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Trainable clustering framework for spatial transcriptomics
<h4>Summary</h4>Spatial transcriptomics (ST) enables high-resolution exploration of tissue architecture by integrating gene expression profiles with spatial information, thereby advancing insights into cellular composition, organization, and interactions. Among ST applications, spatial domain identification is critical for …
Read PDFA spatial transcriptomics comparison of the adult versus metamorphosed axolotl brain
The Mexican axolotl (Ambystoma mexicanum) is an established model for studying tetrapod regeneration and development. Notably, axolotls exhibit remarkable brain regeneration as adults, a trait rarely observed in other adult vertebrates. Adult axolotls can undergo …
Read PDF3D reconstruction of spatial transcriptomics with spatial pattern enhanced graph convolutional neural network
Spatially resolved transcriptomics (SRT) is a promising new technology that enables simultaneous analysis of gene expression and spatial information for biomedical research. However, the existing statistical and deep learning algorithms used for analyzing SRT data …
Read PDFTerpenoids Associated with the Resistance of Poplar to Canker Disease as Revealed by Transcriptomics and Metabolomics Analyses
Poplar (<i>Populus</i> spp.) has a short growth cycle and considerable economic value. Also, it is highly susceptible to various diseases. Of these, the canker disease has a significant impact on the health and productivity of …
Read PDFIdentification and characterisation of an elusive bacterial enzyme system for chloromethane dehalogenation
Chloromethane, a toxic gas primarily produced naturally, contributes to stratospheric ozone destruction. The anaerobic acetogen Acetobacterium dehalogenans can utilise chloromethane as a carbon and energy source, but the associated dehalogenase/methyltransferase has remained elusive. Through comparative …
Read PDFFusobacterium nucleatum-Derived Outer Membrane Vesicles Disrupt Epithelial Barrier in Oral Lichen Planus via JNK/c-JUN Mediated Claudin-4 Downregulation
<h4>Introduction and aims</h4>Oral lichen planus (OLP) is a chronic inflammatory disease of unknown etiology. Recent studies have implicated microbial dysbiosis in its pathogenesis. Our previous research revealed an increased abundance of Fusobacterium nucleatum (F.nucleatum) in …
Read PDFIntegrative Spatial Transcriptomics and Experimental Validation Reveal UBC-Mediated EMT Associated with Immune Evasion in Hepatocellular Carcinoma
<h4>Background</h4>Hepatocellular carcinoma (HCC) exhibits pronounced spatial heterogeneity that limits therapeutic efficacy. The contribution of epithelial-mesenchymal transition (EMT) to regional tumor progression and immune evasion remains incompletely understood.<h4>Methods</h4>We integrated bulk transcriptomic datasets (TCGA, GSE14520), 34 single-cell …
Read PDFGenome-wide identification of genes involved in beetle odoriferous defensive stink gland function recognizes Laccase2 as the phenoloxidase responsible for toxic para-benzoquinone synthesis
Exocrine glands have evolved several times independently in Coleoptera to produce defensive chemical compounds with repellent, antimicrobial, or toxic effects. Research on such glands had focused on morphological or chemical ecology methods. However, modern genetic …
Read PDFCTFacTomo: Reconstructing 3D spatial structures of RNA tomography transcriptomes by collapsed tensor factorization
Cells are organized to form three-dimensional structures of complex tissues. To map the complete 3D organization of a tissue, technologies based on tissue microdissections provide deep bulk RNA sequencing of orthogonally arranged cryosections of a …
Read PDFDysfunction of the neurovascular unit as a temporal driver in Alzheimer's pathogenesis
Extensive studies have shown that cerebrovascular dysfunction is a critical factor in the onset and progression of Alzheimer's disease (AD). Neurovascular unit (NVU) is impaired in AD brains, including damage of tight junction between endothelial …
Read PDFToward a Molecular Reclassification of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Integrating Multi-Omics, Machine Learning, and Precision Medicine
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, multi-system disease characterized by a multitude of symptoms across various organ systems. Diagnosis has relied heavily on heterogeneous clinical symptom presentation and evolving case definitions, with treatment …
Read PDFGenome-Wide Association Studies Data and Transcriptomics Data Link Herpes Simplex Virus 1 Infection and Parkinson's Disease
<h4>Objective</h4>The main goal of this study is to explore the link between herpes simplex virus 1 (HSV-1) infection and Parkinson's disease (PD) from the genome-wide association studies (GWAS) data and find the shared molecular signature …
Read PDFDecoding epithelial-T cell interactions in colorectal cancer through single-cell and spatial transcriptomics
<h4>Background</h4>Colorectal cancer (CRC) is a heterogeneous malignancy shaped by genetic alterations and immune microenvironmental interactions. While single-cell RNA sequencing (scRNA-seq) has uncovered diverse epithelial and T cell subsets, the spatial architecture of their crosstalk remains …
Read PDFSTEER: decoupling kinetics with Spatial-Temporal Explainable Expert model for RNA velocity inference
RNA velocity provides a powerful scope for understanding cell state dynamics by modeling spliced and unspliced mRNA captured by single-cell or spatial transcriptomic technologies. However, prevailing methods relying on restrictive kinetic assumptions often fail in …
Read PDFMulti-Omics Integrated Analysis Reveals Correlative Signatures of Short-Chain PFAS Mixtures on Mouse Midbrain Dopaminergic Neurons Involving the TM/5-HT Pathway
This study aimed to identify candidate molecular pathways mediating dopaminergic dysfunction induced by PFAS mixture exposure, with a focus on the TM/5-HT signaling axis and calcium-linked lipid metabolites, and to explore potential gut-brain axis involvement. …
Read PDFMapping the immune environment: spatiotemporal dynamics in cardiovascular events
Cardiovascular disease remains a leading cause of global mortality despite advances in revascularization, pharmacotherapy, and risk stratification. Immune responses to cardiovascular damage are neither temporally linear nor spatially homogeneous; they evolve across overlapping phases and …
Read PDFElucidating cardiac fibroblasts heterogeneity and activation during experimental autoimmune myocarditis using spatial transcriptomics
Dilated cardiomyopathy (DCM), which develops from myocardial inflammation, is frequently linked to a poor prognosis and fatal outcome. Experimental autoimmune myocarditis (EAM) serves as an animal model of CD4<sup>+</sup> T cells-dependent acute myocarditis that is …
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