SARS-CoV-2 Infection of Pluripotent Stem Cell-Derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response
Jessie Huang, Adam J Hume, Kristine M Abo, Rhiannon B Werder, Carlos Villacorta-Martin, Konstantinos-Dionysios Alysandratos, Mary Lou Beermann, Chantelle Simone-Roach, Jonathan Lindstrom-Vautrin, Judith Olejnik, Ellen L Suder, Esther Bullitt, Anne Hinds, Arjun Sharma, Markus Bosmann, Ruobing Wang, Finn Hawkins, Eric J Burks, Mohsan Saeed, Andrew A Wilson, Elke Mühlberger, Darrell N Kotton, Jessie Huang, Adam J Hume, Kristine M Abo, Rhiannon B Werder, Carlos Villacorta-Martin, Konstantinos-Dionysios Alysandratos, Mary Lou Beermann, Chantelle Simone-Roach, Jonathan Lindstrom-Vautrin, Judith Olejnik, Ellen L Suder, Esther Bullitt, Anne Hinds, Arjun Sharma, Markus Bosmann, Ruobing Wang, Finn Hawkins, Eric J Burks, Mohsan Saeed, Andrew A Wilson, Elke Mühlberger, Darrell N Kotton
Abstract
A hallmark of severe COVID-19 pneumonia is SARS-CoV-2 infection of the facultative progenitors of lung alveoli, the alveolar epithelial type 2 cells (AT2s). However, inability to access these cells from patients, particularly at early stages of disease, limits an understanding of disease inception. Here, we present an in vitro human model that simulates the initial apical infection of alveolar epithelium with SARS-CoV-2 by using induced pluripotent stem cell-derived AT2s that have been adapted to air-liquid interface culture. We find a rapid transcriptomic change in infected cells, characterized by a shift to an inflammatory phenotype with upregulation of NF-κB signaling and loss of the mature alveolar program. Drug testing confirms the efficacy of remdesivir as well as TMPRSS2 protease inhibition, validating a putative mechanism used for viral entry in alveolar cells. Our model system reveals cell-intrinsic responses of a key lung target cell to SARS-CoV-2 infection and should facilitate drug development.
Keywords: COVID-19; SARS-CoV-2; alveolar epithelial cell; alveolar type 2 cell; human induced pluripotent stem cells; iPSCs; inflammation; lung.
Conflict of interest statement
Declaration of Interests The authors declare no competing interests.
Copyright © 2020 Elsevier Inc. All rights reserved.
Figures
References
- Abo K.M., Ma L., Matte T., Huang J., Alysandratos K.D., Werder R.B., Mithal A., Beermann M.L., Lindstrom-Vautrin J., Mostoslavsky G. Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors. bioRxiv. 2020 2020.2006.2003.132639.
- Bao L., Deng W., Huang B., Gao H., Liu J., Ren L., Wei Q., Yu P., Xu Y., Qi F. The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature. 2020;583:830–833.
- Barkauskas C.E., Cronce M.J., Rackley C.R., Bowie E.J., Keene D.R., Stripp B.R., Randell S.H., Noble P.W., Hogan B.L. Type 2 alveolar cells are stem cells in adult lung. J. Clin. Invest. 2013;123:3025–3036.
- Blanco-Melo D., Nilsson-Payant B.E., Liu W.C., Uhl S., Hoagland D., Møller R., Jordan T.X., Oishi K., Panis M., Sachs D. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell. 2020;181:1036–1045.e9.
- Bradley B.T., Maioli H., Johnston R., Chaudhry I., Fink S.L., Xu H., Najafian B., Deutsch G., Lacy J.M., Williams T. Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series. Lancet. 2020;396:320–332.
- Broggi A., Ghosh S., Sposito B., Spreafico R., Balzarini F., Lo Cascio A., Clementi N., De Santis M., Mancini N., Granucci F., Zanoni I. Type III interferons disrupt the lung epithelial barrier upon viral recognition. Science. 2020;369:706–712.
