An Orthologous Epigenetic Gene Expression Signature Derived from Differentiating Embryonic Stem Cells Identifies Regulators of Cardiogenesis

• Published in: PloS one 2015-10, Vol.10 (10), p.e0141066-e0141066
• Main Authors: Busser, Brian W, Lin, Yongshun, Yang, Yanqin, Zhu, Jun, Chen, Guokai, Michelson, Alan M
• Format: Article
• Language: English
• Subjects: Alzheimer's disease; Animals; Binding; Biology; Biomarkers - metabolism; Blood; Cardiomyocytes; Cardiovascular disease; Cell Differentiation - genetics; Cell fate; Cell Lineage - genetics; Chromatin Immunoprecipitation; Congenital diseases; Drosophila; Drosophila - embryology; Drosophila - genetics; Drosophila - growth & development; Embryo cells; Embryo, Nonmammalian - cytology; Embryo, Nonmammalian - metabolism; Embryonic stem cells; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Epigenetics; Epigenomics; Flow Cytometry; Gene expression; Gene Expression Profiling; Gene Expression Regulation; Genes; Genetic aspects; Genetic engineering; Heart; Heart diseases; Homeobox; Homeodomain Proteins - antagonists & inhibitors; Homeodomain Proteins - genetics; Humans; Insects; Mice; Mutation; Myocytes, Cardiac - cytology; Myocytes, Cardiac - metabolism; Oligonucleotide Array Sequence Analysis; Organogenesis - genetics; Physiological aspects; Regulators; Repressor Proteins - antagonists & inhibitors; Repressor Proteins - genetics; RNA Interference - physiology; RNA-mediated interference; Signatures; Specifications; Stem cell transplantation; Stem cells; Structure-function relationships; Transcription factors; Transcription Factors - antagonists & inhibitors; Transcription Factors - genetics; Zinc; Zinc finger proteins
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0141066

Here we used predictive gene expression signatures within a multi-species framework to identify the genes that underlie cardiac cell fate decisions in differentiating embryonic stem cells. We show that the overlapping orthologous mouse and human genes are the most accurate candidate cardiogenic genes as these genes identified the most conserved developmental pathways that characterize the cardiac lineage. An RNAi-based screen of the candidate genes in Drosophila uncovered numerous novel cardiogenic genes. shRNA knockdown combined with transcriptome profiling of the newly-identified transcription factors zinc finger protein 503 and zinc finger E-box binding homeobox 2 and the well-known cardiac regulatory factor NK2 homeobox 5 revealed that zinc finger E-box binding homeobox 2 activates terminal differentiation genes required for cardiomyocyte structure and function whereas zinc finger protein 503 and NK2 homeobox 5 are required for specification of the cardiac lineage. We further demonstrated that an essential role of NK2 homeobox 5 and zinc finger protein 503 in specification of the cardiac lineage is the repression of gene expression programs characteristic of alternative cell fates. Collectively, these results show that orthologous gene expression signatures can be used to identify conserved cardiogenic pathways.