Abstract 714: Mapping the Transcriptional Dynamics of Pluripotent Stem Cell-derived Endothelial Cell Differentiation by Single Cell RNA Sequencing

2019 ◽  
Vol 125 (Suppl_1) ◽  
Author(s):  
Ian R McCracken ◽  
Richard S Taylor ◽  
Fernando De La Cuesta ◽  
Ross Dobie ◽  
Beth E Henderson ◽  
...  
Keyword(s):  
Stem Cell ◽  
Endothelial Cell ◽  
Cell Differentiation ◽  
Single Cell ◽  
Rna Sequencing ◽  
Pluripotent Stem Cell ◽  
Transcriptional Dynamics ◽  
Endothelial Cell Differentiation ◽  
Single Cell Rna Sequencing

scholarly journals Single‐Cell Transcriptomics of Engineered Cardiac Tissues From Patient‐Specific Induced Pluripotent Stem Cell–Derived Cardiomyocytes Reveals Abnormal Developmental Trajectory and Intrinsic Contractile Defects in Hypoplastic Right Heart Syndrome

2020 ◽  
Vol 9 (20) ◽  
Author(s):  
Yin‐Yu Lam ◽  
Wendy Keung ◽  
Chun‐Ho Chan ◽  
Lin Geng ◽  
Nicodemus Wong ◽  
...  
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Pluripotent Stem Cell ◽  
Cardiac Tissue ◽  
Induced Pluripotent Stem Cell ◽  
Developmental Trajectory ◽  
Single Cell Rna Sequencing ◽  
Human Cardiac Tissue ◽  
Induced Pluripotent

Background To understand the intrinsic cardiac developmental and functional abnormalities in pulmonary atresia with intact ventricular septum (PAIVS) free from effects secondary to anatomic defects, we performed and compared single‐cell transcriptomic and phenotypic analyses of patient‐ and healthy subject–derived human‐induced pluripotent stem cell–derived cardiomyocytes (hiPSC‐CMs) and engineered tissue models. Methods and Results We derived hiPSC lines from 3 patients with PAIVS and 3 healthy subjects and differentiated them into hiPSC‐CMs, which were then bioengineered into the human cardiac anisotropic sheet and human cardiac tissue strip custom‐designed for electrophysiological and contractile assessments, respectively. Single‐cell RNA sequencing (scRNA‐seq) of hiPSC‐CMs, human cardiac anisotropic sheet, and human cardiac tissue strip was performed to examine the transcriptomic basis for any phenotypic abnormalities using pseudotime and differential expression analyses. Through pseudotime analysis, we demonstrated that bioengineered tissue constructs provide pro‐maturational cues to hiPSC‐CMs, although the maturation and development were attenuated in PAIVS hiPSC‐CMs. Furthermore, reduced contractility and prolonged contractile kinetics were observed with PAIVS human cardiac tissue strips. Consistently, single‐cell RNA sequencing of PAIVS human cardiac tissue strips and hiPSC‐CMs exhibited diminished expression of cardiac contractile apparatus genes. By contrast, electrophysiological aberrancies were absent in PAIVS human cardiac anisotropic sheets. Conclusions Our findings were the first to reveal intrinsic abnormalities of cardiomyocyte development and function in PAIVS free from secondary effects. We conclude that hiPSC‐derived engineered tissues offer a unique method for studying primary cardiac abnormalities and uncovering pathogenic mechanisms that underlie sporadic congenital heart diseases.

2149-P: Mitochondrial Akt Modulated Human Embryonic Stem Cell Differentiation Lineages—Analysis with Single Cell RNA Sequencing

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 2149-P
Author(s):  
HSIAOCHEN LEE ◽  
YU-HAN CHEN ◽  
HUGO YOU-HSIEN LIN ◽  
ALBERT TA ◽  
PING H. WANG ◽  
...  
Keyword(s):  
Stem Cell ◽  
Cell Differentiation ◽  
Embryonic Stem Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Human Embryonic Stem Cell ◽  
Embryonic Stem ◽  
Stem Cell Differentiation ◽  
Embryonic Stem Cell Differentiation ◽  
Single Cell Rna Sequencing

scholarly journals Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level

2020 ◽  
Author(s):  
Suraj Kannan ◽  
Michael Farid ◽  
Brian L. Lin ◽  
Matthew Miyamoto ◽  
Chulan Kwon
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Pluripotent Stem Cell ◽  
Developmental Trajectory ◽  
Single Cell Level ◽  
Batch Effects ◽  
Cell Level ◽  
Single Cell Rna Sequencing

The immaturity of pluripotent stem cell (PSC)-derived tissues has emerged as a universal problem for their biomedical applications. While efforts have been made to generate adult-like cells from PSCs, direct benchmarking of PSC-derived tissues against in vivo development has not been established. Thus, maturation status is often assessed on an ad-hoc basis. Single cell RNA-sequencing (scRNA-seq) offers a promising solution, though cross-study comparison is limited by dataset-specific batch effects. Here, we developed a novel approach to quantify PSC-derived cardiomyocyte (CM) maturation through transcriptomic entropy. Transcriptomic entropy is robust across datasets regardless of differences in isolation protocols, library preparation, and other potential batch effects. With this new model, we analyzed over 45 scRNA-seq datasets and over 52,000 CMs, and established a cross-study, cross-species CM maturation reference. This reference enabled us to directly compare PSC-CMs with the in vivo developmental trajectory and thereby to quantify PSC-CM maturation status. We further found that our entropy-based approach can be used for other cell types, including pancreatic beta cells and hepatocytes. Our study presents a biologically relevant and interpretable metric for quantifying PSC-derived tissue maturation, and is extensible to numerous tissue engineering contexts.Significance StatementThere is significant interest in generating mature cardiomyocytes from pluripotent stem cells. However, there are currently few effective metrics to quantify the maturation status of a single cardiomyocyte. We developed a new metric for measuring cardiomyocyte maturation using single cell RNA-sequencing data. This metric, called entropy score, uses the gene distribution to estimate maturation at the single cell level. Entropy score enables comparing pluripotent stem cell-derived cardiomyocytes directly against endogenously-isolated cardiomyocytes. Thus, entropy score can better assist in development of approaches to improve the maturation of pluripotent stem cell-derived cardiomyocytes.

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