Erectile dysfunction is a common condition of men in middle and older ages. Twin studies suggest that about one-third of the risk is due to genetic factors, independent of other known erectile dysfunction risk factors. However, studies that have searched for specific genetic contributors have been limited due to small sample sizes, candidate gene approaches, and weak phenotyping. As a result, there are no confirmed genetic risk factors for erectile dysfunction. This study finds a specific genetic cause for erectile dysfunction.

Erectile dysfunction affects millions of men worldwide. Twin studies support the role of genetic risk factors underlying erectile dysfunction, but no specific genetic variants have been identified. We conducted a large-scale genome-wide association study of erectile dysfunction in 36,649 men in the multiethnic Kaiser Permanente Northern California Genetic Epidemiology Research in Adult Health and Aging cohort. We also undertook replication analyses in 222,358 men from the UK Biobank. In the discovery cohort, we identified a single locus (rs17185536-T) on chromosome 6 near the single-minded family basic helix-loop-helix transcription factor 1 (SIM1) gene that was significantly associated with the risk of erectile dysfunction (odds ratio = 1.26, P = 3.4 × 10 −25 ). The association replicated in the UK Biobank sample (odds ratio = 1.25, P = 6.8 × 10 −14 ), and the effect is independent of known erectile dysfunction risk factors, including body mass index (BMI). The risk locus resides on the same topologically associating domain as SIM1 and interacts with the SIM1 promoter, and the rs17185536-T risk allele showed differential enhancer activity. SIM1 is part of the leptin–melanocortin system, which has an established role in body weight homeostasis and sexual function. Because the variants associated with erectile dysfunction are not associated with differences in BMI, our findings suggest a mechanism that is specific to sexual function.

Erectile dysfunction is a common and costly disease of men in middle and older ages (1, 2). Its pathophysiology is tied to psychosocial, neurological, hormonal, and vascular factors (3). Epidemiological studies have shown that age, obesity, diabetes, benign prostatic hyperplasia (BPH), lower urinary tract symptoms, hyperlipidemia, cardiovascular disease, and smoking are important risk factors in erectile dysfunction susceptibility (4). There is also substantial evidence that genetics influence the risk of erectile dysfunction. A twin study in middle-aged male veterans found that about one-third of the risk is heritable, independent of known erectile dysfunction risk factors (5). However, subsequent association studies searching for specific genetic contributors have been limited by small sample sizes, a reliance on limited candidate-gene approaches, and weak phenotyping. As a result, there are no confirmed genetic risk factors for erectile dysfunction (6). Understanding the genetic basis of erectile dysfunction can provide insight into its etiology and lead to the development of new therapies.

Here, we undertook a genome-wide association study (GWAS) of erectile dysfunction in the large and ethnically diverse Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort, which includes 36,649 men from four race/ethnicity groups (non-Hispanic whites, Hispanic/Latinos, East Asians, and African Americans). We then validated genome-wide significant associations in an external independent cohort of 222,358 men from the UK Biobank. We further examined the effect of the validated risk locus in race/ethnicity and phenotype subgroups. Finally, through in silico and in vitro functional investigations, we linked our risk locus to gene function.

We next set out to determine whether the region encompassing rs17185536 or other regions nearby that have SNPs in strong linkage disequilibrium (r 2 >0.8) with rs17185536 function as enhancers and whether the erectile dysfunction-associated variant(s) might lead to differential enhancer activity. We cloned six different regions ( SI Appendix, Table S5 ) containing both the risk and reference alleles into an enhancer assay vector and tested them for enhancer activity in HEK 293T cells. We chose this cell line as SIM1 is known to be expressed in the kidney. We observed differential enhancer activity between the risk and reference alleles for three of the constructs, including the rs17185536-T (risk) allele, which showed significant enhancer activity compared with empty vector, and the rs17185536-C (reference), which did not have significant enhancer activity ( Fig. 3 ). Combined, our results suggest that the rs17185536-T (risk) allele or other erectile dysfunction-associated alleles in this region lead to differential enhancer activity and that this region may regulate the expression of SIM1.

