Replication of association of DENND1A and THADA variants with polycystic ovary syndrome in European cohorts
- Mark O Goodarzi1,2,3,4,
- Michelle R Jones1,
- Xiaohui Li3,
- Angela K Chua1,
- Obed A Garcia5,
- Yii-Der I Chen2,3,
- Ronald M Krauss6,
- Jerome I Rotter3,4,
- Wendy Ankener7,
- Richard S Legro8,
- Ricardo Azziz2,4,9,
- Jerome F Strauss III10,
- Andrea Dunaif5,
- Margrit Urbanek5
- 1Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- 2Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- 3Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- 4Department of Medicine, the David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- 5Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- 6Children's Hospital Oakland Research Institute, Oakland, California, USA
- 7Department of Human Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- 8Department of Obstetrics and Gynecology, Pennsylvania State College of Medicine, Hershey, Pennsylvania, USA
- 9Department of Obstetrics and Gynecology, Medical College of Georgia, Georgia Health Sciences University, Augusta, Georgia
- 10Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
- Correspondence to Dr Margrit Urbanek, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University School of Medicine, 303 E Chicago Avenue, Tarry 15-717, Chicago, IL 60611, USA;
Contributors MOG, MRJ, XL, AC, OAG, YDIC, RMK, JIR, WA, RSL, RA, JFS, AD, and MU contributed to the conception and design, or analysis and interpretation of data; MOG, RSL, RA, JFS, AD, and MU contributed to the drafting the article or revising it critically for important intellectual content; MOG, JFS, and MU contributed to the final approval of the version to be published.
- Received 15 August 2011
- Revised 3 November 2011
- Accepted 26 November 2011
- Published Online First 17 December 2011
Background Polycystic ovary syndrome (PCOS) is a complex endocrine disorder with a strong familial component. PCOS is characterised by hyperandrogenaemia and irregular menses. A recent genome-wide association study (GWAS) of PCOS in a Chinese cohort identified three reproducible PCOS susceptibility loci mapping to 2p16.3 (luteinising hormone/choriogonadotropin receptor; LHCGR), 2p21 (thyroid associated protein; THADA), and 9q33.3 (DENN/MADD domain containing 1A; DENNDIA). The impact of these loci in non-Chinese PCOS cohorts remains to be determined.
Methods and results The study tested association with PCOS of seven single nucleotide polymorphisms mapping to the three Chinese PCOS loci in two European derived PCOS cohorts (cohort A = 939 cases and 957 controls; cohort B = 535 cases and 845 controls). Cases fulfilled the National Institute of Child Health & Human Development criteria for PCOS. Variation in DENND1A was strongly associated with PCOS in the study cohort (pcombined cohorts=10−8); multiple variants in THADA were also associated with PCOS, while there was no significant evidence for association of LHCGR variation with PCOS. The present study had >80% power to detect an effect of similar size as was observed by Chen et al for DENND1A and THADA, but reduced power (at <40%) for LHCGR at p=0.0001. The study had sufficient power (57–88%) for LHCGR at p=0.01.
Conclusions At least two of the PCOS susceptibility loci identified in the Chinese PCOS GWAS (DENND1A and THADA) are also associated with PCOS in European derived populations, and are therefore likely to be important in the aetiology of PCOS regardless of ethnicity. The analysis of the LHCGR gene was not sufficiently powered to detect modest effects.
- genome-wide association study
- genetic epidemiology
- reproductive medicine
- obstetrics and gynaecology
Polycystic ovary syndrome (PCOS) is a common endocrine disorder of women of reproductive age that is characterised by elevated androgens and oligomenorrhoea and amenorrhoea, and is associated with an increased risk of developing insulin resistance, obesity, and type 2 diabetes. PCOS is a complex disorder with both environmental and genetic factors contributing to its aetiology.1 Although numerous attempts have been made to identify genetic susceptibility loci for PCOS, only a few have been reproducibly identified.2
Recently, the first genome-wide association study (GWAS) of PCOS was published. This study identified three loci that were reproducibly associated with PCOS in a Chinese cohort.3 These PCOS susceptibility loci mapped to the genomic areas of three genes, LHCGR, THADA, and DENND1A. LHCGR encodes luteinising hormone/choriogonadotropin receptor, which is the receptor for two glycoprotein hormones, luteinising hormone (LH) and human chorionic gonadotropin (hCG). LH stimulates ovarian theca cells to produce testosterone, which is then converted to oestrogen by granulosa cells. The mid-cycle LH surge triggers ovulation, after which LH also stimulates the corpora lutea of the follicles to produce progesterone; hCG is required for the maintenance of pregnancy. FSHR is the receptor for follicle stimulating hormone (FSH), which stimulates the development of ovarian follicles; the FSHR gene is adjacent to LHCGR. THADA encodes thyroid adenoma associated protein, which is expressed in the pancreas, adrenal medulla, thyroid, adrenal cortex, testis, thymus, small intestine, and stomach; chromosomal aberrations of the genomic region containing THADA have been observed in benign thyroid adenomas. Single nucleotide polymorphisms (SNPs) within THADA have also been associated with type 2 diabetes.4 DENND1A encodes a protein named DENN/MADD domain containing 1A or DENND1A, a member of the connecdenn family, which plays a role in Rab35 activated endocytotic trafficking.
