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Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome …
Read PDFGenome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read …
Read PDF<h4>Background</h4>Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters.<h4>Results</h4>In this study, we …
Read PDFWhile the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing …
Read PDFA modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in …
Read PDF<h4>Background</h4>With over 10,000 recognized species, birds constitute one of the most diverse and widely distributed vertebrate groups. Although avian genomics has advanced rapidly over the past decade, substantial gaps remain across the global avifauna. Filling …
Read PDFTea plants possess a highly heterozygous genome and produce diverse beneficial metabolites, yet the genomic basis of its metabolic diversity remains fully elusive. Here, we show that single-cell sequencing of 107 sperm cells, combined with …
Read PDF<h4>Background</h4>Hypoxic-ischemic (HI) brain injury triggers a dynamic, multi-phase response involving early microglial efferocytosis followed by extracellular matrix (ECM) deposition and scar formation. Arginase-1 (ARG1), a key enzyme in tissue repair, is implicated in both processes, …
Read PDF<h4>Background</h4>The clinical management of lung adenocarcinoma (LUAD) is compromised by post-surgical recurrence and therapeutic resistance, underscoring the urgent need to uncover actionable therapeutic vulnerabilities. By integrating human genetics with multi-omics profiling and experimental validation, this …
Read PDFGenome-wide association studies (GWAS) have identified a large number of variants linked to complex traits and diseases, most of which lie in noncoding regions and act in a tissue- and cell type-specific manner. However, how …
Read PDFRecurrent loss of complex traits such as insect flight offers insights into evolutionary regression, as seen in <i>Bombyx mori</i> domestication from its flight-capable ancestor <i>B. mandarina</i>. By integrating single-cell and spatial transcriptomics of developing flight …
Read PDFDespite significant progress in targeted cancer therapies and conventional imaging methodologies, the effective detection and treatment of solid tumours remain a major clinical challenge. This is thought to be caused by the complexity and heterogeneity …
Read PDFRemodeling of the tumor microenvironment (TME) under therapeutic pressure is a critical determinant of treatment response and resistance in hepatocellular carcinoma (HCC). Triple-combination therapy integrating targeted agents, immune checkpoint inhibitors, and radiotherapy (T+I+R) has shown …
Read PDF<h4>Background</h4>Colorectal cancer (CRC) is a leading cause of cancer-related death, often marked by intratumoral heterogeneity, immune evasion, and therapeutic resistance. Recent advancements in single-cell and spatial transcriptomics have enabled a deeper understanding of the tumor …
Read PDF<h4>Background & aims</h4>Ribosomal protein L8 (RPL8) is up-regulated in hepatocellular carcinoma (HCC), yet its clinical value and microenvironment role remain unclear.<h4>Methods</h4>Multi-omics (TCGA, CPTAC), scRNA-seq (GSE146115) and spatial transcriptomics were integrated; function was tested by RPL8 …
Read PDFTumors are composed of cellular populations with distinct genotypes and phenotypes, which dynamically evolve over time and during treatment. This process is known as clonal evolution, and it is difficult to reveal fine-scale clonal structure …
Read PDFAndrogenetic alopecia (AGA) manifests as progressive hair follicle (HF) miniaturization; however, its drivers remain poorly elucidated. Combining spatial and single-cell transcriptomics, we generate a concise single-cell atlas of anagen HFs in male AGA, revealing early …
Read PDF<h4>Background</h4>Oral squamous cell carcinoma (OSCC) exhibits heterogeneous therapeutic outcomes owing to various tumor microenvironments (TMEs). Previous studies have classified OSCC according to its molecular characteristics; however, clinical practice is limited by technical complexity.<h4>Methods</h4>A total of …
Read PDFMetastatic breast cancer (MBC) remains the primary cause of mortality in breast cancer patients, driven by tumor heterogeneity, cellular evolution, and therapy-resistant clones. Traditional bulk transcriptomics, although informative, fail to capture rare subpopulations and context-specific …
Read PDFMetastasis remains the leading cause of cancer mortality, yet the factors that determine metastatic competence and the timing of its acquisition are not well understood. Using human breast cancer cohorts and multi-omics in preclinical models, …
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