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Functional Investigations of HNF1A Identify Rare Variants As Risk Factors for Type 2 Diabetes in the General Population

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Functional Investigations of HNF1A Identify Rare Variants As Risk Factors for Type 2 Diabetes in the General Population Functional Investigations of HNF1A Identify Rare Variants as Risk Factors for Type 2 Diabetes in the General Population The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Najmi, L. A., I. Aukrust, J. Flannick, J. Molnes, N. Burtt, A. Molven, L. Groop, et al. 2017. “Functional Investigations of HNF1A Identify Rare Variants as Risk Factors for Type 2 Diabetes in the General Population.” Diabetes 66 (2): 335-346. doi:10.2337/db16-0460. http:// dx.doi.org/10.2337/db16-0460. Published Version doi:10.2337/db16-0460 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:35982023 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Diabetes Volume 66, February 2017 335 Laeya Abdoli Najmi,1,2,3 Ingvild Aukrust,1,2 Jason Flannick,4 Janne Molnes,1,5 Noel Burtt,4 Anders Molven,1,6,7 Leif Groop,8 David Altshuler,4,9,10 Stefan Johansson,1,2 Lise Bjørkhaug,1,11 and Pål Rasmus Njølstad1,5 Functional Investigations of HNF1A Identify Rare Variants as Risk Factors for Type 2 Diabetes in the General Population Diabetes 2017;66:335–346 | DOI: 10.2337/db16-0460 Variants in HNF1A encoding hepatocyte nuclear factor 1a Maturity-onset diabetes of the young (MODY) is a domi- (HNF-1A) are associated with maturity-onset diabetes of the nantly inherited subtype of diabetes, estimated to account young form 3 (MODY 3) and type 2 diabetes. We investi- for 1–2% of all diabetes cases and is caused by mutations gated whether functional classification of HNF1A rare cod- across 10 or more genes (1). MODY arises most commonly ing variants can inform models of diabetes risk prediction in from mutations in HNF1A (2) and GCK (3,4), and less com- the general population by analyzing the effect of 27 HNF1A monly from mutations in HNF4A (5), HNF1B (6), and INS fi n METABOLISM variants identi ed in well-phenotyped populations ( =4,115). (7). Genetic studies in multiethnic cohorts have shown that fi Bioinformatics tools classi ed 11 variants as likely patho- variants in MODY genes may also predispose carriers to the genic and showed no association with diabetes risk risk of diabetes later in life (8–10). In the hepatocyte nuclear (combined minor allele frequency [MAF] 0.22%; odds factor 1a (HNF1A) gene, population-specificvariantswith ratio [OR] 2.02; 95% CI 0.73–5.60; P =0.18).However, very low minor allele frequency (MAF) have demonstrated a different set of 11 variants that reduced HNF-1A < an increased risk for type 2 diabetes in selected popula- transcriptional activity to 60% of normal (wild-type) ac- HNF1A tivity was strongly associated with diabetes in the gen- tions. The E508K rare variant (MAF 0.45% in eral population (combined MAF 0.22%; OR 5.04; 95% Mexicans and almost absent in other populations) is asso- CI 1.99–12.80; P = 0.0007). Our functional investiga- ciatedwithtype2diabetesintheMexicanpopulation(odds P 3 27 tions indicate that 0.44% of the population carry HNF1A ratio [OR], 5.48; =4.4 10 ) (11), and the G319S variants that result in a substantially increased risk for de- variant is associated with early-onset type 2 diabetes in veloping diabetes. These results suggest that functional the Oji-Cree population (OR 4.0 in homozygous carriers characterization of variants within MODY genes may over- and OR 1.97 in heterozygous carriers) (12). Meta-analyses come the limitations of bioinformatics tools for the pur- have shown the common variants I27L and A98V slightly poses of presymptomatic diabetesriskpredictioninthe increase the type 2 diabetes risk (I27L: OR 1.09; P =8.13 2 2 general population. 10 15; MAF 33%; A98V: OR 1.22; P =5.13 10 10;MAF 1KG Jebsen Center for Diabetes Research, Department of Clinical Science, Uni- 11Department of Biomedical Laboratory Sciences, Bergen University College, versity of Bergen, Bergen, Norway Bergen, Norway 2 Center for Medical Genetics and Molecular Medicine, Haukeland University Corresponding authors: Pål Rasmus Njølstad, [email protected]., and Lise Hospital, Bergen, Norway Bjørkhaug, [email protected]. 3Department of Biomedicine, University of Bergen, Bergen, Norway Received 11 April 2016 and accepted 18 November 2016. 4Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA This article contains Supplementary Data online at http://diabetes 5Department of Pediatrics, Haukeland University Hospital, Bergen, Norway .diabetesjournals.org/lookup/suppl/doi:10.2337/db16-0460/-/DC1. 