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Artificial intelligence (AI) has become a transformative tool in cell biology, driving discoveries through the analysis of complex biological data. This review explores the diverse applications of AI, including its impact on microscopy, imaging, drug …
Read PDFArecoline, the major alkaloid of areca nut, is a common exposure in chewing products, but its relationship with prostate cancer (PCa) is unclear. We integrated network toxicology, bulk RNA machine learning, single-cell transcriptomics, molecular simulation, …
Read PDFLymph node (LN) function requires the organization of cells into higher-order spatial units. However, the principles governing LN architecture in health and disease remain poorly understood. Here, we used single-cell and spatial mapping to investigate …
Read PDF<h4>Motivation</h4>Understanding spatial organization, intercellular interactions, and regulatory networks within the spatial context of tissues is crucial for uncovering complex biological processes and disease mechanisms. Spatial transcriptomics technologies have revolutionized this field by enabling the spatially …
Read PDFUnderstanding tissue complexity requires spatially resolved multi-omics data at single-cell resolution. Here, we present a workflow integrating high-resolution matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) with Xenium spatial transcriptomics (SPT) on a single tissue …
Read PDFCancer is a highly complex and heterogeneous disease involving multiple pathophysiological events. Despite significant advances in modern medicine, the molecular mechanisms of cancer are still largely unknown. Omics methods have opened new avenues for identifying …
Read PDFThe rise of single-cell transcriptomics and comprehensive reference atlases promised a unifying molecular framework to classify cell identity. Yet transcriptomic identities are often interpreted outside the environmental contexts in which they arise. Here, we analyzed …
Read PDF<h4>Background</h4>Congenital heart disease (CHD) affects approximately 1% of live births worldwide and remains the leading cause of infant mortality from congenital anomalies. Despite advances in diagnosis and therapeutics, the molecular mechanisms underlying CHD pathogenesis remain …
Read PDFThe impact that single-cell and spatial genomic technologies have had on the scientific community since their advent has been widespread and profound. The field of spinal cord injury (SCI) is one such area that has …
Read PDFThe immunoregulatory architecture of human oral tissues remains poorly defined. We present an integrated single-cell and spatial proteotranscriptomic atlas profiling >250,000 single-cell transcriptomes and >4 million spatially resolved cells across 13 niches. Using our AI-enabled …
Read PDF<h4>Background</h4>Gliomas exhibit substantial intratumoral heterogeneity, which limits prognostic precision and therapeutic efficacy. Selenoproteins are key regulators of redox homeostasis, but their role in glioma progression remains insufficiently defined. This study aimed to characterize glioma cells …
Read PDFPancreatic ductal adenocarcinoma (PDAC) is the most complex and aggressive disease with the worst rates of unresectable or metastatic disease at diagnosis, resistance to systemic therapy, and case fatality rate (CFR) among leading cancers. In …
Read PDF<h4>Background</h4>Allergic rhinitis (AR) is a common chronic nasal mucosal inflammatory disorder driven by type 2 immunity, but the spatial stromal-immune cell interactions underlying its pathogenesis remain unclear.<h4>Methods</h4>We used 10x Genomics Xenium <i>In Situ</i> spatial transcriptomics …
Read PDFGastric cancer (GC) remains a major global health burden, with its unfavorable prognosis primarily driven by extensive tumor heterogeneity. Traditional bulk omics, while informative, are inherently limited by the averaging effect of diverse cell populations …
Read PDFIn single-cell transcriptomics, the accurate identification of cell-type-specific marker genes is fundamental for understanding cellular heterogeneity. However, existing approaches often rely on arbitrary thresholds and clustering heuristics, making them sensitive to noise, annotation bias, and …
Read PDFWhite adipose tissue (WAT) is a remarkably plastic organ integrating metabolic, endocrine and immune functions. In humans, perturbations in adipocyte turnover, size regulation and cellular heterogeneity underpin the transition from metabolic health to obesity-related disease. …
Read PDFIntratumor macrophage infiltration plays a crucial role in various aspects of tumor immunity in colorectal cancer (CRC). However, the phenotypic heterogeneity, spatial distribution, and cellular interactions of these macrophages remain elusive. To overcome the limitations, …
Read PDFBACKGROUND: Glioblastoma represents the most aggressive primary brain malignancy, characterized by a profoundly immunosuppressive microenvironment that limits therapeutic efficacy and drives disease progression. Myeloid cells—comprising tumor-associated macrophages, myeloid-derived suppressor cells, and dendritic cells—serve as central …
Read PDF<h4>Background and aims</h4>A comprehensive understanding of the liver niche during development provides insights into a unique, naturally occurring multifunctional multicellular environment. We applied spatial transcriptomic and histologic approaches to identify and histologically validate RNA-based markers …
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