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Principal Investigator: Nir Hacohen
Organization: MASSACHUSETTS GENERAL HOSPITAL
Fiscal Year: 2023
Award: $148,180
Funding agency: National Institute of Allergy and Infectious Diseases
Project Summary
The overall objective of the U19 is to discover the role of the PD-1 pathway in human immunity by studying the
effects of therapeutic PD-1 blockade on immune responses to chronic viruses (Project 1) and preventive
vaccines (Project 2). To monitor adaptive immune responses in patients, we need to track the complex
repertoire of T and B cells since clonotypes may behave differently over time and in response to infection and
therapy. While there are several methods for tracking antigen-specific lymphocytes, large volumes of blood are
needed for monitoring multiple antigens, biopsies have limited material for standard pipelines, and clonotypes
with distinct antigen receptors are not distinguished. Standard bulk sequencing of TCRs and BCRs can provide
quantitative clonotype frequencies; however, its utility is limited because the target antigens are not known for
each TCR/BCR and the activation states of each clonotype cannot be determined. Core D provides an
innovative service for tracking antigen-specific T and B cells in patient blood and tissues, allowing Projects 1
and 2 to quantify the frequency, antigen specificity and activation states of lymphocytes. Aim 1 provides an
approach to match TCRs and BCRs to antigens by sequencing antigen receptors in patient T and B cells
stimulated or tagged with viral or vaccine antigens. Aim 2 uses the more cost-effective bulk TCR- and BCR-seq
to quantify the frequencies of clonotypes in serial samples of patients treated with anti-PD-1 therapy, but takes
advantage of the results in Aim 1 to link antigen receptors from the repertoire with specific viral or vaccine
antigens. Aim 3 uses leading-edge droplet-based RNA-seq to sequence paired antigen receptor chains (TCRα
& β; IgH & IgK/L) along with thousands of mRNAs in single lymphocytes, linking functional pathways with
antigen receptors. The resulting dataset from the three Aims will be integrated to provide the frequencies,
antigen specificities and activation states of T and B cells, allowing us to test the hypothesis that anti-PD-1
therapy differentially impacts the proliferation and activation of each lymphocyte subset depending on its
antigen specificity and pre-therapy differentiation state. In short, Core D enables the monitoring of antigen-
specific lymphocytes at unprecedented resolution, and will help dissect changes in immune protection against
chronic infections (including HBV, HCV, CMV, and EBV), and influenza vaccination as result of anti-PD-1
therapy. The establishment and refinement of these approaches and creation of a Core D infrastructure will
enable interrogation of immune mechanisms and provide insights into development and durability of
immunological memory in the context of checkpoint blockade or any other immunotherapies.
Terms: <Address><Affect><Alleles><Allelomorphs><Antigen Receptors><Antigen Targeting><Antigenic Determinants><Antigens><B blood cells><B cell><B cells><B-Cells><B-Lymphocytes><B-cell><B-cell receptor repertoire sequencing><B-cell receptor sequencing><BCR repertoire sequencing><BCR seq><BCR sequencing><BCRseq><Bar Codes><Binding Determinants><Biological><Biopsy><Blast Transformation><Blastogenesis><Blood><Blood Reticuloendothelial System><Blood Sample><Blood Volume><Blood specimen><Body Tissues><Burkitt Herpesvirus><Burkitt Lymphoma Virus><CMV><Cell Body><Cell Count><Cell Number><Cells><Chronic><Clone Cells><Complex><Cytomegalovirus><Data><Data Set><Development><Differentiation Therapy><EB virus><EBV><ELISPOT><Epitopes><Epstein Barr Virus><Evolution><Exhibits><Flu vaccination><Frequencies><Gene Expression><Genes><HBV><HCMV><HCV><HHV-4><HHV4><HLA Class I Histocompatibility Antigen, A-2 Alpha