sars cov 2 drives jak1 2 dependent local complement hyperactivation CORD-Papers-2022-06-02 (Version 1)

Title: SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation
Abstract: Patients with coronavirus disease 2019 (COVID-19) present a wide range of acute clinical manifestations affecting the lungs liver kidneys and gut. Angiotensin converting enzyme (ACE) 2 the best-characterized entry receptor for the disease-causing virus SARS-CoV-2 is highly expressed in the aforementioned tissues. However the pathways that underlie the disease are still poorly understood. Here we unexpectedly found that the complement system was one of the intracellular pathways most highly induced by SARS-CoV-2 infection in lung epithelial cells. Infection of respiratory epithelial cells with SARS-CoV-2 generated activated complement component C3a and could be blocked by a cell-permeable inhibitor of complement factor B (CFBi) indicating the presence of an inducible cell-intrinsic C3 convertase in respiratory epithelial cells. Within cells of the bronchoalveolar lavage of patients distinct signatures of complement activation in myeloid lymphoid and epithelial cells tracked with disease severity. Genes induced by SARS-CoV-2 and the drugs that could normalize these genes both implicated the interferon-JAK1/2-STAT1 signaling system and NF-B as the main drivers of their expression. Ruxolitinib a JAK1/2 inhibitor normalized interferon signature genes and all complement gene transcripts induced by SARS-CoV-2 in lung epithelial cell lines but did not affect NF-B-regulated genes. Ruxolitinib alone or in combination with the antiviral remdesivir inhibited C3a protein produced by infected cells. Together we postulate that combination therapy with JAK inhibitors and drugs that normalize NF-B-signaling could potentially have clinical application for severe COVID-19.
Published: 2021-04-07
Journal: Sci Immunol
DOI: 10.1126/sciimmunol.abg0833
DOI_URL: http://doi.org/10.1126/sciimmunol.abg0833
Author Name: Yan Bingyu
Author link: https://covid19-data.nist.gov/pid/rest/local/author/yan_bingyu
Author Name: Freiwald Tilo
Author link: https://covid19-data.nist.gov/pid/rest/local/author/freiwald_tilo
Author Name: Chauss Daniel
Author link: https://covid19-data.nist.gov/pid/rest/local/author/chauss_daniel
Author Name: Wang Luopin
Author link: https://covid19-data.nist.gov/pid/rest/local/author/wang_luopin
Author Name: West Erin
Author link: https://covid19-data.nist.gov/pid/rest/local/author/west_erin
Author Name: Mirabelli Carmen
Author link: https://covid19-data.nist.gov/pid/rest/local/author/mirabelli_carmen
Author Name: Zhang Charles J
Author link: https://covid19-data.nist.gov/pid/rest/local/author/zhang_charles_j
Author Name: Nichols Eva Maria
Author link: https://covid19-data.nist.gov/pid/rest/local/author/nichols_eva_maria
Author Name: Malik Nazish
Author link: https://covid19-data.nist.gov/pid/rest/local/author/malik_nazish
Author Name: Gregory Richard
Author link: https://covid19-data.nist.gov/pid/rest/local/author/gregory_richard
Author Name: Bantscheff Marcus
Author link: https://covid19-data.nist.gov/pid/rest/local/author/bantscheff_marcus
Author Name: Ghidelli Disse Sonja
Author link: https://covid19-data.nist.gov/pid/rest/local/author/ghidelli_disse_sonja
Author Name: Kolev Martin
Author link: https://covid19-data.nist.gov/pid/rest/local/author/kolev_martin
Author Name: Frum Tristan
Author link: https://covid19-data.nist.gov/pid/rest/local/author/frum_tristan
Author Name: Spence Jason R
Author link: https://covid19-data.nist.gov/pid/rest/local/author/spence_jason_r
