The online version of this article (doi:10.1186/s13229-017-0130-3) contains supplementary material, which is available to authorized users.
Autism spectrum disorder (ASD) is one of the most highly heritable neuropsychiatric disorders, but underlying molecular mechanisms are still unresolved due to extreme locus heterogeneity. Leveraging meaningful endophenotypes or biomarkers may be an effective strategy to reduce heterogeneity to identify novel ASD genes. Numerous lines of evidence suggest a link between hyperserotonemia, i.e., elevated serotonin (5-hydroxytryptamine or 5-HT) in whole blood, and ASD. However, the genetic determinants of blood 5-HT level and their relationship to ASD are largely unknown.
In this study, pursuing the hypothesis that de novo variants (DNVs) and rare risk alleles acting in a recessive mode may play an important role in predisposition of hyperserotonemia in people with ASD, we carried out whole exome sequencing (WES) in 116 ASD parent-proband trios with most (107) probands having 5-HT measurements.
Combined with published ASD DNVs, we identified USP15 as having recurrent de novo loss of function mutations and discovered evidence supporting two other known genes with recurrent DNVs (FOXP1 and KDM5B). Genes harboring functional DNVs significantly overlap with functional/disease gene sets known to be involved in ASD etiology, including FMRP targets and synaptic formation and transcriptional regulation genes. We grouped the probands into High-5HT and Normal-5HT groups based on normalized serotonin levels, and used network-based gene set enrichment analysis (NGSEA) to identify novel hyperserotonemia-related ASD genes based on LoF and missense DNVs. We found enrichment in the High-5HT group for a gene network module (DAWN-1) previously implicated in ASD, and this points to the TGF-β pathway and cell junction processes. Through analysis of rare recessively acting variants (RAVs), we also found that rare compound heterozygotes (CHs) in the High-5HT group were enriched for loci in an ASD-associated gene set. Finally, we carried out rare variant group-wise transmission disequilibrium tests (gTDT) and observed significant association of rare variants in genes encoding a subset of the serotonin pathway with ASD.
Our study identified USP15 as a novel gene implicated in ASD based on recurrent DNVs. It also demonstrates the potential value of 5-HT as an effective endophenotype for gene discovery in ASD, and the effectiveness of this strategy needs to be further explored in studies of larger sample sizes.
Additional file 1: Table S1. List of DNVs identified in our data. Table S2. Mean and standard deviation used for normalization of WB5HT. Table S3. Serotonin pathway genes. Table S4. Summary of subject demographics and phenotype data. Table S5. GSEA of LoF DNVs in ASC, SSC and ACE. Table S6. Gene lists disrupted by different types of DNVs in the High-5HT and the Normal-5HT groups. Table S7. GSEA of all RAVs and Normal-5HT RAVs. (XLSX 47 kb)13229_2017_130_MOESM1_ESM.xlsx
Additional file 2: Figure S1. The distribution of normalized 5-HT in parents and probands. The two vertical lines at 5-HT = 1.0 and 1.75 are the cutoffs used to define the High group (5HT > 1.75) and the Normal-5HT group (5HT < 1.0). (PDF 19 kb)13229_2017_130_MOESM2_ESM.pdf
Additional file 3: Figure S2. The result of PCA indicates the threshold to identify the individuals with European ancestry. Left panel: PC plot of CEU, CHB, YRI from the 1000 Genome Project. Right panel: PC plot of our data. (PDF 8 kb)13229_2017_130_MOESM3_ESM.pdf
Additional file 4: Figure S3. Gene length distribution of functional/disease gene sets used in GSEA. Most of gene sets have higher median gene length than the set of all genes (background distribution). The red line indicates the median length of all genes in the genome. (PDF 80 kb)13229_2017_130_MOESM4_ESM.pdf
Additional file 5: Figure S4. Burden of RAVs in Fathers, Mothers and Probands. (a) All RAVs. (b) Homozygous RAVs. (c) Compound heterozygous RAVs. (PNG 430 kb)13229_2017_130_MOESM5_ESM.png
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- Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism
Lea K. Davis
Melissa H. Potter
Nancy J. Cox
Edwin H. Cook
James S. Sutcliffe
- BioMed Central