Self-Supervised AI Reveals a Hidden Landscape of Prognostic Spatial Patterns in Multiplex Immunofluorescence Images

作者：Lucas Farndale, Kai Rakovic, Phimmada Hatthakarnkul, Sona Szalma, Leonor Patricia Schubert Santana, Silvia Martinelli, Fiona Ballantyne, Rachel L Baird, Ian Powley, Leah Officer-Jones, Noori Maka, Campbell S.D. Roxburgh, Crispin Miller, David K. Chang, Joanne Edwards, Edward W. Roberts, John Le Quesne, Ke Yuan · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2025 · DOI：10.1101/2025.10.16.682563 · 被引用次数：1 · 研究领域：Image Processing Techniques and Applications、Cell Image Analysis Techniques

Abstract Modern spatial proteomic methods, such as multiplex immunofluorescence (mIF) imaging, offer a data-rich view of spatial biology in intact tissues. However, interpreting its complexity is a major bottleneck, limiting its potential for biological discovery and clinical translation. Current computational methods often rely on segmentation-based approaches that discard crucial morphological information and are limited to testing pre-defined hypotheses. Here, we introduce a self-supervised learning (SSL) framework that enables hypothesis-agnostic, context-aware discovery of biomarkers directly from mIF images. Our approach extracts rich feature representations that capture holistic architectural patterns, which integrate cellular morphology, marker interactions, and microenvironmental context without human supervision. Applying this framework to over 7,000 mIF tissue images from over 1,800 patients in two distinct cancer types, we demonstrate superior prognostic performance over conventional segmentation analyses. The method autonomously identified previously unknown and potentially clinically actionable biological patterns. In lung adenocarcinoma, these include a Ki67-mediated immune evasion phenotype, a sub-cellular pattern of GLB1 expression which aligns with low-grade EGFR -driven tumours, and distinct modes of tumour-immune interaction in PD-L1 + patients. We also find a regulatory T-cell-mediated immunosupressive environment promoting tumour budding in colorectal ca...