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In vivo evaluation of biomaterials largely relies on histology to assess biocompatibility and foreign body responses. While effective for capturing end-stage outcomes, these methods offer limited insight into the cellular mechanisms driving tissue remodeling, hindering …
Read PDFSpatial transcriptomics technologies such as Xenium, MERFISH, and Visium HD enable high-resolution profiling of gene expression while preserving tissue architecture. However, most computational methods for spatial analysis do not explicitly model local tissue context, such …
Read PDFThe spatial organization of chronic liver disease across major etiologic contexts remains incompletely understood. Here we present a pilot spatial case series using sequencing-based spatial transcriptomics to examine alcohol-associated liver disease (ALD), metabolic dysfunction-associated steatohepatitis …
Read PDFDecoding how cells influence and communicate with each other in space is fundamental for understanding tissue organization. However, existing approaches either overlook spatial context entirely or rely solely on local cell-cell adjacency, failing to capture …
Read PDFHuman atherosclerosis is increasingly recognized as a spatially organized inflammatory disease in which macrophages act as central regulators of lesion evolution rather than as a uniform foam-cell population. Recent single-cell and spatial profiling studies have …
Read PDFMicrobial predators obtain energy from killing other living cells. <i>Streptomyces</i> are soil bacteria that are known to produce numerous catabolic enzymes and antimicrobial compounds to defend against competing organisms. Here, we demonstrate that <i>Streptomyces</i> are …
Read PDF<h4>Background</h4>Multiple Sclerosis is a chronic autoimmune disease that attacks the myelin sheath in the central nervous system, with a higher prevalence among female patients. We and others have documented significant changes in microbial taxa in …
Read PDFAutism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition in which human post-mortem cortical transcriptomic studies have identified recurrent but context-sensitive molecular abnormalities. This narrative review synthesises RNA sequencing (RNA-seq) evidence from ASD cortex and …
Read PDFSpatial transcriptomics enables high-resolution gene expression mapping in intact tissues. Xenium is widely adopted for its reliability, accessibility and data quality, yet the properties and limitations of Xenium-derived data remain poorly characterized. Here we present …
Read PDFThe advent of high-throughput technologies has accelerated biomedical research by facilitating the investigation of biological complexity at unprecedented resolution. Single-cell RNA sequencing (scRNA-seq) has transformed our ability to deconstruct cellular heterogeneity in complex diseases. Acute …
Read PDFMeningiomas are the most common primary intracranial tumor in adults. Traditional bulk genomic and histopathological analyses have provided valuable insights into meningioma biology. Recent advances in single-cell sequencing technologies have enabled the comprehensive study of …
Read PDF<h4>Purpose</h4>The purpose of this study was to determine optic nerve head (ONH) laminar collagen and retrolaminar myelin expression change in non-human-primate (NHP) experimental glaucoma (EG) using immunohistochemistry (IHC) and spatial transcriptomics.<h4>Methods</h4>Unilateral EG NHPs (n = …
Read PDFThe global prevalence of gastrointestinal tumours and the bottlenecks in their diagnosis and treatment are being systematically overcome by the multi-omics revolution: high-throughput technologies are driving the multidimensional integration of genomics-transcriptomics-proteomics-metabolomics to comprehensively decode the …
Read PDF<h4>Background</h4>In neoadjuvant chemoradiotherapy (NCRT), only 1/3 of patients with esophageal squamous cell carcinoma (ESCC) achieve pathologic complete response (pCR). Here, we aimed to depict the biological landscape of ESCC with different responses to NCRT and …
Read PDFSequencing an entire spatial transcriptomics slide can cost thousands of dollars per assay, making routine use impractical. Focusing on smaller regions of interest (ROIs) based on adjacent H&E slides offers a practical alternative, but there …
Read PDFCurrent tools for spatial omics analysis often face challenges in performing integrated transcriptomics and metabolomics analysis, in-depth biological interpretation, and user-friendly operation. To address this, we developed SMIntegration, the first web-based graphical platform designed specifically …
Read PDF<h4>Motivation</h4>Capturing spatial structure is fundamental to the analysis of spatial transcriptomics data. However, most existing methods focus on clustering within individual tissue slices and often ignore the high inter-slice similarity inherent in multi-slice datasets.<h4>Results</h4>To address …
Read PDFDeciphering the cellular composition of spatial spots in spatial transcriptomics (ST) data is fundamental for elucidating the heterogeneity of tissue spatial structures. However, existing models often require retraining for each new deconvolution task, reflecting limitations …
Read PDFTumor cell heterogeneity and multicellular interactions critically influence drug resistance, recurrence, and prognosis. Here, CPcellsubpopulation, a computational framework integrating scRNA-seq, bulk RNA-seq, and clinical data was developed to identify cancer progression-associated cell subpopulations. Then, the …
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