Single Cell RNA Sequencing of Blood and CSF of Patients with NeuroAIDS

NIH Pandemic-Era Grants

Pandemic Era Grants

2024

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Principal Investigator: Steven  Jacobson
Organization: NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE
Fiscal Year: 2024
Award: $300,000
Funding agency: National Institute of Neurological Disorders and Stroke

This project builds upon our expertise in determining if there is B and T cell clonal expansion in the cerebrospinal fluid. In the context of HIV infection this will help identify if there is an HIV reservoir in the meninges, which have a large number of macrophages and could could serve as a reservoir for the virus. We will use single cell sequencing of the cells to analyze the B and T cell receptors from a well characterized cohort of people with HIV and controls for this purpose.The diversity of the sequences will help establish clonality. This will also be compared to those in the blood of the same individuals

Terms: <AIDS Virus><Acquired Immune Deficiency Syndrome Virus><Acquired Immunodeficiency Syndrome Virus><Address><Adult T-Cell Leukemia-Lymphoma Virus I><Antibodies><Antigens><B blood cells><B cell><B cell receptor><B cells><B-Cell Antigen Receptor><B-Cells><B-Lymphocytes><B-cell><Blood><Blood Reticuloendothelial System><Brain><Brain Nervous System><CD8 Cell><CD8 T cells><CD8 lymphocyte><CD8+ T cell><CD8+ T-Lymphocyte><CD8-Positive Lymphocytes><CD8-Positive T-Lymphocytes><CDR3-region><Cell Body><Cells><Cerebrospinal Fluid><Chromium><Clinical><Clonal Expansion><Clonality><Clone Cells><Complementarity Determining Region 3><Complementarity Determining Region III><Complementary DNA><Coupled><Cr element><DNA><Deoxyribonucleic Acid><Detection><Disease><Disease Progression><Disorder><Dissection><Encephalon><Evaluation><Evolution><Frequencies><Gene Expression Monitoring><Gene Expression Pattern Analysis><Gene Expression Profiling><Genomics><HIV><HIV 1 associated neurocognitive disorder><HIV Infections><HIV associated neurocognitive deficit><HIV associated neurocognitive impairment><HIV associated neurological disease><HIV associated neurological disorder><HIV induced neurocognitive deficit><HIV induced neurocognitive impairment><HIV neurocognitive impairment><HIV-1 associated neurocognitive deficit><HIV-1 associated neurocognitive disorder><HIV-1 associated neurocognitive impairment><HIV-associated neurocognitive disorder><HTLV-1><HTLV-I><HTLV-III Infections><HTLV-III-LAV Infections><HTLV1><Human Immunodeficiency Viruses><Human T-Cell Leukemia Virus I><Human T-Lymphotropic Virus Type III Infections><Human T-lymphotropic virus 1><Immune><Immune memory><Immune response><Immunes><Immunologic Memory><Immunological Memory><Immunological response><Individual><Infiltration><LAV-HTLV-III><Laboratories><Lymphadenopathy-Associated Virus><MHC Receptor><Macrophage><Major Histocompatibility Complex Receptor><Meninges><Mφ><NIH><National Institutes of Health><Neurocognitive Impairment in HIV><Neurocognitive Impairment in HIV-1><Neurologic><Neurological><ORFs><Open Reading Frames><PASC><PBMC><Pathogenesis><Pathogenicity><Patients><Peripheral Blood Mononuclear Cell><Persons><Post Acute Sequelae of COVID19><Post Acute Sequelae of SARS-CoV-2><Post Acute Sequelae of SARS-CoV2><Post Acute Sequelae of severe acute respiratory syndrome coronavirus 2><Post-Acute Sequelae of SARS-CoV-2 Infection><Process><Protein Coding Region><Reporting><SEQ-AN><Sequence Analyses><Sequence Analysis><Single cell seq><T Cell Specificity><T-Cell Antigen Receptors><T-Cell Immunologic Specificity><T-Cell Receptor><T-Cells><T-Lymphocyte><T-cell receptor repertoire><T8 Cells><T8 Lymphocytes><TCR repertoire><Technology><Time><Transcript Expression Analyses><Transcript Expression Analysis><Type I Human T-Lymphotropic Virus><United States National Institutes of Health><Viral><Viral reservoir><Virus><Virus reservoir><Virus-HIV><Virus-HTLV-I><adverse sequelae of COVID><adverse sequelae of COVID-19><adverse sequelae of coronavirus disease><adverse sequelae of coronavirus disease 2019><analyze gene expression><anamnestic reaction><cDNA><cerebral spinal fluid><chronic COVID-19 sequelae><cohort><complementarity-determining region 3><deep sequencing><exhaustion><gene expression analysis><gene expression assay><host response><human T cell lymphoma virus I><human T cell lymphoma virus type I><human T cell lymphotropic virus  1><human T cell lymphotropic virus type 1><human T lymphotropic virus I><human T-cell leukemia virus type 1><immune system response><immunogen><immunoresponse><inflammatory environment><inflammatory milieu><long haul sequelae of COVID-19><long haul sequelae of coronavirus disease 2019><long-term sequelae of COVID-19><long-term sequelae of SARS-CoV-2><long-term sequelae of coronavirus disease 2019><long-term sequelae of severe acute respiratory syndrome coronavirus 2><lymph organ><lymphatic organ><lymphoid organ><meninge><neural inflammation><neuro-AIDS><neuro-HIV><neuroAIDS><neuroHIV><neuroinflammation><neuroinflammatory><post COVID-19 sequelae><post acute sequelae following COVID-19><post-acute sequelae following SARS-CoV-2 infection><post-acute sequelae of COVID-19><post-acute sequelae of acute COVID infection><post-acute sequelae of coronavirus disease 2019><response><response to therapy><response to treatment><scRNA-seq><secondary immune response><single cell RNA-seq><single cell RNAseq><single cell expression profiling><single cell next generation sequencing><single cell sequencing><single cell transcriptomic profiling><single-cell RNA sequencing><spinal fluid><therapeutic response><therapy response><third complementarity-determining region><thymus derived lymphocyte><tool><transcriptional profiling><treatment response><treatment responsiveness>