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Koraishy FM, Mann FD, Waszczuk MA, Kuan PF, Jonas K, Yang X, Docherty A, Shabalin A, Clouston S, Kotov R, Luft B. Polygenic association of glomerular filtration rate decline in world trade center responders. BMC Nephrol 2022; 23:347. [PMID: 36307804 PMCID: PMC9615399 DOI: 10.1186/s12882-022-02967-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The factors associated with estimated glomerular filtrate rate (eGFR) decline in low risk adults remain relatively unknown. We hypothesized that a polygenic risk score (PRS) will be associated with eGFR decline. METHODS We analyzed genetic data from 1,601 adult participants with European ancestry in the World Trade Center Health Program (baseline age 49.68 ± 8.79 years, 93% male, 23% hypertensive, 7% diabetic and 1% with cardiovascular disease) with ≥ three serial measures of serum creatinine. PRSs were calculated from an aggregation of single nucleotide polymorphisms (SNPs) from a recent, large-scale genome-wide association study (GWAS) of rapid eGFR decline. Generalized linear models were used to evaluate the association of PRS with renal outcomes: baseline eGFR and CKD stage, rate of change in eGFR, stable versus declining eGFR over a 3-5-year observation period. eGFR decline was defined in separate analyses as "clinical" (> -1.0 ml/min/1.73 m2/year) or "empirical" (lower most quartile of eGFR slopes). RESULTS The mean baseline eGFR was ~ 86 ml/min/1.73 m2. Subjects with decline in eGFR were more likely to be diabetic. PRS was significantly associated with lower baseline eGFR (B = -0.96, p = 0.002), higher CKD stage (OR = 1.17, p = 0.010), decline in eGFR (OR = 1.14, p = 0.036) relative to stable eGFR, and the lower quartile of eGFR slopes (OR = 1.21, p = 0.008), after adjusting for established risk factors for CKD. CONCLUSION Common genetic variants are associated with eGFR decline in middle-aged adults with relatively low comorbidity burdens.
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Affiliation(s)
- Farrukh M Koraishy
- Division of Nephrology, Department of Medicine, Stony Brook University, 100 Nicolls Road, HSCT16-080E, Stony Brook, NY, USA.
| | - Frank D Mann
- Department of Family, Population, and Preventative Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Monika A Waszczuk
- Department of Psychology, Rosalind Franklin University, North Chicago, IL, USA
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Katherine Jonas
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, USA
| | - Xiaohua Yang
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anna Docherty
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Andrey Shabalin
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Sean Clouston
- Department of Family, Population, and Preventative Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Roman Kotov
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, USA
| | - Benjamin Luft
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA
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Jefferis J, Pelecanos A, Catts V, Mallett A. The Heritability of Kidney Function using an Older Australian Twin Population. Kidney Int Rep 2022; 7:1819-1830. [PMID: 35967118 PMCID: PMC9366362 DOI: 10.1016/j.ekir.2022.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/31/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Twin studies are unique population models which estimate observed rather than inferred genetic components of complex traits. Nonmonogenic chronic kidney disease (CKD) is a complex disease process with strong genetic and environmental influences, amenable to twin studies. We aimed to assess the heritability of CKD using twin analysis and modeling within Older Australian Twin Study (OATS) data. Methods OATS had 109 dizygotic (DZ) and 126 monozygotic (MZ) twin pairs with paired serum creatinine levels. Heritability of kidney function as estimated glomerular filtration rate (eGFR CKD Epidemiology Collaboration [CKD-EPI]) was modeled using the ACE model to estimate additive heritability (A), common (C), and unique (E) environmental factors. Intratwin pair analysis using mixed effects logistic regression allowed analysis of variation in eGFR from established CKD risk factors. Results The median age was 69.71 (interquartile range 78.4–83.0) years, with 65% female, and a mean CKD-EPI of 82.8 ml/min (SD 6.7). The unadjusted ACE model determined kidney function to be 33% genetically determined (A), 18% shared genetic-environmental (C), and 49% because of unique environment (E). This remained unchanged when adjusted for age, hypertension, and sex. Hypertension was associated with eGFR; however, intertwin variance in hypertension did not explain variance in eGFR. Two or more hypertension medications were associated with decreased eGFR (P = 0.009). Conclusion This study estimates observed heritability at 33%, notably higher than inferred heritability in genome-wide association study (GWAS) (7.1%–18%). Epigenetics and other genomic phenomena may explain this heritability gap. Difference in antihypertension medications explains part of unique environmental exposures, though discordance in hypertension and diabetes does not.
