Identification of SARS-CoV-2 inhibitors using lung and colonic organoids.
Yuling Han, Xiaohua Duan, Liuliu Yang, Benjamin E Nilsson-Payant, Pengfei Wang, Fuyu Duan, Xuming Tang, Tomer M Yaron, Tuo Zhang, Skyler Uhl, Yaron Bram, Chanel Richardson, Jiajun Zhu, Zeping Zhao, David Redmond, Sean Houghton, Duc-Huy T Nguyen, Dong Xu, Xing Wang, Jose Jessurun, Alain Borczuk, Yaoxing Huang, Jared L Johnson, Yuru Liu, Jenny Xiang, Hui Wang, Lewis C Cantley, Benjamin R tenOever, David D Ho, Fong Cheng Pan, Todd Evans, Huanhuan Joyce Chen, Robert E Schwartz, Shuibing Chen
Author Information
Yuling Han: Department of Surgery, Weill Cornell Medicine, New York, NY, USA. ORCID
Xiaohua Duan: Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
Liuliu Yang: Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
Benjamin E Nilsson-Payant: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. ORCID
Pengfei Wang: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
Fuyu Duan: Pritzker School of Molecular Engineering and Ben May Department, University of Chicago, Chicago, IL, USA.
Xuming Tang: Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
Tomer M Yaron: Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. ORCID
Tuo Zhang: Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA. ORCID
Skyler Uhl: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Yaron Bram: Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
Chanel Richardson: Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
Jiajun Zhu: Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
Zeping Zhao: Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
David Redmond: Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.
Sean Houghton: Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.
Duc-Huy T Nguyen: Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
Dong Xu: Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA.
Xing Wang: Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA. ORCID
Jose Jessurun: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA. ORCID
Alain Borczuk: Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Yaoxing Huang: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA. ORCID
Jared L Johnson: Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. ORCID
Yuru Liu: Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA.
Jenny Xiang: Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA.
Hui Wang: State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China. huiwang@shsmu.edu.cn.
Lewis C Cantley: Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. LCantley@med.cornell.edu. ORCID
Benjamin R tenOever: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. benjamin.tenoever@mssm.edu. ORCID
David D Ho: Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA. dh2994@cumc.columbia.edu. ORCID
Fong Cheng Pan: Department of Surgery, Weill Cornell Medicine, New York, NY, USA. fcp2002@med.cornell.edu. ORCID
Todd Evans: Department of Surgery, Weill Cornell Medicine, New York, NY, USA. tre2003@med.cornell.edu. ORCID
Huanhuan Joyce Chen: Pritzker School of Molecular Engineering and Ben May Department, University of Chicago, Chicago, IL, USA. joycechen@uchicago.edu.
Robert E Schwartz: Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA. res2025@med.cornell.edu.
Shuibing Chen: Department of Surgery, Weill Cornell Medicine, New York, NY, USA. shc2034@med.cornell.edu. ORCID
There is an urgent need to create novel models using human disease-relevant cells to study severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) biology and to facilitate drug screening. Here, as SARS-CoV-2 primarily infects the respiratory tract, we developed a lung organoid model using human pluripotent stem cells (hPSC-LOs). The hPSC-LOs (particularly alveolar type-II-like cells) are permissive to SARS-CoV-2 infection, and showed robust induction of chemokines following SARS-CoV-2 infection, similar to what is seen in patients with COVID-19. Nearly 25% of these patients also have gastrointestinal manifestations, which are associated with worse COVID-19 outcomes. We therefore also generated complementary hPSC-derived colonic organoids (hPSC-COs) to explore the response of colonic cells to SARS-CoV-2 infection. We found that multiple colonic cell types, especially enterocytes, express ACE2 and are permissive to SARS-CoV-2 infection. Using hPSC-LOs, we performed a high-throughput screen of drugs approved by the FDA (US Food and Drug Administration) and identified entry inhibitors of SARS-CoV-2, including imatinib, mycophenolic acid and quinacrine dihydrochloride. Treatment at physiologically relevant levels of these drugs significantly inhibited SARS-CoV-2 infection of both hPSC-LOs and hPSC-COs. Together, these data demonstrate that hPSC-LOs and hPSC-COs infected by SARS-CoV-2 can serve as disease models to study SARS-CoV-2 infection and provide a valuable resource for drug screening to identify candidate COVID-19 therapeutics.
References
Pan, L. et al. Clinical characteristics of COVID-19 patients with digestive symptoms in Hubei, China: a descriptive, cross-sectional, multicenter study. Am. J. Gastroenterol. 115, 766���773 (2020).
[DOI: 10.14309/ajg.0000000000000620]
Lamers, M. M. et al. SARS-CoV-2 productively infects human gut enterocytes. Science 369, 50���54 (2020).
[DOI: 10.1126/science.abc1669]
Zhou, J. et al. Infection of bat and human intestinal organoids by SARS-CoV-2. Nat. Med. 26, 1077���1083 (2020).