- Channappanavar R., Fehr A.R., Vijay R., Mack M., Zhao J., Meyerholz D.K., Perlman S. Dysregulated Type I Interferon and Inflammatory Monocyte-Macrophage Responses Cause Lethal Pneumonia in SARS-CoV-Infected Mice. Cell Host Microbe. 2016;19:181–193.
- Chen J., Wu H., Yu Y., Tang N. Pulmonary alveolar regeneration in adult COVID-19 patients. Cell Res. 2020;30:708–710.
- Clementi N., Ferrarese R., Criscuolo E., Diotti R.A., Castelli M., Scagnolari C., Burioni R., Antonelli G., Clementi M., Mancini N. Interferon-β-1a Inhibition of Severe Acute Respiratory Syndrome–Coronavirus 2 In Vitro When Administered After Virus Infection. The Journal of Infectious Diseases. 2020;222:722–725.
- Crawford K.H.D., Eguia R., Dingens A.S., Loes A.N., Malone K.D., Wolf C.R., Chu H.Y., Tortorici M.A., Veesler D., Murphy M. Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays. Viruses. 2020;12:513.
- Dobin A., Davis C.A., Schlesinger F., Drenkow J., Zaleski C., Jha S., Batut P., Chaisson M., Gingeras T.R. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
- Habermann A.C., Gutierrez A.J., Bui L.T., Yahn S.L., Winters N.I., Calvi C.L., Peter L., Chung M.-I., Taylor C.J., Jetter C. Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis. Sci. Adv. 2020;6:eaba1972.
- Harcourt J., Tamin A., Lu X., Kamili S., Sakthivel S.K., Murray J., Queen K., Tao Y., Paden C.R., Zhang J. Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with Coronavirus Disease, United States. Emerg. Infect. Dis. 2020;26:1266–1273.
- Hawkins F., Kramer P., Jacob A., Driver I., Thomas D.C., McCauley K.B., Skvir N., Crane A.M., Kurmann A.A., Hollenberg A.N. Prospective isolation of NKX2-1-expressing human lung progenitors derived from pluripotent stem cells. J. Clin. Invest. 2017;127:2277–2294.
- Hoffmann M., Kleine-Weber H., Schroeder S., Krüger N., Herrler T., Erichsen S., Schiergens T.S., Herrler G., Wu N.H., Nitsche A. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020;181:271–280.e8.
- Hou Y.J., Okuda K., Edwards C.E., Martinez D.R., Asakura T., Dinnon K.H., 3rd, Kato T., Lee R.E., Yount B.L., Mascenik T.M. SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract. Cell. 2020;182:429–446.e14.
- Huang S.X., Islam M.N., O’Neill J., Hu Z., Yang Y.G., Chen Y.W., Mumau M., Green M.D., Vunjak-Novakovic G., Bhattacharya J., Snoeck H.W. Efficient generation of lung and airway epithelial cells from human pluripotent stem cells. Nat. Biotechnol. 2014;32:84–91.
- Hurley K., Ding J., Villacorta-Martin C., Herriges M.J., Jacob A., Vedaie M., Alysandratos K.D., Sun Y.L., Lin C., Werder R.B. Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. Cell Stem Cell. 2020;26:593–608.e8.
- Imai M., Iwatsuki-Horimoto K., Hatta M., Loeber S., Halfmann P.J., Nakajima N., Watanabe T., Ujie M., Takahashi K., Ito M. Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development. Proc. Natl. Acad. Sci. USA. 2020;117:16587–16595.
- Jacob A., Morley M., Hawkins F., McCauley K.B., Jean J.C., Heins H., Na C.L., Weaver T.E., Vedaie M., Hurley K. Differentiation of Human Pluripotent Stem Cells into Functional Lung Alveolar Epithelial Cells. Cell Stem Cell. 2017;21:472–488.e410.
- Jacob A., Vedaie M., Roberts D.A., Thomas D.C., Villacorta-Martin C., Alysandratos K.D., Hawkins F., Kotton D.N. Derivation of self-renewing lung alveolar epithelial type II cells from human pluripotent stem cells. Nat. Protoc. 2019;14:3303–3332.
