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Precision Thyroid Oncology: A Review of Multi-Omics Biomarkers and Spatiotemporal Technologies
Thyroid cancer (TC), the most prevalent endocrine malignancy worldwide, encompasses a broad spectrum of biological behaviors ranging from indolent microcarcinomas to lethal anaplastic variants. Despite advancements in standard care, critical clinical "bottlenecks" persist, including the …
Read PDFSpatial transcriptomic profiling of decalcified murine musculoskeletal samples via Xenium Prime 5K
Successful generation of high-quality spatial transcriptomics data from murine musculoskeletal tissues has been impeded by the challenge of preserving RNA integrity through the harsh tissue processing steps required for histological sectioning. In particular, the need …
Read PDFAdvances in predicting omics profiles from imaging data
While traditional imaging techniques, such as histopathology, are often part of clinical workflows, molecular profiling remains more difficult to conduct and is less cost-effective. Thus, the prediction of molecular 'omics' data directly from imaging has …
Read PDFSingle-Cell and Spatial Omics: Methods and Applications
Single-cell and spatial omics have revolutionized biomedical research by enabling high-resolution molecular profiling across cells and tissues, thereby overcoming key limitations of bulk sequencing and revealing unprecedented cellular heterogeneity and spatial organization central to development, …
Read PDFIntegrative Molecular Analyses of Inflammatory and Autoimmune Signals in Cardiac Sarcoidosis
<h4>Background</h4>Cardiac sarcoidosis (CS) is an enigmatic disorder characterized by unexplained patchy, sterile granulomas intermixed with preserved myocardium and fibrotic regions without granuloma. CS causes arrhythmias, sudden cardiac death, and heart failure. The mechanisms producing this …
Read PDFscTumorDrug: predicting cell-type-specific drug responses for heterogeneous tumors
It is important to predict cell-type-specific drug responses within the heterogeneous tumors for precision medicine. The single-cell RNA sequencing (scRNA-seq) technique together with drug responses data provides opportunities for this mission. The previous methods were …
Read PDFIntegrative single-cell and spatial transcriptomics analysis reveals a baicalein-responsive 10-gene signature for non-small cell lung cancer
<h4>Background</h4>Non‑small cell lung cancer (NSCLC) remains a leading cause of cancer‑related mortality worldwide. Baicalein, a natural flavonoid, has shown anti‑cancer activity but its molecular targets and cell‑type‑specific effects in the tumor microenvironment (TME) are incompletely …
Read PDFPathway-centric visualization of cell-cell communication in single-cell transcriptomics data
Single-nuclei transcriptomics enables investigating ligand-receptor mediated cell-cell communication between different cell-types. However, current tools do not allow for non-programmatic means to access this analysis. Additionally, most methods can not account for molecular pathways involved in …
Read PDFSingle-Cell and Spatial Transcriptomics Reveal That <i>TXNIP</i> and <i>BIRC3</i> Contribute to Human Prostate Tumor Progression
Prostate cancer is one of the most prevalent malignancies among men and remains a major clinical challenge due to the complex tumor microenvironment. Understanding gene expression dynamics at both cellular and spatial levels is essential …
Read PDFGraph convolutional networks for inferring cell-cell communication from spatial transcriptomics data
<h4>Motivation</h4>Single-cell spatial transcriptomics provides gene expression measurements of individual cells while preserving their spatial positions within tissue. Cell-cell communication (CCC) can be inferred by comparing the predictions of held-out gene expression levels by a pair …
Read PDFSpatial multi-omics technologies in gastric cancer: applications and advances
Gastric cancer (GC) is plagued by profound intratumoral heterogeneity and a complex tumor microenvironment (TME), which are the core obstacles to precise diagnosis and treatment. Conventional bulk multi-omics technologies average molecular signals across tissues, thus …
Read PDFSpatial single-cell omics: new insights into liver diseases
The liver is a highly multifunctional organ that can perform many metabolic and immunological functions due to a highly complex spatially organised microarchitecture that is disturbed in many liver diseases. Recent methodological advances in spatial …
Read PDFspRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
The analysis of spatial transcriptomic data is hindered by high noise levels and missing gene measurements, challenges that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome …
Read PDFA cell atlas of the developing human outflow tract of the heart and its adult aortic valve derivatives
The outflow tract (OFT) of the heart carries blood away from the heart into the great arteries. During embryogenesis, the OFT divides to form the aorta and pulmonary trunk, creating the double circulation present in …
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