Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses

Autor: Normandin, Erica, Triana, Sergio, Raju, Siddharth S., Lan, Tammy C.T., Lagerborg, Kim, Rudy, Melissa, Adams, Gordon C., DeRuff, Katherine C., Logue, James, Liu, David, Strebinger, Daniel, Rao, Arya, Messer, Katelyn S., Sacks, Molly, Adams, Ricky D., Janosko, Krisztina, Kotliar, Dylan, Shah, Rickey, Crozier, Ian, Rinn, John L., Melé, Marta, Honko, Anna N., Zhang, Feng, Babadi, Mehrtash, Luban, Jeremy, Bennett, Richard S., Shalek, Alex K., Barkas, Nikolaos, Lin, Aaron E., Hensley, Lisa E., Sabeti, Pardis C., Siddle, Katherine J.

Publikováno v: In Cell Genomics 13 December 2023 3(12)

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A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2.

Autor: Delorey TM; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Ziegler CGK; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA.; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA., Heimberg G; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Normand R; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.; Harvard Medical School, Boston, MA 02115, USA.; Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Yang Y; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., Segerstolpe A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Abbondanza D; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Fleming SJ; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142.; Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Subramanian A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Montoro DT; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Jagadeesh KA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Dey KK; Department of Epidemiology, Harvard School of Public Health., Sen P; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA., Slyper M; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Pita-Juárez YH; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Harvard Medical School, Boston, MA 02115, USA.; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA., Phillips D; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Bloom-Ackerman Z; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Barkas N; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142., Ganna A; Institute for Molecular Medicine Finland, Helsinki, Finland.; Analytical & Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA., Gomez J; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Normandin E; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Harvard Medical School, Boston, MA 02115, USA., Naderi P; Harvard Medical School, Boston, MA 02115, USA.; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA., Popov YV; Harvard Medical School, Boston, MA 02115, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.; Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA., Raju SS; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA., Niezen S; Harvard Medical School, Boston, MA 02115, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.; Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA., Tsai LT; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Harvard Medical School, Boston, MA 02115, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115.; Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA., Siddle KJ; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA., Sud M; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Tran VM; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Vellarikkal SK; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Amir-Zilberstein L; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Atri DS; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Beechem J; NanoString Technologies Inc., Seattle, WA 98109, USA., Brook OR; Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA., Chen J; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA., Divakar P; NanoString Technologies Inc., Seattle, WA 98109, USA., Dorceus P; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Engreitz JM; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Department of Genetics and BASE Initiative, Stanford University School of Medicine., Essene A; Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115.; Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA., Fitzgerald DM; Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., Fropf R; NanoString Technologies Inc., Seattle, WA 98109, USA., Gazal S; Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA., Gould J; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142., Grzyb J; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115., Harvey T; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Hecht J; Harvard Medical School, Boston, MA 02115, USA.; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA., Hether T; NanoString Technologies Inc., Seattle, WA 98109, USA., Jane-Valbuena J; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Leney-Greene M; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Ma H; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., McCabe C; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., McLoughlin DE; Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., Miller EM; NanoString Technologies Inc., Seattle, WA 98109, USA., Muus C; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138., Niemi M; Institute for Molecular Medicine Finland, Helsinki, Finland., Padera R; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115.; Harvard-MIT Division of Health Sciences and Technology, Cambridge MA.; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA., Pan L; NanoString Technologies Inc., Seattle, WA 98109, USA., Pant D; Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.; Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02115.; Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, MA 02115, USA., Pe'er C; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Pfiffner-Borges J; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Pinto CJ; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.; Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., Plaisted J; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115., Reeves J; NanoString Technologies Inc., Seattle, WA 98109, USA., Ross M; NanoString Technologies Inc., Seattle, WA 98109, USA., Rudy M; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Rueckert EH; NanoString Technologies Inc., Seattle, WA 98109, USA., Siciliano M; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115., Sturm A; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Todres E; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Waghray A; Harvard Stem Cell Institute, Cambridge, MA, USA.; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., Warren S; NanoString Technologies Inc., Seattle, WA 98109, USA., Zhang S; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Zollinger DR; NanoString Technologies Inc., Seattle, WA 98109, USA., Cosimi L; Infectious Diseases Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Gupta RM; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Hacohen N; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA., Hide W; Harvard Medical School, Boston, MA 02115, USA.; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA., Price AL; Department of Epidemiology, Harvard School of Public Health., Rajagopal J; Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., Tata PR; Duke University School of Medicine, Durham, NC., Riedel S; Harvard Medical School, Boston, MA 02115, USA.; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA., Szabo G; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Harvard Medical School, Boston, MA 02115, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA., Tickle TL; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142., Hung D; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA., Sabeti PC; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA.; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA., Novak R; Wyss Institute for Biologically Inspired Engineering, Harvard University., Rogers R; Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.; Massachusetts General Hospital, MA 02114, USA., Ingber DE; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138.; Wyss Institute for Biologically Inspired Engineering, Harvard University.; Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA USA., Jiang ZG; Harvard Medical School, Boston, MA 02115, USA.; Department of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.; Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA., Juric D; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.; Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., Babadi M; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142.; Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Farhi SL; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Stone JR; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA., Vlachos IS; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Harvard Medical School, Boston, MA 02115, USA.; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA., Solomon IH; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115., Ashenberg O; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Porter CBM; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA., Li B; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA., Shalek AK; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA.; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA.; Harvard Medical School, Boston, MA 02115, USA.; Harvard Stem Cell Institute, Cambridge, MA, USA.; Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA., Villani AC; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA., Rozenblatt-Rosen O; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.; Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA., Regev A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA.; Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2021 Feb 25. Date of Electronic Publication: 2021 Feb 25.