CITE-seq

A Gene-Program Architecture of Mouse T cells

The paper introduces immgenT-GP, a gene-program framework that identifies 200 reproducible gene programs in mouse T cells, capturing lineage identity, activation states, and tissue location.

Multi-omics reveals a monocyte-macrophage-fibroblast axis in post-COVID-19 fibroinflammatory lung remodelling

This study identifies a monocyte-macrophage-fibroblast axis in post-COVID-19 lung fibrosis using multi-omic profiling and shows its potential as a therapeutic target.

An immunophenotype-coupled transcriptomic atlas of mouse hematopoietic progenitors

This paper constructs a CITE-seq-based atlas of mouse hematopoietic progenitors, identifying 28 progenitor stages across eight lineages and novel surface markers.

Single-cell proteomics maps circulating monocyte dynamics in advanced head and neck squamous cell carcinoma

The paper uses single-cell proteomics to analyze circulating immune cells in HNSCC patients, revealing proteomic changes in monocytes during metastasis.

Integrative single cell analysis of CD8+ T-cells across early and advanced oral cancers reveals signatures of anti-tumour activity

This paper identifies a signature of anti-tumour activity in CD8+ T-cells across oral cancers using single-cell RNA and TCR sequencing, and develops a machine learning classifier to detect these cells from transcriptome data.

Single-cell multi-omics maps clonal IEL expansion and epithelial remodelling in refractory coeliac disease

This study identifies clonal IEL expansion and epithelial remodelling in RCD1 using single-cell multi-omics, showing distinct immune and epithelial states compared to ACD.

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.

High-avidity TCR signaling drives an NKG2A-positive CD8 T cell exhaustion state in human tumors

This study identifies high-avidity TCR signaling via NFAT as a key driver of NKG2A-positive CD8 T cell exhaustion in human tumors, with implications for immunotherapy.

Quantifying the Recoverability of V and J Genes from TCR CDR3 Sequences Using Generative Repertoire Models

This paper quantifies how much V and J gene identity can be recovered from TCR CDR3 sequences using generative models and shows that J genes are nearly determined while V genes are partially recoverable with group-level structure.

Germline-encoded V(D)J gene usage does not impose strict constraints on the epitope-specificity of T cell receptors

The study identifies over 27,000 unique epitope-reactive TCRs from immunized mice, showing that TCR diversity is not constrained by germline VJ combinations but by combinatorial pairing of segments and CDR3 sequences.

Pre-existing Th1 immunity is abrogated by ongoing recruitment of monocytic host cells that are refractory to activation

The paper shows that pre-existing Th1 immunity is overcome by monocyte-derived macrophages that create a pathogen niche, and that checkpoint blockade or depletion of these cells improves parasite control.

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.

alpha2,3-sialylation on human naive T cells restrains bispecific engager-mediated anti-tumor immunity

Desialylation enhances bispecific T cell engager responses by relieving a sialoglycan-dependent restraint in human T cells.

Unlocking Your Programmable and Creative RNA Sequence Designer with RDiffusion

RDiffusion is a generative transformer model for RNA sequence design that outperforms baselines in success rate and diversity, and was used to design therapeutic miRNA mimics for osteoarthritis.

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.

Sepsis Subtypes in Blood and Liver Define Precision Strategy for CXCR2 Blockade

The paper identifies sepsis subtypes in blood and liver and shows that CXCR2 blockade improves survival only in specific subtypes, highlighting the need for precision therapy.

Progressive deterioration of adaptive immune repertoires in Down syndrome linked to interferon hyperactivity and lymphoid tissue disorganization

This study identifies hyperactive interferon signaling and lymphoid tissue disorganization as drivers of adaptive immune dysfunction in Down syndrome across development and aging.

Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics

The paper develops a pipeline for protein-level cell annotation in human PBMCs using mass spectrometry-based single-cell proteomics and validates it on unsorted samples.

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.

Integrative AI-Enabled Virtual Cell Modeling Reveals a Clinically Relevant Latent Effector State of Human CD8 T Cells Undetectable by Conventional Analyses

The paper uses AI to model CD8 T-cell responses during ICI therapy, identifying a latent effector state that conventional methods miss.

CITE-seq of murine bone marrow plasmacytoid dendritic cells and haematopoietic progenitor cells in sepsis

The paper provides CITE-seq data of bone marrow cells from septic and sham mice to study transcriptional and surface marker changes in sepsis.

Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking

This study establishes quality control standards for single-cell proteomics through inter-laboratory benchmarking, identifying software and technical factors affecting data reliability.

Combinatorial adapter targeting enables AND-gate activation of AdCAR T cells in pancreatic cancer but reveals donor-dependent activation thresholds

This study shows that combinatorial adapter targeting in AdCAR T cells can selectively kill pancreatic cancer cells while avoiding off-tumor toxicity, but activation thresholds vary between donors.

Spatial Compartmentalization of TCR Repertoires Between Primary Melanomas and Sentinel Lymph Nodes Reveals Distinct Clonal Architectures and Shared Antigen Recognition

The paper analyzes TCR repertoires in melanoma tumors and sentinel lymph nodes to reveal distinct clonal architectures and shared antigen recognition patterns.

Safe Redosable Low-Immunogenic In Vivo CAR-T Therapy for B Cell Malignancies and Solid Tumors

This paper develops viroVbot, an in vivo CAR-T platform with reduced immunogenicity and safety, showing efficacy in treating multiple myeloma and gastric cancer through sequential redosing.

CyStainer: A transformer-based variational autoencoder for robust marker imputation in high-parameter cytometry

CyStainer imputes markers in high-parameter cytometry data without shared markers, outperforming existing methods in panel merging and dataset integration.

Context-dependent correlations mislead transcriptomic network inference in bulk and single-cell data

The paper shows that pooled correlations in transcriptomic data often reverse sign when analyzed within specific contexts, highlighting the need for context-aware reporting of correlations.