Citations

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.

Abstract Endometriosis (EMS) is an estrogen-dependent, chronic inflammatory disease in which endometrial-like tissue grows outside the uterus, leading to pelvic pain, dysmenorrhea, dyspareunia, and infertility. Increasing evidence shows that these symptoms do not arise from the presence of ectopic tissue alone. Rather, they reflect a sustained neuroimmune process in which inflammatory, neural, and stromal pathways continuously interact. Within the peritoneal cavity of EMS, immune activation elevates cytokines such as IL-1β, IL-6, and TNF-α, which stimulate production of neurotrophic mediators including NGF, BDNF, and IGF-1. These signals induce sensory-nerve sprouting, lower nociceptor thresholds, and convert lesions into hyperinnervated, pain-generating structures. Once these fibers infiltrate lesions, they release neuropeptides such as substance P (SP) and calcitonin gene-related peptide (CGRP). Rather than simply transmitting nociceptive signals, these neurons actively reshape the lesion microenvironment. SP and CGRP amplify inflammation, promote immune-cell recruitment, and drive epithelial–mesenchymal transition and myofibroblast differentiation, accelerating the fibrotic remodeling characteristic of deep infiltrating endometriosis. This neuropeptide-driven activity strengthens the lesion’s neuroimmune profile and forms a feed-forward loop in which inflammation, nerve growth, and fibrosis reinforce one another over time. Persistent nociceptive input from sensitized lesions produces downstream changes in the central nervous system. Within the spinal cord, activated microglia and astrocytes release proinflammatory mediators that enhance excitatory signaling and diminish inhibitory tone. With continued input, spinal and cortical circuits undergo neuroplastic changes that give rise to central sensitization, hyperalgesia, allodynia, and the cross-organ sensitization that links pain across the uterus, bladder, bowel, and pelvic floor. These long-range effects explain why pain may persist even when visible lesions are small or surgically removed. Together, these findings position endometriosis as a chronic systemic neuroimmune disorder maintained by reciprocal signaling between immune cells, sensory neurons, and central pain networks. Viewing EMS through this lens highlights multiple therapeutic entry points. Targeting NGF–TrkA and CGRP–RAMP1 signaling, modulating macrophage and B-cell function, dampening glial activation, or applying neuromodulatory techniques offers a more rational pathway to interrupt the self-reinforcing neuroimmune loop that sustains pain. Integrating immunologic and neurobiologic evidence therefore provides a foundation for mechanism-based therapies capable of delivering more durable relief and improving long-term quality of life. Citation Format: Ariana F. Rahman. Endometriosis as a Neuroimmune Disorder: Integrating Inflammation, Innervation, and Sensitization [abstract]. In: Proceedings of the AACR Immuno-Oncology Conference (AACR IO): Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2026 Feb 18-21; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2026;14(2 Suppl):Abstract nr A062.

Abstract Endometriosis (EMS) is a prevalent systemic disorder impacting 10% of women of reproductive age, characterized by the growth of endometrial-like tissue outside the uterine cavity, chronic inflammation, and fibrosis, leading to pain, infertility, and organ dysfunction. Despite its widespread occurrence, the pathogenesis of EMS remains elusive, and current treatments are inadequate, with recurrence post-surgery being a significant issue. Notably, EMS displays features reminiscent of malignancy, including genetic mutations and clonal cell proliferation. The presence of tertiary lymphoid structures (TLSs) within lesions indicates a potential role of immune dysfunction in disease progression. This study aims to explore immune mechanisms underlying EMS through three specific aims: 1) Analyzing cellular, molecular, and spatial characteristics of T and B cell interactions; 2) Defining the functional phenotype of immune cells involved; and 3) Investigating the B cell antigen receptor repertoire and the specificity of locally produced antibodies. Techniques such as single-cell RNA sequencing, spatial transcriptomics, and multiplex immunofluorescence, are employed. The outcomes provide insights into immune contributions to EMS pathology and guide the development of novel diagnostic and therapeutic strategies. Citation Format: Ariana F Rahman, Khashayarsha Khazaie, Elika Javaheri, Yohannes Woldeamanuel. Characterizing immune dysregulation and tertiary lymphoid structures in endometriosis: Pathogenic insights and therapeutic implications [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B081.