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BACKGROUND: Single cell spatially resolved transcriptomics (ST) has revolutionized molecular profiling by providing the visualization of gene expression within its native tissue architecture, enabling insights into cellular heterogeneity, tumor microenvironment (TME) composition, and the molecular …
Read PDFBiological macromolecules assemble into sophisticated spatial architectures to orchestrate fundamental cellular processes. Understanding this architecture is therefore essential for deciphering the mechanisms of life. Driven by advances in high-throughput sequencing and single-molecule imaging, spatial omics …
Read PDF<h4>Introduction</h4>Cells in tissues interact by direct physical contact or over short and long distances via secreted mediators. Cell-cell communication inference has now become routine in downstream scRNAseq analysis but this mostly fails to capture physical …
Read PDFLung cancer remains a leading cause of cancer-related mortality owing to its aggressiveness and pronounced heterogeneity. Cancer stem cells (CSCs) have been implicated in tumor progression and therapeutic resistance; however, their transcriptional programs and spatial …
Read PDF<h4>Background</h4>Immune checkpoint inhibitors have improved outcomes in several malignancies, yet durable benefit remains limited in most solid tumors because many lesions exhibit immune-excluded or immune-suppressive tumor microenvironments (TMEs). These resistant states are now understood to …
Read PDFThe advent of transcriptomics technologies compatible with formalin-fixed paraffin-embedded tissues has enabled greater opportunities for scientists to interrogate the transcriptome of archived tissues, especially those from rare neurodegenerative diseases. Tissues from brain banks are often …
Read PDFCell-type-specific spatially variable genes (ctSVGs) integrate cell-type composition with spatially varying gene expression, revealing novel insights into molecular mechanisms through spatial transcriptomics. However, the emerging methods devoted to ctSVG detection have not been systematically evaluated, …
Read PDF<h4>Background</h4>Relapsed or refractory (R/R) B-cell non-Hodgkin's lymphoma (B-NHL) remains a major therapeutic challenge despite CD19-directed chimeric antigen receptor (CAR) T-cell therapies, with treatment failure often driven by antigen escape and limited CAR-T persistence. Dual targeting …
Read PDFPituitary tumours are intracranial neoplasms that pose significant clinical challenges due to their potential for recurrence, therapeutic resistance and resultant endocrine dysfunction and mass effects. In the normal anterior pituitary, resident pituitary stem cells (PSCs) …
Read PDFRepeated implantation failure (RIF) presents a significant challenge to in vitro fertilization (IVF), and abnormalities in the endometrium often play a crucial role in RIF. To enhance and deepen our understanding of tissue context in …
Read PDF<h4>Background</h4>Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality. Chromosome 8 open reading frame 33 (C8orf33) has been noted as a potential oncogenic factor in several cancers, but its biological roles and regulatory mechanism …
Read PDFCertain characteristics, such as high heterogeneity, a complex tumor microenvironment, metastatic potential, and drug resistance, render Lung cancer (LC) a formidable challenge for clinical management. With rapid advancements in high-throughput sequencing, medical imaging, and digital …
Read PDFPlant tissues exhibit a layered architecture that makes spatial context decisive for interpreting transcriptional changes. This review explains why the location of gene expression is as important as its magnitude and synthesizes advances uniting single-cell/nucleus …
Read PDFSpatial transcriptomics captures context-dependent gene expression; however, existing workflows do not consistently account for measurement scale and often rely on a user-defined spatial neighbor graph, making results sensitive to this choice and limiting cross-study comparability. …
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