1
|
Pan Y, Sun X, Mi X, Huang Z, Hsu Y, Hixson JE, Munzy D, Metcalf G, Franceschini N, Tin A, Köttgen A, Francis M, Brody JA, Kestenbaum B, Sitlani CM, Mychaleckyj JC, Kramer H, Lange LA, Guo X, Hwang SJ, Irvin MR, Smith JA, Yanek LR, Vaidya D, Chen YDI, Fornage M, Lloyd-Jones DM, Hou L, Mathias RA, Mitchell BD, Peyser PA, Kardia SLR, Arnett DK, Correa A, Raffield LM, Vasan RS, Cupple LA, Levy D, Kaplan RC, North KE, Rotter JI, Kooperberg C, Reiner AP, Psaty BM, Tracy RP, Gibbs RA, Morrison AC, Feldman H, Boerwinkle E, He J, Kelly TN. Whole-exome sequencing study identifies four novel gene loci associated with diabetic kidney disease. Hum Mol Genet 2023; 32:1048-1060. [PMID: 36444934 PMCID: PMC9990994 DOI: 10.1093/hmg/ddac290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Diabetic kidney disease (DKD) is recognized as an important public health challenge. However, its genomic mechanisms are poorly understood. To identify rare variants for DKD, we conducted a whole-exome sequencing (WES) study leveraging large cohorts well-phenotyped for chronic kidney disease and diabetes. Our two-stage WES study included 4372 European and African ancestry participants from the Chronic Renal Insufficiency Cohort and Atherosclerosis Risk in Communities studies (stage 1) and 11 487 multi-ancestry Trans-Omics for Precision Medicine participants (stage 2). Generalized linear mixed models, which accounted for genetic relatedness and adjusted for age, sex and ancestry, were used to test associations between single variants and DKD. Gene-based aggregate rare variant analyses were conducted using an optimized sequence kernel association test implemented within our mixed model framework. We identified four novel exome-wide significant DKD-related loci through initiating diabetes. In single-variant analyses, participants carrying a rare, in-frame insertion in the DIS3L2 gene (rs141560952) exhibited a 193-fold increased odds [95% confidence interval (CI): 33.6, 1105] of DKD compared with noncarriers (P = 3.59 × 10-9). Likewise, each copy of a low-frequency KRT6B splice-site variant (rs425827) conferred a 5.31-fold higher odds (95% CI: 3.06, 9.21) of DKD (P = 2.72 × 10-9). Aggregate gene-based analyses further identified ERAP2 (P = 4.03 × 10-8) and NPEPPS (P = 1.51 × 10-7), which are both expressed in the kidney and implicated in renin-angiotensin-aldosterone system modulated immune response. In the largest WES study of DKD, we identified novel rare variant loci attaining exome-wide significance. These findings provide new insights into the molecular mechanisms underlying DKD.
Collapse
Affiliation(s)
- Yang Pan
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Xiao Sun
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Xuenan Mi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zhijie Huang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Yenchih Hsu
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James E Hixson
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Donna Munzy
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nora Franceschini
- Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Adrienne Tin
- University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center – University of Freiburg, Freiburg 79106, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Michael Francis
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | | | - Jennifer A Brody
- Cardiovascular Health Research Unit, Departments of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Bryan Kestenbaum
- University of Washington, Department of Medicine, Division of Nephrology, Kidney Research Institute, Seattle, WA 98195, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Departments of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Charlottesville, VA 22903, USA
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL 60153, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Centre, Torrance, CA 90502, USA
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL 35233, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dhananjay Vaidya
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Centre, Torrance, CA 90502, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Donna K Arnett
