CITE-seq

Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy

The paper profiles CD8+ T cells in multiple myeloma patients to assess tumor reactivity and exhaustion, finding no evidence of tumor-experienced T cells with hallmark exhaustion or activation features.

A proteogenomic tool uncovers protein markers for human microglial states

The paper introduces a proteomic tool to identify protein markers for human microglial states and validates their utility in purification and differentiation.

Ocelli: an open-source tool for the visualization of developmental multimodal single-cell data

Ocelli is a Python tool for visualizing developmental multimodal single-cell data using diffusion-based modeling, improving computational efficiency and low-dimensional representation quality.

Islet-antigen reactive B cells display a unique phenotype and BCR repertoire in autoantibody positive and recent-onset type 1 diabetes patients

The paper identifies unique phenotypic and BCR repertoire features of pancreatic islet antigen-reactive B cells in prediabetic and recent-onset type 1 diabetes individuals compared to non-diabetic donors.

T-cell receptors identified by a personalized antigen-agnostic screening approach target shared neoantigen KRAS Q61H

The paper identifies T-cell receptors targeting KRAS Q61H neoantigen in NSCLC patients using antigen-agnostic screening and demonstrates their reactivity and potential for adoptive cell therapy.

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

The paper identifies public TCRB sequences expanded in CD or UC, associated with HLA alleles and antigen-specific immune responses, showing differential expansion in CD compared to UC and healthy controls.

Single-Cell Analysis Reveals Tissue-Specific T Cell Adaptation and Clonal Distribution Across the Human Gut-Liver-Blood Axis

The paper tracks T cell clones across gut, liver, and blood using single-cell RNA and TCR sequencing, revealing tissue-specific adaptations and limited overlap between colonic IELs and lamina propria T cells.

Engineering CD3 Subunits with Endoplasmic Reticulum Retention Signal Facilitates Allogeneic CAR T Cell Production

This paper develops a method to reduce TCR expression in CAR T cells using engineered CD3 subunits with an endoplasmic reticulum retention signal, avoiding genome editing and enabling safer allogeneic CAR T cell production.

Convergent and clonotype-enriched mutations in the light chain drive affinity maturation of a public antibody

The paper identifies clonotype-enriched mutations in the light chain of a public antibody that enhance affinity for a conserved viral epitope and increase after repeated vaccinations.

Visual quality control with CytoMDS, a Bioconductor package for low dimensional representation of cytometry sample distances

CytoMDS provides a method for visual quality control of cytometry data by representing samples in low dimensions to detect batch effects and outliers.

Unifying multimodal single-cell data with a mixture-of-experts β-variational autoencoder framework

UniVI integrates multimodal single-cell data using a mixture-of-experts β-variational autoencoder, improving cross-modal alignment and label transfer across various data types and study designs.

Mapping the peripheral immune landscape of Parkinson's disease patients with single-cell sequencing

This study uses single-cell sequencing to analyze peripheral immune cell changes in Parkinson's disease patients, identifying key immune signatures and potential biomarkers.

Single-cell multiomics reveals the distinct properties of neonatal and adult recent thymic emigrants

This study compares neonatal and adult CD8+ recent thymic emigrants using single-cell multiomics, finding distinct phenotypes and functions despite similar post-thymic maturation.

Comprehensive analysis of myeloid reporter mice

This study presents lineage tracing results from 18 myeloid-specific fate-mapping models in mouse peripheral blood and synovial tissue, validating synovial macrophage identification through flow cytometry and CITE-seq.

Detection of PCR chimeras in adaptive immune receptor repertoire sequencing using hidden Markov models

This paper introduces CHMMAIRRa, a hidden Markov model to detect PCR chimeras in AIRR-seq data, incorporating somatic hypermutation and germline references.

Scalable intracellular delivery via microfluidic vortex shedding enhances the function of chimeric antigen receptor T-cells

This study introduces hydroporation as a scalable and efficient method for delivering CAR-T cells, achieving higher yields and viability compared to traditional methods.

Learning single-cell spatial context through integrated spatial multiomics with CORAL

The paper introduces CORAL, a deep generative model for spatial multiomics data that deconvolves low-resolution data into single-cell profiles and identifies spatial domains and cell-cell interactions.

multiHIVE: Hierarchical Multimodal Deep Generative Model for Single-cell Multiomics Integration

multiHIVE integrates CITE-seq data using a hierarchical deep generative model, improving trajectory inference and gene trend identification.

Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning

This paper introduces LIgO, a software suite that simulates adaptive immune receptor repertoires with immune information to aid in developing and benchmarking AIRR machine learning methods.

Mapping cells through time and space with moscot

moscot unifies optimal transport for temporal, spatial and spatiotemporal single-cell mapping, using multimodal cost spaces and low-rank solvers to scale to 1.7 million mouse embryo cells.

Joint single-cell measurements of surface proteins, intracellular proteins and gene expression with icCITE-seq

This paper introduces icCITE-seq, a method that simultaneously measures surface and intracellular proteins and gene expression in single cells, validated in primary human T cells.

Highly potent novel multi-armoured IL13Rα2 CAR-T subverts the immunosuppressive microenvironment of Glioblastoma

This paper develops a novel CAR-T cell therapy for glioblastoma that overcomes immunosuppression and improves persistence through a multi-armoured design.

Maternal type 2 immunity promotes a microchimeric transfer of systemic type 2 immunity to offspring.

This study shows maternal type 2 immunity, independent of antigen exposure, transfers protective immunity to offspring via microchimeric cells.

Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues

This paper introduces MMoCHi, a multimodal classifier for CITE-seq data that improves immune cell subset annotation by integrating transcriptomic and proteomic data.

Temperature-based MHC class-I multimer peptide exchange for human HLA-A, B and C.

The paper introduces a temperature-based peptide exchange method for loading different peptides into MHC-I multimers for HLA-A, B, and C alleles, enabling high-throughput T cell response analysis.

CD6 Regulates CD4 T Follicular Helper Cell Differentiation and Humoral Immunity During Murine Coronavirus Infection

This study shows CD6 suppresses CD4 T cell activation and follicular helper cell differentiation during viral infection, reducing antiviral humoral immunity.

Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn's Disease

The paper uses multi-omics approaches to identify hyperactivated IFNG signaling in PCD, linking it to immune and stromal cell pathogenesis and suggesting IFNG as a therapeutic target.

BMP4 is sufficient to induce a caudal organizer

This study shows that BMP4 alone can induce a caudal organizer in zebrafish embryos and human pluripotent stem cells, replicating developmental processes seen in natural development.

Long noncoding RNA HSCHARME is altered in human cardiomyopathies and promotes stem cell-derived cardiomyocyte differentiation by splicing regulation.

This study identifies HSCHARME, a lncRNA altered in cardiomyopathies, which promotes cardiomyocyte differentiation through splicing regulation.

In vivo engineered quadrivalent CAR-macrophages break tumor barrier,remodel TME and overcome tumor heterogeneity through antigen spreading

This study develops in vivo engineered quadrivalent CAR-macrophages that break tumor barriers, remodel the TME, and overcome tumor heterogeneity through antigen spreading, achieving complete tumor regression.