Evidence map›Paper›PMID 33655247›Full record

ArticlebioRxiv : the preprint server for biology2021

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

Toni M Delorey, Carly G K Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Asa Segerstolpe, Domenic Abbondanza, Stephen J Fleming, Ayshwarya Subramanian, Daniel T Montoro and 92 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed, 43 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

102 authors at 11 institutions in 3 countries.

Toni M DeloreyKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Carly G K ZieglerBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Graham HeimbergKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Rachelly NormandBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Yiming YangKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Asa SegerstolpeKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Domenic AbbondanzaKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Stephen J FlemingData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142.
Ayshwarya SubramanianKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Daniel T MontoroBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Karthik A JagadeeshKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Kushal K DeyDepartment of Epidemiology, Harvard School of Public Health.
Pritha SenBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Michal SlyperKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Yered H Pita-JuárezBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Devan PhillipsKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Zohar Bloom-AckermanInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Nick BarkasData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142.
Andrea GannaInstitute for Molecular Medicine Finland, Helsinki, Finland.
James GomezInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Erica NormandinBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Pourya NaderiHarvard Medical School, Boston, MA 02115, USA.
Yury V PopovHarvard Medical School, Boston, MA 02115, USA.
Siddharth S RajuBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Sebastian NiezenHarvard Medical School, Boston, MA 02115, USA.
Linus T-Y TsaiBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Katherine J SiddleBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Malika SudKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Victoria M TranInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Shamsudheen K VellarikkalBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Liat Amir-ZilbersteinKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Deepak S AtriBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Joseph BeechemNanoString Technologies Inc., Seattle, WA 98109, USA.
Olga R BrookDepartment of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
Jonathan ChenBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Prajan DivakarNanoString Technologies Inc., Seattle, WA 98109, USA.
Phylicia DorceusKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Jesse M EngreitzBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Adam EsseneDepartment of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.
Donna M FitzgeraldMassachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Robin FropfNanoString Technologies Inc., Seattle, WA 98109, USA.
Steven GazalCenter for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
Joshua GouldData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142.
John GrzybDepartment of Pathology, Brigham and Women's Hospital, Boston, MA 02115.
Tyler HarveyKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Jonathan HechtHarvard Medical School, Boston, MA 02115, USA.
Tyler HetherNanoString Technologies Inc., Seattle, WA 98109, USA.
Judit Jane-ValbuenaKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Michael Leney-GreeneBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Hui MaKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Cristin McCabeKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Daniel E McLoughlinMassachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Eric M MillerNanoString Technologies Inc., Seattle, WA 98109, USA.
Christoph MuusBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Mari NiemiInstitute for Molecular Medicine Finland, Helsinki, Finland.
Robert PaderaDepartment of Pathology, Brigham and Women's Hospital, Boston, MA 02115.
Liuliu PanNanoString Technologies Inc., Seattle, WA 98109, USA.
Deepti PantDepartment of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.
Carmel Pe'erKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Jenna Pfiffner-BorgesBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Christopher J PintoDepartment of Medicine, Harvard Medical School, Boston, MA 02115, USA.
Jacob PlaistedDepartment of Pathology, Brigham and Women's Hospital, Boston, MA 02115.
Jason ReevesNanoString Technologies Inc., Seattle, WA 98109, USA.
Marty RossNanoString Technologies Inc., Seattle, WA 98109, USA.
Melissa RudyBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Erroll H RueckertNanoString Technologies Inc., Seattle, WA 98109, USA.
Michelle SicilianoDepartment of Pathology, Brigham and Women's Hospital, Boston, MA 02115.
Alexander SturmInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Ellen TodresKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Avinash WaghrayHarvard Stem Cell Institute, Cambridge, MA, USA.
Sarah WarrenNanoString Technologies Inc., Seattle, WA 98109, USA.
Shuting ZhangInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Daniel R ZollingerNanoString Technologies Inc., Seattle, WA 98109, USA.
Lisa CosimiInfectious Diseases Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
Rajat M GuptaBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Nir HacohenBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Winston HideHarvard Medical School, Boston, MA 02115, USA.
Alkes L PriceDepartment of Epidemiology, Harvard School of Public Health.
Jayaraj RajagopalMassachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Purushothama Rao TataDuke University School of Medicine, Durham, NC.
Stefan RiedelHarvard Medical School, Boston, MA 02115, USA.
Gyongyi SzaboBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Timothy L TickleKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Deborah HungInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Pardis C SabetiBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Richard NovakWyss Institute for Biologically Inspired Engineering, Harvard University.
Robert RogersDepartment of Medicine, Beth Israel Deaconess Medical Center, MA 02115, USA.
Donald E IngberJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138.
Z Gordon JiangHarvard Medical School, Boston, MA 02115, USA.
Dejan JuricDepartment of Medicine, Harvard Medical School, Boston, MA 02115, USA.
Mehrtash BabadiData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142.
Samouil L FarhiKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
James R StoneDepartment of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
Ioannis S VlachosBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Isaac H SolomonDepartment of Pathology, Brigham and Women's Hospital, Boston, MA 02115.
Orr AshenbergKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Caroline B M PorterKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Bo LiKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Alex K ShalekBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Alexandra-Chloé VillaniBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Orit Rozenblatt-RosenKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Aviv RegevKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, USA.
Broad Institute · USBeth Israel Deaconess Medical Center · USNanostring Technologies (United States) · USBrigham and Women's Hospital · USHarvard University · USMassachusetts General Hospital · USBoston Children's Hospital · USDuke University · USInspire · CHInstitute for Molecular Medicine Finland · FIUniversity of Southern California · US

Funding

INSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2M
MicroRNAs in Alcoholic Liver Disease Administrative SupplementR01AA020744 · NIAAA · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI SZABO, GYONGYI · 2011 to 2023
$5.3M
TLR4 Signaling in alcoholic liver diseaseR01AA017729 · NIAAA · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI SZABO, GYONGYI · 2009 to 2021
$4.3M
Deciphering the Achilles Heel of Cancer ImmunotherapyDP2CA247831 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI VILLANI, ALEXANDRA-CHLOE · 2019 to 2019
$2.5M
Biomarkers of Disease in Alcoholic Hepatitis Administrative SupplementU01AA026933 · NIAAA · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI SZABO, GYONGYI · 2018 to 2023
$1.4M
NCI NIH HHS DP2 CA247831NHGRI NIH HHS T32 HG000044NIAAA NIH HHS R01 AA017729NIAAA NIH HHS R01 AA020744NIAAA NIH HHS U01 AA026933
6 · The paper itself

Abstract

The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients' demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63

Identifiers

PMID33655247
PMCPMC7924267
OpenAlexW3132202883

What OpenQuestion holds

Textmetadata
LicenceCC BY-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.