Review of Single-Cell RNA Sequencing in the Heart

Yamada, Shintaro; Nomura, Seitaro

doi:10.3390/ijms21218345

Cited by 60 publications

(39 citation statements)

References 68 publications

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“…Notably, the change in droplet dimensions from ~ 125 to ~ 85 μm lead to impressive 2- to 4-fold increases in the number of nuclei that provided > 1000 UMI counts when different mouse brain regions were profiled. Conversely, increasing droplet dimensions is expected to be beneficial for particularly large cells, such as adult cardiomyctes (~ 100 μM), that have so far required specialised scRNA-seq setups that preclude massively parallal studies 18 , 19 . Due to the smooth pressure-based pump system employed, and like selective other custom 9 and commercial 10 platforms, droplet manipulation is readily achieved with the Nadia and accompanying Innovate.…”

Section: Resultsmentioning

confidence: 99%

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

Davey

Wong²,

Konopacki³

et al. 2021

Sci Rep

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Single cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3′ mRNA capture of ~ 50,000 single cells or individual nuclei in a single run. The precise pressure-based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efficiencies that compare favorably in the field. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of different buffers and barcoded bead configurations to facilitate diverse applications. Finally, by 3′ mRNA profiling asynchronous human and mouse cells at different phases of the cell cycle, we demonstrate the system's ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this provided supportive evidence for multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and flexible technology for future transcriptomic studies, and other related applications, at cell resolution.

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Section: Resultsmentioning

confidence: 99%

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

Davey

Wong²,

Konopacki³

et al. 2021

Sci Rep

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“…The heterogeneity of fibroblasts has been demonstrated using single-cell RNA sequencing (scRNAseq), a relatively new, but rapidly developing, technology [ 28 ]. It allows the comprehensive characterization of gene expression and relationships in individual cells.…”

Section: Classification Of Fibroblastsmentioning

confidence: 99%

Cardiac Fibrosis and Fibroblasts

Kurose

2021

Cells

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Cardiac fibrosis is the excess deposition of extracellular matrix (ECM), such as collagen. Myofibroblasts are major players in the production of collagen, and are differentiated primarily from resident fibroblasts. Collagen can compensate for the dead cells produced by injury. The appropriate production of collagen is beneficial for preserving the structural integrity of the heart, and protects the heart from cardiac rupture. However, excessive deposition of collagen causes cardiac dysfunction. Recent studies have demonstrated that myofibroblasts can change their phenotypes. In addition, myofibroblasts are found to have functions other than ECM production. Myofibroblasts have macrophage-like functions, in which they engulf dead cells and secrete anti-inflammatory cytokines. Research into fibroblasts has been delayed due to the lack of selective markers for the identification of fibroblasts. In recent years, it has become possible to genetically label fibroblasts and perform sequencing at single-cell levels. Based on new technologies, the origins of fibroblasts and myofibroblasts, time-dependent changes in fibroblast states after injury, and fibroblast heterogeneity have been demonstrated. In this paper, recent advances in fibroblast and myofibroblast research are reviewed.

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“…The Chromium system restricts the size of cells to be less than 30μm in diameter. 31 Alternatively, plate-based FACS with a larger nozzle size (up to 130μm) can be used to capture cells of large size such as adult cardiomyocytes (CMs). 32 In addition, single-nuclei RNA sequencing (snRNA-seq), a method for profiling gene expression in cells that are difficult to be dissociated, is an alternative to scRNA-seq to capture adult and large cardiomyocytes.…”

Section: The Workflow Of Scrna-seqmentioning

confidence: 99%

“…The droplet-based Chromium platform is suitable for scRNA-seq studies with cells smaller than 30μm. 31 However, adult CMs in mice and humans are relatively larger than 100μm in diameter, which deterred the use of this single-cell system. 31 Therefore, snRNA-seq, which extracted nuclei rather than intact CMs, or plate-based FACS platform could be…”

Section: Limitations Of Scrna-seq In Cardiac Tissuementioning

confidence: 99%

Single-Cell RNA Sequencing (scRNA-seq) in Cardiac Tissue: Applications and Limitations

Wang¹,

Gu²,

Liu³

et al. 2021

VHRM

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Cardiovascular diseases (CVDs) are a group of disorders of the blood vessels and heart, which are considered as the leading causes of death worldwide. The pathology of CVDs could be related to the functional abnormalities of multiple cell types in the heart. Single-cell RNA sequencing (scRNA-seq) technology is a powerful method for characterizing individual cells and elucidating the molecular mechanisms by providing a high resolution of transcriptomic changes at the single-cell level. Specifically, scRNA-seq has provided novel insights into CVDs by identifying rare cardiac cell types, inferring the trajectory tree, estimating RNA velocity, elucidating the cell-cell communication, and comparing healthy and pathological heart samples. In this review, we summarize the different scRNAseq platforms and published single-cell datasets in the cardiovascular field, and describe the utilities and limitations of this technology. Lastly, we discuss the future perspective of the application of scRNA-seq technology into cardiovascular research.

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Review of Single-Cell RNA Sequencing in the Heart

Cited by 60 publications

References 68 publications

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

Cardiac Fibrosis and Fibroblasts

Single-Cell RNA Sequencing (scRNA-seq) in Cardiac Tissue: Applications and Limitations

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