CITE-seq

NK Cells Engineered with a Chimeric Antigen Receptor Delay HIV Rebound and Reshape HIV Reservoir Composition

This study shows that engineered NK cells with a CD4-based CAR delay HIV rebound and alter the reservoir's composition in humanized mice.

Single-Cell Sequencing in Pediatric Acute Leukemia: A Systematic Review of Biologic Insights and Translational Potential

This review evaluates single-cell sequencing findings in pediatric acute leukemia, highlighting insights into clonal evolution, chemoresistance, and immune dynamics, while noting limitations in study design and bias.

A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

Evidence for reduced somatic T-cell receptor sequence diversity profiles among Midwestern Amish in an aging cohort study

The paper examines T-cell receptor sequence diversity and HLA alleles in Midwestern Amish participants to explore associations with Alzheimer's disease and cognitive status.

Cross-species molecular stratification enables T cell receptor diagnosis of Parkinson's disease

This paper stratifies Parkinson's disease patients using T-cell receptor repertoires and develops classifiers that achieve high AUC for subtype diagnosis.

Single-Cell Multi-Omics Dissects Transcript Isoform and Immune Repertoire Dynamics in Human Immunosenescence

This study uses single-cell multi-omics to analyze transcript isoform and immune repertoire changes in aging human immune cells, identifying age-related molecular features in T cells and B cells.

Humanized FLT3 mice display enhanced tissue engraftment and support HIV-1 persistence and rebound

This study introduces a novel humanized FLT3 mouse model that supports enhanced development of human innate immune cells and HIV-1 persistence, mimicking human viral reservoirs.

Intragenic Transcription from Defective HIV Proviruses Triggers Interferon Responses in Myeloid Cells

This study shows defective HIV proviruses trigger type I interferon responses in myeloid cells through MDA5-dependent pathways, contributing to chronic inflammation in people with HIV.

TSTScope Unifies Single-Cell Multi-Omics to Identify Functional T Cell States Predictive of Immunotherapy Response

TSTScope integrates single-cell transcriptomics and T-cell receptor data to identify functional T cell states predictive of immunotherapy response, finding that functional state, not abundance, determines treatment outcomes.

Interpretable Integration of CITE-seq RNA and ADT Profiles Without Explicit Modality-Weight Tuning via Tensor Decomposition-Based Unsupervised Feature Extraction

The paper introduces a tensor decomposition method for integrating CITE-seq RNA and ADT data without modality-weight tuning, showing competitive but not superior performance compared to existing methods.

Meditope-Enabled Chimeric Antigen Receptors Facilitate Plug-and-Play Control of T Cells

This study develops meditope-enabled CARs to improve T cell functionality and address tumor heterogeneity in CAR therapy.

Helminth infection induces neuroimmune remodeling and clinical remission in a mouse model of multiple sclerosis

This study shows that helminth infection reduces CNS inflammation and demyelination in a mouse model of multiple sclerosis by promoting Th2 cells.

The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors

The paper introduces a data portal and open-source tools for single-cell transcriptomics of pediatric tumors, providing uniformly processed RNA-seq data and metadata from over 700 samples across 55 cancer types.

Directing fratricide within T cell products using an anti-uPAR chimeric antigen receptor to drive the production of potent therapeutic cells

This paper introduces a method to enhance T cell therapy by using a CAR targeting uPAR to eliminate dysfunctional T cells through directed fratricide.

Antigen-reactive CD4+ T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation bias

This study identifies antigen-reactive CD4+ T cells after SARS-CoV-2 vaccination using single-cell RNA and TCR sequencing, revealing phenotypic differences between stimulated and unstimulated states.

Dendritic cells accelerate CAR T cells in irradiated tumors through chimeric synapses

This study shows dendritic cells enhance CAR T cell persistence in irradiated tumors by antigen-dressing and stimulating CAR T cells through chimeric receptors.

CD4+ T cells promote fibrosis during metabolic dysfunction-associated steatohepatitis

This study identifies CD4+ T cells as drivers of fibrosis in MASH by showing their proinflammatory activity and the therapeutic potential of targeting the OX40L-OX40 axis.

Cross-modal Denoising and Integration of Spatial Multi-omics data with CANDIES

CANDIES denoises and integrates spatial multi-omics data using a conditional diffusion model and contrastive learning, improving downstream analysis tasks.

Targeting PD-1+ T-cells with Chimeric Antigen Receptors to reduce the HIV Reservoir

This study designs PD-1-targeting CAR-T-cells to reduce the HIV reservoir by depleting specific T-cell subpopulations in HIV-infected humanized mice.

Clonal overlap and convergent clustering of T-cell receptor signatures in Crohn's disease in monozygotic twins

This study analyzes T-cell receptor repertoires in monozygotic twins with and without Crohn's disease, finding increased TCR overlap in concordant pairs and identifying eight novel TCR clusters potentially linked to the disease.

Genotype-immunophenotype relationships in NPM1-mutant AML clonal evolution uncovered by single cell multiomic analysis

This study uses single-cell multiomic analysis to reveal genotype-immunophenotype relationships and clonal evolution in NPM1-mutant AML across disease stages.

Tracking antigen-specific T cell response to cancer immunotherapy

The paper develops a pipeline to identify and track antigen-specific T cell responses to cancer immunotherapy in mice using TCR repertoire analysis.

Explainable Graph Learning for Multimodal Single-Cell Data Integration

SCPRO-VI integrates multi-omic single-cell data using a variational graph auto-encoder and biologically guided metrics, improving subcluster identification.

Longitudinal TCR repertoires in ulcerative colitis patients show features distinguishing disease states

This study analyzes TCR repertoires from ulcerative colitis patients over time, identifying Vβ gene usage and K-mer enrichment differences between flare and remission states.

Tissue-specific clonal selection and differentiation of CD4+ T cells during infection

This study uses TRACK mice to show tissue-specific clonal selection and differentiation of CD4+ T cells during influenza infection, revealing organ-specific transcriptional programs and memory formation patterns.

HIV-SEQ REVEALS GLOBAL HOST GENE EXPRESSION DIFFERENCES BETWEEN HIV-TRANSCRIBING CELLS FROM VIREMIC AND SUPPRESSED PEOPLE WITH HIV

The paper develops HIV-seq to capture HIV transcripts for scRNA-seq, revealing distinct transcriptional features of HIV-transcribing cells in viremic and ART-suppressed HIV patients.

Antibody responses against bacterial glycans affinity mature and diversify in germinal centers.

The paper shows that glycan-specific B cells undergo class-switching and diversification in germinal centers with age and infection, influencing vaccine design.

Adult mice with neonatal-like T cell subsets exhibit increased susceptibility to Bordetella pertussis and influenza infection

This study shows that adult mice with neonatal-like T cell subsets are more susceptible to Bordetella pertussis but not influenza, highlighting the role of thymic development in immune responses.

Partially Shared Multi-Modal Embedding Learns Holistic Representation of Cell State

APOLLO learns shared and modality-specific information from multi-modal single-cell data to improve understanding of cell state and regulatory mechanisms.

Identification of a type 1 diabetes-associated T cell receptor repertoire signature from the human peripheral blood

The paper identifies TCR subsequence motifs associated with type 1 diabetes using deep learning and shows their enrichment in T1D individuals based on HLA risk alleles.