cell-cell communication

Uncovering Viral Signals Across Cell Populations in Colorectal Cancer

This study maps viral RNA signals across cell types and tissues in colorectal cancer, identifying significant viral associations with specific cell types and tissue conditions.

IL13 critically contributes to the antitumor activity of polyfunctional CD4+ T cells driven by constitutively active Stat5

This study identifies IL13 as a critical cytokine for the antitumor activity of polyfunctional CD4+ T cells modified with constitutively active Stat5, showing its role in enhancing immune responses and tumor control.

Comparative larval single-cell transcriptomics provides insights into the evolutionary origins of sensory-neural programmes in Porifera and Cnidaria

The paper compares larval single-cell transcriptomes of sponges and cnidarians to explore the evolutionary origins of neural and sensory cell types.

Age-associated repression of HNF4α is a driver and potential therapeutic target in liver metabolic dysfunction

This study identifies age-associated repression of HNF4α as a driver of liver metabolic dysfunction and shows that restoring HNF4α can reverse some age-related liver defects.

Cholinergic modulation engages a CHRM1-IL-17 neuroimmune axis to promote diabetic wound repair

The paper identifies a CHRM1-IL-17 neuroimmune axis that promotes diabetic wound healing through cholinergic modulation and local AChE inhibition.

Single-cell multi-omics identify OTP and NOVA1 as regulators of leptin action in hypothalamic feeding circuits

This study uses single-cell multi-omics to identify OTP and NOVA1 as key regulators of leptin action in hypothalamic feeding circuits, revealing cell-type-specific transcriptional and regulatory changes.

A single-cell transcriptomic atlas of paper wasp brains highlights Kenyon cells' role in social behavior

The paper uses single-cell transcriptomics to analyze brain cells in paper wasps, showing that Kenyon cells vary with social roles and respond to social interactions.

Regenerative epithelial spike cells instruct immune niche homeostasis in zebrafish fin epidermis

The paper identifies a novel epithelial cell type in zebrafish fins, spike cells, and shows their role in maintaining immune cell niche homeostasis through interactions with mpeg1+ immune cells.

Multicellular Perturb-seq Reveals Lineage-Specific Transcriptional Control During Human Cardiac Organoid Development

This study uses Perturb-seq with CRISPRi to analyze how cardiac and vascular transcription factors coordinate lineage commitment and cross-lineage signaling in human cardiac organoids.

Single-Cell Transcriptomics Reveals Tumorigenic Lineages and Interactions Persisting and Evolving From Premalignancy to Cancer in the Stomach

The paper uses single-cell transcriptomics to track molecular changes from premalignancy to cancer in gastric tissue, identifying persistent and evolving tumorigenic lineages and markers like EMB.

LCN2+ Astrocytes Mark a Pro-inflammatory Astrocyte State Associated with Secondary Brain Injury After Cerebral Venous Thrombosis

Clonally Convergent Tph/Tfh-like CD4+ T Cells are Shared Across Recovery and Recurrence in Experimental Periodontitis

The paper identifies clonally convergent Tfh/Tph-like CD4+ T cells that persist in the mucosa after recovery from periodontitis and contribute to recurrence.

Aging activates latent enhancers that can be reversed withexercise

This study identifies age-acquired enhancers in mouse hearts and shows that exercise can reverse their activation.

Single-Cell RNA Sequencing Reveals Distinct Cellular and Molecular Features of Steroid-Induced Osteonecrosis of the Femoral Head Compared to Alcohol-Induced Osteonecrosis and Hip Osteoarthritis

This study uses single-cell RNA sequencing to compare cellular and molecular features of steroid-induced and alcohol-induced osteonecrosis of the femoral head with hip osteoarthritis, identifying distinct immune and stromal cell signatures.

Uncovering cross-signal interactions in single-cell and spatial omics

CRISP identifies and localizes interactions between biological signals in single-cell and spatial transcriptomic data, revealing their effects on tissue function and gene regulation.