Genomic and epigenetic annotations of the SIM1 locus. (A) A University of California, Santa Cruz genome browser snapshot of the SIM1 locus showing rs17185536, the TAD in this region, the human–mouse (H–M) synteny breakpoint, and the virtual 4C (circularized chromosome conformation capture) interactions from human GM12878 cells adapted from the 3D Genome Browser ( 54 ). (B) A zoomed-in view of the regions that were cloned for enhancer assays showing the cloned regions, the SNPs, the ENCODE human skeletal muscle cells and myoblasts ChIP-seq peaks (green), ENCODE DNaseI hypersensitivity sites, ENCODE transcription factor ChIP-seq sites, and evolutionary conservation peaks (blue peaks) (B).

We then undertook chromatin interaction and evolutionary conservation analyses to determine whether the region around rs17185536 interacts with nearby genes. Chromosomes are organized into topologically associating domains (TADs); enhancers interact with genes in the same TAD more frequently than with genes located in other parts of the genome ( 10 ). rs17185536 resides within a TAD that includes the genes SIM1, MCHR2, PRDM13, CCNC, and USP45, indicating that the erectile dysfunction risk locus could interact with one of these genes ( 10 ). However, of those genes, only SIM1 is located within a human–mouse synteny block that contains rs17185536. This synteny block is defined at one end by a mouse chromosomal breakpoint ∼93 kb distal to MCHR2 ( 11 ), the next closest gene to rs17185536, which suggests that the physical proximity of the erectile dysfunction risk locus and SIM1 has been preserved over evolutionary time ( Fig. 2A ). Analyses of various chromatin conformation capture assays using the 3D Genome Browser ( 12 ) show that the region around rs17185536 interacts with the SIM1 promoter ( Fig. 2A ). Consistent with this interaction, rs17185536 is located within an evolutionarily conserved sequence that has an H3K27ac ChIP-seq peak in human skeletal muscle cells and myoblasts from ENCODE ( 13 ) data, suggesting that this region may act as an enhancer ( Fig. 2B ).

We also conducted sensitivity analyses to determine whether the effect of this locus was influenced by phenotype definition. Since the self-reported questionnaire included four severity levels, we compared the different response levels, using men who answered that they are “Always” able to get an erection as the reference group ( SI Appendix, Table S4 ). We observed a greater effect of rs17185536-T with each increase in severity level, with odds ratios of 1.15 (1.09–1.21) for the “Usually” group, 1.30 (1.23–1.38) for the “Sometimes” group, and 1.41 (1.31–1.51) for the “Never” group ( SI Appendix, Fig. S1C ). We also observed genome-wide significant associations between rs17185536-T and an EHR-based clinical diagnosis of erectile dysfunction (odds ratio 1.12, 95% CI 1.08–1.17) as well as with the use of PDE5i drugs or other erectile dysfunction treatments (odds ratio 1.16, 95% CI 1.12–1.19). Finally, because of the incomplete concordance across these different phenotype definitions, we conducted an analysis using a strict definition of case and control, requiring cases to meet case criteria for our survey and clinical and treatment definitions and controls to meet control criteria in all three definitions. We observed an even stronger association between the rs17185536-T allele and erectile dysfunction (odds ratio 1.37, 95% CI 1.31–1.43).

Because the risk of erectile dysfunction has been associated with a number of other risk factors, including higher BMI, diabetes, benign prostatic hyperplasia, lower urinary tract symptoms, hyperlipidemia, cardiovascular disease, and smoking status, we conducted analyses adjusting for each of these risk factors individually and combined in GERA to determine whether the risk locus imparted its effect via one of these risk factors. After adjusting for BMI, the effect of rs17185536-T remained similar to the overall GERA result (odds ratio 1.26, 95% CI 1.21–1.32) ( SI Appendix, Fig. S1B ), which is consistent with a lack of association between the SNP and BMI (P = 0.51). Similarly, the association between rs17185536 and erectile dysfunction was similar after adjusting for the other risk factors individually and in a model including all risk factors as covariates at the same time (odds ratio 1.27, 95% CI 1.21–1.33), suggesting that these risk factors do not explain the observed association. In the fully adjusted model, rs17185536 explained 1.6% of the heritability of the risk of ED. Finally, we used LD Hub to conduct a genetic correlation analysis with 177 traits with available GWAS summary statistics ( 9 ). After correcting for multiple testing, there were no significant associations with other traits.

