Genetics

Comprehensive tumour-immune profiling reveals TREM2+ tumour-associated macrophages facilitating lymph node metastasis in head and neck squamous cell carcinoma.

BACKGROUND: Lymph node (LN) metastasis is a well-established independent prognostic factor in head and neck squamous cell carcinoma (HNSCC). Formation of suppressive tumour immune microenvironment (TIME) is a major contributor to tumour immune evasion and metastasis. However, the TIME landscape underlying LN-metastatic HNSCC remains poorly elucidated. METHODS: A total of 688 866 single-cell transc...

Identifying a conserved transcriptional signature of drought and salt stress in Arabidopsis thaliana through meta-analysis, consensus network analysis, and deep learning.

Understanding plant responses to abiotic stress is critical for improving stress resilience. Here, we performed an integrative analysis that uniquely converges three synergistic approaches: meta-analysis, consensus network analysis, and deep learning on Arabidopsis thaliana transcriptomic datasets under drought and salt conditions, comprising 64 samples across multiple studies. This novel framewor...

Comprehensive bioinformatic analysis and experimental validation identify MT1M and MT1X as key metallothioneins in BC pathogenesis.

BACKGROUND: Metallothioneins (MTs) are crucial metal-binding proteins involved in cellular zinc homeostasis and oxidative stress response. However, th...

Contrastive learning of dynamic processing body formation reveals undefined mechanisms of approved compounds.

Membraneless organelles (MLOs) are liquid-like compartments that organize cellular functions through liquid-liquid phase separation of proteins and RN...

Disulfidptosis in osteoarthritis: Role of SLC2A3 downregulation and potential therapeutic implications.

OBJECTIVE: Disulfidptosis is a newly recognized form of regulated cell death characterized by actin cytoskeleton collapse under disulfide stress. Rece...

CYP2C19 genotype-guided dosing of proton pump inhibitors: progress in clinical trials and real-world use.

INTRODUCTION: Proton pump inhibitors (PPIs) are widely used to treat acid-related disorders; however, treatment response varies significantly due to C...

A novel signature of palmitoylation for predicting prognosis and therapeutic response of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) represents an extremely complex and heterogeneous malignant tumor. Protein palmitoylation, a highly conserved and pivot...

Th17-related genes PGAP1 and TMBIM1 serve as potential diagnostic and predictive biomarkers in systemic sclerosis: bioinformatic identification and murine model validation.

BACKGROUND: T helper 17 (Th17) cells participate in all pathological stages of systemic sclerosis (SSc). Molecular markers associated with Th17 cells ...

Metabolomic-driven prediction of the mutational status of healthy individuals with a family history of hereditary breast and ovarian cancer syndrome: the HRRmet study.

Pathogenic variants (PVs) identified in genes involved in the DNA homologous recombination repair (HRR) mechanism are the main cause of hereditary bre...

Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis.

Chronic obstructive pulmonary disease (COPD) is characterized by chronic airway inflammation and is closely linked to oxidative stress. This study aim...

PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.

Alternative polyadenylation (APA) is a pervasive RNA-processing mechanism in eukaryotes that significantly promotes transcriptome and proteome diversi...

Emerging roles of artificial intelligence/machine learning (AI/ML) towards new understandings in molecular crosstalk between circRNA-CUL3-TKI to resensitize chemoresistant cancers.

Cancer arises and is resistant to therapy via intricate molecular networks that are poorly characterised. While individually, Cullin-3 (CUL3) and circ...

A novel explainable deep-learning approach for network analysis of epistatic interactions.

Epistatic interactions of gene loci often determine complex trait phenotypes and may indicate the underlying molecular mechanisms of traits and diseas...

Advancing climate-resilient livestock systems: Next-generation emission mitigation strategies and integrated technological innovations.

Livestock production significantly contributes to global greenhouse gas (GHG) emissions, particularly methane (CH₄), nitrous oxide (N₂O), and carbon d...

Circulating tumor DNA dynamics predict pathological response and guide therapy personalization in the neoadjuvant setting.

Neoadjuvant therapy is a cornerstone of modern oncology, yet its efficacy is traditionally assessed only after treatment completion, creating a "black...

Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.

Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a...

RNA modifications in cancer and their detection: a review.

Ribonucleic acid (RNA) modifications, once viewed as static structural features, are now recognized as dynamic regulators of the 'epitranscriptome' th...

The Emerging Role of Olfactory Receptors: From Genomics to Precision Medicine.

Olfactory receptors (ORs), once considered peripheral to sensory biology, are now recognized as functionally important components of precision medicin...

Update of the Novara Cohort Study (NCS): protocol evolution of a population-based longitudinal study on ageing in Northern Italy - cohort profile.

PURPOSE: The Novara Cohort Study (NCS) was established to investigate the biological, psychological and social factors that influence ageing in the ge...

Identification of diagnostic and prognostic biomarkers in lung adenocarcinoma through integrated bioinformatics analysis and real time PCR validation.

Lung cancer is the third most common cancer in the US with a 5-year survival rate of 17%. Non-small cell lung cancer, especially adenocarcinoma, preva...