- Department of Epidemiology, University of Kentucky, Lexington, KY 40506, USA
| | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - L Adrienne Cupple
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Robert C Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kari E North
- Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Centre, Torrance, CA 90502, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Department of Health Services, University of Washington, Seattle, WA 98195, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Harold Feldman
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiang He
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | | |
Collapse
|
2
|
Kannan V, Misra BK, Kapadia A, Bajpai R, Deshpande S, Almel S, Sankhe M, Desai K, Shaikh M, Anand V, Kannan A, Teo WY, Ross J, Bollo R, Seow WT, Tan AM, Kang SG, Kim DS, Li XN, Lau CC, Mohila CA, Adesina A, Su J, Ichimura K, Fukushima S, Matsushita Y, Tomiyama A, Niwa T, Suzuki T, Nakazato Y, Mukasa A, Kumabe T, Nagane M, Iuchi T, Mizoguchi M, Tamura K, Sugiyama K, Nakada M, Kanemura Y, Yokogami K, Matsutani M, Shibata T, Nishikawa R, Takami H, Fukushima S, Fukuoka K, Yanagisawa T, Nakamura T, Arita H, Narita Y, Shibui S, Nishikawa R, Ichimura K, Matsutani M, Sands S, Guerry W, Kretschmar C, Donahue B, Allen J, Matsutani M, Nishikawa R, Kumabe T, Sugiyama K, Nakamura H, Sawamura Y, Fujimaki T, Hattori E, Arakawa Y, Kawabata Y, Aoki T, Miyamoto S, Kagawa N, Hirayama R, Fujimoto Y, Chiba Y, Kinoshita M, Takano K, Eino D, Fukuya S, Nakanishi K, Yamamoto F, Hashii Y, Hashimoto N, Hara J, Yoshimine T, Murray M, Bartels U, Nishikawa R, Fangusaro J, Matsutani M, Nicholson J, Sumerauer D, Zapotocky M, Churackova M, Cyprova S, Zamecnik J, Malinova B, Kyncl M, Tichy M, Stary J, Lassen-Ramshad Y, von Oettingen G, Agerbaek M, Ohnishi T, Kohno S, Inoue A, Ohue S, Kohno S, Iwata S, Inoue A, Ohue S, Kumon Y, Ohnishi T, Acharya S, DeWees T, Shinohara E, Perkins S, Kato H, Fuji H, Nakasu Y, Ishida Y, Okawada S, Yang Q, Guo C, Chen Z, Alapetite C, Faure-Conter C, Verite C, Pagnier A, Laithier V, Entz-Werle N, Gorde-Grosjean S, Palenzuela G, Lemoine P, Frappaz D, Nguyen HA, Bui L, Ngoc, Cerbone M, Ederies A, Losa L, Moreno C, Sun K, Spoudeas HA, Nakano Y, Okada K, Kosaka Y, Nagashima T, Hashii Y, Kagawa N, Soejima T, Osugi Y, Sakamoto H, Hara J, Nicholson J, Alapetite C, Kortmann RD, Garre ML, Ricardi U, Saran F, Frappaz D, Calaminus G, Muda Z, Menon B, Ibrahim H, Rahman EJA, Muhamad M, Othman IS, Thevarajah A, Cheng S, Kilday JP, Laperriere N, Drake J, Bouffet E, Bartels U, Sakamoto H, Matsusaka Y, Watanabe Y, Umaba R, Hara J, Osugi Y, Alapetite C, Ruffier-Loubiere A, De Marzi L, Bolle S, Claude L, Habrand JL, Brisse H, Frappaz D, Doz F, Bourdeaut F, Dendale R, Mazal A, Fournier-Bidoz N, Fujimaki T, Fukuoka K, Shirahata M, Suzuki T, Adachi JI, Mishima K, Wakiya K, Matsutani M, Nishikawa R, Fukushima S, Yamashita S, Kato M, Nakamura H, Takami H, Suzuki T, Yanagisawa T, Mukasa A, Kumabe T, Nagane M, Sugiyama K, Tamura K, Narita Y, Shibui S, Shibata T, Ushijima T, Matsutani M, Nishikawa R, Ichimura K, Consortium IGA, Calaminus G, Kortmann RD, Frappaz D, Alapetite C, Garre ML, Ricardi U, Saran FH, Nicholson J, Calaminus G, Kortmann RD, Frappaz D, Alapetite C, Garre ML, Ricardi U, Saran FH, Nicholson J, Czech T, Nicholson J, Frappaz D, Kortmann RD, Alapetite C, Garre ML, Ricardi U, Saran F, Calaminus G, Hayden J, Bartels U, Calaminus G, Joseph R, Nicholson J, Hale J, Lindsay H, Kogiso M, Qi L, Yee TW, Huang Y, Mao H, Lin F, Baxter P, Su J, Terashima K, Perlaky L, Lau C, Parsons D, Chintagumpala M, Li XAN, Osorio D, Vaughn D, Gardner S, Mrugala M, Ferreira M, Keene C, Gonzalez-Cuyar L, Hebb A, Rockhill J, Wang L, Yamaguchi S, Burstein M, Terashima K, Ng HK, Nakamura H, He Z, Suzuki T, Nishikawa R, Natsume A, Terasaka S, Dauser R, Whitehead W, Adesina A, Sun J, Munzy D, Gibbs R, Leal S, Wheeler D, Lau C, Dhall G, Robison N, Judkins A, Krieger M, Gilles F, Park J, Lee SU, Kim T, Choi Y, Park HJ, Shin SH, Kim JY, Robison N, Dhir N, Khamani J, Margol A, Wong K, Britt B, Evans A, Nelson M, Grimm J, Finlay J, Dhall G. GERM CELL TUMOURS. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|