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Park JH, Koo BN, Kim MS, Shin D, Kwak YL. Effects of intraoperative dexmedetomidine infusion on renal function in elective living donor kidney transplantation: a randomized controlled trial. Can J Anaesth 2021; 69:448-459. [PMID: 34931289 DOI: 10.1007/s12630-021-02173-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/16/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Ischemia-reperfusion injury is inevitable during donor organ harvest and recipient allograft reperfusion in kidney transplantation, and affects graft outcomes. Dexmedetomidine, an α2-adrenoreceptor agonist, has renoprotective effects against ischemia-reperfusion injury. We investigated the effects of intraoperative dexmedetomidine infusion on renal function and the development of delayed graft function after elective living donor kidney transplantation in a randomized controlled trial. METHODS A total of 104 patients were randomly assigned to receive either an intraoperative infusion of dexmedetomidine 0.4 μg·kg-1·hr-1 or 0.9% saline. The primary outcome was the serum creatinine level on postoperative day (POD) 7. Secondary outcomes were renal function and the degree of inflammation and included the following variables: serum creatinine level and estimated glomerular filtration rate up to six months; incidence of delayed graft function; and levels of serum cystatin C, plasma interleukin (IL)-1β, and IL-18 during the perioperative period. RESULTS The mean (standard deviation) serum creatinine level on POD 7 was comparable between the groups (dexmedetomidine vs control: 1.11 [0.87] mg·dL-1 vs 1.06 [0.73] mg·dL-1; mean difference, 0.05; 95% confidence interval, -0.27 to 0.36; P = 0.77). Delayed graft function occurred in one patient in each group (odds ratio, 1.020; P > 0.99). There were no significant differences in the secondary outcomes between the groups (all P > 0.05). CONCLUSIONS Intraoperative dexmedetomidine infusion did not produce any beneficial effects on renal function or delayed graft function in patients undergoing elective living donor kidney transplantation. STUDY REGISTRATION www.ClinicalTrials.gov (NCT03327389); registered 31 October 2017.
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Affiliation(s)
- Jin Ha Park
- Department of Anesthesiology and Pain Medicine, and Anesthesia and Pain Research Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Bon-Nyeo Koo
- Department of Anesthesiology and Pain Medicine, and Anesthesia and Pain Research Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Min-Soo Kim
- Department of Anesthesiology and Pain Medicine, and Anesthesia and Pain Research Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Dongkwan Shin
- Department of Anesthesiology and Pain Medicine, and Anesthesia and Pain Research Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Young-Lan Kwak
- Department of Anesthesiology and Pain Medicine, and Anesthesia and Pain Research Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea. .,Yonsei Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, South Korea.
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Zhang J, Thio CHL, Gansevoort RT, Snieder H. Familial Aggregation of CKD and Heritability of Kidney Biomarkers in the General Population: The Lifelines Cohort Study. Am J Kidney Dis 2020; 77:869-878. [PMID: 33359149 DOI: 10.1053/j.ajkd.2020.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 11/06/2020] [Indexed: 01/08/2023]
Abstract
RATIONALE & OBJECTIVE Chronic kidney disease (CKD) has a heritable component. We aimed to quantify familial aggregation of CKD in the general population and assess the extent to which kidney traits could be explained by genetic and environmental factors. STUDY DESIGN Cross-sectional 3-generation family study. SETTING & PARTICIPANTS Data were collected at entry into the Lifelines Cohort Study from a sample of the general population of the northern Netherlands, composed predominantly of individuals of European ancestry. EXPOSURE Family history of CKD. OUTCOMES The primary outcome was CKD, defined as estimated glomerular filtration rate (eGFR)<60mL/min/1.73m2, where GFR was estimated using the CKD Epidemiology Collaboration creatinine equation. Among a subsample for which urinary albumin concentration was available (n=59,943), urinary albumin excretion was expressed as the rate of urinary albumin excretion (UAE) per 24 hours or urinary albumin-creatinine ratio (UACR). ANALYTICAL APPROACH Familial aggregation of CKD was assessed by calculating the recurrence risk ratio (RRR), using adapted Cox proportional hazards models. Heritability of continuous kidney-related traits was estimated using linear mixed models and defined as the ratio of the additive genetic variance to total phenotypic variance. All models were adjusted for age, sex, and known risk factors for kidney disease. RESULTS Among 155,911 participants with available eGFR data, the prevalence of CKD was 1.19% (1,862 cases per 155,911). The risk of CKD in those with an affected first-degree relative was 3 timeshigher than the risk in the total sample (RRR, 3.04 [95% CI, 2.26-4.09). In those with an affected spouse, risk of CKD was also higher (RRR, 1.56 [95% CI, 1.20-1.96]), indicative of shared environmental factors and/or assortative mating. Heritability estimates of eGFR, UAE, and UACR were 44%, 20%, and 18%, respectively. For serum urea, creatinine, and uric acid, estimates were 31%, 37%, and 48%, respectively, whereas estimates for serum electrolytes ranged from 22% to 28%. LIMITATIONS Use of estimated rather than measured GFR. UAE data only available in a subsample. CONCLUSIONS In this large population-based family study, a positive family history was strongly associated with increased risk of CKD. We observed moderate to high heritability of kidney traits and related biomarkers. These results indicate an important role of genetic factors in CKD risk.
