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Principal Investigator: Behdad Afzali
Organization: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
Fiscal Year: 2021
Award: $3,000,357
Funding agency: National Institute of Diabetes and Digestive and Kidney Diseases
In this year, we extended the concept of cell-autonomous Complement activity as driver of cell behavior into non-immune cells and infection. We found that SARS-CoV-2 infection of respiratory epithelial cells (RECs) also induces Complement gene transcription as one of the top pathways in response to the virus and such REC Complement production likely contributes to COVID-19 severity. Thus, the intracellular COMPLEMENT pathway is not immune cell-restricted but also present in multiple cell types, reflecting evolutionary conservation. This work was published in Science Immunology. Briefly, we found that viral sensing in respiratory epithelial cells was followed by recruitment of TFs downstream of the type I interferon (IFN) receptor (driven by JAK1/2-STAT1), and NF-kB. These initiated transcription of both C3 and cell-intrinsic complement factor B (CFB), representing an alternative Complement pathway for C3 protein activation within cells. C3 is potently inflammatory and its processed fragments an independent risk factor for death in COVID-19. These findings are important because they indicate that infected cells at the site of inflammation are a key source of Complement during COVID-19. They also shed light on why COVID-19 is hard to treat using COMPLEMENT inhibitors that only block plasma-derived Complement. Accordingly, we showed that cell-permeable CFB inhibitors, and inhibitors of IFN signaling, alone or with antivirals, abrogated intracellular Complement production. We proposed that combinatorial treatments to normalize this excessive response may be effective for management of hyperinflammation in COVID-19.
Since SARS-CoV2-infected lungs are a Complement-rich environment (see above) and we showed that CD4+ T cells are themselves a tissue source of Complement (annual report from 2020), we hypothesized that studying transcriptomes of Complement-activated T cells would reveal the effects of Complement on T cells. We showed that Complement induces a self-contained autocrine/paracrine vitamin D (VitD) system in T cells that is required for appropriate inflammatory T cell shut-down, permitting tissue healing to take place. This paper is currently under revision but available as pre-print. Briefly, Complement induces a cell-intrinsic VitD system permitting T cells to both activate and respond to VitD. Sensing of active VitD causes genome-wide epigenetic changes that generate new and augment existing super-enhancers, and recruit key TFs (principally VDR, c-JUN, STAT3 and BACH2) that shape the VitD response in T cells. We found, again, that BACH2 was a central TF in these events. T cells of patients with COVID-19 showed Th1 hyper-activation and evidence of dysregulation of this VitD shut-down program, indicating either a lack of substrate (VitD deficiency) and/or abnormal regulation of this system. These data may explain the epidemiologic link between vitamin D insufficiency/deficiency and risk of both developing COVID-19 and suffering mortality after infection. They are also noteworthy because they establish cross-regulation between the two main interests of our lab, Complement and the TF BACH2.
Whilst working on REC and T cell responses in COVID-19, we noted that some RNAseq reads in SARS-CoV2-infected cells aligned to both human and viral genomes, representing host-virus chimeric (HVC) transcripts. Others interpreted these as evidence of viral integration into the genome, generating great anxiety about the safety of SARS-CoV2 mRNA vaccines. DNA viruses (e.g. HBV and HPV), and retroviruses (e.g. HIV), have elaborate mechanisms for genome integration as part of their lifecycle. Not only is SARS-CoV2 a positive strand RNA virus without this machinery, but this virus has an exclusively cytoplasmic lifecycle, making genomic integration highly unlikely. We thus hypothesized that HVC reads represent in vitro artifacts of RNAseq. By analyzing RNAseq data from virally infected cells and patients with COVID-19, as well as developing a novel method for enriching RNAs containing viral sequences, we concluded that there is no compelling evidence to support integration of SARS-CoV2 into the human genome and that HVCs were most likely artifacts of RNAseq library preparation. This paper, the first to refute SARS-CoV2 integration, was published in the Journal of Virology, and accepted as cover art. These are important findings because they provide reassurance about viral integration and safety of mRNA vaccines.
