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Subramanian A, Su S, Moding EJ, Binkley MS. Investigating the tissue specificity and prognostic impact of cis-regulatory cancer risk variants. Hum Genet 2023; 142:1395-1405. [PMID: 37474751 DOI: 10.1007/s00439-023-02586-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
The tissue-specific incidence of cancers and their genetic basis are poorly understood. Although prior studies have shown global correlation across tissues for cancer risk single-nucleotide polymorphisms (SNPs) identified through genome-wide association studies (GWAS), any shared functional regulation of gene expression on a per SNP basis has not been well characterized. We set to quantify cis-mediated gene regulation and tissue sharing for SNPs associated with eight common cancers. We identify significant tissue sharing for individual SNPs and global enrichment for breast, colorectal, and Hodgkin lymphoma cancer risk SNPs in multiple tissues. In addition, we observe increasing tissue sharing for cancer risk SNPs overlapping with super-enhancers for breast cancer and Hodgkin lymphoma providing further evidence of tissue specificity. Finally, for genes under cis-regulation by breast cancer SNPs, we identify a phenotype characterized by low expression of tumor suppressors and negative regulators of the WNT pathway associated with worse freedom from progression and overall survival in patients who eventually develop breast cancer. Our results introduce a paradigm for functionally annotating individual cancer risk SNPs and will inform the design of future translational studies aimed to personalize assessment of inherited cancer risk across tissues.
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Affiliation(s)
- Ajay Subramanian
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Shengqin Su
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Sargent Binkley
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA.
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Massignam ET, Dieter C, Assmann TS, Duarte GCK, Bauer AC, Canani LH, Crispim D. The rs705708 A allele of the ERBB3 gene is associated with lower prevalence of diabetic retinopathy and arterial hypertension and with improved renal function in type 1 diabetic patients. Microvasc Res 2022; 143:104378. [PMID: 35594935 DOI: 10.1016/j.mvr.2022.104378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION The Erb-b2 receptor tyrosine kinase 3 (ERBB3) is involved in autoimmune processes related to type 1 diabetes mellitus (T1DM) pathogenesis. Accordingly, some studies have suggested that single nucleotide polymorphisms (SNPs) in the ERBB3 gene confer risk for T1DM. Proliferation-associated protein 2G4 (PA2G4) is another candidate gene for this disease because it regulates cell proliferation and adaptive immunity. Moreover, PA2G4 regulates ERBB3. To date, no study has evaluated the association of PA2G4 SNPs and T1DM. AIM To evaluate the association of ERBB3 rs705708 (G/A) and PA2G4 rs773120 (C/T) SNPs with T1DM and its clinical and laboratory characteristics. METHODS This case-control study included 976 white subjects from Southern Brazil, categorized into 501 cases with T1DM and 475 non-diabetic controls. The ERBB3 and PA2G4 SNPs were genotyped by allelic discrimination-real-time PCR. RESULTS ERBB3 rs705708 and PA2G4 rs773120 SNPs were not associated with T1DM considering different inheritance models and also when controlling for covariables. However, T1DM patients carrying the ERBB3 rs705708 A allele developed T1DM at an earlier age vs. G/G patients. Interestingly, in the T1DM group, the rs705708 A allele was associated with lower prevalence of diabetic retinopathy and arterial hypertension as well as with improved renal function (higher estimated glomerular filtration rate and lower urinary albumin excretion levels) compared to G/G patients. CONCLUSIONS Although no association was observed between the ERBB3 rs705708 and PA2G4 rs773120 SNPs and T1DM, the rs705708 A allele was associated, for the first time in literature, with lower prevalence of diabetic retinopathy and arterial hypertension. Additionally, this SNP was associated with improved renal function.
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Affiliation(s)
- Eloísa Toscan Massignam
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Faculty of Medicine, Department of Internal Medicine, Graduate Program in Medical Sciences: Endocrinology, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristine Dieter
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Faculty of Medicine, Department of Internal Medicine, Graduate Program in Medical Sciences: Endocrinology, Porto Alegre, Rio Grande do Sul, Brazil
| | - Taís Silveira Assmann
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Faculty of Medicine, Department of Internal Medicine, Graduate Program in Medical Sciences: Endocrinology, Porto Alegre, Rio Grande do Sul, Brazil
| | - Guilherme Coutinho Kullmann Duarte
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Faculty of Medicine, Department of Internal Medicine, Graduate Program in Medical Sciences: Endocrinology, Porto Alegre, Rio Grande do Sul, Brazil
| | - Andrea Carla Bauer
- Nephrology Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Luis Henrique Canani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Faculty of Medicine, Department of Internal Medicine, Graduate Program in Medical Sciences: Endocrinology, Porto Alegre, Rio Grande do Sul, Brazil
| | - Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Faculty of Medicine, Department of Internal Medicine, Graduate Program in Medical Sciences: Endocrinology, Porto Alegre, Rio Grande do Sul, Brazil.
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3
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Wnt-Signaling Regulated by Glucocorticoid-Induced miRNAs. Int J Mol Sci 2021; 22:ijms222111778. [PMID: 34769207 PMCID: PMC8584097 DOI: 10.3390/ijms222111778] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Glucocorticoids (GCs) are pleiotropic hormones which regulate innumerable physiological processes. Their comprehensive effects are due to the diversity of signaling mechanism networks. MiRNAs, small, non-coding RNAs contribute to the fine tuning of signaling pathways and reciprocal regulation between GCs and miRNAs has been suggested. Our aim was to investigate the expressional change and potential function of GC mediated miRNAs. The miRNA expression profile was measured in three models: human adrenocortical adenoma vs. normal tissue, steroid-producing H295R cells and in hormonally inactive HeLa cells before and after dexamethasone treatment. The gene expression profile in 82 control and 57 GC-affected samples was evaluated in GC producing and six different GC target tissue types. Tissue-specific target prediction (TSTP) was applied to identify the most relevant miRNA-mRNA interactions. Glucocorticoid treatment resulted in cell type-dependent miRNA expression changes. However, 19.5% of the influenced signaling pathways were common in all three experiments, of which the Wnt-signaling pathway seemed to be the most affected. Transcriptome data and TSTP showed similar results, as the Wnt pathway was significantly altered in both the GC-producing adrenal gland and all investigated GC target tissue types. In different cell types, different miRNAs led to the regulation of similar pathways. Wnt signaling may be one of the most important signaling pathways affected by hypercortisolism. It is, at least in part, regulated by miRNAs that mediate the glucocorticoid effect. Our findings on GC producing and GC target tissues suggest that the alteration of Wnt signaling (together with other pathways) may be responsible for the leading symptoms observed in Cushing's syndrome.
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Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize. PLoS Genet 2021; 17:e1009568. [PMID: 34606492 PMCID: PMC8516254 DOI: 10.1371/journal.pgen.1009568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/14/2021] [Accepted: 09/07/2021] [Indexed: 11/19/2022] Open
Abstract
Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for predicting many complex traits. However, it usually cannot capture the combination of alleles in haplotypes and it has generated little insight about the biological function of polymorphisms. Here we present a novel and cost-effective method for imputing cis haplotype associated RNA expression (HARE), studied their transferability across tissues, and evaluated genomic prediction models within and across populations. HARE focuses on tightly linked cis acting causal variants in the immediate vicinity of the gene, while excluding trans effects from diffusion and metabolism. Therefore, HARE estimates were more transferrable across different tissues and populations compared to measured transcript expression. We also showed that HARE estimates captured one-third of the variation in gene expression. HARE estimates were used in genomic prediction models evaluated within and across two diverse maize panels–a diverse association panel (Goodman Association panel) and a large half-sib panel (Nested Association Mapping panel)–for predicting 26 complex traits. HARE resulted in up to 15% higher prediction accuracy than control approaches that preserved haplotype structure, suggesting that HARE carried functional information in addition to information about haplotype structure. The largest increase was observed when the model was trained in the Nested Association Mapping panel and tested in the Goodman Association panel. Additionally, HARE yielded higher within-population prediction accuracy as compared to measured expression values. The accuracy achieved by measured expression was variable across tissues, whereas accuracy by HARE was more stable across tissues. Therefore, imputing RNA expression of genes by haplotype is stable, cost-effective, and transferable across populations. Genomic marker data is widely used in the prediction of many traits. However, prediction has been primarily carried out within populations and without explicit modeling of RNA or protein expression. In this study, we explored the prediction of field traits within and across populations using estimated RNA expression attributable to only the DNA sequence around a gene. We showed that the estimated RNA expression was more transferable across populations and tissues than measured RNA expression. We improved prediction of field traits up to 15% using estimated gene expression as compared to observed expression or gene sequence alone. Overall, these findings indicate that structural and functional information in the gene sequence is highly transferable.
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5
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Andolfo I, Russo R, Lasorsa VA, Cantalupo S, Rosato BE, Bonfiglio F, Frisso G, Abete P, Cassese GM, Servillo G, Esposito G, Gentile I, Piscopo C, Villani R, Fiorentino G, Cerino P, Buonerba C, Pierri B, Zollo M, Iolascon A, Capasso M. Common variants at 21q22.3 locus influence MX1 and TMPRSS2 gene expression and susceptibility to severe COVID-19. iScience 2021; 24:102322. [PMID: 33748697 PMCID: PMC7968217 DOI: 10.1016/j.isci.2021.102322] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/15/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
The established risk factors of coronavirus disease 2019 (COVID-19) are advanced age, male sex, and comorbidities, but they do not fully explain the wide spectrum of disease manifestations. Genetic factors implicated in the host antiviral response provide for novel insights into its pathogenesis. We performed an in-depth genetic analysis of chromosome 21 exploiting the genome-wide association study data, including 6,406 individuals hospitalized for COVID-19 and 902,088 controls with European genetic ancestry from the COVID-19 Host Genetics Initiative. We found that five single nucleotide polymorphisms within TMPRSS2 and near MX1 gene show associations with severe COVID-19. The minor alleles of the five single nucleotide polymorphisms (SNPs) correlated with a reduced risk of developing severe COVID-19 and high level of MX1 expression in blood. Our findings demonstrate that host genetic factors can influence the different clinical presentations of COVID-19 and that MX1 could be a potential therapeutic target.
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Affiliation(s)
- Immacolata Andolfo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Vito Alessandro Lasorsa
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Sueva Cantalupo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Barbara Eleni Rosato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Ferdinando Bonfiglio
- Dipartimento di Ingegneria chimica, dei Materiali e della Produzione industriale, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Pasquale Abete
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Napoli, Italy
| | - Gian Marco Cassese
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Napoli, Italy
| | - Giuseppe Servillo
- Dipartimento di Neuroscienze e Scienze riproduttive ed odontostomatologiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Gabriella Esposito
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Ivan Gentile
- Dipartimento di Medicina clinica e Chirurgia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, A.O.R.N. ‘Antonio Cardarelli’, Napoli, Italy
| | - Romolo Villani
- Poison Centre, A.O.R.N. ‘Antonio Cardarelli’, Napoli, Italy
| | | | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
| | - Carlo Buonerba
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
| | - Biancamaria Pierri
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana", Università di Salerno, Baronissi, Italy
| | - Massimo Zollo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Mario Capasso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
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6
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Im C, Li N, Moon W, Liu Q, Morton LM, Leisenring WM, Howell RM, Chow EJ, Sklar CA, Wilson CL, Wang Z, Sapkota Y, Chemaitilly W, Ness KK, Hudson MM, Robison LL, Bhatia S, Armstrong GT, Yasui Y. Genome-wide Association Studies Reveal Novel Locus With Sex-/Therapy-Specific Fracture Risk Effects in Childhood Cancer Survivors. J Bone Miner Res 2021; 36:685-695. [PMID: 33338273 PMCID: PMC8044050 DOI: 10.1002/jbmr.4234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022]
Abstract
Childhood cancer survivors treated with radiation therapy (RT) and osteotoxic chemotherapies are at increased risk for fractures. However, understanding of how genetic and clinical susceptibility factors jointly contribute to fracture risk among survivors is limited. To address this gap, we conducted genome-wide association studies of fracture risk after cancer diagnosis in 2453 participants of European ancestry from the Childhood Cancer Survivor Study (CCSS) with 930 incident fractures using Cox regression models (ie, time-to-event analysis) and prioritized sex- and treatment-stratified genetic associations. We performed replication analyses in 1417 survivors of European ancestry with 652 incident fractures from the St. Jude Lifetime Cohort Study (SJLIFE). In discovery, we identified a genome-wide significant (p < 5 × 10-8 ) fracture risk locus, 16p13.3 (HAGHL), among female CCSS survivors (n = 1289) with strong evidence of sex-specific effects (psex-heterogeneity < 7 × 10-6 ). Combining discovery and replication data, rs1406815 showed the strongest association (hazard ratio [HR] = 1.43, p = 8.2 × 10-9 ; n = 1935 women) at this locus. In treatment-stratified analyses in the discovery cohort, the association between rs1406815 and fracture risk among female survivors with no RT exposures was weak (HR = 1.22, 95% confidence interval [CI] 0.95-1.57, p = 0.11) but increased substantially among those with greater head/neck RT doses (any RT: HR = 1.88, 95% CI 1.54-2.28, p = 2.4 × 10-10 ; >36 Gray only: HR = 3.79, 95% CI 1.95-7.34, p = 8.2 × 10-5 ). These head/neck RT-specific HAGHL single-nucleotide polymorphism (SNP) effects were replicated in female SJLIFE survivors. In silico bioinformatics analyses suggest these fracture risk alleles regulate HAGHL gene expression and related bone resorption pathways. Genetic risk profiles integrating this locus may help identify female survivors who would benefit from targeted interventions to reduce fracture risk. © 2020 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Cindy Im
- School of Public Health, University of Alberta, Edmonton, Canada
| | - Nan Li
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wonjong Moon
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qi Liu
- School of Public Health, University of Alberta, Edmonton, Canada
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Wendy M Leisenring
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rebecca M Howell
- Department of Radiation Physic, MD Anderson Cancer Center, Houston, TX, USA
| | - Eric J Chow
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles A Sklar
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wassim Chemaitilly
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Division of Endocrinology, Department of Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, Canada.,Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
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7
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Soeda M, Ohka S, Nishizawa D, Hasegawa J, Nakayama K, Ebata Y, Ichinohe T, Fukuda KI, Ikeda K. Cold pain sensitivity is associated with single-nucleotide polymorphisms of PAR2/ F2RL1 and TRPM8. Mol Pain 2021; 17:17448069211002009. [PMID: 33765896 PMCID: PMC8822448 DOI: 10.1177/17448069211002009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pain sensitivity differs individually, but the mechanisms and genetic factors that underlie these differences are not fully understood. To investigate genetic factors that are involved in sensing cold pain, we applied a cold-induced pain test and evaluated protease-activated receptor 2 (PAR2/F2RL1) and transient receptor potential melastatin 8 (TRPM8), which are related to pain. We statistically investigated the associations between genetic polymorphisms and cold pain sensitivity in 461 healthy patients who were scheduled to undergo cosmetic orthognathic surgery for mandibular prognathism. We found an association between cold pain sensitivity and the rs2243057 polymorphism of the PAR2 gene. We also found a significant association between cold pain sensitivity and the rs12992084 polymorphism of the TRPM8 gene. Carriers of the minor A allele of the rs2243057 polymorphism of PAR2 and minor C allele of the rs12992084 polymorphism of TRPM8 exhibited a longer latency to pain perception in the cold-induced pain test, reflecting a decrease in cold pain sensitivity. These results suggest that genetic polymorphisms of both PAR2 and TRPM8 are involved in individual differences in cold pain sensitivity.
