Nature Protocols, Journal Year: 2025, Volume and Issue: unknown
Published: March 25, 2025
Language: Английский
Nature Protocols, Journal Year: 2024, Volume and Issue: unknown
Published: Sept. 16, 2024
Language: Английский
Citations
94
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: Nov. 5, 2023
Abstract Recent advances in single-cell sequencing technologies offer an opportunity to explore cell-cell communication tissues systematically and with reduced bias. A key challenge is the integration between known molecular interactions measurements into a framework identify analyze complex networks. Previously, we developed computational tool, named CellChat that infers analyzes networks from RNA-sequencing (scRNA-seq) data within easily interpretable framework. quantifies signaling probability two cell groups using simplified mass action-based model, which incorporates core interaction ligands receptors multi-subunit structure along modulation by cofactors. v2 updated version includes direct incorporation of spatial locations cells, if available, infer spatially proximal communication, additional comparison functionalities, expanded database ligand-receptor pairs rich annotations, Interactive Explorer. Here provide step-by-step protocol for can be used both scRNA-seq resolved transcriptomic data, including inference analysis one dataset identification altered across different datasets. The steps applying transcriptomics are described detail. R implementation toolkit tutorials graphic outputs available at https://github.com/jinworks/CellChat . This typically takes around 20 minutes, no specialized prior bioinformatics training required complete task.
Language: Английский
Citations
93
Cell, Journal Year: 2024, Volume and Issue: 187(10), P. 2485 - 2501.e26
Published: April 22, 2024
Glioma contains malignant cells in diverse states. Here, we combine spatial transcriptomics, proteomics, and computational approaches to define glioma cellular states uncover their organization. We find three prominent modes of First, gliomas are composed small local environments, each typically enriched with one major state. Second, specific pairs preferentially reside proximity across multiple scales. This pairing is consistent tumors. Third, these pairwise interactions collectively a global architecture five layers. Hypoxia appears drive the layers, as it associated long-range organization that includes all cancer cell Accordingly, tumor regions distant from any hypoxic/necrotic foci tumors lack hypoxia such low-grade IDH-mutant less organized. In summary, provide conceptual framework for glioma, highlighting tissue organizer.
Language: Английский
Citations
83
Nature, Journal Year: 2024, Volume and Issue: 627(8005), P. 854 - 864
Published: March 13, 2024
Abstract The heart, which is the first organ to develop, highly dependent on its form function 1,2 . However, how diverse cardiac cell types spatially coordinate create complex morphological structures that are crucial for heart remains unclear. Here we integrated single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization resolve identity of develop human heart. This approach also provided a spatial mapping individual cells enables illumination their organization into cellular communities distinct structures. We discovered many these further specified subpopulations exclusive specific communities, support specialization according ecosystem and anatomical region. In particular, ventricular cardiomyocyte displayed an unexpected laminar across wall formed, other subpopulations, several communities. Interrogating cell–cell interactions within using vivo conditional genetic mouse models vitro pluripotent stem systems revealed multicellular signalling pathways orchestrate during morphogenesis. These detailed findings social constructing remodelling offer new insights structural diseases engineering tissues repair.