- Jiang R.D., Liu M.Q., Chen Y., Shan C., Zhou Y.W., Shen X.R., Li Q., Zhang L., Zhu Y., Si H.R. Pathogenesis of SARS-CoV-2 in Transgenic Mice Expressing Human Angiotensin-Converting Enzyme 2. Cell. 2020;182:50–58.e58.
- Korotkevich G., Sukhov V., Sergushichev A. Fast gene set enrichment analysis. bioRxiv. 2019 doi: 10.1101/060012.
- Law C.W., Alhamdoosh M., Su S., Dong X., Tian L., Smyth G.K., Ritchie M.E. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research. 2016;5
- Lei X., Dong X., Ma R., Wang W., Xiao X., Tian Z., Wang C., Wang Y., Li L., Ren L. Activation and evasion of type I interferon responses by SARS-CoV-2. Nat. Commun. 2020;11:3810.
- Leung J.M., Yang C.X., Tam A., Shaipanich T., Hackett T.-L., Singhera G.K., Dorscheid D.R., Sin D.D. ACE-2 expression in the small airway epithelia of smokers and COPD patients: implications for COVID-19. Eur. Respir. J. 2020;55:2000688.
- Longmire T.A., Ikonomou L., Hawkins F., Christodoulou C., Cao Y., Jean J.C., Kwok L.W., Mou H., Rajagopal J., Shen S.S. Efficient derivation of purified lung and thyroid progenitors from embryonic stem cells. Cell Stem Cell. 2012;10:398–411.
- McCauley K.B., Hawkins F., Serra M., Thomas D.C., Jacob A., Kotton D.N. Efficient Derivation of Functional Human Airway Epithelium from Pluripotent Stem Cells via Temporal Regulation of Wnt Signaling. Cell Stem Cell. 2017;20:844–857.e846.
- McCauley K.B., Alysandratos K.D., Jacob A., Hawkins F., Caballero I.S., Vedaie M., Yang W., Slovik K.J., Morley M., Carraro G. Single-Cell Transcriptomic Profiling of Pluripotent Stem Cell-Derived SCGB3A2+ Airway Epithelium. Stem Cell Reports. 2018;10:1579–1595.
- McCauley K.B., Hawkins F., Kotton D.N. Derivation of Epithelial-Only Airway Organoids from Human Pluripotent Stem Cells. Curr. Protoc. Stem Cell Biol. 2018;45:e51.
- Menachery V.D., Eisfeld A.J., Schäfer A., Josset L., Sims A.C., Proll S., Fan S., Li C., Neumann G., Tilton S.C. Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. MBio. 2014;5 e01174–14.
- Mou H., Quinlan B.D., Peng H., Guo Y., Peng S., Zhang L., Davis-Gardner M.E., Gardner M.R., Crynen G., Voo Z.X. Mutations from bat ACE2 orthologs markedly enhance ACE2-Fc neutralization of SARS-CoV-2. bioRxiv. 2020 doi: 10.1101/2020.06.29.178459.
- Mulay A., Konda B., Garcia G., Yao C., Beil S., Sen C., Purkayastha A., Kolls J.K., Pociask D.A., Pessina P., Sainz de Aja J., Garcia-de-Alba C., Kim C.F., Gomperts B., Arumugaswami V., Stripp B.R. SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery. bioRxiv. 2020 doi: 10.1101/2020.06.29.174623.
- Ou X., Liu Y., Lei X., Li P., Mi D., Ren L., Guo L., Guo R., Chen T., Hu J. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat. Commun. 2020;11:1620.
- Pham I., Uchida T., Planes C., Ware L.B., Kaner R., Matthay M.A., Clerici C. Hypoxia upregulates VEGF expression in alveolar epithelial cells in vitro and in vivo. Am. J. Physiol. Lung Cell. Mol. Physiol. 2002;283:L1133–L1142.
- Pruijssers A.J., George A.S., Schäfer A., Leist S.R., Gralinksi L.E., Dinnon K.H., 3rd, Yount B.L., Agostini M.L., Stevens L.J., Chappell J.D. Remdesivir Inhibits SARS-CoV-2 in Human Lung Cells and Chimeric SARS-CoV Expressing the SARS-CoV-2 RNA Polymerase in Mice. Cell Rep. 2020;32:107940.
