Abstract
Autism spectrum disorder (ASD) is a hereditary heterogeneous neurodevelopmental disorder characterized by social and speech dysplasia. We collected the expression profiles of ASD in GSE26415, GSE42133 and GSE123302 from the gene expression omnibus (GEO) database, as well as methylation data of GSE109905. Differentially expressed genes (DEGs) between ASD and controls were obtained by differential expression analysis. Enrichment analysis identified the biological functions and signaling pathways involved by common genes in three groups of DEGs. Protein-protein interaction (PPI) networks were used to identify genes with the highest connectivity as key genes. In addition, we identified methylation markers by associating differentially methylated positions. Key methylation markers were identified using the least absolute shrink and selection operator (LASSO) model. Receiver operating characteristic curves and nomograms were used to identify the diagnostic role of key methylation markers for ASD. A total of 57 common genes were identified in the three groups of DEGs. These genes were mainly enriched in Sphingolipid metabolism and PPAR signaling pathway. In the PPI network, we identified seven key genes with higher connectivity, and used qRT-PCR experiments to verify the expressions. In addition, we identified 31 methylation markers and screened 3 key methylation markers (RUNX2, IMMP2L and MDM2) by LASSO model. Their methylation levels were closely related to the diagnostic effects of ASD. Our analysis identified RUNX2, IMMP2L and MDM2 as possible diagnostic markers for ASD. Identifying different biomarkers and risk genes will contribute to the diagnosis of ASD and the development of new clinical and drug treatments.
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Data availability
The data used in this study can be found in GEO database, including GSE26415, GSE42133, GSE123302 and GSE109905.
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Bei Zhang and Xiaoyuan Hu designed and managed the study. Bei Zhang and Yuefei Li contributed significantly to the data analyses. Xiaoyuan Hu and Yongkang Ni performed methylation analysis. Bei Zhang and Lin Xue wrote the paper. Lin Xue reviewed and edited. All authors contributed to and approved the final manuscript.
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This study was performed at the Fourth People’s Hospital of Urumqi and was approved by the ethics review board of the Fourth People’s Hospital of Urumqi (No: 20200306). Patients gave their approval to be enrolled in this study in an informed written consent. The patient studies were conducted in accordance with the ethical guidelines of the Declaration of Helsinki.
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Zhang, B., Hu, X., Li, Y. et al. Identification of methylation markers for diagnosis of autism spectrum disorder. Metab Brain Dis 37, 219–228 (2022). https://doi.org/10.1007/s11011-021-00805-5
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DOI: https://doi.org/10.1007/s11011-021-00805-5