Author Name: Sexton Jonathan Z
Author link: https://covid19-data.nist.gov/pid/rest/local/author/sexton_jonathan_z
Author Name: Alysandratos Konstantinos D
Author link: https://covid19-data.nist.gov/pid/rest/local/author/alysandratos_konstantinos_d
Author Name: Kotton Darrell N
Author link: https://covid19-data.nist.gov/pid/rest/local/author/kotton_darrell_n
Author Name: Pittaluga Stefania
Author link: https://covid19-data.nist.gov/pid/rest/local/author/pittaluga_stefania
Author Name: Bibby Jack
Author link: https://covid19-data.nist.gov/pid/rest/local/author/bibby_jack
Author Name: Niyonzima Nathalie
Author link: https://covid19-data.nist.gov/pid/rest/local/author/niyonzima_nathalie
Author Name: Olson Matthew R
Author link: https://covid19-data.nist.gov/pid/rest/local/author/olson_matthew_r
Author Name: Kordasti Shahram
Author link: https://covid19-data.nist.gov/pid/rest/local/author/kordasti_shahram
Author Name: Portilla Didier
Author link: https://covid19-data.nist.gov/pid/rest/local/author/portilla_didier
Author Name: Wobus Christiane E
Author link: https://covid19-data.nist.gov/pid/rest/local/author/wobus_christiane_e
Author Name: Laurence Arian
Author link: https://covid19-data.nist.gov/pid/rest/local/author/laurence_arian
Author Name: Lionakis Michail S
Author link: https://covid19-data.nist.gov/pid/rest/local/author/lionakis_michail_s
Author Name: Kemper Claudia
Author link: https://covid19-data.nist.gov/pid/rest/local/author/kemper_claudia
Author Name: Afzali Behdad
Author link: https://covid19-data.nist.gov/pid/rest/local/author/afzali_behdad
Author Name: Kazemian Majid
Author link: https://covid19-data.nist.gov/pid/rest/local/author/kazemian_majid
sha: 4999d439f376bfd55abec9904e9a421e3aa4b13a
license: cc-by
license_url: https://creativecommons.org/licenses/by/4.0/
source_x: Medline; PMC
source_x_url: https://www.medline.com/https://www.ncbi.nlm.nih.gov/pubmed/
pubmed_id: 33827897
pubmed_id_url: https://www.ncbi.nlm.nih.gov/pubmed/33827897
pmcid: PMC8139422
pmcid_url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8139422
url: https://www.ncbi.nlm.nih.gov/pubmed/33827897/ https://doi.org/10.1126/sciimmunol.abg0833
has_full_text: TRUE
Keywords Extracted from Text Content: p-value<0.0005 Non-Essential Amino Acids, 1 mM Sodium Pyruvate HEK293 DMSO C9 coronavirus C1r LPS IFN-a hBOs chromatin S2C-E GSE131300 UCSC hepatocyte-derived patient lung biopsies PBMC pneumocyte intracellular nuclear EHS STAT3 S4A C5a Bovine Serum 609.38 SARS-CoV-2-induced immune cell lungs syncytia Fig. S11A Interferon alpha/beta DSigDB lung biopsy samples ENCFF565WST C1S matrix porcine trypsin JAK-STAT1 S4C USA human IFN-α receptor S4D EDTA ENCFF137KNW La Jolla Complement factor B lung C3a fragment Fig. S3 T helper 1 Fig. 3C JAK1 AddModuleScore CD46 AT2 cells Figs. 1F-H anaphylatoxins monocyte/macrophage cells respiratory epithelial cells IRF7 liver HTB-55 10mM EGTA UMIs human bronchial epithelial cells GSE150728 Fig. S7 RNA18S5 COVID-19 patient lung tissue Cfb 10μM ACE2-transduced A549 cells thrombotic microangiopathy Fig. 7 .Viral ENCFF055YQO C3-deficient animals complement factor B deep-Tools S1A-B S2A-B S4A-B Abcam ENCFF000XLN alveolospheres c2.cp.v7.1 S3A JAK/STAT-dependent serum C3 Reserpine JAK1/2 type II pneumocyte-like serum-derived lymphoid cells baricitinib proximal avdoralimab human bronchial organoids GSM1508095 COVID-19 (12) interstitial fluids basal cells C1 proteases C1R C4d GIBCO immune cells p<0.05 750rpm blood trypsin ruxolitinib cellular A549-ACE2 cells JAK1/2-induced STAT membrane