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Spatial omics integrates molecular profiling with spatial tissue context, enabling high-resolution analysis of gene expression, protein interactions, and epigenetic modifications. This approach provides critical insights into disease mechanisms and therapeutic responses, with applications in cancer, neurology, and immunology. Spatial omics technologies, including spatial transcriptomics, proteomics, and epigenomics, facilitate the study of cellular heterogeneity, tissue organization, and cell-cell interactions within their native environments. Despite challenges in data complexity and integration, advancements in multi-omics pipelines and computational tools are enhancing data accuracy and biological interpretation. This review provides a comprehensive overview of key spatial omics technologies, their analytical methods, validation strategies, and clinical applications. By integrating spatially resolved molecular data with traditional omics, spatial omics is transforming precision medicine, biomarker discovery, and personalized therapy. Future research should focus on improving standardization, reproducibility, and multimodal data integration to fully realize the potential of spatial omics in clinical and translational research.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC12071594 | PMC |
http://dx.doi.org/10.3390/ijms26093949 | DOI Listing |
Gigascience
January 2025
Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria.
Background: Pancreatic ductal adenocarcinoma (PDAC), the most common and aggressive form of pancreatic cancer, exhibits profound intratumor morphological heterogeneity, complicating the elucidation of the underlying molecular mechanisms driving its progression.
Results: We present and validate an optimized framework for RNA sequencing (RNA-seq) of multiple spatially resolved laser micro-dissected tumor areas (LMD-seq), along with methodological and analytical details to maximize reproducibility and data mining. This approach enhances sensitivity in detecting lowly expressed genes, outperforming single-cell RNA-seq methods, particularly in identifying rare tumor cell populations and transcriptional programs with low expression.
Summary: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics.
View Article and Find Full Text PDFFront Immunol
September 2025
Department of Orthopedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China.
Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by sustained synovial inflammation and the gradual destruction of joint structures. Although conventional T cells have historically been viewed as central to RA pathogenesis, increasing attention has recently focused on unconventional T cell subsets, such as natural killer T (NKT) cells, mucosal-associated invariant T (MAIT) cells, and gamma delta T (γδ T) cells. Functioning as a bridge between innate and adaptive immunity, these cells contribute to RA immunopathogenesis by producing cytokines, exerting cytotoxic effects, and interacting with various immune and stromal cells.
View Article and Find Full Text PDFBrain
September 2025
Institute of Neuroscience, Kunming Medical University, Kunming 650500, Yunnan Province, China.
The hippocampus (HC), a central hub for memory and cognition, exhibits unique metabolic resilience during aging despite widespread brain glucose hypometabolism. Here, we report that aged humans and macaques paradoxically display elevated HC glucose uptake (18F-FDG PET SUVR) alongside strengthened connectivity to sensory-motor and limbic networks-an adaptive rewiring revealed by graph-theoretical metabolic network analysis. Integrated multi-omics profiling identified STT3A (oligosaccharyltransferase) and ALG5 (dolichyl-phosphate β-glucosyltransferase) as key regulators of age-related HC adaptation, with their upregulation in aged macaque hippocampi driving N-glycosylation-dependent metabolic reprogramming.
View Article and Find Full Text PDFFront Oncol
August 2025
International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, China.
Tumor draining lymph nodes (TDLNs), as secondary lymphoid organs, are pivotal in initiating and regulating adaptive immune responses. Historically, TDLNs were recognized primarily as metastasis gateways in cancer, promoting radical dissection to prevent recurrence. However, emerging preclinical studies reveals their critical role in orchestrating systemic anti-tumor immune responses during cancer therapy, highlighting the dilemma of balancing lymph nodes (LNs) preservation with metastasis control.
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