| Literature DB >> 31447881 |
Yan Sun1, Xueming Yao1, Michael E March2, Xinyi Meng1, Junyi Li1, Zhi Wei3, Patrick M A Sleiman2,4,5, Hakon Hakonarson2,4,5, Qianghua Xia1, Jin Li1.
Abstract
Autism spectrum disorder (ASD) is a complex neuropsychiatric disorder. A number of genetic risk loci have been identified for ASD from genome-wide association studies (GWAS); however, their target genes in relevant tissues and cell types remain to be investigated. The frontal cortex is a key region in the human brain for communication and cognitive function. To identify risk genes contributing to potential dysfunction in the frontal cortex of ASD patients, we took an in silico approach integrating multi-omics data. We first found genes with expression in frontal cortex tissue that correlates with ASD risk loci by leveraging expression quantitative trait loci (eQTLs) information. Among these genes, we then identified 76 genes showing significant differential expression in the frontal cortex between ASD cases and controls in microarray datasets and further replicated four genes with RNA-seq data. Among the ASD GWAS single nucleotide polymorphisms (SNPs) correlating with the 76 genes, 20 overlap with histone marks and 40 are associated with gene methylation level. Thus, through multi-omics data analyses, we identified genes that may work as target genes of ASD risk loci in the brain frontal cortex.Entities:
Keywords: DNA methylation; GWAS loci; autism; brain frontal cortex; eQTL; histone modification; target gene
Year: 2019 PMID: 31447881 PMCID: PMC6696877 DOI: 10.3389/fgene.2019.00707
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Candidate autism spectrum disorder (ASD) target genes that showed significant differential expression in both microarray and RNA-seq datasets.
| ASD SNP | Target gene | eQTL | Microarray | RNA-seq |
|---|---|---|---|---|
| rs75782365 |
| 0.0015 | 0.0316 | 0.0228 |
| rs3132581 |
| 0.0058 | 0.0121 | 0.00299 |
| rs11587682 |
| 0.017 | 0.0145 | 0.0325 |
| rs4905226 |
| 0.014 | 0.0376 | 0.00629 |
SNP, single nucleotide polymorphism; Target Gene, candidate target gene identified for each ASD GWAS locus; eQTL P-value, P-value of correlation between gene expression level and GWAS SNP genotype in GTEx database or Braineac database; Microarray P-value, P-value of the differentially expressed gene in microarray meta-analysis; RNA-seq P-value, P-value of the differentially expressed gene in RNA-seq analysis.
Figure 1Eleven out of 76 proteins encoded by the autism spectrum disorder (ASD) loci target genes showed protein–protein interactions (PPIs). The PPI network was constructed using NetworkAnalyst with InnateDB as the source of protein interaction data. The nodes represent proteins, and the size of the nodes reflects the number of interaction partners with it. The edges between the nodes indicate known interactions between the proteins.
Within genes HISTI1H1C, HSPA1B, PRPF3, and SERPINA3, single-nucleotide polymorphisms (SNPs) are associated with other neuropsychiatric diseases.
| ADHD | Bipolar | MDD | SCZ | |||||
|---|---|---|---|---|---|---|---|---|
| Gene | Best SNP | P-value | Best SNP | P-value | Best SNP | P-value | Best SNP | P-value |
|
| rs16891264 | 0.0529 | rs10425 | 0.0022 | rs12210098 | 0.0024 | rs3857546 | 1.46E−09 |
|
| rs9267786 | 0.0202 | rs389883 | 0.000322 | rs9368699 | 0.00562 | rs1270942 | 5.00E−07 |
|
| rs10494266 | 0.00081 | rs12138453 | 0.000171 | rs16836940 | 0.00014 | rs16835254 | 0.000105 |
|
| rs2268336 | 0.00107 | rs17091191 | 0.00103 | rs1243533 | 0.0162 | rs11625527 | 0.00403 |
ADHD, attention-deficit hyperactivity disorder; MDD, major depressive disorder; SCZ, schizophrenia.
ASD genome-wide association studies (GWAS) SNPs overlap with histone marks in brain dorsolateral prefrontal cortex, based on ENCODE and ROADMAP datasets.