A549 C3a antibody placenta analyte SRP257667 S1B C5b C3a receptor kidney Interferon CFB myeloid Tween Max SARS-CoV1 SARS-CoV-2-induced lung cellintrinsic factor B blocking antibody pre-ranked NHBE cells type II pneumocytes SARS-CoV-2-infected cells SRAS-COV2 HEPES donors STAT1 TPM -bowtie-n 1 195.10 lung epithelial cells sepharose HepG2 liver cells C5 into C5a cell line mitochondrial IBC C5b-9 FBS CBM20Alite SARS-CoV-2 upper respiratory COVID-19 NC_002023.1 airway epithelial cells Hoechst 33342 Triton X-100 TNF L-glutamine K-562 Calu-3 cell lines Fig. 4B peripheral blood mononuclear cells monolayer Fig. 5C C5aR1 SARS-CoV-2-infected cells C3 CTO-20C column Fig. S6 CA Sino intracellular C3 convertase Cells 40143-R019 Calu-3 cells AT1 Human CD14 Dulbecco's Modified Eagle HeLa cells expressors Human CD4 + T cells bis-benzimide IFN-pathway L15SA-1 HepG2 cell/tissue extract Hoechst-33342 pentahydrate SARS-CoV-2 virus Fig. 1A AT2 AMY-101 DMEM Alexa-488 Coronavirus disease 2019 Survivors alveolar type I GSE145926 H3K27Ac C1R TCID50 ACE2 C3 and C3 GSE122960 gene_set SARS-CoV-2-driven SARS-CoV-2 induced/repressed genes NHBE USA-WA1/2020 ATCC S5A-B Janus kinase SIL-30ACMP autosampler BAL primary lung cells COVID-19 patient Fig. 6C Tween 20 IL-6 Bronchoalveolar lavage cellintrinsic C3 convertase Complement Factor B Fig. S1D competitionbased formic acid IgG1 isotype antibody pluripotent stem myeloid cells CD4 sub-cell line single cell Hycult HM2074BT-B C3 convertase C3 convertase (4 D-glucose basal/club intermediate cells Fig. S9C SARS-CoV-2 (11) intracellular C3a IAV CFH C3a CFBi human C3a epithelial cells C3aR GSK acetonitrile RSV Fig. 4D IL6 extracellular space lung cells JAK1/2-STAT1 CD14 HBECs beta coronavirus peripheral blood ACN 10ug/ml lung biopsies × IL-1β MCF-7 cells lung biopsy sC5b-9 cell lung samples patient cells anti-human C3a neo-epitope CFBi-F JAK-STAT IFN receptor leukocyte NC_045512.2 C3 convertase. gastrointestinal eculizumab K d app STAT1activating type I interferon CO2 nuclei Fig. 1E ENCODE human Fc-silent monoclonal antibody lymphoid histone 3 lysine 27 left panel human plasma lung lymphoid cells ciliated cells NR-52281 cat S8A-C SARS-CoV-2induced R-HSA-909733 Patients patient lung biopsy samples IFN monocytes ENCFF002CTG RNA28S5 C3bBb p-value<0.05 IFNα SCTransform C3b (4 GSEA iPSC lines epithelial RELA cells PCs NHBE samples FaDu cells Ruxolitinib UK RPMI 1640 TFs A118 R50AA-2 Vero E6 cells SARS-CoV-2 (Figs. 1F-H type I IFN bronchoalveolar fluid cells 308.10 club cells lectin NF-κB Calu-3 C3 JAKi human bronchial epithelial IFNs clone SPC2-ST-B2 K d app correction factor C3AR1 S4B coronavirus (SARS-CoV)-2 IFN-α/β mouse anti-nucleocapsid LC-30AD binary pumps S12A-B lung tissues alveolar epithelial type 2 cells Thermo Fisher A21121 Cell Ranger cytoplasm PBMC samples altered-self type II human pneumocytes tissue FindVariableFeatures patients serum nucleotide IFN-α surface complement factor H Fig. S2C C5 JAKi ruxolitinib A549 cells IRF9 FC>1.5 CD55 GSE147507 type I interferons nucleated cells C3b 5mM EDTA type I IFNs Human adenocarcinoma lung epithelial (Calu-3) cells BSA leukocytes iAEC2s 150mM NaCl P.P.M. SARS-CoV-2 N-protein