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Affiliation(s)
- Moe Soeda
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Department of Oral Health and Clinical Science, Tokyo Dental College, Tokyo, Japan
| | - Seii Ohka
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Daisuke Nishizawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Junko Hasegawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kyoko Nakayama
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yuko Ebata
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tatsuya Ichinohe
- Department of Dental Anesthesiology, Tokyo Dental College, Tokyo, Japan
| | - Ken-Ichi Fukuda
- Department of Oral Health and Clinical Science, Tokyo Dental College, Tokyo, Japan
| | - Kazutaka Ikeda
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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8
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Zhang E, Levin AM, Williams LK. How does race and ethnicity effect the precision treatment of asthma? EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2019; 4:337-356. [PMID: 33015363 DOI: 10.1080/23808993.2019.1690396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction Asthma is a common condition that affects large numbers of children and adults, yet the burden of disease is not equally distributed amongst groups. In the United States, African Americans and Puerto Ricans have higher rates of asthma and its complications when compared with European Americans. However, clinical trials and genetic studies have largely focused on the latter group. Areas covered Here we examine what is known regarding differences in asthma treatment response by race-ethnicity. We also review existing genetic studies related to the use of asthma medications, paying special attention to studies that included substantial numbers of non-white population groups. Publicly accessible search engines of the medical literature were queried using combinations of the terms asthma, race, ethnicity, pharmacogenomics, and pharmacogenetics, as well as the names of individual asthma medication classes. The list of articles reviewed was supplemented by bibliographies and expert knowledge. Expert opinion A substantial and coordinated effort is still needed to both identify and validate genetic biomarkers of asthma medication response, as currently there are no clinically actionable genetic markers available for this purpose. The path to identifying such markers in non-white populations is even more formidable, since these groups are underrepresented in existing data.
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Affiliation(s)
- Ellen Zhang
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
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9
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Neavin DR, Lee JH, Liu D, Ye Z, Li H, Wang L, Ordog T, Weinshilboum RM. Single Nucleotide Polymorphisms at a Distance from Aryl Hydrocarbon Receptor (AHR) Binding Sites Influence AHR Ligand-Dependent Gene Expression. Drug Metab Dispos 2019; 47:983-994. [PMID: 31292129 PMCID: PMC7184190 DOI: 10.1124/dmd.119.087312] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/07/2019] [Indexed: 12/17/2022] Open
Abstract
Greater than 90% of significant genome-wide association study (GWAS) single-nucleotide polymorphisms (SNPs) are in noncoding regions of the genome, but only 25.6% are known expression quantitative trait loci (eQTLs). Therefore, the function of many significant GWAS SNPs remains unclear. We have identified a novel type of eQTL for which SNPs distant from ligand-activated transcription factor (TF) binding sites can alter target gene expression in a SNP genotype-by-ligand–dependent fashion that we refer to as pharmacogenomic eQTLs (PGx-eQTLs)—loci that may have important pharmacotherapeutic implications. In the present study, we integrated chromatin immunoprecipitation-seq with RNA-seq and SNP genotype data for a panel of lymphoblastoid cell lines to identify 10 novel cis PGx-eQTLs dependent on the ligand-activated TF aryl hydrocarbon receptor (AHR)—a critical environmental sensor for xenobiotic (drug) and immune response. Those 10 cis PGx-eQTLs were eQTLs only after AHR ligand treatment, even though the SNPs did not create/destroy an AHR response element—the DNA sequence motif recognized and bound by AHR. Additional functional studies in multiple cell lines demonstrated that some cis PGx-eQTLs are functional in multiple cell types, whereas others displayed SNP-by-ligand–dependent effects in just one cell type. Furthermore, four of those cis PGx-eQTLs had previously been associated with clinical phenotypes, indicating that those loci might have the potential to inform clinical decisions. Therefore, SNPs across the genome that are distant from TF binding sites for ligand-activated TFs might function as PGx-eQTLs and, as a result, might have important clinical implications for interindividual variation in drug response.
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Affiliation(s)
- Drew R Neavin
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Jeong-Heon Lee
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Zhenqing Ye
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Hu Li
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Tamas Ordog
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics (D.R.N., D.L., H.L., L.W., R.M.W.), Epigenomics Program, Center for Individualized Medicine (J.-H.L., T.O.), Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology (J.-H.L.), Division of Biomedical Statistics and Informatics (Z.Y.), Department of Physiology and Biomedical Engineering (T.O.), and Division of Gastroenterology and Hepatology, Department of Medicine (T.O.), Mayo Clinic, Rochester, Minnesota
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10
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Gibbon A, Saunders CJ, Collins M, Gamieldien J, September AV. Defining the molecular signatures of Achilles tendinopathy and anterior cruciate ligament ruptures: A whole-exome sequencing approach. PLoS One 2018; 13:e0205860. [PMID: 30359423 PMCID: PMC6201890 DOI: 10.1371/journal.pone.0205860] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/02/2018] [Indexed: 12/22/2022] Open
Abstract
Musculoskeletal soft tissue injuries are complex phenotypes with genetics being one of many proposed risk factors. Case-control association studies using the candidate gene approach have predominately been used to identify risk loci for these injuries. However, the ability to identify all risk conferring variants using this approach alone is unlikely. Therefore, this study aimed to further define the genetic profile of these injuries using an integrated omics approach involving whole exome sequencing and a customised analyses pipeline. The exomes of ten exemplar asymptomatic controls and ten exemplar cases with Achilles tendinopathy were individually sequenced using a platform that included the coverage of the untranslated regions and miRBase miRNA genes. Approximately 200 000 variants were identified in the sequenced samples. Previous research was used to guide a targeted analysis of the genes encoding the tenascin-C (TNC) glycoprotein and the α1 chain of type XXVII collagen (COL27A1) located on chromosome 9. Selection of variants within these genes were; however, not predetermined but based on a tiered filtering strategy. Four variants in TNC (rs1061494, rs1138545, rs2104772 and rs1061495) and three variants in the upstream COL27A1 gene (rs2567706, rs2241671 and rs2567705) were genotyped in larger Achilles tendinopathy and anterior cruciate ligament (ACL) rupture sample groups. The CC genotype of TNC rs1061494 (C/T) was associated with the risk of Achilles tendinopathy (p = 0.018, OR: 2.5 95% CI: 1.2-5.1). Furthermore, the AA genotype of the TNC rs2104772 (A/T) variant was significantly associated with ACL ruptures in the female subgroup (p = 0.035, OR: 2.3 95% CI: 1.1-5.5). An inferred haplotype in the TNC gene was also associated with the risk of Achilles tendinopathy. These results provide a proof of concept for the use of a customised pipeline for the exploration of a larger genomic dataset. This approach, using previous research to guide a targeted analysis of the data has generated new genetic signatures in the biology of musculoskeletal soft tissue injuries.
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Affiliation(s)
- Andrea Gibbon
- Division of Exercise Science and Sports Medicine, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Colleen J. Saunders
- South African National Bioinformatics Institute/SA MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, Cape Town, South Africa
- Division of Emergency Medicine, Department of Surgery, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Malcolm Collins
- Division of Exercise Science and Sports Medicine, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Junaid Gamieldien
- South African National Bioinformatics Institute/SA MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Alison V. September
- Division of Exercise Science and Sports Medicine, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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11
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Integrative approach identifies corticosteroid response variant in diverse populations with asthma. J Allergy Clin Immunol 2018; 143:1791-1802. [PMID: 30367910 PMCID: PMC6482107 DOI: 10.1016/j.jaci.2018.09.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/02/2018] [Accepted: 09/08/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Although inhaled corticosteroid (ICS) medication is considered the cornerstone treatment for patients with persistent asthma, few ICS pharmacogenomic studies have involved nonwhite populations. OBJECTIVE We sought to identify genetic predictors of ICS response in multiple population groups with asthma. METHODS The discovery group comprised African American participants from the Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE) who underwent 6 weeks of monitored ICS therapy (n = 244). A genome-wide scan was performed to identify single nucleotide polymorphism (SNP) variants jointly associated (ie, the combined effect of the SNP and SNP × ICS treatment interaction) with changes in asthma control. Top associations were validated by assessing the joint association with asthma exacerbations in 3 additional groups: African Americans (n = 803 and n = 563) and Latinos (n = 1461). RNA sequencing data from 408 asthmatic patients and 405 control subjects were used to examine whether genotype was associated with gene expression. RESULTS One variant, rs3827907, was significantly associated with ICS-mediated changes in asthma control in the discovery set (P = 7.79 × 10-8) and was jointly associated with asthma exacerbations in 3 validation cohorts (P = .023, P = .029, and P = .041). RNA sequencing analysis found the rs3827907 C-allele to be associated with lower RNASE2 expression (P = 6.10 × 10-4). RNASE2 encodes eosinophil-derived neurotoxin, and the rs3827907 C-allele appeared to particularly influence ICS treatment response in the presence of eosinophilic inflammation (ie, high pretreatment eosinophil-derived neurotoxin levels or blood eosinophil counts). CONCLUSION We identified a variant, rs3827907, that appears to influence response to ICS treatment in multiple population groups and likely mediates its effect through eosinophils.
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12
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Seong KM, Coates BS, Sun W, Clark JM, Pittendrigh BR. Changes in Neuronal Signaling and Cell Stress Response Pathways are Associated with a Multigenic Response of Drosophila melanogaster to DDT Selection. Genome Biol Evol 2018; 9:3356-3372. [PMID: 29211847 PMCID: PMC5737697 DOI: 10.1093/gbe/evx252] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2017] [Indexed: 12/11/2022] Open
Abstract
The adaptation of insect populations to insecticidal control is a continual threat to human health and sustainable agricultural practices, but many complex genomic mechanisms involved in this adaption remain poorly understood. This study applied a systems approach to investigate the interconnections between structural and functional variance in response to dichlorodiphenyltrichloroethane (DDT) within the Drosophila melanogaster strain 91-R. Directional selection in 6 selective sweeps coincided with constitutive gene expression differences in DDT resistant flies, including the most highly upregulated transcript, Unc-115 b, which plays a central role in axon guidance, and the most highly downregulated transcript, the angiopoietin-like CG31832, which is involved in directing vascular branching and dendrite outgrowth but likely may be under trans-regulatory control. Direct functions and protein–protein interactions mediated by differentially expressed transcripts control changes in cell migration, signal transduction, and gene regulatory cascades that impact the nervous system. Although changes to cellular stress response pathways involve 8 different cytochrome P450s, stress response, and apoptosis is controlled by a multifacetted regulatory mechanism. These data demonstrate that DDT selection in 91-R may have resulted in genome-wide adaptations that impacts genetic and signal transduction pathways that converge to modify stress response, cell survival, and neurological functions. This study implicates the involvement of a multigenic mechanism in the adaptation to a chemical insecticide, which impact interconnected regulatory cascades. We propose that DDT selection within 91-R might act systemically, wherein pathway interactions function to reinforce the epistatic effects of individual adaptive changes on an additive or nonadditive basis.
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Affiliation(s)
- Keon Mook Seong
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA
| | - Brad S Coates
- Corn Insects & Crop Genetics Research Unit, USDA-ARS, Iowa State University, Ames, Iowa, USA
| | - Weilin Sun
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA
| | - John M Clark
- Department of Veterinary & Animal Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Barry R Pittendrigh
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA
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13
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Abstract
OBJECTIVES Glucocorticoids such as dexamethasone have pleiotropic effects, including desired antileukemic, anti-inflammatory, or immunosuppressive effects, and undesired metabolic or toxic effects. The most serious adverse effects of dexamethasone among patients with acute lymphoblastic leukemia are osteonecrosis and thrombosis. To identify inherited genomic variation involved in these severe adverse effects, we carried out genome-wide association studies (GWAS) by analyzing 14 pleiotropic glucocorticoid phenotypes in 391 patients with acute lymphoblastic leukemia. PATIENTS AND METHODS We used the Projection Onto the Most Interesting Statistical Evidence integrative analysis technique to identify genetic variants associated with pleiotropic dexamethasone phenotypes, stratifying for age, sex, race, and treatment, and compared the results with conventional single-phenotype GWAS. The phenotypes were osteonecrosis, central nervous system toxicity, hyperglycemia, hypokalemia, thrombosis, dexamethasone exposure, BMI, growth trajectory, and levels of cortisol, albumin, and asparaginase antibodies, and changes in cholesterol, triglycerides, and low-density lipoproteins after dexamethasone. RESULTS The integrative analysis identified more pleiotropic single nucleotide polymorphism variants (P=1.46×10(-215), and these variants were more likely to be in gene-regulatory regions (P=1.22×10(-6)) than traditional single-phenotype GWAS. The integrative analysis yielded genomic variants (rs2243057 and rs6453253) in F2RL1, a receptor that functions in hemostasis, thrombosis, and inflammation, which were associated with pleiotropic effects, including osteonecrosis and thrombosis, and were in regulatory gene regions. CONCLUSION The integrative pleiotropic analysis identified risk variants for osteonecrosis and thrombosis not identified by single-phenotype analysis that may have importance for patients with underlying sensitivity to multiple dexamethasone adverse effects.
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14
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Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Interactions between genetic variation and cellular environment in skeletal muscle gene expression. PLoS One 2018; 13:e0195788. [PMID: 29659628 PMCID: PMC5901994 DOI: 10.1371/journal.pone.0195788] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 03/29/2018] [Indexed: 12/18/2022] Open
Abstract
From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)—genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.
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Affiliation(s)
- D. Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - David A. Knowles
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea H. Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Brooke N. Wolford
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Li Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ricardo D’Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen C. J. Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Peter S. Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Michael R. Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Ryan P. Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leena Kinnunen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Jouko Saramies
- South Karelia Social and Health Care District, Lappeenranta, Finland
| | - Jouko Sundvall
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Timo A. Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Neurosciences and Preventive Medicine, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Dasman Diabetes Institute, Dasman, Kuwait
| | - Heikki A. Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine and Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Haartmaninkatu 4, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, Finland
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (EB); (FSC)
| | - Francis S. Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- * E-mail: (EB); (FSC)
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15
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Müller B, Boltze J, Czepezauer I, Hesse V, Wilcke A, Kirsten H. Dyslexia risk variant rs600753 is linked with dyslexia-specific differential allelic expression of DYX1C1. Genet Mol Biol 2018; 41:41-49. [PMID: 29473935 PMCID: PMC5901500 DOI: 10.1590/1678-4685-gmb-2017-0165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/28/2017] [Indexed: 11/22/2022] Open
Abstract
An increasing number of genetic variants involved in dyslexia development were
discovered during the last years, yet little is known about the molecular
functional mechanisms of these SNPs. In this study we investigated whether
dyslexia candidate SNPs have a direct, disease-specific effect on local
expression levels of the assumed target gene by using a differential allelic
expression assay. In total, 12 SNPs previously associated with dyslexia and
related phenotypes were suitable for analysis. Transcripts corresponding to four
SNPs were sufficiently expressed in 28 cell lines originating from controls and
a family affected by dyslexia. We observed a significant effect of rs600753 on
expression levels of DYX1C1 in forward and reverse sequencing
approaches. The expression level of the rs600753 risk allele was increased in
the respective seven cell lines from members of the dyslexia family which might
be due to a disturbed transcription factor binding sites. When considering our
results in the context of neuroanatomical dyslexia-specific findings, we
speculate that this mechanism may be part of the pathomechanisms underlying the
dyslexia-specific brain phenotype. Our results suggest that allele-specific
DYX1C1 expression levels depend on genetic variants of
rs600753 and contribute to dyslexia. However, these results are preliminary and
need replication.
