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Deciphering the cis-regulatory logic underlying cell type identity remains a key challenge in biology. Single-cell chromatin accessibility (scATAC-seq) atlases enable training of sequence-to-function (S2F) deep learning models to decode enhancer logic. Yet, optimal criteria for …
Read PDF<h4>Background</h4>Osteoarthritis (OA) is a progressive joint disease influenced by macrophage-associated efferocytosis.<h4>Objective</h4>This study aimed to identify key OA biomarkers by integrating transcriptomic and single-cell RNA sequencing (scRNA-seq) data with Mendelian randomization (MR).<h4>Materials and methods</h4>We integrated three …
Read PDFHeterogeneity within clonal cell populations remains a critical bottleneck within bioprocess engineering, notably by undermining bioproduction yields. Efforts to mitigate its impact have, however, been hampered by technological difficulties quantifying metabolism at the single-cell level. …
Read PDFOncogenic mutations shape colorectal cancer (CRC) biology, yet their impact on transcriptional phenotypes remains incompletely understood, and their individual prognostic value is limited. Here, we perform a pooled single-cell transcriptomic screen of over 100,000 CRC …
Read PDF<h4>Background</h4>Lung cancer, particularly the non-small cell lung cancer (NSCLC) subtypes lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD), exhibits high heterogeneity and high mortality. This study aimed to explore their tumor microenvironment (TME) features, …
Read PDFWhereas FMS-like tyrosine kinase-3 (FLT3) inhibitors have significantly improved the treatment of aggressive FLT3-mutated acute myeloid leukemia (AML), the emergence of resistance remains as a major challenge. In this study, we applied our recently developed …
Read PDFGastric cancer remains highly lethal, yet how protein S-palmitoylation shapes tumour ecosystems and clinical outcome is unclear. We integrated single-cell RNA sequencing (119,931 cells from 25 gastric tumours) with spatial transcriptomics and bulk cohorts to …
Read PDF<h4>Background</h4>Osteosarcoma remains lethal for many patients with metastatic or relapsed disease. Post-translational modifications (PTMs) regulate protein signaling and may shape the tumor microenvironment and clinical behavior in osteosarcoma, but PTM-anchored transcriptomic programs are as yet …
Read PDFHuman gastrointestinal (GI) tissues are a major site of HIV-1 viral persistence, but the nature of the GI reservoir remains poorly described. To characterize the GI HIV reservoir, we profiled cells from GI tissue and …
Read PDFSingle-cell sequencing (SCS) techniques have the potential to offer precise insights into cellular diversity by revealing unique genetic and transcriptomic profiles at the single-cell level. This advanced technology has been used extensively in research, but …
Read PDFApproximately 10 million people worldwide suffer from corneal diseases, with endothelial dysfunction being a leading cause of blindness. Current morphological assessments lack sensitivity for detecting early corneal endothelial abnormalities. Here, we present a novel diagnostic …
Read PDFThe cerebellum, essential for motor coordination and increasingly recognized for its role in cognition, is typically considered more resilient to aging and largely spared from hallmark Alzheimer's disease (AD) pathology. However, transcriptomic analyses across fifteen …
Read PDF<h4>Background</h4>Colorectal cancer (CRC) is a malignant disease that poses a significant threat to human health; however, early diagnostic and treatment strategies for it remain limited. Immune evasion is a critical factor contributing to treatment failure …
Read PDFPhenotypic heterogeneity is prevalent during aging, yet its underlying molecular drivers remain poorly understood. In budding yeast, two distinct aging trajectories, characterized by either ribosomal DNA (rDNA) instability or mitochondrial decline, have been proposed to …
Read PDF<h4>Background</h4>Colorectal cancer still causes many cancer deaths, and patient outcomes differ a lot. The tumor microenvironment can shape tumor growth and treatment response. Autophagy is a cell recycling process linked to tumor survival and immune …
Read PDFBiomarkers of aging offer insights into how diseases and interventions affect biological systems. However, most current biomarkers are based on bulk cell measurements, making it difficult to distinguish between changes driven by shifts in cell …
Read PDFEctopic ACTH-secreting pheochromocytomas are rare and life-threatening endocrine tumors responsible for hypertension, paroxysmal symptoms, and Cushing's syndrome. The cellular origin of ACTH and the tumor's molecular characteristics remain poorly understood. Single-cell RNA sequencing was performed …
Read PDF<h4>Introduction</h4>Leukemia is a clonal malignant proliferative disease originating from hematopoietic stem cells. Although its treatment strategy has gradually developed from traditional chemotherapy to a multimodal treatment system including novel targeted therapy and immunotherapy, primary drug …
Read PDFSkeletal muscle development is cornerstone of vertebrate locomotion, relies on the functionally distinct muscle fiber-type. Although the cellular dynamics in myogenesis have been extensively studied, the developmental origins and pathways governing fiber-type diversification remain unresolved. …
Read PDF<h4>Background</h4>Obstructive sleep apnea-hypopnea syndrome (OSAHS) is a prevalent respiratory disorder characterized by intermittent hypoxia (IH), which promotes pulmonary complications. However, the cellular and molecular mechanisms underlying IH-induced lung remodeling remain poorly understood.<h4>Methods</h4>We performed comprehensive single-cell …
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