Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients

Emerging Microbes and Infections

Volumn 9, Issue 1, 2020, Pages 761-770

  Xiong, Yong ^a   Liu, Yuan ^a   Cao, Liu ^b   Wang, Dehe ^a   Guo, Ming ^a   Jiang, Ao ^a   Guo, Dong ^a   Hu, Wenjia ^a   Yang, Jiayi ^a   Tang, Zhidong ^a   Wu, Honglong ^c   Lin, Yongquan ^c   Zhang, Meiyuan ^c   Zhang, Qi ^a   Shi, Mang ^b   Liu, Yingle ^a   Zhou, Yu ^a   Lan, Ke ^a   Chen, Yu ^a  

^a WUHAN UNIVERSITY   (China)

^b SUN YAT SEN UNIVERSITY   (China)

^c BGIShenzhen   (China)

Author keywords

COVID 19; cytokine; inflammation; lymphopenia; transcriptome profiling

Indexed keywords

AREG PROTEIN; CCL3L1 CHEMOKINE; COMPLEMENT COMPONENT C5; CXCL1 CHEMOKINE; CXCL2 CHEMOKINE; CYTOKINE; CYTOKINE RECEPTOR; GAMMA INTERFERON INDUCIBLE PROTEIN 10; IMMUNOGLOBULIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 10; INTERLEUKIN 17; INTERLEUKIN 18; INTERLEUKIN 33; MACROPHAGE INFLAMMATORY PROTEIN 1ALPHA; MACROPHAGE INFLAMMATORY PROTEIN 1BETA; MESSENGER RNA; MONOCYTE CHEMOTACTIC PROTEIN 1; MONOCYTE CHEMOTACTIC PROTEIN 2; NRG1 PROTEIN; PROTEIN P53; TISSUE INHIBITOR OF METALLOPROTEINASE 1; TOLL LIKE RECEPTOR; TRANSCRIPTOME; TUMOR NECROSIS FACTOR RELATED APOPTOSIS INDUCING LIGAND; UNCLASSIFIED DRUG; VIRAL PROTEIN; VIRUS RNA; CHEMOKINE; TP53 PROTEIN, HUMAN;

ADA2 GENE; APOPTOSIS; ARTICLE; AXON GUIDANCE; B LYMPHOCYTE; BRONCHOALVEOLAR LAVAGE FLUID; CARBON METABOLISM; CELLULAR IMMUNITY; COMPLEMENT ACTIVATION; CONTROLLED STUDY; CORONAVIRUS DISEASE 2019; CYTOKINE RELEASE; CYTOKINE STORM; DOWN REGULATION; ENDOPLASMIC RETICULUM; GENE EXPRESSION; GENE FUNCTION; HK1 GENE; HUMAN; HUMAN CELL; HUMORAL IMMUNITY; INFLAMMATION; LUNG PARENCHYMA; LYMPHOCYTOPENIA; LYSOSOME; MGAT1 GENE; PENTOSE PHOSPHATE CYCLE; PERIPHERAL BLOOD MONONUCLEAR CELL; PGD GENE; PHAGOSOME; PLA2G15 GENE; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN TARGETING; QUANTITATIVE ANALYSIS; RNA ISOLATION; RNA SEQUENCING; SEVERE ACUTE RESPIRATORY SYNDROME; SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2; SIGNAL TRANSDUCTION; TRANSCRIPTOME SEQUENCING; UPREGULATION; VIRUS GENE; VIRUS PATHOGENESIS; BETACORONAVIRUS; CORONAVIRUS INFECTION; GENETICS; IMMUNOLOGY; MONONUCLEAR CELL; PANDEMIC; VIRUS PNEUMONIA;

APOPTOSIS; BETACORONAVIRUS; BRONCHOALVEOLAR LAVAGE FLUID; CHEMOKINES; CORONAVIRUS INFECTIONS; CYTOKINES; HUMANS; LEUKOCYTES, MONONUCLEAR; LYMPHOPENIA; PANDEMICS; PNEUMONIA, VIRAL; RNA-SEQ; SIGNAL TRANSDUCTION; TRANSCRIPTOME; TUMOR SUPPRESSOR PROTEIN P53;

EID: 85082568920     PISSN: None     EISSN: 22221751     Source Type: Journal    
DOI: 10.1080/22221751.2020.1747363     Document Type: Article

References (51)

1. Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020 Mar;579(7798):270–273.
2. Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020 Mar;579(7798):265–269.
3. Chen L, Liu W, Zhang Q, et al. RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerg microbes infect. 2020 Dec;9(1):313–319. doi: 10.1080/22221751.2020.1725399
4. Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395(10223):497–506. doi: 10.1016/S0140-6736(20)30183-5
5. Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395(10223):507–513. doi: 10.1016/S0140-6736(20)30211-7
6. Guan WJ, Ni ZY, Hu Y, et al. Clinical characteristics of coronavirus disease 2019 in China. N Engl J med. 2020 Feb 28[Online ahead of print] DOI: 10.1056/NEJMoa2002032.
7. Nelemans T, Kikkert M., Viral innate immune evasion and the pathogenesis of emerging RNA virus infections. Viruses. 2019 Oct 18;11(10):961. doi: 10.3390/v11100961
8. Fehr AR, Channappanavar R, Perlman S., Middle East respiratory syndrome: emergence of a pathogenic human coronavirus. Annu rev med. 2017 Jan 14;68:387–399. doi: 10.1146/annurev-med-051215-031152
9. Newton AH, Cardani A, Braciale TJ., The host immune response in respiratory virus infection: balancing virus clearance and immunopathology. Semin immunopathol. 2016 Jul;38(4):471–482. doi: 10.1007/s00281-016-0558-0
10. Channappanavar R, Zhao J, Perlman S., T cell-mediated immune response to respiratory coronaviruses. Immunol res. 2014 Aug;59(1-3):118–128. doi: 10.1007/s12026-014-8534-z
11. Kindler E, Thiel V., SARS-CoV and IFN: too little, too late. Cell host microbe. 2016 Feb 10;19(2):139–141. doi: 10.1016/j.chom.2016.01.012
12. Channappanavar R, Fehr AR, Vijay R, et al. Dysregulated type I interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in SARS-CoV-infected mice. Cell host microbe. 2016 Feb 10;19(2):181–193. doi: 10.1016/j.chom.2016.01.007
13. Chen Y, Liu Q, Guo D., Emerging coronaviruses: genome structure, replication, and pathogenesis. J med virol. 2020 Apr;92(4):418–423. doi: 10.1002/jmv.25681
14. de Wit E, van Doremalen N, Falzarano D, et al. SARS and MERS: recent insights into emerging coronaviruses. Nat rev microbiol. 2016 Aug;14(8):523–534. doi: 10.1038/nrmicro.2016.81
15. Zhou J, Chu H, Li C, et al. Active replication of Middle East respiratory syndrome coronavirus and aberrant induction of inflammatory cytokines and chemokines in human macrophages: implications for pathogenesis. J infect dis. 2014 May 1;209(9):1331–1342. doi: 10.1093/infdis/jit504
16. Wang D, Hu B, Hu C, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA. 2020 Feb 7[Online ahead of print] DOI: 10.1001/jama.2020.1585.
17. Xu Z, Shi L, Wang Y, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet respir med. 2020 Feb 18[Online ahead of print] DOI: 10.1016/S2213-2600(20)30076-X.
18. Monaco G, Lee B, Xu W, et al. RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types. Cell rep. 2019 Feb 5;26(6):1627–1640. e7. doi: 10.1016/j.celrep.2019.01.041
19. Wilson JA, Prow NA, Schroder WA, et al. RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation. PLoS pathog. 2017 Feb;13(2):e1006155. doi: 10.1371/journal.ppat.1006155
20. Michalovich D, Rodriguez-Perez N, Smolinska S, et al. Obesity and disease severity magnify disturbed microbiome-immune interactions in asthma patients. Nat commun. 2019 Dec 13;10(1):5711. doi: 10.1038/s41467-019-13751-9
21. Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15–21. doi: 10.1093/bioinformatics/bts635
22. Institute B. Picard Toolkit. (2019). Available from: http://broadinstitute.github.io/picard/.
23. Wang L, Wang S, Li W., RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012 Aug 15;28(16):2184–2185. doi: 10.1093/bioinformatics/bts356
24. Lee CM, Barber GP, Casper J, et al. UCSC genome browser enters 20th year. Nucleic acids res. 2020 Jan 8;48(D1):D756–D761.
25. Liao Y, Smyth GK, Shi W., Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923–930. doi: 10.1093/bioinformatics/btt656
26. Love MI, Huber W, Anders S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biol. 2014;15(12):550. doi: 10.1186/s13059-014-0550-8
27. Yu G, Wang LG, Han Y, et al. Clusterprofiler: an R package for comparing biological themes among gene clusters. Omics: J integr biol. 2012 May;16(5):284–287. doi: 10.1089/omi.2011.0118
