{"paper_id":"83f7644e-bf1f-4e7d-9bbb-99017235062f","body_text":"Evidence of shared genetic factors in the aetiology of gastrointestinal \ndisorders and endometriosis and clinical implications for disease \nmanagement \n \nFei Yang 1, Yeda Wu 1, Richard Hockey 2, Jenny Doust 2, Gita D. Mishra 2, Grant W. \nMontgomery1 on behalf of the International Endometriosis Genetics Consortium and Sally \nMortlock1 \n1. The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD \n4072, Australia \n2. The University of Queensland, NHMRC Centre for Research Excellence on Women and \nNon-communicable Diseases (CREWaND), School of Public Health, Herston Road, \nHerston, QLD, Australia. \n \nGraphical abstract \n \n \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \nNOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.\n\n 2 \nAbstract \nIn clinical practice, the co-existence of endometriosis and gastrointestinal symptoms is often \nobserved; however, the factors driving this link remain largely unknown. Here, using large-\nscale multifaceted data including observational, genetic, and pharmaceutical datasets, we \nreport a positive phenotypic and genetic association of endometriosis with peptic ulcer \ndisease (PUD), gastro-oesophageal reflux disease (GORD), a combined GORD/PUD \nMedicated (GPM) phenotype and irritable bowel syndrome (IBS), but not with inflammatory \nbowel disease (IBD). Mendelian randomization analysis identified a causal effect of the GPM \nphenotype on endometriosis and a bidirectional causal association between endometriosis and \nIBS. Cross-trait meta-analysis and colocalization along with comprehensive functional \nannotation confirmed two shared genetic loci ( FN1, \nTACSTD2) for endometriosis with IBS \nand twelve loci (ETAA1, HOXC4, RERG, SEMA3F, SPAG16, HIST1H2BC, RAB5B, CCKBR \nand PDE4B ) with GORD and PUD. Shared genetic loci may contribute to risk of both \nendometriosis and digestive disorders through the involvement of DNA damage, estrogen \nregulated cell-proliferation and inflammation, and barrier dysfunction. Analyses of \nmedication usage identified a higher use of drugs for IBS, GORD and PUD in women \ndiagnosed with endometriosis as well as a higher use of hormone therapies in women \ndiagnosed with IBS, GORD and PUD but not for IBD, which strongly supports the co-\noccurrence of these conditions and highlights the potential for drug repositioning and caution \naround drug contraindications in clinical practice. Taken together, the combined evidence \nrobustly suggests a shared disease aetiology and provides important clinical implications for \ndiagnostic and treatment decisions for endometriosis and digestive disorders.  \n \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 3 \nWHAT IS ALREADY KNOWN ON THIS TOPIC?  \n• Both endometriosis and gastrointestinal disorders affect a large proportion of people \nworldwide and the co-existence of endometriosis and gastrointestinal symptoms (eg, \nabnormal pain, bloating, constipation) is often observed in clinical practice.  \n• The association of these two diseases was supported but also limited to previous \nobservational evidence which highlights a three-fold increase in the prevalence of \nirritable bowel syndrome (IBS) in women with endometriosis.  \n• Observational study is easily subject to measurement error, confounding and reverse \ncausation. Therefore, it is important to assess the association using multidimensional \ndatasets and more accurate approaches, such as the use of genetic data in a mendelian \nrandomisation framework as well as the analysis from a perspective of medication usage.  \n \nWHAT THIS STUDY ADDS \n• Genetic risk factors for endometriosis and gastrointestinal disorders, two leading causes \nof discomfort and chronic pelvic pain, are correlated.  \n• Mendelian randomisation analyses supported a causal relationship between genetic \npredisposition to gastrointestinal disorders (gastro-oesophageal reflux disease (GORD) \nand peptic ulcer diseases (PUD)) and endometriosis risk, and evidence for a bidirectional \ncausal relationship between endometriosis and IBS, which might explain in part the co-\noccurrence of these diseases.  \n• The identification of shared risk loci highlighted biological pathways that may contribute \nto the pathogenesis of both diseases, including estrogen regulation and inflammation, as \nwell as potential therapeutic drug targets such as CCKBR and PDE4B.  \n• The higher use of drugs for IBS, GORD and PUD in women diagnosed with \nendometriosis as well as the higher use of hormone therapies in women diagnosed with \nIBS, GORD and PUD, support the co-occurrence of these conditions and shared disease \naetiology but also highlights the potential for drug repositioning and caution around drug \ncontraindications.  \n \nIntroduction  \nEndometriosis is a common gynaecological disease affecting around 11% of reproductive \naged women, significantly impacting quality of life and work productivity 1 2 . The clinical \nmanifestations of endometriosis are diverse. Many of the symptoms are non-specific, which \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 4 \npreclude timely diagnosis and further prognosis 1 3 . It has often been observed that many \nwomen diagnosed with endometriosis also experience symptoms associated with \ngastrointestinal disorders (GI) including abdominal pain, bloating, constipation, heartburn, \ndyspepsia, vomiting, painful bowel movements, diarrhea, and nausea\n4-6. Studies have shown \nthat whilst these symptoms do not necessarily involve bowel lesions associated with \nendometriosis, symptoms such as cyclic-related bloating, constipation and diarrhea can get \nworse during menstruation\n5-8. Inevitably, this presents challenges for clinicians to accurately \ndiagnosis both diseases among women. Understanding shared disease aetiology critically \nimpacts both disease diagnosis and management.  \n \nPrevious observational studies have provided some evidence for the associations between \nendometriosis and digestive disorders. Meta-analyses have reported a three-fold increase in \nthe prevalence of IBS in women with endometriosis compared to women without \nendometriosis\n9 10. This was supported by a recent retrospective study using a large nationwide \nbiobank-based cohort, the Estonian Biobank (EstBB), that reported a notable proportion of \nwomen diagnosed with endometriosis or IBS also suffered from IBS (13.6%) or \nendometriosis (9.0%), respectively\n11. A nationwide Danish cohort study found a significantly \nincreased risk of inflammatory bowel disease (IBD) in endometriosis patients with a \nstandardised incidence ratio (SIR) of 1.5 (95% confidence interval 1.4 to 1.7), and the \nrelationship became stronger when restricted to surgically confirmed endometriosis\n12. \nCurrently, very few observational studies have investigated the association between \nendometriosis and other gastrointestinal disorders. However, endometriosis symptoms \noverlap with other common gastrointestinal disorders, including peptic ulcer disease (PUD) \nand gastro-oesophageal reflux disease (GORD)\n13.  \n \nDespite studies showing endometriosis patients are more likely than people without \nendometriosis to present gastrointestinal symptoms or have a diagnosis of gastrointestinal \ndisorders, it is uncertain whether this is due to 1) a direct effect of endometriosis itself; 2) \nshared aetiological factors between endometriosis and gastrointestinal diseases; 3) side \neffects of medical treatments; or 4) the inevitable association bias in observational studies, \nsuch as the measurement error, reverse causation, residual or unmeasured confounding\n14. For \nexample, therapeutic use of gonadotropin-releasing hormone (GnRH) analogues and \nnonsteroidal anti-inflammatory drugs (NSAIDs), to manage symptoms of endometriosis, has \nbeen widely reported to aggravate the severity of gastrointestinal symptoms and contribute to \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 5 \ngastrointestinal disorders including PUD 6 15-18 . Therefore, using a more accurate approach \nand multidimensional dataset to validate the relationship between endometriosis and \ngastrointestinal disorders has important implications, not only for understanding shared \ndisease mechanisms but also for informing therapeutic strategies in clinical practice. \n \nEndometriosis and gastrointestinal diseases mentioned above are common multifactorial \ndiseases with environmental and genetic risk factors both playing roles in the development of \nthese diseases\n19 20 . Twin and family studies have shown a heritable component of \nendometriosis, IBS, PUD, IBD and GORD 21-26. Genome-wide association study (GWAS), \nwhich have been widely used to identify disease associated genetic risk variants 27, also \nenable the use of mendelian randomisation (MR) approaches to assess the causal effect of \ncumulative genetic predisposition to one disease on other disease risk. Given the advantage \nthat genetic alleles are randomly determined at conception and free from potential \nenvironmental confounders (eg. medication usage) and measurement error due to self-report, \nMR analysis can minimize the biases that frequently weaken results obtained from \nobservational approachs\n14 28.  Therefore, application of GWAS data and an MR framework is \nof great value in understanding shared aetiology.  \n \nOne study recently implicated causal links between endometriosis and depression with gastric \nmucosa abnormalities using genetic data29. However, the relationship between endometriosis \nand other common GI disorders, like IBS and IBD and PUD, were not investigated.  