Integrative Analysis of Genomic, Epigenomic and Phenotypic Data for Disease Stratification of Endometriosis

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Project Summary/Abstract Endometriosis is a common disease causing pelvic pain and infertility. It affects the quality of life of millions of women and has a major impact on the U.S. health economy. Most disease derives from retrograde menstrual seeding of endometrial tissue and cells from the lining of the uterus (eutopic endometrium) onto pelvic structures that develop as lesions and elicit an inflammatory response and scarring. It is surgically diagnosed, is heterogeneous in appearance and staging and is characterized by unpredictable responses to surgical and medical therapies. Abnormalities within the uterus predisposing to establishing the disease are either inherent (genetic) or acquired (environmental/lifestyle), and if the latter, raise the possibility of life-style modification to alter disease risk and progression. The NIH Human Genome Project and NIH Roadmap Epigenomics Project are generating genomic and epigenomic data, and with powerful bioinformatics and biostatistical tools, are providing novel insights into multiple diseases. However, no studies have utilized these combined technologies at the scale required to address fundamental questions related to endometriosis - a scientific gap addressed herein. A growing number of human diseases are associated with acquired defects in DNA methylation, and epigenetic changes provide a biological link between individual exposures and phenotype. Our proposal addresses identifying endometriosis-specific, eutopic endometrial DNA methylation signals, their associations with surgical disease phenotypes and specific patient characteristics, genetic and non-genetic contributions to these DNA methylation signals and potentially identifying modifiable disease risk factors. Our team involves a collaboration among global leading genomic and epidemiological research centers focused on endometriosis (UCSF, Harvard, Oxford, QIMR, and University of Melbourne (the “Consortium”)) to address the hypotheses that 1) environmental and genetic influences contribute to endometriosis and leave long-term signatures in the DNA methylome in the eutopic endometrium that contribute to disease pathogenesis and pathophysiology; and 2) these can serve to stratify disease risk and inform new avenues for drug target discoveries and diagnostic development. We propose to perform genome-wide DNA methylation analyses and genotyping of nearly 1000 well annotated, existing eutopic endometrium samples (and ongoing accrual for a 400 sample replication study), collected by standard operating procedures and extensive phenotyping, established by our World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project (WERF-EPHect).