GeoMX : Metabolic and Inflammatory Niches Driving Recurrence in Adjuvant-Treated NSCLC

While there have been therapeutic advancements in treatments for non-small cell lung cancer (NSCLC), we have a limited understanding of how the tumour composition and spatial heterogeneity influences clinical outcomes. Here, we perform multiomic analysis of 61 NSCLC patients treated with adjuvant chemotherapy and curative resection, integrating spatial transcriptomics, spatial proteomics, and deep learning to profile the tumour microenvironment (TME). We identify spatial-metabolic states associated with disease recurrence in and between cells in the TME, involving glutamine import, glycolytic, and lipid oxidation pathways. Based on protein expression, we find spatially distinct regions linked to tumour recurrence, implicating specific roles for tumour associated macrophages, metabolic pathways, and major histocompatibility complex (MHC) proteins. Moreover, transcriptomic analysis reveals histology-specific gene expression changes and metabolic and inflammation pathway associations with tumour recurrence. This multiomic analysis highlights the complex immunological and metabolic dynamics characteristic of disease recurrence in adjuvant chemotherapy treated NSCLC.This dataset is the GeoMx DSP whole transcriptome assay data of 52 patients, consisting of the raw counts matrix, log normalised count matrix and matching metadata.