| SNP | Chromatin marks | |||
|---|---|---|---|---|
| rs1080500 | H3K4me1 | H3K27ac | ||
| rs1104918 | H3K4me1 | H3K27ac | ||
| rs12045323 | H3K4me1 | H3K27ac | ||
| rs12826178 | H3K4me1 | |||
| rs133047 | H3K4me1 | |||
| rs1550976 | H3K4me1 | |||
| rs169738 | H3K4me3 | H3K4me1 | H3K27ac | |
| rs17292804 | H3K4me3 | H3K4me1 | H3K27ac | H3K9ac |
| rs2021722 | H3K4me1 | H3K27ac | H3K9ac | |
| rs2233375 | H3K27ac | |||
| rs2297909 | H3K4me1 | H3K27ac | H3K9ac | |
| rs2898883 | H3K27ac | H3K9ac | ||
| rs4150167 | H3K4me1 | H3K27ac | ||
| rs4702 | H3K4me3 | H3K4me1 | H3K27ac | H3K9ac |
| rs548181 | H3K4me3 | H3K4me1 | H3K27ac | H3K9ac |
| rs609412 | H3K4me1 | |||
| rs73416724 | H3K4me3 | H3K4me1 | H3K27ac | H3K9ac |
| rs760648 | H3K4me1 | |||
| rs8321 | H3K4me1 | H3K9ac | ||
| rs880446 | H3K4me3 | H3K4me1 | H3K27ac | H3K9ac |
ASD GWAS SNPs correlate with target gene methylation level at nominal significance level.
| eQTL_SNP | Gene | Methylation probe | Methylation beta | Methylation |
|---|---|---|---|---|
| rs385492 |
| cg09296453 | −0.204 | 1.25E−16 |
| rs12887734 |
| cg01651570 | 0.33 | 9.61E−07 |
| rs4650608 |
| cg07107453 | −0.0964 | 3.93E−06 |
| rs2021722 |
| cg20408505 | −0.0653 | 0.000391 |
| rs8054556 |
| cg09584855 | 0.0426 | 0.000398 |
| rs7746199 |
| cg20029652 | 0.0364 | 0.000721 |
| rs1080500 |
| cg02011912 | 0.0449 | 0.000883 |
| rs11587682 |
| cg04633021 | −0.0633 | 0.00107 |
| rs880446 |
| cg03946671 | −0.141 | 0.00162 |
| rs1550976 |
| cg04307764 | −0.0481 | 0.00208 |
| rs4150167 |
| cg08941639 | −0.253 | 0.00223 |
| rs2332700 |
| cg12963168 | 0.0372 | 0.00239 |
| rs2535629 |
| cg09254361 | 0.0693 | 0.00261 |
| rs221902 |
| cg16339264 | 0.033 | 0.00265 |
| rs11191419 |
| cg11453585 | −0.0485 | 0.00329 |
| rs11587682 |
| cg04212235 | 0.106 | 0.00405 |
| rs6538761 |
| cg09725090 | 0.0222 | 0.00502 |
| rs12871532 |
| cg20776540 | −0.0244 | 0.00547 |
| rs11587682 |
| cg17724175 | 0.108 | 0.00597 |
| rs72934570 |
| cg24533565 | −0.0718 | 0.00636 |
| rs880446 |
| cg04630273 | 0.0518 | 0.00655 |
| rs8009147 |
| cg21190363 | 0.0317 | 0.00854 |
| rs8321 |
| cg05385119 | 0.148 | 0.00896 |
| rs1080500 |
| cg09890989 | 0.0324 | 0.0116 |
| rs4773054 |
| cg02673355 | 0.0716 | 0.0118 |
| rs609412 |
| cg17175376 | 0.022 | 0.0128 |
| rs169738 |
| cg25055477 | 0.0178 | 0.0152 |
| rs2851447 |
| cg26682900 | −0.0185 | 0.0167 |
| rs548181 |
| cg27218829 | −0.0302 | 0.0202 |
| rs72687362 |
| cg08860119 | −0.0361 | 0.0215 |
| rs7914558 |
| cg07168060 | 0.0332 | 0.0217 |
| rs2233375 |
| cg12315466 | 0.034 | 0.0226 |
| rs12826178 |
| cg08163918 | −0.133 | 0.025 |
| rs548181 |
| cg21050392 | −0.0281 | 0.0281 |
| rs10255295 |
| cg14341575 | 0.034 | 0.0287 |
| rs1797052 |
| cg19990379 | −0.0364 | 0.0306 |
| rs3849046 |
| cg07368507 | 0.0279 | 0.0308 |
| rs1104918 |
| cg21347380 | −0.0318 | 0.0371 |
| rs6453278 |
| cg15817406 | −0.0526 | 0.0384 |
| rs7254215 |
| cg01282080 | −0.0401 | 0.0388 |
| rs7184114 |
| cg25645462 | −0.0301 | 0.0396 |
| rs11735612 |
| cg06787716 | −0.0219 | 0.0398 |
| rs2898883 |
| cg08001899 | 0.0471 | 0.0412 |
| rs133047 |
| cg26919805 | 0.0557 | 0.0428 |
| rs73416724 |
| cg01847614 | −0.0244 | 0.0456 |