bulk RNA-seq

Cannabidiol Impairs Glucagon Trafficking and Secretion Through the Lysosomal System in Murine αTC1-6 cells

This study shows that CBD reduces glucagon secretion in mouse αTC1-6 cells by altering lysosomal trafficking and secretion pathways.

JAK1/2 Inhibition Restores Tissue Integrity by Rewiring Type 1/2 Immunity Toward Targetable IL-17 Responses

This study shows JAK1/2 inhibition reduces pathogenic immune responses and restores tissue integrity in chronic skin inflammation by shifting immunity toward IL-17 responses.

Divergent Pontine and Cerebellar Pathology in Preterm Infants With Necrotizing Enterocolitis

This study identifies divergent brain pathology in preterm infants with NEC, showing distinct cellular and molecular changes in the pons and cerebellum.

TREM2 encodes plaque macrophage plasticity to mediate atherosclerosis regression

This study identifies TREM2's role in atherosclerosis regression by enhancing efferocytosis in lipid-experienced macrophages, suggesting TREM2 as a therapeutic target for plaque stabilization.

Butyrate reverts Chlamydia pneumoniae -induced transcriptional suppression of macrophage polarization markers and promotes chlamydial clearance in macrophages

This study shows butyrate reduces C. pneumoniae genome copy numbers and enhances antibiotic efficacy in macrophages, while reversing transcriptional suppression of polarization markers and antimicrobial peptides.

The cyclin-G associated kinase (GAK) is a novel mitotic kinase and therapeutic target in diffuse large B-cell lymphoma

This paper identifies GAK as a novel mitotic kinase and therapeutic target in DLBCL, showing that GAK inhibition causes mitotic defects and that existing drugs can be repurposed for its targeting.

Genomic context tunes sequence-encoded RNA processing

The paper shows that genomic context influences RNA processing by demonstrating that introns retain splicing across ectopic positions, while cryptic polyadenylation sites are less frequently used outside their native context.

TROP2 and immune gene expression by African ancestry in triple-negative breast cancer

The paper examines TROP2 and immune gene expression differences by African ancestry in TNBC, finding no significant TACSTD2 differences by race or ancestry but a link between higher African ancestry and higher PDCD1 expression.

XRN1-dependent RNA homeostasis regulates hepatitis D virus

This study identifies XRN1 as a key regulator of HDV infection, showing it controls viral replication through dsRNA homeostasis and innate immune activation.

Multi-omics in the All Of Us Research Program expands mapping genetic mechanisms in health and disease

The paper reports on the All of Us multi-omics cohort, identifying 182,246 QTLs and demonstrating rare variant effects across proteomic and transcriptomic data.

Unravelling genomic and environmental contributions to nitrogen-use efficiency in tropical maize through Bayesian causal forests

This paper uses Bayesian causal forests to estimate the causal effect of nitrogen levels on maize traits, finding that environmental factors largely drive trait variation while genomic background influences baseline levels.

Metabolic dysfunction and metformin modify plasma extracellular vesicle signaling to prostate cancer cells

This study investigates how metabolic dysfunction and metformin affect plasma extracellular vesicle signaling to prostate cancer cells, identifying specific miRNAs and their effects on tumor progression.

Gene Embedding Hub: a standardized resource for human gene representations

The paper introduces a standardized resource of human gene embeddings derived from diverse biological data sources, enabling comparison and use across modalities.

Partial epithelial-to-mesenchymal transition mediates profound gap closure through growth and fluidization

The paper shows that growth-mediated compressive stresses drive millimeter-scale gap closure in MEC1 cells, with fluid-like tissue remodeling enhancing collective closure.

Single-cell transcriptome-wide association analysis reveals epithelial cell-specific genetic susceptibility to colorectal cancer

The paper performs single-cell transcriptome-wide association analysis to identify cell-type-specific genetic susceptibility genes for colorectal cancer, finding 546 gene-cell-type associations and 347 candidate susceptibility genes.

