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Spatially resolved single-cell transcriptomic profiling of human colorectal cancer using NanoString CosMx SMI

ABSTRACT: This study used the NanoString CosMx Spatial Molecular Imager (SMI) to perform spatially resolved single-cell transcriptomic profiling of FFPE human colorectal tissue. Seventeen samples were analyzed, including three colorectal polyp samples (CA), eleven stage I colorectal cancer samples (CCP1–CCP4), and three colorectal cancer-adjacent tissue samples (HCT). CosMx SMI enabled in situ detection and spatial localization of RNA transcripts at single-cell and subcellular resolution. The processed dataset includes per-cell gene expression matrices, transcript coordinates, cell metadata, field-of-view (FOV) positions, and cell segmentation polygon data, providing a resource for investigating spatial cellular heterogeneity and the tumor microenvironment in colorectal cancer. This study used the NanoString CosMx Spatial Molecular Imager (SMI) to perform spatially resolved single-cell transcriptomic profiling of FFPE human colorectal tissue. Seventeen samples were analyzed, including three colorectal polyp samples (CA), eleven stage I colorectal cancer samples (CCP1–CCP4), and three colorectal cancer-adjacent tissue samples (HCT). CosMx SMI enabled in situ detection and spatial localization of RNA transcripts at single-cell and subcellular resolution. The processed dataset includes per-cell gene expression matrices, transcript coordinates, cell metadata, field-of-view (FOV) positions, and cell segmentation polygon data, providing a resource for investigating spatial cellular heterogeneity and the tumor microenvironment in colorectal cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE348495 | GEO | 2026/09/30

REPOSITORIES: GEO

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Project description:Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer-related mortality. CRC can be classified into DNA mismatch repair proficient (MMRp) and deficient (MMRd) subtypes, with only ~50% of MMRd tumours responding to immunotherapy. Tumour architecture is spatially heterogeneous, ranging from the necrotic core to the invasive front, accompanied by diverse stromal and immune responses that influence tumour progression and treatment outcomes. To explore the spatial organisation of the tumour-immune microenvironment, we profiled the expression of ~1,000 genes in 846,469 cells from 23 tumour and normal tissue samples using the CosMx Spatial Molecular Imager (SMI). Using a custom bioinformatic pipeline, we performed quality control, cell type annotation, identified 9 spatial niches and provide an interactive web application to explore this data. Spatial niches included normal colonic crypts, tumour masses, neutrophil-rich regions, and lymphoid aggregates. Differential gene expression analysis revealed niche-specific changes to chemokine signalling, T cell infiltration and myeloid cell polarisation could either support or inhibit tumours depending on the niche. To expand the analysis, we integrated public single-cell RNA-Seq datasets, identifying increased tumour stemness in samples with higher neutrophil content that appeared to be driven by inflammation-mediated stromal reprogramming. Additionally, samples enriched in lymphoid aggregates, as defined by a spatial lymphoid aggregate signature, displayed heightened interferon signalling and an increased abundance of proliferating B cells. Finally, we identify gene expression patterns that distinguish tumour cells from normal epithelial cells within tumours. Our analysis reveals that many of the most pronounced changes in tumour gene expression originate from alterations in the tumour microenvironment, while also revealing tumour-intrinsic gene expression. By studying the spatial niches of CRC, we reveal niche-specific dynamics that drive tumours through innate stromal signalling and suggest both tumour-specific and stromally-mediated potential therapeutic targets.

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Spatially resolved single-cell transcriptomic profiling of human colorectal cancer using NanoString CosMx SMI

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