Spatial omics technology integrates the concept of space into omics research and retains the spatial information of tissues or organs while obtaining molecular information. It is characterized by the ability to visualize changes in molecular information and yields intuitive and vivid visual results. Spatial omics technologies include spatial transcriptomics, spatial proteomics, spatial metabolomics, and other technologies, the most widely used of which are spatial transcriptomics and spatial proteomics. The tumor microenvironment refers to the surrounding microenvironment in which tumor cells exist, including the surrounding blood vessels, immune cells, fibroblasts, bone marrow-derived inflammatory cells, various signaling molecules, and extracellular matrix. A key issue in modern tumor biology is the application of spatial omics to the study of the tumor microenvironment, which can reveal problems that conventional research techniques cannot, potentially leading to the development of novel therapeutic agents for cancer. This paper summarizes the progress of research on spatial transcriptomics and spatial proteomics technologies for characterizing the tumor immune microenvironment.
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http://dx.doi.org/10.32604/or.2023.029494 | DOI Listing |
Nat Commun
January 2025
Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
Spatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of such technologies offers the opportunity to delineate cell-type spatial relationships, particularly across different length scales, and enhance our understanding of tissue organization and function. To quantify such multi-scale cell-type spatial relationships, we present CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
University of Washington, Seattle, WA, USA.
Background: The BRAIN Initiative has stimulated development of novel single cell and spatial molecular approaches to understand human brain structure and function. However, traditional methods for human brain specimen collection, including retrospective archival tissues, have not been optimized for these latest methods. A modernized approach that optimizes tissue quality, anatomical precision, and comprehensive, quantitative neuropathological assessments is needed to maximize the impact of the tremendous investment and remarkable technological advances in human neuroscience research.
View Article and Find Full Text PDFNat Commun
January 2025
Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
Recent advancements in biological technologies have enabled the measurement of spatially resolved multi-omics data, yet computational algorithms for this purpose are scarce. Existing tools target either single omics or lack spatial integration. We generate a graph neural network algorithm named COSMOS to address this gap and demonstrated the superior performance of COSMOS in domain segmentation, visualization, and spatiotemporal map for spatially resolved multi-omics data integration tasks.
View Article and Find Full Text PDFZhonghua Kou Qiang Yi Xue Za Zhi
January 2025
The Stomatology Center and Research Center of Oral and Maxillofacial Development and Regeneration of Xiangya Hospital; Academician Workstation for Oral & Maxillofacial Regenerative Medicine, Central South University, Changsha410008, China.
Single-cell and spatial multi-omics technologies enable the simultaneous analysis of thousands of cells in various states, revealing their transcriptional profiles, chromatin accessibility, and spatial positioning. Recent advances in single-cell multi-omics have led to significant discoveries regarding the definition, function, evolution, and interaction of various cell subtypes during tooth development. We summarize key findings from recent single-cell multi-omics studies on tooth development, highlighting their contributions to the field and discussing future perspectives in dental developmental genomics research.
View Article and Find Full Text PDFJ Adv Res
December 2024
State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China. Electronic address:
Introduction: The periodontal ligament (PDL), a dynamic connective tissue that anchors teeth to the alveolar bone, enables tooth retention and facilitates continuous turnover. The integrity of the periodontium is maintained by periodontal ligament stem cells (PDLSCs), whose dysfunction and senescence with age can disrupt tissue homeostasis, hinder injury repair, and lead to tooth loss, ultimately impacting overall health. Transforming growth factor-β1 (TGF-β1) is known for its regenerative properties and as a functional paracrine factor in stem cell therapy, but its precise role in modulating PDLSC activity remains controversial and poorly understood.
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