Multimodal Analysis of Transcriptional Regulation in the Dorsolateral Prefrontal Cortex Enhances Alzheimer's Disease Risk Gene Discovery

This study uses multimodal transcriptomic data to enhance Alzheimer's disease risk gene discovery, identifying 161 risk genes with proteomic support and an interconnected network of hub genes.

Repurposing Regulatory Toxicology Safety Data to Identify Potential Pro-Longevity Substances

This paper uses pesticide toxicity data to identify substances that improve survival and healthspan by affecting mitochondrial bioenergetics.

Sup4h5-L19 activation tagging line partially restores root hair growth in p4h5 mutant by introducing small transcriptomic changes in Arabidopsis thaliana

The paper identifies an activation-tagging line that partially restores root hair growth in a p4h5 mutant by altering gene expression, particularly at low temperatures.

Phenotypic screening in Parkinson's iPSC-dopamine neurons identifies the FASN-SREBP1 axis as a potential therapeutic target

The paper uses patient-derived iPSC-dopamine neurons to screen compounds and identifies the FASN-SREBP1 axis as a potential therapeutic target for Parkinson's disease.

Engineered trophoblast organoids recapitulate molecular and functional features of preeclampsia

This paper develops a genetically engineered trophoblast organoid model of preeclampsia that recapitulates molecular and functional features of the disease.

Farm exposure is associated with human breast milk immune profile and microbiome

The paper compares immune profiles and microbiomes of breast milk from mothers with different farm exposures to identify associations with immune development and atopic disease.

Developmental IL7/IL7R signaling in fetal resident tissue macrophages regulates adaptive responses to liver injury

This study shows that IL7/IL7R signaling during fetal development programs liver-resident macrophages, which are critical for postnatal immune responses to liver injury.

Rev-erb-alpha inhibits vascular calcification by repressing osteogenic reprogramming in atherosclerosis

This study identifies Rev-erb-alpha as a repressor of vascular calcification by inhibiting osteogenic reprogramming of vascular smooth muscle cells in atherosclerosis.

tWhEEL: a transcript-aware workflow for quantifying CRISPR knockout feasibility using transcriptome assembly

tWhEEL quantifies CRISPR knockout feasibility by integrating transcriptome data with guide RNA design and functional annotations to prioritize tractable biological functions and organisms.

THERAPY RESISTANCE IN MELANOMA DRIVES CILIOGENESIS AND GLUTAMINE/ASPARTATE METABOLISM DEPENDENCY

This study identifies a link between therapy resistance in melanoma and increased ciliogenesis and glutamine/aspartate metabolism dependency.

Evasion of Hepatic ILC1 Immunosurveillance Drives Breast Cancer Liver Metastasis

This study identifies liver-resident ILC1s as a critical barrier against breast cancer liver metastasis, showing that DR5 expression and host metabolism influence this immunosurveillance.

Trisomy 21 Perturbs Oligodendrocyte Developmental States and Oligo-Neuron Communication in Human Forebrain Assembloids

This study investigates how trisomy 21 affects oligodendrocyte development and neuron-glia communication in human forebrain assembloids, finding a shift toward a pre-myelinating state and disrupted myelination.

Siderophore-Mediated Competition Between Cystic Fibrosis Pathogens Increases Virulence Factor Production

This study shows Achromobacter spp. enhance Pseudomonas aeruginosa virulence by inducing siderophore production through iron competition in CF airways.

Integrative multi-omics re-analysis of public sequencing and metabolomics repositories defines the mucosal immune and metabolic landscape of Helicobacter pylori infection and supports CagW as a rational mRNA-LNP vaccine antigen

The paper re-analyses public multi-omics data to characterize the gastric mucosal immune and metabolic landscape of H. pylori infection and identifies CagW as a promising mRNA-LNP vaccine antigen.

Shared and Specific miRNA-mRNA in Human and Murine Acute Kidney Injury

The paper compares miRNA-mRNA profiles across human and murine AKI models to identify shared and specific molecular programs associated with different injury etiologies and biological heterogeneity.