While these three loci show reproducible evidence for association in the Chinese population, it is not known whether they also contribute to PCOS susceptibility in non-Chinese populations. In this study we sought to replicate the three PCOS susceptibility loci identified by GWAS in the Chinese population in PCOS case–control cohorts of European ancestry. We tested for association between PCOS and one SNP in LHCGR, four SNPs in THADA, and two SNPs in DENND1A in two cohorts consisting in total of 1474 women with PCOS and 1802 controls. These seven SNPs were among the most significant associations in the Chinese GWAS, and THADA and DENND1A variants are also associated with PCOS in women of European ancestry.
Patients and methods
This study was approved by the institutional review boards of the Brigham and Women's Hospital, Northwestern University Feinberg School of Medicine, Pennsylvania State University (PSU) College of Medicine, and University of Pennsylvania Medical Center, University of Alabama at Birmingham (UAB), Cedars-Sinai Medical Center (CSMC), Virginia Commonwealth University, the Pregnancy in PCOS (PPCOS) trial,5 and the Cholesterol and Pharmacogenetics (CAP) study.6 Written informed consent was obtained from all participants.
The first case–control cohort (no overlap with cohort B) consisted of 939 index cases (probands) with PCOS and 957 control women (109 intensively phenotyped subjects recruited in parallel to the PCOS probands and 848 minimally phenotyped from a DNA repository) of European Caucasian ancestry. Subjects were recruited at Brigham and Women's Hospital, Northwestern University, and Pennsylvania State University. Phenotypic characteristics of cases and controls are given in table 1.
PCOS was defined according to the classic National Institute of Child Health & Human Development (NICHD) criteria as previously implemented by us.7–10 All women with PCOS had hyperandrogenaemia and chronic anovulation, with the exclusion of specific disorders of the ovaries, adrenal or pituitary,7–10 and therefore satisfied the NICHD, Rotterdam, and Androgen Excess Society criteria for the diagnosis of PCOS.11–13
Intensively phenotyped, reproductively normal control women (n=109) were phenotyped as previously reported.8 10 They had normal androgen values, regular menses, and were of similar age, weight, and ethnicity to the PCOS cases. To increase the number of control subjects, we used minimally phenotyped women (n=848) selected from NUgene, a large scale genebank (http://www.nugene.org) that combines a centralised genomic DNA sample collection and storage system with the ability to update participants' health status from electronic medical records. The majority of the minimally phenotyped subjects (>80%) were queried by questionnaire, had no history of irregular menses, and did not carry a diagnosis of PCOS. We therefore expect that our control cohort included fewer women with PCOS than the population prevalence of PCOS (5–10%).14
None of the intensively phenotyped subjects were receiving medications known to alter reproductive hormone levels or glucose homeostasis for at least 1 month before study. Contraceptive steroids were stopped at least 3 months before the study. Anthropometric measurements (weight and height) were taken as reported.15 Circulating concentrations of total testosterone (T), non-sex hormone-binding globulin-bound testosterone (uT), and dehydroepiandrosterone sulfate (DHEAS) were determined from a fasting blood sample.7 8
The second case–control cohort (no overlap with cohort A) consisted of 535 unrelated white PCOS patients and 845 white controls. Sources of subjects included UAB (241 PCOS and 147 controls), CSMC (179 PCOS and 27 controls), PSU (recruited by RS Legro separately from above; 46 PCOS and 68 controls),7 the PPCOS trial (69 cases),5 and the CAP study (603 controls).6 All PCOS subjects met NICHD criteria.13 Parameters for defining hirsutism, hyperandrogenaemia, ovulatory dysfunction, and exclusion of related disorders were previously reported for the UAB and CSMC,14 the additional PSU,7 and the PPCOS5 samples. The CAP samples (271 women and 332 men) consisted of general community controls. Table 1 presents the clinical characteristics of cohort B.