To investigate whether the effect of the replicated erectile dysfunction risk locus was influenced by race/ethnicity, we examined the association of rs17185536 separately by GERA race/ethnicity group. The T allele of rs17185536 (rs17185536-T) was associated with an increase in the risk of erectile dysfunction in non-Hispanic whites (odds ratio 1.25, 95% CI 1.19–1.31), Hispanic/Latinos (odds ratio 1.35, 95% CI 1.16–1.57), East Asians (odds ratio 1.05, 95% CI 0.65–1.71), and African Americans (odds ratio 1.36, 95% CI 1.07–1.71) ( SI Appendix, Fig. S1A ). While the association was not significant (P > 0.05) in the East Asian group, this appears to be due to the lower frequency of the T allele in that group (2%) than in the other race/ethnicity groups (26% in non-Hispanic whites, 19% in Hispanic/Latinos, and 21% in African Americans). We also examined the association of rs17185536 by decade of age. We observed significant associations across each decade, with the strongest effect in men aged 50–59 y (odds ratio 1.32, 95% CI 1.24–1.41).

Manhattan plot of the GERA discovery cohort multiethnic genome-wide association meta-analysis of erectile dysfunction. A GWAS of erectile dysfunction was conducted in 36,649 men (14,215 cases and 22,434 controls) from four race/ethnicity groups (non-Hispanic white, Latino, East Asian, and African American). Association results (−log 10 P values) are plotted for each chromosome. The SIM1 gene name at the locus associated with erectile dysfunction is indicated.

In our discovery multiethnic GWAS analysis, we identified a single locus on chromosome 6 with multiple noncoding SNPs that were associated at a genome-wide level of significance with erectile dysfunction (P < 5 × 10 −8 ) ( Fig. 1 ). To prioritize associated SNPs for follow up analyses, we used a Bayesian approach to derive the smallest set of variants that included the causal variant with 95% probability (95% credible set) ( 7 ). Five SNPs were included in this 95% credible set ( SI Appendix, Table S1 ). We then conducted a replication association analysis of these five SNPs in an independent cohort of 222,358 men (2,957 cases and 219,401 controls) from the UK Biobank ( SI Appendix, Table S2 ). All five credible set SNPs were significantly associated with erectile dysfunction in the replication analysis (P < 0.01 required for multiple testing; all SNPs were associated P < 10 −13 ) in the same direction as the GERA cohort results ( SI Appendix, Table S3 ). As evolutionary conservation is a strong marker of functional genomic sequences, we focused our follow-up analyses on one of the five SNPs, rs17185536, which was the only SNP located in an evolutionarily conserved region ( 8 ).

We conducted the primary-discovery erectile dysfunction GWAS using the survey phenotype definition in 36,349 men from four race/ethnicity groups (non-Hispanic whites, 81.4%; Hispanic/Latinos, 8.1%; East Asians, 7.5%; and African Americans, 3.0%) in the GERA cohort ( Table 1 ). Cases were older than controls (68.9 ± 10.8 vs. 56.1 ± 11.4 y), had slightly higher body mass indices (BMIs) (27.7 ± 4.7 vs. 26.9 ± 4.3), were more likely to have diabetes (29.8% vs. 14.6%), and were more likely to be current smokers (6.2% vs. 5.5%) or former smokers (53.1% vs. 37.2%). Cases were also more likely than controls to have a clinical diagnosis recorded in the electronic health record (EHR) (39.3% vs. 23.3%) and were more likely to have filled a phosphodiesterase type 5 inhibitor (PDE5i) prescription to treat erectile dysfunction (59.2% vs. 29.0%).

Discussion

We identified a single locus near the SIM1 gene that was significantly associated with the risk of erectile dysfunction and confirmed that association in a large, independent cohort. The association was robust to changes in phenotype definition and was independent of known erectile dysfunction risk factors. Through a series of analyses, we showed that the region containing the lead variant likely interacts with the promoter of the SIM1 gene and that the risk allele of the lead variant alters an enhancer.

