Journal
MOLECULAR AUTISM
Volume 9, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13229-018-0213-9
Keywords
Autism spectrum disorder; Alu elements; Retrotransposon; DNA methylation; Epigenetic regulation; Gene expression profiles; Subgrouping; Lymphoblastoid cell lines; Sex bias; Neuroinflammation
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Funding
- Ratchadaphiseksomphot Endowment Fund part of the Research Grant for New Scholar CU Researcher's Project [GDNS 57-034-37-002]
- Faculty of Allied Health Sciences Research Fund [AHS-CU 58003]
- 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund) [GCUGR1125601055M 53-1, GCUGR1125601058M 53-4, GCUGR1125601056M 53-2]
- Scholarship from the Graduate School, Chulalongkorn University to commemorate the 72nd anniversary of His Majesty King Bhumibala Aduladeja
- NIEHS [R21 ES023061]
- Thailand Research Fund [DPG5980005, BRG5980001]
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Background: Alu elements are a group of repetitive elements that can influence gene expression through CpG residues and transcription factor binding. Altered gene expression and methylation profiles have been reported in various tissues and cell lines from individuals with autism spectrum disorder (ASD). However, the role of Alu elements in ASD remains unclear. We thus investigated whether Alu elements are associated with altered gene expression profiles in ASD. Methods: We obtained five blood-based gene expression profiles from the Gene Expression Omnibus database and human Alu-inserted gene lists from the TranspoGene database. Differentially expressed genes (DEGs) in ASD were identified from each study and overlapped with the human Alu-inserted genes. The biological functions and networks of Alu-inserted DEGs were then predicted by Ingenuity Pathway Analysis (IPA). A combined bisulfite restriction analysis of lymphoblastoid cell lines (LCLs) derived from 36 ASD and 20 sex-and age-matched unaffected individuals was performed to assess the global DNA methylation levels within Alu elements, and the Alu expression levels were determined by quantitative RT-PCR. Results: In ASD blood or blood-derived cells, 320 Alu-inserted genes were reproducibly differentially expressed. Biological function and pathway analysis showed that these genes were significantly associated with neurodevelopmental disorders and neurological functions involved in ASD etiology. Interestingly, estrogen receptor and androgen signaling pathways implicated in the sex bias of ASD, as well as IL-6 signaling and neuroinflammation signaling pathways, were also highlighted. Alu methylation was not significantly different between the ASD and sex-and age-matched control groups. However, significantly altered Alu methylation patterns were observed in ASD cases sub-grouped based on Autism Diagnostic Interview-Revised scores compared with matched controls. Quantitative RT-PCR analysis of Alu expression also showed significant differences between ASD subgroups. Interestingly, Alu expression was correlated with methylation status in one phenotypic ASD subgroup. Conclusion: Alu methylation and expression were altered in LCLs from ASD subgroups. Our findings highlight the association of Alu elements with gene dysregulation in ASD blood samples and warrant further investigation. Moreover, the classification of ASD individuals into subgroups based on phenotypes may be beneficial and could provide insights into the still unknown etiology and the underlying mechanisms of ASD.
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