Extracted Text Content in Record: First 5000 Characters:Coronavirus disease 2019 (COVID)-19, a viral pneumonia caused by a beta coronavirus named severe acute respiratory syndrome coronavirus (SARS-CoV)-2, is now a pandemic. Patients with COVID-19 present variable clinical symptoms, ranging from a mild upper respiratory tract illness to a CORONAVIRUS SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation significant disease with severe and life-threatening complications, characterized by combinations of acute respiratory distress syndrome, coagulopathy, vasculitis, kidney, liver and gastrointestinal injury (1) . Survivors, and those with milder presentations, may suffer from loss of normal tissue function due to persistent inflammation and/or fibrosis. (2, 3) . The pathogenesis of COVID-19 and the causes of its variable severity are poorly understood, thus a better mechanistic understanding of the disease will help identify at-risk patients and allow for the development and refinement of muchneeded treatments. The complement system is an evolutionarily conserved component of innate immunity, required for pathogen recognition and removal (4) . The key components are complement (C)3 and C5, which circulate in their pro-enzyme forms in blood and interstitial fluids. C3 is activated through the classical (antibody signal), lectin (pattern recognition signal) and/or alternative (altered-self and tick-over) pathways into bio-active C3a and C3b via cleavage by an enzyme complex called C3 convertase. Complement factor B (CFB) is a key component of the alternative pathway C3 convertase. C3b generation triggers subsequent activation of C5 into C5a and C5b, with the latter seeding the formation of the lytic membrane attack complex (MAC) on pathogens or target cells. C3a and C5a are anaphylatoxins and induce a general inflammatory reaction by binding to their respective receptors, C3a receptor (C3aR) and C5aR1 expressed on immune cell. C3b binds its canonical receptor, CD46, which is expressed on nucleated cells and acts as both a complement regulator and a driver of T helper 1 differentiation in CD4 + T cells (5, 6) . Although the traditional view of complement is as a hepatocytederived and serum-effective system, the complement system is also expressed and biologically active within cells (7) . Patients with severe COVID-19 have high circulating levels of terminal activation fragments of complement (C5a and sC5b-9) (8) (9) (10) , which correlate to disease severity (8) . Single nucleotide variants in two complement regulators, decay accelerating factor (CD55) and complement factor H, are risk factors for morbidity and mortality from SARS-CoV-2 (11) . This is concordant with a recent report, which shows that serum C3 hyperactivation is an independent risk factor for inhospital mortality (12) . Despite these reports, the mechanisms behind the overactivation and conversion of the normally protective complement system into a harmful component of COVID-19 are currently unclear. Here, we examined the transcriptomes of respiratory epithelial cells infected with SARS-CoV-2 and found that the complement system was one of the intracellular pathways most highly induced in response to infection. C3 protein was processed to active fragments by expression of an inducible alternative pathway convertase (CFB) and that was normalized by a cell-permeable inhibitor of CFB. Interferon signaling via the JAK1/2-STAT1 pathway was principally responsible for transcription of complement genes in this setting and ruxolitinib, a JAK1 inhibitor, alone or in combination with remdesivir, an anti-viral agent, normalized this transcriptional response and production of processed C3 fragments from infected cells. To gain insights into the pathophysiologic mechanisms of COVID-19, we sourced bulk RNA-seq data from lung tissues of two patients with SARS-CoV-2 infection and uninfected controls (Table S1A) (13) . We compared the