- Qian Z., Travanty E.A., Oko L., Edeen K., Berglund A., Wang J., Ito Y., Holmes K.V., Mason R.J. Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus. Am. J. Respir. Cell Mol. Biol. 2013;48:742–748.
- Riva L., Yuan S., Yin X., Martin-Sancho L., Matsunaga N., Pache L., Burgstaller-Muehlbacher S., De Jesus P.D., Teriete P., Hull M.V. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature. 2020:1–7.
- Schaefer I.-M., Padera R.F., Solomon I.H., Kanjilal S., Hammer M.M., Hornick J.L., Sholl L.M. In situ detection of SARS-CoV-2 in lungs and airways of patients with COVID-19. Mod. Pathol. 2020 doi: 10.1038/s41379-020-0595-z. Published online June 19, 2020.
- Serra M., Alysandratos K.D., Hawkins F., McCauley K.B., Jacob A., Choi J., Caballero I.S., Vedaie M., Kurmann A.A., Ikonomou L. Pluripotent stem cell differentiation reveals distinct developmental pathways regulating lung- versus thyroid-lineage specification. Development. 2017;144:3879–3893.
- Shang J., Wan Y., Luo C., Ye G., Geng Q., Auerbach A., Li F. Cell entry mechanisms of SARS-CoV-2. Proc. Natl. Acad. Sci. USA. 2020;117:11727–11734.
- Sia S.F., Yan L.M., Chin A.W.H., Fung K., Choy K.T., Wong A.Y.L., Kaewpreedee P., Perera R.A.P.M., Poon L.L.M., Nicholls J.M. Pathogenesis and transmission of SARS-CoV-2 in golden hamsters. Nature. 2020;583:834–838.
- Sun S.-H., Chen Q., Gu H.-J., Yang G., Wang Y.-X., Huang X.-Y., Liu S.-S., Zhang N.-N., Li X.-F., Xiong R. A mouse model of SARS-CoV-2 infection and pathogenesis. Cell Host Microbe. 2020;28:124–133.e4.
- Sungnak W., Huang N., Bécavin C., Berg M., Queen R., Litvinukova M., Talavera-López C., Maatz H., Reichart D., Sampaziotis F., HCA Lung Biological Network SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat. Med. 2020;26:681–687.
- Thi Nhu Thao T., Labroussaa F., Ebert N., V’kovski P., Stalder H., Portmann J., Kelly J., Steiner S., Holwerda M., Kratzel A. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature. 2020;582:561–565.
- Wang M., Cao R., Zhang L., Yang X., Liu J., Xu M., Shi Z., Hu Z., Zhong W., Xiao G. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30:269–271.
- Wang N., Zhan Y., Zhu L., Hou Z., Liu F., Song P., Qiu F., Wang X., Zou X., Wan D. Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients. Cell Host Microbe. 2020;28:455–464.e2.
- Weinreb C., Wolock S., Klein A.M. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. Bioinformatics. 2018;34:1246–1248.
- Wu D., Smyth G.K. Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research. 2012;40:e133.
- Yamamoto Y., Gotoh S., Korogi Y., Seki M., Konishi S., Ikeo S., Sone N., Nagasaki T., Matsumoto H., Muro S. Long-term expansion of alveolar stem cells derived from human iPS cells in organoids. Nat. Methods. 2017;14:1097–1106.
- Zhu N., Zhang D., Wang W., Li X., Yang B., Song J., Zhao X., Huang B., Shi W., Lu R., China Novel Coronavirus Investigating and Research Team A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. 2020;382:727–733.
- Ziegler C.G.K., Allon S.J., Nyquist S.K., Mbano I.M., Miao V.N., Tzouanas C.N., Cao Y., Yousif A.S., Bals J., Hauser B.M., HCA Lung Biological Network. Electronic address. lung-network@humancellatlas.org. HCA Lung Biological Network 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. 2020;181:1016–1035.e19.
Source: PubMed