic Twins Suggests Differentially Methylated Regions to Associate with Hand Grip Strength

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University of Southern Denmark Epigenome-wide exploratory study of monozygotic twins suggests differentially methylated regions to associate with hand grip strength Soerensen, Mette; Li, Weilong; Debrabant, Birgit; Nygaard, Marianne; Mengel-From, Jonas; Frost, Morten; Christensen, Kaare; Christiansen, Lene; Tan, Qihua Published in: Biogerontology DOI: 10.1007/s10522-019-09818-1 Publication date: 2019 Document version: Final published version Document license: CC BY Citation for pulished version (APA): Soerensen, M., Li, W., Debrabant, B., Nygaard, M., Mengel-From, J., Frost, M., Christensen, K., Christiansen, L., & Tan, Q. (2019). Epigenome-wide exploratory study of monozygotic twins suggests differentially methylated regions to associate with hand grip strength. Biogerontology, 20(5), 627-647. https://doi.org/10.1007/s10522- 019-09818-1 Go to publication entry in University of Southern Denmark's Research Portal Terms of use This work is brought to you by the University of Southern Denmark. Unless otherwise specified it has been shared according to the terms for self-archiving. If no other license is stated, these terms apply: • You may download this work for personal use only. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying this open access version If you believe that this document breaches copyright please contact us providing details and we will investigate your claim. Please direct all enquiries to [email protected] Download date: 29. Sep. 2021 Biogerontology (2019) 20:627–647 https://doi.org/10.1007/s10522-019-09818-1 (0123456789().,-volV)( 0123456789().,-volV) RESEARCH ARTICLE Epigenome-wide exploratory study of monozygotic twins suggests differentially methylated regions to associate with hand grip strength Mette Soerensen . Weilong Li . Birgit Debrabant . Marianne Nygaard . Jonas Mengel-From . Morten Frost . Kaare Christensen . Lene Christiansen . Qihua Tan Received: 15 April 2019 / Accepted: 24 June 2019 / Published online: 28 June 2019 Ó The Author(s) 2019 Abstract Hand grip strength is a measure of mus- significant CpG sites or pathways were found, how- cular strength and is used to study age-related loss of ever two of the suggestive top CpG sites were mapped physical capacity. In order to explore the biological to the COL6A1 and CACNA1B genes, known to be mechanisms that influence hand grip strength varia- related to muscular dysfunction. By investigating tion, an epigenome-wide association study (EWAS) of genomic regions using the comb-p algorithm, several hand grip strength in 672 middle-aged and elderly differentially methylated regions in regulatory monozygotic twins (age 55–90 years) was performed, domains were identified as significantly associated to using both individual and twin pair level analyses, the hand grip strength, and pathway analyses of these latter controlling the influence of genetic variation. regions revealed significant pathways related to the Moreover, as measurements of hand grip strength immune system, autoimmune disorders, including performed over 8 years were available in the elderly diabetes type 1 and viral myocarditis, as well as twins (age 73–90 at intake), a longitudinal EWAS was negative regulation of cell differentiation. The genes conducted for this subsample. No genome-wide contributing to the immunological pathways were HLA-B, HLA-C, HLA-DMA, HLA-DPB1, MYH10, ERAP1 and IRF8, while the genes implicated in the negative regulation of cell differentiation were IRF8, Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10522-019-09818-1) con- CEBPD, ID2 and BRCA1. In conclusion, this tains supplementary material, which is available to authorized users. M. Soerensen (&) Á W. Li Á B. Debrabant Á M. Soerensen Á M. Nygaard Á J. Mengel-From Á M. Nygaard Á J. Mengel-From Á K. Christensen Á K. Christensen Á Q. Tan L. Christiansen Á Q. Tan Department of Clinical Genetics, Odense University Epidemiology, Biostatistics and Biodemography, Hospital, J.B. Winsløws Vej 4, 5000 Odense C, Denmark Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9B, 5000 Odense C, M. Frost Denmark Endocrine Research Unit, KMEB, University of Southern e-mail: [email protected] Denmark, J.B. Winsløws Vej 4, 5000 Odense C, Denmark M. Soerensen L. Christiansen Department of Clinical Biochemistry and Pharmacology, Department of Clinical Immunology, Copenhagen Center for Individualized Medicine in Arterial Diseases, University Hospital, Rigshospitalet, Blegdamsvej 9, Odense University Hospital, J.B. Winsløws Vej 4, 2100 Copenhagen Ø, Denmark 5000 Odense C, Denmark 123 628 Biogerontology (2019) 20:627–647 exploratory study suggests hand grip strength to Wang et al. 2005; Bohannon et al. 2012). In associate with differentially methylated regions accordance, the average hand grip strength peaks in enriched in immunological and cell differentiation early adulthood, followed by a period of continuance, pathways, and hence merits further investigations. and then starts declining from midlife and throughout life (Frederiksen et al. 2006; Dodds et al. 2014). Hand Keywords Epigenome-wide association study Á grip strength has been associated with a number of Hand grip strength Á Twin data Á Longitudinal data Á adverse health outcomes, such as depression (van Pathway analyses Á Comb-p Milligen et al. 2011; Fukumori et al. 2015), cardio- metabolic risk markers and diseases (Mainous et al. 2015; Lawman et al. 2016; Lee et al. 2016), and multi- Abbreviations morbidity (Cheung et al. 2013; Yorke et al. 2015), as EWAS Epigenome-wide association study well as with an increased overall mortality risk GWAS Genome-wide association study (Newman et al. 2006; Arvandi et al. 2016). In a study TWAS Transcriptome-wide association study of almost 140,000 individuals from 17 different MADT The Study of Middle Aged Danish countries, Leong et al. (2015) found associations Twins between hand grip strength and incident cardiovascu- LSADT The Longitudinal Study of Aging lar disease and further confirmed that hand grip Danish Twins strength is a strong predictor of all-cause and in BWD The Study of Birth Weight Discordant particular cardiovascular mortality. Recently, a study Twins of 502,293 participants from the UK Biobank confirms PCA Principle component analysis an association to all cause mortality and cause specific DMRs Differentially methylated regions mortality from cardiovascular disease, yet also puts FDR False discovery rate forward associations to cause specific mortality from TSS Transcription start site respiratory disease, chronic obstructive pulmonary KEGG The Kyoto Encyclopedia of Genes and disease and cancers, as well as to incidences of Genomes database cardiovascular disease, respiratory diseases, chronic WebGestalt The WEB-based GEne SeT AnaLysis obstructive pulmonary disease and cancers (Celis- Toolkit Morales et al. 2018). In addition, recent literature MSigDB Molecular Signatures Database reviews firmly validate the associations between hand GREAT Genomic regions enrichment grip strength and cognitive decline (Fritz et al. 2017; annotation tool Rijk et al. 2016) and functional status such as activity ORA Overrepresentation enrichment of daily living (Rijk et al. 2016). analysis Previous studies have estimated that the heritability GREA Genomic regions enrichment analysis of hand grip strength is approximately 50–60% (Frederiksen et al. 2002). However, very few consis- tent genetic associations have been found, and large Introduction genome-wide association studies (GWAS) of hand grip strength are scarce compared to other traits, thus Aging is accompanied by a general loss of physical leaving the molecular background of hand grip capacity that is often associated with adverse age- strength largely unaccounted for (Garatachea and related outcomes and thus may have significant Lucı´a 2013; Chan et al. 2015). The very first hand grip influences on the quality of life. For example, age- strength GWAS included 2088 adults (aged related decline in skeletal muscle strength, which is an 55–85 years) and revealed no genome-wide signifi- important component of sarcopenia and frailty, is cant results (Chan et al. 2015). Later, a meta-analysis associated with physical disability, morbidity and of 27,581 individuals over 65 years of age from 14 mortality (Beaudart et al. 2017). different cohorts discovered one genome-wide signif- Hand grip strength is a simple and easily admin- icant association, rs752045, in an intergenic region on istered measurement of muscle strength that correlates chromosome 8, which was replicated in 6363 individ- well with overall muscle strength (Visser et al. 2000; uals from three additional cohorts (Matteini et al. 123 Biogerontology (2019) 20:627–647 629 2016). rs752045 is located in a DNase hypersensitivity associated differentially methylated genomic regions, site known to affect a binding motif of the CCAAT/ of which some showed replication in 1196 individuals: enhancer-binding protein-b (CEBPB), which has been these included the DNAH12, ZFP64, TP63 and implicated in muscle cell differentiation and muscle GUSBP11 genes, which have previously been linked repair (Matteini et al. 2016). Recently, an even larger to muscle differentiation and function (Livshits et al. multi-center GWAS of 195,180 individuals identified 2016). Hence, the latter study suggests the importance 16 loci including genes involved in processes such as of epigenetic
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  • Comparative Mrna and Mirna Expression in European