transcriptomes of patients to controls using gene set enrichment analysis (GSEA) (14) and found 36 canonical pathways curated by the Molecular Signatures Database (MSigDB) to be induced in patients compared to controls ( Fig. 1A and Table S1B ). Five of the 36 (14%) enriched pathways were annotated as complement pathways. Traditionally, complement is considered a mostly hepatocyte-derived and serum-effective system (4) . Thus, the dominance of the SARS-CoV-2-induced lung cellintrinsic complement signature was unexpected. Since the patient lung biopsy samples contained a mixed population of lung cells, we next defined the cellular source of the complement signature in the affected lungs. To this end, we examined the transcriptomes of primary human bronchial epithelial (NHBE) cells infected in vitro with SARS-CoV-2, which again identified several complement pathways as highly enriched in infected cells. In fact, hierarchical classification of enriched pathways by significance (FDR q-value) showed that complement pathways were among the most highly enriched of all pathways fo
Keywords Extracted from PMC Text: coronavirus nucleated cells lectin A549 cells IRF9 ACE2-transduced A549 cells ruxolitinib 40143-R019 C3a antibody EDTA Fig. 1E IFN-a HeLa cells lymphoid cells myeloid cat USA leukocyte iAEC2s acetonitrile PCs IFN-pathway Alexa-488 Fig. 7 CFB Dulbeccos SCTransform monocytes proximal HBECs SARS-CoV-2-induced SARS-CoV-2-driven COVID-19 (12) DSigDB HepG2 cell/tissue extract Triton X-100 A118 C3 and C3 coronavirus (SARS-CoV)-2 STAT1-activating type I interferon JAKi NF-B CFBi-F AT2 cells L-glutamine H3K27Ac cell line S3A RELA SARS-CoV-2 virus patients cells deepTools lymphoid CD46 sepharose C3 convertase IgG1 isotype antibody R50AA-2 line airway epithelial cells BD FACS ciliated cells Tween Reserpine CO2 RSV human bronchial epithelial HEK293 mitochondrial Fig. 5C STAT3 donors CD4 cell 308.10 type II pneumocytes IL6 ATCC FCS nuclei lung T helper 1 RPMI 1640 C3 convertase. STAT1 GSK C1r lung cells type I interferons Coronavirus disease 2019 bis-benzimide TCID50 CFBi, 2 M bronchoalveolar fluid cells p<0.05 lines Cfb La Jolla type I IFN S4A Calu-3 cell lines EHS Cell Ranger NC_002023.1 serum C3 STAT1/ cells PBMC IFN- receptor syncytia C5 SRAS-COV2 Interferon IFNs patients avdoralimab Ruxolitinib SARS-CoV-2 (11) nucleotide IFN- S4B HEPES immune cell serum-derived intracellular C3a epithelial Calu-3 cells C3-deficient animals surface Fig. S11A Complement factor B MCF-7 cells C3a fragment Fig. 3C right panel Fig. S1D gastrointestinal AddModuleScore cytoplasm GlaxoSmithKline p-value<0.05 IFN BSA c2.cp.v7.1 cellular human bronchial organoids Hycult HM2074BT-B lung lymphoid cells DMSO JAK1/2STAT1 ENCFF137KNW JAK1 Max hepatocyte-derived patient cells FC>1.5 Abcam single cell CD14 C3 TFs UCSC table browser SARS-CoV-2 (Figs. 1F-H club cells 750rpm IAV ENCFF565WST DMEM JAK1/2-induced STAT C4d UK human C3a S4A-B clone SPC2-ST-B2 analyte FSC CTO-20C column CBM20Alite SARS-CoV-2 induced/repressed genes chromatin alveolospheres human BAL type I IFNs Hoechst-33342 pentahydrate C1S upper respiratory S5A-B respiratory epithelial cells P.P.M. cells C3a receptor A549 AMY-101 liver C3/ LC-30AD binary pumps S2C-E GSE145926 FindVariableFeatures NHBE samples C3bBb mouse Cells C1R IC50-values GSE131300 Fig. 1A Fig. 4D Thermo Fisher A21121 S1A-B type II pneumocyte-like Calu-3 C3b (4 porcine trypsin basal/club intermediate cells STAT1/ K-562 10mM EGTA p-value<0.0005 PBMC samples ENCFF002CTG CD55 myeloid cells LPS STAT1+/+ primary lung cells