RESEARCH ARTICLE

Host metabolism dysregulation and cell tropism identification in human airway and alveolar organoids upon SARS-CoV-2 infection

  • Rongjuan Pei 2 ,
  • Jianqi Feng 1 ,
  • Yecheng Zhang 2 ,
  • Hao Sun 2 ,
  • Lian Li 1 ,
  • Xuejie Yang 5,7 ,
  • Jiangping He 5,6 ,
  • Shuqi Xiao 2 ,
  • Jin Xiong 2 ,
  • Ying Lin 1 ,
  • Kun Wen 8 ,
  • Hongwei Zhou 8 ,
  • Jiekai Chen 5,6,7 ,
  • Zhili Rong , 1,3,4 ,
  • Xinwen Chen , 2,5
Expand
  • 1. Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
  • 2. Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
  • 3. Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
  • 4. Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
  • 5. Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
  • 6. The Centre of Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou 510530, China
  • 7. Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
  • 8. Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China

Received date: 07 Oct 2020

Accepted date: 13 Nov 2020

Published date: 15 Sep 2021

Copyright

2020 The Author(s) 2020

Abstract

The coronavirus disease 2019 (COVID-19) pandemic is caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is spread primary via respiratory droplets and infects the lungs. Currently widely used cell lines and animals are unable to accurately mimic human physiological conditions because of the abnormal status of cell lines (transformed or cancer cells) and species differences between animals and humans. Organoids are stem cell-derived selforganized three-dimensional culture in vitro and model the physiological conditions of natural organs. Here we showed that SARS-CoV-2 infected and extensively replicated in human embryonic stem cells (hESCs)-derived lung organoids, including airway and alveolar organoids which covered the complete infection and spread route for SARS-CoV-2 within lungs. The infected cells were ciliated, club, and alveolar type 2 (AT2) cells, which were sequentially located from the proximal to the distal airway and terminal alveoli, respectively. Additionally, RNA-seq revealed early cell response to virus infection including an unexpected downregulation of the metabolic processes, especially lipid metabolism, in addition to the well-known upregulation of immune response. Further, Remdesivir and a human neutralizing antibody potently inhibited SARS-CoV-2 replication in lung organoids. Therefore, human lung organoids can serve as a pathophysiological model to investigate the underlying mechanism of SARS-CoV-2 infection and to discover and test therapeutic drugs for COVID-19.

Cite this article

Rongjuan Pei , Jianqi Feng , Yecheng Zhang , Hao Sun , Lian Li , Xuejie Yang , Jiangping He , Shuqi Xiao , Jin Xiong , Ying Lin , Kun Wen , Hongwei Zhou , Jiekai Chen , Zhili Rong , Xinwen Chen . Host metabolism dysregulation and cell tropism identification in human airway and alveolar organoids upon SARS-CoV-2 infection[J]. Protein & Cell, 2021 , 12(9) : 717 -733 . DOI: 10.1007/s13238-020-00811-w

1
Anderson CM, Stahl A (2013) SLC27 fatty acid transport proteins. Mol Aspects Med 34:516–528

DOI

2
Banu N, Panikar SS, Leal LR, Leal AR (2020) Protective role of ACE2 and its downregulation in SARS-CoV-2 infection leading to macrophage activation syndrome: therapeutic implications. Life Sci 256:117905

DOI

3
Bao L, Deng W, Huang B, Gao H, Liu J, Ren L, Wei Q, Yu P, Xu Y, Qi F (2020) The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature 583:830–833

DOI

4
Beigel JH, Tomashek KM, Dodd LE, Mehta AK, Zingman BS, Kalil AC, Hohmann E, Chu HY, Luetkemeyer A, Kline S (2020) Remdesivir for the treatment of Covid-19—preliminary report. N Engl J Med.

