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The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of single-cell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications, particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.
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http://dx.doi.org/10.1007/s11427-024-2770-x | DOI Listing |
Neurol Res
September 2025
Henan Provincial People's Hospital, Department of Surgery of Spine and Spinal Cord, People's Hospital of Zhengzhou University, Zhengzhou, China.
Background: Immunotherapy holds significant yet underexplored potential for low-grade glioma (LGG) treatment. We therefore interrogated the role of Fanconi Anemia Complementation Group C (FANCC) as a novel immune checkpoint regulator given its spatial correlation with tumor microenvironments and clinical associations with immunosuppressive markers.
Objectives: FANCC is implicated in various tumor progressions; its role in LGG remains unexplored.
J Pathol
September 2025
Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA.
Serous endometrial carcinoma (SEC) is one of the most lethal types of uterine cancer, responsible for about 40% of all endometrial cancer-related deaths. Cell state dynamics during the early stages of SEC remain largely unknown, thereby hindering early detection and treatment of this disease. Here, we provide a comprehensive census of cell types and their states for normal, predysplastic, and dysplastic endometrium in a genetic mouse model of SEC.
View Article and Find Full Text PDFNew Phytol
September 2025
Institute of Plant Biochemistry and Cluster of Excellences on Plant Science (CEPLAS), Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Düsseldorf, 40225, Germany.
In mammals, blood sugar levels are tightly controlled by two hormones: insulin and glucagon. In flowering plants, a comparable regulatory mechanism exists, mediated by the sugar-signalling molecule trehalose 6-phosphate (Tre6P). Similar to insulin, Tre6P functions as a signal and negative feedback regulator of sucrose, the main transport sugar in vascular plants.
View Article and Find Full Text PDFAnal Chem
September 2025
State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
Deciphering the multicomponent of cell membranes at the single-cell level is critical for understanding pathological mechanisms such as tumor metastasis, yet remains technically daunting due to the membrane's nanoscale thickness and ultralow molecular abundance. Here, we introduce a surface-assisted vacuum ultraviolet laser desorption-ionization mass spectrometry imaging (SAVUVDI-MSI) platform that overcomes long-standing challenges of cytoplasmic interference and insufficient sensitivity. Leveraging the nanoscale depth profiling capability of VUV-LDI, we achieve precise ablation of a single-cell membrane.
View Article and Find Full Text PDFPLoS Comput Biol
September 2025
OmnibusXLab, OmnibusX Company Limited, Ho Chi Minh City, Vietnam.
OmnibusX is an integrated, privacy-centric platform that enables code-free multi-omics data analysis by bridging computational methodologies with user-friendly interfaces. Designed to overcome challenges posed by fragmented analytical tools and high computational barriers, OmnibusX consolidates workflows for diverse technologies - including bulk RNA-seq, single-cell RNA-seq, single-cell ATAC-seq, and spatial transcriptomics - into a single, cohesive application. The application integrates established open-source tools such as Scanpy, DESeq2, SciPy, and scikit-learn into transparent, reproducible pipelines, offering users control over analytical parameters.
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