scholarly journals scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-cell Graph Entropy

Author(s):  
Jiayuan Zhong ◽  
Chongyin Han ◽  
Xuhang Zhang ◽  
Pei Chen ◽  
Rui Liu
2020 ◽  
Author(s):  
Jiayuan Zhong ◽  
Chongyin Han ◽  
Xuhang Zhang ◽  
Pei Chen ◽  
Rui Liu

AbstractCell fate commitment occurs during early embryonic development, that is, the embryonic differentiation sometimes undergoes a critical phase transition or “tipping point” of cell fate commitment, at which there is a drastic or qualitative shift of the cell populations. In this study, we presented a novel computational approach, the single-cell graph entropy (SGE), to explore the gene-gene associations among cell populations based on single-cell RNA sequencing (scRNA-seq) data. Specifically, by transforming the sparse and fluctuating gene expression data to the stable local network entropy, the SGE score quantitatively characterizes the criticality of gene regulatory networks among cell populations, and thus can be employed to predict the tipping point of cell fate or lineage commitment at the single cell level. The proposed SGE method was applied to five scRNA-seq datasets. For all these datasets of embryonic differentiation, SGE effectively captures the signal of the impending cell fate transitions, which cannot be detected by gene expressions. Some “dark” genes that are non-differential but sensitive to SGE values were revealed. The successful identification of critical transition for all five datasets demonstrates the effectiveness of our method in analyzing scRNA-seq data from a network perspective, and the potential of SGE to track the dynamics of cell differentiation.


PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8054 ◽  
Author(s):  
Vanessa Cheng ◽  
Subham Dasgupta ◽  
Aalekhya Reddam ◽  
David C. Volz

Peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated transcription factor that regulates lipid/glucose homeostasis and adipocyte differentiation. While the role of PPARγ in adipogenesis and diabetes has been extensively studied, little is known about PPARγ function during early embryonic development. Within zebrafish, maternally-loaded pparγ transcripts are present within the first 6 h post-fertilization (hpf), and de novo transcription of zygotic pparγ commences at ~48 hpf. Since maternal pparγ transcripts are elevated during a critical window of cell fate specification, the objective of this study was to test the hypothesis that PPARγ regulates gastrulation and dorsoventral patterning during zebrafish embryogenesis. To accomplish this objective, we relied on (1) ciglitazone as a potent PPARγ agonist and (2) a splice-blocking, pparγ-specific morpholino to knockdown pparγ. We found that initiation of ciglitazone—a potent human PPARγ agonist—exposure by 4 hpf resulted in concentration-dependent effects on dorsoventral patterning in the absence of epiboly defects during gastrulation, leading to ventralized embryos by 24 hpf. Interestingly, ciglitazone-induced ventralization was reversed by co-exposure with dorsomorphin, a bone morphogenetic protein signaling inhibitor that induces strong dorsalization within zebrafish embryos. Moreover, mRNA-sequencing revealed that lipid- and cholesterol-related processes were affected by exposure to ciglitazone. However, pparγ knockdown did not block ciglitazone-induced ventralization, suggesting that PPARγ is not required for dorsoventral patterning nor involved in ciglitazone-induced toxicity within zebrafish embryos. Our findings point to a novel, PPARγ-independent mechanism of action and phenotype following ciglitazone exposure during early embryonic development.


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