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Affiliation(s)
- Jia Zhang
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Shenzhen Center for Chronic Disease Control, Shenzhen, Guangdong, China; Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, and School of Basic Medicine, Peking Union, Medical College, Beijing, China
| | - Chris H L Thio
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Ron T Gansevoort
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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Tunbridge EM, Narajos M, Harrison CH, Beresford C, Cipriani A, Harrison PJ. Which Dopamine Polymorphisms Are Functional? Systematic Review and Meta-analysis of COMT, DAT, DBH, DDC, DRD1-5, MAOA, MAOB, TH, VMAT1, and VMAT2. Biol Psychiatry 2019; 86:608-620. [PMID: 31303260 DOI: 10.1016/j.biopsych.2019.05.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/11/2019] [Accepted: 05/01/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND Many polymorphisms in dopamine genes are reported to affect cognitive, imaging, or clinical phenotypes. It is often inferred or assumed that such associations are causal, mediated by a direct effect of the polymorphism on the gene product itself. However, the supporting evidence is not always clear. METHODS We conducted systematic reviews and meta-analyses to assess the empirical evidence for functional polymorphisms in genes encoding dopaminergic enzymes (COMT, DBH, DDC, MAOA, MAOB, and TH), dopamine receptors (DRD1, DRD2, DRD3, DRD4, and DRD5), the dopamine transporter (DAT), and vesicular transporters (VMAT1 and VMAT2). We defined functionality as an effect of the polymorphism on the expression, abundance, activity, or affinity of the gene product. RESULTS We screened 22,728 articles and identified 255 eligible studies. We found robust and medium to large effects for polymorphisms in 4 genes. For catechol-O-methyltransferase (COMT), the Val158Met polymorphism (rs4680) markedly affected enzyme activity, protein abundance, and protein stability. Dopamine β-hydroxylase (DBH) activity was associated with rs1611115, rs2519152, and the DBH-STR polymorphism. Monoamine oxidase A (MAOA) activity was associated with a 5' VNTR polymorphism. Dopamine D2 receptor (DRD2) binding was influenced by the Taq1A (rs1800497) polymorphism, and rs1076560 affected DRD2 splicing. CONCLUSIONS Some widely studied dopaminergic polymorphisms clearly and substantially affect the abundance or activity of the encoded gene product. However, for other polymorphisms, evidence of such an association is negative, inconclusive, or lacking. These findings are relevant when selecting polymorphisms as "markers" of dopamine function, and for interpreting the biological plausibility of associations between these polymorphisms and aspects of brain function or dysfunction.
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Affiliation(s)
- Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Marco Narajos
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom
| | | | - Charles Beresford
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andrea Cipriani
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom.
