1
|
Functional Genomics of Epileptogenesis in Animal Models and Humans. Cell Mol Neurobiol 2020; 41:1579-1587. [PMID: 32725455 DOI: 10.1007/s10571-020-00927-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 07/20/2020] [Indexed: 12/14/2022]
Abstract
It has been estimated that epilepsies are among the top five neurological diseases with the highest burden of disease. In recent years, genome-wide expression studies (GWES) have been carried out in experimental models of epilepsy and in samples from human patients. In this study, I carried out meta-analyses and analyses of convergence for available GWES for epileptogenesis in humans and in mouse, rat, zebrafish and fruit fly models. Multiple lines of evidence (such as genome-wide association data and known druggable genes) were integrated to prioritize top candidate genes for epileptogenesis and a functional enrichment analysis was carried out. Several top candidate genes, which are supported by multiple lines of genomic evidence, such as GRIN1, KCNAB1 and STX1B, were identified. Druggable genes of potential interest (such as GABRA2, GRIK1, KCNAB1 and STX4) were also identified. An enrichment of genes regulated by the MEF2 and SOX5 transcription factors and the miR-106b-5p and miR-101-3p miRNAs was found. The current work is the first meta-analysis and convergent analysis of GWES for epileptogenesis in humans and in multiple animal models, integrating results from several genomic studies. Novel candidate genes and pathways for epileptogenesis were identified in this analysis.
Collapse
|
2
|
Romdhane L, Bouhamed H, Ghedira K, Ben Hamda C, Louhichi A, Jmel H, Romdhane S, Charfeddine C, Mokni M, Abdelhak S, Rebai A. The morbid cutaneous anatomy of the human genome revealed by a bioinformatic approach. Genomics 2020; 112:4232-4241. [PMID: 32650097 DOI: 10.1016/j.ygeno.2020.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 03/28/2020] [Accepted: 07/02/2020] [Indexed: 01/05/2023]
Abstract
Computational approaches have been developed to prioritize candidate genes in disease gene identification. They are based on different pieces of evidences associating each gene with the given disease. In this study, 648 genes underlying genodermatoses have been compared to 1808 genes involved in other genetic diseases using a bioinformatic approach. These genes were studied at the structural, evolutionary and functional levels. Results show that genes underlying genodermatoses present longer CDS and have more exons. Significant differences were observed in nucleotide motif and amino-acid compositions. Evolutionary conservation analysis revealed that genodermatoses genes have less paralogs, more orthologs in Mouse and Dog and are less conserved. Functional analysis revealed that genodermatosis genes seem to be involved in immune system and skin layers. The Bayesian network model returned a rate of good classification of around 80%. This computational approach could help investigators working in the field of dermatology by prioritizing positional candidate genes for mutation screening.
Collapse
Affiliation(s)
- Lilia Romdhane
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia; Department of Biology, Faculty of Sciences of Bizerte, Jarzouna, Université Tunis Carthage, Tunis, Tunisia.
| | - Heni Bouhamed
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Amel Louhichi
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Haifa Jmel
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Safa Romdhane
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Chérine Charfeddine
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia; High Institut of Biotechnology of Sidi Thabet, University of Manouba, BiotechPole of Sidi Thabet, Ariana, Tunisia
| | - Mourad Mokni
- Department of Dermatology, CHU La Rabta Tunis, Tunis, Tunisia; Public health and infection Research Laboratory, La Rabta Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Ahmed Rebai
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| |
Collapse
|
3
|
Forero DA, González-Giraldo Y. Integrative In Silico Analysis of Genome-Wide DNA Methylation Profiles in Schizophrenia. J Mol Neurosci 2020; 70:1887-1893. [PMID: 32451840 DOI: 10.1007/s12031-020-01585-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022]
Abstract
Schizophrenia (SZ) is a complex and severe psychiatric disorder, which has a global lifetime prevalence of 0.4% and a heritability of around 0.81. A number of epigenome-wide association studies (EWAS) have been carried out for SZ, with discordant results. The main aim of this study was to carry out an integrative in silico analysis of available genome-wide DNA methylation profiles in schizophrenia. In this work, an integration of multiple lines of evidence (top candidate genes from several EWAS and genome-wide expression and association data) was carried out, in order to identify top differentially methylated (DM) genes for SZ. In addition, functional enrichment and protein-protein interaction analyses were carried out. Several top differentially methylated genes, such as APC, CACNB2, and PRKN, were found, and an enrichment of binding sites for brain-expressed transcription factors, such as FOXO1, MYB, and ZIC3, was also observed. Moreover, a protein-protein interaction network showed a central role for DISC1 and ZNF688 genes, and experimentally validated targets of MIR-137, such as and KCNB2, NRXN1, and SYN2, were identified among DM genes. This is the first integrative in silico analysis of available genome-wide DNA methylation profiles in schizophrenia. This work identified novel candidate genes and pathways for SZ and provides the basis to explore their role in the pathogenesis of SZ in future studies.
Collapse
Affiliation(s)
- Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia.
| | - Yeimy González-Giraldo
- Center for Psychosocial Studies for Latin America and the Caribbean, School of Psychosocial Therapies, Universidad Antonio Nariño, Bogotá, Colombia
| |
Collapse
|