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Affiliation(s)
- Bent Müller
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Johannes Boltze
- Fraunhofer Research Institution for Marine Biotechnology, Department of Medical Cell Technology, Lübeck, Germany.,Institute for Medical and Marine Biotechnology, University of Lübeck, Lübeck, Germany
| | - Ivonne Czepezauer
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Volker Hesse
- German Center for Growth, Development and Health Encouragement in Childhood and Adolescence, Berlin, Germany.,Charité-University Medicine Berlin, Institute for Experimental Paediatric Endocrinolgy, Berlin
| | | | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Holger Kirsten
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
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16
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Li XC, Fay JC. Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species. Genome Biol Evol 2018; 9:1120-1129. [PMID: 28431042 PMCID: PMC5554586 DOI: 10.1093/gbe/evx072] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2017] [Indexed: 12/19/2022] Open
Abstract
Gene regulation is a ubiquitous mechanism by which organisms respond to their environment. While organisms are often found to be adapted to the environments they experience, the role of gene regulation in environmental adaptation is not often known. In this study, we examine divergence in cis-regulatory effects between two Saccharomycesspecies, S. cerevisiaeand S. uvarum, that have substantially diverged in their thermal growth profile. We measured allele specific expression (ASE) in the species’ hybrid at three temperatures, the highest of which is lethal to S. uvarumbut not the hybrid or S. cerevisiae. We find that S. uvarumalleles can be expressed at the same level as S. cerevisiaealleles at high temperature and most cis-acting differences in gene expression are not dependent on temperature. While a small set of 136 genes show temperature-dependent ASE, we find no indication that signatures of directional cis-regulatory evolution are associated with temperature. Within promoter regions we find binding sites enriched upstream of temperature responsive genes, but only weak correlations between binding site and expression divergence. Our results indicate that temperature divergence between S. cerevisiaeand S. uvarumhas not caused widespread divergence in cis-regulatory activity, but point to a small subset of genes where the species’ alleles show differences in magnitude or opposite responses to temperature. The difficulty of explaining divergence in cis-regulatory sequences with models of transcription factor binding sites and nucleosome positioning highlights the importance of identifying mutations that underlie cis-regulatory divergence between species.
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Affiliation(s)
- Xueying C Li
- Molecular Genetics and Genomics Program, Division of Biological and Biomedical Sciences, Washington University, St. Louis, MO
| | - Justin C Fay
- Department of Genetics, Washington University, St. Louis, MO.,Center for Genome Sciences and System Biology, Washington University, St. Louis, MO
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17
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McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, Conti D, Gauderman WJ, Hsu L, Hutter CM, Jankowska MM, Kerr J, Kraft P, Montgomery SB, Mukherjee B, Papanicolaou GJ, Patel CJ, Ritchie MD, Ritz BR, Thomas DC, Wei P, Witte JS. Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. Am J Epidemiol 2017; 186:753-761. [PMID: 28978193 PMCID: PMC5860428 DOI: 10.1093/aje/kwx227] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 03/14/2017] [Accepted: 03/16/2017] [Indexed: 12/25/2022] Open
Abstract
Recently, many new approaches, study designs, and statistical and analytical methods have emerged for studying gene-environment interactions (G×Es) in large-scale studies of human populations. There are opportunities in this field, particularly with respect to the incorporation of -omics and next-generation sequencing data and continual improvement in measures of environmental exposures implicated in complex disease outcomes. In a workshop called "Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases," held October 17-18, 2014, by the National Institute of Environmental Health Sciences and the National Cancer Institute in conjunction with the annual American Society of Human Genetics meeting, participants explored new approaches and tools that have been developed in recent years for G×E discovery. This paper highlights current and critical issues and themes in G×E research that need additional consideration, including the improved data analytical methods, environmental exposure assessment, and incorporation of functional data and annotations.
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Affiliation(s)
| | - Leah E. Mechanic
- Correspondence to Dr. Leah E. Mechanic, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, 9609 Medical Center Drive, Room 4E104, MSC 9763, Bethesda, MD 20892 (e-mail: )
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18
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Munz M, Chen H, Jockel-Schneider Y, Adam K, Hoffman P, Berger K, Kocher T, Meyle J, Eickholz P, Doerfer C, Laudes M, Uitterlinden A, Lieb W, Franke A, Schreiber S, Offenbacher S, Divaris K, Bruckmann C, Loos BG, Jepsen S, Dommisch H, Schäefer AS. A haplotype block downstream of plasminogen is associated with chronic and aggressive periodontitis. J Clin Periodontol 2017; 44:962-970. [DOI: 10.1111/jcpe.12749] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Matthias Munz
- Department of Periodontology; Institute of Dental, Oral and Maxillary Medicine; Charité - University Medicine Berlin; Berlin Germany
- Institute for Integrative and Experimental Genomics; University Medical Center Schleswig-Holstein - Campus Lübeck; Lübeck Germany
| | - Hong Chen
- Department of Periodontology; Institute of Dental, Oral and Maxillary Medicine; Charité - University Medicine Berlin; Berlin Germany
- Department of Stomatology; Zhejiang Provincial People's Hospital; Hangzhou China
| | - Yvonne Jockel-Schneider
- Department of Periodontology; Clinic of Preventive Dentistry and Periodontology; University Medical Center of the Julius-Maximilians-University; Würzburg Germany
| | - Knut Adam
- Department of Conservative Dentistry, Periodontology and Preventive Dentistry; Hannover Medical School; Hannover Germany
| | - Per Hoffman
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Human Genomics Research Group; Department of Biomedicine; University Hospital of Basel; Basel Switzerland
| | - Klaus Berger
- Institute of Epidemiology and Social Medicine; University of Münster; Münster Germany
| | - Thomas Kocher
- Unit of Periodontology; Department of Restorative Dentistry, Periodontology, Endodontology, Preventive Dentistry and Pedodontics, Dental School; University Medicine Greifswald; Greifswald Germany
| | - Jörg Meyle
- Department of Periodontology; University Medical Center Giessen and Marburg; Gießen Germany
| | - Peter Eickholz
- Department of Periodontology, Centre for Dental, Oral Medicine (Carolinum); Johann Wolfgang Goethe-University; Frankfurt am Main Germany
| | - Christof Doerfer
- Department of Operative Dentistry and Periodontology; University Medical Center Schleswig-Holstein; Campus Kiel Germany
| | - Matthias Laudes
- Clinic of Internal Medicine I; University Clinic Schleswig-Holstein; Kiel Germany
| | | | - Wolfgang Lieb
- Institute of Epidemiology; Biobank PopGen; Christian-Albrechts-University; Kiel Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology; Christian-Albrechts-University; Kiel Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology; Christian-Albrechts-University; Kiel Germany
| | - Steven Offenbacher
- Department of Periodontology; UNC School of Dentistry; Chapel Hill NC USA
| | - Kimon Divaris
- Department of Pediatric Dentistry; UNC School of Dentistry; Chapel Hill NC USA
- Department of Epidemiology; UNC Gillings School of Global Public Health; Chapel Hill NC USA
| | - Corinna Bruckmann
- Department of Conservative Dentistry and Periodontology; University Clinic of Dentistry; Vienna Austria
| | - Bruno G. Loos
- Department of Periodontology and Oral Biochemistry; Academic Centre for Dentistry Amsterdam (ACTA); University of Amsterdam and VU University Amsterdam; Amsterdam The Netherlands
| | - Søeren Jepsen
- Department of Periodontology, Operative and Preventive Dentistry; Center of Dento-Maxillo-Facial Medicine Rheinische-Friedrich-Wilhelms-University Bonn; Bonn Germany
| | - Henrik Dommisch
- Department of Periodontology; Institute of Dental, Oral and Maxillary Medicine; Charité - University Medicine Berlin; Berlin Germany
| | - Arne S. Schäefer
- Department of Periodontology; Institute of Dental, Oral and Maxillary Medicine; Charité - University Medicine Berlin; Berlin Germany
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Quispe X, Tapia SM, Villarroel C, Oporto C, Abarca V, García V, Martínez C, Cubillos FA. Genetic basis of mycotoxin susceptibility differences between budding yeast isolates. Sci Rep 2017; 7:9173. [PMID: 28835621 PMCID: PMC5569051 DOI: 10.1038/s41598-017-09471-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/25/2017] [Indexed: 01/29/2023] Open
Abstract
Micophenolic acid (MPA) is an immunosuppressant mycotoxin which impairs yeast cell growth to variable degrees depending on the genetic background. Such variation could have emerged from several phenomena, including MPA gene resistance mutations and variations in copy number and localisation of resistance genes. To test this, we evaluated MPA susceptibility in four S. cerevisiae isolates and genetically dissected variation through the identification of Quantitative Trait Loci. Via linkage analysis we identified six QTLs, majority of which were located within subtelomeres and co-localised with IMD2, an inosine monophosphate dehydrogenase previously identified underlying MPA drug resistance in yeast cells. From chromosome end disruption and bioinformatics analysis, it was found that the subtelomere localisation of IMD2 within chromosome ends is variable depending on the strain, demonstrating the influence of IMD2 on the natural variation in yeast MPA susceptibility. Furthermore, GxE gene expression analysis of strains exhibiting opposite phenotypes indicated that ribosome biogenesis, RNA transport, and purine biosynthesis were impaired in strains most susceptible to MPA toxicity. Our results demonstrate that natural variation can be exploited to better understand the molecular mechanisms underlying mycotoxin susceptibility in eukaryote cells and demonstrate the role of subtelomeric regions in mediating interactions with the environment.
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Affiliation(s)
- Xtopher Quispe
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Sebastián M Tapia
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Carlos Villarroel
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Christian Oporto
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile
| | - Valentina Abarca
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Verónica García
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco A Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile. .,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla, 114-D, Santiago, Chile. .,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
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20
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Qiu W, Guo F, Glass K, Yuan GC, Quackenbush J, Zhou X, Tantisira KG. Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma. J Allergy Clin Immunol 2017; 141:1250-1258. [PMID: 28736268 DOI: 10.1016/j.jaci.2017.05.052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/02/2017] [Accepted: 05/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Variations in drug response between individuals have prevented us from achieving high drug efficacy in treating many complex diseases, including asthma. Genetics plays an important role in accounting for such interindividual variations in drug response. However, systematic approaches for addressing how genetic factors and their regulators determine variations in drug response in asthma treatment are lacking. OBJECTIVE We sought to identify key transcriptional regulators of corticosteroid response in asthma using a novel systems biology approach. METHODS We used Passing Attributes between Networks for Data Assimilations (PANDA) to construct the gene regulatory networks associated with good responders and poor responders to inhaled corticosteroids based on a subset of 145 white children with asthma who participated in the Childhood Asthma Management Cohort. PANDA uses gene expression profiles and published relationships among genes, transcription factors (TFs), and proteins to construct the directed networks of TFs and genes. We assessed the differential connectivity between the gene regulatory network of good responders versus that of poor responders. RESULTS When compared with poor responders, the network of good responders has differential connectivity and distinct ontologies (eg, proapoptosis enriched in network of good responders and antiapoptosis enriched in network of poor responders). Many of the key hubs identified in conjunction with clinical response are also cellular response hubs. Functional validation demonstrated abrogation of differences in corticosteroid-treated cell viability following siRNA knockdown of 2 TFs and differential downstream expression between good responders and poor responders. CONCLUSIONS We have identified and validated multiple TFs influencing asthma treatment response. Our results show that differential connectivity analysis can provide new insights into the heterogeneity of drug treatment effects.
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Affiliation(s)
- Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Feng Guo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Guo Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Mass; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Mass; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
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21
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Deming Y, Li Z, Kapoor M, Harari O, Del-Aguila JL, Black K, Carrell D, Cai Y, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Huang KL, Bertelsen S, Fagan AM, Holtzman DM, Morris JC, Kim S, Saykin AJ, De Jager PL, Albert M, Moghekar A, O'Brien R, Riemenschneider M, Petersen RC, Blennow K, Zetterberg H, Minthon L, Van Deerlin VM, Lee VMY, Shaw LM, Trojanowski JQ, Schellenberg G, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Peskind ER, Li G, Di Narzo AF, Kauwe JSK, Goate AM, Cruchaga C. Genome-wide association study identifies four novel loci associated with Alzheimer's endophenotypes and disease modifiers. Acta Neuropathol 2017; 133:839-856. [PMID: 28247064 PMCID: PMC5613285 DOI: 10.1007/s00401-017-1685-y] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/08/2017] [Accepted: 02/14/2017] [Indexed: 01/20/2023]
Abstract
More than 20 genetic loci have been associated with risk for Alzheimer's disease (AD), but reported genome-wide significant loci do not account for all the estimated heritability and provide little information about underlying biological mechanisms. Genetic studies using intermediate quantitative traits such as biomarkers, or endophenotypes, benefit from increased statistical power to identify variants that may not pass the stringent multiple test correction in case-control studies. Endophenotypes also contain additional information helpful for identifying variants and genes associated with other aspects of disease, such as rate of progression or onset, and provide context to interpret the results from genome-wide association studies (GWAS). We conducted GWAS of amyloid beta (Aβ42), tau, and phosphorylated tau (ptau181) levels in cerebrospinal fluid (CSF) from 3146 participants across nine studies to identify novel variants associated with AD. Five genome-wide significant loci (two novel) were associated with ptau181, including loci that have also been associated with AD risk or brain-related phenotypes. Two novel loci associated with Aβ42 near GLIS1 on 1p32.3 (β = -0.059, P = 2.08 × 10-8) and within SERPINB1 on 6p25 (β = -0.025, P = 1.72 × 10-8) were also associated with AD risk (GLIS1: OR = 1.105, P = 3.43 × 10-2), disease progression (GLIS1: β = 0.277, P = 1.92 × 10-2), and age at onset (SERPINB1: β = 0.043, P = 4.62 × 10-3). Bioinformatics indicate that the intronic SERPINB1 variant (rs316341) affects expression of SERPINB1 in various tissues, including the hippocampus, suggesting that SERPINB1 influences AD through an Aβ-associated mechanism. Analyses of known AD risk loci suggest CLU and FERMT2 may influence CSF Aβ42 (P = 0.001 and P = 0.009, respectively) and the INPP5D locus may affect ptau181 levels (P = 0.009); larger studies are necessary to verify these results. Together the findings from this study can be used to inform future AD studies.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Manav Kapoor
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - David Carrell
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Yefei Cai
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Shengmei Ma
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Benjamin Saef
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Bill Howells
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Kuan-Lin Huang
- Department of Medicine, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Sarah Bertelsen
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anne M Fagan
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Sungeun Kim
- Indiana Alzheimer Disease Center and Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Electrical and Computer Engineering, State University of New York, Oswego, NY, 13126, USA
| | - Andrew J Saykin
- Indiana Alzheimer Disease Center and Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Institute for the Neurosciences, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard University and M.I.T., Cambridge, MA, 02142, USA
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard O'Brien
- Department of Neurology, Duke Medical Center, Box 2900, Durham, NC, 27710, USA
| | | | | | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, University of Gothenburg, Mölndal, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Lennart Minthon
- Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Vivianna M Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia Man-Yee Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan L Haines
- Department of Molecular Physiology and Biophysics, Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
| | - Richard Mayeux
- Department of Neurology, Taub Institute on Alzheimer's Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, and Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Lindsay A Farrer
- Departments of Biostatistics, Medicine (Genetics Program), Ophthalmology, Epidemiology, and Neurology, Boston University, Boston, MA, USA
| | - Elaine R Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- VISN-20 Mental Illness Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Ge Li
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- VISN-20 Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Alison M Goate
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA.
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.