DOI

5
Bustamante-Marin XM, Ostrowski LE (2017) Cilia and mucociliary clearance. Cold Spring Harb Perspect Biol 9:a028241

DOI

6
Cairns RA, Harris IS, Mak TW (2011) Regulation of cancer cell metabolism. Nat Rev Cancer 11:85–95

DOI

7
Calkin AC, Tontonoz P (2012) Transcriptional integration of metabolism by the nuclear sterol-activated receptors LXR and FXR. Nat Rev Mol Cell Biol 13:213–224

DOI

8
Cantuti-Castelvetri L, Ojha R, Pedro LD, Djannatian M, Franz J, Kuivanen S, van der Meer F, Kallio K, Kaya T, Anastasina M (2020) Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science 370:6518

DOI

9
Chandrashekar A, Liu J, Martinot AJ, McMahan K, Mercado NB, Peter L, Tostanoski LH, Yu J, Maliga Z, Nekorchuk M (2020) SARS-CoV-2 infection protects against rechallenge in rhesus macaques. Science 369:812–817

DOI

10
Chen Y, Feng J, Zhao S, Han L, Yang H, Lin Y, Rong Z (2018) Longterm engraftment promotes differentiation of alveolar epithelial cells from human embryonic stem cell derived lung organoids. Stem Cells Dev 27:1339–1349

DOI

11
Clevers H (2016) Modeling development and disease with organoids. Cell 165:1586–1597

DOI

12
Daly JL, Simonetti B, Plagaro CA, Williamson MK, Shoemark DK, Simon-Gracia L, Klein K, Bauer M, Hollandi R, Greber UF (2020) Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science

DOI

13
Damiani C, Rovida L, Maspero D, Sala I, Rosato L, Di Filippo M, Pescini D, Graudenzi A, Antoniotti M, Mauri G (2020) MaREA4-Galaxy: metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy. Comput Struct Biotechnol J 18:993–999

DOI

14
Dawson PA, Hubbert ML, Rao A (2010) Getting the mOST from OST: role of organic solute transporter, OSTalpha-OSTbeta, in bile acid and steroid metabolism. Biochim Biophys Acta 1801:994–1004

DOI

15
Diamond DL, Syder AJ, Jacobs JM, Sorensen CM, Walters KA, Proll SC, McDermott JE, Gritsenko MA, Zhang Q, Zhao R (2010) Temporal proteome and lipidome profiles reveal hepatitis C virusassociated reprogramming of hepatocellular metabolism and bioenergetics. PLoS Pathog 6:e1000719

DOI

16
Dutta D, Clevers H (2017) Organoid culture systems to study hostpathogen interactions. Curr Opin Immunol 48:15–22

DOI

17
Eastman RT, Roth JS, Brimacombe KR, Simeonov A, Shen M, Patnaik S, Hall MD (2020) Remdesivir: a review of its discovery and development leading to emergency use authorization for treatment of COVID-19. ACS Cent Sci 6:672–683

DOI

18
Fehr AR, Perlman S (2015) Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol 1282:1–23

DOI

19
Feingold KR, Grunfeld C (2000) Introduction to lipids and lipoproteins. In: Feingold KR, Anawalt B, Boyce A, Chrousos G, de Herder WW, Dungan K, Grossman A, Hershman JM, Hofland HJ, Kaltsas G et al (eds) Endotext. MDText.com, South Dartmouth

20
Furuhashi M, Hotamisligil GS (2008) Fatty acid-binding proteins: role in metabolic diseases and potential as drug targets. Nat Rev Drug Discov 7:489–503

DOI

21
Glowacka I, Bertram S, Herzog P, Pfefferle S, Steffen I, Muench MO, Simmons G, Hofmann H, Kuri T, Weber F (2010) Differential downregulation of ACE2 by the spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus NL63. J Virol 84:1198–1205

DOI

22
Harcourt J, Tamin A, Lu X, Kamili S, Sakthivel SK, Murray J, Queen K, Tao Y, Paden CR, Zhang J (2020) Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient. bioRxiv

DOI

23
Heaton NS, Randall G (2011) Multifaceted roles for lipids in viral infection. Trends Microbiol 19:368–375

DOI

24
Heurich A, Hofmann-Winkler H, Gierer S, Liepold T, Jahn O, Pohlmann S (2014) TMPRSS2 and ADAM17 cleave ACE2 differentially and only proteolysis by TMPRSS2 augments entry driven by the severe acute respiratory syndrome coronavirus spike protein. J Virol 88:1293–1307