    Comparative Mrna and Mirna Expression in European

    Heredity (2019) 122:172–186 https://doi.org/10.1038/s41437-018-0090-1 ARTICLE Comparative mRNA and miRNA expression in European mouflon (Ovis musimon) and sheep (Ovis aries) provides novel insights into the genetic mechanisms for female reproductive success 1 1,2 1,2 3 1,2 1,2 1,2 Ji Yang ● Xin Li ● Yin-Hong Cao ● Kisun Pokharel ● Xiao-Ju Hu ● Ze-Hui Chen ● Song-Song Xu ● 3 3 3 1 Jaana Peippo ● Mervi Honkatukia ● Juha Kantanen ● Meng-Hua Li Received: 12 January 2018 / Revised: 20 March 2018 / Accepted: 18 April 2018 / Published online: 21 May 2018 © The Author(s) 2018. This article is published with open access Abstract Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis 1234567890();,: 1234567890();,: musimon) and performed an mRNA–miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep. We identified several novel genes with differentially expressed mRNAs (e.g., EREG, INHBA, SPP1, AMH, TDRD5, and ZP2) between the wild and domestic sheep, which are functionally involved in oocyte and follicle development and fertilization, and are significantly (adjusted P-value < 0.05) enriched in the Gene Ontology (GO) terms of various reproductive process, including the regulation of fertilization, oogenesis, ovarian follicle development, and sperm–egg recognition.