C5aR1 SARS-CoV-2 N-protein NR-52281 altered-self Vero E6 cells iPSC competition-based leukocytes Fig. S2C Biolegend ENCFF055YQO CFBi complement factor B inhibitor kidney TPM Survivors Sino thrombotic microangiopathy COVID-19 patient lung tissue CA Fig. 4B membrane peripheral blood IL-6 AT1 histone 3 lysine 27 C3a complement factor B SARS-CoV-2 HepG2 liver cells matrix C5b-9 Janus kinase CFH HTB-55 D-glucose IBC ACN pluripotent stem factor B blocking antibody SRP257667 alveolar type I FBS anaphylatoxins extracellular space NC_045512.2 C3AR1 GSM1508095 RNA28S5 COVID-19 anti-human C3a neo-epitope TNF placenta GSE147507 C5a Non-Essential Amino Acids, 1 mM Sodium Pyruvate C3b monolayer Fig. S9C interstitial fluids COVID-19 patient A549-ACE2 cells human bronchial epithelial cells NHBE beta coronavirus IL-1 serum Figs. 1F-H lung tissues peripheral blood mononuclear cells patient lung biopsy samples hBOs tissue SIL-30ACMP autosampler sC5b-9 human Fc-silent monoclonal antibody S4C 5mM EDTA 1M Bronchoalveolar lavage lungs AT2 USA-WA1/2020 C3aR trypsin C9 S4D SARS-CoV-2induced S1B R-HSA-909733 S2A-B GSE150728 ENCFF000XLN immune cells 195.10 IC50/ Kdapp correction factor lung biopsies patient lung biopsies S12A-B baricitinib 1g/ml anti-CD3 antibody gene_set GSE122960 lung samples epithelial cells Fig. S6 formic acid sub-cell lung biopsy samples anti-nucleocapsid RNA18S5 C1 proteases C1R JAKi ruxolitinib Complement Factor B SARS-CoV-2-induced lung human plasma lung biopsy C5b NHBE cells IRF7 GSEA UMIs blood 609.38 monocyte/macrophage cells Bovine Serum complement factor H Hoechst 33342 Human CD14 Human adenocarcinoma lung epithelial (Calu-3) cells eculizumab FaDu cells pneumocyte Fig. 3C JAK-STAT expressors Tween 20 intracellular Patients ENCODE intracellular C3 convertase JAK/STAT-dependent RSV-infected A549 cells JAK-STAT1 alveolar epithelial type 2 cells left panel 10ug/ml lung epithelial cells L15SA-1 150mM NaCl S8A-C Human CD4+ T cells C5 into C5a GIBCO basal cells ACE2 SARS-CoV1 type II human pneumocytes nuclear
Extracted PMC Text Content in Record: First 5000 Characters:Coronavirus disease 2019 (COVID)-19, a viral pneumonia caused by a beta coronavirus named severe acute respiratory syndrome coronavirus (SARS-CoV)-2, is now a pandemic. Patients with COVID-19 present variable clinical symptoms, ranging from a mild upper respiratory tract illness to a significant disease with severe and life-threatening complications, characterized by combinations of acute respiratory distress syndrome, coagulopathy, vasculitis, kidney, liver and gastrointestinal injury (1). Survivors, and those with milder presentations, may suffer from loss of normal tissue function due to persistent inflammation and/or fibrosis. (2, 3). The pathogenesis of COVID-19 and the causes of its variable severity are poorly understood, thus a better mechanistic understanding of the disease will help identify at-risk patients and allow for the development and refinement of much-needed treatments. The complement system is an evolutionarily conserved component of innate immunity, required for pathogen recognition and removal (4). The key components are complement (C)3 and C5, which circulate in their pro-enzyme forms in blood and interstitial fluids. C3 is activated through the classical (antibody signal), lectin (pattern recognition signal) and/or alternative (altered-self and tick-over) pathways into bio-active C3a and C3b via cleavage by an enzyme complex called C3 convertase. Complement factor B (CFB) is a key component of the alternative pathway C3 convertase. C3b