Genotyping in cohort A was carried out using the Applied Biosystems Assays by Design (ABD) or Assays on Demand (AOD) 5′nuclease Taqman technology (Applied Biosystems, Foster City, California, USA), as recommended by the manufacturer on the 7900HT DNA analysis system (Applied Biosystems). Duplicate genotyping of a HapMap CEU trio yielded a 99.7% concordance rate. The genotyping success rate was 97%. All SNPs were in Hardy–Weinberg equilibrium. We genotyped seven markers, consisting of the SNPs most associated with PCOS in the Chinese GWAS or proxies for these SNPs (table 2). Rs13405728 maps to 2p13.6 (LHCGR), rs12468394, rs13429458, rs6544661, and rs11891936 map to 2p21 (THADA), and rs2479106 and rs10818854 map to 19q33.3 (DENND1A). Rs6544661 was used as a proxy for rs12478601 with which it is in complete linkage disequilibrium (LD) (r2=1) in the CEU population of the HapMap database (release 24, http://hapmap.ncbi.nlm.nih.gov/). A third SNP, rs10986105, associated with PCOS in the Chinese GWAS was not genotyped herein, because, unlike in Asian populations, in European populations it is in high LD with rs10818854 (r2=0.83 in HapMap CEU). In some cases, technical reasons necessitated genotyping of proxy SNPs in linkage disequilibrium with the SNPs of interest; r2 values in table 2 are linkage disequilibrium (HapMap CEU) of the genotyped SNP with the Chinese GWAS SNP. Seven SNPs genotyped in each cohort captured the variation of the eight SNPs of interest.
In cohort B, genotyping was carried out using iSelect Infinium technology, following the manufacturer's protocol (Illumina, San Diego, California, USA).16 17 SNPs were excluded if the genotyping failure rate was >10% or if the minor allele frequency was <3%. Duplicate genotyping of 12 samples yielded a 100% concordance rate. The genotyping success rate was 99.97%. A total of seven SNPs were examined (table 2), all of which were in Hardy–Weinberg equilibrium. In the 2p13.6 locus (LHCGR), we genotyped rs6732721, a proxy for rs13405728 (r2=0.87 in HapMap CEU). In the 2p21 locus (THADA), we genotyped rs12468394, rs13429458, rs11891936, and rs6544661. In the 9q33.3 (DENND1A) locus, we genotyped rs2479106 and rs12337273, a proxy for two of the Chinese GWAS SNPs (r2=0.83 with rs10818854 and r2=1 with rs10986105 in HapMap CEU).
Unpaired t tests were used to compare clinical characteristics between cases and controls; quantitative traits were log- or square-root-transformed as appropriate to reduce non-normality. Quantitative trait data are presented as median (IQR).
Separately in cohorts A and B, association analyses were conducted using logistic regression; the dependent variable was PCOS status, and the independent variable was genotype (additive model). To assess whether the effects of the seven SNPs were independent of body mass index (BMI), adjusted analyses were conducted with inclusion of BMI as an additional independent variable. Furthermore, we directly evaluated the seven SNPs for an effect on BMI by conducting linear regression wherein BMI was the dependent variable. Meta-analyses were conducted on the logistic regression results of cohort A and cohort B using inverse variance weighting.
