Single-cell RNA sequencing (scRNA-seq)

Overview

Single-cell RNA sequencing (scRNA-seq) enables transcriptome-wide gene expression profiling at single-cell resolution, enabling cell type deconvolution, identification of rare cell populations, and analysis of intratumoral heterogeneity PMID:37406106.

Used by

  • PMID:41941260 — scRNA-seq of pre- and post-RT PBMCs from ImmunoRad rectal-cancer MCT1 patients showed RT-induced stress responses in B cells, ECM-remodeling and immune activation in monocytes, and MYC-driven activation in CD8+ T cells — interpreted as RT-induced trained immunity PMID:41941260.
  • PMID:37406106 — scRNA-seq on paired pre- and on-treatment biopsies from 7 HER2-positive metastatic esophagogastric cancer patients (3 receiving CAPOX + trastuzumab, 4 without trastuzumab) from MSK and Samsung Medical Center; identified a transcriptional resistance program characterized by upregulation of MT1H, MT1E, MT2A, and MSMB via GeneVector analysis PMID:37406106.
  • PMID:27806376 — plate-based Smart-Seq2 scRNA-seq on 4,347 FACS-sorted live single cells from 6 untreated IDH-mutant, 1p/19q co-deleted oligodendrogliomas (MGH36/53/54/60/93/97); identified three transcriptional states (oligodendrocytic, astrocytic, stem/progenitor) constituting a developmental hierarchy conserved across genetic subclones PMID:27806376.
  • PMID:34493726 — Smart-Seq2 scRNA-seq and snRNA-seq (nuc-Seq) on 11 neuroblastoma tumors (4,224 nuclei) and 3 postnatal human adrenal glands (1,536 nuclei); identified an undifferentiated nC3 cluster in high-risk tumors transcriptionally resembling a novel postnatal human cholinergic progenitor (hC1), distinguishing high- from low-risk disease PMID:34493726.
  • Applied to 156 multi-site HGSOC biopsy samples (~930k cells total) from 42 treatment-naive patients; resolved site-specific T cell phenotypic states: adnexal sites enriched for dysfunctional CD8+ T cells, non-adnexal/metastatic sites enriched for naive/memory T cells PMID:36517593
  • Single-cell RNA-seq performed on 259,441 cells from three public ccRCC cohorts to validate FGES signatures; a subset of 22,456 cells used for spatial validation in the HiTME ccRCC subtyping study PMID:22138691
  • Applied to 147,045 FAC-sorted tdTomato+ cells from Vhl/HIF conditional knockout mice (4 genotypes, 12 mice) to resolve HIFα-isoform–specific transcriptional programs in proximal tubular cells; revealed HIF1A drives glycolysis while HIF2A drives dedifferentiation PMID:23797736
  • Re-analyzed public scRNA-seq dataset (National Omics Data Encyclopedia OEP00001237, 13 GBC patients) to identify 16 cell types including ACTA2+ and MFAP5+ CAF subpopulations with co-expression of YAP1 and SEMA7A PMID:24997986
  • Single-cell RNA sequencing with consensus hierarchical clustering (Deng M, cited) classified CCA into BA-active vs BA-inactive metabolic subtypes; BA-active subtype showed shorter OS and immunotherapy resistance with SLCO1B3 and CEACAM1 as prognostic markers PMID:25608663
  • 10x Chromium Single Cell Gene Expression 3’v3.1 applied across multiple AAV-CRISPR rat breast tumor genotypes; UMAP showed genotype-driven immune microenvironment differences: adaptive immune enrichment in single-edit tumors, myeloid-dominated immunosuppression (macrophage vs neutrophil dichotomy) in multi-edit tumors PMID:26437033

Notes

  • scRNA-seq revealed cancer-cell-intrinsic resistance programs associated with trastuzumab + chemotherapy that could not be identified by bulk sequencing PMID:37406106.
  • Corpus-grown slug; not present in canonical ontology.

Sources

This page was processed by crosslinker on 2026-05-14.

This page was processed by crosslinker on 2026-05-14. - PMID:36517593

This page was processed by crosslinker on 2026-05-14. - PMID:22138691

This page was processed by crosslinker on 2026-05-14. - PMID:23797736

This page was processed by crosslinker on 2026-05-14. - PMID:24997986

This page was processed by crosslinker on 2026-05-14. - PMID:25608663

This page was processed by crosslinker on 2026-05-14. - PMID:26437033

This page was processed by wiki-cli on 2026-05-14.