{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:01:54Z","timestamp":1785423714486,"version":"3.56.0"},"posted":{"date-parts":[[2025,9,18]]},"group-title":"Systems Biology","reference-count":55,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T00:00:00Z","timestamp":1758153600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["R01HD110367"],"award-info":[{"award-number":["R01HD110367"]}],"id":[{"id":"https:\/\/ror.org\/04byxyr05","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/01fnrgf58","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,9,18]]},"abstract":"<jats:title>Structured Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>Endometriosis is a chronic, estrogen-dependent disease characterized by the presence of endometrial-like tissue growing outside the uterus. The molecular and clinical heterogeneity of endometriosis complicate diagnostic and treatment options -- diagnostic delays of seven to ten years are common and therapies often lack long-term efficacy. Estrogen signaling and estrogen receptor beta (ER\u03b2) expression is thought to be increased in endometriosis, contributing to increased cell proliferation in lesions. The \u201cER\u03b2 dominance hypothesis\u201d is a prevailing hypothesis in the field, setting ER\u03b2 as a high-priority therapeutic target. If effectively modulated, ER\u03b2 could be the first therapy to directly target lesion biology, rather than only managing symptoms.<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Objective(s)<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>We aimed to characterize ER\u03b2\u2019s expression in endometriosis by cell type and evaluate its therapeutic relevance, primarily assessing the validity of the ER\u03b2 dominance hypothesis.<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Study Design<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>We reanalyzed scRNAseq data from eight previously published studies. Our final filtered dataset included 557,061 cells, the largest endometriosis single cell atlas ever constructed. We quantified gene expression levels of ESR1 and ESR2, which encode ER\u0251 and ER\u03b2 respectively, across each tissue and cell type, to identify cell-type specific drivers of ESR2\/ER\u03b2 expression across diseased and healthy tissues. To characterize the differences between cells that uniquely express ESR1 versus those that uniquely express ESR2, we performed differential gene expression and pathway enrichment analyses.<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>Count and distribution analyses revealed no significant ESR2\/ER\u03b2 dominance in any cell or tissue type by Fisher\u2019s Exact Tests and Wilcoxon Rank Sum Tests. Differential gene expression and pathway enrichment analyses suggest distinct roles of each estrogen receptor isoform.<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusion(s)<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>Overall, our results argue against a simplified model of ER\u03b2 dominance and instead propose a dual-isoform and cell and tissue-specific framework for understanding estrogen receptor signaling in endometriosis. These findings hold important implications for future therapeutic strategies. Specifically, treatments that target ER\u03b2 alone may fail to account for the functional role and relative abundance of ER\u03b1. In the future, therapeutic approaches that consider isoform-specific, tissue-specific, and cell-specific expression patterns may prove most effective in reducing recurrence and improving outcomes for patients.<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Condensation page<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Tweetable statement<\/jats:title>\n                    <jats:p>Single cell RNA Sequencing meta-analysis shows estrogen receptor beta is not dominantly expressed in most endometriosis tissues. Estrogen receptor alpha to estrogen receptor beta ratios vary by cell type and tissue type. Each isoform directs cell-type specific behavior in endometriosis and disease-free tissues.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>AJOG at a Glance<\/jats:title>\n                    <jats:list list-type=\"alpha-upper\">\n                      <jats:list-item>\n                        <jats:p>Why was this study conducted?<\/jats:p>\n                        <jats:list list-type=\"bullet\">\n                          <jats:list-item>\n                            <jats:p>We wanted to characterize estrogen receptor beta\u2019s expression in endometriosis and evaluate its therapeutic relevance.<\/jats:p>\n                          <\/jats:list-item>\n                        <\/jats:list>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>What are the key findings?<\/jats:p>\n                        <jats:list list-type=\"bullet\">\n                          <jats:list-item>\n                            <jats:p>Estrogen receptor beta is not dominantly expressed in any tissue. Estrogen receptor alpha and estrogen receptor beta have disease- and cell-type specific behaviors.<\/jats:p>\n                          <\/jats:list-item>\n                        <\/jats:list>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>What does this study add to what is already known?<\/jats:p>\n                        <jats:list list-type=\"bullet\">\n                          <jats:list-item>\n                            <jats:p>It characterizes estrogen receptor isoform expression and signaling by cell type. It also challenges the current estrogen receptor beta dominance hypothesis, meaning estrogen receptor beta may not be a key driver of endometriosis.<\/jats:p>\n                          <\/jats:list-item>\n                        <\/jats:list>\n                      <\/jats:list-item>\n                    <\/jats:list>\n                  <\/jats:sec>\n                <\/jats:sec>","DOI":"10.1101\/2025.09.15.676330","type":"posted-content","created":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T23:05:18Z","timestamp":1758236718000},"source":"Crossref","is-referenced-by-count":0,"title":["Rethinking the Estrogen Receptor Beta Dominance Hypothesis in Endometriosis: Insights from Single Cell RNA Sequencing 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