We used the Genetic Power Calculator package to calculate the power to detect an association between SNPs tested and PCOS in our cohort.18 The allele frequencies in the power analysis are those for the PCOS associated allele (or corresponding proxy SNP alleles) at each SNP in the Hapmap CEU cohort (rs13405728 allele G = 0.058; rs6732721 allele C = 0.067; rs12468394 allele A = 0.508; rs13429458 allele C = 0.096; rs12478601 allele T = 0.600; rs11891936 allele A = 0.200; rs6544661 allele G = 0.600; rs2479106 allele G = 0.300; rs10818854 allele A = 0.050; rs10986105 allele C = 0.042; rs12337273 allele G = 0.034). Other parameters used for this analyses were: 957 controls, 939 cases for cohort A, 845 controls, 535 cases for cohort B, 1802 controls, 1474 cases for the complete cohort, genotype relative risk (RR) of 1.5 and 2.0 under an additive model. Assuming these parameters, we had 88% power to detect an effect at p<1×10−4 in the complete cohort for at least one SNP mapping to DENND1A and THADA with genotype RRs of 1.5 and 2.0. For LHCGR we had 57% power to detect an effect at p=0.01 in the complete cohort for a genotype RR of 1.5 and >80% power detect an effect at p=0.01 in the complete sample for a genotype RR of 2.0. We therefore had modest to sufficient power to detect a relevant effect in our cohort.
Quantitative trait association analyses
Exploratory association analyses of the seven SNPs against BMI, total testosterone, DHEAS, fasting insulin, and fasting glucose were conducted within each cohort. Because these analyses are not in replication of results from the Chinese GWAS, we applied a multiple testing corrected p value of 0.001 (=0.05/35; accounting for seven SNPs against five traits).
Allele frequencies and genotype frequencies for each SNP are shown in table 3. In cohort A, of the seven SNPs genotyped, four variants (three in THADA, one in DENND1A) were associated with PCOS (table 4). These associations remained significant after adjustment for BMI (table 5). The highest level of significance and greatest effect size were observed for the DENND1A SNP rs10818854. This was the only SNP associated with PCOS in cohort B, with a similar odds ratio; adjustment for BMI did not materially alter this association (tables 4 and 5). None of the seven SNPs was associated with BMI itself.
Meta-analysis results of the two cohorts are shown in tables 4 and 5. The DENND1A SNP rs10818854 was highly associated with PCOS (unadjusted p=9.8×10−8, BMI adjusted p=6.5×10−8). Three SNPs in the THADA locus, rs12468394, rs6544661, and rs11891936, were significantly associated with PCOS at lower levels of significance (tables 4 and 5). The magnitude and direction of effects of the European PCOS associated DENND1A and THADA SNPs were similar to those observed in the Chinese GWAS (table 2).
None of the seven SNPs were associated with total testosterone, DHEAS, fasting insulin, or fasting glucose (data not shown).
In this study, we performed a meta-analysis of two case–control cohorts examining whether variants recently identified in a GWAS for PCOS in Chinese Han subjects would be associated with PCOS in non-Hispanic whites. Of the seven SNPs tested, one—rs10818854 in the DENND1A gene—was highly associated with PCOS in the present analysis; three SNPs in THADA were associated with PCOS in the meta-analysis. Finding variants in two of three genes associated with PCOS in both Chinese and Europeans is not unexpected, because the remarkably similar prevalence of PCOS around the globe suggests it might be an ancient disorder, for which the existence of common susceptibility genes and alleles in different races would be predicted.19 Indeed, among the four SNPs associated with PCOS in both Chinese and Europeans, the same alleles were associated with PCOS with similar odds ratios.
Until recently, the field of PCOS genetics was dominated by candidate gene studies, which examined over 100 genes of which only a few have been replicated.2 20–24 Given the modest success of candidate gene studies in PCOS, GWAS for this condition have been highly anticipated. The first was conducted in a cohort of cases and controls from China, with two levels of replication.3 That study identified SNPs in three loci, at chromosomes 2p13.1, 2p21, and 9q33.3, as replicated loci for PCOS. Genes found at these loci include LHCGR, THADA, and DENND1A, respectively. The three DENND1A SNPs associated with PCOS in the Chinese GWAS, rs10818854, rs2479106, rs10986105, are independent (r2<0.7) of each other in Asian populations.3 Since in white populations, rs10818854 and rs10986105 are highly correlated (r2=0.83 in HapMap CEU), we examined only the former in this study and found it to be associated with PCOS.
