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Benchek P, Igo RP, Voss-Hoynes H, Wren Y, Miller G, Truitt B, Zhang W, Osterman M, Freebairn L, Tag J, Taylor HG, Chan ER, Roussos P, Lewis B, Stein CM, Iyengar SK. Association between genes regulating neural pathways for quantitative traits of speech and language disorders. NPJ Genom Med 2021; 6:64. [PMID: 34315907 PMCID: PMC8316336 DOI: 10.1038/s41525-021-00225-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Speech sound disorders (SSD) manifest as difficulties in phonological memory and awareness, oral motor function, language, vocabulary, reading, and spelling. Families enriched for SSD are rare, and typically display a cluster of deficits. We conducted a genome-wide association study (GWAS) in 435 children from 148 families in the Cleveland Family Speech and Reading study (CFSRS), examining 16 variables representing 6 domains. Replication was conducted using the Avon Longitudinal Study of Parents and Children (ALSPAC). We identified 18 significant loci (combined p < 10-8) that we pursued bioinformatically. We prioritized 5 novel gene regions with likely functional repercussions on neural pathways, including those which colocalized with differentially methylated regions in our sample. Polygenic risk scores for receptive language, expressive vocabulary, phonological awareness, phonological memory, spelling, and reading decoding associated with increasing clinical severity. In summary, neural-genetic influence on SSD is primarily multigenic and acts on genomic regulatory elements, similar to other neurodevelopmental disorders.
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Affiliation(s)
- Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Robert P Igo
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Heather Voss-Hoynes
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Yvonne Wren
- Bristol Dental School, Faculty of Health Sciences, University of Bristol, and Bristol Speech and Language Therapy Research Unit, North Bristol NHS Trust, Bristol, UK
| | - Gabrielle Miller
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara Truitt
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Wen Zhang
- Department of Psychiatry, Friedman Brain Institute, and Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Osterman
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lisa Freebairn
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jessica Tag
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - H Gerry Taylor
- Department of Pediatrics, Case Western Reserve University, and Rainbow Babies & Children's Hospital, University Hospital Case Medical Center, Cleveland, OH, USA
- Nationwide Children's Hospital Research Institute and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - E Ricky Chan
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Panos Roussos
- Department of Psychiatry, Friedman Brain Institute, and Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Barbara Lewis
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Hearing and Speech Center, Cleveland, OH, USA
| | - Catherine M Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Sudha K Iyengar
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
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Wan JY, Goodman DL, Willems EL, Freedland AR, Norden-Krichmar TM, Santorico SA, Edwards KL. Genome-wide association analysis of metabolic syndrome quantitative traits in the GENNID multiethnic family study. Diabetol Metab Syndr 2021; 13:59. [PMID: 34074324 PMCID: PMC8170963 DOI: 10.1186/s13098-021-00670-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To identify genetic associations of quantitative metabolic syndrome (MetS) traits and characterize heterogeneity across ethnic groups. METHODS Data was collected from GENetics of Noninsulin dependent Diabetes Mellitus (GENNID), a multiethnic resource of Type 2 diabetic families and included 1520 subjects in 259 African-American, European-American, Japanese-Americans, and Mexican-American families. We focused on eight MetS traits: weight, waist circumference, systolic and diastolic blood pressure, high-density lipoprotein, triglycerides, fasting glucose, and insulin. Using genotyped and imputed data from Illumina's Multiethnic array, we conducted genome-wide association analyses with linear mixed models for all ethnicities, except for the smaller Japanese-American group, where we used additive genetic models with gene-dropping. RESULTS Findings included ethnic-specific genetic associations and heterogeneity across ethnicities. Most significant associations were outside our candidate linkage regions and were coincident within a gene or intergenic region, with two exceptions in European-American families: (a) within previously identified linkage region on chromosome 2, two significant GLI2-TFCP2L1 associations with weight, and (b) one chromosome 11 variant near CADM1-LINC00900 with pleiotropic blood pressure effects. CONCLUSIONS This multiethnic family study found genetic heterogeneity and coincident associations (with one case of pleiotropy), highlighting the importance of including diverse populations in genetic research and illustrating the complex genetic architecture underlying MetS.
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Affiliation(s)
- Jia Y Wan
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA
| | - Deborah L Goodman
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA
| | - Emileigh L Willems
- Department of Mathematical and Statistical Sciences, University of Colorado, Denver, CO, USA
| | - Alexis R Freedland
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA
| | - Trina M Norden-Krichmar
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA
| | - Stephanie A Santorico
- Department of Mathematical and Statistical Sciences, University of Colorado, Denver, CO, USA
- Human Medical Genetics and Genomics Program, University of Colorado, Denver, CO, USA
- Department of Biostatistics & Informatics, University of Colorado, Denver, CO, USA
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Karen L Edwards
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA.
