title: Dissection of Regulatory Elements During Direct Conversion of Somatic Cells Into Neurons.
abstract: A revolutionary approach that involves direct conversion of somatic cells into almost any other types of cells showed promising results for regenerative medicine. Currently, producing valuable cell types including neurons, cardiomyocytes, and hepatocytes through direct conversion of somatic cells appear to be a feasible option for regenerative medicine. The process involves inducing the cells by chemical cocktails or by expression of different types of transcription factors. In this concept, in vitro neurogenesis considered to be able to produce neuron cells to replace damaged neurons especially in Alzheimer and Parkinson disease. However, early successful experiments followed by major drawbacks such as low differentiation efficiency in producing neurons and detection of various undesirable types of cells in the culture. Therefore, there is not a single optimized common protocol for producing high quality neurons in vitro so far. This is partly due to the lack of our understanding about the precise cellular, genetic, and molecular mechanisms underlying neurogenesis via direct conversion. In the current work, we have employed meta-analysis tools and extensive gene regulatory network analysis on the high throughput gene expression data obtained from previous reprogramming protocols to identify central gene regulatory components involved in direct conversion of fibroblasts into neurons. Our results identified miR-9, miR-30 as the most important miRNA and TP53, MYC, JUN, SP1, and SMAD2 considered to be the most important transcription factors. These findings would be useful for direct targeting these hub regulatory elements in order to increase the efficacy and specificity of the conversion protocols. J. Cell. Biochem. 118: 3158-3170, 2017. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Bioinformatics Lab, Department of Biology, School of Sciences, Razi University, Kermanshah, Iran.
authors.forename: Tahereh
authors.initials: T
authors.lastname: Soleimani
authors.affiliation: Bioinformatics Lab, Department of Biology, School of Sciences, Razi University, Kermanshah, Iran.
authors.forename: Nafiseh
authors.initials: N
authors.lastname: Falsafi
authors.affiliation: Bioinformatics Lab, Department of Biology, School of Sciences, Razi University, Kermanshah, Iran.
authors.forename: Hossein
authors.identifier: 0000-0002-8754-3491
authors.initials: H
authors.lastname: Fallahi
mesh_terms: D000818:Animals; D065150:Cellular Reprogramming; D000067470:Cellular Reprogramming Techniques / Q000379:methods*; D006801:Humans; D009474:Neurons / Q000166:cytology / Q000378:metabolism*; D020218:Response Elements; D014157:Transcription Factors / Q000096:biosynthesis / Q000235:genetics
chemical_list: D014157:Transcription Factors
keywords: CHEMICAL COCKTAILS; CORE REGULATORY NETWORK; DIRECT CONVERSION; REPROGRAMMING; SOMATIC NEUROGENESIS