T-cell and B-cell Immunology

Distribution-modeling quantifies collective Th cell decision circuits in chronic inflammation

The paper develops a mathematical framework to analyze collective immune-cell dynamics and applies it to model Th1 vs. Tfh cell fate decisions in chronic inflammation.

Modulation of antigen discrimination by duration of immune contacts in a kinetic proofreading model of T cell activation with extreme statistics.

The paper develops a stochastic model of T cell activation incorporating kinetic proofreading and finite contact duration to study antigen discrimination under extreme statistics.

A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion

The paper uses a Boolean model to analyze gene regulatory interactions in CD8+ T cell exhaustion, identifying gene expression states and pathways leading to T cell exhaustion.

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences

The paper presents a cost-effective, non-commercial protocol for normalizing TCRβ CDR3 sequencing data to correct amplification bias in bulk TCR repertoire profiling.

Transcriptional reprogramming by IL-2 variant generates metabolically active stem-like T cells

This study shows that a variant of IL-2 (IL-2v) induces a stem-like, metabolically active T-cell state with improved therapeutic potential in adoptive cell therapy.

The RNA helicase DDX39B activates FOXP3 RNA splicing to control T regulatory cell fate

This study identifies DDX39B as a regulator of FOXP3 RNA splicing, which influences T regulatory cell fate and immune tolerance, linking it to multiple sclerosis risk.

Quantitative Annotations of T-Cell Repertoire Specificity

This paper introduces TCRanno, a tool to quantify TCR repertoire specificity, revealing insights into infections, autoimmunity, and cancer through analysis of 4,195 repertoires.

Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function

The paper uses CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function, finding BATF3 as a key gene that enhances memory T cell features and improves CAR T cell therapy outcomes.

Quantifying B-cell Clonal Diversity In Repertoire Data

This study compares clone identification methods for B-cell repertoires and finds Shannon entropy to be the most robust diversity index, with alignment-free methods preferred for shorter reads.

ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intra-clonal diversities: application to human B-cell tumors

Foxn1 overexpression promotes thymic epithelial progenitor cell proliferation and mTEC maintenance, but does not prevent thymic involution

This study shows Foxn1 overexpression in TECs promotes proliferation and differentiation but does not prevent aging-related thymic involution.

Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation

This study integrates proteomic and transcriptomic data from human T-cells to show time-dependent metabolic reprogramming and divergence in gene expression during activation.

TCR_Explore: a novel webtool for T cell receptor repertoire analysis

TCR_Explore is a webtool for TCR repertoire analysis that automates quality control and analysis, enabling non-expert users to generate publication-ready figures.

Forward genetic screen of homeostatic antibody levels in the Collaborative Cross identifies MBD1 as a novel regulator of B cell homeostasis

The paper identifies MBD1 as a regulator of homeostatic IgG1 levels and marginal zone B cell differentiation through a genetic screen in Collaborative Cross mice.

Non-coding autoimmune risk variant accelerates T peripheral helper cell development via ICOS

The paper identifies a non-coding variant that increases ICOS expression, leading to more T peripheral helper cells and contributing to autoimmune diseases.

Alternative paths to immune activation: the role of costimulatory risk genes for polygenic inflammatory disease in T helper cells

This study examines how different costimulatory receptors affect T cell activation and identifies genetic risk factors for inflammatory diseases through RNA-seq and ATAC-seq in human CD4+ T cells.

Stepwise progression of beta-selection during T cell development as revealed by histone deacetylation inhibition

This study uses histone deacetylase inhibition to reveal a new stage in T cell β-selection, showing how CD28, CD5, Lef1, and CD2 coordinate to regulate the checkpoint.

Development in context: interferon response networks regulate human fetal thymic epithelial cell differentiation

This study uses single-cell transcriptomics to identify gene regulatory networks and lineage trajectories in human fetal thymic epithelial cells, revealing interferon response pathways that distinguish thymic epithelium from other anterior foregut-derived organs.

Co-stimulatory molecules decide T cell fate through regulations of their invigoration and impairment

The paper shows that differences in co-stimulatory molecule avidity lead to distinct T cell fates through variations in downstream signaling and gene expression.

High-throughput TCRB enrichment sequencing of human cord blood exhibited a distinct fetal T cell repertoire in the third trimester of pregnancy

This study analyzes the TCRB repertoire in human cord blood from 24-38 weeks gestation, finding fetal TCRB repertoires have lower diversity and shorter CDR3s compared to adults, with CDR3 length increasing with gestational age.

Reference-based comparison of adaptive immune receptor repertoires

The paper introduces immuneREF, a method to quantify immune repertoire similarity across health and disease, finding that healthy and diseased repertoires are more similar than previously thought.

TCR-pMHC complex formation triggers CD3 dynamics

This study identifies an allosteric mechanism where TCR-pMHC binding induces CD3 dynamics through conformational changes, with the TCRβ FG loop acting as a gatekeeper and the connecting peptide as a hinge.

miR-155 exerts posttranscriptional control of autoimmune regulator (Aire) and tissue-restricted antigen genes in medullary thymic epithelial cells

The paper identifies miR-155 as a posttranscriptional regulator of Aire and TRA genes in mTECs, affecting chemotaxis.

Mathematical Characterization of Private and Public Immune Repertoire Sequences

The paper quantifies the publicness or privateness of T and B cell clones using information-theoretic metrics applied to synthetic and empirical TCR data.

Low-dose IL-2 reduces IL-21+ T cells and induces a long-lived anti-inflammatory gene expression signature inversely modulated in COVID-19 patients

Mechanisms underlying the reprogramming of mouse embryonic fibroblasts to thymic epithelial cells

This study characterizes the reprogramming of mouse fibroblasts into thymic epithelial cells (TECs) by analyzing gene expression changes and identifying factors that enhance the process.

Single-cell multi-omic analysis of thymocyte development reveals drivers of CD4/CD8 lineage commitment

This study uses CITE-seq to analyze thymocyte development and identifies TCR signaling waves and the TCR/calcineurin/NFAT/GATA3 axis as drivers of CD4/CD8 lineage commitment.

Gene regulatory network of human GM-CSF secreting T helper cells

The paper identifies gene regulatory networks in human GM-CSF-secreting CD4 T cells using ATAC-seq and RNA-seq data, linking them to autoimmune disease.

Multivalent, asymmetric IL-2-Fc fusions provide optimally enhanced regulatory T cell selectivity

This paper systematically evaluates IL-2-Fc fusions to enhance Treg selectivity by exploring valency, orientation, and binding kinetics, identifying multivalency and asymmetry as key factors for improved specificity.

In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity

The paper introduces Compass, an algorithm that uses single-cell RNA-Seq and flux balance analysis to characterize metabolic states in Th17 cells, revealing a metabolic switch and novel anti-inflammatory regulators.