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Multi-dimensional omics integrated machine learning framework identifies macrophage-fibroblast-tumor co-infiltration patterns to predict prognosis in gastric cancer
Gastric cancer (GC), of which cases with peritoneal metastasis are particularly challenging, retains its position of being highly complex and remarkably resistant to therapy. Understanding the spatial heterogeneity and leveraging recent technologies such as machine …
Read PDFSpatial multi-omics mapping of tumor microanatomy dynamics following radiotherapy combined with targeted-immunotherapy in hepatocellular carcinoma
Remodeling 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 PDFMulti-omics profiling of sodium-overload (NECSO) programs identifies NEK8 as a central driver of colorectal cancer progression through single-cell and spatial transcriptomics
<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 PDFIntegrated spatial and single-cell transcriptomics reveals RPL8 as a prognostic biomarker and therapeutic target in hepatocellular carcinoma
<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 PDFSingle-cell Profiling Reveals Cooperative Participation of <i>SPP1<sup>+</sup></i> Myeloid and <i>POSTN<sup>+</sup></i> Fibroblast Subsets in Inflammation and Remodeling in Thoracic Aortic Aneurysm
Thoracic aortic aneurysm (TAA) is a life-threatening condition characterized by aortic dilation, inflammation, and extracellular matrix degradation. Despite advances in surgical management, effective pharmacological therapies are still lacking, largely due to an incomplete understanding of …
Read PDFSpatial Transcriptional Heterogeneity in the Infarct Core and Its Surrounding Regions Targeting Piezo1 Signals in Rats With Myocardial Ischemia-Reperfusion Injury
Myocardial ischemia-reperfusion (MIR) injury is a major cause of cardiac dysfunction, but the spatial heterogeneity of its underlying molecular programs remains unclear. In this study, we applied Visium spatial transcriptomics to generate gene expression maps …
Read PDFAn ELIXIR scoping review on domain-specific evaluation metrics for synthetic data in life sciences
Synthetic data (SD) has become an increasingly important asset in the life sciences, helping address data scarcity, privacy concerns, and barriers to data access. Creating artificial datasets that mirror the characteristics of real data allows …
Read PDFHuman multi-tissue transcriptomics identifies galectin-1 and follistatin-like 1 as exerkines with distinct transcript-to-serum coupling after exercise
Exercise-induced secreted factors (exerkines) are proposed to coordinate systemic health benefits, yet their human tissue sources and the physiological rules governing transcript-to-serum coupling remain incompletely defined. We integrated multi-tissue transcriptomics with matched serial serum profiling …
Read PDFNon-destructive transcriptomics via vesicular export
Transcriptomics enables comprehensive, multiplexed characterization of cellular states, yet prevailing methods typically require cell fixation or lysis, precluding longitudinal analysis of RNA expression in living cells. Here, we present non-destructive transcriptomics by vesicular export (NTVE), …
Read PDFUnraveling TIME: CD8+ T cell- and CXCL11-driven endocrine resistance in breast cancer
A major unmet need in estrogen receptor-positive (ER+) breast cancer is understanding the mechanisms that underlie resistance to endocrine therapy. Although accumulating evidence suggests an association between the tumor immune microenvironment (TIME) and endocrine response, …
Read PDFDifferential expression analysis for spatially correlated data using smiDE
Differential expression is a key application of imaging spatial transcriptomics, moving analysis beyond cell type localization to examining cell state responses to microenvironments. However, spatial data poses new challenges to differential expression: segmentation errors cause …
Read PDFDe Novo Detection of Clonal Structure and Evolution in Single-Cell and Spatial Transcriptomes
Tumors 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 PDFPrognostic genes in hepatocellular carcinoma and their function: an analysis integrating high-throughput-based spatial transcriptomics and single-cell RNA-sequencing
<h4>Background</h4>Identifying novel prognostic indicators for patients with hepatocellular carcinoma (HCC) is critical to improving patient outcomes. Mapping the spatial composition of HCC tumors remains challenging. Therefore, this study aimed to identify prognostic genes and assess …
Read PDFSingle-cell transcriptomics reveals hair growth retardation mediated by aberrant connective tissue sheath contraction in male androgenetic alopecia
Androgenetic 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 PDFInvestigating Low-Temperature Stress Responses in Crustacea Aquatic Species Through Comparative Transcriptomics
Crustaceans, such as shrimp and crabs, are pivotal to global aquaculture, yet their productivity is severely impacted by low-temperature stress. This study employs comparative transcriptomic and genomic analyses to elucidate the molecular mechanisms underlying crustacean …
Read PDFCBX3:IL1RN Reflects Distinct Cellular States That Defines the Clinical Outcome of Oral Squamous Cell Carcinoma
<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 PDFIntegrated analysis of transcriptome and proteome reveal that PDCoV infection induces autophagy-dependent ferroptosis to facilitate viral replication
Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus that causes severe diarrhea in swine industries worldwide. However, the interactions between PDCoV and host cells remain poorly understood. In this study, we employed transcriptomic and proteomic …
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