Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma

PLoS One. 2017 Mar 6;12(3):e0172427. doi: 10.1371/journal.pone.0172427. eCollection 2017.

Abstract

Purpose: To identify biological processes associated with POAG and its subtypes, high-tension (HTG) and normal-tension glaucoma (NTG), by analyzing rare potentially damaging genetic variants.

Methods: A total of 122 and 65 unrelated HTG and NTG participants, respectively, with early onset advanced POAG, 103 non-glaucoma controls and 993 unscreened ethnicity-matched controls were included in this study. Study participants without myocilin disease-causing variants and non-glaucoma controls were subjected to whole exome sequencing on an Illumina HiSeq2000. Exomes of participants were sequenced on an Illumina HiSeq2000. Qualifying variants were rare in the general population (MAF < 0.001) and potentially functionally damaging (nonsense, frameshift, splice or predicted pathogenic using SIFT or Polyphen2 software). Genes showing enrichment of qualifying variants in cases were selected for pathway and network analysis using InnateDB.

Results: POAG cases showed enrichment of rare variants in camera-type eye development genes (p = 1.40×10-7, corrected p = 3.28×10-4). Implicated eye development genes were related to neuronal or retinal development. HTG cases were significantly enriched for key regulators in the unfolded protein response (UPR) (p = 7.72×10-5, corrected p = 0.013). The UPR is known to be involved in myocilin-related glaucoma; our results suggest the UPR has a role in non-myocilin causes of HTG. NTG cases showed enrichment in ion channel transport processes (p = 1.05×10-4, corrected p = 0.027) including calcium, chloride and phospholipid transporters involved in plasma membrane homeostasis. Network analysis also revealed enrichment of the MHC Class I antigen presentation pathway in HTG, and the EGFR1 and cell-cycle pathways in both HTG and NTG.

Conclusion: This study suggests that mutations in eye development genes are enriched in POAG. HTG can result from aberrant responses to protein misfolding which may be amenable to molecular chaperone therapy. NTG is associated with impaired plasma membrane homeostasis increasing susceptibility to apoptosis.

MeSH terms

  • Adult
  • Apoptosis / genetics
  • Case-Control Studies
  • Cell Membrane / metabolism*
  • Computational Biology / methods
  • Exome
  • Female
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Gene Ontology
  • Gene Regulatory Networks
  • Genetic Predisposition to Disease
  • Glaucoma, Open-Angle / genetics*
  • Glaucoma, Open-Angle / metabolism*
  • High-Throughput Nucleotide Sequencing
  • Homeostasis / genetics*
  • Humans
  • Male
  • Middle Aged
  • Mutation
  • Organogenesis / genetics*
  • Unfolded Protein Response / genetics*

Grant support

This project is supported by The National Health and Medical Research Council (NHMRC) Centres of Research Excellence scheme (APP1023911) and project grant (APP1107098). SM is supported by an Australian Research Council Future Fellowship. DJL is supported by an EMBL Australia Group Leader award. JEC is supported by an NHMRC Practitioner Fellowship (APP1065433). The funding organizations had no role in the design or conduct of this research.