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Time-dependent genetic effects on gene expression implicate aging processes. Genome Res 2017; 27:545-552. [PMID: 28302734 PMCID: PMC5378173 DOI: 10.1101/gr.207688.116] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 01/23/2017] [Indexed: 01/04/2023]
Abstract
Gene expression is dependent on genetic and environmental factors. In the last decade, a large body of research has significantly improved our understanding of the genetic architecture of gene expression. However, it remains unclear whether genetic effects on gene expression remain stable over time. Here, we show, using longitudinal whole-blood gene expression data from a twin cohort, that the genetic architecture of a subset of genes is unstable over time. In addition, we identified 2213 genes differentially expressed across time points that we linked with aging within and across studies. Interestingly, we discovered that most differentially expressed genes were affected by a subset of 77 putative causal genes. Finally, we observed that putative causal genes and down-regulated genes were affected by a loss of genetic control between time points. Taken together, our data suggest that instability in the genetic architecture of a subset of genes could lead to widespread effects on the transcriptome with an aging signature.
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23
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Sabik OL, Farber CR. Using GWAS to identify novel therapeutic targets for osteoporosis. Transl Res 2017; 181:15-26. [PMID: 27837649 PMCID: PMC5357198 DOI: 10.1016/j.trsl.2016.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 12/14/2022]
Abstract
Osteoporosis is a common, increasingly prevalent, global health burden characterized by low bone mineral density (BMD) and increased risk of fracture. Despite its significant impact on human health, there is currently a lack of highly effective treatments free of side effects for osteoporosis. Therefore, a major goal in the field is to identify new drug targets. Genetic discovery has been shown to be effective in the unbiased identification of novel drug targets and genome-wide association studies (GWASs) have begun to provide insight into genetic basis of osteoporosis. Over the last decade, GWASs have led to the identification of ∼100 loci associated with BMD and other bone traits related to risk of fracture. However, there have been limited efforts to identify the causal genes underlying the GWAS loci or the mechanisms by which GWAS loci alter bone physiology. In this review, we summarize the current state of the field and discuss strategies for causal gene discovery and the evidence that the novel genes underlying GWAS loci are likely to be a new source of drug targets.
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Affiliation(s)
- Olivia L Sabik
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Va; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Va
| | - Charles R Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Va; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Va; Department of Public Health Science, School of Medicine, University of Virginia, Charlottesville, Va.
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24
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Hamdi Y, Soucy P, Kuchenbaeker KB, Pastinen T, Droit A, Lemaçon A, Adlard J, Aittomäki K, Andrulis IL, Arason A, Arnold N, Arun BK, Azzollini J, Bane A, Barjhoux L, Barrowdale D, Benitez J, Berthet P, Blok MJ, Bobolis K, Bonadona V, Bonanni B, Bradbury AR, Brewer C, Buecher B, Buys SS, Caligo MA, Chiquette J, Chung WK, Claes KBM, Daly MB, Damiola F, Davidson R, De la Hoya M, De Leeneer K, Diez O, Ding YC, Dolcetti R, Domchek SM, Dorfling CM, Eccles D, Eeles R, Einbeigi Z, Ejlertsen B, Engel C, Gareth Evans D, Feliubadalo L, Foretova L, Fostira F, Foulkes WD, Fountzilas G, Friedman E, Frost D, Ganschow P, Ganz PA, Garber J, Gayther SA, Gerdes AM, Glendon G, Godwin AK, Goldgar DE, Greene MH, Gronwald J, Hahnen E, Hamann U, Hansen TVO, Hart S, Hays JL, Hogervorst FBL, Hulick PJ, Imyanitov EN, Isaacs C, Izatt L, Jakubowska A, James P, Janavicius R, Jensen UB, John EM, Joseph V, Just W, Kaczmarek K, Karlan BY, Kets CM, Kirk J, Kriege M, Laitman Y, Laurent M, Lazaro C, Leslie G, Lester J, Lesueur F, Liljegren A, Loman N, Loud JT, Manoukian S, Mariani M, Mazoyer S, McGuffog L, Meijers-Heijboer HEJ, Meindl A, Miller A, Montagna M, Mulligan AM, Nathanson KL, Neuhausen SL, Nevanlinna H, Nussbaum RL, Olah E, Olopade OI, Ong KR, Oosterwijk JC, Osorio A, Papi L, Park SK, Pedersen IS, Peissel B, Segura PP, Peterlongo P, Phelan CM, Radice P, Rantala J, Rappaport-Fuerhauser C, Rennert G, Richardson A, Robson M, Rodriguez GC, Rookus MA, Schmutzler RK, Sevenet N, Shah PD, Singer CF, Slavin TP, Snape K, Sokolowska J, Sønderstrup IMH, Southey M, Spurdle AB, Stadler Z, Stoppa-Lyonnet D, Sukiennicki G, Sutter C, Tan Y, Tea MK, Teixeira MR, Teulé A, Teo SH, Terry MB, Thomassen M, Tihomirova L, Tischkowitz M, Tognazzo S, Toland AE, Tung N, van den Ouweland AMW, van der Luijt RB, van Engelen K, van Rensburg EJ, Varon-Mateeva R, Wappenschmidt B, Wijnen JT, Rebbeck T, Chenevix-Trench G, Offit K, Couch FJ, Nord S, Easton DF, Antoniou AC, Simard J. Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3. Breast Cancer Res Treat 2017; 161:117-134. [PMID: 27796716 PMCID: PMC5222911 DOI: 10.1007/s10549-016-4018-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/08/2016] [Indexed: 12/13/2022]
Abstract
PURPOSE Cis-acting regulatory SNPs resulting in differential allelic expression (DAE) may, in part, explain the underlying phenotypic variation associated with many complex diseases. To investigate whether common variants associated with DAE were involved in breast cancer susceptibility among BRCA1 and BRCA2 mutation carriers, a list of 175 genes was developed based of their involvement in cancer-related pathways. METHODS Using data from a genome-wide map of SNPs associated with allelic expression, we assessed the association of ~320 SNPs located in the vicinity of these genes with breast and ovarian cancer risks in 15,252 BRCA1 and 8211 BRCA2 mutation carriers ascertained from 54 studies participating in the Consortium of Investigators of Modifiers of BRCA1/2. RESULTS We identified a region on 11q22.3 that is significantly associated with breast cancer risk in BRCA1 mutation carriers (most significant SNP rs228595 p = 7 × 10-6). This association was absent in BRCA2 carriers (p = 0.57). The 11q22.3 region notably encompasses genes such as ACAT1, NPAT, and ATM. Expression quantitative trait loci associations were observed in both normal breast and tumors across this region, namely for ACAT1, ATM, and other genes. In silico analysis revealed some overlap between top risk-associated SNPs and relevant biological features in mammary cell data, which suggests potential functional significance. CONCLUSION We identified 11q22.3 as a new modifier locus in BRCA1 carriers. Replication in larger studies using estrogen receptor (ER)-negative or triple-negative (i.e., ER-, progesterone receptor-, and HER2-negative) cases could therefore be helpful to confirm the association of this locus with breast cancer risk.
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Affiliation(s)
- Yosr Hamdi
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, 2705 Laurier Boulevard, Quebec, QC, G1V 4G2, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, 2705 Laurier Boulevard, Quebec, QC, G1V 4G2, Canada
| | - Karoline B Kuchenbaeker
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1HH, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Arnaud Droit
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, 2705 Laurier Boulevard, Quebec, QC, G1V 4G2, Canada
| | - Audrey Lemaçon
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, 2705 Laurier Boulevard, Quebec, QC, G1V 4G2, Canada
| | - Julian Adlard
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, HUS, Meilahdentie 2, P.O. BOX 160, 00029, Helsinki, Finland
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Adalgeir Arason
- Department of Pathology hus 9, Landspitali-LSH v/Hringbraut, 101, Reykjavík, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavík, Iceland
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts University Kiel, Campus Kiel, 24105, Kiel, Germany
| | - Banu K Arun
- Department of Breast Medical Oncology and Clinical Cancer Genetics Program, University of Texas MD Anderson Cancer Center, 1515 Pressler Street CBP 5, Houston, TX, 77030, USA
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133, Milan, Italy
| | - Anita Bane
- Department of Pathology & Molecular Medicine, Juravinski Hospital and Cancer Centre, McMaster University, 711 Concession Street, Hamilton, ON, L8V 1C3, Canada
| | - Laure Barjhoux
- Bâtiment Cheney D, Centre Léon Bérard, 28 rue Laënnec, 69373, Lyon, France
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Javier Benitez
- Human Genetics Group, Spanish National Cancer Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), 28029, Madrid, Spain
- Human Genotyping (CEGEN) Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Pascaline Berthet
- Centre François Baclesse, 3 avenue Général Harris, 14076, Caen, France
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Kristie Bobolis
- City of Hope Clinical Cancer Genomics Community Research Network, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Valérie Bonadona
- Unité de Prévention et d'Epidémiologie Génétique, Centre Léon Bérard, 28 rue Laënnec, 69373, Lyon, France
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Via Ripamonti 435, 20141, Milan, Italy
| | - Angela R Bradbury
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Carole Brewer
- Department of Clinical Genetics, Royal Devon & Exeter Hospital, Exeter, EX1 2ED, UK
| | - Bruno Buecher
- Service de Génétique Oncologique, Institut Curie, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Maria A Caligo
- Section of Genetic Oncology, Department of Laboratory Medicine, University and University Hospital of Pisa, Pisa, Italy
| | - Jocelyne Chiquette
- Unité de recherche en santé des populations, Centre des maladies du sein Deschênes-Fabia, Hôpital du Saint-Sacrement, 1050 chemin Sainte-Foy, Quebec, QC, G1S 4L8, Canada
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, 1150 St. Nicholas Avenue, New York, NY, 10032, USA
| | - Kathleen B M Claes
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Mary B Daly
- Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Francesca Damiola
- Bâtiment Cheney D, Centre Léon Bérard, 28 rue Laënnec, 69373, Lyon, France
| | - Rosemarie Davidson
- Department of Clinical Genetics, South Glasgow University Hospitals, Glasgow, G51 4TF, UK
| | - Miguel De la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Martin Lagos s/n, Madrid, Spain
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Clinical and Molecular Genetics Area, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Riccardo Dolcetti
- Cancer Bioimmunotherapy Unit, Department of Medical Oncology, Centro di Riferimento Oncologico, IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) National Cancer Institute, Via Franco Gallini 2, 33081, Aviano, PN, Italy
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, Australia
| | - Susan M Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Cecilia M Dorfling
- Cancer Genetics Laboratory, Department of Genetics, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton, UK
| | - Ros Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Sutton, SM2 5NG, UK
| | - Zakaria Einbeigi
- Department of Oncology, Sahlgrenska University Hospital, 41345, Göteborg, Sweden
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107, Leipzig, Germany
- LIFE, Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - D Gareth Evans
- Genomic Medicine, Manchester Academic Health Sciences Centre, Institute of Human Development, Manchester University, Central Manchester University Hospitals, NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Lidia Feliubadalo
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Gran Via de l'Hospitalet, 199-203, L'Hospitalet, 08908, Barcelona, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653, Brno, Czech Republic
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, (INRASTES) Institute of Nuclear and Radiological Sciences and Technology, National Centre for Scientific Research "Demokritos", Patriarchou Gregoriou & Neapoleos str., Aghia Paraskevi Attikis, Athens, Greece
| | - William D Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, QC, Canada
| | - George Fountzilas
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki School of Medicine, Thessaloníki, Greece
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, 52621, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, 69978, Ramat Aviv, Israel
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Pamela Ganschow
- Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Patricia A Ganz
- UCLA Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Center, 650 Charles Young Drive South, Room A2-125 HS, Los Angeles, CA, 90095-6900, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Anne-Marie Gerdes
- Department of Clincial Genetics, Rigshospitalet, Blegdamsvej 9, 4062, Copenhagen, Denmark
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Boulevard, 4019 Wahl Hall East, MS 3040, Kansas City, Kansas, USA
| | - David E Goldgar
- Department of Dermatology, University of Utah School of Medicine, 30 North 1900 East, SOM 4B454, Salt Lake City, UT, 84132, USA
| | - Mark H Greene
- Clinical Genetics Branch, DCEG, NCI NIH, 9609 Medical Center Drive, Room 6E-454, Bethesda, MD, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Polabska 4, 70-115, Szczecin, Poland
| | - Eric Hahnen
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, 50931, Cologne, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100, Copenhagen, Denmark
| | - Steven Hart
- Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - John L Hays
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH, 43210, USA
- Comprehensive Cancer Center Arthur C. James Cancer Hospital and Richard J. Solove Research Institute Biomedical Research Tower, Room 588, 460 West 12th Avenue, Columbus, OH, 43210, USA
| | - Frans B L Hogervorst
- Family Cancer Clinic, Netherlands Cancer Institute, P.O. Box 90203, 1006 BE, Amsterdam, The Netherlands
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, University of Chicago Pritzker School of Medicine, 1000 Central Street, Suite 620, Evanston, IL, 60201, USA
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, 3800 Reservoir Road NW, Washington, DC, 20007, USA
| | - Louise Izatt
- Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, SE1 9RT, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Polabska 4, 70-115, Szczecin, Poland
| | - Paul James
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Ramunas Janavicius
- Hematology, Oncology and Transfusion Medicine Center, Department of Molecular and Regenerative Medicine, Vilnius University Hospital Santariskiu Clinics, Santariskiu st. 2, 08661, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Zygymantu st. 9, Vilnius, Lithuania
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21C, Århus N, Denmark
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, 2201 Walnut Avenue Suite 300, Fremont, CA, 94538, USA
- Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Vijai Joseph
- Clinical Genetics Research Laboratory, Department of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10044, USA
| | - Walter Just
- Institute of Human Genetics, University of Ulm, 89091, Ulm, Germany
| | - Katarzyna Kaczmarek
- Department of Genetics and Pathology, Pomeranian Medical University, Polabska 4, 70-115, Szczecin, Poland
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, 90048, USA
| | - Carolien M Kets
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Judy Kirk
- Westmead Hospital, Familial Cancer Service, Hawkebury Road, P.O. Box 533, Wentworthville, NSW, 2145, Australia
| | - Mieke Kriege
- Department of Medical Oncology, Family Cancer Clinic, Erasmus University Medical Center, P.O. Box 5201, 3008 AE, Rotterdam, The Netherlands
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, 52621, Ramat Gan, Israel
| | - Maïté Laurent
- Service de Génétique Oncologique, Institut Curie, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Gran Via de l'Hospitalet, 199-203, L'Hospitalet, 08908, Barcelona, Spain
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, 90048, USA
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer Team, INSERM U900, Institut Curie Mines ParisTech, PSL University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Annelie Liljegren
- Department of Oncology, Karolinska University Hospital, 17176, Stockholm, Sweden
| | - Niklas Loman
- Department of Oncology, Lund University Hospital, 22185, Lund, Sweden
| | - Jennifer T Loud
- Clinical Genetics Branch, DCEG, NCI NIH, 9609 Medical Center Drive, Room 6E-454, Bethesda, MD, USA
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133, Milan, Italy
| | - Milena Mariani
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133, Milan, Italy
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, INSERM U1028, CNRS UMR5292, University of Lyon, Lyon, France
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Hanne E J Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - Alfons Meindl
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts University Kiel, Campus Kiel, 24105, Kiel, Germany
| | - Austin Miller
- NRG Oncology Statistics and Data Management Center, Roswell Park Cancer Institute, Elm St & Carlton St, Buffalo, NY, 14263, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Via Gattamelata 64, 35128, Padua, Italy
| | - Anna Marie Mulligan
- Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and the Keenan Research Centre of the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Katherine L Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Biomedicum Helsinki, Haartmaninkatu 8, HUS, P.O. BOX 700, 00029, Helsinki, Finland
| | - Robert L Nussbaum
- Department of Medicine and Genetics, University of California, 513 Parnassus Ave., HSE 901E, San Francisco, CA, 94143-0794, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Olufunmilayo I Olopade
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, MC 2115, Chicago, IL, USA
| | - Kai-Ren Ong
- West Midlands Regional Genetics Service, Birmingham Women's Hospital Healthcare NHS Trust, Edgbaston, Birmingham, UK
| | - Jan C Oosterwijk
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB, Groningen, The Netherlands