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Neumeyer S, Popanda O, Butterbach K, Edelmann D, Bläker H, Toth C, Roth W, Herpel E, Jäkel C, Schmezer P, Benner A, Burwinkel B, Hoffmeister M, Brenner H, Chang-Claude J. DNA methylation profiling to explore colorectal tumor differences according to menopausal hormone therapy use in women. Epigenomics 2019; 11:1765-1778. [PMID: 31755748 DOI: 10.2217/epi-2019-0051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: Use of menopausal hormone therapy (MHT) has been associated with a reduced risk for colorectal cancer, but mechanisms underlying this relationship are not well understood. In the colon, MHT appears to act through estrogen receptor β (ERβ) which may influence DNA methylation by binding to DNA. Using genome-wide methylation profiling data, we aimed to identify genes that may be differentially methylated according to MHT use. Materials & methods: DNA methylation was measured using Illumina HumanMethylation450k arrays in two independent tumor sample sets of colorectal cancer patients. Differential methylation was determined using R/limma. Results: In the discovery analysis, two CpG sites showed differential DNA methylation according to MHT use, both were not replicated. In stratified analyses, 342 CpG sites were associated with current MHT use only in ERβ-positive tumors. Conclusion: The suggestive findings of differential methylation according to current MHT use in ERβ-positive tumors warrant further investigation.
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Affiliation(s)
- Sonja Neumeyer
- Division of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Odilia Popanda
- Division of Epigenomics & Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Katja Butterbach
- Division of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Division of Clinical Epidemiology & Aging Research, German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité University Medicine, Charitéplatz 1, 10117 Berlin, Germany
| | - Csaba Toth
- Institute of Pathology, Heidelberg University, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Wilfried Roth
- Institute of Pathology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Esther Herpel
- Institute of Pathology, Heidelberg University, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany.,NCT Tissue Bank, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Cornelia Jäkel
- Division of Epigenomics & Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Peter Schmezer
- Division of Epigenomics & Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Barbara Burwinkel
- Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Gynecology & Obstetrics, Molecular Biology of Breast Cancer, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology & Aging Research, German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology & Aging Research, German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Genetic Tumour Epidemiology Group, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistraße 54, 20251 Hamburg, Germany
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4
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Neumeyer S, Popanda O, Edelmann D, Butterbach K, Toth C, Roth W, Bläker H, Jiang R, Herpel E, Jäkel C, Schmezer P, Jansen L, Alwers E, Benner A, Burwinkel B, Hoffmeister M, Brenner H, Chang-Claude J. Genome-wide DNA methylation differences according to oestrogen receptor beta status in colorectal cancer. Epigenetics 2019; 14:477-493. [PMID: 30931802 DOI: 10.1080/15592294.2019.1595998] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Involvement of sex hormones in colorectal cancer (CRC) development has been linked to oestrogen receptor β (ERβ). Expression of ERβ is found reduced in tumour tissue and inversely related to mortality. However, mechanisms are not well understood. Our study aimed to detect differentially methylated genes associated with ERβ expression, which could point to mechanisms by which ERβ could influence risk and prognosis of CRC. Epigenome-wide DNA methylation profiling was performed using Illumina HumanMethylation450k BeadChip arrays in two independent tumour sample sets of CRC patients recruited in 2003-2010 by the German DACHS study (discovery cohort n = 917, replication cohort n = 907). ERβ expression was measured using immunohistochemistry and scored as negative, moderate and high. Differentially methylated CpG sites and genomic regions were determined using limma in the R-package RnBeads. For the comparison of tumours with moderate/high ERβ versus negative expression, differentially methylated CpG sites were identified but not confirmed by replication. Comparing tumours of high with tumours of negative ERβ expression revealed 2,904 differentially methylated CpG sites of which 403 were replicated (FDR adjusted p-value<0.05). Replicated CpGs were annotated to genes such as CD36, HK1 or LRP5. A survival analysis indicates that 30 of the replicated CpGs are also associated with overall survival (FDR-adjusted p-value<0.05). The regional analysis identified 60 differentially methylated promotor regions. The epigenome-wide analysis identified both novel genes as well as genes already implicated in CRC. Follow-up mechanistic studies to better understand the regulatory role of ERβ could inform potential targets for improving treatment or prevention of CRC.
