Abstract A044: Decoding the endometriosis immune–pain axis: A single-cell pipeline for neuroimmune hub discovery and drug prioritization

Abstract Endometriosis affects an estimated 10% of reproductive-age women and girls worldwide, approximately 190 million individuals, yet its molecular pathogenesis remains incompletely understood and current treatments rely largely on hormonal suppression, surgery, and symptom management. We developed a multi-stage single-cell transcriptomic pipeline to identify lesion-associated cellular niches that may coordinate immune tolerance, failed lesion clearance, fibrotic remodeling, and chronic pelvic pain, with the goal of prioritizing non-hormonal therapeutic hypotheses. Using the public Tan et al. atlas, GSE179640, comprising more than 122,000 cells from 14 individuals across control endometrium, eutopic endometrium, peritoneal lesions, adjacent peritoneal tissue, and ovarian lesions, the workflow combines Harmony integration, GenoRefine dimensionality reduction, unsupervised clustering, tissue-type stratification, and donor-aware pseudobulk differential expression. A mechanism-anchored scoring framework ranks GenoRefine clusters across T-cell suppression, macrophage tolerance, neuroimmune pain, CGRP/RAMP1 macrophage reprogramming, efferocytosis context, perivascular angiogenic remodeling, fibrosis, and lesion-type enrichment. Candidate immune-pain hubs are evaluated using curated ligand-receptor and mediator-axis analyses and exported for CellPhoneDB/LIANA validation, enabling complex-aware communication scoring across cytotoxic T-cell and neuroimmune-responsive compartments. The prostaglandin pathway is modeled as PTGS2/PTGES-driven PGE2 production coupled to PTGER2/PTGER4 receptor response, avoiding an incorrect direct ligand-receptor representation. Drug mapping proceeds by consolidating hub markers, pseudobulk-supported genes, ligand-receptor partners, and mediator-axis targets into disease-axis target sets; annotating them through DGIdb-informed drug-gene interactions and druggability classes; and formatting lesion up/down signatures for CLUE/LINCS perturbational reversal. Drug prioritization generates separate shortlists for pain/neuroimmune signaling, immune tolerance, fibrosis/angiogenesis, CGRP/RAMP1 macrophage biology, and efferocytosis-context targets. Each candidate is annotated by desired intervention direction, evidence level, lesion-type enrichment, cell-type specificity, pseudobulk support, communication support, and translation caution. CGRP/RAMP1 is prioritized as a clinically tractable neuroimmune axis because CGRP-pathway agents are approved in migraine and preclinical endometriosis models implicate nociceptor-to-macrophage CGRP signaling in pain and lesion growth; however, endometriosis-specific efficacy and reproductive safety require validation. Neuronal markers are interpreted as lesion-context signals pending spatial validation. This framework provides a reproducible drug-discovery strategy for identifying immune-pain hubs and prioritizing druggable non-hormonal axes in endometriosis. Citation Format: Ariana F. Rahman. Decoding the endometriosis immune–pain axis: A single-cell pipeline for neuroimmune hub discovery and drug prioritization [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr A044.