28. Carbon S, Ireland A, Mungall CJ, et al. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009 Jan 15;25(2):288–289. doi: 10.1093/bioinformatics/btn615
29. Kanehisa M, Sato Y, Furumichi M, et al. New approach for understanding genome variations in KEGG. Nucleic acids res. 2019 Jan 8;47(D1):D590–D595. doi: 10.1093/nar/gky962
30. Wang Y, Song F, Zhu J, et al. GSA: genome sequence archive. Genom proteom bioinform. 2017 Feb;15(1):14–18. doi: 10.1016/j.gpb.2017.01.001
31. National Genomics Data Center M, Partners. Database resources of the National Genomics Data Center in 2020. Nucleic acids res. 2020 Jan 8;48(D1):D24–D33.
32. Jiang Y, Xu J, Zhou C, et al. Characterization of cytokine/chemokine profiles of severe acute respiratory syndrome. Am J respir crit care med. 2005 Apr 15;171(8):850–857. doi: 10.1164/rccm.200407-857OC
33. Thaker SK, Ch'ng J, Christofk HR., Viral hijacking of cellular metabolism. BMC biol. 2019 Jul 18;17(1):59. doi: 10.1186/s12915-019-0678-9
34. Huang KJ, Su IJ, Theron M, et al. An interferon-gamma-related cytokine storm in SARS patients. J med virol. 2005 Feb;75(2):185–194. doi: 10.1002/jmv.20255
35. Teijaro JR, Walsh KB, Rice S, et al. Mapping the innate signaling cascade essential for cytokine storm during influenza virus infection. Proc. natl. acad. sci. U.S.A. 2014 Mar 11;111(10):3799–3804. doi: 10.1073/pnas.1400593111
36. Okabayashi T, Kariwa H, Yokota S, et al. Cytokine regulation in SARS coronavirus infection compared to other respiratory virus infections. J med virol. 2006 Apr;78(4):417–424. doi: 10.1002/jmv.20556
37. Griffith JW, Sokol CL, Luster AD., Chemokines and chemokine receptors: positioning cells for host defense and immunity. Annu rev immunol. 2014;32:659–702. doi: 10.1146/annurev-immunol-032713-120145
38. Sheahan T, Morrison TE, Funkhouser W, et al. Myd88 is required for protection from lethal infection with a mouse-adapted SARS-CoV. PLoS pathog. 2008 Dec;4(12):e1000240. doi: 10.1371/journal.ppat.1000240
39. Ng PC, Lam CW, Li AM, et al. Inflammatory cytokine profile in children with severe acute respiratory syndrome. Pediatrics. 2004 Jan;113(1 Pt 1):e7–14. doi: 10.1542/peds.113.1.e7
40. Zhang Y, Li J, Zhan Y, et al. Analysis of serum cytokines in patients with severe acute respiratory syndrome. Infect immun. 2004 Aug;72(8):4410–4415. doi: 10.1128/IAI.72.8.4410-4415.2004
41. Bordon J, Aliberti S, Fernandez-Botran R, et al. Understanding the roles of cytokines and neutrophil activity and neutrophil apoptosis in the protective versus deleterious inflammatory response in pneumonia. Int J infect dis. 2013 Feb;17(2):e76–e83. doi: 10.1016/j.ijid.2012.06.006
42. Saxena V, Lienesch DW, Zhou M, et al. Dual roles of immunoregulatory cytokine TGF-beta in the pathogenesis of autoimmunity-mediated organ damage. J immunol. 2008 Feb 1;180(3):1903–1912. doi: 10.4049/jimmunol.180.3.1903
43. Yu X, Buttgereit A, Lelios I, et al. The cytokine TGF-beta promotes the development and homeostasis of alveolar macrophages. Immunity. 2017 Nov 21;47(5):903–912 e4. doi: 10.1016/j.immuni.2017.10.007
44. Panesar NS., What caused lymphopenia in SARS and how reliable is the lymphokine status in glucocorticoid-treated patients? Med hypotheses. 2008 Aug;71(2):298–301. doi: 10.1016/j.mehy.2008.03.019
45. O'Donnell R, Tasker RC, Roe MF., SARS: understanding the coronavirus: apoptosis may explain lymphopenia of SARS. Br med J. 2003 Sep 13;327(7415):620. doi: 10.1136/bmj.327.7415.620-b
46. Panesar NS., Lymphopenia in SARS. Lancet. 2003 Jun 7;361(9373):1985. doi: 10.1016/S0140-6736(03)13557-X
47. Cui W, Fan Y, Wu W, et al. Expression of lymphocytes and lymphocyte subsets in patients with severe acute respiratory syndrome. Clin infect dis. 2003 Sep 15;37(6):857–859. doi: 10.1086/378587
48. Gu J, Gong E, Zhang B, et al. Multiple organ infection and the pathogenesis of SARS. J exp med. 2005 Aug 1;202(3):415–424. doi: 10.1084/jem.20050828
49. Stockman LJ, Bellamy R, Garner P., SARS: systematic review of treatment effects. PLoS med. 2006 Sep;3(9):e343. doi: 10.1371/journal.pmed.0030343
50. Panesar NS., Glucocorticoid treatment of patients with SARS: implications for mechanisms of immunopathology. Nat rev immunol. 2006 2006/04/01;6(4):334–334. doi: 10.1038/nri1835-c1
51. Russell CD, Millar JE, Baillie JK., Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury. Lancet. 2020 Feb 15;395(10223):473–475. doi: 10.1016/S0140-6736(20)30317-2