A fibroblast-CD8+ T cell circuit drives a Type 1 shift in allergic inflammatory memory

This study identifies a fibroblast-CD8+ T cell circuit that drives a Type 1 immune shift in allergic inflammatory memory through mechanistic and translational analysis in murine and human models.

Early Progression Cells mark a stem-like state associated with pancreatic cancer initiation and progression

The paper identifies Early Progression Cells (EPCs) as stem-like cells in pancreatic cancer that drive progression and are associated with specific gene programs and interactions.

Comparative molecular analysis of histopathologic subtypes reveals shared epithelial remodeling yet distinct fibroblast programs in scleroderma lung disease

This study compares molecular features of SSc-NSIP and SSc-UIP with IPF, finding shared epithelial changes and distinct fibroblast programs.

Distinct processing of visual motion by transcriptomic cell types in the superior colliculus

The paper identifies how three transcriptomic cell types in the superior colliculus process visual motion with distinct feature selectivity, morphology, and connectivity.

irAEGIS: Pathway-guided interpretable prediction of immune-related adverse events

irAEGIS predicts immune-related adverse events from pre-treatment scRNA-seq data using a pathway-guided interpretable model, outperforming existing methods and identifying biologically relevant immune programs.

KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells

This study assesses whether hydroquinone induces aneuploidy in hematopoietic stem cells using KaryoTap and FISH, finding no reproducible increase in whole-chromosome aneuploidy.

Loss of stromal VEGFR2 protects against ischemic acute kidney injury by preserving the renal microvasculature

This study shows that loss of stromal VEGFR2 protects against ischemic AKI by preserving the renal microvasculature through enhanced endothelial function and communication.

NEPTUNE: a neuronal cell death pathway prediction tool used to decipher neurodegeneration using single cell RNA-seq datasets

NEPTUNE identifies neuronal cell death markers from single-cell RNA-seq data, revealing non-apoptotic mechanisms in photoreceptor degeneration in rd1 mice.

GraphExperiment: infrastructure for high-dimensional quantitative data and associated networks in R/Bioconductor

GraphExperiment provides an R/Bioconductor package to store and manipulate high-dimensional quantitative data alongside associated networks in a unified framework.

Pathological levels of α-synuclein increase basal mitophagy in Parkinson's dopamine neurons

This study shows that elevated α-synuclein increases basal mitophagy in Parkinson's dopamine neurons, leading to mitochondrial dysfunction and neuronal activity deficits, which can be reversed by DRP1 inhibition.

Single-nucleus transcriptomics links telencephalic cell signatures to ocean acidification effects on social behaviour in a coral reef fish

The paper uses single-nucleus transcriptomics to identify neural cell type responses to elevated CO2 in cleaner wrasse, revealing disruptions in myelination, glutamatergic signalling, and cell-cell communication.

Regionalisation of muscle nucleus heterogeneity in foetal skeletal muscle

The paper identifies transcriptionally distinct muscle nuclei in fetal chicken limb muscles, showing tip and central domain identities and signaling roles in muscle development.

Elevated mitochondrial metabolism in Down syndrome iPSCs reduces commitment to neuroectoderm

This study shows that increased mitochondrial metabolism in Down syndrome iPSCs impairs neuroectoderm commitment by reducing ciliation, and this effect can be reversed by inhibiting mitochondrial calcium uptake.

De novo lipogenesis controls antigen presentation and metastatic immune escape in triple-negative breast cancer.

FASN-driven lipogenesis sustains EGFR palmitoylation and PI3K-AKT-mTOR signaling, suppressing tumor MHC-I antigen presentation; blocking it curbs TNBC metastasis in mice via CD8 T cell recognition.

Keratin 17 Defines an Epithelial-Mesenchymal Transition-Associated Migratory Cell State in Pancreatic Ductal Adenocarcinoma

This study identifies K17 as a marker of an EMT-associated migratory cell state in PDAC, showing its role in promoting tumor-cell migration and poor prognosis.