COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.
Adult
Aged
Aged, 80 and over
Atlases as Topic
Autopsy
Biological Specimen Banks
COVID-19
/ genetics
Endothelial Cells
Epithelial Cells
/ pathology
Female
Fibroblasts
Genome-Wide Association Study
Heart
/ virology
Humans
Inflammation
/ pathology
Kidney
/ pathology
Liver
/ pathology
Lung
/ pathology
Male
Middle Aged
Myocardium
/ pathology
Organ Specificity
Phagocytes
Pulmonary Alveoli
/ pathology
RNA, Viral
/ analysis
Regeneration
SARS-CoV-2
/ immunology
Single-Cell Analysis
Viral Load
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
received:
16
11
2020
accepted:
19
04
2021
pubmed:
30
4
2021
medline:
9
7
2021
entrez:
29
4
2021
Statut:
ppublish
Résumé
COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure
Identifiants
pubmed: 33915569
doi: 10.1038/s41586-021-03570-8
pii: 10.1038/s41586-021-03570-8
pmc: PMC8919505
mid: NIHMS1771808
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
107-113Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIMH NIH HHS
ID : R37 MH107649
Pays : United States
Organisme : NIAAA NIH HHS
ID : U01 AA026933
Pays : United States
Organisme : NCI NIH HHS
ID : K08 CA222663
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007753
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK046200
Pays : United States
Organisme : NIAAA NIH HHS
ID : R01 AA017729
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA013696
Pays : United States
Organisme : NHLBI NIH HHS
ID : UH3 HL141797
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH107649
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH101244
Pays : United States
Organisme : NIAAA NIH HHS
ID : R01 AA020744
Pays : United States
Organisme : NCI NIH HHS
ID : R37 CA258829
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA225088
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009379
Pays : United States
Organisme : NCI NIH HHS
ID : DP2 CA247831
Pays : United States
Commentaires et corrections
Type : CommentIn
Références
Guan, W.-J. et al. Clinical characteristics of coronavirus disease 2019 in China. N. Engl. J. Med. 382, 1708–1720 (2020).
pubmed: 32109013
doi: 10.1056/NEJMoa2002032
Puelles, V. G. et al. Multiorgan and renal tropism of SARS-CoV-2. N. Engl. J. Med. 383, 590–592 (2020).
pubmed: 32402155
doi: 10.1056/NEJMc2011400
Huang, C. et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 395, 497–506 (2020).
pubmed: 31986264
pmcid: 7159299
doi: 10.1016/S0140-6736(20)30183-5
Xu, Z. et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir. Med. 8, 420–422 (2020).
pubmed: 32085846
pmcid: 7164771
doi: 10.1016/S2213-2600(20)30076-X
Varga, Z. et al. Endothelial cell infection and endotheliitis in COVID-19. Lancet 395, 1417–1418 (2020).
pubmed: 32325026
pmcid: 7172722
doi: 10.1016/S0140-6736(20)30937-5
Chen, G. et al. Clinical and immunological features of severe and moderate coronavirus disease 2019. J. Clin. Invest. 130, 2620–2629 (2020).
pubmed: 32217835
pmcid: 7190990
doi: 10.1172/JCI137244
Qin, C. et al. Dysregulation of immune response in patients with coronavirus 2019 (COVID-19) in Wuhan, China. Clin. Infect. Dis. 71, 762–768 (2020).
pubmed: 32161940
doi: 10.1093/cid/ciaa248
Hadjadj, J. et al. Impaired type I interferon activity and exacerbated inflammatory responses in severe COVID-19 patients. Science 369, 718–724 (2020).
Bian, X.-W. et al. Autopsy of COVID-19 patients in China. Natl. Sci. Rev. 7, 1414–1418 (2020).
pmcid: 7313767
pubmed: 34192086
doi: 10.1093/nsr/nwaa123
Menter, T. et al. Postmortem examination of COVID-19 patients reveals diffuse alveolar damage with severe capillary congestion and variegated findings in lungs and other organs suggesting vascular dysfunction. Histopathology 77, 198–209 (2020).
pubmed: 32364264
pmcid: 7496150
doi: 10.1111/his.14134
Wichmann, D. et al. Autopsy findings and venous thromboembolism in patients with COVID-19: a prospective cohort study. Ann. Intern. Med. 173, 268–277 (2020).
pubmed: 32374815
doi: 10.7326/M20-2003
Bösmüller, H. et al. The evolution of pulmonary pathology in fatal COVID-19 disease: an autopsy study with clinical correlation. Virchows Arch. 477, 349–357 (2020).
pubmed: 32607684
pmcid: 7324489
doi: 10.1007/s00428-020-02881-x
Slyper, M. et al. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat. Med. 26, 792 –802 (2020).
pubmed: 32405060
pmcid: 7220853
doi: 10.1038/s41591-020-0844-1
Fleming, S. J., Marioni, J. C. & Babadi, M. CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. Preprint at https://doi.org/10.1101/791699 (2019).