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Guvercin G, Karakus V, Aksit M, Dere Y, Aktar M, Alpay H, Bozkaya G, Tatar E. Matrix metalloproteinase-9, 10, and stress hyperglycaemia in acute kidney injury. Eur J Clin Invest 2018; 48:e12963. [PMID: 29856477 DOI: 10.1111/eci.12963] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 05/30/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND This study investigated the effect of matrix metalloproteinase (MMP)-9 and 10, and stress hyperglycaemia on the necessity of emergency renal replacement therapy (RRT) and mortality in nondiabetic geriatric patients with acute kidney injury (AKI). MATERIALS AND METHODS The present observational and longitudinal study included 101 nondiabetic geriatric patients (age >65 years) with AKI. The serum levels of MMP-9 and MMP-10 were evaluated in these patients. Serum glucose level >140 mg/dL at the time of admission was accepted as stress hyperglycaemia. RESULTS The average age of patients was 81 ± 7.1 years. Stress hyperglycaemia was diagnosed in 34.6% of the cases; the majority of these cases were patients with high-serum urea, CRP, and chronic kidney disease. The average levels of MMP-9 and MMP-10 were found to be 199 ± 38 and 16.5 ± 7.5 ng/mL, respectively. Thirty-one cases (30.6%) mortality during hospitalization and 20 cases (20%) underwent emergency RRT. Multiregression analysis showed the serum urea (P < .001) and stress hyperglycaemia (P = .03) to be independently associated with mortality. Also, serum urea (P = .01), potassium level (P = .03), and MMP-10 levels (P = .03) were independently associated with the necessity of the emergency RRT. The MMP-9 levels exhibited no relation with the necessity of emergency RRT and mortality. CONCLUSION Stress hyperglycaemia is a common condition among nondiabetic geriatric patients with AKI and is related to mortality. Serum MMP-10 levels serve as an important predictor of the necessity of emergency RRT in these patients.
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Affiliation(s)
- Guray Guvercin
- Department of Internal Medicine, Izmir Bozyaka Education and Research Hospital, Health Sciences University, Izmir, Turkey
| | - Volkan Karakus
- Division of Hematology, Mugla Sitki Kocman University Training and Research Hospital, Mugla, Turkey
| | - Murat Aksit
- Department of Biochemistry, Izmir Bozyaka Education and Research Hospital, Health Sciences University, Izmir, Turkey
| | - Yelda Dere
- Division of Pathology, Mugla Sitki Kocman University Training and Research Hospital, Mugla, Turkey
| | - Merve Aktar
- Department of Internal Medicine, Izmir Bozyaka Education and Research Hospital, Health Sciences University, Izmir, Turkey
| | - Hasan Alpay
- Department of Internal Medicine, Izmir Bozyaka Education and Research Hospital, Health Sciences University, Izmir, Turkey
| | - Giray Bozkaya
- Department of Biochemistry, Izmir Bozyaka Education and Research Hospital, Health Sciences University, Izmir, Turkey
| | - Erhan Tatar
- Department of Nephrology, Izmir Bozyaka Education and Research Hospital, Health Sciences University, Izmir, Turkey
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7
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Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer KA. iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Stem Cell Reports 2017; 8:1086-1100. [PMID: 28410642 PMCID: PMC5390244 DOI: 10.1016/j.stemcr.2017.03.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 03/08/2017] [Accepted: 03/13/2017] [Indexed: 11/18/2022] Open
Abstract
Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines.
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Affiliation(s)
- Athanasia D Panopoulos
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paola Benaglio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Roy Williams
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sherin I Hashem
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernhard M Schuldt
- Zentrum für Integrative Psychiatrie, Universitätsklinikum Schleswig-Holstein, 24105 Kiel, Germany
| | - Christopher DeBoever
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelo D Arias
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Melvin Garcia
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bradley C Nelson
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Harismendy
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - David A Jakubosky
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - William W Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - KathyJean Farnam
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Megan Cook
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Victor Borja
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carl A Miller
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan D Grinstein
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Frauke Drees
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan Okubo
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Yuriko Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Veronica Modesto
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Carl T Dargitz
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rachel Feiring
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Chang Zhao
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aitor Aguirre
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas J McGarry
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - He Li
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joaquin Reyna
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fangwen Rao
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel T O'Connor
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sylvia M Evans
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neil C Chi
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Naoki Nariai
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Franz-Josef Müller
- Zentrum für Integrative Psychiatrie, Universitätsklinikum Schleswig-Holstein, 24105 Kiel, Germany
| | - Lawrence S B Goldstein
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Eric Adler
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeanne F Loring
- Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - W Travis Berggren
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Erin N Smith
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Panopoulos AD, Smith EN, Arias AD, Shepard PJ, Hishida Y, Modesto V, Diffenderfer KE, Conner C, Biggs W, Sandoval E, D'Antonio-Chronowska A, Berggren WT, Izpisua Belmonte JC, Frazer KA. Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. Cell Stem Cell 2017; 20:505-517.e6. [PMID: 28388429 PMCID: PMC5444384 DOI: 10.1016/j.stem.2017.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 01/06/2017] [Accepted: 03/15/2017] [Indexed: 01/24/2023]
Abstract
Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming.
