Abstract 5000: Single cell and spatial mapping of the fallopian tube with insight into origin of high grade serous carcinoma

Abstract High-grade serous “ovarian” carcinoma (HGSC), the most lethal gynecologic cancer, typically presents at advanced stages owing to lack of symptoms in early-stage disease. Additionally, no effective screening strategies exist. Despite the misnomer, most HGSC arise from fallopian tube epithelium (FTE). Better understanding early steps in pathogenesis of serous tubal intraepithelial carcinoma (STIC) and cell of origin for HGSC will inform early detection strategies and lead to new insights for effective screening approaches. HGSC and STIC are characterized by TP53 mutation and chromosomal instability. Earlier lesions in the FTE, such as “p53 signatures, ” benign lesions harboring TP53 mutation, are less well understood. We aimed to study STIC, p53 signatures, and the benign FT at the single cell and spatial level, considering not only epithelial and lesional cells but also the surrounding stromal and immune microenvironment. We employed single-cell RNA sequencing (scRNA-seq) in combination with single-nuclei RNA sequencing using 10x flex and single-cell spatial transcriptomics (scST), on formalin-fixed paraffin-embedded (FFPE) tissues to analyze normal and neoplastic fallopian tubes. scST data from 84 fields of view representing 8 patients (5 benign, 3 STIC) were used to define epithelial subtypes within the FTE, considering both gene expression profiles and spatial distributions correlating to histopathological findings. Furthermore, scRNA-seq data from fresh non-neoplastic FT and FFPE STIC samples were integrated to construct comprehensive atlases. The epithelial subtypes within the scST data were mapped on to the integrated atlas using gene module scores.Seven distinct epithelial subtypes were identified, with transcriptional diversity linked to HGSC precursors. Subtype-specific gene expression profiles were linked to histological features, revealing cellular heterogeneity in normal epithelium in contrast to clonal expansions and STIC. In the microenvironment, we found epithelial subtype-specific stromal and immune interactions. Furthermore, four subclusters of macrophages were identified with distinct expression programs; some subtypes were only abundant in association with STIC. We implemented scST in clinical FT samples including STIC, and integrated ST features with a large atlas of scRNA-seq data to refine single cell characterization of benign FT, p53 signatures, and STIC. Our spatially informed analyses recognized distinct subsets of epithelial, immune, and stromal cells that change over the course of STIC/HGSC development. Additionally, the trajectory of epithelial subtypes demonstrates the most likely epithelial cell subtype from which STIC may form. Our integrated FT atlas provides a critical resource for others seeking to understand early events in HGSC pathogenesis, advancing early detection and therapeutic strategies. Citation Format: Sahar Nasr, Jacob Gutierrez, Caleb lareau, Brooke Howitt. Single cell and spatial mapping of the fallopian tube with insight into origin of high grade serous carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5000.