The Spectrum of PAX6 Mutations and Genotype-Phenotype Correlations in the Eye

Abstract

The transcription factor PAX6 is essential in ocular development in vertebrates, being considered the master regulator of the eye. During eye development, it is essential for the correct patterning and formation of the multi-layered optic cup and it is involved in the developing lens and corneal epithelium. In adulthood, it is mostly expressed in cornea, iris, and lens. PAX6 is a dosage-sensitive gene and it is highly regulated by several elements located upstream, downstream, and within the gene. There are more than 500 different mutations described to affect PAX6 and its regulatory regions, the majority of which lead to PAX6 haploinsufficiency, causing several ocular and systemic abnormalities. Aniridia is an autosomal dominant disorder that is marked by the complete or partial absence of the iris, foveal hypoplasia, and nystagmus, and is caused by heterozygous PAX6 mutations. Other ocular abnormalities have also been associated with PAX6 changes, and genotype-phenotype correlations are emerging. This review will cover recent advancements in PAX6 regulation, particularly the role of several enhancers that are known to regulate PAX6 during eye development and disease. We will also present an updated overview of the mutation spectrum, where an increasing number of mutations in the non-coding regions have been reported. Novel genotype-phenotype correlations will also be discussed.

Keywords: PAX6; aniridia; enhancers; genotype-phenotype correlations; haploinsufficiency; microphthalmia; non-coding variants; paired domain; premature termination codon; regulatory regions.

Figure 1

Human PAX6 locus. (A) PAX6 gene structure in 11p13, with 14 exons (boxes, colours represent respective protein domains), promoters P0, P1 and Pα (boxes with diagonal lines) and regulatory elements (oval shapes with horizontal lines) including ectodermal enhancer (EE), located upstream PAX6, and Downstream Regulatory Region (DRR) and SIMO, within the introns of neighbour gene ELP4 (last four exons represented by orange boxes). EE: ectodermal enhancer; DRR: downstream regulatory region. (B) Main PAX6 isoforms, canonical PAX6 and PAX6(5a) and their respective structure with functional domains. PD: paired domain; NTS: N-terminal subdomain; CTS: C-terminal subdomain; LNK: linker region; HD: homeodomain; PST: proline-serine-threonine domain; aa: amino acids.

Figure 2

Schematic representation of previously reported deletions in 11p13 encompassing regulatory regions 3’ of PAX6. Genes are represented by grey boxes and arrows indicate direction of transcription. PAX6 is highlighted in black. Known PAX6 enhancers are indicated by oval shapes with horizontal lines with focus on SIMO and E180B. Coloured bars represent deletions identified in different cohorts of aniridia patients without PAX6 mutations [68,72,73,75,76,77]. The vertical dashed lines indicate a common region deleted in all mentioned aniridia patients, which was defined first as 245 Kb long by Ansari et al. (blue dashed lines) and later reduced to 18 Kb by Plaisancie et al. (red dashed lines) [72,75]. Genomic coordinates are based on human genome assembly hg19.

Figure 3

Distribution of different mutation types in the PAX6 Mutation Database. (A) All of the mutations reported in the database. (B) Mutation frequencies associated to aniridia. (C) PAX6 mutation distribution in non-aniridia phenotypes. PTC (premature termination codon) include all mutations predicted to cause a premature stop codon and include nonsense, frameshift and splice site variants. CTE refer to variants that cause C-terminal extension of PAX6.

Figure 4

Phenotypic spectrum of patients with PAX6 mutations. (A) Classical aniridia phenotype showing complete iris hypoplasia with central corneal opacity and vascularisation, (B) fundus imaging indicating absence of foveal reflex and (C) optical coherence tomography (OCT) of the macula showing foveal hypoplasia. (D) Left eye of a patient diagnosed with bilateral microphthalmia with microcornea. (E) Patient diagnosed with dominant nystagmus with no iris abnormalities and (F) foveal hypoplasia on OCT.

Figure 5

Spectrum of coding PAX6 mutations causing non-aniridia phenotypes. A representation of canonical PAX6 structure is shown with respective domains and amino acid distribution. Mutations and respective phenotypes were collected from the PAX6 Mutation Database and the Human Genome Mutation Database (HGMD). The majority of mutations are included in the paired domain (NTS and CTS) and constitute missense mutations (squares). Mutations in alternative exon 5a are shown in blue. ^a Isolated foveal hypoplasia and nystagmus without iris abnormalities; variants shown in grey show cases presenting full iris but with possible mild structural defects [86]; ^b Optic nerve malformations include optic nerve coloboma, aplasia, and morning glory disc; NTS: N-terminal subdomain; CTS: C-terminal subdomain; LNK: linker region; HD: homeodomain; PSTD: proline-serine-threonine domain; aa: amino acids; ASD: anterior segment dysgenesis.