Language: Английский
Citations
70
Cell, Journal Year: 2024, Volume and Issue: 187(17), P. 4488 - 4519
Published: Aug. 1, 2024
Language: Английский
Citations
30
Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)
Published: June 4, 2024
Abstract Semaglutide, a glucagon-like peptide-1 receptor agonist, is clinically used as glucose-lowering and weight loss medication due to its effects on energy metabolism. In heart failure, production impaired altered mitochondrial function increased glycolysis. However, the impact of semaglutide cardiomyocyte metabolism under pressure overload remains unclear. Here we demonstrate that improves cardiac reduces hypertrophy fibrosis in mouse model overload-induced failure. Semaglutide preserves structure chronic stress. Metabolomics reveals damage, lipid accumulation, ATP deficiency by promoting pyruvate entry into tricarboxylic acid cycle increasing fatty oxidation. Transcriptional analysis shows regulates myocardial through Creb5/NR4a1 axis PI3K/AKT pathway, reducing NR4a1 expression translocation mitochondria. knockdown ameliorates dysfunction abnormal glucose heart. These findings suggest may be therapeutic agent for improving remodeling modulating
Language: Английский
Citations
26
Genome Medicine, Journal Year: 2024, Volume and Issue: 16(1)
Published: Jan. 18, 2024
Abstract Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome parallel or even same tissue section. This review focuses on recent advancements spatial multi-omics technologies, including novel computational approaches. We discuss low-resolution high-resolution methods which can resolve up 10,000 individual molecules at subcellular level. By applying integrating these techniques, researchers recently gained valuable insights into molecular circuits mechanisms govern cell biology along cardiovascular disease spectrum. provide an overview current approaches, with focus integration datasets, highlighting strengths weaknesses various pipelines. These tools play crucial role analyzing interpreting facilitating discovery new findings, enhancing translational research. Despite nontrivial challenges, such need for standardization experimental setups, analysis, improved tools, application holds tremendous potential revolutionizing our understanding human processes identification biomarkers therapeutic targets. Exciting opportunities lie ahead field will likely contribute advancement personalized medicine diseases.
Language: Английский
Citations
25
Nature, Journal Year: 2024, Volume and Issue: 628(8009), P. 854 - 862
Published: April 3, 2024
Abstract The intestinal immune system is highly adapted to maintaining tolerance the commensal microbiota and self-antigens while defending against invading pathogens 1,2 . Recognizing how diverse network of local cells establish homeostasis maintains it in complex environment gut critical understanding can be re-established following dysfunction, such as inflammatory disorders. Although cell molecular interactions that control T regulatory (T reg ) development function have been identified 3,4 , less known about cellular neighbourhoods spatial compartmentalization shapes microorganism-reactive function. Here we used vivo live imaging, photo-activation-guided single-cell RNA sequencing 5–7 transcriptomics follow natural history are reactive towards Helicobacter hepaticus through space time settings inflammation. antigen stimulation occur anywhere tissue, lamina propria—but not embedded lymphoid aggregates—is key microniche supports effector (eT eT stable once their niche established; however, unleashing inflammation breaks down compartmentalization, leading dominance CD103 + SIRPα dendritic propria. We identify validate putative tolerogenic interaction between CD206 macrophages propria receptor–ligand pairs likely govern interaction. Our results reveal a mechanism demonstrate knowledge may contribute next generation tolerance-inducing therapies.
Language: Английский
Citations
25
Biomarker Research, Journal Year: 2024, Volume and Issue: 12(1)
Published: Sept. 27, 2024
Abstract Cells, as the fundamental units of life, contain multidimensional spatiotemporal information. Single-cell RNA sequencing (scRNA-seq) is revolutionizing biomedical science by analyzing cellular state and intercellular heterogeneity. Undoubtedly, single-cell transcriptomics has emerged one most vibrant research fields today. With optimization innovation technologies, intricate details concealed within cells are gradually unveiled. The combination scRNA-seq other multi-omics at forefront field. This involves simultaneously measuring various omics data individual cells, expanding our understanding across a broader spectrum dimensions. precisely captures aspects transcriptomes, immune repertoire, spatial information, temporal epitopes, in diverse contexts. In addition to depicting cell atlas normal or diseased tissues, it also provides cornerstone for studying differentiation development patterns, disease heterogeneity, drug resistance mechanisms, treatment strategies. Herein, we review traditional technologies outline latest advancements multi-omics. We summarize current status challenges applying biological clinical applications. Finally, discuss limitations potential strategies address them.
Language: Английский
Citations
23
Nature Cardiovascular Research, Journal Year: 2024, Volume and Issue: 3(3), P. 283 - 300
Published: Feb. 14, 2024
Language: Английский
Citations
19