A universal pipeline to combine spatial transcriptomics, proteomics, and diagnostic H&E assays on a single tissue section to study tissue microenvironment.

作者：Li Yen Chong, Craig Ryan Joseph, Felicia Wee, Zhen Wei Neo, Jeffrey Chun Tatt Lim, Yang Wu, Willa Wen‐You Yim, Melvin L.K. Chua, Nye Thane Ngo, Tony Kiat Hon Lim, Joe Yeong · 发表于：Journal of Clinical Oncology · 年份：2024 · DOI：10.1200/jco.2024.42.16_suppl.e14657 · 被引用次数：2 · 研究领域：Single-cell and spatial transcriptomics

e14657 Background: Spatial multi-omics approaches, including spatial transcriptomics (ST) and spatial proteomics (SP), that elucidate the complex tissue microenvironment (TME) are gaining traction in cancer research studies. However, combining these approaches onto one tissue section remains challenging. ST methods visualize, locate and quantify RNA targets, evaluating the transcriptome of the TME at the subcellular level while SP methods stain and visualize protein biomarkers at the cellular level. Here we show a pipeline that combines these ST and SP methods with Hematoxylin and Eosin (H&E) approach on a single tissue section to achieve single slide multi-omics data with high resolution tissue morphology images. Methods: 5µm formalin-fixed paraffin-embedded sections of human lung cancer samples were placed on a Xenium (10x Genomics, Pleasanton, CA) slides and treated to expose RNA molecules. Probe hybridization was performed with a human lung panel kit containing 289 barcoded DNA padlock probes. Downstream ligation and amplification generated copies of the barcode and thereafter, the Xenium Analyzer performed imaging and data collection. The same tissue section was then stained and imaged in COMET (Lunaphore Technologies SA, Switzerland) using sequential immunofluorescence (seqIF) method to detect 40 protein targets in situ. Serial sections of the specimens were used for direct H&E and seqIF staining for comparative validation. Results: Multi-omics images generated ...