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Laura Papi
- Unit of Medical Genetics, Department of Biomedical Experimental and Clinical Sciences, University of Florence, Viale Morgagni 50, 50134, Florence, Italy
| | - Sue Kyung Park
- Department of Preventive Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 110-799, Korea
| | - Inge Sokilde Pedersen
- Section of Molecular Diagnostics, Department of Biochemistry, Aalborg University Hospital, Reberbansgade 15, Ålborg, Denmark
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133, Milan, Italy
| | - Pedro Perez Segura
- Department of Oncology, Hospital Clinico San Carlos, IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Martin Lagos s/n, Madrid, Spain
| | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, c/o IFOM-IEO Campus, Via Adamello 16, 20139, Milan, Italy
| | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), c/o Amaedeolab via GA Amadeo 42, 20133, Milan, Italy
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, L5:03, 171 76, Stockholm, Sweden
| | | | - Gad Rennert
- Clalit National Israeli Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, 7 Michal St., 34362, Haifa, Israel
| | - Andrea Richardson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mark Robson
- Clinical Genetics, Services Department of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Gustavo C Rodriguez
- Division of Gynecologic Oncology, NorthShore University HealthSystem, University of Chicago, 2650 Ridge Avenue, Suite 1507, Walgreens, Evanston, IL, 60201, USA
| | - Matti A Rookus
- Department of Epidemiology, Netherlands Cancer Institute, P.O. Box 90203, 1006 BE, Amsterdam, The Netherlands
| | - Rita Katharina Schmutzler
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, 50931, Cologne, Germany
- Center for Hereditary Breast and Ovarian Cancer, Medical Faculty, University Hospital Cologne, 50931, Cologne, Germany
- Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Nicolas Sevenet
- Oncogénétique, Institut Bergonié, 229 cours de l'Argonne, 33076, Bordeaux, France
| | - Payal D Shah
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Christian F Singer
- Department of OB/GYN, Medical University of Vienna, Waehringer Guertel 18-20, A, 1090, Vienna, Austria
| | - Thomas P Slavin
- Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Katie Snape
- Medical Genetics Unit, St George's, University of London, London, SW17 0RE, UK
| | - Johanna Sokolowska
- Laboratoire de génétique médicale Nancy Université, Centre Hospitalier Régional et Universitaire, Rue du Morvan cedex 1, 54511, Vandoeuvre-les-Nancy, France
| | - Ida Marie Heeholm Sønderstrup
- Department of Pathology Region Zealand Section Slagelse, Slagelse Hospital, Ingemannsvej 18 Slagelse, Cpoenhagen, Denmark
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston Road, Brisbane, QLD, 4006, Australia
| | - Zsofia Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | | | - Grzegorz Sukiennicki
- Department of Genetics and Pathology, Pomeranian Medical University, Polabska 4, 70-115, Szczecin, Poland
| | - Christian Sutter
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Yen Tan
- Department of OB/GYN, Medical University of Vienna, Waehringer Guertel 18-20, A, 1090, Vienna, Austria
| | - Muy-Kheng Tea
- Department of OB/GYN, Medical University of Vienna, Waehringer Guertel 18-20, A, 1090, Vienna, Austria
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Alex Teulé
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Gran Via de l'Hospitalet, 199-203, L'Hospitalet, 08908, Barcelona, Spain
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 1 Jalan SS12/1A, 47500, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, University Malaya, 1 Jalan SS12/1A, 50603, Kuala Lumpur, Malaysia
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Sonder Boulevard 29, Odense C, Denmark
| | - Laima Tihomirova
- Latvian Biomedical Research and Study Centre, Ratsupites str 1, Riga, Latvia
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, QC, Canada
- Department of Medical Genetics Level 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Hills Road, Box 134, Cambridge, CB2 0QQ, UK
| | - Silvia Tognazzo
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Via Gattamelata 64, 35128, Padua, Italy
| | - Amanda Ewart Toland
- Division of Human Genetics, Departments of Internal Medicine and Cancer Biology and Genetics Comprehensive Cancer Center, The Ohio State University, 998 Biomedical Research Tower, Columbus, OH, 43210, USA
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA
| | - Ans M W van den Ouweland
- Department of Clinical Genetics, Family Cancer Clinic, Erasmus University Medical Center, 330 Brookline Avenue, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Rob B van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Klaartje van Engelen
- Department of Clinical Genetics, Academic Medical Center, P.O. Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Elizabeth J van Rensburg
- Cancer Genetics Laboratory, Department of Genetics, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa
| | - Raymonda Varon-Mateeva
- Institute of Human Genetics, Charite Berlin, Campus Virchov Klinikum, 13353, Berlin, Germany
| | - Barbara Wappenschmidt
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, 50931, Cologne, Germany
| | - Juul T Wijnen
- Department of Human Genetics & Department of Clinical Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Timothy Rebbeck
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Georgia Chenevix-Trench
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston Road, Brisbane, QLD, 4006, Australia
| | - Kenneth Offit
- Clinical Genetics Research Laboratory, Department of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10044, USA
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0372, Oslo, Norway
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, 2705 Laurier Boulevard, Quebec, QC, G1V 4G2, Canada.
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Moreno-Moral A, Pesce F, Behmoaras J, Petretto E. Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease. Methods Mol Biol 2017; 1488:337-362. [PMID: 27933533 DOI: 10.1007/978-1-4939-6427-7_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.
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Affiliation(s)
- Aida Moreno-Moral
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Francesco Pesce
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, Hammersmith Campus, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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miR-203 and miR-320 Regulate Bone Morphogenetic Protein-2-Induced Osteoblast Differentiation by Targeting Distal-Less Homeobox 5 (Dlx5). Genes (Basel) 2016; 8:genes8010004. [PMID: 28025541 PMCID: PMC5294999 DOI: 10.3390/genes8010004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/24/2016] [Accepted: 12/15/2016] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs (miRNAs) are a family of small, non-coding RNAs (17–24 nucleotides), which regulate gene expression either by the degradation of the target mRNAs or inhibiting the translation of genes. Recent studies have indicated that miRNA plays an important role in regulating osteoblast differentiation. In this study, we identified miR-203 and miR-320b as important miRNAs modulating osteoblast differentiation. We identified Dlx5 as potential common target by prediction algorithms and confirmed this by knock-down and over expression of the miRNAs and assessing Dlx5 at mRNA and protein levels and specificity was verified by luciferase reporter assays. We examined the effect of miR-203 and miR-320b on osteoblast differentiation by transfecting with pre- and anti-miRs. Over-expression of miR-203 and miR-320b inhibited osteoblast differentiation, whereas inhibition of miR-203 and miR-320b stimulated alkaline phosphatase activity and matrix mineralization. We show that miR-203 and miR-320b negatively regulate BMP-2-induced osteoblast differentiation by suppressing Dlx5, which in turn suppresses the downstream osteogenic master transcription factor Runx2 and Osx and together they suppress osteoblast differentiation. Taken together, we propose a role for miR-203 and miR-320b in modulating bone metabolism.
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Hamdi Y, Soucy P, Adoue V, Michailidou K, Canisius S, Lemaçon A, Droit A, Andrulis IL, Anton-Culver H, Arndt V, Baynes C, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borresen-Dale AL, Brand JS, Brauch H, Brenner H, Broeks A, Burwinkel B, Chang-Claude J, Couch FJ, Cox A, Cross SS, Czene K, Darabi H, Dennis J, Devilee P, Dörk T, Dos-Santos-Silva I, Eriksson M, Fasching PA, Figueroa J, Flyger H, García-Closas M, Giles GG, Goldberg MS, González-Neira A, Grenaker-Alnæs G, Guénel P, Haeberle L, Haiman CA, Hamann U, Hallberg E, Hooning MJ, Hopper JL, Jakubowska A, Jones M, Kabisch M, Kataja V, Lambrechts D, Marchand LL, Lindblom A, Lubinski J, Mannermaa A, Maranian M, Margolin S, Marme F, Milne RL, Neuhausen SL, Nevanlinna H, Neven P, Olswold C, Peto J, Plaseska-Karanfilska D, Pylkäs K, Radice P, Rudolph A, Sawyer EJ, Schmidt MK, Shu XO, Southey MC, Swerdlow A, Tollenaar RA, Tomlinson I, Torres D, Truong T, Vachon C, Van Den Ouweland AMW, Wang Q, Winqvist R, Investigators KC, Zheng W, Benitez J, Chenevix-Trench G, Dunning AM, Pharoah PDP, Kristensen V, Hall P, Easton DF, Pastinen T, Nord S, Simard J. Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21. Oncotarget 2016; 7:80140-80163. [PMID: 27792995 PMCID: PMC5340257 DOI: 10.18632/oncotarget.12818] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/13/2016] [Indexed: 12/02/2022] Open
Abstract
There are significant inter-individual differences in the levels of gene expression. Through modulation of gene expression, cis-acting variants represent an important source of phenotypic variation. Consequently, cis-regulatory SNPs associated with differential allelic expression are functional candidates for further investigation as disease-causing variants. To investigate whether common variants associated with differential allelic expression were involved in breast cancer susceptibility, a list of genes was established on the basis of their involvement in cancer related pathways and/or mechanisms. Thereafter, using data from a genome-wide map of allelic expression associated SNPs, 313 genetic variants were selected and their association with breast cancer risk was then evaluated in 46,451 breast cancer cases and 42,599 controls of European ancestry ascertained from 41 studies participating in the Breast Cancer Association Consortium. The associations were evaluated with overall breast cancer risk and with estrogen receptor negative and positive disease. One novel breast cancer susceptibility locus on 4q21 (rs11099601) was identified (OR = 1.05, P = 5.6x10-6). rs11099601 lies in a 135 kb linkage disequilibrium block containing several genes, including, HELQ, encoding the protein HEL308 a DNA dependant ATPase and DNA Helicase involved in DNA repair, MRPS18C encoding the Mitochondrial Ribosomal Protein S18C and FAM175A (ABRAXAS), encoding a BRCA1 BRCT domain-interacting protein involved in DNA damage response and double-strand break (DSB) repair. Expression QTL analysis in breast cancer tissue showed rs11099601 to be associated with HELQ (P = 8.28x10-14), MRPS18C (P = 1.94x10-27) and FAM175A (P = 3.83x10-3), explaining about 20%, 14% and 1%, respectively of the variance inexpression of these genes in breast carcinomas.
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Affiliation(s)
- Yosr Hamdi
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
| | - Véronique Adoue
- Institut National de la Santé et de la Recherche Médicale U1043, Toulouse, France
- Centre National de la Recherche Scientifique, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Sander Canisius
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Audrey Lemaçon
- Centre de Recherche du CHU de Québec – Université Laval, Faculté de Médecine, Département de Médecine Moléculaire, Université Laval, Quebec, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec – Université Laval, Faculté de Médecine, Département de Médecine Moléculaire, Université Laval, Quebec, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlevand Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Anne-Lise Borresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Judith S. Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - NBCS Collaborators
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
- Section of Oncology, Institute of Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
- Department of Breast-Endocrine Surgery, Akershus University Hospital, Lørenskog, Norway
- Department of Breast and Endocrine Surgery, Oslo University Hospital, Ullevål, Oslo, Norway
- Department of Research, Vestre Viken, Drammen, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- National Advisory Unit on Late Effects after Cancer Treatment, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Oncology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter A. Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | | | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Mark S. Goldberg
- Department of Medicine, McGill University, Montreal, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, Canada
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Grethe Grenaker-Alnæs
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, VilleJuif, France
| | - Lothar Haeberle
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Michael Jones
- Division of Genetics and Epidemiology, the Institute of Cancer Research, London, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Vesa Kataja
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Central Finland Hospital District, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Diether Lambrechts
- Vesalius Research Center, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | | | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mel Maranian
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Patrick Neven
- Multidisciplinary Breast Center, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dijana Plaseska-Karanfilska
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione Istituto Di Ricovero e Cura a Carattere, Scientifico, Istituto Nazionale Tumori, Milan, Italy
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Elinor J. Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology & Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rob A.E.M. Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, VilleJuif, France
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras, Valencia, Spain
| | | | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Vessela Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
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28
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Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23. Genome Biol 2016; 17:212. [PMID: 27799070 PMCID: PMC5088679 DOI: 10.1186/s13059-016-1078-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/05/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific assays in T and B cell lines, we provide compelling evidence that redefines causal genes at the 6q23 locus, one of the most important loci that confers autoimmunity risk. RESULTS Although the function of disease-associated non-coding single nucleotide polymorphisms (SNPs) at 6q23 is unknown, the association is generally assigned to TNFAIP3, the closest gene. However, the DNA fragment containing the associated SNPs interacts through chromatin looping not only with TNFAIP3, but also with IL20RA, located 680 kb upstream. The risk allele of the most likely causal SNP, rs6927172, is correlated with both a higher frequency of interactions and increased expression of IL20RA, along with a stronger binding of both the NFκB transcription factor and chromatin marks characteristic of active enhancers in T-cells. CONCLUSIONS Our results highlight the importance of gene assignment for translating GWAS findings into biologically meaningful mechanisms of disease and potential therapeutic targets; indeed, monoclonal antibody therapy targeting IL-20 is effective in the treatment of rheumatoid arthritis and psoriasis, both with strong GWAS associations to this region.
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Moyerbrailean GA, Richards AL, Kurtz D, Kalita CA, Davis GO, Harvey CT, Alazizi A, Watza D, Sorokin Y, Hauff N, Zhou X, Wen X, Pique-Regi R, Luca F. High-throughput allele-specific expression across 250 environmental conditions. Genome Res 2016; 26:1627-1638. [PMID: 27934696 PMCID: PMC5131815 DOI: 10.1101/gr.209759.116] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/13/2016] [Indexed: 11/24/2022]
Abstract
Gene-by-environment (GxE) interactions determine common disease risk factors and biomedically relevant complex traits. However, quantifying how the environment modulates genetic effects on human quantitative phenotypes presents unique challenges. Environmental covariates are complex and difficult to measure and control at the organismal level, as found in GWAS and epidemiological studies. An alternative approach focuses on the cellular environment using in vitro treatments as a proxy for the organismal environment. These cellular environments simplify the organism-level environmental exposures to provide a tractable influence on subcellular phenotypes, such as gene expression. Expression quantitative trait loci (eQTL) mapping studies identified GxE interactions in response to drug treatment and pathogen exposure. However, eQTL mapping approaches are infeasible for large-scale analysis of multiple cellular environments. Recently, allele-specific expression (ASE) analysis emerged as a powerful tool to identify GxE interactions in gene expression patterns by exploiting naturally occurring environmental exposures. Here we characterized genetic effects on the transcriptional response to 50 treatments in five cell types. We discovered 1455 genes with ASE (FDR < 10%) and 215 genes with GxE interactions. We demonstrated a major role for GxE interactions in complex traits. Genes with a transcriptional response to environmental perturbations showed sevenfold higher odds of being found in GWAS. Additionally, 105 genes that indicated GxE interactions (49%) were identified by GWAS as associated with complex traits. Examples include GIPR–caffeine interaction and obesity and include LAMP3–selenium interaction and Parkinson disease. Our results demonstrate that comprehensive catalogs of GxE interactions are indispensable to thoroughly annotate genes and bridge epidemiological and genome-wide association studies.
