CITE-seq

Identification of B cell subsets based on antigen receptor sequences using deep learning

This paper introduces BCR-SORT, a deep learning model that predicts B cell subsets from BCR sequences, revealing inter-individual heterogeneity in memory B cell evolution post-COVID-19 vaccination.

Gene editing of CD3 epsilon gene to redirect regulatory T cells for adoptive T cell transfer

This paper develops a non-viral CRISPR-Cas12a method to redirect Tregs with CARs by integrating an antigen-binding domain into the CD3 epsilon gene, showing improved antigen-specific function and graft protection in a mouse model.

Protein-based cell population discovery and annotation for CITE-seq data identifies cellular phenotypes associated with critical COVID-19 severity

The paper applies a flow cytometry analysis tool to CITE-seq data to identify protein-based cell phenotypes linked to critical COVID-19 severity.

Computationally accelerated identification of P-glycoprotein inhibitors

This study identifies nine novel P-gp inhibitors using a computationally accelerated drug discovery pipeline, showing they reverse multidrug resistance in cancer cells with minimal toxicity to non-cancerous cells.

Single-cell multimodal profiling of monocytes reveals diverse phenotypes and alterations linked to cardiovascular disease risks

The paper uses multimodal single-cell profiling to identify diverse monocyte subtypes and links them to cardiovascular disease risk factors.

AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes

The paper curates high-quality human immunoglobulin germline gene reference sets to improve AIRR-seq analysis accuracy and facilitate immunoglobulin gene studies.

Selective Translation Orchestrates Key Signaling Pathways in Primed Pluripotency

This study identifies EIF3D as a key regulator of primed pluripotency through selective translational control of signaling pathways and p53 regulators.

Tumor-derived hypoxic small extracellular vesicles promote endothelial cell migration and tube formation via ALS2/Rab5/β-catenin signaling

This study shows hypoxic tumor cells release extracellular vesicles containing ALS2, which activate Rab5 in endothelial cells to promote angiogenesis via β-catenin stabilization.

A Novel Therapeutic Approach using CXCR3 Blockade to Treat Immune Checkpoint Inhibitor-mediated Myocarditis

This study identifies CXCR3-CXCL9/10 axis as a therapeutic target for ICI-mediated myocarditis using mouse models and human patient data.

First-in-class Transactivator-Free, Doxycycline-inducible IL-18-engineered CAR-T cells for relapsed/refractory B-cell lymphomas

This paper develops doxycycline-inducible IL-18 CAR-T cells (iTRUCK19.18) that enhance antitumor activity while controlling IL-18 release through dual mechanisms.

Diverse competitor B cell responses to a germline-targeting priming immunogen in human Ig loci transgenic mice

The paper analyzes B cell responses to a germline-targeting immunogen in human Ig loci transgenic mice, finding diverse non-VRC01-class B cells and competitor B cells recognizing epitopes near the VRC01 epitope.

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

DiffModeler uses diffusion models to accurately model protein complex structures from low-resolution cryo-EM maps, achieving high TM-Scores across various resolutions.

CD62L-selected umbilical cord blood universal CAR T cells

This paper describes the production of CD62L-selected UCB-derived CAR T cells using machine-based manufacturing, showing high CAR19 expression and anti-leukaemic activity comparable to peripheral blood-derived CAR T cells.

Cortical microinfarcts potentiate recurrent ischemic injury through NLRP3-dependent trained immunity

This study shows that microinfarcts in mice enhance recurrent stroke severity via NLRP3-dependent trained immunity in microglia.

Machine Learning Based Modelling of Human and Insect Olfaction Screens Millions of compounds to Identify Pleasant Smelling Insect Repellents

The paper uses machine learning to predict odor valence in humans and insects, screening millions of compounds to identify pleasant-smelling insect repellents.