DOI

25
Hilgenfeld R, Peiris M (2013) From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses. Antiviral Res 100:286–295

DOI

26
Hoffmann M, Kleine-Weber H, Schroeder S, Kruger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu NH, Nitsche A (2020) SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181(271–280):e278

DOI

27
Hollenbaugh JA, Munger J, Kim B (2011) Metabolite profiles of human immunodeficiency virus infected CD4+ T cells and macrophages using LC-MS/MS analysis. Virology 415:153–159

DOI

28
Hotamisligil GS, Bernlohr DA (2015) Metabolic functions of FABPs–mechanisms and therapeutic implications. Nat Rev Endocrinol 11:592–605

DOI

29
Hou YXJ, Okuda K, Edwards CE, Martinez DR, Asakura T, DinnonKH T, Kato RE, Lee BL, Yount TM, Mascenik (2020) SARSCoV-2 reverse genetics reveals a variable infection gradient in the respiratory tract. Cell 182:429

DOI

30
Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X (2020) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet 395:497–506

DOI

31
Hutchins AP, Jauch R, Dyla M, Miranda-Saavedra D (2014) glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data. Cell Regen (Lond) 3:1

DOI

32
Jiang RD, Liu MQ, Chen Y, Shan C, Zhou YW, Shen XR, Li Q, Zhang L, Zhu Y, Si HR(2020) Pathogenesis of SARS-CoV-2 in transgenic mice expressing human angiotensin-converting enzyme 2. Cell 182(50–58):e58

DOI

33
Jia MR, Wei T, Xu WF (2010) The analgesic activity of bestatin as a potent APN inhibitor. Front Neurosci 4:50

DOI

34
Kaye M (2006) SARS-associated coronavirus replication in cell lines. Emerg Infect Dis 12:128–133

DOI

35
Ketter E, Randall G (2019) Virus impact on lipids and membranes. Annu Rev Virol 6:319–340

DOI

36
Kim JM, Chung YS, Jo HJ, Lee NJ, Kim MS, Woo SH, Park S, Kim JW, Kim HM, Han MG (2020) Identification of Coronavirus Isolated from a Patient in Korea with COVID-19. Osong Public Health Res Perspect 11:3–7

DOI

37
Kroemer G, Pouyssegur J (2008) Tumor cell metabolism: cancer’s Achilles’ heel. Cancer Cell 13:472–482

DOI

38
Kuba K, Imai Y, Rao S, Gao H, Guo F, Guan B, Huan Y, Yang P, Zhang Y, Deng W (2005) A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nat Med 11:875–879

DOI

39
Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J, Breugem TI, Ravelli RBG, Paul van Schayck J, Mykytyn AZ, Duimel HQ (2020) SARS-CoV-2 productively infects human gut enterocytes. Science 369:50–54

DOI

40
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

DOI

41
Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323–323

DOI

42
Li JY, You Z, Wang Q, Zhou ZJ, Qiu Y, Luo R, Ge XY (2020) The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future. Microbes Infect 22:80–85

DOI

43
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550

DOI

44
Martic-Kehl MI, Schibli R, Schubiger PA (2012) Can animal data predict human outcome? Problems and pitfalls of translational animal research. Eur J Nucl Med Mol Imaging 39:1492–1496

DOI

45
McCauley KB, Hawkins F, Serra M, Thomas DC, Jacob A, Kotton DN (2017) Efficient derivation of functional human airway epithelium from pluripotent stem cells via temporal regulation of Wnt signaling. Cell Stem Cell 20(844–857):e846

DOI

46
Monteil V, Kwon H, Prado P, Hagelkruys A, Wimmer RA, Stahl M, Leopoldi A, Garreta E, Hurtado Del Pozo C, Prosper F (2020) Inhibition of SARS-CoV-2 infections in engineered human tissues using clinical-grade soluble human ACE2. Cell 181(905–913):e907

