Abstract Esophageal squamous cell carcinoma (ESCC) is the world’s 7th most common malignancy, yet survival remains dismal owing to late detection, frequent relapse, and a lack of targeted therapies. While Wnt signalling is commonly dysregulated in ESCC, the specific roles of its facultative components Lgr5 and Lgr6 remain poorly understood. We combined single-cell transcriptomic analyses from patient biopsies, a chemically induced murine ESCC model, and primary three-dimensional tumour organoids to define how Lgr5+ and Lgr6+ epithelial cells shape disease course. Single-cell profiling of patient tumours located the majority of LGR5+ and LGR6+ cells within stem-like clusters enriched for cell-cycle and stress-adaptation programmes. In mice, reporter models showed that the proportion of Lgr5+ and Lgr6+ cells increases sharply between healthy tissues, dysplastic tissues, and tumours, while lineage tracing models confirmed their direct contribution to tumour outgrowth and long-term retention. In vitro organoid assays revealed functional complementarity: Lgr5+ cells enhanced organoid initiation, while Lgr6+ cells sustained long-term self-renewal. Collectively, these results label Lgr5+ and Lgr6+ populations as non-redundant drivers of tumour initiation and progression. Joint assessment of both markers sharpens prognostic resolution and exposes a dual-target vulnerability that could dismantle the cellular reservoir underpinning ESCC maintenance and relapse. This integrative study provides a rationale for precision interventions aimed at stem-like epithelial populations in ESCC and lays the groundwork for biomarker-guided therapeutic strategies. Citation Format: Lana Kostic, Snezhina Kancheva, Katzrin Murad, Kaushal Krishna Kaslikar, Bernett Lee, Nick Barker. Lgr5+ and Lgr6+ Cells as Prognostic Markers and Therapeutic Targets in Esophageal Squamous Cell Carcinoma (ESCC) abstract. In: Proceedings of Frontiers in Cancer Science 2025; 2025 Nov 5-7; Singapore. Philadelphia (PA): AACR; Cancer Res 2026;86 (13Suppl): Abstract nr P14.
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