DENND1A (also known as connecdenn) encodes a protein involved in endosomal membrane trafficking.25 Its N-terminus contains a DENN (differentially expressed in neoplastic vs normal cells) motif, which is found in many proteins but whose function is uncertain.26 At the plasma membrane, DENND1A interacts with clathrin and the clathrin adaptor protein AP-1, via residues in the C-terminal end.27 28 DENND1A also functions as a guanine nucleotide exchange factor (GEF) for the small GTPase Rab35, serving to link Rab35 with clathrin mediated endocytosis.28 DENND1A has been found in neuronal clathrin coated vesicles, where it plays a role in synaptic vesicle endocytosis.27 DENND1A is ubiquitously expressed, with highest levels in kidney and brain.29 Genetic variation in DENND1A has been associated with personality traits (rs7852296, p=9×10−6 30) and weakly with cleft lip/palate (rs1928482, p=0.03, in only one of multiple cohorts studied31). Because a protein such as this would be expected to affect diverse processes, it is not surprising to find it associated with PCOS, a syndrome characterised by dysfunction in multiple organ systems (ovary, adrenal, hypothalamus, pituitary, insulin responsive tissues). It has been speculated that DENND1A may affect the development of PCOS via altered activity of endoplasmic reticulum aminopeptidase 1.3
While it is possible that DENND1A contributes directly to the PCOS phenotype, alternatively the positive association signal may be related to variation in another gene in linkage disequilibrium with the positive SNP. One such candidate gene encodes a microRNA, miR601, which is co-localised with DENND1A. mIR601 up-regulates expression of actin cytoskeleton, down-regulates the Fas induced apoptosis pathway, and represses nuclear factor-kappaB transcription factor dependent reporter expression.32 The control of these signalling pathways might directly or indirectly contribute to the PCOS phenotype.
DENND1A has a paralog, DENND1C, located on chromosome 19p13, a region that we previously suggested harbours a risk allele for PCOS21; however, SNPs in the DENND1C gene were not associated with PCOS (data not shown).
Multiple SNPs in the THADA locus were associated with PCOS. Of interest, rs7578597, a missense variant in THADA, was associated with type 2 diabetes in a large GWAS meta-analysis.4 However, the THADA SNPs associated with PCOS in our data are not in LD with the diabetes variant in the HapMap and 1000 Genomes Project databases.33 This resembles the situation with the gene TCF7L2, wherein different variants affect diabetes susceptibility and PCOS susceptibility.34
Of the three genes considered, only LHCGR did not show association with PCOS in our European derived cohorts. The SNP genotyped is rare in Europeans (minor allele frequency 0.05 in HapMap CEU) but common in Han Chinese (frequency 0.23 in HapMap), resulting in reduced power to detect association of this SNP with PCOS in our cohorts, as our meta-analysis effect size (OR 0.8) was similar to that observed in the Chinese study (OR 0.7).3 LHCGR might contain susceptibility SNPs for PCOS in whites not tagged by SNP rs13405728 in Chinese. A similar finding was observed in the gene TCF7L2, wherein different variants were associated with type 2 diabetes in whites and Chinese.35 Alternatively, the LD pattern in the Caucasian populations may be sufficiently different from that in the Chinese so that the genotyped SNP is not detecting the same causal variant in the two populations. Comprehensive fine mapping is needed to evaluate this possibility in PCOS.
In conclusion, the GWAS era has finally arrived in PCOS genetics. By discovering loci that would not otherwise be considered in traditional candidate gene approaches, GWAS will open new avenues in genetic and physiologic research in PCOS. DENND1A and THADA appear to affect PCOS risk in at least two different racial groups.
We thank all the women and their families for their participation. Some of the hormone assays were performed at the University of Virginia, Center for Research in Reproduction, Ligand Assay and Analysis Core which is supported by NICHD Grant U54-HD28934.
Funding This study was supported by National Institutes of Health (U54-HD034449 to RSL, JFS, AD, and MU, P50-HD044405 to AD and MU, RR10732 and C06-RR016499 to Pennsylvania State University General Clinical Research Center (GCRC), M01-RR00048 to Northwestern University GCRC, M01-RR10732 and M01-RR02635 to Brigham and Women's Hospital GCRC, R01-HD029364 and K24-HD001346 to RA, R01-HL069757 to RMK, R01-DK079888 to MOG, R01-HD057450 to MU and OAG, and M01-RR00425 to the Harbor-UCLA/CSMC GCRC) and the Winnick Clinical Scholars Award to MOG.
Competing interests None.
Ethics approval Ethics approval was provided by Massachusetts, California, Pennsylvania, Illinois, Alabama.
Provenance and peer review Not commissioned; externally peer reviewed.
Data sharing statement Specific genotype and phenotype information will be made available as requested.