GWAS \nstudies have identified risk variants for endometriosis and gastrointestinal disorders \nindependently30-32,  including one female-specific IBS risk locus at 9q31.2, which was also \npreviously reported as more strongly associated with early age at menarche32, a risk factor for \nendometriosis. This study presents a comprehensive evaluation of the relationship between \nendometriosis and gastrointestinal disorders through analysis of large-scale genetic datasets, \nand epidemiological and pharmaceutical data in the UK Biobank (UKB) and Australian \nLongitudinal Study on Women’s Health (ALSWH)\n33 34.  \n \nMethod  \nData resources \nThe large-scale GWAS summary statistics for endometriosis and five gastrointestinal \ndisorder phenotypes, utilized in this study, have been well described in previous studies 30 31. \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 6 \nSummary data for endometriosis were restricted to eight European ancestry cohorts 31 35 for \nthe purpose of this analysis. A total number of 14,926 cases and 189,715 controls genotyped \nacross 7,899,415 SNPs were included in the endometriosis meta-analysis.  GWAS summary \nstatistics for four gastrointestinal disorders, gastro-oesophageal reflux disease (GORD) (n\ncase \n= 39,851, ncontrol  =  416,563), peptic ulcer disease (PUD) (n case  = 12,226, ncontrol  =  444,188), \nirritable bowel syndrome (IBS) (n case = 14994, n control = 441420) and inflammatory bowel \ndisease (IBD) (n case  =  6,115, n control  =  450,299), were previously generated using genetic \ndata from individuals in the UK Biobank (UKB), using the health-related outcomes data from \ncombing self-reported, primary care, death register and hospital reported diagnoses. As \nmedications used for PUD also have a therapeutic effect on GORD, a fifth phenotype for \ngastrointestinal disorders is the combined GORD and PUD and individuals taking \nmedications for GORD/PUD making a total of 75,192 cases and 381,222 controls in the \nGORD/PUD Medicated (GPM) phenotype\n30. Sex stratified GWAS summary statistics for \nIBS were also generated in this study for the purpose of exploring potential sex bias in the \nrelationship between endometriosis and IBS.  \n \nComorbidity analysis  \nAs a cross-sectional analysis, the comorbid relationship between endometriosis and each \ngastrointestinal disorder (IBS, IBD, GORD and PUD) described above were investigated \namong unrelated European female individuals in the UKB, with ancestry definition described \npreviously36. Phenotypes were defined using self-reported, hospital admission, death register \nor primary care record data. Endometriosis cases were defined using date and source of \nendometriosis reported (UKB data fields:132122 & 132123), ICD10 diagnosis (UKB data \nfield:41270), ICD9 diagnosis (UKB data field: 41271) and self-report (UKB data field: \n20002), totalling 5,392 cases (excluding endometriosis of the uterus/adenomyosis). \nGastrointestinal disorders definitions were similar as previously described by Wu et al. 30 \nhowever, these were also restricted to females. A total of 16,330 IBS cases were included \n(UKB data field: 131639) alongside 22,383 GORD cases (UKB data field: 131585). IBD and \nPUD were defined using a combination of disease codes, IBD cases were a combination of \nCrohn’s diseases (UKB data field: 131627) and ulcerative colitis (UKB data field: 131629) \ndiagnoses totalling 2,708 cases and PUD cases were a combination of gastric ulcer cases \n(UKB data field : 131591), duodenal ulcer cases (UKB data field: 131593), other site peptic \nulcer cases (UKB data field: 131595) and gastro-jejunal ulcer cases (UKB data field : \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 7 \n131597) totalling 5,208. We firstly measured whether individuals diagnosed with \nendometriosis were more likely to have a diagnosis of IBS, IBD, GORD and/or PUD using \nFisher’s exact test. Next, we conducted a competitive comorbidity analysis to test which \ndigestive disorder is more prone to be comorbid with endometriosis among these four \ndisorders. Briefly, the proportion of endometriosis cases in each of the four digestive diseases \nwere calculated and then compared in pairs using a two-proportion Z-test. To meet the \nprerequisite of this analysis that samples in each pair are independent, we removed \noverlapping samples when calculating the proportion. \n \nGenetic correlation  \nGenetic correlation attributable to the genome-wide common SNPs between endometriosis \nand each of the other five gastrointestinal disorder phenotypes (IBS, IBD, GORD, PUD, \nGPM) was estimated using bivariate linkage disequilibrium score regression (LDSC)\n37 and \ntheir respective GWAS summary statistics. GWAS summary data was formatted using the \nfunction ‘munge_sumstats.py’ outlined in the LDSC manual and the genetic correlation for \neach pair was estimated. The European 1000 genome reference data was adopted in the \ncalculation of linkage disequilibrium (LD) scores. A sex-stratified analysis was conducted to \nfurther investigate whether the genetic correlation between endometriosis and IBS is sex \ndependent. Given that there was no sample overlap in GWAS studies of endometriosis and \ngastrointestinal disorders and all participants are of European ancestry, we also reduced \nstandard error of genetic correlations by constraining the intercept, which was used to protect \nbias from population stratification and sample overlap in different GWAS studies. \n \nAssessing potential causal relationships  \nMendelian randomisation (MR) uses genetic variants that are robustly associated with \nexposure of interest to test whether those genetic variants also increase the risk of another \ntrait \n14. MR has emerged as a valuable tool to assess the causal effect of one trait on another. \nThe genetic variants selected are robust and are not associated with other confounders and \nwill only influence the outcome trait through the trait of interest if there is a causal \nassociation, thus less susceptible to confounding, measurement error, and reverse causation \nwhen compared with conventional observation studies\n14 38 39 . In this study, the causal \nrelationships between endometriosis and gastrointestinal disorder phenotypes (IBS, GORD, \nPUD, GPM) was investigated using one wildly-accepted MR method called Generalised \nSummary-data-based Mendelian randomization (GSMR)\n40. The combined phenotype of \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 8 \nGPM was used in place of individual GWAS for PUD and GORD to increase study power. \nGSMR uses all significantly associated SNPs as SNP instruments to test for causality. To \nreduce the influence of horizontal pleiotropy (a single locus directly affecting multiple \nphenotypes), one potential confounding factor for Mendelian randomization analysis, we also \napplied the HEIDI-outlier analysis to detect SNPs having obvious pleotropic effect on both \nrisk factor and diseases. To remove potential confounding from the correlation between the \nGI traits, we applied mtCOJO\n40 on both the exposure and outcome trait. We further used the \nadjusted GWAS summary statistics to repeat the GSMR analysis again. A P-value of < 0.05 \nwas considered significant. In some cases there was an insufficient number of SNPs to use as \ninstruments and so the GWAS threshold was relaxed to allow at least ten SNPs for each \nphenotype, following the author’s recommendation to include at least 10 SNP instruments \nduring GSMR analysis to achieve robust results.   \n \nCross-trait meta-analysis of endometriosis and gastrointestinal diseases \nWe next adopted two complementary cross-trait meta-analysis methods, MetABF\n41 and Eskin \nrandom-effects model (RE2C) 42, to identify whether there are shared risk loci between \nendometriosis and the digestive disorders (IBS, GPM), as well as potential novel risk loci for \neach disease. MetABF performs the multi-trait meta-analysis based on the Bayesian \nframework. Effect alleles were harmonised across all three GWAS. Both fixed and \nindependent effect models were used when performing this meta-analysis. The prior \nparameter accounting for effects of heterogeneity in two diseases was set as 0.1, which is \ntypically used in complex diseases. As a result, SNPs with a logABF > 4 and at least a \nnormally significant P-value < 0.05 in each individual disease GWAS analysis were defined \nas significant in the MetABF analysis.  \n \nTo validate the MetABF results, we used a complementary cross-trait meta-analysis \napproach, RE2C, which dramatically increases power when statistics among different studies \nare correlated compared with other methods. RE2C also accounts for the heterogeneous \neffects within studies using a novel statistic model. Similar to MetABF, effect alleles were \nharmonised across the GWAS prior to being used as input for the RE2C analysis. As a result, \na SNP meeting the P -value threshold of < 5e-8 in either fixed (Lin-Sullivan method) or \nrandom (RE2C) effects model and having at least a normally significant P-value < 0.05 in the \nindividual disease GWAS, were deemed as significant in the meta-analysis. SNPs meeting \nboth thresholds of MetABF and RE2C were selected for the further fine mapping analysis in \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 9 \nFunctional Mapping and Annotation (FUMA) 43 to identify independent risk loci using a \nthreshold of r2/i1 </i1 0.6 and then the lead SNPs at a threshold of r2/i1 </i1 0.1.  The maximum \ndistance between LD blocks to merge into a locus were set as 250kb.  \n \nColocalization analysis \nTo identify specific genomic regions that have the same causal variant for each disease we \nconducted a pairwise GWAS (GWAS-PW) 44 analysis. Again, this analysis was restricted to \ncomparisons with IBS and GPM. The input to GWAS-PW is a set of estimated effect sizes \nand standard error for each SNP on each of the paired diseases. The whole genome was split \ninto 1,703 LD independent blocks, and the probability is estimated for four models extended \nfrom Giambartolomei et al\n45, that a given region (a) contains a genetic variant that impacts \nfirst disease (PPA1); (b) contains a genetic variant that impacts the second disease (PPA2); \n(c) contains a genetic variant that affects both diseases; (PPA3) or (d) contains two distinct \nvariants that influences each disease separately (PPA4). Paired summary statistics for \nendometriosis with IBS or GPM were analysed. Any regions that were identified with a \nPPA3/PPA4 >0.5 were considered to show evidence of a shared causal variant and two \ndistinct causal variants respectively.   \n \nFunctional annotation and gene mapping \nIn order to identify potential target genes associated with both endometriosis and IBS or \nGPM, we used FUMA to perform Multi-marker Analysis of GenoMic Annotation \n(MAGMA) gene-set analysis and two additional annotation approaches, positional mapping \nwith combined annotation-dependent depletion (CADD) score and cis-expression \nquantitative trait loci (eQTL) mapping for independent SNPs and SNPs in LD identified in \nthe above cross-trait meta-analysis. Gene sets were adopted from Genotype-Tissue \nExpression (GTEx) project which collects 54 non-diseased tissue sites across nearly 1000 \nindividuals\n46. Cis-eQTL information of 12 digestive and reproductive tissues (Supplementary \nTable 1) in the GTEx Project 46, endometrium eQTLs 47 and a large blood eQTL dataset, \neQTLGen48 were used for the eQTL mapping analysis. Variants with a CADD score of more \nthan 12.7 were defined as potentially pathogenic. \n \nSMR analysis is a powerful approach to identify likely causal relationship between the trait-\nassociated SNPs and gene expression. SMR analysis was performed on endometriosis, IBS \nand GPM respectively using eQTL data from 12 digestive and reproductive tissues in the \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 10\nGTEx project46 and endometrium 47. Associations were defined as significant if PSMR < 0.05 \nand PHEIDI > 0.05. We determined if any SMR significant genes were shared between the \ndiseases. Shared causal associations indicated that SNPs may be associated with both \ndiseases through the regulation of expression of the same gene. \n \nAdditional epigenomic functional annotation was performed with EpiMap\n49 using epigenome \nmaps from relevant tissues (uterus, ovary, gastroesophageal sphincter, Peyer’s patch, \noesophagus, stomach, colon, intestine, rectum) to define chromatin states, enhancers, \nupstream regulators and downstream target genes.\n \n \nPathway-based enrichment analysis \nTo identify which biological pathways are associated with both endometriosis and IBS or \nGPM, we firstly performed a gene-set enrichment analysis using MAGMA implemented in \nFUMA. Significant SNPs from the cross-trait meta-analysis were used as input for MAGMA \nand a window of 0kb outside of a gene was adopted in the gene-set analysis. In addition, \ngenes annotated to significant loci from the cross-trait meta-analysis were included in a \nGENE2FUNCTION analysis in FUMA to identify whether these genes were enriched in any \ncurated gene sets.  \n \nPhenome-wide association \nIn order to investigate whether the correlation between endometriosis and each of IBS and \nGPM can be explained by the genetic susceptibility to any other traits or diseases, we \nsearched traits that were associated with genome-wide significant independent SNPs and \nSNPs in LD (r\n2 > 0.8) from the cross-trait meta-analysis. We used information from GWAS \ncatalogue and PhenoScanner 50.  \n \nDrug target analysis  \nUsing the online Open-targets drug database (www.targetvalidation.org\n), we investigated if \nany known drug targets are common across endometriosis and gastrointestinal disorders \n(GORD, PUD, IBS) and if any genes functionally annotated to shared risk loci are potential \ndrug targets for either endometriosis and/or digestive disorders. \n \nMedication usage  \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 11\nTo investigate the implications of medication use on the relationship between endometriosis \nand gastrointestinal disorders we analysed Pharmaceutical Benefits Scheme (PBS) data by \nendometriosis status from the 1973-78 and 1989-95 cohorts in the Australian Longitudinal \nStudy on Women’s Health (ALSWH)\n33 34 . The frequency of medications used in these \nwomen was calculated. In addition, we characterized the medication use (UKB data field: \n20003) in unrelated women in the UK Biobank, including 5,392 women diagnosed with \nendometriosis, 15,881 women with IBS, 22,383 women with GORD, 5,208 women with \nPUD and 2,708 women with IBD. We randomly selected age-matched controls to avoid the \npotential bias caused by differences in age distribution between cases and controls. \nDifferences in the proportion of women, with and without an above diagnosis, using reported \nmedications was tested using fisher test. After correcting for multiple testing using \nBonferroni analysis, a P-value of < 0.05 was considered significant.  \n \nResults  \nSignificant comorbid relationship between endometriosis and GI disorders \nUsing data from 188,461 unrelated females in UKB, we found a bidirectional \nepidemiological relationship between endometriosis and each of the four GI disorders (IBS, \nIBD, GORD, PUD). GORD and IBS remained significant after accounting for multiple tests. \nOf those associations (Table 1), women with endometriosis were two times more likely to \nhave an IBS diagnosis (OR = 2.01, 95% CI 1.86 to 2.16; P-value = 3.90e-68), and 1.4 times \nmore likely to have a GORD diagnosis (OR = 1.40, 95% CI 1.30 to 1.50; p = 3.54e-18), than \nthose free of endometriosis. The competitive comorbidity analyses confirmed that women \nwith endometriosis are more prone to be comorbid with IBS, followed by GORD, when \ncompared with PUD (OR = 1.22, 95% CI 1.05 to 1.42; p = 0.01) and IBD (OR = 1.25, 95% \nCI 1.01 to 1.53; p = 0.04) (Figure 1).  \n \nGenetic correlation between endometriosis and GI disorders \nCompared with comorbidity relationship identified above, the LDSC analysis only provided \nevidence of a significant positive genetic correlation (rg) between endometriosis and IBS (rg \n= 0.22, p = 0.005), GORD (rg = 0.16, p = 0.004), PUD (rg = 0.23, p = 0.003) and GPM (rg = \n0.22, p =\n 2.17e-06) (Figure 2A). There was no evidence of significant correlation between \nendometriosis and IBD. Constraining the intercept due to no sample overlap, resulted in a \nsmaller standard error whereas there was little change in the genetic correlation (Figure 2A).  \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 12\nAlthough endometriosis is rarely observed in males, males do carry endometriosis risk \nalleles, as such we also conducted the genetic correlation analysis separately for females and \nmales. The results remained significant between endometriosis and both the separate female \n(rg = 0.28, p = 0.003) and male (rg = 0.21, p = 0.014) IBS GWAS cohorts (Figure 2B).\n \n \nComplex causal relationship between endometriosis and GI disorders \nFollowing the identification of shared genetic correlation, we applied an MR method 40 to \nestimate the causal relationship between GPM, IBS, and endometriosis (Figure 3). We \nidentified evidence of a significant association between GPM and endometriosis whereby \ngenetic variants contributing to the risk of GPM (genetic predisposition to GPM) also \nincreased risk of endometriosis (odds ratio = 1.56 (95% CI 1.35 to 1.76), p = 2.47e-5) (Table \n2). The reverse MR analysis (the genetic effect of endometriosis on GPM) was not \nstatistically significant (odds ratio = 0.98 (95% CI 0.94 to 1.02), p = 0.32). Due to the limited \nnumber of SNP instruments available for IBS when using a genome-wide significant level (P \n< 5e-8), we were unable to estimate the effect of IBS on endometriosis risk. However, using \nendometriosis as the exposure we identified that genetic variants contributing to the risk of \nendometriosis had a small effect on risk to IBS (odds ratio=1.07 (95% CI 1.01 to 1.13), p = \n0.042). This effect was no longer significant following stringent Bonferroni correction for \nmultiple testing. \n \nTo increase the number of SNP instruments in the analysis we relaxed the SNP inclusion \nthreshold to P < 5e-6 and repeated the GSMR analysis. The relationship between GPM and \nendometriosis, and endometriosis and IBS, was consistent, although attenuated, compared \nwith that estimated using the genome-wide significant level ( P < 5e-8) (Table 2). \nInterestingly, we also found evidence of bi-directional relationship between IBS and \nendometriosis. Genetic variants that increased risk of IBS had a significant risk effect on \nendometriosis (odds ratio=1.15 (95% CI 1.03 to 1.28), p = 0.028) however, this effect was no \nlonger significant following stringent Bonferroni correction for multiple testing. \n \nA genetic correlation  and strong bi-directional association between IBS and GPM has been \npreviously reported\n30 , with genetic predisposition to IBS having a causal effect on GPM \n(odds ratio = 1.20 (95% CI 1.15 to 1.24), p = 1.93e-14) and genetic predisposition to GPM \nhaving a causal effect on IBS (odds ratio = 1.34 (95% CI 1.28 to 1.40), p = 7.29e-23). The \ncomplex causal relationship among the three diseases is illustrated in Figure 3. The \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 13\nrelationship between GI disorders may act as a confounder impacting the results of each pair \nof MR analyses. To avoid the potential effect of GPM on the relationship between \nendometriosis and IBS, we adjusted the GWAS data of both endometriosis and IBS for the \neffects of GPM using mtCOJO to identify disease specific variant associations independent \nof GPM. Following this conditional analysis, evidence for the bi-directional causal \nrelationship between IBS and endometriosis remained (Table 2, Figure 4). The causal \nrelationship between GPM and endometriosis, following adjustment for the genetic effects of \nIBS, was only significant when the less stringent SNP inclusion p-value threshold was used \nbut did not pass correction for multiple testing (odds ratio = 1.16 (95% CI 1.05 to 1.27), p = \n0.008) (Table 2, Figure 4).  \n \nMR was run separately for GORD and PUD to test if the relationship between GPM and \nendometriosis was driven by one particular phenotype. There was evidence of a significant \nrelationship between GORD and endometriosis which remained when conditioning both \ntraits on PUD (OR=1.15 (95% CI 1.10 to 1.21), p=1.69e-6) however, there was no evidence \nof a causal relationship between PUD and endometriosis (Supplementary Table 2). More \npowerful GWAS studies may be required to validate these causal relationships. \n \nGenomic loci associated with both endometriosis and GI disorders  \nTo identify if there are any risk loci associated with both endometriosis and IBS or GPM, we \ncarried out a cross-trait meta-analysis using two different methods, MetABF and RE2C. \nSNPs were considered associated with both diseases at a genome-wide significant level if \nthey had a logABF > 4 in MetABF and a P -value < 5e-8 in RE2C models and a P-value < \n0.05 in each individual GWAS analysis. As a result, a total number of 477 SNPs met criteria \nfor endometriosis and GPM while only 32 SNPs were significant for endometriosis and IBS. \nUsing FUMA, 12 genomic risk loci (21 independent signals) were identified as significantly \nassociated with both endometriosis and GPM and three with endometriosis and IBS (Table \n3). Among those loci identified by the cross-trait meta-analysis, the SNP on chr2:67845739 \n(rs2861694) within ETAA1 was previously reported as associated with both endometriosis \nand GPM, another five SNPs were significantly associated with either endometriosis or \nGPM.  The remaining nine risk loci were identified for the first time at a genome-wide level \nof significance for endometriosis and GPM and IBS (Table 3).  \n \nEvidence of shared causal variants between endometriosis and GI disorders \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 14\nGWAS-PW was used to perform a colocalization analysis to assess if any of the genomic \nregions jointly affected endometriosis and IBS. Results (Table 4) showed that there were \nthree regions with PPA3 > 0.5 and three regions with PPA4 > 0.5, suggesting that 3 regions \ncontain the same causal variant for both endometriosis and IBS whereas another three regions \ncontain distinct and independent causal variants for endometriosis and IBS respectively. \nAnalysing endometriosis and GPM, we identified six regions with PPA3 > 0.5 and 60 regions \nwith PPA4 > 0.5. None of the regions with PPA3 > 0.5 in endometriosis and GPM \noverlapped with the three regions identified between endometriosis and IBS.  Regions with \nevidence of a single casual variant (PPA3 > 0.5) for both endometriosis and either IBS or \nGPM are shown in Table 4. Among these identified regions, the two loci ( TACSTD2 and \nFN1) with the highest probability of a shared causal variant for endometriosis and IBS and \nthe three loci (ETAA1 , HOXC4 and RERG) with the highest probability of a shared causal \nvariant for endometriosis and GPM were also identified by the cross-trait meta-analysis \ndescribed above. Specifically, the region with the strongest pleiotropic effect on \nendometriosis and GPM is located near ETAA1/LINCO1812 on chromosome 2 (Figure 5) , \nSNPs in this region are significantly associated with these two diseases and the index SNPs in \nthe individual GWAS studies are in strong LD (r\n2 = 0.88). Other regions identified by both \ncross-trait meta-analysis and GWAS-PW are shown in Supplementary Figure 1A-G.  \n \nGene mapping and functional annotation of shared risk loci  \nWe performed a gene-based analysis using MAGMA to identify potential genes associated \nwith both endometriosis and IBS or GPM. A total of 19 protein coding genes mapped to \nSNPs from the endometriosis and GPM cross-trait meta-analysis reached genome-wide \nsignificance (Supplementary Table 3). Only FN1 passed the MAGMA analysis for SNPs \nfrom endometriosis and IBS meta-analysis.  \n \nTo better understand the potential regulatory function of identified risk loci associated with \nboth diseases, we mapped risk SNPs to cis-eQTLs in different tissues for genes up to 1MB on \neither side of the variant using FUMA. Lead SNPs in three loci ( RAB5B, ETAA1 and HOXC) \nfrom the cross-trait meta-analysis were found to impact gene expression in either blood or \nboth digestive and reproductive tissues. In detail, we identified eQTLs for four genes in \ndigestive tissues that contained SNPs associated with risk of endometriosis and IBS from the \nGWAS meta-analysis (Supplementary Table 4).  Similarly, we identified eQTLs for 37 genes \nthat contained SNPs associated with risk of endometriosis and GPM from the GWAS meta-\n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 15\nanalysis (Supplementary Table 4). Seven are expressed both in digestive and reproductive \ntissues. Using a more powerful blood eQTL dataset from the eQTLGen project we identified \na total of 8 and 162 genes with eQTLs containing SNPs associated with risk of endometriosis \nand IBS, and GPM, respectively (Supplementary Table 4). Whilst 70% of genes with eQTLs \nin digestive and reproductive tissues were also in blood, indicating genetic regulation of gene \nexpression can be shared across tissues, 12 were not identified in blood and may represent \ntissue specific effects. For example, the lead SNP, rs773111, in RAB5B locus shared by \nendometriosis and GPM is an eQTL for RAB5B expression in blood and for nearby SUOX \ngene expressed in blood, digestive, and reproductive tissues.  \n \nCombined annotation-dependent depletion (CADD) scores, which inform the deleterious \neffect of a SNP on protein function, were used to further understand the function of shared \nSNPs using FUMA. Our results showed that risk variants shared between endometriosis and \nIBS located in WNT4 on chromosome 1 and FN1  on chromosome 2 had at least one SNP \nwith CADD score greater than 12.7 using positional gene mapping (Supplementary Table 5). \nRisk variants shared between endometriosis and GPM located in 33 different genes had at \nleast one SNP with CADD score greater than 12.7 (Supplementary Table 5).  \n \nTo investigate the shared functional mechanism of SNPs associated with both endometriosis \nand digestive disorders, we applied the Summary data-based Mendelian randomization \n(SMR) method. SMR integrates the GWAS summary statistics of disease with SNP-gene \nassociations (eQTL), and the significant SMR association indicates that the SNP is causal for \nthe disease as mediated through gene expression or has a pleiotropic effect on both disease \nand gene expression. We aimed to identify common associations between individual \nendometriosis and IBS and GPM SMR analyses. eQTL information in digestive and \nreproductive tissues in the GTEx project and in endometrium were used in this study. Our \nresults identified 155 genes with normally significant SMR associations ( P-SMR < 0.05; P -\nHEIDI > 0.05) for which variants were associated with risk of endometriosis and GPM and \nexpression in digestive and reproductive tissues simultaneously (Supplementary Table 6). Of \nthe 155 significant SMR associations, one variant (rs2344609), significantly associated with \nCNGA4 expression, was significant in the cross-trait meta-analysis and another (rs9873183), \nassociated with expression of RNF123, was in LD (r\n2 > 0.5) with significant SNPs in the \ncross-trait meta-analysis. When applied to endometriosis and IBS, we identified 91 genes \nwith nominally significant SMR associations for variants associated with both diseases and \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 16\nexpression in digestive and reproductive tissues (Supplementary Table 6). Of the 91 \nsignificant SMR associations, one variant (rs232877) associated with expression of MYSM1 \nwas in LD (r 2 > 0.65) with the lead SNP of TACSTD2  loci identified in the cross-trait meta-\nanalysis, demonstrating that it may contribute to the risk of both endometriosis and IBS \nmediated through MYSM1 expression.   \n \nRisk SNPs from the cross-trait metanalyses were also mapped to regulatory regions in \nreproductive and gastrointestinal tissues using EpiMap\n49. Of 477 SNPs significant in the \nendometriosis and GPM meta-analysis, 35 were located in predicted enhancers and nine of \nthese enhancers were predicted in both reproductive and gastrointestinal tissues \n(Supplementary Table 7). Gene targets of these enhancers included 10 genes on chromosome \n3 (CYB561D2, GNAI2, HYAL3, NAT6, NPRL2, RBM5, RBM6, SEMA3F, SLC38A3, TUSC2) \nand nine genes on chromosome 12 ( RERG, HOXC4, HOXC5, HOXC6, HOXC8, HOXC9, \nHOXC10, HOXC11, HOXC13) including a cluster of HOXC genes (Supplementary Table 8). \nFive SNPs were located in predicter promoter regions for RBM5 and RBM6 on chromosome \n3 and HOXC-AS1, RERG and SUOX on chromosome 12. Only one SNP significant in the \nendometriosis and IBS meta-analysis was located in a regulatory region, a predicted enhancer \nand promoter region in FN1 on chromosome 2 in colon and esophagus (Supplementary Table \n7).  \n \nIn total, 218 genes were mapped to 24 shared risk loci using at least one annotation method \nabove (Supplementary Table 9) and 37 genes had evidence from at least two methods (Table \n5). \n \nPathways enriched for genes in shared risk loci \nThe MAGMA gene-set analysis, which uses the full distribution of input SNP p-values to \nidentify whether curated gene sets and GO terms from MsigDB were significantly associated \nwith both diseases, found no gene set remained significant after multiple testing. We instead \nused another pathway enrichment approach, GENE2FUNC, to test whether 204 prioritized \ngenes (eQTL, CADD, MAGMA, SMR) linked to endometriosis and GPM were enriched in \npre-defined pathways based on their gene expression. As a result, a total number of five \nKEGG gene sets passed adjusted p-value threshold of P < 0.05, including “leukocyte \ntransendothelial migration”, “oxidative phosphorylation”, “epithelial cell signalling in \nhelicobacter pylori infection”, and “chemokine_signaling pathway” (Supplementary Table \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 17\n10). Genes were also enriched in 40 GWAS Catalog reported gene sets, including fat \ndistribution, BMI, intelligence, and depression (Supplementary Table 10).  The 14 genes \nlinked to endometriosis and IBS were enriched in two KEGG pathways including “pathway \nin cancer” and “ECM receptor interaction” and 17 GWAS Catalog gene sets (Supplementary \nTable 11). \n \nAdditional phenotypes associated with shared risk loci   \nGiven the nature of SNP pleiotropy, we further investigated whether there were previously \nreported trait associations with SNPs related to risk of both endometriosis and gastrointestinal \ndiseases through PhenoScanner and GWAS Catalog. Interestingly, as shown from the results \nin Supplementary Table 12, our results identified that fat and estrogen related traits (BMI, \nbody fat percentage, waist circumference, hip circumference, WHR, weight, age at first birth \nand age at menarche) are associated with six (WNT4, SEMA3F, HIST1H2BC, RERG, RAB5B, \nHOXC4/5/6) of twelve regions shared between endometriosis and GPM, which consistently \nsupported that those identified regions might contribute to the risk of both endometriosis and \nGPM through the dysregulation of estrogen and inflammation. The precise interaction \nmechanism of estrogen and fat related traits with endometriosis and GPM is unknown and \nrequires further investigation.   \n \nPotential for drug repositioning \nThe online Open-target drug platform was used to assess if any of the genes linked to both \nendometriosis and the GI disorders were potential drug targets \n(https://www.targetvalidation.org). A total of 218 unique genes with evidence from gene \nmapping and functional annotation (Supplementary Table 9) were used to search for known \nendometriosis and gastrointestinal disorder (GORD, PUD, IBS) drug targets. One gene, \nCCKBR encoded a protein that was targeted by two drugs Proglumide (ATC code: \nA02BX06) and Netzepide (NCT01298999 and NCT02597712) for the clinical treatment of \nGORD and PUD. In addition, PDE4B with its encoded protein cAMP-specific 3',5'-cyclic \nphosphodiesterase 4B being targeted by Pentoxifylline, acts as an inhibitor targeting the \nimmune system and has been clinically trialled for the treatment of both endometriosis (phase \nIII) and IBS (Phase IV) separately (Table 6).  Compared with IBS which has multiple sources \nof evidence to support the promising treatment effect of Pentoxifylline\n51 52, there is limited \nevidence on whether Pentoxifylline impacts endometriosis related pain reduction 53. Notably, \nwhen not restricted to the aforementioned gene set, 34 genes with encoded proteins were \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 18\ntargets of both endometriosis and IBS/GORD/PUD drugs (Supplementary Table 13).  This \nstudy may provide novel insights and evidence for the further investigation of therapeutic \ntargets for both endometriosis and GI traits. \n \nInsights from medication use in both diseases \nIdentified comorbid relationships between endometriosis and gastrointestinal disorders and \nshared symptomology as well as shared genetic components also raise questions around the \npotential effects of medication use on disease aetiology and management. We investigated \nprescription medication use in women by endometriosis status using data from the PBS \nrecords for both the 1973-78 and the 1989-95 ALSWH cohorts. Interestingly, drugs for peptic \nulcer and gastro-oesophageal reflux were within the top 10 most frequently used drugs in \nboth cohorts and such drug usage rate was significantly higher in women with endometriosis \nthan those without in 1989-95 ALSWH cohort after multiple testing (Supplementary Table \n14), further evidence of the likely co-occurrence of the diseases and disease symptoms. \nConsistently, using age-matched medication data of unrelated European women within the \nUK biobank revealed that in addition to the expected hormonal therapies and NSAIDs, up to \nseven medications for treatments of GORD, PUD and IBS were also significantly higher in \nwomen with endometriosis compared with women without (Table 7 & Supplementary Table \n15). More interestingly, when comparing medication usage between women with and without \ngastrointestinal disorders in the UK biobank, we also found a significantly higher use of \nhormone therapies among IBS, GORD, and PUD, but not for IBD (Table 7 & Supplementary \nTable 16), which is consistent with genetic results in this study. We next searched for the \ntarget genes of those drugs used for GI disorders identified above, and found that SLC22A1, \none of their transporters, has also been identified by our cross-trait meta-analysis and \nsubsequent functional mapping (Supplementary Table 4 & Supplementary Table 9).  \n \nDiscussion  \nSummary findings of this study \nThis is the first study to comprehensively illustrate the link between endometriosis and \ngastrointestinal disorders which both affect a large proportion of people worldwide, using \nlarge-scale multi-dimensional data including clinical, genetic, and pharmaceutical datasets. \nWe confirmed both a bidirectional epidemiological association and a shared genetic basis of \nendometriosis with each of the three GI traits (IBS, GORD, and PUD). Evidence of \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 19\nmedication use further supported the co-occurrence and shared disease aetiology of these \nconditions but also highlights the potential for drug repositioning and caution around drug \ncontraindications in clinical practice.  \n \nEvidence for comorbid relationships \nEndometriosis and IBS, two of the leading causes of chronic pelvic pain, are often \nmisdiagnosed in clinics due to non-specific symptoms\n54. Several epidemiological studies \nindicated women with endometriosis have an increased risk of a diagnosis of IBS 55 56. For \nexample, one nationwide UK case-control study demonstrated women diagnosed with \nendometriosis were two and half times more likely to receive a new diagnosis of IBS when \ncompared with controls (OR = 2.5, 95% CI 2.2 to 2.8)\n54. Few studies have investigated if \nwomen with IBS are more likely to be diagnosed with endometriosis. Our analysis using \ndiagnoses reported in UKB supported the epidemiological association between endometriosis \nand IBS. We identified a bidirectional association between endometriosis and all four \ngastrointestinal disorders. Of those associations, endometriosis showed a stronger \nrelationship with IBS and GORD when compared with PUD and IBD. Therefore, in addition \nto the clinically reported shared symptomology, this study provides further evidence of a \ncomplex phenotypic association between endometriosis and gastrointestinal disorders.  \n \nEvidence of shared genetic aetiology and potential drug candidates  \nA previous study investigating the shared genetic basis between endometriosis and \ndepression has implicated gastric mucosa abnormalities in this casual pathway\n29. Adewuyi et \nal. reported a strong genetic correlation between endometriosis and GORD using two early \npublished GWAS summary datasets in the UKB29 however, other common GI disorders such \nas IBS were not measured. Consistent with previous reports, our study, which included one \nthird more individuals from the UKB, also identified a significant genetic correlation between \nendometriosis and GORD. In addition, our study identified novel genetic correlations \nbetween endometriosis and IBS and PUD, but not for IBD. This is in line with known genetic \ndifferences between IBD and the other three GI disorders identified using both partitioned \nSNP-based heritability analysis and bivariate LDSC analysis\n30. When using a more powerful \nphenotype GPM, a combination of diagnosis of PUD and/or GORD as two acid-related \ndiseases that share treatment therapy in clinical practice, we found a stronger genetic \ncorrelation with endometriosis. Many observational studies are subject to the confounding \neffects of environment and lifestyle factors. In contrast, our analysis based on genotype-level \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 20\ndata are unlikely to suffer from such methodological bias. Therefore, the estimated one-fifth \nof the genetic contribution to endometriosis, which is shared with the genetic contribution to \nIBS or GPM, may partly explain the significant comorbid relationship between the diseases.  \n \nIn addition to a genetic correlation between endometriosis and IBS and GPM we identified a \nbidirectional causal relationship between genetic risk of IBS and endometriosis and a \nunidirectional causal relationship between GPM and endometriosis. The MR framework is a \npowerful and cost-effective method for inferring causality due to its advantage that genetic \nalleles are determined at conception, so that MR results are free from potential environmental \nconfounders (eg. medication usage) and bias which are often found in observational studies\n57. \nIn this study, the identification of bidirectional causality (vertical pleiotropy) between \nendometriosis and IBS suggests that the increased risks of endometriosis in IBS patients and \nvice versa are, in part, mediated by the genetic liability to the other disease. The estimated \ncausal relationship between traits can also be affected by violations of MR assumptions \nwhich occur when genetic variants are also associated with confounding factors or influence \nthe outcome through a confounding factor. A strength of our study is that we conducted the \nmtCOJO conditional analysis which takes into account the correlation between traits given \nthe previously reported complexity among GI disorders\n30, and the significant bidirectional \nrelationship between IBS and GPM in this study using both standard and reverse MR analysis \n(Figure 3). The MR results remained similar after conditioning on GPM, indicating that the \nbidirectional causal relationship between endometriosis and IBS at the genetic level were not \ndriven by their relationship with GPM.  \n \nMoreover, the subsequent identification of shared genomic loci using cross-trait meta-\nanalysis and colocalization approaches further provides clues as to the possible biological \nmechanisms and specific pathways driving the causal relationships between the different \ngastrointestinal disorders and endometriosis. For example, both TACSTD2 on chromosome 1 \nand FN1 on chromosome 2 shared by endometriosis and IBS are involved in various cellular \nprocesses including cell proliferation, motility, invasion and migration \n58,59. TACSTD2 is a \nnovel region that has not been implicated in IBS or endometriosis GWAS analyses \npreviously. The intracellular calcium signal transducer TACSTD2 was reported to be \noverexpressed in endometrioid-type endometrial carcinoma and gastrointestinal cancers \n60 61. \nAnother shared locus FN1 has been previously linked to the risk of endometriosis at a \ngenome-wide significance threshold of P < 5e-8 in both the latest GWAS study62 and a recent \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 21\nGreek population-based GWAS study 63.  Despite FN1  not having been identified in IBS \nGWAS meta-analyses, there are studies demonstrating a significant down-regulation of \nexpression of FN1 in IBS patients compared with controls, which may be responsible for the \nincreased mucosal permeability and visceral hypersensitivity of IBS through its mediation in \nbarrier dysfunction \n64 65 . Functional annotations in this study also suggest a possible \npathogenic effect of these two regions, providing evidence that the lead SNP (rs6661808) at \nthe TASCTD2 locus is an eQTL in both blood and digestive tissues, while the lead SNP in the \nFN1 region was within a predicted enhancer or promoter in digestive tissues and had a \nCADD score over 12.7.   \n \nThree genomic loci shared by endometriosis and GPM were identified in this study using \nboth cross-trait meta-analysis and GWAS-PW, including ETAA1 on chromosome 2, HOXC \nand RERG on chromosome 12.  ETAA1 is an activator of ATR kinase which plays a key role \nin protecting the genome against both intrinsic replication problems and substantial extrinsic \nDNA damage\n66, while the other two regions  are closely associated with receptor signalling \nand estrogen metabolism 67-70. The ETAA1  locus has been previously reported to be \nassociated with risk of both traits at genome-wide significance level 30 62 . Functional \nannotation of independent SNPs in the HOXC  region suggest that these variants impact \nregulatory elements in both digestive and reproductive tissues and regulate expression of \nseveral HOXC genes (HOXC4, HOXC5, HOXC6, HOXC8, HOXC9, HOXC10, HOXC-AS1) . \nAltered expression of the HOXC cluster has been found in ectopic and eutopic tissues from \nendometriosis patients vs. control\n71-73, as well as in gastrointestinal disorders such as \nulcerative colitis, colorectal cancer and gastric cancer 74-77 . Even though RERG, and nearby \nPTPRO, were not implicated in any GWAS studies of the separate traits, P-values for the lead \nSNP were close to genome-wide significance ( PEndometriosis = 9.24E-06, PGPM = 8.80E-07) \nsuggesting the increased power from combining the traits was able to identify a novel risk \nlocus for both diseases. Moreover, experiments have shown that the upregulated ER β  \nexpression and attenuated ERα  expression in endometriosis lesions indicated that insufficient \nexpression of PTPRO may be involved in the progression of endometriosis 78. Research \nfindings on the association between estrogen and GORD and PUD have been contradictory79-\n84, evidenced by some studies reporting a higher prevalence rate of GORD and PUD in men \ncompared with women before the age of menopause 81 85  and others reporting a positive \ncorrelation between GORD symptoms and postmenopausal hormone therapy 86. In this study, \nwe provided additional evidence that this estrogen related loci on chromosome 12 may be \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 22\ninvolved in the progression of both endometriosis and GORD and PUD however, the \nunderlying molecular mechanism remains unclear.  \n \nIn addition to the five highlighted regions shared by endometriosis and IBS/GPM, another six \nregions (SEMA3F, SPAG16, HIST1H2BC, RAB5B, CCKBR and PDE4B) identified by cross-\ntrait meta-analysis and at least two functional annotation analyses also implicate potential \npathways that are associated with the two traits. With the exception of HIST1H2BC and \nSPAG16 loci, the remaining four loci have been implicated in previous GORD or PUD \nGWAS studies \n30 87 . The lead SNPs in these six regions are all nominally significantly \nassociated with endometriosis and have not been linked to endometriosis in previous GWAS \nstudies. They may represent novel target genes or pathways involved in endometriosis \nprogression. For example, HIST1H2BC, SPAG16, SEMA3F and RAB5B themselves or genes \nnearby those regions may be associated with endometriosis by either being the estradiol \nresponsive gene, or related to steroid hormone treatment and metabolism, and further regulate \nthe proliferation of endometrial stromal cells\n88-95.  \n \nEvidence for the potential of drug repositioning in clinics \nTo verify whether the 218 candidate genes identified have any implications in the clinic, we \nsearched the online drug target databases and identified CCKBR and PDE4B with their \nencoded proteins as drug targets. While the former is currently used  for treatment of PUD \nand GORD, the latter has been clinically trialled for both IBS and endometriosis. PDE4B is \nmainly present in immune and epithelial cells and has a role modulating inflammation and \nepithelial integrity \n96 while CCKBR encodes a G-protein coupled receptor for gastrin and \ncholecystokinin. Even though CCKBR has not been targeted for treatment of endometriosis,  \na recent study has demonstrated that reduction of gastrin is associated with inactivation of \nCCKBR/ERK/P65 signalling in estrogen receptor positive breast cancer cells, and lower \nexpression of gastrin and CCKBR was correlated to worse prognosis in breast cancer\n97. \nTherefore, the involvement of gastrin and CCKBR in estrogen metabolism may implicate this \ngene as a potential drug target for endometriosis. Moreover, considering the low quality of \ncurrent evidence for Pentoxifylline which was used to treat endometriosis by targeting \nPDE4B encoded protein\n53, this study provides more evidence and novel insight for the further \ninvestigation of PDE4B for the purpose of treating both endometriosis and GI disorders. \n \nEvidence for associations with medication usage \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 23\nIn the present study, our ability to link diagnoses with drug usage further revealed overlap in \nmedication use between endometriosis and GI disorders, providing novel insights for disease \naetiology and management in clinics. The identification of a higher use of drugs for IBS, \nGORD and PUD in women diagnosed with endometriosis as well as the higher use of \nhormone therapies in women diagnosed with IBS, GORD and PUD but not for IBD, strongly \nsupports the coexistence and potential manifestations of underlying pathophysiological and \ngenetic correlations between the diseases. Whilst not unexpected, the frequent use of \nNSAIDs by women with endometriosis highlights potential confounding from \ncontraindicated therapies as the frequent use of NSAIDs during endometriosis treatment is a \nwell-known risk factor for PUD by destroying the mucus layer in the digestive tract\n15. \nHowever, the genetic correlation between the diseases suggests the relationship is not driven \nby a consequence of medical therapies alone. Additionally, we also identified that the \nfrequency of other treatments for gastrointestinal disorders such as omeprazole and laxatives \nwas also significantly higher in women with endometriosis than women without. One of the \ngene targets of omeprazole, ATP4A, is a member of the ATPase family responsible for \noxidative phosphorylation. Evidence from the cross-trait meta-analysis and functional \nannotation methods highlighted ATP6V0E1 and ATP6V0E2 as potential target genes involved \nin both endometriosis and GPM.  ATP6V0E1 and ATP6V0E2  also belong to ATPase family \nsuggesting targeting this pathway may have effects on both GI disorders and endometriosis. \nOther evidence towards the potential of drug repositioning includes that visceral sensitivity \nand chronic low-grade inflammatory state have been key characteristics in both IBS and \nendometriosis\n98 and therapies targeted at relieving pain in IBS can also relieve pain during \nmenstruation99. Similarly, a New Zealand based study reported that women with IBS and \nconcurrent endometriosis had a significantly higher response rate to a low FODMAP diet, \none therapy for IBS, than those IBS patients with no known endometriosis100.  \n \nClinical implications \nAt least three types of clinical implication can be drawn from this study. First, regarding \ndiagnosis for both endometriosis and GI disorders, shared aetiology suggests joint or \nalternative diagnoses should considered for patients presenting symptoms related to either \ndisease. Second, evidence from medication use suggest caution around contraindications for \nsome drugs, as NASIDs, often used for endometriosis, are a well-known risk factor for PUD. \nTherefore, it may be worthwhile for clinicians to consider potential contraindications when \nprescribing NASIDs for female patients presenting with symptoms shared between the \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 24\ndiseases such as abnormal pain, bloating or constipation, etc.  Third, support for PDE4B as a \nshared drug target for the treatment of both IBS and endometriosis, suggest comorbidity of \nendometriosis and IBS should be considered in the design and recruitment for clinical trials.  \n \nStrengths and limitations  \nOne major strength of the current study is the use of large-scale population data, genetic and \nmedication usage data for both gastrointestinal disorders and endometriosis, to \ncomprehensively illustrate the association between these two disorders. Integrating these \ndatasets provides more convincing evidence for the association of diseases, as well as \nimportant clinical implications. Despite these interesting findings, we acknowledge serval \nlimitations. First, endometriosis is a highly heterogeneous condition with variation in lesion \nlocation and grade\n101. Similarly, the four GI phenotypes derived from UKB may also \nintroduce further heterogeneity 30. It is not clear if certain subtypes of endometriosis share \nmore genetic risk factors with digestive disorders.  Therefore, the associations identified in \nthis study should be validated in larger endometriosis datasets with more detailed phenotype \ninformation when these are available. Second, as mentioned in Wu et al.\n30, the existence of \nco-reporting of some diagnoses, including two gastrointestinal disorders, may bias the \nassociation with specific digestive disorders. However, the sensitivity tests carried out in the \nstudy, which excluded those individuals with more than one diagnosis, demonstrated that the \nco-existence did not impact conclusions. We concluded that GWAS summary statistics for \nIBS and GPM phenotypes are robust, and identified different genetic risk factors shared \nbetween endometriosis and IBS and GPM.  Third, compared with the other four phenotypes, \nthere are fewer IBD cases available in UKB, which may limit the power for both genetic and \nepidemiological analyses. Results for the IBD GWAS were highly consistent with previously \npublished GWAS\n30 suggesting results in this study are robust.  \n \nConclusions  \nThis study comprehensively assesses the observational, genetic, and pharmaceutical usage \nassociations between endometriosis and gastrointestinal disorders using various statistical \napproaches and multidimensional large-scale datasets. We provide strong evidence for the \nshared aetiology of endometriosis and digestive disorders and highlight target genes and \npathways contributing to the shared aetiology. The results suggest potential targets for \ntreatment, considerations for disease management and caution around contraindications for \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 25\nsome drugs. The clinical implications could facilitate better clinical outcomes for women \nwith both endometriosis and gastrointestinal diseases. \n \nData Availability  \nThis study includes no data deposited in external repositories.  \n \nAuthor Contributions \nF.Y, S.M and G.W.M designed the study with input from the other authors. G.W.M, S.M, \nY.W, R.H and G.D.M coordinated data collection, quality control of data, data management \nand analysis of the original datasets. F.Y, S.M, R.H and Y.W ran additional quality control \nand filtering of datasets. Data analysis was performed by F.Y which was interpreted by all \nauthors. F.Y, S.M, and G.W.M drafted the report with input from all other authors. The final \nmanuscript has been critically revised and approved by all authors.  \n \nFunding \nThis work was supported by the National Health and Medical Research Council of Australia \n[Project Grants GNT1147846, GNT1105321 and GNT1049472, Investigator Grant 1177194 \nto G.W.M and Medical Research Future Fund Research Grant MRF1199785 to G.D.M and \nS.M]. For funding details of the endometriosis meta-analysis please see Sapkota et al., \n(2017). \n \nAcknowledgements \nThis research has been conducted using the UK Biobank Resource under Application \nNumber 54861 and 12505. Summary statistics from the endometriosis GWAS used in this \nstudy contain data from 23andMe. We would like to thank the research participants and \nemployees of 23andMe, Inc. for making this work possible. \n \nThe research on which this paper is partly based was conducted as part of the Australian \nLongitudinal Study on Women’s Health by the University of Queensland and The University \nof Newcastle. We are grateful to the Australian Government Department of Health and Aged \nCare for funding and to the women who provided the survey data. \n \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 26\nWe acknowledge the Department of Health and Medicare Australia for providing MBS and \nPBS data and the Australian Institute of Health and Welfare (AIHW) as the integrating \nauthority. We also acknowledge the following:  \n• Centre for Health Record Linkage (CHeReL), NSW Ministry of Health and ACT \nHealth, for the NSW Admitted Patients Data Collection, and the ACT Admitted \nPatient Care Data Collections. \n• Queensland Health, including the Statistical Services Branch, for the Qld Hospital \nAdmitted Patient Data Collection. \n• Department of Health Western Australia, including the Data Linkage Branch, and the \nWA Hospital Morbidity Data Collection. \n• SA NT Datalink, and SA Department for Health and Wellbeing and Northern \nTerritory Department of Health, for the SA Public Hospital Separations and NT \nPublic Hospital Inpatient Activity Data Collections. \n• Tasmanian Data Linkage Unit, and the Department of Health, Tasmania, for the \nPublic Hospital Admitted Patient Episodes Data Collection. \n• Victorian Department of Health as the source of the Victorian Admitted Episodes \nDataset, and the Centre for Victorian Data Linkage (Victorian Department of Health) \nfor the provision of data linkage. \n \nThe International Endometriosis Genetics Consortium (IEGC) \nThe following are members of the International Endogene Consortium (IEC): Yadav Sapkota, \nValgerdur Steinthorsdottir, Andrew P. Morris, Amelie Fassbender, Nilufer Rahmioglu, \nImmaculata De Vivo, Julie E. Buring, Futao Zhang, Todd L. Edwards, Sarah Jones, Dorien O, \nDaniëlle Peterse, Kathryn M. Rexrode, Paul M. Ridker, Andrew J. Schork, Stuart MacGregor, \nNicholas G. Martin, Christian M. Becker, Sosuke Adachi, Kosuke Yoshihara, Takayuki \nEnomoto, Atsushi Takahashi, Yoichiro Kamatani, Koichi Matsuda, Michiaki Kubo, Gudmar \nThorleifsson, Reynir T. Geirsson, Unnur Thorsteinsdottir, Leanne M. Wallace, iPSYCH-SSI-\nBroad Groupw, Jian Yang, Digna R. Velez Edwards, Mette Nyegaard, Siew-Kee Low, Krina \nT. Zondervan, Stacey A. Missmer, Thomas D’Hooghe, Grant W. Montgomery, Daniel I. \nChasman, Kari Stefansson, Joyce Y. Tung, and Dale R. Nyholt \n \nConflict of interest  \nThe authors declare that they have no conflict of interest.\n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n \nFigure 1.  Competitive comorbidity analysis for endometriosis and four gastrointestinal \ndisorders in unrelated female European individuals. The Venn diagram shows the number of \nindividuals with diagnosis of gastrointestinal disorders. At the bottom of Venn diagram is the \nproportion of endometriosis cases (n=5,392) in each of the digestive diseases after removing \nthe overlapped individuals for these four diseases, ranking from highest proportion to the \nleast. Paired comparison was conducted using a two-proportion Z test, with the \ncorresponding P-value under each comparison.  \n \n \n \n \n \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n \n \nFigure 2.  Results of genetic correlation between endometriosis and a) gastrointestinal \ndisorders (irritable bowel syndrome (IBS), peptic ulcer disease (PUD), gastro-oesophageal \nreflux disease (GORD), GORD/PUD Medicated (GPM) inflammatory bowel disease (IBD)) \nand b) separate male and female IBS GWAS datasets. The x-axis indicates the value of \ngenetic correlation, and the error bar indicates its 95% confidence interval. All red lines \nrepresent the results after constraining the heritability intercept to one considering no sample \noverlap for each comparison. \n \n \nFigure 3.  Simplified causal relationship identified by GSMR (Generalised Summary-data-\nbased Mendelian Randomisation). Different arrow colour represents the specific direction of \ncausal relationship. \n \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n \n \nFigure 4.  GSMR results for gastrointestinal disorders and endometriosis. The first row \nrepresents results using original GWAS data while the second row used the GWAS data \nconditioned on GPM or IBS. GWAS threshold for SNP instrument was set as P < 5e-6. bxy \nis the effect of exposure on outcome free of confounding from non-genetic factors and can be \napproximately interpreted as log(odds ratio).  \n \n \n \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 30\n \n \nFigure 5 . Mirror plot of first two GWAS-PW regions containing same causal variants for \nendometriosis and GPM. The left is the genomic locus near ETAA1 on chromosome 2, while \nthe right is the locus around HOXC4 on chromosome 12. \n \n  \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 31\nTable 1. Comorbid relationship between endometriosis and gastrointestinal disorders (GI) in \nunrelated European women in the UK Biobank. Association between diseases was tested \nusing the fisher’s exact test. \n GORD \n(n=22,383) \nIBS \n(n=16,330) \nPUD \n(n=5,208) \nIBD \n(n=2,708) \nEndo vs GI 1.40 (1.30-1.50) \nP=3.54e-18 \n2.01 (1.86-2.15) \nP=3.90e-68 \n1.22 (1.05-1.42) \nP=0.01 \n \n1.25 (1.01-1.53) \nP=0.04 \nGI vs Endo 1.45 (1.35-1.57) \nP=5.94e-22 \n2.13 (1.98-2.30) \nP=7.14e-79 \n1.22 (1.05-1.42) \nP=0.01 \n1.24 (1.0-1.53) \nP=0.04 \nNote: GORD (Gastro-oesophageal Reflux Disease), IBS (Irritable Bowel Disease), PUD (Peptic Ulcer \nDisease) and IBD (Inflammatory bowel disease), Endo (Endometriosis). The number in the bracket below \neach disease represent the number of women diagnosed with this disease. There are a total number of 5,392 \nwomen diagnosed with endometriosis. Fisher’s exact results are represented by OR, 95% CI values within \nbrackets and P-value. \n \n \nTable 2. Summary of GSMR results for endometriosis (Endo), irritable bowel syndrome \n(IBS) and GORD/PUD Medicated (GPM) using different SNP instrument GWAS p-value \nthresholds. \nExposure  Outcome  Odds Ratio \n(95% CI) SE P-value No. SNP \nInstruments \nSNP instrument GWAS p-value<5e-8 \nGPM Endo 1.56 (1.35, 1.76) 0.104 2.47e-05 20 \nGPM_IBS Endo_IBS 1.22 (1.00, 1.44) 0.112 0.073 17 \nEndo IBS 1.07 (1.01, 1.13) 0.031 0.042 10 \nEndo_GPM IBS_GPM 1.09 (1.03, 1.14) 0.028 0.003 12 \nSNP instrument GWAS p-value<5e-6 \nGPM Endo 1.18 (1.08, 1.27) 0.049 0.001 132 \nGPM_IBS Endo _IBS 1.16 (1.05, 1.27) 0.055 0.008 103 \nEndo IBS 1.04 (1.01, 1.07) 0.016 0.012 54 \nEndo_GPM IBS _GPM 1.03 (1.00, 1.06) 0.016 0.050 48 \nIBS Endo 1.15 (1.03, 1.28) 0.066 0.028 30 \nIBS_GPM Endo _GPM 1.23 (1.09, 1.38) 0.074 0.004 25 \n_IBS = primary trait conditioned on IBS using mtCOJO \n_GPM = primary trait conditioned on GPM using mtCOJO \n95% CI = 95% confidence interval  \n \n \nTable 3. Significant SNP loci identified by endometriosis (Endo), irritable bowel syndrome \n(IBS) and GORD/PUD Medicated (GPM) cross-trait meta-analysis. \n    Beta P.value  \nrsID Nearest gene Chr BP Endo GI Endo GI Meta \nEndometriosis & IBS \nrs12407439 LINCO1635 1 22347396 -0.14 -0.03 6.57E-08 0.025 3.98E-08 \nrs6661808 TACSTD2 1 59089534 -0.08 -0.07 0.002 1.20E-06 7.67E-09 \nrs1250244 FN1 2 216297796 0.10 0.03 8.73E-08 0.001 9.09E-10 \nEndometriosis & GPM \nrs7515106 WNT4 1 22473410 -0.10 0.01 1.89E-09 0.045 5.93E-09 \nrs7547294 PDE4B 1 66351735 -0.03 -0.03 0.035 2.40E-07 2.53E-08 \nrs11675830 ETAA1 2 67776860 0.07 0.02 2.57E-06 9.60E-06 5.41E-10 \nrs4260227 ETAA1 2 67843537 0.07 0.04 2.21E-05 2.10E-09 1.20E-12 \nrs2861694 ETAA1 2 67845739 0.07 0.04 7.77E-07 1.00E-10 1.05E-15 \nrs13031614 SPAG16 2 215068514 0.03 0.03 0.022 4.20E-07 3.06E-08 \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 32\nrs7613360 CAMKV 3 49916710 -0.05 -0.03 0.001 7.40E-07 7.61E-09 \nrs2008877 SEMA3F-AS1 3 50162291 0.04 0.03 0.002 6.50E-08 8.00E-10 \nrs2526388 SEMA3F-AS1 3 50174886 0.03 0.03 0.046 1.70E-07 2.20E-08 \nrs1046953 SEMA3F 3 50197097 0.04 0.03 0.003 3.00E-08 5.15E-10 \nrs12631337 SEMA3F 3 50198537 0.05 0.03 0.001 1.50E-10 7.38E-13 \nrs71557318 HIST1H2BC 6 26118570 0.05 -0.03 0.024 1.30E-09 1.03E-09 \nrs10811669 CDKN2B-\nAS1 \n9 22172893 -0.08 -0.01 1.68E-08 0.03 2.04E-08 \nrs10500661 CCKBR 11 6273744 0.05 -0.04 0.006 9.70E-12 2.63E-12 \nrs1479406 RERG 12 15387543 -0.06 -0.03 9.24E-06 8.80E-07 1.06E-10 \nrs11056461 PTPRO 12 15558466 -0.08 -0.02 2.12E-06 0.00048 2.66E-08 \nrs3803042 MIR196A2 12 54387947 -0.06 -0.02 4.54E-06 0.0001 1.65E-08 \nrs11170785 HOXC8 12 54407290 -0.06 -0.02 3.46E-05 8.20E-06 3.25E-09 \nrs736825 HOXC4/5/6 12 54417576 -0.08 -0.03 1.98E-05 3.00E-06 1.53E-09 \nrs773111 RAB5B 12 56375740 0.03 0.03 0.028 8.10E-08 6.80E-09 \nrs9807058 LINC01982 17 50338523 -0.04 -0.03 0.04997 1.50E-07 2.18E-08 \n \n \nTable 4. Genomic regions that contain a same causal variant jointly influencing \nendometriosis with irritable bowel syndrome (IBS) and GORD/PUD Medicated (GPM) \nrespectively. \n     Risk loci (P < 5e-8) \nChr Start End PPA-3 Nearest gene Endo GI Meta \nEndometriosis & IBS \n2 215573795 217715180 0.818 FN1 Yes No Yes \n1 58865399 59889341 0.766 OMA1/ TACSTD2/MYSM1 No No Yes \n6 30798252 31565648 0.532 HLA-C No No No \nEndometriosis & GPM \n2 67227143 68009259 0.983 ETAA1/ LINCO1812 Yes Yes Yes \n12 53039757 54777633 0.932 HOXC4/ HOXC-AS1 No No Yes \n12 15248516 16309290 0.755 RERG/PTPRO No No Yes \n3 47729665 49314960 0.628 DALRD3/KLHDC8B/P4HTM/RBM6 No No No \n1 76729016 79660928 0.618 FUBP1/ADGRL4 No No No \n10 19717815 22772115 0.551 CASC10 No No No \n \n \nTable 5. Functionally mapped genes for significant risk loci identified in the cross-trait meta-\nanalysis of endometriosis and gastrointestinal disorders. \nChr Gene Closest gene \nto lead SNP \nposMap \nMaxCADD \neQTL MAGMA SMR EpiMap \nEndometriosis & IBS \n1 MYSM1  12.9 Yes  Yes  \n1 OMA1   Yes    \n1 TACSTD2 Yes  Yes    \n2 FN1 Yes 22  Yes  Yes \nEndometriosis & GPM \n1 PDE4B Yes   Yes   \n2 SPAG16 Yes 17.74  Yes   \n2 ETAA1 Yes  Yes    \n3 CAMKV Yes 18.51 Yes Yes   \n3 MST1R  18.51 Yes Yes   \n3 CTD-2330K9.3  13.15 Yes Yes   \n3 MON1A  13.15 Yes Yes   \n3 RBM6  17.77 Yes Yes  Yes \n3 RBM5  18.47 Yes Yes  Yes \n3 SEMA3F Yes 19.09 Yes Yes  Yes \n3 CYB561D2   Yes   Yes \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 33\n3 RNF123   Yes  Yes  \n3 HYAL3   Yes   Yes \n3 NAT6   Yes   Yes \n6 HIST1H3B  13.84 Yes    \n6 HFE  14.95 Yes    \n6 HIST1H2BC  14.07 Yes Yes   \n6 HIST1H1T Yes 14.95     \n11 FAM160A2  12.74 Yes    \n11 CNGA4  11.83 Yes  Yes  \n11 C11orf42  12.74  Yes   \n12 RERG Yes 17.74 Yes Yes  Yes \n12 PTPRO Yes 17.74 Yes Yes   \n12 HOXC6 Yes 21.7 Yes Yes  Yes \n12 HOXC9  21.7 Yes Yes  Yes \n12 HOXC8 Yes 19.36 Yes Yes  Yes \n12 HOXC4 Yes 22 Yes Yes  Yes \n12 HOXC5 Yes 17.09 Yes   Yes \n12 RAB5B Yes 21.2 Yes Yes   \n12 SUOX  21.2 Yes   Yes \n12 RP11-834C11.12  21.7  Yes   \n12 HOXC10  21.7    Yes \n \n \nTable 6. Existing drug targets for endometriosis and gastrointestinal disorders.  \nHuman \nTarget \nDrug Phase Type Mechanism \nof Action  \nIndication Source  \nCCKBR PROGLUMIDE Phase IV Small \nmolecule \nCholecystokin\nin receptor \nGORD ATC:A02BX06 \nCCKBR NETAZEPIDE Phase I Protein Cholecystokin\nin receptor \nPUD NCT01298999 \nNCT02597712 \nPDE4B PENTOXIFYLLINE Phase \nIII/IV \nSmall \nmolecule \n3',5'-cyclic \nphosphodieste\nrase inhibitor \nEndo/ IBS NCT00632697 \nNCT01542268 \nNote: GORD (Gastro-oesophageal Reflux Disease); IBS (Irritable Bowel Disease); PUD \n(Peptic Ulcer Disease); Endo (Endometriosis) \n \n \n \nTable 7. Comparison of medication usage in UKB unrelated European women with and \nwithout a diagnosis of endometriosis or gastrointestinal disorders.  \nMedication Diagnoses Controls P.Value  BF.P.value Description \n Med No Med No    \nEndometriosis \nOmeprazole 540 4852 5521 86823 1.49E-28 1.73E-25 GORD/PUD Treatment \nLaxatives 353 5039 3749 88595 1.52E-16 1.76E-13 Constipation Treatment \nLansoprazole 266 5126 2881 89463 6.96E-12 8.05E-09 GORD/PUD treatment \nMebeverine 73 5319 558 91786 3.84E-09 4.45E-06 IBS Treatment \nRanitidine 163 5229 1765 90579 1.06E-07 0.0001 GORD/PUD treatment \nSenna 30 5362 176 92168 1.25E-06 0.0015 Constipation Treatment \nEsomeprazole 33 5359 242 92102 2.88E-05 0.0334 GORD/PUD treatment \nParacetamol 1914 3478 25462 66882 8.16E-35 9.45E-32 Painkiller \nPremarin  132 5260 595 91749 1.49E-33 1.73E-30 Hormone Therapy \nIrritable Bowel Disease \nVagifem  200 15679 758 126274 2.29E-18 2.91E-15 Hormone Therapy \nPremarin  185 15694 891 126141 2.31E-09 2.94E-06 Hormone Therapy \n . CC-BY-ND 4.0 International licenseIt is made available under a \n is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint \n\n 34\nEstraderm  80 15799 291 126741 6.54E-09 8.31E-06 Hormone Therapy \nOvestin  51 15828 151 126881 1.59E-08 2.03E-05 Hormone Therapy \nEstradiol product 99 15780 430 126602 2.33E-07 0.0003 Hormone Therapy \nEvorel 25 patch 82 15797 346 126686 9.59E-07 0.0012 Hormone Therapy \nConjugated oestrogens 18 15861 29 127003 1.22E-06 0.0016 Hormone Therapy \nClimaval 1mg tablet 65 15814 258 126774 2.08E-06 0.0026 Hormone Therapy \nEstriol product 37 15842 114 126918 3.17E-06 0.0040 Hormone Therapy \nOmeprazole 2242 13637 4209 122823 0 0 GI disorder treatment \nGastro-oesophageal Reflux Disease \nEstradiol product 134 22248 317 89211 8.50E-07 0.0010 Hormone Therapy \nEstraderm  94 22288 217 89311 1.81E-05 0.0207 Hormone Therapy \nPremarin  233 22149 672 88856 2.44E-05 0.0279 Hormone Therapy \nLansoprazole 3705 18677 1640 87888 0 0 GI disorder treatment \nOmeprazole  6948 15434 3335 86193 0 0 GI disorder treatment \nRanitidine 1596 20786 1081 88447 0 0 GI disorder treatment \nGaviscon liquid 714 21668 237 89291 1.01E-295 1.15E-292 GI disorder treatment \nParacetamol 7900 14482 21440 68088 1.92E-249 2.20E-246 Painkiller \nEsomeprazole 434 21948 99 89429 3.35E-205 3.83E-202 GI disorder treatment \nPeptic Ulcer Disease \nEstraderm  35 5173 205 72707 1.26E-05 0.0135 Hormone Therapy \nOmeprazole  1375 3833 2821 70091 0 0 GI disorder treatment \nLansoprazole 711 4497 1426 71486 2.34E-306 2.49E-303 GI disorder treatment \nRanitidine  351 4857 942 71970 3.67E-118 3.91E-115 GI disorder treatment \nParacetamol 1963 3245 17305 55607 1.74E-103 1.86E-100 Painkiller \nEsomeprazole 107 5101 88 72824 1.62E-72 1.73E-69 GI disorder treatment \nTramadol 217 4991 665 72247 1.10E-64 1.17E-61 Opioid \nCo-codamol 348 4860 1608 71304 4.27E-64 4.55E-61 Opioid \nAmitriptyline 326 4882 1477 71435 1.03E-61 1.10E-58 Antidepressants \n \n  \n . 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(which was not certified by peer review)\nThe copyright holder for this preprint this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.22281201doi: medRxiv preprint","source_license":"CC0","license_restricted":false}