Chemotherapy synergizes with cancer vaccines and expands stem-like TCF1+CD8+ T cells

This study shows that chemotherapy, specifically CarboTaxol, synergizes with cancer vaccines and anti-PD-1 to improve tumor control and survival by expanding stem-like TCF1+CD8+ T cells.

Single cell analysis reveals CD45RClow/-TNFR2+CD29lowCD8+ Tregs with superior activity

The paper identifies and characterizes three subsets of human CD8+ regulatory T cells using single-cell CITE-seq and VDJ sequencing, highlighting a subset with superior suppressive activity.

Targeted inCITE-Seq Analysis Identifies the Loss of Nuclear TDP-43 in Endothelium as a Mediator of Blood Brain Barrier Signaling Pathway Dysfunction in Neurodegeneration

The paper identifies loss of nuclear TDP-43 in endothelial cells as a mediator of BBB signaling pathway dysfunction in neurodegenerative diseases using inCITE-seq.

Gravity-based microfiltration reveals unexpected prevalence of circulating tumor cell clusters in ovarian and colorectal cancer

This study introduces gravity-based microfiltration to isolate CTC clusters, finding they are prevalent in ovarian and colorectal cancer patients.

Deciphering abdominal aortic diseases through T-cell clonal repertoire of perivascular adipose tissue

The paper analyzes T-cell receptor beta diversity in perivascular adipose tissue of AAA and AOD patients, finding distinct clonal repertoires that differentiate the diseases.

Robust diagnosis of infectious disease, autoimmunity and cancer from the paratope networks of adaptive immune receptors

This paper develops a novel representation of adaptive immune receptors to improve disease classification from blood samples, achieving higher accuracy for infectious disease, autoimmunity, and cancer.

Paired single-cell multi-omics data integration with Mowgli

Mowgli integrates paired single-cell multi-omics data using a combination of NMF and OT, improving clustering and interpretability, and is benchmarked against state-of-the-art methods.

scSniper: Single-cell Deep Neural Network-based Identification of Prominent Biomarkers

scSniper identifies disease biomarkers using a deep neural network, outperforming traditional methods on real-world datasets.

Prenatal inflammation reprograms hyperactive ILC2s that promote allergic lung inflammation and airway dysfunction

Prenatal inflammation induces hyperactivated ILC2s in the developing lung, leading to increased asthma susceptibility through immune remodeling.

Intestinal cDC1s provide IL-12 dependent and independent functions required for CD4+ T cell mediated resistance to Cryptosporidium

The paper investigates the role of intestinal cDC1s in CD4+ T cell-mediated resistance to Cryptosporidium, showing they support T cell expansion and effector function through IL-12-dependent and -independent mechanisms.

Step-wise epigenetic signal integration governs adaptive programming of cytotoxic lymphocytes

This study shows that interleukin-12 signaling integrates with antigen receptor signals in a context-dependent manner to determine the epigenetic and functional fate of cytotoxic lymphocytes.

A single-cell multi-omic and spatial atlas of B cell lymphomas reveals differentiation drives intratumor heterogeneity

This study reveals that cellular differentiation drives intratumor heterogeneity in B-cell lymphomas, with distinct maturation states associated with different survival outcomes.

One infusion of engineered long-lasting and multifunctional T cells cures asthma in mice

This paper shows that engineered T cells can cure asthma in mice by targeting eosinophils and blocking inflammatory cytokines.

Yclon: Ultrafast clustering of B cell clones from high-throughput immunoglobulin repertoire sequencing data

YClon is a fast and efficient method for clonotyping Ig repertoire data, outperforming existing methods by being 30 to 5000 times faster and handling up to 2 million sequences on a standard laptop.

LSD1 inhibition improves efficacy of adoptive T cell therapy by enhancing CD8+ T cell responsiveness.

This study shows that inhibiting LSD1 enhances CD8+ T cell function in adoptive T cell therapy, leading to improved antitumor immunity and synergistic effects with anti-PDL1 therapy.