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Affiliation(s)
- Athanasia D Panopoulos
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Erin N Smith
- Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelo D Arias
- Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peter J Shepard
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; BioSpyder Technologies, Inc., Carlsbad, CA 92008, USA
| | - Yuriko Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Veronica Modesto
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Clay Conner
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | | | | | - W Travis Berggren
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Kelly A Frazer
- Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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9
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Stafford-Smith M, Li YJ, Mathew JP, Li YW, Ji Y, Phillips-Bute BG, Milano CA, Newman MF, Kraus WE, Kertai MD, Shah SH, Podgoreanu MV. Genome-wide association study of acute kidney injury after coronary bypass graft surgery identifies susceptibility loci. Kidney Int 2015; 88:823-32. [PMID: 26083657 PMCID: PMC4589439 DOI: 10.1038/ki.2015.161] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 03/18/2015] [Accepted: 04/09/2015] [Indexed: 12/25/2022]
Abstract
Acute kidney injury (AKI) is a common, serious complication of cardiac surgery. Since prior studies have supported a genetic basis for postoperative AKI, we conducted a genome-wide association study (GWAS) for AKI following coronary bypass graft (CABG) surgery. The discovery dataset consisted of 873 non-emergent CABG surgery patients with cardiopulmonary bypass (PEGASUS), while a replication dataset had 380 cardiac surgical patients (CATHGEN). Single nucleotide polymorphism (SNP) data were based on Illumina Human610-Quad (PEGASUS) and OMNI1-Quad (CATHGEN) BeadChips. We used linear regression with adjustment for a clinical AKI risk score to test SNP associations with the postoperative peak rise relative to preoperative serum creatinine concentration as a quantitative AKI trait. Nine SNPs meeting significance in the discovery set were detected. The rs13317787 in GRM7|LMCD1-AS1 intergenic region (3p21.6) and rs10262995 in BBS9 (7p14.3) were replicated with significance in the CATHGEN data set and exhibited significantly strong overall association following meta-analysis. Additional fine-mapping using imputed SNPs across these two regions and meta-analysis found genome wide significance at the GRM7|LMCD1-AS1 locus and a significantly strong association at BBS9. Thus, through an unbiased GWAS approach, we found two new loci associated with post-CABG AKI providing new insights into the pathogenesis of perioperative AKI.
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Affiliation(s)
- Mark Stafford-Smith
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA.,Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Joseph P Mathew
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Yen-Wei Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Yunqi Ji
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Carmelo A Milano
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Mark F Newman
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - William E Kraus
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Miklos D Kertai
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Svati H Shah
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Mihai V Podgoreanu
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
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10
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Barrie ES, Weinshenker D, Verma A, Pendergrass SA, Lange LA, Ritchie MD, Wilson JG, Kuivaniemi H, Tromp G, Carey DJ, Gerhard GS, Brilliant MH, Hebbring SJ, Cubells JF, Pinsonneault JK, Norman GJ, Sadee W. Regulatory polymorphisms in human DBH affect peripheral gene expression and sympathetic activity. Circ Res 2014; 115:1017-25. [PMID: 25326128 DOI: 10.1161/circresaha.116.304398] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
RATIONALE Dopamine β-hydroxylase (DBH) catalyzes the conversion of dopamine to norepinephrine in the central nervous system and peripherally. DBH variants are associated with large changes in circulating DBH and implicated in multiple disorders; yet causal relationships and tissue-specific effects remain unresolved. OBJECTIVE To characterize regulatory variants in DBH, effect on mRNA expression, and role in modulating sympathetic tone and disease risk. METHODS AND RESULTS Analysis of DBH mRNA in human tissues confirmed high expression in the locus coeruleus and adrenal gland, but also in sympathetically innervated organs (liver>lung>heart). Allele-specific mRNA assays revealed pronounced allelic expression differences in the liver (2- to 11-fold) attributable to promoter rs1611115 and exon 2 rs1108580, but only small differences in locus coeruleus and adrenals. These alleles were also associated with significantly reduced mRNA expression in liver and lung. Although DBH protein is expressed in other sympathetically innervated organs, mRNA levels were too low for analysis. In mice, hepatic Dbh mRNA levels correlated with cardiovascular risk phenotypes. The minor alleles of rs1611115 and rs1108580 were associated with sympathetic phenotypes, including angina pectoris. Testing combined effects of these variants suggested protection against myocardial infarction in 3 separate clinical cohorts. CONCLUSIONS We demonstrate profound effects of DBH variants on expression in 2 sympathetically innervated organs, liver and lung, but not in adrenals and brain. Preliminary results demonstrate an association of these variants with clinical phenotypes responsive to peripheral sympathetic tone. We hypothesize that in addition to endocrine effects via circulating DBH and norepinephrine, the variants act in sympathetically innervated target organs.
