Document text
Principal Investigator: RUTH R MONTGOMERY
Organization: YALE UNIVERSITY
Fiscal Year: 2023
Award: $531,460
Funding agency: National Institute of Allergy and Infectious Diseases
Abstract
We propose single-cell technologies to quantify multiparameter immune markers that provide in-
depth single-cell data for analysis of immune responses to vaccination in our study cohorts. The
shared platforms in this service core provide efficient and reproducible profiling in support of our
research projects with greatly expanded sensitivity and cell-type specificity. To define cell
phenotypes, we will employ mass cytometry or CyTOF (Cytometry by Time-Of-Flight) for
multiparameter single-cell analysis, which uses heavy metal ions as antibody labels and provides
tremendous detail for cellular analysis of immune subsets. To further profile and correlate the
transcriptomes of targeted single cells with immunophenotype, we will employ single-cell cellular
indexing of transcriptomes and epitopes by sequencing (CITE-Seq) for circulating blood cells and
spatial-resolution proteo-transcriptomics via deterministic barcoding (DBiT-seq) in biopsies from
tissues (skin, lymph node). These transcriptomics include in depth sequencing of BCR and TCR
to investigate clonal expansion in the tissue compared to the circulation. To identify molecular
signatures of vaccine responses across our cohorts, we will use a mass spectrometry (MS)-based
MStern blotting-based serum proteomics platform for unbiased discovery of several hundred
proteins with immunological function as an excellent reflection of the immunological state.
Standardization, both at the assay and analytical levels, will allow comparisons and integration of
data across projects. The goals of Core C are to provide a unique and essential resource to
enable the comprehensive characterization of circulating immune cells from blood as well as cells
available from tissue biopsies, with comparative data by CyTOF and RNA-sequencing (RNA-seq),
and matched profiles of proteomic milieu.
Terms: <Adaptive Immune System><Antibodies><Assay><B cell receptor><B-Cell Antigen Receptor><B-cell receptor repertoire sequencing><B-cell receptor sequencing><BCR repertoire sequencing><BCR seq><BCR sequencing><BCRseq><Bar Codes><Bioassay><Biologic Assays><Biological Assay><Biopsy><Blood><Blood Cells><Blood Plasma><Blood Reticuloendothelial System><Blood Sample><Blood Serum><Blood specimen><Body Tissues><CITE sequencing><CITE-seq><CITEseq><Cell Body><Cell Communication and Signaling><Cell Signaling><Cell Surface Proteins><Cells><Cellular Immune Function><Cellular Indexing of Transcriptomes and Epitopes by Sequencing><Characteristics><Circulation><Clinical><Clonal Expansion><Cohort Studies><Collaborations><Complex><Concurrent Studies><Cytometry><Data><Data Analyses><Data Analysis><Data Banks><Databanks><Detection><Dimensions><Disease><Disorder><Expression Signature><Frequencies><Gene Expression><Gene Expression Profile><Gene Transcription><Genes><Genetic Transcription><Goals><Heavy Metals><Immune><Immune Markers><Immune response><Immunes><Immunochemical Immunologic><Immunologic><Immunologic Markers><Immunologic Subtyping><Immunological><Immunological response><Immunologically><Immunologics><Immunophenotyping><Innate Immune System><Intracellular Communication and Signaling><Investigation><Ions><Knowledge><Label><Lymph Node Reticuloendothelial System><Lymph node proper><Lymphatic nodes><Manuals><Maps><Mass Photometry/Spectrum Analysis><Mass Spectrometry><Mass Spectroscopy><Mass Spectrum><Mass Spectrum Analyses><Mass Spectrum Analysis><Measurement><Membrane Protein Gene><Membrane Proteins><Membrane-Associated Proteins><Messenger RNA><Molecular><Molecular Fingerprinting><Molecular Profiling><NIAID><National Institute of Allergy and Infectious Disease><PBMC><Pathogenesis><Pathway interactions><Peripheral Blood Cell><Peripheral Blood Mononuclear Cell><Phenotype><Plasma><Plasma Serum><Population><Process><Proteins><Proteome><Proteomics><Quality Control><R-Series Research Projects><R01 Mechanism><R01 Program><RNA Expression><RNA Seq><RNA sequencing><RNAseq><Reproducibility><Research Grants><Research Project Grants><Research Projects><Research Resources><Resolution><Resources><Reticuloendothelial System, Serum, Plasma><Sampling><Serum><Services><Signal Pathway><Signal Transduction><Signal Transduction Systems><Signaling><Site><Skin><Specificity><Standardization><Surface Proteins><T-Cells><T-Lymphocyte><Technology><Time><Tissue Sample><Tissues><Transcription><Vaccination><Vaccines><Visualization><Vulnerable Populations><Weight><acquired immune system><barcode><biological signal transduction><biomarker discovery><cell type><cellular indexing of transcriptomes and epitopes by single cell sequencing><clinical relevance><clinically relevant><cohort><comparative><computational tools><computerized tools><data depository><data integration><data interpretation><data management><data repository><data set repository><dataset repository><dimensional analysis><feeding><functional status><gene expression pattern><gene expression signature><global gene expression><global transcription profile><high dimensionality><host response><human disease><immune function><immune system response><immune-based biomarkers><immunological biomarkers><immunological markers><immunological status><immunophenotype><immunoresponse><insight><interest><lymph gland><lymph nodes><lymphnodes><mRNA><molecular profile><molecular signature><multiomics><multiple omics><new technology><novel technologies><pathway><protein expression><resolutions><response><response biomarker><response markers><shareable platform><sharing platform><single cell analysis><single cell technology><study population><thymus derived lymphocyte><transcriptional profile><transcriptional signature><transcriptome><transcriptome profiling><transcriptome sequencing><transcriptomic profiling><transcriptomic sequencing><transcriptomics><vaccine response><vaccine responsiveness><vaccine-induced response><vulnerable group><vulnerable individual><vulnerable people><weights>