|
1
|
Kim N, Kim KH, Lim WJ, Kim J, Kim SA, Yoo HJ. Whole Exome Sequencing Identifies Novel De Novo Variants Interacting with Six Gene Networks in Autism Spectrum Disorder. Genes (Basel) 2020; 12:genes12010001. [PMID: 33374967 PMCID: PMC7822011 DOI: 10.3390/genes12010001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable condition caused by a combination of environmental and genetic factors such as de novo and inherited variants, as well as rare or common variants among hundreds of related genes. Previous genome-wide association studies have identified susceptibility genes; however, most ASD-associated genes remain undiscovered. This study aimed to examine rare de novo variants to identify genetic risk factors of ASD using whole exome sequencing (WES), functional characterization, and genetic network analyses of identified variants using Korean familial dataset. We recruited children with ASD and their biological parents. The clinical best estimate diagnosis of ASD was made according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5TM), using comprehensive diagnostic instruments. The final analyses included a total of 151 individuals from 51 families. Variants were identified and filtered using the GATK Best Practices for bioinformatics analysis, followed by genome alignments and annotation to the reference genome assembly GRCh37 (liftover to GRCh38), and further annotated using dbSNP 154 build databases. To evaluate allele frequencies of de novo variants, we used the dbSNP, gnomAD exome v2.1.1, and genome v3.0. We used Ingenuity Pathway Analysis (IPA, Qiagen) software to construct networks using all identified de novo variants with known autism-related genes to find probable relationships. We identified 36 de novo variants with potential relations to ASD; 27 missense, two silent, one nonsense, one splice region, one splice site, one 5′ UTR, and one intronic SNV and two frameshift deletions. We identified six networks with functional relationships. Among the interactions between de novo variants, the IPA assay found that the NF-κB signaling pathway and its interacting genes were commonly observed at two networks. The relatively small cohort size may affect the results of novel ASD genes with de novo variants described in our findings. We did not conduct functional experiments in this study. Because of the diversity and heterogeneity of ASD, the primary purpose of this study was to investigate probable causative relationships between novel de novo variants and known autism genes. Additionally, we based functional relationships with known genes on network analysis rather than on statistical analysis. We identified new variants that may underlie genetic factors contributing to ASD in Korean families using WES and genetic network analyses. We observed novel de novo variants that might be functionally linked to ASD, of which the variants interact with six genetic networks.
Collapse
Affiliation(s)
- Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Soon Ae Kim
- Department of Pharmacology, School of Medicine, Eulji University, Daejeon 34824, Korea
- Correspondence: (S.A.K.); (H.J.Y.); Tel.: +82-42-259-1672 (S.A.K.); +82-31-787-7436 (H.J.Y.)
| | - Hee Jeong Yoo
- Department of Psychiatry, College of Medicine, Seoul National University, Seoul 03080, Korea
- Department of Psychiatry, Seoul National University Bundang Hospital, Gyeonggi 13620, Korea
- Correspondence: (S.A.K.); (H.J.Y.); Tel.: +82-42-259-1672 (S.A.K.); +82-31-787-7436 (H.J.Y.)
| |
Collapse
|
|
2
|
Lungba RM, Khan SZA, Ajibawo-Aganbi U, Perez Bastidas MV, Veliginti S, Saleem S, Cancarevic I. The Role of the Gut Microbiota and the Immune System in the Development of Autism. Cureus 2020; 12:e11226. [PMID: 33269154 PMCID: PMC7707059 DOI: 10.7759/cureus.11226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/28/2020] [Indexed: 12/28/2022] Open
Abstract
Autism spectrum disorders (ASDs) are neurodevelopmental disorders that present with social skills and communication challenges, restricted interest, and repetitive behavior. The specific cause of autism is not well understood yet. However, numerous studies indicated that environmental and genetic factors, dysregulated immune response, and alterations to the balance and content of the gut microbiota are implemented in the development of autism. Many non-pharmacological interventions are nominated to manage autism, including family support services and psychoeducational methods. Moreover, different pharmacological therapy modalities are recommended for children with ASD. Learning more about the brain, immune system, and gut connections could assist in early diagnosis and treatment of this devastating neurodevelopmental disorders as an early intervention in ASD could improve a child's overall development. We gathered data from relevant previously published articles on PubMed to evaluate the role of the gut microbiota and the immune system on the development of autism..
Collapse
Affiliation(s)
- Rayan M Lungba
- Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Seyad Zulficar Ali Khan
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
- Family Medicine, Ministry of Health Oman, Salalah, OMN
| | - Uvie Ajibawo-Aganbi
- Faculty of Health Sciences, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | | | - Swathi Veliginti
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Sania Saleem
- Research and Development, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Ivan Cancarevic
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| |
Collapse
|