generation triggers subsequent activation of C5 into C5a and C5b, with the latter seeding the formation of the lytic membrane attack complex (MAC) on pathogens or target cells. C3a and C5a are anaphylatoxins and induce a general inflammatory reaction by binding to their respective receptors, C3a receptor (C3aR) and C5aR1 expressed on immune cell. C3b binds its canonical receptor, CD46, which is expressed on nucleated cells and acts as both a complement regulator and a driver of T helper 1 differentiation in CD4+ T cells (5, 6). Although the traditional view of complement is as a hepatocyte-derived and serum-effective system, the complement system is also expressed and biologically active within cells (7). Patients with severe COVID-19 have high circulating levels of terminal activation fragments of complement (C5a and sC5b-9) (810), which correlate to disease severity (8). Single nucleotide variants in two complement regulators, decay accelerating factor (CD55) and complement factor H, are risk factors for morbidity and mortality from SARS-CoV-2 (11). This is concordant with a recent report, which shows that serum C3 hyperactivation is an independent risk factor for in-hospital mortality (12). Despite these reports, the mechanisms behind the overactivation and conversion of the normally protective complement system into a harmful component of COVID-19 are currently unclear. Here, we examined the transcriptomes of respiratory epithelial cells infected with SARS-CoV-2 and found that the complement system was one of the intracellular pathways most highly induced in response to infection. C3 protein was processed to active fragments by expression of an inducible alternative pathway convertase (CFB) and that was normalized by a cell-permeable inhibitor of CFB. Interferon signaling via the JAK1/2STAT1 pathway was principally responsible for transcription of complement genes in this setting and ruxolitinib, a JAK1 inhibitor, alone or in combination with remdesivir, an anti-viral agent, normalized this transcriptional response and production of processed C3 fragments from infected cells. To gain insights into the pathophysiologic mechanisms of COVID-19, we sourced bulk RNA-seq data from lung tissues of two patients with SARS-CoV-2 infection and uninfected controls (Table S1A) (13). We compared the transcriptomes of patients to controls using gene set enrichment analysis (GSEA) (14) and found 36 canonical pathways curated by the Molecular Signatures Database (MSigDB) to be induced in patients compared to controls (Fig. 1A and Table S1B). Five of the 36 (14%) enriched pathways were annotated as complement pathways. Traditionally, complement is considered a mostly hepatocyte-derived and serum-effective system (4). Thus, the dominance of the SARS-CoV-2-induced lung cell-intrinsic complement signature was unexpected. Since the patient lung biopsy samples contained a mixed population of lung cells, we next defined the cellular source of the complement signature in the affected lungs. To this end, we examined the transcriptomes of primary human bronchial epithelial (NHBE) cells infected in vitro with SARS-CoV-2, which again identified several complement pathways as highly enriched in infected cells. In fact, hierarchical classification of enriched pathways by significance (FDR q-value) showed that complement pathways were among the most highly enriched of all pathways following SARS-CoV-2 infection (Fig. 1B). One of the cell types infected by SARS-CoV-2 are type II p
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