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Spatial proteomics is a multidimensional technique that studies the spatial distribution and function of proteins within cells or tissues across both spatial and temporal dimensions. This field multidimensionally reveals the complex structure of the human proteome, including the characteristics of protein spatial distribution, dynamic protein translocation, and protein interaction networks. Recently, as a crucial method for studying protein spatial localization, spatial proteomics has been applied in the clinical investigation of various diseases. This review summarizes the fundamental concepts and characteristics of tissue-level spatial proteomics, its research progress in common human diseases such as cancer, neurological disorders, cardiovascular diseases, autoimmune diseases, and anticipates its future development trends. The aim is to highlight the significant impact of spatial proteomics on understanding disease pathogenesis, advancing diagnostic methods, and developing potential therapeutic targets in clinical research.
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http://dx.doi.org/10.1186/s12953-024-00231-2 | DOI Listing |
Cell Syst
September 2025
Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA. Electronic address:
Identifying cell types in highly multiplexed images is essential for understanding tissue spatial organization. Current cell-type annotation methods often rely on extensive reference images and manual adjustments. In this work, we present a tool, the Robust Image-Based Cell Annotator (RIBCA), that enables accurate, automated, unbiased, and fine-grained cell-type annotation for images with a wide range of antibody panels without requiring additional model training or human intervention.
View Article and Find Full Text PDFElife
September 2025
Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig Maximilians-Universität München, Munich, Germany.
The rapid emergence of mineralized structures in diverse animal groups during the late Ediacaran and early Cambrian periods likely resulted from modifications of pre-adapted biomineralization genes inherited from a common ancestor. As the oldest extant phylum with mineralized structures, sponges are key to understanding animal biomineralization. Yet, the biomineralization process in sponges, particularly in forming spicules, is not well understood.
View Article and Find Full Text PDFJ Leukoc Biol
September 2025
School of Pharmacy and Medical Science and Central Facility for Genomics, Griffith University, Parklands Drive, QLD, Australia.
There is limited understanding of the impact of anti-IL5 treatment on nasal polyp tissue biology in chronic rhinosinusitis with nasal polyps (CRSwNP). This study examined nasal polyp tissue cellular proteome and transcriptome responses to anti-IL5 treatment in CRSwNP utilising spatial profiling. GeoMx™ Digital Spatial Profiling (DSP) of 80 proteins and 1,833 mRNA targets in the polyp stroma and the whole transcriptome (18,815 mRNA targets) in polyp epithelia was undertaken on sinonasal biopsies collected from 20 individuals with eosinophilic CRSwNP before and after 16 and 24 weeks of mepolizumab treatment.
View Article and Find Full Text PDFBioinform Adv
August 2025
Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
Motivation: Advances in high-throughput technologies have shifted the focus from bulk to single cell or spatial transcriptomic and proteomic analysis of tissues and cell cultures. The resulting increase in gene and/or protein lists leads to the subsequent growth of up- and downregulated pathways lists. This trend creates the need for pathway-network based integration strategies that allow quick exploration of shared and distinct mechanisms across datasets.
View Article and Find Full Text PDFConnect Tissue Res
September 2025
Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland.
Osteoarthritis (OA) is a multifactorial, mechano-inflammatory joint disorder characterized by cartilage degradation, synovial inflammation, and subchondral bone remodeling. Despite its high prevalence and significant impact on quality of life, no disease-modifying treatments have been approved. In many other disease areas, advanced omics technologies are impacting the development of advanced therapies.
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