Genotype:Phenotype Correlations of Social Deficits of Relevance for Autism Spectrum Disorder (ASD) in an NHP Model
Despite the important mechanistic information on neurodevelopmental processes provided to date by genetic rodent models of autism spectrum disorder (ASD), it is necessary to examine those processes in nonhuman primate (NHP) models with social behaviors and brain anatomy, function and development that more closely resemble that of our species. One NHP well-suited to such analyses is the macaque [rhesus monkey (M. mulatta)], where both typical and atypical social behaviors can be observed in complex social groups and genomic similarity to humans is much higher than in rodents. The macaque Social Responsiveness Scale (mSRS) has also been adapted to adult macaques from the human SRS used for clinical ASD assessments. Both genotypic and phenotypic analyses, particularly during development, are critical to further develop a NHP animal model of genetic risk for ASD of high translational value to humans.
The purpose of the present study is to identify genetic variants in a clinically relevant juvenile macaque NHP model housed in a semi-naturalistic environment, and compare variants to social behavioral phenotypes of relevance for ASD. We focused first on correlations between social phenotypes and variants identified in a list of 87 genes of interest in ASD in humans.
We made behavioral observations by two methods: first, at the Yerkes National Primate Research Center breeding colony, we collected 30-minute behavioral observations on 4 different days using a detailed and well-established ethogram for rhesus monkeys based on published methods. In addition, social impairments were assessed using a modified version of the adult mSRS adapted to juvenile macaques. For genomic analyses on 91 individuals, we enriched rhesus macaque DNA samples for exome sequences using the Rhexome v2 capture reagent and sequenced using the Illumina NovaSeq system. Reads were aligned to the rhesus Mmul_8.01 (rheMac8) reference genome using BWAmem. We called genomic variants using GATK and annotated them with VEP; associations with social phenotypes were made with PLINK and FaST-LMM. We further examined variants of interest by lifting the rhesus positions over to the orthologous human position and performing CADD analysis that predicts the functional impact of variants.
Our behavioral observations, including the mSRS, identified outliers on the social behavior spectrum in our macaque colony. Exploratory exome sequencing yielded a total of 169,240 SNVs and 7,201 indels in the 91 individuals. This includes 1,350 SNVs and 95 indels in the 87 genes of interest. We saw single-hit SNVs in several genes of top interest in humans (Satterstrom et al. 2018, https://www.biorxiv.org/content/early/2018/12/01/484113), including KDM6B and ASH1L, and these corresponded to observable changes in social behavior. We also observed individuals with combinations of common variants in a number of the 87 genes of interest.
Our pilot study indicates that we are able to identify juvenile macaques on extreme ends of a social behavior phenotype spectrum using different behavioral approaches. We also saw correlations between behavioral phenotypes of several animals and variants in genes associated with ASD in humans, particularly when the variants were also predicted to be damaging in the macaques.