the landscape of lung bronchoalveolar immune cells in covid 19 revealed by single cell CORD-Papers (Version 1)

Title: The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing
Abstract: The novel coronavirus SARS-CoV-2 etiological agent of recently named Coronavirus infected disease (COVID-19) by WHO has caused more than 2 000 deaths worldwide since its emergency in Wuhan City Hubei province China in December 2019. The symptoms of COVID-19 varied from modest mild to acute respiratory distress syndrome (ARDS) and the latter of which is generally associated with deregulated immune cytokine production; however we currently know little as to the interplay between the extent of clinical symptoms and the compositions of lung immune microenvironment. Here we comprehensively characterized the lung immune microenvironment with the bronchoalveolar lavage fluid (BALF) from 3 severe and 3 mild COVID-19 patients and 8 previously reported healthy lung controls through single-cell RNA sequence (scRNA-seq) combined with TCR-seq. Our data shows that monocyte-derived FCN1+ macrophages whereas notFABP4+ alveolar macrophages that represent a predominant macrophage subset in BALF from patients with mild diseases overwhelm in the severely damaged lungs from patients with ARDS. These cells are highly inflammatory and enormous chemokine producers implicated in cytokine storm. Furthermore the formation of tissue resident highly expanded clonal CD8+ T cells in the lung microenvironment of mild symptom patients suggests a robust adaptive immune response connected to a better control of COVID-19. This study first reported the cellular atlas of lung bronchoalveolar immune microenvironment in COVID-19 patients at the single-cell resolution and unveiled the potential immune mechanisms underlying disease progression and protection in COVID-19.
Published: 2020-02-26
DOI: 10.1101/2020.02.23.20026690
DOI_URL: http://doi.org/10.1101/2020.02.23.20026690
Author Name: Liao M
Author link: https://covid19-data.nist.gov/pid/rest/local/author/liao_m
Author Name: Liu Y
Author link: https://covid19-data.nist.gov/pid/rest/local/author/liu_y
Author Name: Yuan J
Author link: https://covid19-data.nist.gov/pid/rest/local/author/yuan_j
Author Name: Wen Y
Author link: https://covid19-data.nist.gov/pid/rest/local/author/wen_y
Author Name: Xu G
Author link: https://covid19-data.nist.gov/pid/rest/local/author/xu_g
Author Name: Zhao J
Author link: https://covid19-data.nist.gov/pid/rest/local/author/zhao_j
Author Name: Chen L
Author link: https://covid19-data.nist.gov/pid/rest/local/author/chen_l
Author Name: Li J
Author link: https://covid19-data.nist.gov/pid/rest/local/author/li_j
Author Name: Wang X
Author link: https://covid19-data.nist.gov/pid/rest/local/author/wang_x
Author Name: Wang F
Author link: https://covid19-data.nist.gov/pid/rest/local/author/wang_f
Author Name: Liu L
Author link: https://covid19-data.nist.gov/pid/rest/local/author/liu_l
Author Name: Zhang S
Author link: https://covid19-data.nist.gov/pid/rest/local/author/zhang_s
Author Name: Zhang Z
Author link: https://covid19-data.nist.gov/pid/rest/local/author/zhang_z
sha: 8f81392c0b84774a0907127a08737c94f780afb7
license: medrxiv
source_x: MedRxiv; WHO
source_x_url: https://www.who.int/
url: https://doi.org/10.1101/2020.02.23.20026690 http://medrxiv.org/cgi/content/short/2020.02.23.20026690v1?rss=1
has_full_text: TRUE
Keywords Extracted from Text Content: samples Slingshot [33 TCR alpha macrophages left coronavirus https://doi.org/10.1101/2020.02.23.20026690 doi lung XCL2 medRxiv preprint Table 1 SARS-CoV-2 C11, C13, C14, PPARG ITGA1 SPP1 KLRC1 lumps Figure 1E-1F UMAP T145 BHLHE41 NK cells mouse alveolar macrophage Macrophages clusterProfiler [36] ITGAE CREB1 SARS-CoV-2-specific T cells COVID-19 C12 TCR V(D)J C15 tissue human CDR3 C9 lung CD8 + T cells ORF1ab 3' V2 chemistry kit patients human lung macrophage influenza infections S3B myeloid cell T lymphocytes Cell Ranger Software Suite (Version 3.1.0 CCR7 + cells C20 lung bronchoalveolar lavage fluid T cells macrophage NK XCL1 LogNormalize C0 C5 S100A9 Cell lung immune M2-like TFs CD8B throat swab FABP4 T-cell IL2RA CTLA4 V(D)J MKI67 SARS-CoV lung tissue https://github.com/tmoerman/arboreto human ACE2 GSE122960 [12 Cells C22 T HOPX donors CD8A bats [3 patient macrophage lineage C19 NK cell FASLG STAT2 CXCL11 lungs tissue samples CD8 immune cells AM C6, FCN1 CCL2 B IRFs tissue macrophage acute respiratory infections lung AMs PPARγ human GRCh38 Proliferating T cells M1-M3 feature-barcode matrix CCR7 + T cells epithelial cells AMs CD4 FASTQs STAT1 multiple IFN regulatory factors lung macrophage VCAN T cell clones Seurat v3 [31 COVID-19 patients GRNBoost2 IL-8 C16 NK lymphocytes CXCR6 Chromium Single cell KLRD1 lung BALF FOXP3 S2B KLRF1 CXCL10 monocyte SARS patients Wuhan nasal swab proliferating cells monocytes beta chains TYMS human subjects BALF Figure 2E Figure 2G M2 pySCENIC Treg cells GZMA medRxiv TCR T cell cell medRxiv preprint HC1-HC8 gene-barcode matrix immune defense ( Figure S4 ZNF683 IL7R calcium medRxiv preprint cells central memory cells SCENIC [34] lung AM medRxiv preprint patients clones cells CCL5 monocyte-derived FCN1 + macrophages Figure 4E MERS-CoV BALF) cells dendritic cell Figure 1F and human lungs C10 3F CXCL9 memory cells cellular TFs lung macrophages re-clustered CCL3 RPMI 1640 monocyte-like GZMK SCENIC JAML sputum C21 medRxiv preprint effector Cell Ranger vdj pipeline ( patient samples specimens medRxiv preprint S100A8 SPP1 + macrophages macrophage cells lung immune cell compartments C17, preprint medRxiv preprint medRxiv preprint
