Investigation of both epidemiological and genetic risk factors for endometriosis: novel insights and important clinical implications

Endometriosis is a chronic gynaecological disorder that affects one in nine women of reproductive age. The disease has a complex aetiology with 50% of variation in disease risk attributed to genetics and the remaining 50% attributed to environmental and lifestyle factors. Many endometriosis risk factors and comorbidities have been reported by epidemiological studies however, most have not been confirmed by randomised control studies or genetic analyses. In addition to reported epidemiological risk factors, mapped genetic risk factors for endometriosis lie in regulatory regions of the genome, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic regulation in endometrium are limited, especially transcript-level expression and RNA splicing. Therefore, to better understand the relationship between endometriosis and potential risk factors and comorbidities, this thesis firstly investigated whether suggested epidemiological risk factors for endometriosis may have a causative effect on the disease and share underlying genetic mechanisms with endometriosis through common molecular pathways. Secondly, transcriptional regulation in endometriosis was investigated by integrating genetic (genotypes) and transcript expression (RNA sequencing) data in endometrium samples from 206 women of European ancestry, with and without endometriosis, the largest endometriosis transcriptomic dataset to date.

With the aim to further investigate epidemiological risk factors for endometriosis, Chapter 2 evaluated the genetic correlation and causal relationship with melanoma. Epidemiological studies have observed that risk of endometriosis is associated with history of cutaneous melanoma and vice versa. Here, using summary statistics from separate female and male melanoma cohorts, this chapter identified a significant positive genetic correlation between melanoma in females and endometriosis (rg = 0.144, se = 0.065, p = 0.025), as well as a causal relationship whereby genetic predisposition to melanoma in females has a causal effect on endometriosis. However, no evidence of a correlation between endometriosis and melanoma in males or a combined male and female melanoma dataset was found.

Chapter 3 continued investigating the relationship between endometriosis and potential risk factors this time focusing on gastrointestinal disorders. In clinical practice, the co-existence of endometriosis and gastrointestinal symptoms is often observed; however, the factors driving this link remain largely unknown. Here, using large-scale datasets, we report a genetic correlation between endometriosis and irritable bowel syndrome (IBS), peptic ulcer disease (PUD), gastro-oesophageal reflux disease (GORD) and a combined GORD/PUD Medicated (GPM) phenotype. Mendelian randomisation (MR) analyses support a causal relationship between genetic predisposition to endometriosis and IBS and GPM. The identification of shared risk loci highlights biological pathways that may contribute to the pathogenesis of both diseases, including estrogen regulation and inflammation, and potential therapeutic drug targets (CCKBR & PDE4B). The higher use of IBS, GORD and PUD medications in women with endometriosis and the higher use of hormone therapies in women with IBS, GORD and PUD, support the co-occurrence of these conditions and highlight the potential for drug repositioning and caution around drug contraindications. Our results provide evidence of shared disease aetiology and have important clinical implications for diagnostic and treatment decisions for both diseases.

With the aim to better understand the underlying regulatory mechanism of mapped genetic risk factors for endometriosis, Chapter 4 comprehensively investigated the role of transcription regulation in endometriosis using transcript expression (RNA sequencing) data in endometrium. Results firstly demonstrate the dynamic nature of transcriptomic changes in endometrium throughout the menstrual cycle at gene-, transcript- and splicing-levels as well as their predictable functional consequences on downstream protein isoforms. Subsequently, both network and individual transcriptome analyses revealed transcriptomic changes between women with (n=143) and without endometriosis (n=63). Larger differences were identified in the mid-secretory phase (MS) of the menstrual cycle, with significant candidate genes related to endometriosis and implantation failure. We identified genetic effects on splicing within endometrium in the form of 3,296 splicing QTLs (sQTLs) and demonstrated that splicing may be an important mediator of genetic effects on endometriosis. Integration of transcriptomic and GWAS data suggested endometriosis risk is, in part, mediated by cis effects on exon 15 skipping of GREB1 in endometrium. Taken together, this transcriptome-wide study provides novel insights into the dynamic changes in endometrium and its association with endometriosis and infertility.

In conclusion, this thesis identified a genetic relationship between reported epidemiological risk factors, melanoma and gastrointestinal disorders, and endometriosis, which provides novel insights into shared molecular and biological pathways between these diseases and has important clinical implications for disease management. Identification of transcriptional differences in endometriosis highlights new therapeutic targets and potential disease pathways.