ReviewAmerican journal of physiology. Gastrointestinal and liver physiology2023
Spatial transcriptomics add a new dimension to our understanding of the gut.
Review in American journal of physiology. Gastrointestinal and liver physiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it, 15 citations in OpenAlex.
- Understanding heterogeneity in the pathogenesis and drug responses of ulcerative colitis through single-cell and spatial transcriptomics.Frontiers in immunology · 2026Pooled it
- A spatial and temporal transcriptomic atlas of mouse intestinal regeneration in the jejunum.Nature communications · 2026Article
- RETROFIT: Reference-free deconvolution of cell-type mixtures in spatial transcriptomics.Nature communications · 2026Article
- Integrative single-cell and spatial multi-Omics analyses identify NETs-driven colon cancer subtypes with distinct metabolic features and prognostic implications.Journal of translational medicine · 2026Article
- Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.Nature microbiology · 2026Article
- Molecular mechanisms and therapeutic potential of tryptophan metabolism in gut-brain signaling transduction: a narrative review.Journal of neuroinflammation · 2026Review
- Spatial immune archetypes in gastric and colorectal cancer: a proposed conceptual framework for immunotherapy resistance and therapeutic remodeling.Frontiers in immunology · 2026Review
- Single-nucleus and spatial transcriptomics reveal intestinal cellular heterogeneity, differentiation, and cell communication mechanisms in SAP-induced intestinal injury.Frontiers in immunology · 2026Article
- Spatial transcriptomics reveals regionally altered gene expression that drives retinal degeneration.Communications biology · 2025Article
- Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner.NPJ biofilms and microbiomes · 2024Article
- Cellular and molecular basis of proximal small intestine disorders.Nature reviews. Gastroenterology & hepatology · 2024Review
- Review
- Key elements determining the intestinal region-specific environment of enteric neurons in type 1 diabetes.World journal of gastroenterology · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The profound complexity of the intestinal mucosa demands a spatial approach to the study of gut transcriptomics. Although single-cell RNA sequencing has revolutionized our ability to survey the diverse cell types of the intestine, knowledge of cell type alone cannot fully describe the cells that make up the intestinal mucosa. During homeostasis and disease, dramatic gradients of oxygen, nutrients, extracellular matrix proteins, morphogens, and microbiota collectively dictate intestinal cell state, and only spatial techniques can articulate differences in cellular transcriptomes at this level. Spatial transcriptomic techniques assign transcriptomic data to precise regions in a tissue of interest. In recent years, these protocols have become increasingly accessible, and their application in the intestinal mucosa has exploded in popularity. In the gut, spatial transcriptomics typically involve the application of tissue sections to spatially barcoded RNA sequencing or laser capture microdissection followed by RNA sequencing. In combination with single-cell RNA sequencing, these spatial sequencing approaches allow for the construction of spatial transcriptional maps at pseudosingle-cell resolution. In this review, we describe the spatial transcriptomic technologies recently applied in the gut and the previously unattainable discoveries that they have produced.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.