Li, B. et al. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Nat. Methods 17, 793–798 (2020).
pubmed: 32719530
pmcid: 7437817
doi: 10.1038/s41592-020-0905-x
Shaffer, A. L. et al. Blimp-1 orchestrates plasma cell differentiation by extinguishing the mature B cell gene expression program. Immunity 17, 51–62 (2002).
pubmed: 12150891
doi: 10.1016/S1074-7613(02)00335-7
Martins, G. & Calame, K. Regulation and functions of Blimp-1 in T and B lymphocytes. Annu. Rev. Immunol. 26, 133–169 (2008).
pubmed: 18370921
doi: 10.1146/annurev.immunol.26.021607.090241
Schupp, J. C. et al. Integrated single cell atlas of endothelial cells of the human lung. Preprint at https://doi.org/10.1101/2020.10.21.347914 (2020).
Travaglini, K. J. et al. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature 587, 619–625 (2020).
pubmed: 33208946
pmcid: 7704697
doi: 10.1038/s41586-020-2922-4
Strunz, M. et al. Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis. Nat. Commun. 11, 3559 (2020).
pubmed: 32678092
pmcid: 7366678
doi: 10.1038/s41467-020-17358-3
Kobayashi, Y. et al. Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis. Nat. Cell Biol. 22, 934–946 (2020).
pubmed: 32661339
pmcid: 7461628
doi: 10.1038/s41556-020-0542-8
Choi, J. et al. Inflammatory signals induce AT2 cell-derived damage-associated transient progenitors that mediate alveolar regeneration. Cell Stem Cell 27, 366–382.e7 (2020).
pubmed: 32750316
pmcid: 7487779
doi: 10.1016/j.stem.2020.06.020
Ziegler, C. G. K. et al. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues. Cell 181, 1016–1035.e19 (2020).
pubmed: 32413319
pmcid: 7252096
doi: 10.1016/j.cell.2020.04.035
Sungnak, W. et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat. Med. 26, 681–687 (2020).
pubmed: 32327758
pmcid: 8637938
doi: 10.1038/s41591-020-0868-6
Muus, C. et al. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat. Med. 27, 546–559 (2021).
pubmed: 33654293
doi: 10.1038/s41591-020-01227-z
Xu, J. et al. SARS-CoV-2 induces transcriptional signatures in human lung epithelial cells that promote lung fibrosis. Respir. Res. 21, 182 (2020).
pubmed: 32664949
pmcid: 7359430
doi: 10.1186/s12931-020-01445-6
Grillo, F., Barisione, E., Ball, L., Mastracci, L. & Fiocca, R. Lung fibrosis: an undervalued finding in COVID-19 pathological series. Lancet Infect. Dis. 21, e72 (2021).
pubmed: 32735785
doi: 10.1016/S1473-3099(20)30582-X
Vaughan, A. E. et al. Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury. Nature 517, 621–625 (2015).
pubmed: 25533958
doi: 10.1038/nature14112
Fernanda de Mello Costa, M., Weiner, A. I. & Vaughan, A. E. Basal-like progenitor cells: a review of dysplastic alveolar regeneration and remodeling in lung repair. Stem Cell Reports 15, 1015–1025 (2020).
pubmed: 33065046
pmcid: 7560757
doi: 10.1016/j.stemcr.2020.09.006
Wölfel, R. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469 (2020).
pubmed: 32235945
doi: 10.1038/s41586-020-2196-x
Walsh, K. A. et al. SARS-CoV-2 detection, viral load and infectivity over the course of an infection. J. Infect. 81, 357–371 (2020).
pubmed: 32615199
pmcid: 7323671
doi: 10.1016/j.jinf.2020.06.067
Blanco-Melo, D. et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181, 1036–1045.e9 (2020).
