Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Furong Qi, Shen Qian, Shuye Zhang, Zheng Zhang, Furong Qi, Shen Qian, Shuye Zhang, Zheng Zhang

Abstract

The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.

Keywords: ACE2; Co-receptor; Coronaviruses; Macrophage; SARS-CoV-2; scRNA-seq.

Conflict of interest statement

Declaration of competing interest We declare that we do not have any commercial or associative interest that represents a conflict of interest in connection with the work submitted.

Copyright © 2020 Shenzhen Third People\\u0019s Hospital. Published by Elsevier Inc. All rights reserved.

Figures

Fig. 1
Fig. 1
The expression profiles of ACE2 in 13 human tissues. The single cell expression maps of ACE2 in lung, liver, stomach, ileum, rectum, colon, blood, bone marrow, spleen, esophagus, kidney, skin and eye. ACE2 is expressed in lung AT2 (Alveolar cells Type2), liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs (enterocytes), rectum ECs, stomach epithelial cells, and kidney proximal tubules. None of the ACE2 transcripts was found in bone marrow and blood. PMCs, pit mucous cells; GMCs, antral basal gland mucous cells; PCs, proliferative cells in stomach and Paneth cells in ileum; EECs, enteroendocrine cells; Gs, goblet cells; PROs, progenitor cells; SCs, stem cells; TAs, transient amplifying; EECs, enteroendocrine cells; RPEs, retinal pigment epithelium.
Fig. 2
Fig. 2
Pearson correlation coefficients between the curated ssRNA viral receptors and membrane proteins. The warm colors mean positive correlation, and the cold colors mean negative correlation. The stars represent the correlation coefficients greater than 0.8. ANPEP, ENPEP and DPP4 show highest correlation with ACE2.
Fig. 3
Fig. 3
Cell-cell interactions between cell types in 8 tissues expressing ACE2. (A) The cell-cell interaction analysis was conducted by CellPhoneDB. Cell types are nodes and interactions are edges. Red nodes indicate major cell types expressing ACE2 in each tissue. Size of cell type is proportional to the total number of interactions with the red nodes. (B) The cytokines that connected ACE2-expressing cells and the macrophages. Macrophages expression receptors and ACE2-expressing cells express ligands.
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References

    1. Ahlquist P., et al. Host factors in positive-strand RNA virus genome replication. J. Virol. 2003;77(15):8181–8186.
    1. Huang C., et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395(10223):497–506.
    1. Chazal N., Gerlier D. Virus entry, assembly, budding, and membrane rafts. Microbiol. Mol. Biol. Rev. 2003;67(2):226–237. table of contents.
    1. Lu R., et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395(10224):565–574.
    1. Hoffmann M., et al. 2020. The Novel Coronavirus 2019 (2019-nCoV) Uses the SARS-Coronavirus Receptor ACE2 and the Cellular Protease TMPRSS2 for Entry into Target Cells; p. 2020. bioRxiv. 01.31.929042.
    1. Xin Zou, K.C., Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han, The single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to Wuhan 2019-nCoV infection. Front. Med. [Epub ahead of print] doi: 10.1007/s11684-020-0754-0.
    1. Zhang Z., et al. Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors. Bioinformatics. 2019;35(5):723–728.
    1. Reyfman P.A., et al. Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 2019;199(12):1517–1536.
    1. MacParland S.A., et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat. Commun. 2018;9(1):4383.
    1. Wang Y., et al. Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J. Exp. Med. 2020;217(2)
    1. Dobie R., et al. Single-cell transcriptomics uncovers zonation of function in the mesenchyme during liver fibrosis. Cell Rep. 2019;29(7):1832–1847 e8.
    1. Oetjen K.A., et al. Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry. JCI Insight. 2018;3(23)
    1. Kim D., et al. Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report. Nat. Med. 2020;26:236–243.
    1. Madissoon E., et al. scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation. Genome Biol. 2019;21(1):1.
    1. Parikh K., et al. Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature. 2019;567(7746):49–55.
    1. Voigt A.P., et al. Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration. Proc. Natl. Acad. Sci. U. S. A. 2019;116(48):24100–24107.
    1. Zhang P., et al. Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer. Cell Rep. 2019;27(6):1934–1947 e5.
    1. Liao J., et al. Single-cell RNA sequencing of human kidney. Sci Data. 2020;7(1):4.
    1. Stuart T., et al. Comprehensive integration of single-cell data. Cell. 2019;177(7):1888–1902 e21.
    1. Korsunsky I., et al. Fast, sensitive and accurate integration of single-cell data with harmony. Nat. Methods. 2019;16(12):1289–1296.
    1. Efremova M., et al. 2019. v2.0: Inferring Cell-Cell Communication from Combined Expression of Multi-Subunit Receptor-Ligand Complexes. bioRxiv.
    1. Lomize A.L., et al. Membranome: a database for proteome-wide analysis of single-pass membrane proteins. Nucleic Acids Res. 2017;45(D1):D250–D255.
    1. Holmes R.S., Spradling-Reeves K.D., Cox L.A. Mammalian Glutamyl aminopeptidase genes (ENPEP) and proteins: comparative studies of a major contributor to arterial hypertension. J. Data Min. Genom. Proteonomics. 2017;8(2)
    1. Li F. Receptor recognition mechanisms of coronaviruses: a decade of structural studies. J. Virol. 2015;89(4):1954–1964.
    1. Smith R.D. Responding to global infectious disease outbreaks: lessons from SARS on the role of risk perception, communication and management. Soc. Sci. Med. 2006;63(12):3113–3123.
    1. Middle East Respiratory Syndrome Coronavirus (MERS-CoV). World Health Organization, Retrieved 10 April 2017.
    1. Chen N., 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.
    1. Wang S., et al. Endocytosis of the receptor-binding domain of SARS-CoV spike protein together with virus receptor ACE2. Virus Res. 2008;136(1–2):8–15.
    1. Yang Z.Y., et al. pH-dependent entry of severe acute respiratory syndrome coronavirus is mediated by the spike glycoprotein and enhanced by dendritic cell transfer through DC-SIGN. J. Virol. 2004;78(11):5642–5650.
    1. Gramberg T., et al. LSECtin interacts with filovirus glycoproteins and the spike protein of SARS coronavirus. Virology. 2005;340(2):224–236.
    1. Marzi A., et al. DC-SIGN and DC-SIGNR interact with the glycoprotein of Marburg virus and the S protein of severe acute respiratory syndrome coronavirus. J. Virol. 2004;78(21):12090–12095.
    1. Peck K.M., et al. Permissivity of dipeptidyl peptidase 4 orthologs to Middle East respiratory syndrome coronavirus is governed by glycosylation and other complex determinants. J. Virol. 2017;91(19)
    1. Le Page C., et al. Interferon activation and innate immunity. Rev. Immunogenet. 2000;2(3):374–386.
    1. Perry A.K., et al. The host type I interferon response to viral and bacterial infections. Cell Res. 2005;15(6):407–422.
    1. McNab F., et al. Type I interferons in infectious disease. Nat. Rev. Immunol. 2015;15(2):87–103.
    1. Hansen T.H., Bouvier M. MHC class I antigen presentation: learning from viral evasion strategies. Nat. Rev. Immunol. 2009;9(7):503–513.
    1. Goulder P.J., Watkins D.I. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat. Rev. Immunol. 2008;8(8):619–630.

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