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.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/s11427-024-2770-x | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy.
Sci Immunol
January 2025
Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA.
Understanding how intratumoral immune populations coordinate antitumor responses after therapy can guide treatment prioritization. We systematically analyzed an established immunotherapy, donor lymphocyte infusion (DLI), by assessing 348,905 single-cell transcriptomes from 74 longitudinal bone marrow samples of 25 patients with relapsed leukemia; a subset was evaluated by both protein- and transcriptome-based spatial analysis. In acute myeloid leukemia (AML) DLI responders, we identified clonally expanded CD8 cytotoxic T lymphocytes with in vitro specificity for patient-matched AML.
View Article and Find Full Text PDFAn ancient apical patterning system sets the position of the forebrain in chordates.
Sci Adv
January 2025
Department of Zoology, University of Cambridge, Cambridge, UK.
The evolutionary origin of the vertebrate brain remains a major subject of debate, as its development from a dorsal tubular neuroepithelium is unique to chordates. To shed light on the evolutionary emergence of the vertebrate brain, we compared anterior neuroectoderm development across deuterostome species, using available single-cell datasets from sea urchin, amphioxus, and zebrafish embryos. We identified a conserved gene co-expression module, comparable to the anterior gene regulatory network (aGRN) controlling apical organ development in ambulacrarians, and spatially mapped it by multiplexed in situ hybridization to the developing retina and hypothalamus of chordates.
View Article and Find Full Text PDFAnalysis of Drug Molecules in Living Cells.
Crit Rev Anal Chem
January 2025
Department of Bioengineering, Faculty of Engineering, The University of Edinburgh, Edinburgh, UK.
Cells are the fundamental units of life, comprising a highly concentrated and complex assembly of biomolecules that interact dynamic ally across spatial and temporal scales. Living cells are constantly undergoing dynamic processes, therefore, to understand the interactions between drug molecules and living cells is of paramount importance in the biomedical sciences and pharmaceutical development. Compared with traditional end-point assays and fixed cell analysis, analysis of drug molecules in living cells can provide more insight into the effects of drugs on cells in real-time and allowing for a better understanding of drug mechanisms and effects, which will contribute to the development of drug developing and testing and personalize medicine.
View Article and Find Full Text PDFRoles of Cellular Neighborhoods in Hepatocellular Carcinoma Pathogenesis.
Annu Rev Pathol
January 2025
Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
The development of hepatocellular carcinoma (HCC) involves an intricate interplay among various cell types within the liver. Unraveling the orchestration of these cells, particularly in the context of various etiologies, may hold the key to deciphering the underlying mechanisms of this complex disease. The advancement of single-cell and spatial technologies has revolutionized our ability to determine cellular neighborhoods and understand their crucial roles in disease pathogenesis.
View Article and Find Full Text PDFResolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges.
Microbiol Mol Biol Rev
January 2025
General Microbiology, Technische Universität Dresden, Dresden, Germany.
SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in eukaryotes, it originates in prokaryotes. Coordinated aggregation of individual cells within the confines of a colony results in emerging, higher-level functions that benefit the population as a whole.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!