Visualization of trans-interactions of a protocadherin-α between processes originating from single neurons

Genome Wide and Rare Variant Association Studies of Amblyopia in the All of Us Research Program

OBJECTIVE

Amblyopia is characterized by decreased visual acuity due to abnormal visual experience during development. It affects approximately three percent of the population and is associated with abnormal development of the visual cortex. Despite treatment, many patients have residual visual acuity deficits. This study aimed to explore the genetic contributions to amblyopia.

DESIGN

Case-control.

PARTICIPANTS

The All of Us Research Program includes genotypic and phenotypic data from a diverse population of adults (age ≥ 18 years) across the United States. 764 subjects with amblyopia (based on ICD and SNOMED codes) and 122,305 controls with no record of amblyopia and whole genome sequencing were compared. Only participants of European genetic ancestry were included due to small numbers of affected participants in other ancestral groups.

METHODS

Genome wide association study (GWAS) of common variants (minor allele frequency >1%) and rare variant association study (RVAS) at the gene level for amblyopia of participants in the All of Us Research Program.

MAIN OUTCOME MEASURES

Individual single-nucleotide polymorphisms (SNPs) significantly associated with amblyopia and genes with significant burden of rare variants in amblyopia RESULTS: The GWAS revealed 4 loci that approached statistical significance defined as p = 5e-8: rs56105618, rs1349660, rs7958343, and rs138693522. Each of the variants is an expression quantitative trait locus (eQTL) for a gene expressed in the brain or related to neural development. RVAS revealed 15 genes with a statistically significant (p-value = 5e-05) different burden of variants: DCP1B, OR12D2, PCDHA4, ALKBH8, NMUR2, OR52P1P, NEU1, CACNB2, PSMA7, LRR1, ZNF831, FSIP2, ZNF654, CES5A, and MPV17, several of which have known roles in neurodevelopment.

CONCLUSIONS

The identification of genes linked to amblyopia with roles in neurodevelopment suggests that the neurodevelopmental changes in amblyopia are not only secondary to abnormal visual experience but may result from the interaction of primary neurodevelopmental deficits with abnormal experience. This potentially explains why some children develop amblyopia and others do not with the same ocular risk factors, may explain differences in treatment outcomes, and suggests new avenues for amblyopia treatment.

Protocol to visualize trans-interaction of clustered protocadherin using cIPAD, a fluorescent indicator, in cultured human cells and mouse neurons

cIPAD is a fluorescent indicator that allows the visualization of trans-interactions of clustered protocadherin (Pcdh), a cell adhesion molecule that mediates neuronal self-recognition. We describe steps for using HEK293T cells to visualize Pcdh trans-interactions across cells as a preliminary experiment before using dissociated mouse neurons. We then detail procedures for visualizing Pcdh trans-interactions between processes originating from the same neurons, which are considered as Pcdh-mediated neuronal self-recognition. For complete details on the use and execution of this protocol, please refer to Kanadome et al.1.