DOI

47
Ou X, Liu Y, Lei X, Li P, Mi D, Ren L, Guo L, Guo R, Chen T, Hu J (2020) Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun 11:1620

DOI

48
Pan C, Kumar C, Bohl S, Klingmueller U, Mann M (2009) Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions. Mol Cell Proteomics 8:443–450

DOI

49
Ramani S, Crawford SE, Blutt SE, Estes MK (2018) Human organoid cultures: transformative new tools for human virus studies. Curr Opin Virol 29:79–86

DOI

50
Risso D, Schwartz K, Sherlock G, Dudoit S (2011) GC-content normalization for RNA-Seq data.BMC Bioinformatics 12:480–480

DOI

51
Rockx B, Kuiken T, Herfst S, Bestebroer T, Lamers MM, Oude Munnink BB, de Meulder D, van Amerongen G, van den Brand J, Okba NMA (2020) Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model. Science 368:1012–1015

DOI

52
Rock JR, Randell SH, Hogan BL (2010) Airway basal stem cells: a perspective on their roles in epithelial homeostasis and remodeling. Dis Model Mech 3:545–556

DOI

53
Rossi G, Manfrin A, Lutolf MP (2018) Progress and potential in organoid research. Nat Rev Genet 19:671–687

DOI

54
Ruprecht JJ, Kunji ERS (2020) The SLC25 mitochondrial carrier family: structure and mechanism. Trends Biochem Sci 45:244–258

DOI

55
Sanchez EL, Lagunoff M (2015) Viral activation of cellular metabolism. Virology 479–480:609–618

DOI

56
Schmitz G, Muller G (1991) Structure and function of lamellar bodies, lipid-protein complexes involved in storage and secretion of cellular lipids. J Lipid Res 32:1539–1570

57
Shi JZ, Wen ZY, Zhong GX, Yang HL, Wang C, Huang BY, Liu RQ, He XJ, Shuai L, Sun ZR (2020a) Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2. Science 368:1016

DOI

58
Shi R, Shan C, Duan X, Chen Z, Liu P, Song J, Song T, Bi X, Han C, Wu L (2020b) A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2. Nature 584:120–124

DOI

59
Sia SF, Yan LM, Chin AWH, Fung K, Choy KT, Wong AYL, Kaewpreedee P, Perera R, Poon LLM, Nicholls JM (2020) Pathogenesis and transmission of SARS-CoV-2 in golden hamsters. Nature 583:834–838

DOI

60
Song Z, Xu Y, Bao L, Zhang L, Yu P, Qu Y, Zhu H, Zhao W, Han Y, Qin C (2019) From SARS to MERS, thrusting coronaviruses into the spotlight. Viruses 11:59

DOI

61
Song JW, Lam SM, Fan X, Cao WJ, Wang SY, Tian H, Chua GH, Zhang C, Meng FP, Xu Z (2020) Omics-driven systems interrogation of metabolic dysregulation in COVID-19 pathogenesis. Cell Metab 32(188–202):e185

DOI

62
Sun D, Lennernas H, Welage LS, Barnett JL, Landowski CP, Foster D, Fleisher D, Lee KD, Amidon GL (2002) Comparison of human duodenum and Caco-2 gene expression profiles for 12,000 gene sequences tags and correlation with permeability of 26 drugs. Pharm Res 19:1400–1416

DOI

63
Suzuki T, Ito Y, Sakai Y, Saito A, Okuzaki D, Motooka D, Minami S, Kobayashi T, Yamamoto T, Okamoto T (2020) Generation of human bronchial organoids for SARS-CoV-2 research. bioRxiv

DOI

64
Takayama K (2020) In vitro and animal models for SARS-CoV-2 research. Trends Pharmacol Sci 41:513–517

DOI

65
Thaker SK, Ch’ng J, Christofk HR (2019) Viral hijacking of cellular metabolism. BMC Biol 17:59

DOI

66
Vaduganathan M, Vardeny O, Michel T, McMurray JJV, Pfeffer MA, Solomon SD (2020) Renin-angiotensin-aldosterone system inhibitors in patients with Covid-19. N Engl J Med 382:1653–1659