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Affiliation(s)
- Gregory A Moyerbrailean
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Allison L Richards
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Daniel Kurtz
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Gordon O Davis
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Chris T Harvey
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Donovan Watza
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Yoram Sorokin
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Nancy Hauff
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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Horikoshi M, Beaumont RN, Day FR, Warrington NM, Kooijman MN, Fernandez-Tajes J, Feenstra B, van Zuydam NR, Gaulton KJ, Grarup N, Bradfield JP, Strachan DP, Li-Gao R, Ahluwalia TS, Kreiner E, Rueedi R, Lyytikäinen LP, Cousminer DL, Wu Y, Thiering E, Wang CA, Have CT, Hottenga JJ, Vilor-Tejedor N, Joshi PK, Boh ETH, Ntalla I, Pitkänen N, Mahajan A, van Leeuwen EM, Joro R, Lagou V, Nodzenski M, Diver LA, Zondervan KT, Bustamante M, Marques-Vidal P, Mercader JM, Bennett AJ, Rahmioglu N, Nyholt DR, Ma RCW, Tam CHT, Tam WH, Ganesh SK, van Rooij FJ, Jones SE, Loh PR, Ruth KS, Tuke MA, Tyrrell J, Wood AR, Yaghootkar H, Scholtens DM, Paternoster L, Prokopenko I, Kovacs P, Atalay M, Willems SM, Panoutsopoulou K, Wang X, Carstensen L, Geller F, Schraut KE, Murcia M, van Beijsterveldt CE, Willemsen G, Appel EVR, Fonvig CE, Trier C, Tiesler CM, Standl M, Kutalik Z, Bonas-Guarch S, Hougaard DM, Sánchez F, Torrents D, Waage J, Hollegaard MV, de Haan HG, Rosendaal FR, Medina-Gomez C, Ring SM, Hemani G, McMahon G, Robertson NR, Groves CJ, Langenberg C, Luan J, Scott RA, Zhao JH, Mentch FD, MacKenzie SM, Reynolds RM, Lowe WL, Tönjes A, Stumvoll M, Lindi V, Lakka TA, van Duijn CM, Kiess W, Körner A, Sørensen TI, Niinikoski H, Pahkala K, Raitakari OT, Zeggini E, Dedoussis GV, Teo YY, Saw SM, Melbye M, Campbell H, Wilson JF, Vrijheid M, de Geus EJ, Boomsma DI, Kadarmideen HN, Holm JC, Hansen T, Sebert S, Hattersley AT, Beilin LJ, Newnham JP, Pennell CE, Heinrich J, Adair LS, Borja JB, Mohlke KL, Eriksson JG, Widén EE, Kähönen M, Viikari JS, Lehtimäki T, Vollenweider P, Bønnelykke K, Bisgaard H, Mook-Kanamori DO, Hofman A, Rivadeneira F, Uitterlinden AG, Pisinger C, Pedersen O, Power C, Hyppönen E, Wareham NJ, Hakonarson H, Davies E, Walker BR, Jaddoe VW, Jarvelin MR, Grant SF, Vaag AA, Lawlor DA, Frayling TM, Davey Smith G, Morris AP, Ong KK, Felix JF, Timpson NJ, Perry JR, Evans DM, McCarthy MI, Freathy RM. Genome-wide associations for birth weight and correlations with adult disease. Nature 2016; 538:248-252. [PMID: 27680694 PMCID: PMC5164934 DOI: 10.1038/nature19806] [Citation(s) in RCA: 325] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 09/02/2016] [Indexed: 12/12/2022]
Abstract
Birth weight (BW) has been shown to be influenced by both fetal and maternal factors and in observational studies is reproducibly associated with future risk of adult metabolic diseases including type 2 diabetes (T2D) and cardiovascular disease. These life-course associations have often been attributed to the impact of an adverse early life environment. Here, we performed a multi-ancestry genome-wide association study (GWAS) meta-analysis of BW in 153,781 individuals, identifying 60 loci where fetal genotype was associated with BW (P < 5 × 10-8). Overall, approximately 15% of variance in BW was captured by assays of fetal genetic variation. Using genetic association alone, we found strong inverse genetic correlations between BW and systolic blood pressure (Rg = -0.22, P = 5.5 × 10-13), T2D (Rg = -0.27, P = 1.1 × 10-6) and coronary artery disease (Rg = -0.30, P = 6.5 × 10-9). In addition, using large -cohort datasets, we demonstrated that genetic factors were the major contributor to the negative covariance between BW and future cardiometabolic risk. Pathway analyses indicated that the protein products of genes within BW-associated regions were enriched for diverse processes including insulin signalling, glucose homeostasis, glycogen biosynthesis and chromatin remodelling. There was also enrichment of associations with BW in known imprinted regions (P = 1.9 × 10-4). We demonstrate that life-course associations between early growth phenotypes and adult cardiometabolic disease are in part the result of shared genetic effects and identify some of the pathways through which these causal genetic effects are mediated.
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Affiliation(s)
- Momoko Horikoshi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Felix R Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Nicole M Warrington
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
- School of Women's and Infants' Health, The University of Western Australia, Perth, Australia
| | - Marjolein N Kooijman
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | | | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
| | - Natalie R van Zuydam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Kyle J Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David P Strachan
- Population Health Research Institute, St George's University of London, London, Cranmer Terrace, UK
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tarunveer S Ahluwalia
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center, Gentofte, Denmark
| | - Eskil Kreiner
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Rico Rueedi
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Diana L Cousminer
- Institute for Molecular Medicine, Finland (FIMM), University of Helsinki, Helsinki, Finland
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Elisabeth Thiering
- Institute of Epidemiology I, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Carol A Wang
- School of Women's and Infants' Health, The University of Western Australia, Perth, Australia
| | - Christian T Have
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jouke-Jan Hottenga
- Netherlands Twin Register, Department of Biological Psychology, VU University, Amsterdam, the Netherlands
| | - Natalia Vilor-Tejedor
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | - Peter K Joshi
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK
| | - Eileen Tai Hui Boh
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Niina Pitkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Elisabeth M van Leeuwen
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Raimo Joro
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
| | - Vasiliki Lagou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- KUL - University of Leuven, Department of Neurosciences, Leuven, Belgium
- Translational Immunology Laboratory, VIB, Leuven, Belgium
| | - Michael Nodzenski
- Department of Preventive Medicine, Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Louise A Diver
- Institute of Cardiovascular & Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Krina T Zondervan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology, University of Oxford, Oxford, UK
| | - Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
- Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Pedro Marques-Vidal
- Department of Internal Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Josep M Mercader
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Nilufer Rahmioglu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dale R Nyholt
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - Ronald Ching Wan Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Claudia Ha Ting Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong, China
| | - Wing Hung Tam
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, Hong Kong, China
| | - Santhi K Ganesh
- Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank Ja van Rooij
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Samuel E Jones
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Po-Ru Loh
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Katherine S Ruth
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Marcus A Tuke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
- European Centre for Environment and Human Health, University of Exeter, Truro, UK
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Denise M Scholtens
- Department of Preventive Medicine, Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK
| | - Peter Kovacs
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Mustafa Atalay
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
| | - Sara M Willems
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | | | - Xu Wang
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | - Lisbeth Carstensen
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
| | - Katharina E Schraut
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mario Murcia
- CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
- FISABIO-Universitat Jaume I-Universitat de València, Joint Research Unit of Epidemiology and Environmental Health, Valencia, Spain
| | | | - Gonneke Willemsen
- Netherlands Twin Register, Department of Biological Psychology, VU University, Amsterdam, the Netherlands
| | - Emil V R Appel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cilius E Fonvig
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children's Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
| | - Caecilie Trier
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children's Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
| | - Carla Mt Tiesler
- Institute of Epidemiology I, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Marie Standl
- Institute of Epidemiology I, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sílvia Bonas-Guarch
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - David M Hougaard
- Danish Center for Neonatal Screening, Statens Serum Institute, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Friman Sánchez
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
- Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - David Torrents
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Johannes Waage
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Mads V Hollegaard
- Danish Center for Neonatal Screening, Statens Serum Institute, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Hugoline G de Haan
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Susan M Ring
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - George McMahon
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Neil R Robertson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Christopher J Groves
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Scott M MacKenzie
- Institute of Cardiovascular & Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Rebecca M Reynolds
- BHF Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, Scotland, UK
| | - William L Lowe
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Anke Tönjes
- Medical Department, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Medical Department, University of Leipzig, Leipzig, Germany
| | - Virpi Lindi
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
| | - Timo A Lakka
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Wieland Kiess
- Pediatric Research Center, Department of Women´s & Child Health, University of Leipzig, Leipzig, Germany
| | - Antje Körner
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Pediatric Research Center, Department of Women´s & Child Health, University of Leipzig, Leipzig, Germany
| | - Thorkild Ia Sørensen
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research and Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Harri Niinikoski
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Department of Physiology, University of Turku, Turku, Finland
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Paavo Nurmi Centre, Sports and Exercise Medicine Unit, Department of Physical Activity and Health, Turku, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | | | - George V Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
- Department of Medicine, Stanford School of Medicine, Stanford, California, USA
| | - Harry Campbell
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK
| | - James F Wilson
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Martine Vrijheid
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | - Eco Jcn de Geus
- Netherlands Twin Register, Department of Biological Psychology, VU University, Amsterdam, the Netherlands
- EMGO Institute for Health and Care Research, VU University and VU University Medical Center, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, VU University, Amsterdam, the Netherlands
| | - Haja N Kadarmideen
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens-Christian Holm
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children's Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Finland
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Lawrence J Beilin
- School of Medicine and Pharmacology, Royal Perth Hospital Unit, The University of Western Australia, Perth, Australia
| | - John P Newnham
- School of Women's and Infants' Health, The University of Western Australia, Perth, Australia
| | - Craig E Pennell
- School of Women's and Infants' Health, The University of Western Australia, Perth, Australia
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Inner City Clinic, University Hospital Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Linda S Adair
- Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Judith B Borja
- USC-Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
- Department of Nutrition and Dietetics, University of San Carlos, Cebu City, Philippines
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Johan G Eriksson
- National Institute for Health and Welfare, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Elisabeth E Widén
- Institute for Molecular Medicine, Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hopital, Tampere, Finland
- Department of Clinical Physiology, University of Tampere School of Medicine, Tampere, Finland
| | - Jorma S Viikari
- Division of Medicine, Turku University Hospital, Turku, Finland
- Department of Medicine, University of Turku, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Peter Vollenweider
- Department of Internal Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
- Epidemiology Section, BESC Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Albert Hofman
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - André G Uitterlinden
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Charlotta Pisinger
- Research Center for Prevention and Health Capital Region, Center for Sundhed, Rigshospitalet - Glostrup, Copenhagen University, Glostrup, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christine Power
- Population, Policy and Practice, UCL Institute of Child Health, University College London, London, UK
| | - Elina Hyppönen
- Population, Policy and Practice, UCL Institute of Child Health, University College London, London, UK
- Centre for Population Health Research, School of Health Sciences, and Sansom Institute, University of South Australia, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eleanor Davies
- Institute of Cardiovascular & Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Brian R Walker
- BHF Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, Scotland, UK
| | - Vincent Wv Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Struan Fa Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Allan A Vaag
- Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Debbie A Lawlor
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Ken K Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Nicholas J Timpson
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - John Rb Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - David M Evans
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
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Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Brümmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. eLife 2016; 5. [PMID: 27623010 PMCID: PMC5053804 DOI: 10.7554/elife.15614] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 09/12/2016] [Indexed: 12/19/2022] Open
Abstract
Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals both local and trans expression Quantitative Trait Loci (eQTLs) demonstrating 2 trans eQTL 'hotspots' associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provide a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation. DOI:http://dx.doi.org/10.7554/eLife.15614.001 Metabolism is a term that describes all the chemical reactions that are involved in keeping a living organism alive. Diseases related to metabolism – such as obesity, heart disease and diabetes – are a major health problem in the Western world. The causes of these diseases are complex and include both environmental factors, such as diet and exercise, and genetics. Indeed, many genetic variants that contribute to obesity have been uncovered in both humans and mice. However, it is only dimly understood how these genetic variants affect the underlying networks of interacting genes that cause metabolic disorders. Measuring gene activity or expression, and tracing how genetic instructions are carried from DNA into RNA and proteins, can reliably identify groups of genes that correlate with metabolic traits in specific organs. This strategy was successfully used in previous studies to reveal new information about abnormalities linked to obesity in specific tissues such as the liver and fat tissues. It was also shown that this approach might suggest new molecules that could be targeted to treat metabolic disorders. A brain region called the hypothalamus is key to the control of metabolism, including feeding behavior and obesity. Hasin-Brumshtein et al. set out to explore gene expression in the hypothalamus of 99 different strains of mice, in the hope that the data will help identify new connections between gene expression and metabolism. This approach showed that thousands of new and known genes are expressed in the mouse hypothalamus, some of which coded for proteins, and some of which did not. Hasin-Brumshtein et al. uncovered two genetic variants that controlled the expression of hundreds of other genes. Further analysis then revealed thousands of genetic variants that regulated the expression of, and type of RNA (so-called "spliceforms") produced from neighboring genes. Also, the expression of many individual genes showed significant similarities with about 150 metabolic measurements that had been evaluated previously in the mice. This new dataset is a unique resource that can be coupled with different approaches to test existing ideas and develop new ones about the role of particular genes or genetic mechanisms in obesity. Future studies will likely focus on new genes that show strong associations with attributes that are relevant to metabolic disorders, such as insulin levels, weight and fat mass. DOI:http://dx.doi.org/10.7554/eLife.15614.002
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Affiliation(s)
- Yehudit Hasin-Brumshtein
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Department of Microbiology, University of California, Los Angeles, Los Angeles, United states.,Department of Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Arshad H Khan
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, United States
| | - Farhad Hormozdiari
- Department of Computer Science, University of California, Los Angeles, Los Angeles, United States
| | - Calvin Pan
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Brian W Parks
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Department of Microbiology, University of California, Los Angeles, Los Angeles, United states.,Department of Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
| | - Anneke Brümmer
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, United States
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
| | - Aldons J Lusis
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Department of Microbiology, University of California, Los Angeles, Los Angeles, United states.,Department of Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Desmond J Smith
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, United States
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Laxman N, Rubin CJ, Mallmin H, Nilsson O, Tellgren-Roth C, Kindmark A. Second generation sequencing of microRNA in Human Bone Cells treated with Parathyroid Hormone or Dexamethasone. Bone 2016; 84:181-188. [PMID: 26748295 DOI: 10.1016/j.bone.2015.12.053] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/21/2015] [Accepted: 12/27/2015] [Indexed: 01/21/2023]
Abstract
We investigated the impact of treatment with parathyroid hormone (PTH) and dexamethasone (DEX) for 2 and 24h by RNA sequencing of miRNAs in primary human bone (HOB) cells. A total of 207 million reads were obtained, and normalized absolute expression retrieved for 373 most abundant miRNAs. In naïve control cells, 7 miRNAs were differentially expressed (FDR<0.05) between the two time points. Ten miRNAs exhibited differential expression (FDR <0.05) across two time points and treatments after adjusting for expression in controls and were selected for downstream analyses. Results show significant effects on miRNA expression when comparing PTH with DEX at 2h with even more pronounced effects at 24h. Interestingly, several miRNAs exhibiting differences in expression are predicted to target genes involved in bone metabolism e.g. miR-30c2, miR-203 and miR-205 targeting RUNX2, and miR-320 targeting β-catenin (CTNNB1) mRNA expression. CTNNB1and RUNX2 levels were decreased after DEX treatment and increased after PTH treatment. Our analysis also identified 2 putative novel miRNAs in PTH and DEX treated cells at 24h. RNA sequencing showed that PTH and DEX treatment affect miRNA expression in HOB cells and that regulated miRNAs in turn are correlated with expression levels of key genes involved in bone metabolism.
