ArticleGenome biology2023
Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 25 citations in OpenAlex.
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- ProbeST: a custom probe design pipeline for dual host-pathogen Spatial Transcriptomics.BMC genomics · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Review
- Venezuelan equine encephalitis virus infection causes chronic neurobehavioral outcomes, cellular remodeling, and hippocampal single-cell transcriptomic changes.PLoS pathogens · 2026Article
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- Exploring microorganism-host interactions: Emerging organoid models and analytical approaches.mLife · 2026Review
- Spatial transcriptomics of developing human lungs defines cellular phenotypes associated with age, lineage and location.Scientific reports · 2026Article
- Spatial Transcriptomics to Study Virus-Host Interactions.Annual review of virology · 2025Review
- Spatial Transcriptomics and Single Cell-RNASeq Reveals Cellular Heterogeneity of SARS-CoV-2 in Lung Tissues and Global Mutational Patterns in COVID-19 Patients.Journal of medical virology · 2025Article
- Spatial-Omics Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Alveolar epithelial type 2 cells in acute lung injury and acute respiratory distress syndrome: spatiotemporal fate and regulation.Burns & trauma · 2025Review
- Decoding immune low-response states in sepsis: single-cell and 3D spatial transcriptomic insights into immunoparalysis.Frontiers in immunology · 2025Review
- Dual spatial host-bacterial gene expression in Mycobacterium abscessus respiratory infections.Communications biology · 2024Article
- Single cell spatial profiling of FFPE splenic tissue from a humanized mouse model of HIV infection.Biomarker research · 2024Article
- Leave no transcripts behind.Nature reviews. Microbiology · 2024Article
- Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis.Nature genetics · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Multiplexed spatial transcriptomics methods and the application of expansion microscopy.Frontiers in cell and developmental biology · 2024Review
- Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.Genome biology · 2023Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Technologies to study localized host-pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host-pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.
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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.