We also collaborated with a number of other labs, leveraging our expertise in gene regulation and transcriptional output. Outputs from these collaborations include co-authot publications in Nature Immunology, Science, Immunity and BMC Genomics.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><AIDS Virus><Acquired Immune Deficiency Syndrome Virus><Acquired Immunodeficiency Syndrome Virus><Alpha-Beta-Omega Interferon Receptor-1><Alternative Complement Pathway><Alternative Pathway Complement Factor B><Annual Reports><Anti-Inflammatories><Anti-Inflammatory Agents><Anti-inflammatory><Antiinflammatories><Antiinflammatory Agents><Antiviral Agents><Antiviral Drugs><Antiviral Protein Alpha Type><Antivirals><Anxiety><Artifacts><Arts><Autocrine Systems><Autoimmune><Autoimmune Diseases><Autoimmune Status><Autoimmunity><Automobile Driving><BACH2><BACH2 gene><BTB and CNC Homology 2><Basal Transcription Factor><Basal transcription factor genes><Basic Leucine Zipper Transcription Factor 2><Behavior><Blood Plasma><Body Tissues><C 3-5 Converting Enzyme><C3 Proactivator><C3PA><CD4 Cells><CD4 Positive T Lymphocytes><CD4 T cells><CD4 helper T cell><CD4 lymphocyte><CD4+ T-Lymphocyte><CD4-Positive Lymphocytes><COVID disease severity><COVID infected patient><COVID patient><COVID positive patient><COVID severity><COVID-19><COVID-19 associated death><COVID-19 associated fatality><COVID-19 associated mortality><COVID-19 death><COVID-19 disease severity><COVID-19 fatality><COVID-19 induced death><COVID-19 induced fatality><COVID-19 induced mortality><COVID-19 infected patient><COVID-19 infection><COVID-19 mortality><COVID-19 patient><COVID-19 positive patient><COVID-19 related death><COVID-19 related fatality><COVID-19 related mortality><COVID-19 severity><COVID-19 virus><COVID19><COVID19 associated death><COVID19 associated fatality><COVID19 associated mortality><COVID19 death><COVID19 disease severity><COVID19 fatality><COVID19 induced death><COVID19 induced fatality><COVID19 induced mortality><COVID19 infection><COVID19 mortality><COVID19 patient><COVID19 positive patient><COVID19 related death><COVID19 related fatality><COVID19 related mortality><COVID19 severity><COVID19 virus><CV-19><CV19><CVFBb><Cell Body><Cell Communication and Signaling><Cell Lineage><Cell Signaling><Cells><Cicatrix><CoV-2><CoV2><Collaborations><Complement><Complement 3 Proactivator><Complement Factor B><Complement Inactivators><Complement Inhibitors><Complement Protein B><Complement Protein Factor B><Complement Proteins><DNA Viruses><Data><Discipline><Disease><Disorder><Enhancers><Environment><Epidemiology><Epigenetic><Epigenetic Change><Epigenetic Mechanism><Epigenetic Process><Epithelial Cells><Event><Factor B><Failure><Functional impairment><Gene Action Regulation><Gene Expression><Gene Expression Regulation><Gene Regulation><Gene Regulation Process><Gene Transcription><General Transcription Factor Gene><General Transcription Factors><Genetic Transcription><Genome><Genomics><HBV><HIV><HPV><Hepatitis B Virus><Homologous Serum Hepatitis Virus><HuIFN-Alpha-Rec><Human Genome><Human Immunodeficiency Viruses><Human Papilloma Virus><Human Papillomavirus><IFN><IFNBR><IFRC><Immune><Immune 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infection><Severe acute respiratory syndrome related corona virus 2><Shapes><Signal Transduction><Signal Transduction Systems><Signaling><Site><Source><Structure of respiratory epithelium><System><T cell differentiation><T cell response><T-Cells><T-Lymphocyte><T4 Cells><T4 Lymphocytes><Tissues><Transcript><Transcription><Transcription Factor NF-kB><Transcription Factor Proto-Oncogene><Transcription factor genes><Transcriptional Regulatory Elements><Treg><Tyrosine-Protein Kinase JAK1><VIT D><Viral><Viral Genome><Virus><Virus Integration><Virus-HIV><Virus-Retrovirus><Vitamin D><Vitamin D Deficiency><Work><Wuhan coronavirus><allergic/immunologic body system><allergic/immunologic organ system><anti-viral agents><anti-viral drugs><anti-virals><antiinflammatory><autocrine><autoimmune condition><autoimmune disorder><biological signal transduction><c jun><c-jun Gene><cell behavior><cell type><cellular behavior><combinatorial><complement pathway><corona virus disease 2019><coronavirus disease 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coronavirus disease 2019><patient with severe acute respiratory distress syndrome coronavirus 2><prevent><preventing><programs><protein activation><pulmonary><recruit><regulatory T-cells><regulatory gene><renal><renal disorder><response><severe acute respiratory syndrome coronavirus 2 associated death><severe acute respiratory syndrome coronavirus 2 associated fatality><severe acute respiratory syndrome coronavirus 2 associated mortality><severe acute respiratory syndrome coronavirus 2 death><severe acute respiratory syndrome coronavirus 2 disease severity><severe acute respiratory syndrome coronavirus 2 fatality><severe acute respiratory syndrome coronavirus 2 induced death><severe acute respiratory syndrome coronavirus 2 induced fatality><severe acute respiratory syndrome coronavirus 2 induced mortality><severe acute respiratory syndrome coronavirus 2 infected patient><severe acute respiratory syndrome coronavirus 2 mortality><severe acute respiratory syndrome coronavirus 2 patient><severe acute respiratory syndrome coronavirus 2 positive patient><severe acute respiratory syndrome coronavirus 2 related death><severe acute respiratory syndrome coronavirus 2 related fatality><severe acute respiratory syndrome coronavirus 2 related mortality><severe acute respiratory syndrome coronavirus 2 severity><social role><thymus derived lymphocyte><trans acting element><transcription factor><transcriptome><transcriptome sequencing><type I IFN receptor><type I interferon receptor><viral integration><virology><virus genome><wart virus>