Supplementary_tables.xlsx

Description

Supplementary tables for "Enhancer Malfunction Underlies Transcriptional Dysregulation in Uterine Leiomyoma"

Abstract

Uterine leiomyomas (fibroids) are a major source of gynaecologic morbidity in reproductive age women and are characterised by the excessive deposition of a disorganised extracellular matrix, resulting in rigid benign tumours. Clinically, leiomyoma patients usually present with pelvic pain, urinary incontinence, as well as heavy cyclic and non-cyclic bleeding. Curative treatment options are limited, with hysterectomies currently the only guaranteed treatment to prevent reoccurrence.Uterine fibroid tumours are composed primarily of smooth muscle cells and fibroblasts. They have also been shown to be clonal, with multiple tumours from the same patient sometimes originating from different tumour initiating cells. Leiomyomas fall into four main mutational subtypes: tumours with genetic aberrations in either fumarate hydratase (FH), mediator of transcription subunit 12 (MED12), high mobility group AT-hook 2 (HMGA2), or type IV collagens. Somatic mutations in Mediator complex subunit MED12 have been implicated as the causal genetic lesion in the majority of leiomyoma. The functional consequence of this mutation with respect to altered epigenetic events and subsequent transcriptional dysregulation remains poorly understood.Epigenetic control of gene expression by promoter-distal cis-regulatory elements such as enhancers is an established and important mechanism of gene regulation, with aberrant epigenetic changes at distal sites being implicated in human disease. Despite this, the role of enhancer regulation in uterine leiomyomas remains unexplored. In this study, optimised extraction procedures for fibrotic tissues, coupled with high resolution ChIP-sequencing, promoter capture Hi-C, and RNA-sequencing of matched normal myometrium and diseased leiomyoma tissues, are used to provide an integrative analysis of transcriptional dysregulation mechanisms in leiomyomas. Through the characterisation of the first chromatin interactome in uterine leiomyomas, this study demonstrates that modified enhancer architecture is an important mechanism of transcriptional dysregulation in uterine fibroids.Activator protein 1 (AP-1) is a dimeric transcription factor that responds to varied stimuli and is responsible for the regulation of many cellular processes such as proliferation and differentiation. AP-1 subunits belonging to JUN, FOS and ATF gene families have previously been demonstrated to be down regulated in uterine leiomyomas. This study highlights the link between decreased AP-1 subunit gene expression and modifications in leiomyoma tissue enhancer architecture. The loss of AP-1 expression results in the depletion of AP-1 occupancy on chromatin in leiomyoma tissue samples, which correlates with changes in H3K27 acetylation at distal cis-regulatory elements.Importantly, this study also demonstrates that silencing of AP-1 subunits in primary human uterine smooth muscle cells leads to large-scale transcriptional dysregulation. In addition, loss of AP-1 causes significant alteration to the H3K27Ac cistrome in uterine smooth muscle cells, primarily at promoter-distal sites, thereby partially recapitulating epigenetic changes seen in leiomyoma tissue samples. The data supports the hypothesis that AP-1 plays an important mechanistic role in enhancer maintenance and the loss of AP-1 results in altered enhancer architecture in uterine smooth muscle cells. These findings establish AP-1 driven aberrant enhancer regulation as an important mechanism of leiomyoma disease pathogenesis.

Files

Additional details