Several different lines of evidence suggest a biologically plausible role for SIM1 in erectile dysfunction susceptibility. SIM1 encodes a transcription factor that is active in the leptin–melanocortin pathway, a system that plays a central role in body weight homeostasis and sexual function (14). The melanocortin peptides alpha melanocortin-stimulating hormone (α-MSH) and adrenocorticotrophic hormone (ACTH) have long been known to stimulate penile erection in male animals (15, 16); MT-II, a synthetic analog of α-MSH, has been shown to induce penile erection in men (17).

While both MT-II and α-MSH are nonselective melanocortin agonists, it is believed that their effect on sexual function is mediated by the melanocortin 4 receptor (MC4R). Mice lacking Mc4r display impaired copulatory behavior (18), an effect that is reversed when MC4Rs are reexpressed only on SIM1-expressing neurons (19). In the latter study, SIM1-dependent expression of MC4R was observed in the paraventricular nucleus of the hypothalamus and medial amygdala. Rare mutations in the coding sequences of both MC4R and SIM1 cause severe forms of human obesity (20), and neurons coexpressing MC4R and SIM1 in the paraventricular nucleus of the hypothalamus have been shown to be both necessary and sufficient for the regulation of feeding and body weight in mice (21).

In our study, the SNPs in the erectile dysfunction risk locus were not associated with variation in BMI, nor was the effect of this locus on the risk of erectile dysfunction changed after adjusting for BMI. We hypothesize that the SIM1 enhancer harboring rs17185536 or the other erectile dysfunction-associated alleles that show differential enhancer activity are active in neurons that control erectile function but not in those controlling feeding and body weight homeostasis. Melanocortin agonists have been shown to initiate penile erection when administered in both the brain and the spinal cord (22). Determining whether the neurons that are sufficient for erectile function are located in the brain, the spinal cord, or both will be essential to understand the specificity of the erectile dysfunction risk locus identified in this study. Further in vivo analyses of enhancers in this region have the potential to address these questions.

An important limitation of the current investigation is the potential for phenotype misclassification when using a self-reported, survey-based phenotype. We addressed this limitation by conducting a number of sensitivity analyses using alternative phenotype definitions based on EHRs and replication in an independent cohort with a different phenotype definition. While the difference in phenotype definition can reduce power to confirm associations, we observed strong confirmation of the discovery association, which provides further support for the robustness of the observed association to changes in phenotype definition. The incomplete concordance between the survey, clinical, and treatment-based phenotype definitions is expected and has been described previously in the literature (2). Many men with erectile dysfunction do not seek medical care for the condition. For this reason, the absence of a clinical diagnosis or PDE5i prescription is not on its own an indicator of an absence of erectile dysfunction. To limit the potential presence of cases among our control group, and vice versa, we conducted an analysis using strict case and controls definitions in which each strict case met the case criteria for the survey and clinical and treatment-based phenotype definitions, and each strict control met the control criteria for all three definitions. We again observed a significant association with the same locus, with a modestly stronger effect size.

While MC4R and SIM1 loss of function are associated with erectile dysfunction, we observed increased enhancer activity for the rs17185536 erectile dysfunction-associated allele. This could be due to this SNP not being the causative variant, to interaction between this variant and other SNPs, or to this region having an additional, as yet uncharacterized function. Further analyses of this region will be needed to characterize its functional role.

Another limitation is that we did not have a comparable phenotype available in women. Based on both human and animal studies of the effects of melanocortin agonists on sexual function in females, it is possible that our erectile dysfunction risk locus may also affect female sexual function, including sexual desire and sexual arousal (23, 24).

Our study is a large-scale investigation of the genetics of erectile dysfunction. We anticipate that future studies involving even larger samples will uncover additional risk loci, providing further insights into the etiology of erectile dysfunction. Our functional analyses, along with previous studies in the literature, point toward a previously unknown mechanism underlying erectile dysfunction, which opens the possibility of developing drug therapies with a more specific target. Those treatments may have the potential to improve sexual function in both men and women.