Spatial transcriptomics

Overview

Spatial transcriptomics technologies enable gene expression profiling while preserving the spatial context of cells within tissue sections. Platforms include 10X Visium (spot-based) and GeoMx (ROI-based), enabling integration of transcriptomic data with tissue architecture and morphology PMID:39091884 PMID:39386723.

Used by

  • PMID:39091884 — 10X Visium spatial transcriptomics was performed on 5 cSCC-AK matched tissue cases with resolved clonal relationships; revealed high expression of immune checkpoint ligands (PVR, NECTIN2, CD274, CD80, CD86) on tumor cells and checkpoint receptors (CTLA4, TIGIT, PDCD1) on lymphocytes at the invasive front of cSCC PMID:39091884.
  • PMID:39386723 — NanoString GeoMx WTA spatial transcriptomics was applied to 35 fallopian tube specimens (HGSOC precursors) with >600 ROIs; complemented CyCIF multiplexed immunofluorescence to characterize the immune microenvironment of HGSOC precursor lesions PMID:39386723.
  • PMID:41941260 — Spatial transcriptomics (10x Visium HD) was applied to 140+ biopsies from the ImmunoRad MCT1 rectal-cancer trial (NCT05943210); identified RT-associated spatial reorganization of lymphocytes and altered macrophage wound-healing signals after short-course radiotherapy PMID:41941260.
  • PMID:39975212 — 10X Xenium single-cell spatial profiling on FFPE skin from a 63-year-old melanoma patient (two adjacent sections, ~96M transcripts, ~300K cells) using a custom 360-gene panel (predesigned 10X human skin panel + 100 custom probes); showed HighMut melanocytes are almost exclusively in the interfollicular epidermis while LowMut melanocytes are enriched in hair follicles, validating in-vitro morphology/mutation burden dimorphism in situ PMID:39975212.
  • Spatial transcriptomics applied in HCC genomic characterization to map intratumoral heterogeneity and gene expression patterns PMID:22634756
  • 10x Genomics Visium CytAssist spatial transcriptomics applied to FFPE experimental Ewing sarcoma tumors (GEO GSE272958); confirmed ~70% transcriptome sharing between primary and metastatic sites and identified BCL11B and ITM2A as Ewing-specific markers. PMID:25186949

Notes

  • Spatial transcriptomics is particularly valuable for characterizing the tumor-immune interface and identifying checkpoint expression patterns at the invasive front PMID:39091884.
  • Corpus-grown slug; not present in canonical ontology.

Sources

This page was processed by crosslinker on 2026-04-30. - PMID:22634756

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