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Principal Investigator: Philip Murphy
Organization: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Fiscal Year: 2024
Award: $210,857
Funding agency: National Institute of Allergy and Infectious Diseases
The aim of this project is to test the hypothesis that specific chemokines and chemokine receptors drive either immunopathology or immune control of SARS-CoV-2 infection in a mouse model. The motivation for this aim is that chemokines regulate leukocyte trafficking and covid-19 disease pathogenesis involves severe immunopathology in the lung dependent on leukocyte influx. We are using huACE2 transgenic mice on a C57BL/6 background infected with the Wuhan strain of the virus as well as non-huACE2 mice infected with the MA-10 mouse adapted strain of the virus. Our goal is to test a WT LD50 dose first, screening for receptor knockouts that increase survival, since any positive results will have translational potential. Receptors that screen negative will be rescreened at an LDzero looking for protective chemokine receptors in the model. Both females and males will be tested and are expected to have differences in clinical progression of coronaviral disease and histopathology, based on other infectious disease models in mice, and differences between the sexes observed in humans infected with SARS-CoV and SARS-CoV-2. In all subsequent experiments, clinical disease progression will be assessed by virus recovery from throat swabs, blood and stool; serum antibody titers, hemograms, blood chemistries and serum cytokines before and at multiple intervals after infection; as well as physical appearance, weight loss, and progression to moribundity and survival for a month after infection. Animals will be euthanized by CO2 and cervical dislocation at the latest one-month post-infection. In our experience, to observe significant differences in survival we will need 20 mice/cohort in each experiment and repeat the experiment 3 times due to the variance in survival between experiments. These numbers should be sufficient to observe significant differences in the other clinical data as well. Fewer non-infected mice will be needed since there is expected to be less variance among these controls. In this reporting period, the results of our ko screen has revealed protective effects of Ackr1 deficiency and harmful effects of Ccr2, Ccr5 and Cxcl10 deficiency.
A secondary goal is to characterize the local immune response in cultured human lung explants infected with SARS-CoV-2. We have succeeded in collaboration with L Margolis from NICHD in establishing this system and demonstrating productive infection in epithelial cells.
In FY24, we extended our analysis of chemokine regulation of mouse-adapted SARS-CoV-2 pathogenesis. In FY23 we had reported in BioRxiv that atypical chemokine receptor 1 (Ackr1, also known as Duffy antigen receptor for chemokines/DARC) was the most highly upregulated chemokine receptor in infected lung, where it localized to endothelial cells of veins and arterioles. We have now completed screening all chemokine receptors encoded by genes located in the GWAS hospot for severe COVID-19 at human 3p21, as well as several other chemokine receptors and chemokines. Ackr1-/- mice were unique in having lower mortality after SARS-CoV-2 infection, particularly in males. ACKR1 is a non-signaling chemokine receptor that in addition to endothelium is also expressed on erythrocytes and Purkinje cells of the cerebellum. It binds promiscuously to both inflammatory CC and CXC chemokines and has been reported to control chemokine availability which may influence the shape of chemotactic gradients and the ability of leukocytes to extravasate and produce immunopathology. Of note, erythrocyte ACKR1 deficiency is fixed in sub-Saharan African populations where COVID-19 has been reported to result in low mortality compared to worldwide data. Our data suggest the possibility of a causal contribution of ACKR1 deficiency to low sub-Saharan COVID-19 mortality and identify ACKR1 as a possible drug target in the disease.
In FY24 we also contributed to work from the Notarangelo lab investigating functional T-cell responses in patients with COVID-19 and inborn errors of immunity (IEIs) who had received COVID-19 mRNA vaccine.
