H. Jabran Zahid

The Separable Organization of Immune Transcriptional Responses

H. Jabran Zahid

Abstract Immune function depends on coordinated responses across diverse cell types, yet the organizing principles underlying this coordination remain uncertain. Here we analyze single-cell data of peripheral blood mononuclear cells from 12 donors exposed in vitro to 90 cytokines and find that, …

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Immune Organization is Encoded in Coordinated Transcriptional Variation Across Cell Types

H. Jabran Zahid

Abstract Immune responses are often interpreted as cell type-specific transcriptional programs driven by external stimuli, with variation typically analyzed within each cell type. Here we show that immune organization is reflected in coordinated changes in gene expression across cell types within individuals, …

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HLA Alleles Imprint Distinct Biases in the Usage Preferences of TCR Vβ segments

Leonardo V. Castorina, Matthew T. Noakes, Lorenzo Pisani, Julia Greissl et autres

Abstract T cells must co-recognize peptide and HLA, yet the extent to which this specificity is shaped by germline-encoded TCR–HLA contacts versus selection during thymic development has remained difficult to quantify. Leveraging population-scale TCR β repertoires linked to donor HLA genotypes, we …

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A fundamental relationship between TCR diversity, repertoire size and systemic clonal expansion: insights from 30,000 TCRβ repertoires

H. Jabran Zahid, Damon May, Harlan Robins, Julia Greissl

Introduction: T cell receptor (TCR) diversity is essential for immune defense, yet the mechanisms underlying its decline with age and its variation among individuals remain poorly understood. These patterns are typically attributed to passive processes such as thymic atrophy and cumulative immune …

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Large-scale statistical mapping of T-cell receptor β sequences to human leukocyte antigens

H. Jabran Zahid, Ruth Taniguchi, Peter Ebert, I‐Ting Chow et autres

Introduction T-cell receptors (TCRs) interacting with peptides presented by human leukocyte antigens (HLAs) are the foundation of the adaptive immune system, but population-level analysis of TCR–HLA interactions is lacking. Methods We statistically associated approximately 106 public TCRβs to specific HLAs using TCRβ …

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A Fundamental Relationship between TCR Diversity, Repertoire Size and Systemic Clonal Expansion: Insights from 30,000 TCR β Repertoires

H. Jabran Zahid, Damon May, Harlan Robins, Julia Greissl

Abstract TCR diversity is essential for immune defense, yet the mechanisms underlying its decline with age, its dependence on sex and its variation among individuals remain poorly understood. These patterns are often attributed to passive loss from factors such as thymic atrophy …

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Antigen-driven expansion of public clonal T-cell populations in inflammatory bowel diseases

Mitchell W. Pesesky, Ramit Bharanikumar, Lionel Le Bourhis, Hesham ElAbd et autres

BACKGROUND AND AIMS: Inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis (UC), are known to involve shifts in the T-cell repertoires of affected individuals, including clonal expansion of abundant T-cell populations in CD mucosal tissue. There are also differential …

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Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels

Thomas M. Snyder, Rachel M. Gittelman, Mark R. Klinger, Damon May et autres

Introduction: T cells are involved in the early identification and clearance of viral infections and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to SARS-CoV-2 …

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The Immune-Mutation Axis of Cancer Incidence: Insights from 30,000 TCR β Repertoires

H. Jabran Zahid, Ruth Taniguchi, Marco Garcia Noceda, Harlan Robins et autres

Abstract Immunoediting posits that mutation and immunity jointly shape cancer evolution, yet their population-level interplay remains uncertain. Here we analyze T cell receptor (TCR) β repertoires from 30,000 individuals and find that TCR diversity, essential for recognizing and eliminating malignant cells, declines …

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Antigen-driven expansion of public clonal T cell populations in inflammatory bowel diseases

Mitchell W. Pesesky, Ramit Bharanikumar, Lionel Le Bourhis, Hesham ElAbd et autres

ABSTRACT Background Inflammatory Bowel Diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are known to involve shifts in the T-cell repertoires of affected individuals. These include a reduction in regulatory T cells in both diseases, increase in TNFα production in …

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Tu1742 ILEAL CROHN'S DISEASE INVOLVES BROAD AND SPECIFIC CHANGES IN THE PERIPHERAL BLOOD T CELL REPERTOIRE NOT SHARED BY OTHER IBD TYPES

Mitchell W. Pesesky, Ramit Bharanikumar, Elisa Rosati, Bernd Bokemeyer et autres

Large-scale statistical mapping of T-cell receptor β sequences to Human Leukocyte Antigens

H. Jabran Zahid, Ruth Taniguchi, Peter Ebert, I‐Ting Chow et autres

Abstract T-cell receptors (TCRs) interacting with peptides presented by human leukocyte antigens (HLAs) are the foundation of the adaptive immune system but population-level analysis of TCR-HLA interactions is lacking. Here we statistically associate ∼ 10 6 public TCRs to specific HLAs using …

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