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Coefficient of Variation
››COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

By Maureen Bellinger
April 29, 2021
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  • Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Toni M. Delorey, Graham Heimberg, Yiming Yang, Åsa Segerstolpe, Domenic Abbondanza, Ayshwarya Subramanian, Karthik A. Jagadeesh, Michal Slyper, Devan Phillips, Malika Sud, Liat Amir-Zilberstein, Phylicia Dorceus, Joshua Gould, Tyler Harvey, Judit Jané-Valbuena, Hui Ma, Cristin McCabe, Carmel Pe’er, Jenna Pfiffner-Borges, Ellen Todres, Timothy L. Tickle, Samouil L. Farhi, Orr Ashenberg, Caroline B. M. Porter, Bo Li, Orit Rozenblatt-Rosen & Aviv Regev

  • Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Carly G. K. Ziegler, Rachelly Normand, Daniel T. Montoro, Pritha Sen, Yered H. Pita-Juárez, Erica Normandin, Siddharth S. Raju, Linus T.-Y. Tsai, Katherine J. Siddle, Shamsudheen K. Vellarikkal, Deepak S. Atri, Jonathan Chen, Jesse M. Engreitz, Michael Leney-Greene, Christoph Muus, Melissa Rudy, Rajat M. Gupta, Nir Hacohen, Gyongyi Szabo, Pardis C. Sabeti, Ioannis S. Vlachos, Alex K. Shalek & Alexandra-Chloé Villani

  • Program in Health Sciences & Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA, USA

    Carly G. K. Ziegler & Alex K. Shalek

  • Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA

    Carly G. K. Ziegler & Alex K. Shalek

  • Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA

    Carly G. K. Ziegler, Alex K. Shalek & Aviv Regev

  • Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA

    Carly G. K. Ziegler & Alex K. Shalek

  • Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA

    Carly G. K. Ziegler & Alex K. Shalek

  • Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA

    Rachelly Normand, Yiming Yang, Pritha Sen, Hui Ma, Bo Li & Alexandra-Chloé Villani

  • Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA

    Rachelly Normand, Nir Hacohen & Alexandra-Chloé Villani

  • Harvard Medical School, Boston, MA, USA

    Rachelly Normand, Yered H. Pita-Juárez, Erica Normandin, Pourya Naderi, Yury V. Popov, Sebastian Niezen, Linus T.-Y. Tsai, Jonathan Hecht, Winston Hide, Stefan Riedel, Gyongyi Szabo, Z. Gordon Jiang, Ioannis S. Vlachos & Alex K. Shalek

  • Massachusetts Institute of Technology, Cambridge, MA, USA

    Rachelly Normand

  • Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Stephen J. Fleming, Nikolaos Barkas, Joshua Gould, Timothy L. Tickle & Mehrtash Babadi

  • Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Stephen J. Fleming & Mehrtash Babadi

  • Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA

    Kushal K. Dey & Alkes L. Price

  • Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA

    Pritha Sen

  • Department of Medicine, Harvard Medical School, Boston, MA, USA

    Pritha Sen, Christopher J. Pinto, Dejan Juric, Bo Li & Alexandra-Chloé Villani

  • Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA

    Yered H. Pita-Juárez, Pourya Naderi, Jonathan Hecht, Winston Hide, Stefan Riedel & Ioannis S. Vlachos

  • Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA

    Yered H. Pita-Juárez, Pourya Naderi, Winston Hide & Ioannis S. Vlachos

  • Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA

    Yered H. Pita-Juárez, Winston Hide & Ioannis S. Vlachos

  • Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA

    Jana Biermann, Johannes C. Melms, Yiping Wang & Benjamin Izar

  • Columbia Center for Translational Immunology, New York, NY, USA

    Jana Biermann, Johannes C. Melms, Yiping Wang & Benjamin Izar

  • Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Zohar Bloom-Ackermann, James Gomez, Victoria M. Tran, Alexander Sturm, Shuting Zhang & Deborah Hung

  • Institute for Molecular Medicine Finland, Helsinki, Finland

    Andrea Ganna & Mari Niemi

  • Analytical & Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA

    Andrea Ganna

  • Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA

    Igor Katsyv & Hanina Hibshoosh

  • Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA

    Yury V. Popov, Sebastian Niezen, Linus T.-Y. Tsai, Adam Essene, Deepti Pant, Gyongyi Szabo, Robert Rogers & Z. Gordon Jiang

  • Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA

    Yury V. Popov, Sebastian Niezen & Z. Gordon Jiang

  • Department of Systems Biology, Harvard Medical School, Boston, MA, USA

    Siddharth S. Raju

  • FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA

    Siddharth S. Raju

  • Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA

    Linus T.-Y. Tsai, Adam Essene & Deepti Pant

  • Boston Nutrition and Obesity Research Center Functional Genomics and Bioinformatics Core Boston, Boston, MA, USA

    Linus T.-Y. Tsai, Adam Essene & Deepti Pant

  • Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA

    Katherine J. Siddle & Pardis C. Sabeti

  • Divisions of Cardiovascular Medicine and Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    Shamsudheen K. Vellarikkal, Deepak S. Atri & Rajat M. Gupta