Using high-throughput sequencing and bioinformatics tools to characterize the T-cell receptor β repertoire signatures in 540 individuals after SARS-CoV-2 infection, 31 IEI recipients of COVID-19 mRNA vaccine, and healthy controls, we quantified HLA class I- and class II-restricted SARS-CoV-2-specific responses and also identified several HLA allele-clonotype motif associations in patients with COVID-19, including a subcohort of anti-type 1 interferon (IFN-1)-positive patients. The analysis revealed that elderly patients with COVID-19 with critical disease manifested lower SARS-CoV-2 T-cell clonotype diversity as well as T-cell responses with reduced magnitude, whereas the SARS-CoV-2-specific clonotypes targeted a broad range of HLA class I- and class II-restricted epitopes across the viral proteome. The presence of anti-IFN-I antibodies was associated with certain HLA alleles. Finally, COVID-19 mRNA immunization induced an increase in the breadth of SARS-CoV-2-specific clonotypes in patients with IEIs, including those who had failed to seroconvert. In conclusion, elderly individuals have impaired capacity to develop broad and sustained T-cell responses after SARS-CoV-2 infection. Genetic factors may play a role in the production of anti-IFN-1 antibodies. COVID-19 mRNA vaccines are effective in inducing T-cell responses in patients with IEIs.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><3p21><4q Chemokine><African><Alleles><Allelomorphs><Animals><Antibodies><Antibody titer measurement><Antigen Receptors><Antigenic Determinants><Appearance><Binding><Binding Determinants><Blood><Blood Chemical Analyses><Blood Chemical Analysis><Blood Reticuloendothelial System><Blood Serum><Blood erythrocyte><Blood leukocyte><Body Weight decreased><C-C Chemokines><C-X-C Chemokines><CC Chemokines><CO2><COVID infected patient><COVID patient><COVID positive patient><COVID-19><COVID-19 associated death><COVID-19 associated fatality><COVID-19 associated mortality><COVID-19 death><COVID-19 fatality><COVID-19 immune response><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 virus><COVID-19 virus infection><COVID19 associated death><COVID19 associated fatality><COVID19 associated mortality><COVID19 death><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 virus><CV-19><CXC Chemokines><Carbon Dioxide><Carbonic Anhydride><Cerebellum><Cervical><Chemokine Receptor Gene><Chemotactic Cytokines><Clinical><Clinical Data><CoV-2><CoV2><Collaborations><Coronavirus Infectious Disease 2019><Data><Differences between sexes><Differs between sexes><Disease><Disease Progression><Dislocations><Disorder><Dose><Drug Targeting><Drugs><Elderly><Endothelial Cells><Endothelium><Epithelial Cells><Epitopes><Erythrocytes><Erythrocytic><Euthanasia><Extravasation><Feces><Female><GWA study><GWAS><Genes><Genetic><Goals><High-Throughput Nucleotide Sequencing><High-Throughput Sequencing><Histopathology><Homologous Chemotactic Cytokines><Human><IFN><Immune><Immune response><Immunes><Immunological response><Immunomodulation><Individual><Infection><Inflammatory><Intercrines><Interferons><Knock-out><Knockout><LD-50><LD50><Leakage><Lethal Dose 50><Leukocyte Trafficking><Leukocytes><Leukocytes Reticuloendothelial System><Lung><Lung Respiratory System><Marrow erythrocyte><Marrow leukocyte><Medication><Mercy Killing><Mice><Mice Mammals><Modeling><Modern Man><Molecular Interaction><Motivation><Murine><Mus><NICHD><National Institute of Child Health and Human Development><National Institute of Children's Health and Human Development><Pathogenesis><Patients><Pharmaceutical Preparations><Pharyngeal structure><Pharynx><Play><Population><Primary Immunodeficiency><Production><Productivity><Proteome><Purkinje Cells><Purkinje's Corpuscles><RNA immunization><RNA vaccination><RNA vaccine><RNA-based vaccine><Receptor Protein><Recovery><Red Blood Cells><Red 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Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome Virus><Severe Acute Respiratory Syndrome corona virus><Severe Acute Respiratory Syndrome coronavirus><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 immune response><Severe acute respiratory syndrome coronavirus 2 infection><Severe acute respiratory syndrome related corona virus 2><Sex Differences><Sexual differences><Shapes><Site><Spillage><Swab><System><T cell response><T-Cell Receptor Beta><T-Cell Receptors beta-Chain><T-Cells><T-Lymphocyte><Techniques><Testing><Throat><Transgenic Mice><Veins><Viral><Viral Pathogenesis><Virus><Weight Loss><Weight Reduction><White Blood Cells><White Cell><Work><Wuhan coronavirus><advanced age><after COVID-19 infection><after SARS-CoV-2 infection><after SARS-CoV2 infection><after infection by SARS-CoV-2><after severe acute respiratory distress syndrome CoV-2 infection><alpha-Chemokines><antibody titering><arteriole><beta Chain Antigen T Cell Receptor><beta-Chemokines><bio-informatics tool><bioinformatics tool><blood chemistry><blood corpuscles><body weight loss><cerebellar Purkinje cell><chemoattractant cytokine><chemokine><chemokine receptor><cohort><congenital immune deficiency><congenital immunodeficiency><coronavirus disease 2019><coronavirus disease 2019 associated death><coronavirus disease 2019 associated fatality><coronavirus disease 2019 associated mortality><coronavirus disease 2019 death><coronavirus disease 2019 fatality><coronavirus disease 2019 immune response><coronavirus disease 2019 induced death><coronavirus disease 2019 induced fatality><coronavirus disease 2019 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infection><primary immune defect><primary immune deficiency><prior COVID-19 infection><prior SARS-CoV-2 infection><prior SARS-CoV2 infection><prior severe acute respiratory distress syndrome CoV-2 infection><protective effect><pulmonary><receptor><response><screening><screenings><senior citizen><serious COVID><serious COVID-19><serious SARS-CoV-2><serious coronavirus disease><serious coronavirus disease 2019><serious severe acute respiratory syndrome coronavirus 2><seroconversion><severe COVID><severe COVID-19><severe COVID19><severe SARS-CoV-2><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 fatality><severe acute respiratory syndrome coronavirus 2 induced death><severe acute respiratory syndrome coronavirus 2 induced 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pathogenesis><white blood cell><white blood corpuscle><whole genome association analysis><whole genome association studies><whole genome association study><wt-loss><β-Chemokines>