LRFN5 locus structure is influenced by the individual’s sex and associated with autism

BackgroundLRFN5 is a brain-specific gene needed for synaptic development and plasticity. It is the only gene in a large 5.4 Mb topologically associating domain (TAD) on chromosome 14, which we term the LRFN5 locus. This locus is highly conserved, but has extensive copy number variation. MethodsLocus structure was studied by chromatin immunoprecipitation (chIP-onchip) in fibroblasts from individuals with autism and controls, supplemented with a capture-HiC determination of TAD structures in a family trio. LRFN5 expression was studied in foetal brain cell cultures. In addition, locus interaction was studied in four large and independent cohorts by measuring deviations from Hardy-Weinberg equilibrium of a common deletion polymorphism. ResultsWe found that locus structural changes are associated with developmental delay (DD) and autism spectrum disorders (ASD). In a large family, ASD in males segregated with a chromosome 14 haplotype carrying a 172 kb deletion upstream of LRFN5 . In a fibroblast capture-HiC study on an ASD-patient-parent trio, the ASDsusceptible haplotype (in the mother and her autistic son) had a TAD pattern different from both the father and a female control. When the trimethylated histone-3-lysine-9 chromatin (H3K9me3) profiles in fibroblasts from control males (n=6) and females (n=7) were compared, a male-female difference was observed around the LRFN5 gene itself (p<0.01). Intriguingly, in three cohorts of individuals with DD (n=8757), the number of heterozygotes of a common deletion polymorphism upstream of LRFN5 was 20-26% lower than expected from Hardy-Weinberg equilibrium. This indicates early allelic interaction, and the genomic conversions from heterozygosity to wildtype or deletion homozygosity were of equal magnitudes. In a control group of medical students (n=1416), such conversions were three times more common than in the DD-patient cohorts (p=0.00001). Hypothetically, such allelic interaction is needed to establish monoallelic expression, which we found in foetal brain cell cultures. LimitationsThe male-female difference in H3K9me3 profiles was based on fibroblast data from a small number of individuals, and the monoallelic expression data on a single experiment. ConclusionsTaken together, allelic interaction, monoallelic expression and sexdependent differences make the LRFN5 locus attractive for exploring the genetic basis of synaptic memory and high-functioning male autism.