| Autism spectrum disorder?ASD?is a kind of neurodevelopmental disorders,which starts in early childhood and lasts for whole life.The etiology and pathogenesis of ASD is not clear now.Nowadays,there is no special treatment or drug for ASD.Thus,it is necessary to determine the etiology of ASD.Copy number variation?CNV?is a kind of variation which can change gene dosage and contribute to the ASD-related phenotypes.CNV is an important source of risk for ASD.Single nucleotide polymorphism?SNP?is another important variation that leads to ASD.Our previous studies explored the association between polymorphisms of SHANK2 and SHANK3and ASD.However,the association of SHANK1 SNPs with ASD susceptibility in North Han Chinese is not clear.Objective:To analyze the patterns of CNVs within ASD in north Han Chinese and find potential pathogenic CNVs,pathogenic genes and ASD-related microRNAs?miRNAs?.To investigate SHANK1 polymorphisms and gene-gene interactions among SHANK family in ASD among North Han Chinese population.This study aimed to provide clues and evidences to the study of ASD etiology.Methods:Array-based comparative genomic hybridization?aCGH?technology was used for genome-wide CNVs screening of 16 ASD patients.Agilent CytoGenomics software 4.0.3.12 was used to analyze CNVs.Some CNVs were considered of strong putative interest after comparing with databases and the results of classification,which was classified according to American College of Medical Genetics guideline.Potential pathogenic genes were selected based on the following criteria:?1?genes were enriched in ASD related pathways;and?2?they were ASD-related genes.Mature miRNAs,which have functions related to brain or nervous system and were encoded by miRNA-genes in pathogenic CNVs regions were further analyzed.Online databases were used to predict putative target genes of miRNAs.Enrichment analysis of ASD-related target genes was performed.A total of 470 subjects?229 cases and 241 controls?were included in this case-control study.Four SHANK1 SNPs?rs73042561,rs3745521,rs4801846,and rs12461427?were genotyped by improved multiple ligase detection reaction.Chi-squared and Fisher's exact test was performed to evaluate genotype and allele frequency distributions in the cases and the controls.The linkage disequilibrium degree between the loci was calculated by online SNPStats analysis program.The associations between the four SHANK1 SNPs and ASD risk under five different genetic models were analyzed by the SNPStats online analysis program.Haplotype analysis was performed by the SNPStats online analysis program.The interactions between 18 SNPs of SHANK family and ASD were assessed by multifactor dimensionality reduction method.Results:1.A total of 115 kinds of CNVs?70 duplications and 45 deletions?were identified in our subjects.The CNVs were distributed in all chromosomes except chromosome 9 and 20.2.Sixteen pathogenic CNVs?duplication?according to the screening criteria in methods were identified.Six pathogenic CNVs?deletion?according to the screening criteria in methods were identified.3.The results of enrichment analysis on 511 genes in pathogenic CNVs showed that most genes played roles in synaptic and the regulation of synaptic-related signaling,neurotransmitter activity,transport and binding,sphingolipid signaling pathway and m TOR signaling pathway.Based on the results of enrichment analysis and comparison with ASD-related genes,5 genes were pathogenic genes,including HRAS,PTEN,SHANK3,SLC6A3,and TSC2.4.There were 12 mature miRNAs with functions related to brain or nervous system.The results of enrichment analysis showed that target genes of these miRNAs were involved in synaptic and the regulation of synaptic-related signaling,neurotransmitter activity,sphingolipid signaling pathway,glutamatergic synapse and WNT signal pathway.5.Genotypic and allelic frequencies of SHANK1 SNPs?rs73042561,rs3745521,rs4801846,and rs12461427?in patients with ASD were not different from those in controls?P>0.05?.6.Results of genetic models showed that:?1?ASD risk was not associated with rs73042561?P?29?0.0025?.?2?Subjects carrying the mutant homozygote?GG?of rs3745521 had a lower risk of developing ASD than those carrying wild-type homozygote?AA?or mutant heterozygote?GA?(Recessive,ORGG vs AA/GA=0.59,95%CI 0.37–0.93)and had a lower risk of developing ASD than those carrying mutant heterozygote?GA??Codominant model,GG vs.GA:OR=0.58,95%CI=0.34–0.98?.However,after bonferroni correction,ASD risk was not associated with rs3745521?P?29?0.0025?.?3?ASD risk was not associated with rs4801846?P?29?0.0025?.?4?ASD risk was not associated with rs12461427?P?29?0.0025?.7.Haplotype-based association analysis on SHANK1 showed that there was no significant association between haplotypes?2 SNPs,3 SNPs,and 4 SNPs?and ASD risk after bonferroni correction.8.There was no significant association between models of gene-gene interaction?18 SNPs of SHANK family?and ASD risk?P?29?0.05?.Conclusion:1.Duplications at 1p36.31,1p36.33,1q42.13,5p15.33,5p15.33–p15.2,7p22.3,7p22.3–p22.2,10q26.2–q26.3,11p15.5,11q25,16p13.3,16q21,22q13.31–q13.33,and Xq12–q13.1 and deletions at 2p23.1–p22.3,7q22.1–q22.2,10q23.2–q23.31,12p12.1–p11.23,14q11.2,and 15q13.3 were pathogenic CNVs associated with ASD in north Han Chinese population.The number of duplications was more than that of deletions in ASD among north Han Chinese population.2.Duplications of HRAS,SHANK3,SLC6A3,and TSC2 and deletion of PTEN were pathogenic genes associated with ASD in north Han Chinese population.3.Duplications of miR-202-3p,miR-202-5p,miR-210-3p,miR-3178,miR-339-3p,miR-339-5p,miR-4516,miR-4717-3p,miR-4717-5p,miR-483-3p,miR-483-5p,miR-675-3p,miR-675-5p,and miR-940 and deletions of miR-107 and miR-558 were pathogenic genes associated with ASD in north Han Chinese population.4.There was no association between the polymorphisms of rs73042561,rs3745521,rs4801846,and rs12461427 and susceptibility to ASD in North Han Chinese population.There was no significant association between haplotypes?2 SNPs,3 SNPs,and 4 SNPs?and susceptibility to ASD in North Han Chinese population.5.There was no significant association between gene-gene interaction of SHANK family and susceptibility to ASD in North Han Chinese population. |
PDF Full Text Request