CITE-seq

TSNR: Protein-Specific Signals with Broad Molecular Context for Spatial Protein Prediction

The paper introduces TSNR, a method for spatial protein prediction that uses protein-specific signals and broad molecular context, achieving high correlation on a benchmark.

Building virtual cell dynamics that evolve with biological measurements

CellCompass, an agentic AI system, models cell dynamics from single-cell measurements and improves predictions by integrating new biological constraints and experimental data.

A computable probability landscape for T cell receptor repertoire sampling and comparison

The paper introduces BEAM, a probability model for TCRβ sequences that enables depth-aware sampling calculations and interpretable repertoire comparison.

Stealth CAR-Tregs evade CD3 antibody therapy and skew immune responses toward regulation

This study shows that TRAC-/-CAR-Tregs survive CD3 antibody therapy better than TRAC+/+CAR-Tregs, shifting immune responses toward regulation.

Tfh dysfunction is associated with poor responses to HBV vaccination

HBV vaccine-draining lymph node biopsies tie low antibody titers to reduced, interferon-skewed GNG4+ germinal center T follicular helper cells; public B cell clonotypes did not track response.

Genetically inducible coordinators of cytokine signaling pathways for interrogating T cell motility

The paper develops CAMPs, genetically inducible receptors to control cytokine signaling in T cells, to study motility and signaling pathways without paracrine interference.

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.

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.

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.

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.

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.

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

HoloCell is a generative foundation model that integrates epigenomics, transcriptomics, and proteomics data across single-cell multi-omics modalities, demonstrating superior performance in representation learning and cross-modal generation.

Sensory neurons encode long-term inflammatory memory that promotes gastric regeneration and tumorigenesis

This paper shows that sensory neurons form long-term inflammatory memory, enhancing gastric regeneration and tumor susceptibility after injury.

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.

Human neonatal CITE-seq atlas identifies an immune transition at 32 weeks' gestation from CD15+ myeloid-dominated to interferon-primed immunity

The paper presents a CITE-seq atlas of human neonatal immune development, identifying a 32-week gestational transition to interferon-primed immunity.

Magnetic field-induced ER stress reprograms the tumor microenvironment to improve triple-negative breast cancer survival

Asha therapy induces ER stress in tumor cells, reprograms the tumor microenvironment, and improves survival in triple-negative breast cancer models.

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.

Single Cell Transcriptomics and Surface Protein Expression Reveal Distinct Cellular and Molecular Phenotypes in Human RPESC-RPE and PSC-RPE

The paper compares single-cell transcriptomic and surface protein profiles of RPESC-RPE and PSC-RPE, finding differences in gene expression and surface markers that suggest functional and immunomodulatory differences.

Programmable and Switchable RNA Scaffolds for Synthetic Condensate Engineering in Mammalian Cells

This paper develops programmable RNA scaffolds that form synthetic condensates in mammalian cells, showing that double-stranded RNA stems drive assembly and introducing an allosteric switch for reversible control.

Antigen-specificity of clonally-enriched CD8+ T cells in multiple sclerosis

Paired CSF and blood scRNA/TCR-seq in treatment-naive MS shows a small set of expanded, cytotoxic CSF-enriched CD8+ clonotypes, two of which recognize EBV epitopes.

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Single-cell and spatial maps of human coronary arteries identify FAP as a marker of SMC-derived modulated cells; an anti-FAP BiTE reduced plaque burden in mouse models.

4D multimodal wound healing atlas reveals organ-level controls of repair phase transitions

The paper presents OWHA, a 4D multimodal atlas of wound healing in mice, revealing a conserved Basal IV/SEMA3C circuit that coordinates repair, and shows its disruption in diabetic wounds.

Regulatory T cells clonally expand and contribute to stromal cell function in fibrotic response to synthetic implants

The paper identifies Treg clonal expansion and immunosuppressive functions in fibrosis induced by synthetic implants, showing their role in modulating stromal cell behavior.

Co-Stimulatory Blockade Prevents Intragraft Accrual of Class-Switched, Activated B Cells Despite Failing to Prevent T-Cell Mediated Rejection

The paper investigates the effects of co-stimulatory blockade on B cell accrual and T cell subsets during T-cell-mediated renal allograft rejection using single-cell RNA sequencing.

Cleanet: robust doublet detection in cytometry data based on protein expression patterns

Cleanet detects and classifies doublets in cytometry data using protein expression patterns, improving accuracy over traditional bivariate gating methods.

A rare HSC-derived megakaryocyte progenitor accumulates via enhanced survival and contributes to exacerbated thrombopoiesis upon aging

The paper identifies a rare HSC-derived megakaryocyte progenitor that accumulates with age, contributing to exaggerated thrombopoiesis and age-related platelet-mediated morbidities.

Simultaneous Profiling of the Blood and Gut T and B Cell Repertoires in Crohn's Disease and Symptomatic Controls Illustrates Tissue-specific Alterations in the Immune Repertoire of Crohn's Disease Patients

Antigen stimulation drives clonal expansion of latent CD4+ T cells using a full-length HIV latency reporter

This study shows antigen stimulation drives clonal expansion of latent HIV-infected CD4+ T cells through TCR and co-stimulatory signals, with IL-7 and CD28 playing key roles.

Analyzing the T cell receptor repertoire of 2,804 individuals with inflammatory bowel disease identifies public T cell responses involved in the pathogenesis

The paper identifies and validates T cell receptor clonotypes associated with Crohn's disease and ulcerative colitis, suggesting they are potential therapeutic targets.