6Gade Laboratory for Pathology, Department of Clinical Medicine, University of L.B. and P.R.N. are both last authors. Bergen, Bergen, Norway D.A. is currently affiliated with Vertex Pharmaceuticals, Boston, MA. 7Department of Pathology, Haukeland University Hospital, Bergen, Norway 8Department of Clinical Sciences, Diabetes and Endocrinology, Clinical Research © 2017 by the American Diabetes Association. Readers may use this article as fi Center, Lund University, Malmö, Sweden long as the work is properly cited, the use is educational and not for pro t, and 9Departments of Genetics and Medicine, Harvard Medical School, Boston, MA the work is not altered. More information is available at http://www.diabetesjournals 10Departments of Molecular Biology and Diabetes Unit, Massachusetts General .org/content/license. Hospital, Boston, MA 336 Functional Investigation of HNF1A Rare Variants Diabetes Volume 66, February 2017 2.7%) (13). Although concurrent large association studies RESEARCH DESIGN AND METHODS conclude that common variants in HNF1A (MAF .5%) do Study Design not associate with type 2 diabetes (14,15), certain combina- We sought to investigate whether the functional classifi- tions of variants (I27L and A98V) have, in vivo, shown a cation of HNF1A rare variants can inform models of fi modest but signi cant association with impairment in glucose- diabetes risk prediction in the general population. By studying stimulated insulin secretion. I27L alone has been associated all protein-coding HNF1A rare variants identified by exome P with an increased type 2 diabetes risk (OR 1.5; =0.002)in sequencing in the three well-phenotyped population cohorts . 2 elderly (age 60) and overweight (BMI 25 kg/m ) patients (described below), using 1) bioinformatics tools used to aid P (OR 2.3; = 0.002) (16). medical diagnostics or 2) functional assays assessing trans- The spectrum of the in vitro functional consequence of activation, DNA binding ability, and nuclear localization, we HNF1A HNF1A variants differs largely. Analyses of muta- could estimate the effect of individual variants and diabetes tions that cosegregate with familial early-onset diabetes risk. We reasoned that risk variants could be validated based (MODY) have demonstrated that they most often cause fi on statistics from a public knowledge base for type 2 dia- diabetes as a result of HNF-1A haploinsuf ciency (loss betes genetics (http://www.type2diabetesgenetics.org). of function), by none or severely impaired binding and transactivation of HNF-1A target genes (,;30% com- Variant Selection and Phenotypic Description of the pared with wild-type), and/or by reducing HNF-1A protein Study Populations stability (17–19). Similar investigations of the type 2 risk We studied protein-coding rare variants in HNF1A iden- variants G319S and E508K have shown a milder effect tified by exon sequencing and reported in a recent study on HNF-1A function compared with MODY variants by (23). The variants were identified in 4,115 random indi- reducing the HNF-1A transactivation potential to ,40–60% viduals from the Framingham Heart Study (FHS) Off- (11,20), whereas DNA binding properties have remained in- spring cohort (n = 1,653), the Jackson Heart Study tact. The functional consequence of common variants, how- (JHS) cohort (n = 1,691), and type 2 diabetes case and ever, are mild when assessed alone (;70% transactivation control patients ascertained from the extremes of genetic by L27 and ;60% by V98) compared with combined risk (extreme type 2 diabetes [T2D] cohort, n = 771). (;50% by L27 and V98) variants (16). The DNA binding The FHS is a three-generation prospective family study properties and protein levels of these common variants of individuals of European ancestry designed to identify have remained intact. factors that contribute to cardiovascular disease, and the A diagnosis of MODY can alter treatment and is im- Offspring cohort consists of 5,124 adult children and portant for prognostic evaluation (21), and identification spouses (enrolled in 1971) of the original participants of individuals at risk for diabetes later in life can target (26). The JHS is a large community-based observational lifestyle interventions (22). The increasing availability of study of participants who are of African American origin. next-generation sequencing offers an opportunity to iden- The study participants, who were recruited from urban tify individuals who carry variants that may cause MODY and rural areas of the Jackson, Mississippi, metropolitan sta- or elevate the diabetes risk. tistical area, consist of 6,500 men and women and 400 fam- The spectrum of rare coding variants in seven of the most ilies (27). The extreme T2D cohort was originally selected common MODY genes was recently investigated in well- from 27,500 individuals in three prospective cohorts: the phenotyped cohorts of the general population (23). This study Malmö Preventive Project (Sweden) (28), the Scania Diabetes – concluded that 0.5 1.5% of randomly selected individuals Registry (Sweden), and the Botnia Study (Finland), selecting carry rare variants that are interpreted as causal for MODY lean and young case patients with type 2 diabetes and old and fi in the Human Gene Mutation Database (HGMD) or ful ll obese control patients.
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