ArticlebioRxiv : the preprint server for biology2026
Spatially resolved transcriptomic and proteomic profiling reveals cell interaction programs that predict Barrett's esophagus progression.
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Barrett's esophagus (BE) is the precursor lesion of esophageal adenocarcinoma (EAC). It affects approximately 5% of adults in the United States and significantly increases the risk of developing EAC. However, current surveillance strategies cannot reliably distinguish patients who will progress from those who will remain stable. Direct studies of progressor BE are extremely limited due to availability of tissue with known progression outcomes, and have largely been restricted to genomic profiling approaches. The premalignant cellular landscape of progressor BE remains poorly understood. Here, we used complementary spatial transcriptomic and proteomic imaging to profile 34 non-dysplastic BE patients under endoscopic surveillance, including those who subsequently progressed to dysplasia or EAC, termed "Progressors" and those who remained stable, termed "Non-progressors". Transcriptomics based Xenium analysis captured 974,604 cells across 70 whole-biopsy regions, while protein based imaging mass cytometry profiled 372,242 cells across 119 selected regions. FUME-TCRseq further quantified T cell clonotypes from matched tissues scrolls. Cellular composition was generally similar between Progressors and Non-progressors. However, Progressors showed increased intestinal Barrett's columnar cells, B cells and gastric progenitor-like cells, together with enhanced immune-epithelial interactions, whereas Non-progressors retained coordinated stromal organization. Spatial interaction features strongly outperformed cell composition and density for progression prediction. Combined spatial interaction model achieved an area under the curve (AUC) of 0.97, compared with 0.62 and 0.68 for comparison and density alone. Complementary imaging mass cytometry further resolved the underlying immune programs, identifying cytotoxic and antigen presenting myeloid features enriched in progressors, and CD56
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