{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Klotzer KA"],"funding":["NIDDK NIH HHS","NIA NIH HHS","Deutsche Forschungsgemeinschaft (German Research Foundation)","Österreichische Agentur für Internationale Mobilität und Kooperation in Bildung, Wissenschaft und Forschung (Austrian Agency for International Cooperation in Education and Research)","U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)","Marshallplan-Jubiläumsstiftung (Austrian Marshall Plan Foundation)"],"pagination":["1922-1934"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12415535"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["57(8)"],"pubmed_abstract":["The use of single-cell RNA sequencing in clinical and translational research is limited by the challenge of identifying cell-type-specific, targetable molecular changes in individual patients and cross-species differences. Here we created an integrated single-cell kidney atlas including over 1 million cells from 140 samples, defining more than 70 conserved cell states in human and rodent models. We developed CellSpectra, a computational tool that quantifies changes in gene expression coordination across cellular functions, which we applied to kidney and lung cancer data. This tool powers our patient-level single-cell functional profiling report, which highlights cell-type-specific changes in the coordination of pathway gene expression in individuals. Our cross-species atlas facilitates the selection of a rodent model that closely reflects the cellular and pathway-level signatures observed in patient samples, advancing the application of single-cell methodologies in clinical precision medicine. Finally, using experimental models, we demonstrate how our informatics approach can be applied for the potential selection of suitable therapeutics."],"journal":["Nature genetics"],"pubmed_title":["Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas."],"pmcid":["PMC12415535"],"funding_grant_id":["5R01DK105821-08","R01 DK087635","2R01DK076077-15","5R01DK132630-02","Marietta-Blau Grant","BA 6205/2-1","5R01DK087635-15","R01 DK076077","P50 DK114786","Austrian Marshall Plan Foundation scholarship","R01 DK105821","5P50DK114786-07","R01 DK132630","R56 AG081351"],"pubmed_authors":["Liang X","Susztak K","Balzer MS","Hogan JJ","Eller K","Bloom RD","Abedini A","Zhang NR","Halmos B","Schuller M","Levinsohn J","Li S","Dumoulin B","Quinn G","Ha E","Klotzer KA"],"additional_accession":[]},"is_claimable":false,"name":"Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas.","description":"The use of single-cell RNA sequencing in clinical and translational research is limited by the challenge of identifying cell-type-specific, targetable molecular changes in individual patients and cross-species differences. Here we created an integrated single-cell kidney atlas including over 1 million cells from 140 samples, defining more than 70 conserved cell states in human and rodent models. We developed CellSpectra, a computational tool that quantifies changes in gene expression coordination across cellular functions, which we applied to kidney and lung cancer data. This tool powers our patient-level single-cell functional profiling report, which highlights cell-type-specific changes in the coordination of pathway gene expression in individuals. Our cross-species atlas facilitates the selection of a rodent model that closely reflects the cellular and pathway-level signatures observed in patient samples, advancing the application of single-cell methodologies in clinical precision medicine. Finally, using experimental models, we demonstrate how our informatics approach can be applied for the potential selection of suitable therapeutics.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Aug","modification":"2026-06-04T16:14:24.832Z","creation":"2026-05-13T14:24:11.845Z"},"accession":"S-EPMC12415535","cross_references":{"pubmed":["40775269"],"doi":["10.1038/s41588-025-02285-0"]}}