A systems genetics approach identifies select candidates as modulators of retinal ganglion cell axonal viability

Abstract

Purpose : Glaucoma is a complex disease characterized by progressive degeneration of the optic nerve (ON) and the loss of retinal ganglion cells (RGCs). The BXD recombinant inbred family represents a murine genetic reference population derived from crosses between C57BL/6J and DBA/2J mice. Several glaucoma endophenotypes segregate in this family. Our study applies a system genetics approach glaucoma to identify genes involved in RGC viability.

Methods : ONs were harvested from 75 BXD strains aged 13 to 19 months. Following tissue processing, we quantified the intact axons per ON cross-section (N = 246). Next, quantitative trait locus (QTL) mapping was performed to identify a locus of interest. Gene expression data from whole eye and retina databases were used for expression QTL (eQTL) analysis. Candidates identified in the locus interval were narrowed using several criteria: a cis-acting eQTL, presence of nonsynonymous single nucleotide polymorphism(s) (SNP), and a significant correlation between gene expression and phenotype (partial r [p(r)] ≥ |0.2|; P < 0.05). Finally, we identified biologically relevant networks in which each high-priority gene operates within.

Results : Across strains, the number of intact axons per ON ranged from nearly 25,000 to 78,000. A single genome-wide significant peak QTL was identified on chromosome 9 at 103.84 Mb [95% CI: 97.27 to 106.02 Mb] with a –logP linkage of 4.88 (P < 0.05). Of 784 positional candidates in this region, six genes met criteria: nephronophthisis 3 (Nphp3), mitochondrial ribosomal protein L3 (Mrpl3), Copine 4 (Cpne4), Gm47106, Fas Apoptotic Inhibitory Molecule 1 (Faim), and EPH Receptor B1 (Ephb1). Nonsynonymous SNPs were found in all candidates except for Gm47106. Using a consensus classifier, amino acid substitutions were predicted to be deleterious to gene function in two candidates: Mrpl3 and Cpne4. Gene set enrichment analysis (GSEA) revealed strong connections to biological networks in neuroinflammation and mitochondrial dysfunction.

Conclusions : Using systems genetics, we identify a single significant QTL regulating the number of live axons in ONs. We suggest two high-priority genes that warrant further exploration for their role in the pathophysiology of glaucoma.

This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.