A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients.
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| Title: | A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. |
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| Authors: | Pita-Juarez Y; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Karagkouni D; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Kalavros N; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Spatial Technologies Unit, HMS Initiative for RNA Medicine / Beth Israel Deaconess Medical Center, Boston, MA, USA., Melms JC; Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.; Columbia Center for Translational Immunology, New York, NY, USA., Niezen S; Harvard Medical School, Boston, MA, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA., Delorey TM; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Essene AL; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA., Brook OR; Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA, USA., Pant D; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA., Skelton-Badlani D; Harvard Medical School, Boston, MA, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA., Naderi P; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Huang P; Harvard Medical School, Boston, MA, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA., Pan L; NanoString Technologies, Inc., Seattle, WA, USA., Hether T; NanoString Technologies, Inc., Seattle, WA, USA., Andrews TS; Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada., Ziegler CGK; Harvard Medical School, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA.; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA.; Harvard Stem Cell Institute, Cambridge, MA, USA.; Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.; Program in Immunology, Harvard Medical School, Boston, MA, USA.; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA., Reeves J; NanoString Technologies, Inc., Seattle, WA, USA., Myloserdnyy A; Harvard Medical School, Boston, MA, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA., Chen R; Harvard Medical School, Boston, MA, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA., Nam A; NanoString Technologies, Inc., Seattle, WA, USA., Phelan S; NanoString Technologies, Inc., Seattle, WA, USA., Liang Y; NanoString Technologies, Inc., Seattle, WA, USA., Gregory M; NanoString Technologies, Inc., Seattle, WA, USA., He S; NanoString Technologies, Inc., Seattle, WA, USA., Patrick M; NanoString Technologies, Inc., Seattle, WA, USA., Rane T; NanoString Technologies, Inc., Seattle, WA, USA., Wardhani A; NanoString Technologies, Inc., Seattle, WA, USA., Amin AD; Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.; Columbia Center for Translational Immunology, New York, NY, USA., Biermann J; Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.; Columbia Center for Translational Immunology, New York, NY, USA., Hibshoosh H; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA., Veregge M; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA., Kramer Z; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA., Jacobs C; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA., Yalcin Y; Harvard Medical School, Boston, MA, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA., Phillips D; Present Address: Genentech, 1 DNA Way, South San Francisco, CA, USA., Slyper M; Present Address: Genentech, 1 DNA Way, South San Francisco, CA, USA., Subramanian A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Ashenberg O; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Bloom-Ackermann Z; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Tran VM; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Gomez J; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Sturm A; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Zhang S; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Fleming SJ; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Warren S; NanoString Technologies, Inc., Seattle, WA, USA., Beechem J; NanoString Technologies, Inc., Seattle, WA, USA., Hung D; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Genetics, Harvard Medical School, Boston, MA, USA.; Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA., Babadi M; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Padera RF Jr; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA., MacParland SA; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA.; Department of Immunology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, ON, Canada.; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada., Bader GD; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, Toronto, ON, Canada., Imad N; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA., Solomon IH; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA., Miller E; NanoString Technologies, Inc., Seattle, WA, USA., Riedel S; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Porter CBM; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Villani AC; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.; Department of Medicine, Harvard Medical School, Boston, MA, USA., Tsai LT; Harvard Medical School, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA., Hide W; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Szabo G; Harvard Medical School, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA., Hecht J; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Rozenblatt-Rosen O; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Present Address: Genentech, 1 DNA Way, South San Francisco, CA, USA., Shalek AK; Harvard Medical School, Boston, MA, USA. shalek@mit.edu.; Broad Institute of MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu.; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA. shalek@mit.edu.; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA. shalek@mit.edu.; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA. shalek@mit.edu.; Harvard Stem Cell Institute, Cambridge, MA, USA. shalek@mit.edu.; Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.; Program in Immunology, Harvard Medical School, Boston, MA, USA. shalek@mit.edu.; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu., Izar B; Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA. bi2175@cumc.columbia.edu.; Columbia Center for Translational Immunology, New York, NY, USA. bi2175@cumc.columbia.edu.; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA. bi2175@cumc.columbia.edu.; Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA. bi2175@cumc.columbia.edu.; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA. bi2175@cumc.columbia.edu., Regev A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. aviv.regev.sc@gmail.com.; Present Address: Genentech, 1 DNA Way, South San Francisco, CA, USA. aviv.regev.sc@gmail.com., Popov YV; Harvard Medical School, Boston, MA, USA. ypopov@bidmc.harvard.edu.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA. ypopov@bidmc.harvard.edu.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA. ypopov@bidmc.harvard.edu., Jiang ZG; Harvard Medical School, Boston, MA, USA. zgjiang@bidmc.harvard.edu.; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA. zgjiang@bidmc.harvard.edu.; Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Boston, MA, USA. zgjiang@bidmc.harvard.edu., Vlachos IS; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA. ivlachos@bidmc.harvard.edu.; Harvard Medical School, Boston, MA, USA. ivlachos@bidmc.harvard.edu.; Broad Institute of MIT and Harvard, Cambridge, MA, USA. ivlachos@bidmc.harvard.edu.; Spatial Technologies Unit, HMS Initiative for RNA Medicine / Beth Israel Deaconess Medical Center, Boston, MA, USA. ivlachos@bidmc.harvard.edu.; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA. ivlachos@bidmc.harvard.edu.; Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA. ivlachos@bidmc.harvard.edu. |
| Source: | Genome biology [Genome Biol] 2025 Mar 14; Vol. 26 (1), pp. 56. Date of Electronic Publication: 2025 Mar 14. |
| Publication Type: | Journal Article |
| Journal Info: | Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE |
| Database: | MEDLINE Ultimate |
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| ISSN: | 1474-760X |
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| DOI: | 10.1186/s13059-025-03499-5 |