[DOI: 10.1038/s41591-020-0912-6]
Monteil, V. et al. Inhibition of SARS-CoV-2 infections in engineered human tissues using clinical-grade soluble human ACE2. Cell 181, 905���913 (2020).
[DOI: 10.1016/j.cell.2020.04.004]
Chen, Y. W. et al. A three-dimensional model of human lung development and disease from pluripotent stem cells. Nat. Cell Biol. 19, 542���549 (2017).
[DOI: 10.1038/ncb3510]
Huang, S. X. et al. Efficient generation of lung and airway epithelial cells from human pluripotent stem cells. Nat. Biotechnol. 32, 84���91 (2014).
[DOI: 10.1038/nbt.2754]
Jacob, A. et al. Differentiation of human pluripotent stem cells into functional lung alveolar epithelial cells. Cell Stem Cell 21, 472���488 (2017).
[DOI: 10.1016/j.stem.2017.08.014]
Mou, H. et al. Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs. Cell Stem Cell 10, 385���397 (2012).
[DOI: 10.1016/j.stem.2012.01.018]
McCauley, K. B. et al. Efficient derivation of functional human airway epithelium from pluripotent stem cells via temporal regulation of Wnt signaling. Cell Stem Cell 20, 844���857 (2017).
[DOI: 10.1016/j.stem.2017.03.001]
Hurley, K. et al. Reconstructed single-cell fate trajectories define lineage plasticity windows during differentiation of human PSC-derived distal lung progenitors. Cell Stem Cell 26, 593���608 (2020).
[DOI: 10.1016/j.stem.2019.12.009]
Jacob, A. et al. Derivation of self-renewing lung alveolar epithelial type II cells from human pluripotent stem cells. Nat. Protoc. 14, 3303���3332 (2019).
[DOI: 10.1038/s41596-019-0220-0]
Dye, B. R. et al. In vitro generation of human pluripotent stem cell derived lung organoids. eLife 4, e05098 (2015).
Chen, H. J. et al. Generation of pulmonary neuroendocrine cells and SCLC-like tumors from human embryonic stem cells. J. Exp. Med. 216, 674���687 (2019).
[DOI: 10.1084/jem.20181155]
Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271���280 (2020).
[DOI: 10.1016/j.cell.2020.02.052]
Shang, J. et al. Cell entry mechanisms of SARS-CoV-2. Proc. Natl Acad. Sci. USA 117, 11727���11734 (2020).
[DOI: 10.1073/pnas.2003138117]
Whitt, M. A. Generation of VSV pseudotypes using recombinant ��G-VSV for studies on virus entry, identification of entry inhibitors, and immune responses to vaccines. J. Virol. Methods 169, 365���374 (2010).
[DOI: 10.1016/j.jviromet.2010.08.006]
Nie, J. et al. Establishment and validation of a pseudovirus neutralization assay for SARS-CoV-2. Emerg. Microbes Infect. 9, 680���686 (2020).
[DOI: 10.1080/22221751.2020.1743767]
Blanco-Melo, D. et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181, 1036���1045 (2020).
[DOI: 10.1016/j.cell.2020.04.026]
Crespo, M. et al. Colonic organoids derived from human induced pluripotent stem cells for modeling colorectal cancer and drug testing. Nat. Med. 23, 878���884 (2017).
[DOI: 10.1038/nm.4355]
Munera, J. O. et al. Differentiation of human pluripotent stem cells into colonic organoids via transient activation of BMP signaling. Cell Stem Cell 21, 51���64 (2017).
[DOI: 10.1016/j.stem.2017.05.020]
Gordon, D. E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459���468 (2020).
Zhao, X. et al. Immunization-elicited broadly protective antibody reveals ebolavirus fusion loop as a site of vulnerability. Cell 169, 891���904 (2017).
[DOI: 10.1016/j.cell.2017.04.038]
Liu, L. et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature 584, 450���456 (2020).
[DOI: 10.1038/s41586-020-2571-7]
Yang, L. et al. 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 (2020).
[DOI: 10.1016/j.stem.2020.06.015]
Lun, A. T., Bach, K. & Marioni, J. C. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17, 75 (2016).
[DOI: 10.1186/s13059-016-0947-7]
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888���1902 (2019).
[DOI: 10.1016/j.cell.2019.05.031]
van den Brink, S. C. et al. Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations. Nat. Methods 14, 935���936 (2017).
[DOI: 10.1038/nmeth.4437]
Travaglini, K. J. et al. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature 587, 619���625 (2020).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139���140 (2010).
[DOI: 10.1093/bioinformatics/btp616]
Liao, Y., Wang, J., Jaehnig, E. J., Shi, Z. & Zhang, B. WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. Nucleic Acids Res. 47, W199���W205 (2019).
[DOI: 10.1093/nar/gkz401]
