Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism.
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 identifiedUSP15as having recurrent de novo loss of function mutations and discovered evidence supporting two other known genes with recurrent DNVs (FOXP1andKDM5B). 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 identifiedUSP15as 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.
Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.|Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.
Rui
R
Chen
Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.|Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN USA.
Lea K
LK
Davis
Department of Psychiatry, University of Illinois at Chicago, Chicago, IL USA.
Stephen
S
Guter
Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.|Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.
Qiang
Q
Wei
Department of Psychiatry, University of Minnesota, Minneapolis, MN USA.
Suma
S
Jacob
Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.|Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.
Melissa H
MH
Potter
Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.|Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN USA.
Nancy J
NJ
Cox
Department of Psychiatry, University of Illinois at Chicago, Chicago, IL USA.
Edwin H
EH
Cook
Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.|Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.
James S
JS
Sutcliffe
Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.|Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.
Bingshan
B
Li
D000067877:Autism Spectrum Disorder / Q000235:genetics* / Q000378:metabolism; D058068:Endophenotypes / Q000097:blood; D059472:Exome; D005260:Female; D051858:Forkhead Transcription Factors / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D006801:Humans; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics*; D008297:Male; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012701:Serotonin / Q000097:blood*; D015398:Signal Transduction; D064570:Ubiquitin-Specific Proteases / Q000235:genetics*
C486626:FOXP1 protein, human; D051858:Forkhead Transcription Factors; D009687:Nuclear Proteins; D012097:Repressor Proteins; D012701:Serotonin; D056484:Jumonji Domain-Containing Histone Demethylases; C119611:KDM5B protein, human; C579226:USP15 protein, human; D064570:Ubiquitin-Specific Proteases
5-HT; Autism; Autism spectrum disorder; Compound heterozygotes; De novo mutation; Endophenotype; Group-wise transmission/disequilibrium test; Hyperserotonemia; Rare variants; Serotonin; Whole exome sequencing