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Affiliation(s)
- Navya Laxman
- Department of Medical Sciences, Uppsala University, Uppsala, 75185, Sweden; Science for Life Laboratory, Department of Medical Sciences, Uppsala University Hospital, SE-75185, Uppsala, Sweden.
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 75185, Sweden
| | - Hans Mallmin
- Department of Surgical Sciences, Uppsala University, Uppsala, 75185, Sweden
| | - Olle Nilsson
- Department of Surgical Sciences, Uppsala University, Uppsala, 75185, Sweden
| | - Christian Tellgren-Roth
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75185, Sweden
| | - Andreas Kindmark
- Department of Medical Sciences, Uppsala University, Uppsala, 75185, Sweden; Science for Life Laboratory, Department of Medical Sciences, Uppsala University Hospital, SE-75185, Uppsala, Sweden
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Ward LD, Kellis M. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res 2015; 44:D877-81. [PMID: 26657631 PMCID: PMC4702929 DOI: 10.1093/nar/gkv1340] [Citation(s) in RCA: 698] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/16/2015] [Indexed: 12/21/2022] Open
Abstract
More than 90% of common variants associated with complex traits do not affect proteins directly, but instead the circuits that control gene expression. This has increased the urgency of understanding the regulatory genome as a key component for translating genetic results into mechanistic insights and ultimately therapeutics. To address this challenge, we developed HaploReg (http://compbio.mit.edu/HaploReg) to aid the functional dissection of genome-wide association study (GWAS) results, the prediction of putative causal variants in haplotype blocks, the prediction of likely cell types of action, and the prediction of candidate target genes by systematic mining of comparative, epigenomic and regulatory annotations. Since first launching the website in 2011, we have greatly expanded HaploReg, increasing the number of chromatin state maps to 127 reference epigenomes from ENCODE 2012 and Roadmap Epigenomics, incorporating regulator binding data, expanding regulatory motif disruption annotations, and integrating expression quantitative trait locus (eQTL) variants and their tissue-specific target genes from GTEx, Geuvadis, and other recent studies. We present these updates as HaploReg v4, and illustrate a use case of HaploReg for attention deficit hyperactivity disorder (ADHD)-associated SNPs with putative brain regulatory mechanisms.
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Affiliation(s)
- Lucas D Ward
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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Park HW, Ge B, Tse S, Grundberg E, Pastinen T, Kelly HW, Tantisira KG. Genetic risk factors for decreased bone mineral accretion in children with asthma receiving multiple oral corticosteroid bursts. J Allergy Clin Immunol 2015; 136:1240-6.e1-8. [PMID: 26025128 PMCID: PMC4641004 DOI: 10.1016/j.jaci.2015.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND Long-term intermittent oral corticosteroid (OCS) use in children with asthma leads to significant decreases in bone mineral accretion (BMA). OBJECTIVE We aimed to identify genetic factors influencing OCS dose effects on BMA in children with asthma. METHODS We first performed a gene-by-OCS interaction genome-wide association study (GWAS) of BMA in 489 white participants in the Childhood Asthma Management Program trial who took short-term oral prednisone bursts when they experienced acute asthma exacerbations. We selected the top-ranked 2000 single nucleotide polymorphisms (SNPs) in the GWAS and determined whether these SNPs also had cis-regulatory effects on dexamethasone-induced gene expression in osteoblasts. RESULTS We identified 2 SNPs (rs9896933 and rs2074439) associated with decreased BMA and related to the tubulin γ pathway. The rs9896933 variant met the criteria for genome-wide significance (P = 3.15 × 10(-8) in the GWAS) and is located on the intron of tubulin folding cofactor D (TBCD) gene. The rs2074439 variant (P = 2.74 × 10(-4) in the GWAS) showed strong cis-regulatory effects on dexamethasone-induced tubulin γ gene expression in osteoblasts (P = 8.64 × 10(-4)). Interestingly, we found that BMA worsened with increasing prednisone dose as the number of mutant alleles of the 2 SNPs increased. CONCLUSIONS We have identified 2 novel tubulin γ pathway SNPs, rs9896933 and rs2074439, showing independent interactive effects with cumulative corticosteroid dose on BMA in children with asthma receiving multiple OCS bursts.
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Affiliation(s)
- Heung-Woo Park
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Bing Ge
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Szeman Tse
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Pediatrics, Sainte-Justine University Health Center, University of Montreal, Montreal, Quebec, Canada
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Department of Medical Genetics, McGill University, Montreal, Quebec, Canada
| | - H William Kelly
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
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Abstract
There is evidence that genetic factors are implicated in the observed differences in therapeutic responses to the common classes of asthma therapy such as β2-agonists, corticosteroids, and leukotriene modifiers. Pharmacogenomics explores the roles of genetic variation in drug response and continues to be a field of great interest in asthma therapy. Prior studies have focused on candidate genes and recently emphasized genome-wide association analyses. Newer integrative omics and system-level approaches have recently revealed novel understanding of drug response pathways. However, the current known genetic loci only account for a fraction of variability in drug response and ongoing research is needed. While the field of asthma pharmacogenomics is not yet fully translatable to clinical practice, ongoing research should hopefully achieve this goal in the near future buttressed by the recent precision medicine efforts in the USA and worldwide.
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Maranville JC, Di Rienzo A. Combining genetic and nongenetic biomarkers to realize the promise of pharmacogenomics for inflammatory diseases. Pharmacogenomics 2015; 15:1931-40. [PMID: 25495413 DOI: 10.2217/pgs.14.129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many drugs used to treat inflammatory diseases are ineffective in a substantial proportion of patients. Identifying patients that are likely to respond to specific therapies would facilitate personalized treatment strategies that could improve outcomes while reducing costs and risks of adverse events. Despite these clear benefits, there are limited examples of predictive biomarkers of drug efficacy currently implemented into clinical practice for inflammatory diseases. We review efforts to identify genetic and nongenetic biomarkers of drug response in these diseases and consider potential benefits from combining multiple sources of biological data into multifeature predictive models.
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Affiliation(s)
- Joseph C Maranville
- Committee on Clinical Pharmacology & Pharmacogenomics, The University of Chicago, Chicago, IL, USA
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Laxman N, Rubin CJ, Mallmin H, Nilsson O, Pastinen T, Grundberg E, Kindmark A. Global miRNA expression and correlation with mRNA levels in primary human bone cells. RNA (NEW YORK, N.Y.) 2015; 21:1433-1443. [PMID: 26078267 PMCID: PMC4509933 DOI: 10.1261/rna.049148.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators that have recently introduced an additional level of intricacy to our understanding of gene regulation. The aim of this study was to investigate miRNA-mRNA interactions that may be relevant for bone metabolism by assessing correlations and interindividual variability in miRNA levels as well as global correlations between miRNA and mRNA levels in a large cohort of primary human osteoblasts (HOBs) obtained during orthopedic surgery in otherwise healthy individuals. We identified differential expression (DE) of 24 miRNAs, and found 9 miRNAs exhibiting DE between males and females. We identified hsa-miR-29b, hsa-miR-30c2, and hsa-miR-125b and their target genes as important modulators of bone metabolism. Further, we used an integrated analysis of global miRNA-mRNA correlations, mRNA-expression profiling, DE, bioinformatics analysis, and functional studies to identify novel target genes for miRNAs with the potential to regulate osteoblast differentiation and extracellular matrix production. Functional studies by overexpression and knockdown of miRNAs showed that, the differentially expressed miRNAs hsa-miR-29b, hsa-miR-30c2, and hsa-miR-125b target genes highly relevant to bone metabolism, e.g., collagen, type I, α1 (COL1A1), osteonectin (SPARC), Runt-related transcription factor 2 (RUNX2), osteocalcin (BGLAP), and frizzled-related protein (FRZB). These miRNAs orchestrate the activities of key regulators of osteoblast differentiation and extracellular matrix proteins by their convergent action on target genes and pathways to control the skeletal gene expression.
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Affiliation(s)
- Navya Laxman
- Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden Science for Life Laboratory, Department of Medical Sciences, Uppsala University Hospital, SE-75185 Uppsala, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75185 Uppsala, Sweden
| | - Hans Mallmin
- Department of Surgical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
| | - Olle Nilsson
- Department of Surgical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 1B1 Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada H3A 0G1
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 1B1 Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada H3A 0G1
| | - Andreas Kindmark
- Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden Science for Life Laboratory, Department of Medical Sciences, Uppsala University Hospital, SE-75185 Uppsala, Sweden
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38
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Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015; 16:197-212. [DOI: 10.1038/nrg3891] [Citation(s) in RCA: 684] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Harvey CT, Moyerbrailean GA, Davis GO, Wen X, Luca F, Pique-Regi R. QuASAR: quantitative allele-specific analysis of reads. ACTA ACUST UNITED AC 2014; 31:1235-42. [PMID: 25480375 DOI: 10.1093/bioinformatics/btu802] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 11/26/2014] [Indexed: 12/30/2022]
Abstract
MOTIVATION Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. RESULTS We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. AVAILABILITY AND IMPLEMENTATION http://github.com/piquelab/QuASAR. CONTACT fluca@wayne.edu or rpique@wayne.edu SUPPLEMENTARY INFORMATION Supplementary Material is available at Bioinformatics online.
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Affiliation(s)
- Chris T Harvey
- Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540 E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gregory A Moyerbrailean
- Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540 E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gordon O Davis
- Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540 E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoquan Wen
- Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540 E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540 E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, 540 E Canfield, Scott Hall, Detroit, MI 48201, USA and Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
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Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I, Loudet O. Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. THE PLANT CELL 2014; 26:4298-310. [PMID: 25428981 PMCID: PMC4277215 DOI: 10.1105/tpc.114.130310] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.
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Affiliation(s)
- Francisco A Cubillos
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile, Santiago, Chile
| | - Oliver Stegle
- Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tuebingen, Germany European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Cécile Grondin
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
| | - Matthieu Canut
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
| | - Sébastien Tisné
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
| | - Isabelle Gy
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
| | - Olivier Loudet
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
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Adoue V, Schiavi A, Light N, Almlöf JC, Lundmark P, Ge B, Kwan T, Caron M, Rönnblom L, Wang C, Chen SH, Goodall AH, Cambien F, Deloukas P, Ouwehand WH, Syvänen AC, Pastinen T. Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs. Mol Syst Biol 2014; 10:754. [PMID: 25326100 PMCID: PMC4299376 DOI: 10.15252/msb.20145114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Most complex disease-associated genetic variants are located in non-coding regions and are
therefore thought to be regulatory in nature. Association mapping of differential allelic expression
(AE) is a powerful method to identify SNPs with direct cis-regulatory impact
(cis-rSNPs). We used AE mapping to identify cis-rSNPs regulating
gene expression in 55 and 63 HapMap lymphoblastoid cell lines from a Caucasian and an African
population, respectively, 70 fibroblast cell lines, and 188 purified monocyte samples and found
40–60% of these cis-rSNPs to be shared across cell types. We uncover
a new class of cis-rSNPs, which disrupt footprint-derived de novo
motifs that are predominantly bound by repressive factors and are implicated in disease
susceptibility through overlaps with GWAS SNPs. Finally, we provide the proof-of-principle for a new
approach for genome-wide functional validation of transcription factor–SNP interactions. By
perturbing NFκB action in lymphoblasts, we identified 489 cis-regulated
transcripts with altered AE after NFκB perturbation. Altogether, we perform a comprehensive
analysis of cis-variation in four cell populations and provide new tools for the
identification of functional variants associated to complex diseases.
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Affiliation(s)
- Veronique Adoue
- Institute National de la Santé et de la Recherche Médicale (INSERM), U1043, Toulouse, France
| | - Alicia Schiavi
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Nicholas Light
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Lundmark
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Lars Rönnblom
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Chuan Wang
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Shu-Huang Chen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Alison H Goodall
- Department of Cardiovascular Science, University of Leicester, Leicester, UK Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, UK Cardiogenics Consortium
| | - Francois Cambien
- Cardiogenics Consortium INSERM UMRS 937 Pierre and Marie Curie University and Medical School, Paris, France
| | - Panos Deloukas
- Cardiogenics Consortium Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Willem H Ouwehand
- Cardiogenics Consortium Department of Haematology, University of Cambridge, Cambridge, UK National Health Service Blood and Transplant, Cambridge Centre, Cambridge, UK
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
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Park HW, Tantisira KG, Weiss ST. Pharmacogenomics in asthma therapy: where are we and where do we go? Annu Rev Pharmacol Toxicol 2014; 55:129-47. [PMID: 25292431 DOI: 10.1146/annurev-pharmtox-010814-124543] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The response to drug treatment in asthma is a complex trait and is markedly variable even in patients with apparently similar clinical features. Pharmaco-genomics, which is the study of variations of human genome characteristics as related to drug response, can play a role in asthma therapy. Both a traditional candidate-gene approach to conducting genetic association studies and genome-wide association studies have provided an increasing list of genes and variants associated with the three major classes of asthma medications: β2-agonists, inhaled corticosteroids, and leukotriene modifiers. Moreover, a recent integrative, systems-level approach has offered a promising opportunity to identify important pharmacogenomics loci in asthma treatment. However, we are still a long way away from making this discipline directly relevant to patients. The combination of network modeling, functional validation, and integrative omics technologies will likely be needed to move asthma pharmacogenomics closer to clinical relevance.
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Affiliation(s)
- Heung-Woo Park
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115; , ,
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43
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Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T. Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping. Epigenetics 2014; 9:1238-51. [PMID: 25055051 DOI: 10.4161/epi.29920] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment.