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Affiliation(s)
- Elizabeth S Barrie
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - David Weinshenker
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Anurag Verma
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Sarah A Pendergrass
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Leslie A Lange
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Marylyn D Ritchie
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - James G Wilson
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Helena Kuivaniemi
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Gerard Tromp
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - David J Carey
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Glenn S Gerhard
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Murray H Brilliant
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Scott J Hebbring
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Joseph F Cubells
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Julia K Pinsonneault
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Greg J Norman
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.)
| | - Wolfgang Sadee
- From the Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus (E.S.B., J.K.P., W.S.); Department of Human Genetics, Emory University School of Medicine, Atlanta, GA (D.W., J.F.C.); Center for Systems Genomics, Pennsylvania State University, University Park (A.V., S.A.P., M.D.R.); Department of Genetics, University of North Carolina School of Medicine, Chapel Hill (L.A.L.); Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson (J.G.W.); The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA (H.K., G.T., D.J.C.); Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey (G.S.G.); Center for Human Genetics, Marshfield Clinic Research Foundation, WI (M.H.B., S.J.H.); and Department of Psychology, The University of Chicago, IL (G.J.N.).
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11
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Mustapic M, Maihofer AX, Mahata M, Chen Y, Baker DG, O'Connor DT, Nievergelt CM. The catecholamine biosynthetic enzyme dopamine β-hydroxylase (DBH): first genome-wide search positions trait-determining variants acting additively in the proximal promoter. Hum Mol Genet 2014; 23:6375-84. [PMID: 24986918 DOI: 10.1093/hmg/ddu332] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dopamine beta-hydroxylase (DBH) is the biosynthetic enzyme catalyzing formation of norepinephrine. Changes in DBH expression or activity have been implicated in the pathogenesis of cardiovascular and neuropsychiatric disorders. Genetic determination of DBH enzymatic activity and its secretion are only incompletely understood. We began with a genome-wide association search for loci contributing to DBH activity in human plasma. Initially, in a population sample of European ancestry, we identified the proximal DBH promoter as a region harboring three common trait-determining variants (top hit rs1611115, P = 7.2 × 10(-51)). We confirmed their effects on transcription and showed that the three variants each acted additively on gene expression. Results were replicated in a population sample of Native American descent (top hit rs1611115, P = 4.1 × 10(-15)). Jointly, DBH variants accounted for 57% of DBH trait variation. We further identified a genome-wide significant SNP at the LOC338797 locus on chromosome 12 as trans-quantitative trait locus (QTL) (rs4255618, P = 4.62 × 10(-8)). Conditional analyses on DBH identified a third genomic region contributing to DBH variation: a likely cis-QTL adjacent to DBH in SARDH (rs7040170, P = 1.31 × 10(-14)) on chromosome 9q. We conclude that three common SNPs in the DBH promoter act additively to control phenotypic variation in DBH levels, and that two additional novel loci (SARDH and LOC338797) may also contribute to the expression of this catecholamine biosynthetic trait. Identification of DBH variants with strong effects makes it possible to take advantage of Mendelian randomization approaches to test causal effects of this intermediate trait on disease.
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Affiliation(s)
- Maja Mustapic
- Department of Psychiatry and Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA, Ruđer Bošković Institute, Zagreb HR-10000, Croatia
| | | | - Manjula Mahata
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Yuqing Chen
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Dewleen G Baker
- Department of Psychiatry and VA San Diego Healthcare System, VA Center of Excellence for Stress and Mental Health (CESAMH), La Jolla, CA 92161, USA and
| | - Daniel T O'Connor
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Caroline M Nievergelt
- Department of Psychiatry and VA San Diego Healthcare System, VA Center of Excellence for Stress and Mental Health (CESAMH), La Jolla, CA 92161, USA and
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