The diversification of methods for studying cell–cell interactions and communication

Armingol, Erick; Baghdassarian, Hratch M.; Lewis, Nathan E.

doi:10.1038/s41576-023-00685-8

Cited by 21 publications

(6 citation statements)

References 211 publications

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“…Cell:cell communication inferred from single-cell data sets can be contextualized with knowledge of distribution of cell types and cell neighborhoods from spatial approaches. 148 Figure 5 summarizes key signaling interactions in three cardiac tissue niches explored using single-cell and spatial approaches.…”

Section: Cardiac Tissue Microenvironmentsmentioning

confidence: 99%

Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics

Palmer,

Rosenthal,

Teichmann

et al. 2024

Circulation Research

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Throughout our lifetime, each beat of the heart requires the coordinated action of multiple cardiac cell types. Understanding cardiac cell biology, its intricate microenvironments, and the mechanisms that govern their function in health and disease are crucial to designing novel therapeutical and behavioral interventions. Recent advances in single-cell and spatial omics technologies have significantly propelled this understanding, offering novel insights into the cellular diversity and function and the complex interactions of cardiac tissue. This review provides a comprehensive overview of the cellular landscape of the heart, bridging the gap between suspension-based and emerging in situ approaches, focusing on the experimental and computational challenges, comparative analyses of mouse and human cardiac systems, and the rising contextualization of cardiac cells within their niches. As we explore the heart at this unprecedented resolution, integrating insights from both mouse and human studies will pave the way for novel diagnostic tools and therapeutic interventions, ultimately improving outcomes for patients with cardiovascular diseases.

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Section: Cardiac Tissue Microenvironmentsmentioning

confidence: 99%

Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics

Palmer,

Rosenthal,

Teichmann

et al. 2024

Circulation Research

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“…The factors driving fibrogenesis are complex, including the communication pathways between neighbouring cells and the effects of surrounding microenvironments [ 20 , 21 ]. Therefore, investigation of cell-cell communication is essential for a comprehensive understanding of the molecular mechanisms of renal fibrogenesis, which is not only restricted to the single-cell level but also needs to encompass other aspects such as ligand-receptor interactions and spatial context [ 22 ]. Since a variety of new techniques are available selecting an appropriate method according to the tissue type and the scientific question is important.…”

Section: Spatial Analysis Of Cell-cell Communicationmentioning

confidence: 99%

New tools to study renal fibrogenesis

Liao,

Scheidereit,

Kuppe

2024

Current Opinion in Nephrology &Amp; Hypertension

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Purpose of the review Kidney fibrosis is a key pathological aspect and outcome of chronic kidney disease (CKD). The advent of multiomic analyses using human kidney tissue, enabled by technological advances, marks a new chapter of discovery in fibrosis research of the kidney. This review highlights the rapid advancements of single-cell and spatial multiomic techniques that offer new avenues for exploring research questions related to human kidney fibrosis development. Recent findings We recently focused on understanding the origin and transition of myofibroblasts in kidney fibrosis using single-cell RNA sequencing (scRNA-seq) [1]. We analysed cells from healthy human kidneys and compared them to patient samples with CKD. We identified PDGFRα+/PDGFRβ+ mesenchymal cells as the primary cellular source of extracellular matrix (ECM) in human kidney fibrosis. We found several commonly shared cell states of fibroblasts and myofibroblasts and provided insights into molecular regulators. Novel single-cell and spatial multiomics tools are now available to shed light on cell lineages, the plasticity of kidney cells and cell-cell communication in fibrosis. Summary As further single-cell and spatial multiomic approaches are being developed, opportunities to apply these methods to human kidney tissues expand similarly. Careful design and optimisation of the multiomic experiments are needed to answer questions related to cell lineages, plasticity and cell-cell communication in kidney fibrosis.

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“…The goal of the group was to run multiple spatial CCC methods and compare evaluations/visualizations and results. We selected the methods from Armingol et al (2024). A more detailed table can be found on the separate GitHub repository of this workgroup.…”

Section: Workgroup Cell-cell Communicationmentioning

confidence: 99%

VIB Hackathon on spatial omics tools and methods

Rombaut,

Pollaris,

Sang-aram

et al. 2024

Preprint

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During a three-day hackathon, work was performed on various topics within the field of spatial omics data analysis. The topics were organized in five workgroups and included benchmarking, pipelines, spatial transcriptomics, spatial proteomics, spatial multi-omics and cell-cell communication. Most tools and methods were considered in the context of the Python ecosystem for spatial (SpatialData) and single-cell (scverse) data analysis.

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The diversification of methods for studying cell–cell interactions and communication

Cited by 21 publications

References 211 publications

Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics

Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics

New tools to study renal fibrogenesis

VIB Hackathon on spatial omics tools and methods

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