CITE-seq

Human T cells employ conserved AU-rich elements to fine-tune IFN-γ production

This study shows that AU-rich elements in the IFNG 3UTR regulate IFN-γ production in human T cells, with ARE deletion increasing sustained cytokine production and anti-tumor responses.

Comprehensive analysis of antiviral adaptive immunity formation and reactivation down to single-cell level

The paper tracks T-cell clone dynamics and TCR repertoire changes after primary and secondary yellow fever vaccination using single-cell RNAseq and TCRseq.

Syncytins enable novel possibilities to transduce human or mouse primary B cells and to achieve well-tolerated in vivo gene transfer

This paper demonstrates that syncytins can pseudotype lentiviral vectors for efficient B cell transduction and reduced in vivo immunogenicity.

Large-scale Analysis of 2,152 dataset reveals key features of B cell biology and the antibody repertoire

This study analyzes 2,152 antibody repertoires to identify key features of B cell biology, revealing gene usage patterns, sex preferences, and mutability mechanisms in the antibody repertoire.

A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells

The paper introduces totalVI, a probabilistic framework for analyzing CITE-seq data by jointly modeling RNA and protein measurements, addressing technical noise and enabling batch correction.

Detection and quantification of GPCR mRNA: An assessment and implications of data from high-content methods

The paper compares methods for detecting and quantifying GPCR mRNA expression, finding RNA-seq and TaqMan arrays outperform microarrays in accuracy and correlation with functional outcomes.

Efficient CRISPR/Cas9 gene ablation in uncultured naive mouse T cells for in vivo studies

This paper demonstrates efficient CRISPR/Cas9 gene ablation in uncultured naive mouse T cells for in vivo studies, showing gene deletion occurs independently of T cell activation.

Engineering of Chimeric Antigen Receptor T Cells with integrin αEβ7 Results in Augmented Therapeutic Efficacy against E-cadherin positive tumor

This study shows that engineering CAR-T cells with CD103 improves their anti-tumor efficacy against E-cadherin positive tumors by enhancing infiltration, expansion, and persistence in vivo.

Immune Profiling of Atherosclerotic Plaques Identifies Innate and Adaptive Dysregulations Associated with Ischemic Cerebrovascular Events

The paper identifies immune dysregulations in atherosclerotic plaques linked to ischemic cerebrovascular events using single-cell analyses of T cells and macrophages.

A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level

The paper introduces a targeted multi-omic approach that measures protein and low abundance transcript expression on single cells, requiring less sequencing depth than whole transcriptome methods.

The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes

The paper estimates the distribution of clone sizes in the human naive T-cell receptor repertoire and finds that while most clones are small, some large clones exist due to peripheral selection.

Comprehensive integration of single cell data

Seurat v3 finds scored mutual-nearest-neighbor anchors in canonical correlation space to integrate scRNA-seq batches and transfer labels, protein levels and transcriptome-wide expression across modalities.

Clonal replacement of tumor-specific T cells following PD-1 blockade

This study tracks T cell clonal dynamics before and after PD-1 blockade in cancer patients, finding that new T cell clones, not pre-existing ones, expand in response to treatment.

Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity

The paper evaluates how CDR3 sequence similarity can balance sensitivity and specificity in distinguishing TCR groups, showing it effectively classifies repertoires by antigen specificity and pathology.

SISUA: SemI-SUpervised generative Autoencoder for single cell data

The paper introduces a semi-supervised generative model for single-cell data using CITE-seq protein counts to improve gene expression analysis.

Genetic modification of primary human B cells generates translationally-relevant models of high-grade lymphoma

This study generates synthetic lymphoma models by genetically modifying primary human B cells to investigate oncogenic mutations in DLBCL.

Viral infection overcomes ineffectiveness of anti-tumoral CD8+ T cell mediated cytotoxicity

This study shows that viral infection can restore MHC-I expression and enhance T cell function, leading to tumor regression in a mouse melanoma model.

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

OLGA calculates amino acid sequence generation probabilities for B- and T-cell receptors using dynamic programming, showing agreement with published data and potential for vaccine design.

Precursor miRNAs are trafficked along axons associated with vesicles and locally processed to regulate growth cone steering

The paper shows that precursor miRNAs are transported along axons, processed into mature miRNAs, and regulate growth cone steering by inhibiting TUBB3 translation.

Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay

The paper introduces ECCITE-seq, a method that simultaneously captures transcriptomes, immune clonotypes, surface markers, sample identity, and CRISPR perturbations from single cells.

Multifaceted influence of pre-mitotic cytotoxicity of primed CD8 T cells on immunity and infection

This study investigates how pre-mitotic cytotoxic CD8 T cells (PMCs) influence immune responses and infection outcomes by killing antigen-bearing dendritic cells.

High-throughput determination of the antigen specificities of T cell receptors in single cells

This paper introduces TetTCR-Seq to link TCR sequences to their antigens in single cells and identifies neo-antigen-specific TCRs with no cross-reactivity.

Reprogramming the antigen specificity of B cells using genome-editing technologies

This study reprograms B cells to express HIV-specific BCRs by editing immunoglobulin genes with CRISPR-Cas9, enabling improved anti-HIV neutralizing activity.

Therapeutic blockade of Activin-A improves NK cell function and anti-tumor immunity

This study shows Activin-A inhibits NK cell function, promotes transdifferentiation into ILC1-like cells, and suppresses anti-tumor immunity, with therapeutic blockade improving outcomes.

T cell immunity does not age in a long-lived rodent species

This study compares T cell receptor diversity across species, finding that long-lived rodents maintain stable TCR diversity with age, unlike humans and mice.

Strong selection of a few dominant CD8 clones in a TLR7-dependent autoimmune mouse model

The paper identifies strong clonal selection of CD8+ T cells in TLR7tg mice, with some clones reaching 30% of the repertoire, suggesting impaired anti-viral responses in autoimmune disease.

Mice developing mammary tumors evolve T cell sequences shared with human breast cancer patients

The paper tracks TCR repertoire evolution in mice with mammary tumors and finds shared tumor-exclusive TCR sequences with human breast cancer patients.

Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells

MetaCyto enables meta-analysis of flow and mass cytometry data, revealing racial differences in immune cell populations across 2926 samples.

Plasmodium-specific atypical memory B cells are not part of the long-lived memory response

The paper shows Plasmodium-specific atypical memory B cells are short-lived and disappear after infection resolution, not part of the long-lived memory response.

Single-cell Map of Diverse Immune Phenotypes Driven by the Tumor Microenvironment

The paper maps immune cell phenotypes in breast cancer using single-cell RNA-seq and identifies continuous tumor-specific expansions driven by environmental cues.