ArticleNature communications2024
High resolution spatial profiling of kidney injury and repair using RNA hybridization-based in situ sequencing.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Next-generation kidney tissue analysis - spatial omics and digital pathology.Nature reviews. Nephrology · 2026Review
- Synchronization of the 12-h circatidal rhythm maintains the kidney through repeated cycles of warm reperfusion in the hibernating ground squirrel.Function (Oxford, England) · 2026Article
- Shared mechanisms of organ fibrosis.JCI insight · 2026Review
- Single-cell RNA sequencing and spatial transcriptomics in the discovery of kidney disease potential biomarkers: a narrative review.BMC nephrology · 2026Review
- Single-cell Stereo-seq reveals regulatory mechanisms driving regeneration of injured proximal tubules during AKI.Nature communications · 2026Article
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Article
- Metabolic beneficial effects of targeting a long non-coding RNA, lnc-megacluster, in obesity.Molecular therapy. Nucleic acids · 2026Article
- Cell-cell crosstalk in kidney health and disease.Nature reviews. Nephrology · 2026Review
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- Defining the urine proteome in boys with posterior urethral valves: a pilot study.Frontiers in cell and developmental biology · 2026Article
- Article
- Genome doubling as a dynamic driver of ovarian cancer evolution: insights from single-cell sequencing.Journal of ovarian research · 2025Review
- A Holistic Approach to AKI: Integrating Clinical and Molecular Data in the Human Kidney.Seminars in nephrology · 2025Review
- Chronic kidney disease of unknown aetiology: a real-world study.BMC nephrology · 2025Observational
- Integration of spatial protein imaging and transcriptomics in the human kidney tracks the regenerative potential of proximal tubules.Science advances · 2025Article
- Multimodal spatial transcriptomic characterization of mouse kidney injury and repair.Nature communications · 2025Article
- SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics.BMC bioinformatics · 2025Article
- Role of local complement activation in kidney fibrosis and repair.The Journal of clinical investigation · 2025Review
- The secret life of complement: challenges and opportunities in exploring functions of the complosome in disease.The Journal of clinical investigation · 2025Review
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Authors and funding
10 authors.
Funding
Abstract
Emerging spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ at cellular resolution. We apply direct RNA hybridization-based in situ sequencing (dRNA HybISS, Cartana part of 10xGenomics) to compare male and female healthy mouse kidneys and the male kidney injury and repair timecourse. A pre-selected panel of 200 genes is used to identify cell state dynamics patterns during injury and repair. We develop a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting dataset allows us to resolve 13 kidney cell types within distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. At late timepoints after injury, C3+ leukocytes are enriched near pro-inflammatory, failed-repair proximal tubule cells. Integration of snRNA-seq dataset from the same injury and repair samples also allows us to impute the spatial localization of genes not directly measured by dRNA HybISS.
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