Extracted Text Content in Record: First 5000 Characters:Since December, 2019, a disease outbreak caused by a novel coronavirus (now given the name SARS-CoV-2) started in Wuhan, and has quickly spread in China and subsequently inmany other countries [1] . The WHO has declared the new coronavirus (CoV) infection as a global public health emergency and named the coronavirus infected disease-19 . The genome analysis showed that the SARS-CoV-2 is a SARS-CoV like β-lineage coronavirus [2] and likely originates from bats [3] . SARS-CoV-2 uses human ACE2 protein as their receptors [4] , which explains its similarly high transmissibility. The clinical data indicated that the COVID-19 varied from asymptomatic to acute respiratory distress syndrome (ARDS), similar as SARS-CoV infection [5] [6] [7] . Although researchers are racing against time to develop vaccines and test anti-viral drugs in clinical trials [8] , there is no effective prophylactic and clinical treatment for COVID-19 yet. Generally, the COVID-19 is less severe and less fatal than the SARS, however, some patients, especially aged populations with co-morbidities are prone to develop more severe symptoms and require emergent medical interventions [9] . It is not completely understood why some patients develop severe but others have mild or even asymptomatic diseases by the same SARS-CoV-2 infections. The immunopathogenesis of hCoVs-induced respiratory distress syndrome may involve deranged interferon production, hyper-inflammatory response and cytokine storms, inefficient or delayed induction of neutralizing antibody and specific T cell responses [10, 11] . However, due to biosafety and ethics issues and technical limitations, most of the current knowledge was generated from animal model studies, and not directly from human subjects. More investigations using patient samples are needed to explore the relevant protective or pathogenic mechanisms in clinical settings. Here, we applied the emerging single-cell RNA sequence (scRNA-seq) and single-cell TCR-seq to comprehensively characterize the lung bronchoalveolar lavage fluid (BALF) cells from 6 of COVID-19 patients, including 3 severe and 3 mild cases. Our study depicts a high-resolution transcriptome atlas of lung resident immune subsets in response to SARS-CoV-2 infections. It reveals that compared to the lung immune microenvironment of mild symptom patients, monocyte-derived FCN1 + macrophages replacing the FABP4 + alveolar macrophages predominate macrophage lineage compostions in the severely damaged lung, which are highly inflammatory and potent chemokine producers. Furthermore, the lung resident highly expanded clonal CD8 + T All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 23.20026690 doi: medRxiv preprint cells formed in the mildly infected patients support the notion that a rapid and robust adaptive immune response is potentially critical for controlling COVID-19. To characterize the immune microenvironment of the SARS-CoV-2-infected lung, we performed scRNA-seq analysis of single cells in the lung BALF (37, 820 cells) using the 10X Genomics platform, from 3 of recovered mild cases and 3 of severe cases ( Figure 1A , Table 1 ). We also collected public available scRNA-seq data (43, 627 cells) of 8 normal lungs as control [12] . This dataset passed stringent high-quality filtering ( Figure S1 ), yielding a mean of 188K reads/cell with median gene and unique molecular identifier (UMI) counts of 2, 070 and 6, 852, respectively (Table S1 ). Figure 1D and S2B). We were also able to detect low levels of SARS-CoV-2 transcripts in various cell populations from severe COVID-19 patients but not mild cases and controls ( Figure S2C ). We assumed that these viral transcripts were likely ambient contaminations of viral loads in the BALF. We then compared the distribution of different cellular compartments among control, mild and severe group. There were higher proportions of T and NK cells in the COVID-19 patients than those in controls, while epithelial cells in patients are fewer. As compared to mild cases, severe patients contained more macrophages but less proportion of T and NK cells ( Figure 1E-1F ). Together, our data showed an increased recruitment of immune cells to the lung in response to SARS-CoV-2 infection, and that the lung immune cell compartments differed between mild and severe COVID-19 patients. All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.02. 23.20026690 doi: medRxiv preprint The increased lung macrophage population was present in severe COVID-19 patients. To further understand the macrophage heterogeneity, we re-clustered the macrophages
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