Chain><HLA-A Class I Antigen 2><HLA-A Histocompatibility Type Antigen 2><HLA-A2><HLA-A2 Antigen><Hepatitis B Virus><Hepatitis C virus><Homologous Serum Hepatitis Virus><Human><Human Herpesvirus 4><IgK><Immune><Immune mediated therapy><Immune memory><Immune response><Immunes><Immunity><Immunologic Memory><Immunological Memory><Immunological response><Immunologically Directed Therapy><Immunotherapy><Individual><Infection><Infectious Mononucleosis Virus><Influenza immunization><Influenza vaccination><Infrastructure><Label><Leukapheresis><Leukocytapheresis><Link><Liver lesion biopsy><Lymphatic cell><Lymphoblast Transformation><Lymphocyte><Lymphocyte Activation><Lymphocyte Stimulation><Lymphocyte Subpopulations><Lymphocyte Subset><Lymphocyte Transformation><Lymphocytic><Major Histocompatibility Complex, Class I, A2 Antigen><Messenger RNA><Methods><Modeling><Modern Man><Monitor><PBMC><PD-1 antibody therapy><PD-1 blockade><PD-1 checkpoint pathway><PD-1 pathway><PD-1 signaling pathway><PD-1 therapy><PD1 antibody therapy><PD1 based treatment><PD1 blockade><PD1 checkpoint pathway><PD1 pathway><PD1 signaling pathway><Pathway interactions><Patients><Peripheral Blood Mononuclear Cell><Preventative vaccine><Preventive vaccine><Proliferating><Property><Prophylactic vaccination against influenza><Prophylactic vaccine><RNA Seq><RNA sequencing><RNAseq><Receptor Protein><Resolution><Role><Salivary Gland Viruses><Sampling><Services><Sorting><Specificity><Staining method><Stains><Standardization><T cell receptor repertoire sequencing><T cell receptor sequencing><T-Cell Activation><T-Cells><T-Lymphocyte><TCR repertoire sequencing><TCR sequencing><TCR-seq><TCRseq><Technical Expertise><Technology><Testing><Therapeutic Effect><Therapeutic Leukopheresis><Time><Tissue Sample><Tissues><Vaccination><Vaccine Antigen><Vaccines><Viral><Viral Antigens><Viral Receptor><Virus><Virus Receptors><aPD-1><aPD-1 therapy><aPD-1 treatment><aPD1><aPD1 therapy><aPD1 treatment><activate T cells><adaptive immune response><anamnestic reaction><anti programmed cell death 1><anti programmed cell death protein 1 checkpoint pathway><anti programmed cell death protein 1 pathway><anti programmed cell death protein 1 signaling pathway><anti-PD-1><anti-PD-1 blockade><anti-PD-1 therapy><anti-PD-1 treatment><anti-PD1><anti-PD1 blockade><anti-PD1 therapy><anti-PD1 treatment><anti-programmed cell death 1 therapy><anti-programmed cell death protein 1><anti-programmed cell death protein 1 therapy><antiPD-1><antiPD1><antigen binding><antigen bound><antigen-specific T cells><barcode><biologic><check point blockade><check point immunotherapy><check point inhibitor therapy><check point inhibitory therapy><check point therapy><checkpoint blockade><checkpoint immunotherapy><checkpoint inhibitor therapy><checkpoint inhibitory therapy><checkpoint therapy><chronic infection><cohort><cost effective><cytokine><cytomegalovirus group><developmental><enzyme linked immunospot assay><flu immunisation><host response><immune check point blockade><immune check point therapy><immune checkpoint blockade><immune checkpoint therapy><immune system response><immune therapeutic approach><immune therapeutic interventions><immune therapeutic regimens><immune therapeutic strategy><immune therapy><immune-based therapies><immune-based treatments><immuno therapy><immunogen><immunoresponse><influenza virus vaccination><innovate><innovation><innovative><insight><liver biopsy><lymph cell><mRNA><pathogen><pathway><persistent infection><programmed cell death protein 1 therapy><receptor><resolutions><response><scRNA-seq><scale up><secondary immune response><single cell RNA-seq><single cell RNAseq><single cell expression profiling><single cell transcriptomic profiling><single-cell RNA sequencing><social role><technical skills><thymus derived lymphocyte><tool><transcriptome sequencing><transcriptomic sequencing><vaccination against influenza><virus antigen><αPD-1><αPD1>