pubmed: 32416070
pmcid: 7227586
doi: 10.1016/j.cell.2020.04.026
Johnson, N. F. Release of lamellar bodies from alveolar type 2 cells. Thorax 35, 192–197 (1980).
pubmed: 6247775
pmcid: 471252
doi: 10.1136/thx.35.3.192
Grant, R. A. et al. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Nature 590, 635–641 (2021).
pubmed: 33429418
pmcid: 7987233
doi: 10.1038/s41586-020-03148-w
Butler, D. et al. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat. Commun. 12, 1660 (2021).
pubmed: 33712587
pmcid: 7954844
doi: 10.1038/s41467-021-21361-7
Park, J. et al. Systemic tissue and cellular disruption from SARS-CoV-2 infection revealed in COVID-19 autopsies and spatial omics tissue maps. Preprint at https://doi.org/10.1101/2021.03.08.434433 (2021).
Rendeiro, A. F. et al. The spatio-temporal landscape of lung pathology in SARS-CoV-2 infection. Preprint at https://doi.org/10.1101/2020.10.26.20219584 (2020).
Karki, R. et al. Synergism of TNF-α and IFN-γ triggers inflammatory cell death, tissue damage, and mortality in SARS-CoV-2 infection and cytokine shock syndromes. Cell 184, 149–168.e17 (2021).
pubmed: 33278357
doi: 10.1016/j.cell.2020.11.025
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
pubmed: 16199517
pmcid: 1239896
doi: 10.1073/pnas.0506580102
Mootha, V. K. et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273 (2003).
pubmed: 12808457
doi: 10.1038/ng1180
van de Sandt, C. E. et al. Human CD8
pubmed: 28613916
doi: 10.1165/rcmb.2016-0377OC
Short, K. R. et al. Influenza virus damages the alveolar barrier by disrupting epithelial cell tight junctions. Eur. Respir. J. 47, 954–966 (2016).
pubmed: 26743480
doi: 10.1183/13993003.01282-2015
Lemieux, J. E. et al. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science 371, eabe3261 (2021).
pubmed: 33303686
doi: 10.1126/science.abe3261
Yu, H. H. & Zallen, J. A. Abl and Canoe/Afadin mediate mechanotransduction at tricellular junctions. Science 370, eaba5528 (2020).
pubmed: 33243859
pmcid: 8559527
doi: 10.1126/science.aba5528
COVID-19 Host Genetics Initiative. The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic. Eur. J. Hum. Genet. 28, 715–718 (2020).
doi: 10.1038/s41431-020-0636-6
Severe Covid-19 GWAS Group. Genomewide association study of severe Covid-19 with respiratory failure. N. Engl. J. Med. 383, 1522–1534 (2020).
doi: 10.1056/NEJMoa2020283
Jagadeesh, K. A. et al. Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics. Preprint at https://doi.org/10.1101/2021.03.19.436212 (2021).
Melms, J. C. et al. A molecular single-cell lung atlas of lethal COVID-19. Nature https://doi.org/10.1038/s41586-021-03569-1 (2021).
Speranza, E. et al. SARS-CoV-2 infection dynamics in lungs of African green monkeys. Preprint at https://doi.org/10.1101/2020.08.20.258087 (2020).
Desai, N. et al. Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection. Preprint at https://doi.org/10.1101/2020.07.30.20165241 (2020).
Liu, T.-M. et al. Hypermorphic mutation of phospholipase C, γ2 acquired in ibrutinib-resistant CLL confers BTK independency upon B-cell receptor activation. Blood 126, 61–68 (2015).
pubmed: 25972157
pmcid: 4492196
doi: 10.1182/blood-2015-02-626846
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
pubmed: 29409532
pmcid: 5802054
doi: 10.1186/s13059-017-1382-0
Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
pubmed: 31740819
pmcid: 6884693
doi: 10.1038/s41592-019-0619-0
Schiller, H. B. et al. The Human Lung Cell Atlas: a high-resolution reference map of the human lung in health and disease. Am. J. Respir. Cell Mol. Biol. 61, 31–41 (2019).
pubmed: 30995076
pmcid: 6604220
doi: 10.1165/rcmb.2018-0416TR
Brill, B., Amir, A. & Heller, R. Testing for differential abundance in compositional counts data, with application to microbiome studies. Preprint at https://arxiv.org/abs/1904.08937 (2019).
Ravindra, N. G. et al. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium. Preprint at https://doi.org/10.1101/2020.05.06.081695 (2020).