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Affiliation(s)
- Nicholas Light
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Véronique Adoue
- Institut National de la Santé et de la Recherche Médicale (Inserm); U1043; Toulouse, France
| | - Bing Ge
- McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Shu-Huang Chen
- McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Tony Kwan
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Tomi Pastinen
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
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44
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Hasin-Brumshtein Y, Hormozdiari F, Martin L, van Nas A, Eskin E, Lusis AJ, Drake TA. Allele-specific expression and eQTL analysis in mouse adipose tissue. BMC Genomics 2014; 15:471. [PMID: 24927774 PMCID: PMC4089026 DOI: 10.1186/1471-2164-15-471] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/07/2014] [Indexed: 11/17/2022] Open
Abstract
Background The simplest definition of cis-eQTLs versus trans, refers to genetic variants that affect expression in an allele specific manner, with implications on underlying mechanism. Yet, due to technical limitations of expression microarrays, the vast majority of eQTL studies performed in the last decade used a genomic distance based definition as a surrogate for cis, therefore exploring local rather than cis-eQTLs. Results In this study we use RNAseq to explore allele specific expression (ASE) in adipose tissue of male and female F1 mice, produced from reciprocal crosses of C57BL/6J and DBA/2J strains. Comparison of the identified cis-eQTLs, to local-eQTLs, that were obtained from adipose tissue expression in two previous population based studies in our laboratory, yields poor overlap between the two mapping approaches, while both local-eQTL studies show highly concordant results. Specifically, local-eQTL studies show ~60% overlap between themselves, while only 15-20% of local-eQTLs are identified as cis by ASE, and less than 50% of ASE genes are recovered in local-eQTL studies. Utilizing recently published ENCODE data, we also find that ASE genes show significant bias for SNPs prevalence in DNase I hypersensitive sites that is ASE direction specific. Conclusions We suggest a new approach to analysis of allele specific expression that is more sensitive and accurate than the commonly used fisher or chi-square statistics. Our analysis indicates that technical differences between the cis and local-eQTL approaches, such as differences in genomic background or sex specificity, account for relatively small fraction of the discrepancy. Therefore, we suggest that the differences between two eQTL mapping approaches may facilitate sorting of SNP-eQTL interactions into true cis and trans, and that a considerable portion of local-eQTL may actually represent trans interactions. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-471) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yehudit Hasin-Brumshtein
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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45
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Kemp JP, Medina-Gomez C, Estrada K, St Pourcain B, Heppe DHM, Warrington NM, Oei L, Ring SM, Kruithof CJ, Timpson NJ, Wolber LE, Reppe S, Gautvik K, Grundberg E, Ge B, van der Eerden B, van de Peppel J, Hibbs MA, Ackert-Bicknell CL, Choi K, Koller DL, Econs MJ, Williams FMK, Foroud T, Carola Zillikens M, Ohlsson C, Hofman A, Uitterlinden AG, Davey Smith G, Jaddoe VWV, Tobias JH, Rivadeneira F, Evans DM. Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. PLoS Genet 2014; 10:e1004423. [PMID: 24945404 PMCID: PMC4063697 DOI: 10.1371/journal.pgen.1004423] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 04/14/2014] [Indexed: 11/19/2022] Open
Abstract
Heritability of bone mineral density (BMD) varies across skeletal sites, reflecting different relative contributions of genetic and environmental influences. To quantify the degree to which common genetic variants tag and environmental factors influence BMD, at different sites, we estimated the genetic (rg) and residual (re) correlations between BMD measured at the upper limbs (UL-BMD), lower limbs (LL-BMD) and skull (SK-BMD), using total-body DXA scans of ∼ 4,890 participants recruited by the Avon Longitudinal Study of Parents and their Children (ALSPAC). Point estimates of rg indicated that appendicular sites have a greater proportion of shared genetic architecture (LL-/UL-BMD rg = 0.78) between them, than with the skull (UL-/SK-BMD rg = 0.58 and LL-/SK-BMD rg = 0.43). Likewise, the residual correlation between BMD at appendicular sites (r(e) = 0.55) was higher than the residual correlation between SK-BMD and BMD at appendicular sites (r(e) = 0.20-0.24). To explore the basis for the observed differences in rg and re, genome-wide association meta-analyses were performed (n ∼ 9,395), combining data from ALSPAC and the Generation R Study identifying 15 independent signals from 13 loci associated at genome-wide significant level across different skeletal regions. Results suggested that previously identified BMD-associated variants may exert site-specific effects (i.e. differ in the strength of their association and magnitude of effect across different skeletal sites). In particular, variants at CPED1 exerted a larger influence on SK-BMD and UL-BMD when compared to LL-BMD (P = 2.01 × 10(-37)), whilst variants at WNT16 influenced UL-BMD to a greater degree when compared to SK- and LL-BMD (P = 2.31 × 10(-14)). In addition, we report a novel association between RIN3 (previously associated with Paget's disease) and LL-BMD (rs754388: β = 0.13, SE = 0.02, P = 1.4 × 10(-10)). Our results suggest that BMD at different skeletal sites is under a mixture of shared and specific genetic and environmental influences. Allowing for these differences by performing genome-wide association at different skeletal sites may help uncover new genetic influences on BMD.
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Affiliation(s)
- John P. Kemp
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), The Netherlands
| | - Karol Estrada
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Beate St Pourcain
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- School of Oral and Dental Sciences, University of Bristol, Bristol, United Kingdom
- School of Experimental Psychology, University of Bristol, Bristol, United Kingdom
| | - Denise H. M. Heppe
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Paediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicole M. Warrington
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Ling Oei
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), The Netherlands
| | - Susan M. Ring
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Claudia J. Kruithof
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Lisa E. Wolber
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Sjur Reppe
- Department of Medical Biochemistry, Oslo University Hospital, Ullevaal, Oslo, Norway
| | - Kaare Gautvik
- Department of Medical Biochemistry, Oslo University Hospital, Ullevaal, Oslo, Norway
- Department of Medical Biochemistry, Oslo Deacon Hospital, Oslo, Norway
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montréal, Canada
- McGill University and Genome Québec Innovation Centre, Montréal, Canada
| | - Bing Ge
- McGill University and Genome Québec Innovation Centre, Montréal, Canada
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Matthew A. Hibbs
- Department of Computer Science, Trinity University, San Antonio, Texas, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Kwangbom Choi
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Daniel L. Koller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Michael J. Econs
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Frances M. K. Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - M. Carola Zillikens
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), The Netherlands
| | - Claes Ohlsson
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Albert Hofman
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), The Netherlands
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), The Netherlands
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Vincent W. V. Jaddoe
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Paediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jonathan H. Tobias
- School of Clinical Sciences, University of Bristol, Bristol, United Kingdom
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), The Netherlands
| | - David M. Evans
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
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46
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Battle A, Montgomery SB. Determining causality and consequence of expression quantitative trait loci. Hum Genet 2014; 133:727-35. [PMID: 24770875 DOI: 10.1007/s00439-014-1446-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 04/09/2014] [Indexed: 12/18/2022]
Abstract
Expression quantitative trait loci (eQTLs) are currently the most abundant and systematically-surveyed class of functional consequence for genetic variation. Recent genetic studies of gene expression have identified thousands of eQTLs in diverse tissue types for the majority of human genes. Application of this large eQTL catalog provides an important resource for understanding the molecular basis of common genetic diseases. However, only now has both the availability of individuals with full genomes and corresponding advances in functional genomics provided the opportunity to dissect eQTLs to identify causal regulatory variants. Resolving the properties of such causal regulatory variants is improving understanding of the molecular mechanisms that influence traits and guiding the development of new genome-scale approaches to variant interpretation. In this review, we provide an overview of current computational and experimental methods for identifying causal regulatory variants and predicting their phenotypic consequences.
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Affiliation(s)
- A Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA,
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47
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Qiu W, Rogers AJ, Damask A, Raby BA, Klanderman BJ, Duan QL, Tyagi S, Niu S, Anderson C, Cahir-Mcfarland E, Mariani TJ, Carey V, Tantisira KG. Pharmacogenomics: novel loci identification via integrating gene differential analysis and eQTL analysis. Hum Mol Genet 2014; 23:5017-24. [PMID: 24770851 DOI: 10.1093/hmg/ddu191] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nearly one-half of asthmatic patients do not respond to the most commonly prescribed controller therapy, inhaled corticosteroids (ICS). We conducted an expression quantitative trait loci (eQTL) analysis using >300 expression microarrays (from 117 lymphoblastoid cell lines) in corticosteroid (dexamethasone) treated and untreated cells derived from asthmatic subjects in the Childhood Asthma Management Program (CAMP) clinical trial. We then tested the associations of eQTL with longitudinal change in airway responsiveness to methacholine (LnPC20) on ICS. We identified 2484 cis-eQTL affecting 767 genes following dexamethasone treatment. A significant over-representation of lnPC20-associated cis-eQTL [190 single-nucleotide polymorphisms (SNPs)] among differentially expressed genes (odds ratio = 1.76, 95% confidence interval: 1.35-2.29) was noted in CAMP Caucasians. Forty-six of these 190 clinical associations were replicated in CAMP African Americans, including seven SNPs near six genes meeting criteria for genome-wide significance (P < 2 × 10(-7)). Notably, the majority of genome-wide findings would not have been uncovered via analysis of untreated samples. These results indicate that identifying eQTL after relevant environmental perturbation enables identification of true pharmacogenetic variants.
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Affiliation(s)
| | - Angela J Rogers
- Division of Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford CA 94305-5236, USA
| | - Amy Damask
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine and Pulmonary Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston MA 02115, USA
| | | | | | - Shiva Tyagi
- Division of Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford CA 94305-5236, USA
| | - Simin Niu
- Channing Division of Network Medicine and
| | | | | | - Thomas J Mariani
- Division of Neonatology and Program in Pediatric Molecular and Personalized Medicine, Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA
| | | | - Kelan G Tantisira
- Channing Division of Network Medicine and Pulmonary Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston MA 02115, USA
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48
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Das SK, Sharma NK. Expression quantitative trait analyses to identify causal genetic variants for type 2 diabetes susceptibility. World J Diabetes 2014; 5:97-114. [PMID: 24748924 PMCID: PMC3990322 DOI: 10.4239/wjd.v5.i2.97] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/21/2014] [Accepted: 03/14/2014] [Indexed: 02/05/2023] Open
Abstract
Type 2 diabetes (T2D) is a common metabolic disorder which is caused by multiple genetic perturbations affecting different biological pathways. Identifying genetic factors modulating the susceptibility of this complex heterogeneous metabolic phenotype in different ethnic and racial groups remains challenging. Despite recent success, the functional role of the T2D susceptibility variants implicated by genome-wide association studies (GWAS) remains largely unknown. Genetic dissection of transcript abundance or expression quantitative trait (eQTL) analysis unravels the genomic architecture of regulatory variants. Availability of eQTL information from tissues relevant for glucose homeostasis in humans opens a new avenue to prioritize GWAS-implicated variants that may be involved in triggering a causal chain of events leading to T2D. In this article, we review the progress made in the field of eQTL research and knowledge gained from those studies in understanding transcription regulatory mechanisms in human subjects. We highlight several novel approaches that can integrate eQTL analysis with multiple layers of biological information to identify ethnic-specific causal variants and gene-environment interactions relevant to T2D pathogenesis. Finally, we discuss how the eQTL analysis mediated search for “missing heritability” may lead us to novel biological and molecular mechanisms involved in susceptibility to T2D.
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49
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van de Peppel J, van Leeuwen JPTM. Vitamin D and gene networks in human osteoblasts. Front Physiol 2014; 5:137. [PMID: 24782782 PMCID: PMC3988399 DOI: 10.3389/fphys.2014.00137] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 03/20/2014] [Indexed: 12/27/2022] Open
Abstract
Bone formation is indirectly influenced by 1,25-dihydroxyvitamin D3 (1,25D3) through the stimulation of calcium uptake in the intestine and re-absorption in the kidneys. Direct effects on osteoblasts and bone formation have also been established. The vitamin D receptor (VDR) is expressed in osteoblasts and 1,25D3 modifies gene expression of various osteoblast differentiation and mineralization-related genes, such as alkaline phosphatase (ALPL), osteocalcin (BGLAP), and osteopontin (SPP1). 1,25D3 is known to stimulate mineralization of human osteoblasts in vitro, and recently it was shown that 1,25D3 induces mineralization via effects in the period preceding mineralization during the pre-mineralization period. For a full understanding of the action of 1,25D3 in osteoblasts it is important to get an integrated network view of the 1,25D3-regulated genes during osteoblast differentiation and mineralization. The current data will be presented and discussed alluding to future studies to fully delineate the 1,25D3 action in osteoblast. Describing and understanding the vitamin D regulatory networks and identifying the dominant players in these networks may help develop novel (personalized) vitamin D-based treatments. The following topics will be discussed in this overview: (1) Bone metabolism and osteoblasts, (2) Vitamin D, bone metabolism and osteoblast function, (3) Vitamin D induced transcriptional networks in the context of osteoblast differentiation and bone formation.
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Affiliation(s)
- Jeroen van de Peppel
- Department of Internal Medicine, Bone and Calcium Metabolism Erasmus MC, Rotterdam, Netherlands
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50
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Zhang K, Huentelman MJ, Rao F, Sun EI, Corneveaux JJ, Schork AJ, Wei Z, Waalen J, Miramontes-Gonzalez JP, Hightower CM, Maihofer AX, Mahata M, Pastinen T, Ehret GB, Schork NJ, Eskin E, Nievergelt CM, Saier MH, O'Connor DT. Genetic implication of a novel thiamine transporter in human hypertension. J Am Coll Cardiol 2014; 63:1542-55. [PMID: 24509276 DOI: 10.1016/j.jacc.2014.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/29/2013] [Accepted: 01/07/2014] [Indexed: 12/27/2022]
Abstract
OBJECTIVES This study coupled 2 strategies-trait extremes and genome-wide pooling-to discover a novel blood pressure (BP) locus that encodes a previously uncharacterized thiamine transporter. BACKGROUND Hypertension is a heritable trait that remains the most potent and widespread cardiovascular risk factor, although details of its genetic determination are poorly understood. METHODS Representative genomic deoxyribonucleic acid (DNA) pools were created from male and female subjects in the highest- and lowest-fifth percentiles of BP in a primary care population of >50,000 patients. The peak associated single-nucleotide polymorphisms were typed in individual DNA samples, as well as in twins/siblings phenotyped for cardiovascular and autonomic traits. Biochemical properties of the associated transporter were evaluated in cellular assays. RESULTS After chip hybridization and calculation of relative allele scores, the peak associations were typed in individual samples, revealing an association between hypertension, systolic BP, and diastolic BP and the previously uncharacterized solute carrier SLC35F3. The BP genetic association at SLC35F3 was validated by meta-analysis in an independent sample from the original source population, as well as the International Consortium for Blood Pressure Genome-Wide Association Studies (across North America and western Europe). Sequence homology to a putative yeast thiamine (vitamin B1) transporter prompted us to express human SLC35F3 in Escherichia coli, which catalyzed [(3)H]-thiamine uptake. SLC35F3 risk-allele homozygotes (T/T) displayed decreased erythrocyte thiamine content on microbiological assay. In twin pairs, the SLC35F3 risk allele predicted heritable cardiovascular traits previously associated with thiamine deficiency, including elevated cardiac stroke volume with decreased vascular resistance, and elevated pressor responses to environmental (cold) stress. Allelic expression imbalance confirmed that cis variation at the human SLC35F3 locus influenced expression of that gene, and the allelic expression imbalance peak coincided with the hypertension peak. CONCLUSIONS Novel strategies were coupled to position a new hypertension-susceptibility locus, uncovering a previously unsuspected thiamine transporter whose genetic variants predicted several disturbances in cardiac and autonomic function. The results have implications for the pathogenesis and treatment of systemic hypertension.
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Affiliation(s)
- Kuixing Zhang
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Matthew J Huentelman
- Division of Neurogenomics, Translational Genomics Research Institute, Phoenix, Arizona
| | - Fangwen Rao
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Eric I Sun
- Department of Biology, UCSD, La Jolla, California
| | - Jason J Corneveaux
- Division of Neurogenomics, Translational Genomics Research Institute, Phoenix, Arizona
| | - Andrew J Schork
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Zhiyun Wei
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Jill Waalen
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | | | - C Makena Hightower
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Adam X Maihofer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California; Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Manjula Mahata
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California
| | - Tomi Pastinen
- Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Georg B Ehret
- Center for Complex Disease Genomics, McKusick-Nathans, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Nicholas J Schork
- Department of Psychiatry, UCSD, La Jolla, California; Departments of Computer Science and Human Genetics, University of California at Los Angeles, Los Angeles, California
| | - Eleazar Eskin
- Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Caroline M Nievergelt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California; Departments of Human and Medical Genetics, McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | | | - Daniel T O'Connor
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, California; Veterans Affairs San Diego Healthcare System, San Diego, California; Department of Pharmacology and the Institute for Genomic Medicine, UCSD, La Jolla, California.
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