  • NanoString Technologies Inc, Seattle, WA, USA

    Joseph Beechem, Prajan Divakar, Robin Fropf, Tyler Hether, Eric M. Miller, Liuliu Pan, Jason Reeves, Marty Ross, Erroll H. Rueckert, Sarah Warren & Daniel R. Zollinger

  • Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA, USA

    Olga R. Brook

  • Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA

    Jonathan Chen & James R. Stone

  • Department of Genetics and BASE Initiative, Stanford University School of Medicine, Stanford, CA, USA

    Jesse M. Engreitz

  • Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA

    Donna M. Fitzgerald, Daniel E. McLoughlin, Christopher J. Pinto, Jayaraj Rajagopal & Dejan Juric

  • Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

    Steven Gazal

  • Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA

    John Grzyb, Robert Padera, Jacob Plaisted, Michelle Siciliano & Isaac H. Solomon

  • John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA

    Christoph Muus & Donald E. Ingber

  • Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA

    Robert Padera

  • Department of Pathology, Harvard Medical School, Boston, MA, USA

    Robert Padera

  • Harvard Stem Cell Institute, Cambridge, MA, USA

    Avinash Waghray & Alex K. Shalek

  • Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA

    Avinash Waghray

  • Infectious Diseases Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA

    Lisa Cosimi

  • Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA

    Nir Hacohen

  • Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA

    Purushothama Rao Tata

  • Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Patrick T. Ellinor

  • Department of Genetics, Harvard Medical School, Boston, MA, USA

    Deborah Hung

  • Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA

    Deborah Hung

  • Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA

    Pardis C. Sabeti

  • Howard Hughes Medical Institute, Chevy Chase, MD, USA

    Pardis C. Sabeti & Aviv Regev

  • Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA

    Pardis C. Sabeti

  • Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA

    Richard Novak & Donald E. Ingber

  • Massachusetts General Hospital, Boston, MA, USA

    Robert Rogers

  • Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA

    Donald E. Ingber

  • Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA

    Benjamin Izar

  • Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY, USA

    Benjamin Izar

  • Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

    Alex K. Shalek

  • Program in Immunology, Harvard Medical School, Boston, MA, USA

    Alex K. Shalek

  • Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA

    Alex K. Shalek

    • A.K.S., A.-C.V., I.S.V., Z.G.J., O.R.-R. and A.R. conceived and led the study. These authors contributed equally as co-second authors: Z.B.-A., N.B., A.G., J.G., J.C.M., I.K., E.N., P.N., Y.V.P., S.S.R., S.N., L.T.-Y.T., K.J.S., M.Su., V.M.T., S.K.V., Y.W. T.M.D., C.G.K.Z., Ã….S., D.A. designed protocols and carried out experiments together with D.P., Z.B.-A., V.M.T., A.S., S.Z., J.G., J.H., E.N., M.Su., C.M., L.T., A.E., D.Pa., L.P., J.C.M., L.A.-Z. C.B.M.P., C.G.K.Z., O.A., R.N., G.H., K.J., K.S., B.L., Y.Y., S.F., A.S., P.N., Y.P.J., P.N., T.He., J.R., W.H., I.S.V., T.M.D. and J.B. designed and performed computational analysis. M.B., N.B., J.G., Y.W., R.G., S.S.R., H.M., P.S., A.W., C.M., M.L.-G., T.H., D.T.M., S.W., D.R.Z., E.R., M.R., E.M., R.F., P.Di., A.G., C.Pe. and M.N. provided input to and assisted with computational analysis. K.J., K.D., A.G., J.E., S.G., A.R. and A.P. contributed methods and performed integrated analysis for GWAS. P.R.T., D.T.M., Z.G.J., Y.P., G.S., S.N., S.R. and J.R. provided clinical and biological expertise. D.F., D.J., D.E.M., C.P., S.K.V., E.K. and J.S. provided clinical expertise, performed sample acquisition and/or administrative coordination at MGH. J.H., R.R., R.N., O.R.B., Z.G.J., Y.P. and D.I. provided clinical expertise, performed sample acquisition and/or administrative coordination at BIDMC. I.H.S., D.A., L.C., J.G., R.P., M.Si., provided clinical expertise, performed sample acquisition and/or administrative coordination at BWH. I.G., H.H. and B.I. provided clinical expertise, performed sample acquisition and/or administrative coordination at CUIMC/NYP. P.D., D.P., J.J-V. and J.B. helped with sample coordination and sample receipt at the Broad Institute. N.B and S.R. performed bulk RNA-Seq deconvolution analysis. E.N., M.R. and K.S. performed viral qPCR, whole-genome sequencing and phylogenetic analyses. M.S. provided input for sc/snRNA-Seq experiments and protocols. J.J.-V., E.T., O.R.R. and A.-C.V. managed the study and tissue acquisition. T.L.T. contributed computational expertise and advice. T.M.D., C.B.M.P., C.G.K.Z., G.H., R.N., K.J., O.A., B.L., Z.G.J., I.S.V, Y.Y., S.F., A.S., D.T.M., A.K.S., A.-C.V., O.R.-R. and A.R. wrote the manuscript, with input from all authors. D.H., P.C.S., N.H. and P.T.E. supervised research.

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