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Multi-Omics Integration Reveals the Genetic Mechanisms of Periodontitis and Predicts Therapeutic Drugs
<h4>Background</h4>Periodontitis is a chronic inflammatory disease driven by host immune dysregulation. However, the specific genetic regulatory mechanisms underlying this disease remain unclear. Identifying key molecular targets is crucial for precise therapeutic intervention.<h4>Methods</h4>This study integrated genome-wide …
Read PDFMulti-Omics reveals SPP1 + malignant and CXCR4<sup>+</sup> TAM crosstalk predicts immunotherapy response in lung adenocarcinoma
<h4>Background</h4>Lung adenocarcinoma (LUAD), a common lung cancer subtype, is significantly influenced by the immune microenvironment. Immune checkpoint inhibitors have shown limited efficacy in Lung adenocarcinoma due to the immunosuppressive tumor microenvironment (TME). Identifying predictive biomarkers …
Read PDFNephrotoxicity of Evodiamine in Mice: Mechanistic Insights from Integrated Network Toxicology and Transcriptomic Profiling
The aim of this study was to evaluate the nephrotoxicity and molecular mechanism of Evodiamine (EVO). We combined RNA sequencing (RNA-seq) and network toxicology (NT) screening of potential target genes and signaling pathways, used molecular …
Read PDFAtherosclerotic Fibrous Plaques in Women Present ECM Remodeling Linked to TGF-β
<h4>Background</h4>Sex and atherosclerotic plaque histology are intertwined, with fibrous plaques being more prevalent in women. Plaque erosion, a significant contributor to acute coronary syndromes, is linked to fibrous plaques and is more prevalent in women …
Read PDFUntangling the fusion of spatial omics and mechanobiology
Cellular biophysical properties are increasingly linked to disease development, including muscular dystrophy, cancer, glaucoma, and other conditions. Transcription profiles of various types have been utilized to elucidate the relationship between genes and their regulatory functions. …
Read PDFSpatial mapping of barcoded, brain-tropic AAVs using multiplexed RNA <i>in situ</i> hybridization
Gene therapy cargo delivery to specific cell types in the central nervous system (CNS) remains a major challenge for the development of adeno-associated virus (AAV) vectors as a therapeutic modality. Here, we leverage high-plex <i>in …
Read PDFProtocol for dual spatial transcriptomic profiling of infected tissues
Dual spatial transcriptomics analysis offers profiling of host- and pathogen-specific transcriptional patterns in infected tissues to establish pathoadaptation signatures and predict infection outcomes. Here, we present a protocol for tissue processing, imaging, selection of regions …
Read PDFSingle-Cell Multi-Omics Profiling of Human Septal Myectomy Tissue: Toward Precision Medicine in Obstructive Hypertrophic Cardiomyopathy
Hypertrophic cardiomyopathy (HCM) is an inherited cardiac disorder most commonly caused by pathogenic variants in sarcomeric genes, yet many patients remain genotype-negative and the mechanisms linking genetic alterations to disease pathology are not fully understood. …
Read PDFEnhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies
Spatial transcriptomics technology represents a groundbreaking advancement in the life sciences, enabling the analysis of gene expression patterns within their native spatial context. However, inefficiencies in RNA capture from tissue samples have historically limited its …
Read PDFMAGNET: Multi-view graph autoencoder with cell-gene attention for cell interaction network reconstruction from spatial transcriptomics
Accurately inferring cell-cell interactions from spatial transcriptomics data remains challenging due to tissue complexity and spatial heterogeneity. Recent deep learning models have started to combine different types of cellular information, such as spatial proximity, gene …
Read PDFRobust transcriptomic signatures of Alzheimer's disease progression: validated explainable AI approach
The lack of validated stage-specific biomarkers hampers the understanding of Alzheimer's disease (AD) progression and clinical translation. Current transcriptomic methods often produce unstable results with limited stage discrimination. We aimed to develop an explainable machine …
Read PDFSpatial transcriptomics of cerebral amyloid angiopathy and amyloid‐β related angiitis
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Read PDFNeighborhood nonnegative matrix factorization identifies patterns and spatially-variable genes in large-scale spatial transcriptomics data
Methods for identifying complex multicellular spatial neighborhoods do not scale to existing spatial transcriptomics data, and often divide tissues into distinct neighborhoods with hard borders. We develop neighborhood NMF (NNMF) that identifies functionally coherent neighborhoods …
Read PDFHelicobacter pylori-linked gene CFAP73 rewires epithelial programs and shapes the gastric cancer microenvironment
<h4>Background</h4>Helicobacter pylori (HP) infection is the strongest environmental driver of gastric cancer, yet the epithelial programs that are progressively disrupted during infection and are associated with malignant transformation remain unclear.<h4>Methods</h4>Trend-associated genes across HP-infection datasets (GSE60662, …
Read PDFDLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma
BACKGROUND: The neuroactive ligand–receptor signaling pathway is increasingly recognized as a regulator of tumor–immune interactions, yet its contribution to lung adenocarcinoma (LUAD) progression and immune evasion remains poorly defined. METHODS: We integrated multi‑cohort transcriptomic datasets, …
Read PDFInvestigating uncharacterised genes in Saccharomyces cerevisiae using robot scientists
Despite extensive research on Saccharomyces cerevisiae functional genomics, approximately 880 out of ~6,000 open reading frames (ORFs) remain uncharacterised. In this study we propose a method for characterising genes with limited prior functional knowledge using …
Read PDFCurrent evidence on the cell of origin of meningiomas disputes the arachnoid cap cell dogma
<h4>Background</h4>For over a century, the dominant hypothesis has maintained that meningiomas arise exclusively from arachnoid cap cells. However, emerging evidence from single-cell transcriptomics, spatial sequencing, developmental biology, and transgenic animal models suggests a significantly more …
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