Novel phenotypes and loci identified through clinical genomics approaches to pediatric cataract

Abstract

Pediatric cataract is highly heterogeneous clinically and etiologically. While mostly isolated, cataract can be part of many multisystem disorders, further complicating the diagnostic process. In this study, we applied genomic tools in the form of a multi-gene panel as well as whole-exome sequencing on unselected cohort of pediatric cataract (166 patients from 74 families). Mutations in previously reported cataract genes were identified in 58% for a total of 43 mutations, including 15 that are novel. GEMIN4 was independently mutated in families with a syndrome of cataract, global developmental delay with or without renal involvement. We also highlight a recognizable syndrome that resembles galactosemia (a fulminant infantile liver disease with cataract) caused by biallelic mutations in CYP51A1. A founder mutation in RIC1 (KIAA1432) was identified in patients with cataract, brain atrophy, microcephaly with or without cleft lip and palate. For non-syndromic pediatric cataract, we map a novel locus in a multiplex consanguineous family on 4p15.32 where exome sequencing revealed a homozygous truncating mutation in TAPT1. We report two further candidates that are biallelically inactivated each in a single cataract family: TAF1A (cataract with global developmental delay) and WDR87 (non-syndromic cataract). In addition to positional mapping data, we use iSyTE developmental lens expression and gene-network analysis to corroborate the proposed link between the novel candidate genes and cataract. Our study expands the phenotypic, allelic and locus heterogeneity of pediatric cataract. The high diagnostic yield of clinical genomics supports the adoption of this approach in this patient group.

Fig. 1

Expanding the allelic and locus heterogeneity of pediatric cataract. Distribution for mutations identified in known and novel candidate genes for cataract by NGS

Fig. 2

The mouse orthologs of the novel cataract candidate genes TAPT1, RIC1, CYP51A1, GEMIN4, TAF1A, WDR87 (4932431P20Rik) are expressed and enriched in lens development. (a) Lens expression of candidate genes Tapt1, Ric1, Cyp51a1, Gemin4, Taf1a, and 4932431P20Rik (WDR87) was analyzed in whole lens microarray datasets at mouse embryonic day (E) 10.5, E16.5 and postnatal day (P) 0, and P56, as well as isolated lens epithelium (Epi.) dataset at P28. The red dotted line in “a” indicates expression cut-off score of 100 fluorescence intensity units. (b) Lens-enrichment of candidate genes was evaluated by comparing their fluorescence expression intensity scores in the lens against that in the mouse whole embryonic body (WB) reference dataset. The color intensities in the heat map indicate the fold-change differences between lens expression over WB. (c) RNA-seq expression of newborn (P0) mouse isolated lens epithelium (epi) and fiber cells (FC). Error bars represent standard error of mean (SEM). Asterisk represents significant difference between comparisons in FC and Epi. expression (p < 0.05)

Fig. 3

Tapt1, Ric1, Cyp51a1, Gemin4 and Taf1a are mis-regulated in targeted gene deletion mouse mutants with lens defects. Expression of candidate genes in various mouse mutants that exhibit lens defects including Pax6 lens-conditional null (Pax6 cKO) at E9.5 and E10.5, Notch2 cKO at E19.5, E2f1−/−:E2f2−/−:E2f3−/− triple cKO (E2f1/2/3 cKO) at P0, Sparc null at P28 (isolated lens epithelium only), Tdrd7 null at P30, Mafg−/−:Mafk+/− compound mutant at P60, Klf4 cKO at P56, Foxe3 lens overexpression mutant at P2, Cpb:p300 cKO mutant at E9.5, dnBrg1 mutant at E15.5 and Hsf4 null at P0. Differential expression in fold-change of candidate genes between mutant and control is plotted. Error bars represent standard error of mean (SEM). Asterisk represents significant expression differences between mutant vs. control lens datasets (p < 0.05)