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| Status |
Public on Sep 01, 2015 |
| Title |
Genome-wide transcription profiling of 22q11.2 deletion syndrome reveals functional pathways related to phenotypic expression of psychosis and autism spectrum disorder |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
22q11.2 Deletion Syndrome (22q11DS) represents one of the most common known genetic risk factors for the development of psychotic illness, and is also associated with high rates of autistic spectrum disorders (ASD) in childhood. We performed integrated genomic analyses of 22q11DS to identify genes and pathways related to specific phenotypes. Eighty percent of 22q11DS individuals (n=37) carried the typical 3 Mb deletion, with significant variability in the deletion characteristics in the remainder of the sample (n=9). Both analysis of differential expression and weighted gene coexpression network analysis (WGCNA) identified peripheral changes in gene expression related to psychotic symptom expression in patients, including a module of co-expressed genes which was associated with psychosis in 22q11DS and involved in pathways associated with transcriptional regulation. Remarkably, this 22q11DS psychosis module was significantly enriched for brain-expressed genes, was not related to antipsychotic medication use, and showed significant overlap with transcriptional changes occurring in idiopathic schizophrenia in an independent dataset. In those with 22q11DS-ASD, both differential expression and WGCNA analyses pointed towards dysregulation of immune response pathways. The ASD-associated module showed overlap with a neuronal module enriched for known autism susceptibility genes identified in brain transcriptome data from individuals with idiopathic autism. These findings further support the use of peripheral tissue in the study of major mutational models of diseases affecting the brain, and point towards specific pathways dysregulated in 22q11DS carriers with psychosis and ASD, warranting their further investigation in idiopathic illness.
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| Overall design |
Participants. Forty-six patients with a molecularly confirmed diagnosis of a 22q11.2 deletion and 66 controls (24 unrelated controls and 42 first-degree relatives of 22q11DS patients) were recruited from an ongoing longitudinal study. Comparative Genomic Hybridization Arrays. To characterize the boundaries of the 22q11.2 deletion, we designed a custom NimbleGen 12*135 HX12 array. Microarray-based gene expression analysis. Whole-genome transcriptional profiling was performed using Illumina Human HT-12 microarrays.Gene ontology annotation was performed using DAVID (http://david.abcc.ncifcrf.gov/) and pathway analysis was performed by using the Functional Analysis Annotation tool in the Ingenuity Pathways Analysis (IPA) software (Ingenuity Systems, www.ingenuity.com). Because the healthy control group included parents of 22q11DS patients, there were significant age differences between groups (Table 1, p<.001); thus, we corrected for age in all analyses.Weighted Gene Co-expression Network Analysis (WGCNA). We conducted WGCNA, a systems biology approach used to identify networks of co-expressed genes in relation to phenotypic data, using the R package. Phenotypic traits examined within the 22q11DS group included: categorical and dimensional indicators of psychosis (i.e. psychosis diagnosis and SIPS psychotic symptom severity score), ASD, and gender. For modules that showed a statistically significant relationship with any phenotypic trait (p<.05), GO analyses and IPA were conducted. Validation with published datasets. In order to validate our gene expression and WGCNA results, we overlapped gene lists obtained from microarray differential expression analysis for 22q11DS vs. Controls,
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| Contributor(s) |
Jalbrzikowski M, Lazaro MT, Gao F, Huang A, Chow C, Geschwind DH, Coppola G, Bearden CE |
| Citation(s) |
26201030 |
| Submission date |
Jul 08, 2014 |
| Last update date |
Aug 16, 2018 |
| Contact name |
Giovanni Coppola |
| E-mail(s) |
gcoppola@ucla.edu
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| Phone |
310-794-4172
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| Organization name |
UCLA
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| Department |
Psychiatry and Neurology
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| Lab |
Neurogenetics
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| Street address |
1524 Gonda, 695 Charles Young Drive South
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (2) |
| GPL6947 |
Illumina HumanHT-12 V3.0 expression beadchip |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (112)
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| Relations |
| BioProject |
PRJNA254737 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE59216_RAW.tar |
32.4 Mb |
(http)(custom) |
TAR |
| GSE59216_normalizedData_log2transformed_HT12v3_21samples.csv.gz |
6.3 Mb |
(ftp)(http) |
CSV |
| GSE59216_normalizedData_log2transformed_HT12v4_91samples.csv.gz |
30.7 Mb |
(ftp)(http) |
CSV |
| GSE59216_normalizedData_log2transformed_adjustedBatchEffect_detectionPval.csv.gz |
20.3 Mb |
(ftp)(http) |
CSV |
| GSE59216_normalized_ageOut.csv.gz |
20.8 Mb |
(ftp)(http) |
CSV |
| GSE59216_rawData_HT12v3_21samples.csv.gz |
6.5 Mb |
(ftp)(http) |
CSV |
| GSE59216_rawData_HT12v4_91samples.csv.gz |
26.1 Mb |
(ftp)(http) |
CSV |
| GSE59216_rawData_combinedPlatformV3V4.csv.gz |
27.4 Mb |
(ftp)(http) |
CSV |
| Processed data are available on Series record |
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