Dataset Information

Identification of the Key Genes of Autism Spectrum Disorder Through Protein-Protein Interaction Network.

ABSTRACT:

Background

Currently, the prevalence of autism spectrum disorder (ASD) is increasing, which widely spurs the interest in the molecular investigation. Thereby, a better understanding of the given disorder mechanisms is likely to be achieved. Bioinformatics suiting protein-protein interactions analysis via the application of high-throughput studies, such as protein array, is one of these achievements.

Materials and methods

The gene expression data from Gene Expression Omnibus (GEO) database were downloaded, and the expression profile of patients with developmental delay and autistic features were analyzed via Cytoscape and its relevant plug-ins.

Results

Our findings indicated that EGFR, ACTB, RHOA, CALM1, MAPK1, and JUN genes as the hub-bottlenecks and their related terms could be important in ASD risk. In other words, any expression modification in these genes could trigger dysfunctions in the corresponding biological processes.

Conclusion

We suggest that differentially expressed genes could be used as suitable targets for ASD after being validated.

SUBMITTER: Zamanian Azodi M

PROVIDER: S-EPMC8343959 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Studies of individuals with autism spectrum disorder (ASD) have revealed a strong multigenic basis with the identification of hundreds of ASD susceptibility genes. ASD is characterized by social deficits and a range of other phenotypes, implicating complex genetics and involvement of a variety of brain regions. However, how mutations and mis-expression of select gene sets are associated with the behavioral components of ASD remains unknown. We reasoned that for genes to be associated with ASD core behaviors they must be: (1) expressed in brain regions relevant to ASD social behaviors and (2) expressed during the ASD susceptible window of brain development. METHODS:Focusing on the amygdala, a brain region whose dysfunction has been highly implicated in the social component of ASD, we mined publicly available gene expression databases to identify ASD-susceptibility genes expressed during human and mouse amygdala development. We found that a large cohort of known ASD susceptibility genes is expressed in the developing human and mouse amygdala. We further performed analysis of single-nucleus RNA-seq (snRNA-seq) data from microdissected amygdala tissue from five ASD and five control human postmortem brains ranging in age from 4 to 20?years to elucidate cell type specificity of amygdala-expressed genes and their dysregulation in ASD. RESULTS:Our analyses revealed that of the high-ranking ASD susceptibility genes, 80 are expressed in both human and mouse amygdala during fetal to early postnatal stages of development. Our human snRNA-seq analyses revealed cohorts of genes with altered expression in the ASD amygdala postnatally, especially within excitatory neurons, with dysregulated expression of seven genes predicted from our datamining pipeline. LIMITATIONS:We were limited by the ages for which we were able to obtain human tissue; therefore, the results from our datamining pipeline approach will require validation, to the extent possible, in human tissue from earlier developmental stages. CONCLUSIONS:Our pipeline narrows down the number of amygdala-expressed genes possibly involved in the social pathophysiology of ASD. Our human single-nucleus gene expression analyses revealed that ASD is characterized by changes in gene expression in specific cell types in the early postnatal amygdala.