DOI

67
van Doremalen N, Lambe T, Spencer A, Belij-Rammerstorfer S, Purushotham JN, Port JR, Avanzato V, Bushmaker T, Flaxman A, Ulaszewska M (2020) ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques. bioRxiv

DOI

68
van Hemert MJ, van den Worm SH, Knoops K, Mommaas AM, Gorbalenya AE, Snijder EJ (2008) SARS-coronavirus replication/transcription complexes are membrane-protected and need a host factor for activity in vitro. PLoS Pathog 4:e1000054

DOI

69
Verdecchia P, Cavallini C, Spanevello A, Angeli F (2020) The pivotal link between ACE2 deficiency and SARS-CoV-2 infection. Eur J Intern Med 76:14–20

DOI

70
Wang Y, Zhang D, Du G, Du R, Zhao J, Jin Y, Fu S, Gao L, Cheng Z, Lu Q (2020b) Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. Lancet 395:1569–1578

71
Wang H, Airola MV, Reue K (2017) How lipid droplets “TAG” along: Glycerolipid synthetic enzymes and lipid storage. Biochim Biophys Acta Mol Cell Biol Lipids 1862:1131–1145

DOI

72
Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, Shi Z, Hu Z, Zhong W, Xiao G (2020a) Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res 30:269–271

DOI

73
Warren HS, Tompkins RG, Moldawer LL, Seok J, Xu W, Mindrinos MN, Maier RV, Xiao W, Davis RW (2015) Mice are not men. Proc Natl Acad Sci USA 112:E345

DOI

74
Wiersinga WJ, Rhodes A, Cheng AC, Peacock SJ, Prescott HC (2020) Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19): a review. JAMA 324:782–793

DOI

75
Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T (2020) A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat Med 26:1070–1076

DOI

76
Williamson BN, Feldmann F, Schwarz B, Meade-White K, Porter DP, Schulz J, van Doremalen N, Leighton I, Yinda CK, Perez-Perez L (2020) Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2. Nature 585:273–276

DOI

77
Xiao L, Sakagami H, Miwa N (2020) ACE2: the key molecule for understanding the pathophysiology of severe and critical conditions of COVID-19: demon or angel? Viruses 12:491

DOI

78
Yamamoto Y, Gotoh S, Korogi Y, Seki M, Konishi S, Ikeo S, Sone N, Nagasaki T, Matsumoto H, Muro S (2017) Long-term expansion of alveolar stem cells derived from human iPS cells in organoids. Nat Methods 14:1097–1106

DOI

79
Yang L, Han Y, Nilsson-Payant BE, Gupta V, Wang P, Duan X, Tang X, Zhu J, Zhao Z, Jaffre F (2020) A human pluripotent stem cell-based platform to study SARS-CoV-2 tropism and model virus infection in human cells and organoids. Cell Stem Cell 27(125–136):e127

DOI

80
Yu G, Wang L-G, Han Y, He Q-Y (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. Omics 16:284–287

DOI

81
Yu J, Tostanoski LH, Peter L, Mercado NB, McMahan K, Mahrokhian SH, Nkolola JP, Liu J, Li Z, Chandrashekar A (2020) DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science 369:806–811

DOI

82
Zhao B, Ni C, Gao R, Wang Y, Yang L, Wei J, Lv T, Liang J, Zhang Q, Xu W (2020) Recapitulation of SARS-CoV-2 infection and cholangiocyte damage with human liver ductal organoids. Protein Cell

DOI

83
Zhou X, Jiang W, Liu Z, Liu S, Liang X (2017) Virus infection and death receptor-mediated apoptosis. Viruses 9:316

DOI

84
Zhou J, Li C, Liu X, Chiu MC, Zhao X, Wang D, Wei Y, Lee A, Zhang AJ, Chu H (2020a) Infection of bat and human intestinal organoids by SARS-CoV-2. Nat Med 26:1077–1083

DOI

85
Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL (2020b) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270–273

DOI

86
Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R (2020) A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 382:727–733

DOI

Outlines

/