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Abu-Elmagd M, Assidi M, Alrefaei AF, Rebai A. Editorial: Advances in genomic and genetic tools, and their applications for understanding embryonic development and human diseases. Front Cell Dev Biol 2022; 10:1016400. [PMID: 36478744 PMCID: PMC9720382 DOI: 10.3389/fcell.2022.1016400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/04/2022] [Indexed: 10/10/2023] Open
Abstract
Significant advances have been recently made in the development of the genetic and genomic platforms. This has greatly contributed to a better understanding of gene expression and regulation machinery. Consequently, this led to considerable progress in unraveling evidence of the genotype-phenotype correlation between normal/abnormal embryonic development and human disease complexity. For example, advanced genomic tools such as next-generation sequencing, and microarray-based CGH have substantially helped in the identification of gene and copy number variants associated with diseases as well as in the discovery of causal gene mutations. In addition, bioinformatic analysis tools of genome annotation and comparison have greatly aided in data analysis for the interpretation of the genetic variants at the individual level. This has unlocked potential possibilities for real advances toward new therapies in personalized medicine for the targeted treatment of human diseases. However, each of these genomic and bioinformatics tools has its limitations and hence further efforts are required to implement novel approaches to overcome these limitations. It could be possible that the use of more than one platform for genotype-phenotype deep analysis is an effective approach to disentangling the cause and treatment of the disease complexities. Our research topic aimed at deciphering these complexities by shedding some light on the recent applications of the basic and advanced genetic/genomic and bioinformatics approaches. These include studying gene-gene, protein-protein, and gene-environment interactions. We, in addition, aimed at a better understanding of the link between normal/abnormal embryonic development and the cause of human disease induction.
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Affiliation(s)
- Muhammad Abu-Elmagd
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulmajeed F. Alrefaei
- Department of Biology, Jamoum University College, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Ahmed Rebai
- Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Xu J, Feng L, Han Z, Li Y, Wu A, Shao T, Ding N, Li L, Deng W, Di X, Wang J, Zhang L, Li X, Zhang K, Cheng S. Extensive ceRNA-ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues. Nucleic Acids Res 2016; 44:9438-9451. [PMID: 27365046 PMCID: PMC5100587 DOI: 10.1093/nar/gkw587] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 06/19/2016] [Indexed: 12/14/2022] Open
Abstract
Crosstalk between RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in development. In this study, we analyzed time series expression data for coding genes and long non-coding RNAs (lncRNAs) to identify thousands of interactions among competitive endogenous RNAs (ceRNAs) in four rhesus tissues. The ceRNAs exhibited dynamic expression and regulatory patterns during each tissue development process, which suggests that ceRNAs might work synergistically during different developmental stages or tissues to control specific functions. In addition, lncRNAs exhibit higher specificity as ceRNAs than coding-genes and their functions were predicted based on their competitive coding-gene partners to discover their important developmental roles. In addition to the specificity of tissue development, functional analyses demonstrated that the combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in multiple tissues, especially transcription-related functions where competitive interactions. Moreover, ceRNA interactions could sequentially and/or synergistically mediate the crosstalk among different signaling pathways during brain development. Analyzing ceRNA interactions during the development of multiple tissues will provideinsights in the regulation of normal development and the dysregulation of key mechanisms during pathogenesis.
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Affiliation(s)
- Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Aetiology and Carcinogenesis, Cancer Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Zujing Han
- BGI Tech Solutions Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Aiwei Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Tingting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Lili Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Wei Deng
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 10021, China
| | - Xuebing Di
- State Key Laboratory of Molecular Oncology, Department of Aetiology and Carcinogenesis, Cancer Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jian Wang
- BGI Tech Solutions Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Lianfeng Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 10021, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Aetiology and Carcinogenesis, Cancer Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Shujun Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China .,State Key Laboratory of Molecular Oncology, Department of Aetiology and Carcinogenesis, Cancer Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing 100021, China
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Itin PH. Etiology and pathogenesis of ectodermal dysplasias. Am J Med Genet A 2014; 164A:2472-7. [PMID: 24715647 DOI: 10.1002/ajmg.a.36550] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/28/2014] [Indexed: 02/04/2023]
Abstract
Ectodermal dysplasias are a large group of heterogeneous heritable conditions characterized by congenital defects of one or more ectodermal structures and their appendages. The skin and its appendages are mainly composed by ectodermal components but development initiation of appendages is orchestrated by signals of the mesoderm with the help of placodes. A complex network of signaling pathways coordinates the formation and function of ectodermal structures. In recent years much has been discovered regarding the molecular mechanisms of ectodermal embryogenesis and this facilitates a rational basis for classification of ectodermal dysplasia. Interestingly, not only complex ectodermal syndromes but also mono- or oligosymptomatic ectodermal malformations may result from a mutation in a gene that is critical for ectodermal development. Mesodermal, and occasionally endodermal malformations may coexist. Embryogenesis occurs in distinct tissue organizational fields and specific interactions among the germ layers exist that may lead to a wide range of ectodermal dysplasias. Of the approximately 200 different ectodermal dysplasias, about 80 have been characterized at the molecular level with identification of the genes that are mutated in these disorders. Modern molecular genetics will increasingly elucidate the basic defects of these distinct syndromes and shed more light into the regulatory mechanisms of embryology. The upcoming classification of ectodermal dysplasias will combine detailed clinical and molecular knowledge.
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Affiliation(s)
- Peter H Itin
- Department of Dermatology, University Hospital Basel, Basel, Switzerland; Research Group of Dermatology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
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