Single-Cell Resolution of Temporal Gene Expression during Heart Development

DeLaughter, Daniel M.; Bick, Alexander; Wakimoto, Hiroko; McKean, David; Gorham, Joshua M.; Kathiriya, Irfan S.; Hinson, J. Travis; Homsy, Jason; Gray, Jesse; Pu, William T.; Bruneau, Benoit G.; Seidman, Jonathan G.; Seidman, Christine E.

doi:10.1016/j.devcel.2016.10.001

Cited by 380 publications

(430 citation statements)

References 53 publications

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“…17,18 To introduce a single base pair mutation at Chr7: 128494628 (G>A) in hESCs, we designed a single guide RNA (sgRNA) targeting the vicinity of Chr7: 128494628 using the online CRISPR Design tool (http://crispr.mit.edu/) and cloned the sgRNA sequence into plasmid PX458 (Addgene, USA; 48138), 19 which carries the nuclease spCas9 fused with an EGFP reporter. A single-stranded oligodeoxynucleotide (ssODN) was synthesized and used as a repair template for homology-directed repair.…”

Section: Methodsmentioning

confidence: 99%

Novel Mutation in FLNC (Filamin C) Causes Familial Restrictive Cardiomyopathy

Tucker

McLellan

et al. 2017

Circ Cardiovasc Genet

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Background Restrictive cardiomyopathy (RCM) is a rare cardiomyopathy characterized by impaired diastolic ventricular function resulting in a poor clinical prognosis. Rarely, heritable forms of RCM have been reported and mutations underlying RCM have been identified in genes that govern the contractile function of the cardiomyocytes. Methods and Results We evaluated 8 family members across four generations by history, physical examination, electrocardiography and echocardiography. Affected individuals presented with a pleitropic syndrome of progressive RCM, atrioventricular septal defects, and a high prevalence of atrial fibrillation. Exome sequencing of 5 affected members identified a single novel missense variant in a highly conserved residue of FLNC (p.V2297M). FLNC encodes Filamin C, a protein that acts as both a scaffold for the assembly and organization of the central contractile unit of striated muscle, and also as a mechanosensitive signaling molecule during cell migration and shear stress. Immunohistochemical analysis of Filamin C localization in cardiac tissue from an affected family member revealed a diminished localization at the z-disk, whereas traditional localization at the intercalated disk was preserved. Stem-cell derived cardiomyocytes mutated to carry the effect allele had diminished contractile activity when compared to controls. Conclusion We have identified a novel variant in FLNC as pathogenic variant for familial RCM, a finding that further expands upon the genetic basis of this rare and morbid cardiomyopathy.

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Section: Methodsmentioning

confidence: 99%

Novel Mutation in FLNC (Filamin C) Causes Familial Restrictive Cardiomyopathy

Tucker

McLellan

et al. 2017

Circ Cardiovasc Genet

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“…Most strikingly, scRNA-seq approaches offer unique opportunities to study transcriptome dynamics with high (pseudo)temporal resolution, providing single cells can be obtained from successive stages along developmental trajectories of interest. In the past few years, scRNA-seq-based analyses have been extensively used to characterized developmental transitions in the hematopoietic system (Bendall et al, 2014;Moignard et al, 2015) , during muscle differentiation (Trapnell et al, 2014) , in early mesoderm development in the mouse (Scialdone et al, 2016) , and during cardiac organogenesis in the mouse, and in vitro cardiomyocyte differentiation from human embryonic stem cells (DeLaughter et al, 2016;Li et al, 2016) . The latter two studies provided insights into the transition between the earliest multipotent progenitors and initial cardiomyocyte differentiation.…”

Section: Introductionmentioning

confidence: 99%

A single cell transcriptional roadmap for cardiopharyngeal fate diversification

Wang

Niu

Jullian

et al. 2017

Preprint

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SummaryDynamic gene expression programs determine multipotent cell states and fate choices during development. Multipotent progenitors for cardiomyocytes and branchiomeric head muscles populate the pharyngeal mesoderm of vertebrate embryos, but the mechanisms underlying cardiopharyngeal multipotency and heart vs. head muscle fate choices remain elusive. The tunicate Ciona emerged as a simple chordate model to study cardiopharyngeal development with unprecedented spatio-temporal resolution. We analyzed the transcriptome of single cardiopharyngeal lineage cells isolated at successive time points encompassing the transitions from multipotent progenitors to distinct first and second heart, and pharyngeal muscle precursors. We reconstructed the three cardiopharyngeal developmental trajectories, and characterized gene expression dynamics and regulatory states underlying each fate choice.Experimental perturbations and bulk transcriptome analyses revealed that ongoing FGF/MAPK signaling maintains cardiopharyngeal multipotency and promotes the pharyngeal muscle fate, whereas signal termination permits the deployment of a full pan-cardiac program and heart fate specification. We identified the Dach1/2 homolog as a novel evolutionarily conserved second-heart-field-specific factor and demonstrate, through lineage tracing and CRISPR/Cas9 perturbations, that it operates downstream of Tbx1/10 to actively suppress the first heart lineage program. This data indicates that the regulatory state of multipotent cardiopharyngeal progenitors determines the first vs. second heart lineage choice, and that Tbx1/10 acts as a bona fide regulator of cardiopharyngeal multipotency.2 All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

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“…These investigations range from defining the molecular profiles of hematopoietic stem cells (HSCs) from mouse embryos (Zhou et al, 2016) and the transcriptional landscape of heart development (DeLaughter et al, 2016;Li et al, 2016a), to comparing cell type diversity in the embryonic midbrain between human and mouse (La Manno et al, 2016) and obtaining initial cellular censuses of the murine spleen (Jaitin et al, 2014), cortex and hippocampus (Zeisel et al, 2015). We list many of these studies in Table 2 but note that more studies are being published every month.…”

Section: Transcriptional Heterogeneity and Pluripotencymentioning

confidence: 99%

Understanding development and stem cells using single cell-based analyses of gene expression

2017

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In recent years, genome-wide profiling approaches have begun to uncover the molecular programs that drive developmental processes. In particular, technical advances that enable genome-wide profiling of thousands of individual cells have provided the tantalizing prospect of cataloging cell type diversity and developmental dynamics in a quantitative and comprehensive manner. Here, we review how singlecell RNA sequencing has provided key insights into mammalian developmental and stem cell biology, emphasizing the analytical approaches that are specific to studying gene expression in single cells.

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Single-Cell Resolution of Temporal Gene Expression during Heart Development

Cited by 380 publications

References 53 publications

Novel Mutation in FLNC (Filamin C) Causes Familial Restrictive Cardiomyopathy

Novel Mutation in FLNC (Filamin C) Causes Familial Restrictive Cardiomyopathy

A single cell transcriptional roadmap for cardiopharyngeal fate diversification

Understanding development and stem cells using single cell-based analyses of gene expression

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