Single-cell analysis identifies distinct macrophage phenotypes associated with pro-disease and pro-resolving functions in the endometriotic niche

Endometriosis negatively impacts the health-related quality of life of 190 million women worldwide. Novel advances in non-hormonal treatments for this debilitating condition are desperately needed. Macrophages play a vital role in the pathophysiology of endometriosis and represent a promising therapeutic target. In the current study, we revealed the full transcriptomic complexity of endometriosis-associated macrophage subpopulations using single-cell analyses in a preclinical mouse model of experimental endometriosis. We have identified two key lesion-resident populations that resemble i) tumour-associated macrophages (characterized by expression of Folr2, Mrc1, Gas6 and Ccl8+) that promoted expression of Col1a1 and Tgfb1 in human endometrial stromal cells and increased angiogenic meshes in human umbilical vein endothelial cells, and ii) scar-associated macrophages (Mmp12, Cd9, Spp1, Trem2+) that exhibited a phenotype associated with fibrosis and matrix remodelling. We also described a population of pro-resolving large peritoneal macrophages (LpM) that align with a lipid-associated macrophage phenotype (Apoe, Saa3, Pid1) concomitant with altered lipid metabolism and cholesterol efflux. Gain of function experiments using an Apoe mimetic resulted in decreased lesion size and fibrosis, and modification of peritoneal macrophage populations in the preclinical model. Using cross-species analysis of mouse and human single-cell datasets, we determined the concordance of peritoneal and lesion-resident macrophage subpopulations, identifying key similarities and differences in transcriptomic phenotypes. Ultimately, we envisage that these findings will inform the design and use of specific macrophage-targeted therapies and open new avenues for the treatment of endometriosis. We used a menses mouse model of endometriosis. From donor endometrium (+4-6 hours P4 withdrawal; n=5 mice), endometriosis lesions (lesions from n=10 mice) and peritoneal lavage from Sham (n=5) and Endometriosis mice (n=5), 200,000 CD45+ cells were FACS sorted into 1ml PBS + 2% FBS using a FACS Fusion. Cells were barcoded using a 10X Genomics Chromium ControllerTM using established pipelines. Libraries were sequenced by Edinburgh Genomics using a NovaSeq 6000 sequencing system (Illumina®, San Diego, USA)