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DNA methylation is a fundamental epigenetic modification that regulates gene expression and maintains genomic stability. Consequently, DNA methylation remains a key biomarker in cancer research, playing a vital role in diagnosis, prognosis, and tailored treatment …
Read PDFProstate cancer is a common malignancy that in 5%-30% leads to treatment-resistant and highly aggressive disease. Metastasis-potential and treatment-resistance is thought to rely on increased plasticity of the cancer cells-a mechanism whereby cancer cells alter …
Read PDF<h4>Motivation</h4>Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly …
Read PDFTumor-derived circulating cell-free DNA (ctDNA) has emerged as a pivotal biomarker for non-invasive cancer diagnosis, treatment monitoring, and prognostic evaluation. However, its inherently low abundance, high fragmentation, and rapid degradation impose stringent requirements on assay …
Read PDFChromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory elements that underlie genetic effects on gene expression and metabolic traits. However, caQTL discovery has been limited by small sample sizes. Here, we map caQTLs …
Read PDFTobacco use, alcohol consumption, and infection with human papilloma virus (HPV) are well-established risk factors for head and neck squamous cell carcinomas (HNSCC). However, the incidence of oral cancer, particularly in the mobile tongue, has …
Read PDFFuchs' endothelial corneal dystrophy (FECD) is a progressive eye disease characterized by accelerated loss of endothelial cells and the development of focal excrescence (guttae) on Descemet's membrane, resulting in cornea opacity and vision deterioration. The …
Read PDFAllergic diseases are a significant global health concern. These disorders result from abnormal immune responses to environmental allergens, influenced by genetic, environmental, and epigenetic factors. Among these, histone acetylation has emerged as a key epigenetic …
Read PDFLiposarcoma (LPS) is the most common soft-tissue sarcoma in adults, and well-differentiated liposarcoma (WDLPS) and dedifferentiated liposarcoma (DDLPS) are the most frequent subtypes. These LPSs are considered to develop due to disturbances in the adipogenic …
Read PDF<h4>Importance</h4>Most pancreatic cancer (PC) cases are diagnosed at a late stage, leading to poor prognosis. New-onset diabetes (NOD) increases the risk of PC by 6- to 8-fold within the first 3 years of diagnosis. This …
Read PDFInfants with severe bronchiolitis (i.e., bronchiolitis requiring hospitalization) face increased risks of respiratory diseases in childhood. We conduct epigenome-wide association studies in a multi-ethnic cohort of these infants. We identify 61 differentially methylated regions in …
Read PDFDeciphering 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 PDFSingle-cell multiomics (scMultiomics) technologies and methods encompassing transcriptomics, genomics, epigenomics, proteomics, and metabolomics, together with associated computational tools have profoundly revolutionized disease research, enabling unprecedented dissection of cellular heterogeneity and dynamic biological responses. The use …
Read PDFCells within the same tissue exhibit heterogeneity, influenced by several factors including enhancers. Enhancers regulate precise spatial and temporal patterns of gene expression by switching between active or inactive states. Therefore, it is imperative to …
Read PDFThe rapid advancement of transposase-accessible chromatin using sequencing (ATAC-seq) technology, particularly with the emergence of single-cell ATAC-seq (scATAC-seq), accelerates the studies of gene regulation. However, the absence of a generic feature reference for ATAC-seq data …
Read PDF<h4>Background</h4>Chronic lymphocytic leukemia (CLL) develops from physiologic B cells through low- and high-count monoclonal B cell lymphocytosis (LC-/HC-MBL). The timing and nature of early B cell expansion and molecular evolution remain unclear, limiting prediction of …
Read PDFDistinct regional functionality of the human cortex is orchestrated by diverse cellular and molecular processes, yet the underlying regulatory mechanisms remain poorly understood. We performed multiomic single-cell and spatial characterization of nine regions of the …
Read PDFEstablishing a cell type-specific chromatin landscape is crucial for the maintenance of cell identity during embryonic development. However, our knowledge of how this landscape is set during vertebrate embryogenesis has been limited, due to the …
Read PDFRecent advancements in single-cell DNA methylation (scDNAm) sequencing technologies have enabled the profiling of epigenetic landscapes at unprecedented resolution, offering insights into cellular heterogeneity, differentiation and evolution. Trajectory inference, which orders cells along pseudotime, allows …
Read PDFSingle-cell spatial transcriptomes have demonstrated molecular and cellular diversity in the brain, but gene regulatory mechanisms underlying transcriptomic profiles and disease pathogenesis remain largely unknown in primates. Here we performed single-nucleus Assay for Transposase-Accessible Chromatin …
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