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Affiliation(s)
- Sonja Neumeyer
- a Division of Cancer Epidemiology , German Cancer Research Center , Heidelberg , Germany.,b Medical Faculty Heidelberg , Heidelberg University , Heidelberg , Germany
| | - Odilia Popanda
- c Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Dominic Edelmann
- d Division of Biostatistics , German Cancer Research Center , Heidelberg , Germany
| | - Katja Butterbach
- a Division of Cancer Epidemiology , German Cancer Research Center , Heidelberg , Germany.,e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany
| | - Csaba Toth
- f Institute of Pathology , Heidelberg University , Heidelberg , Germany
| | - Wilfried Roth
- g Institute of Pathology , Universitätsmedizin der Johannes Gutenberg-Universität Mainz , Mainz , Germany
| | - Hendrik Bläker
- h Institute of Pathology , Charité University Medicine , Berlin , Germany
| | - Ruijingfang Jiang
- a Division of Cancer Epidemiology , German Cancer Research Center , Heidelberg , Germany
| | - Esther Herpel
- f Institute of Pathology , Heidelberg University , Heidelberg , Germany.,i NCT Tissue Bank , National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Cornelia Jäkel
- c Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Peter Schmezer
- c Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Lina Jansen
- e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany
| | - Elizabeth Alwers
- e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany
| | - Axel Benner
- d Division of Biostatistics , German Cancer Research Center , Heidelberg , Germany
| | - Barbara Burwinkel
- j Division of Molecular Epidemiology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,k Department of Gynecology and Obstetrics, Molecular Biology of Breast Cancer , University of Heidelberg , Heidelberg , Germany
| | - Michael Hoffmeister
- e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany
| | - Hermann Brenner
- e Division of Clinical Epidemiology and Aging Research , German Cancer Research Center , Heidelberg , Germany.,l Division of Preventive Oncology , German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) , Heidelberg , Germany.,m German Cancer Consortium (DKTK) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jenny Chang-Claude
- a Division of Cancer Epidemiology , German Cancer Research Center , Heidelberg , Germany.,n Cancer Epidemiology Group , University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
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Adams CD, Jordahl KM, Copeland W, Mirick DK, Song X, Sather CL, Kelsey K, Houseman A, Davis S, Randolph T, Bhatti P. Nightshift work, chronotype, and genome-wide DNA methylation in blood. Epigenetics 2017; 12:833-840. [PMID: 28837395 DOI: 10.1080/15592294.2017.1366407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Molecular mechanisms underlying the negative health effects of shift work are poorly understood, which remains a barrier to developing intervention strategies to protect the long-term health of shift workers. We evaluated genome-wide differences in DNA methylation (measured in blood) between 111 actively employed female nightshift and 86 actively employed female dayshift workers from the Seattle metropolitan area. We also explored the effect of chronotype (i.e., measure of preference for activity earlier or later in the day) on DNA methylation among 110 of the female nightshift workers and an additional group of 131 male nightshift workers. Methylation data were generated using the Illumina Infinium HumanMethylation450 BeadChip (450K) Array. After applying the latest methylation data processing methods, we compared methylation levels at 361,210 CpG loci between the groups using linear regression models adjusted for potential confounders and applied the false-discovery rate (FDR) ≤ 0.05 to account for multiple comparisons. No statistically significant associations at the genome-wide level were observed with shift work or chronotype, though based on raw P values and absolute effect sizes, there were suggestive associations in genes that have been previously linked with cancer (e.g., BACH2, JRK, RPS6KA2) and type-2 diabetes (e.g., KCNQ1). Given that our study was underpowered to detect moderate effects, examining these suggestive results in well-powered independent studies or in pooled data sets may improve our understanding of the pathways underlying the negative health effects of shift work and the influence of personal factors such as chronotype. Such an approach may help identify potential interventions that can be used to protect the long-term health of shift workers.
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Affiliation(s)
- Charleen D Adams
- a MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol , Bristol , UK.,b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Kristina M Jordahl
- b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Wade Copeland
- c Program in Biostatistics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Dana K Mirick
- b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Xiaoling Song
- d Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Cassandra L Sather
- e Genomics Resource, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Karl Kelsey
- f Department of Community Health , Brown University , Providence , RI , USA
| | - Andres Houseman
- g College of Public Health and Human Sciences, Oregon State University , Corvallis , OR , USA
| | - Scott Davis
- b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Timothy Randolph
- c Program in Biostatistics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Parveen Bhatti
- b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
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