PurposeTo demonstrate the utility of an amplification-free long-read sequencing method to characterize the Fuchs endothelial corneal dystrophy (FECD)-associated intronic TCF4 triplet repeat (CTG18.1).MethodsWe applied an amplification-free method, utilizing the CRISPR/Cas9 system, in combination with PacBio single-molecule real-time (SMRT) long-read sequencing, to study CTG18.1. FECD patient samples displaying a diverse range of CTG18.1 allele lengths and zygosity status (n = 11) were analyzed. A robust data analysis pipeline was developed to effectively filter, align, and interrogate CTG18.1-specific reads. All results were compared with conventional polymerase chain reaction (PCR)-based fragment analysis.ResultsCRISPR-guided SMRT sequencing of CTG18.1 provided accurate genotyping information for all samples and phasing was possible for 18/22 alleles sequenced. Repeat length instability was observed for all expanded (≥50 repeats) phased CTG18.1 alleles analyzed. Furthermore, higher levels of repeat instability were associated with increased CTG18.1 allele length (mode length ≥91 repeats) indicating that expanded alleles behave dynamically.ConclusionCRISPR-guided SMRT sequencing of CTG18.1 has revealed novel insights into CTG18.1 length instability. Furthermore, this study provides a framework to improve the molecular diagnostic accuracy for CTG18.1-mediated FECD, which we anticipate will become increasingly important as gene-directed therapies are developed for this common age-related and sight threatening disease.

Fuchs endothelial corneal dystrophy (FECD) is a common cause for heritable visual loss in the elderly. Since the first description of an association between FECD and common polymorphisms situated within the transcription factor 4 ( TCF4 ) gene, genetic and molecular studies have implicated an intronic CTG trinucleotide repeat (CTG18.1) expansion as a causal variant in the majority of FECD patients. To date, several non-mutually exclusive mechanisms have been proposed that drive and/or exacerbate the onset of disease. These mechanisms include (i) TCF4 dysregulation; (ii) toxic gain-of-function from TCF4 repeat-containing RNA; (iii) toxic gain-of-function from repeat-associated non-AUG dependent (RAN) translation; and (iv) somatic instability of CTG18.1. However, the relative contribution of these proposed mechanisms in disease pathogenesis is currently unknown. In this review, we summarise research implicating the repeat expansion in disease pathogenesis, define the phenotype-genotype correlations between FECD and CTG18.1 expansion, and provide an update on research tools that are available to study FECD as a trinucleotide repeat expansion disease. Furthermore, ongoing international research efforts to develop novel CTG18.1 expansion-mediated FECD therapeutics are highlighted and we provide a forward-thinking perspective on key unanswered questions that remain in the field.

The predominant cause of Fuchs endothelial corneal dystrophy (FECD) is a CTG repeat expansion (termed CTG18.1) situated within an intron of the transcription factor encoding gene,TCF4. Here we use a primary FECD case-derived corneal endothelial cell (CEC) system to enhance our understanding of multiple pathogenic processes underlying CTG18.1-mediated FECD. We define differential gene expression and alternative splice events using long- and short-read RNA-seq datasets generated from 15 biologically independent primary CEC lines, comprehensively characterizing aberrant splicing-related aspects of the disease. Further targeted analysis of these data, alongside a complementary spatial transcriptomics approach, reveals a unique and distinctive pattern ofTCF4-specific dysregulation that underpins expansion-positive FECD and isolates downstream consequences of this shift as an important pathogenic component of disease. To explore whetherTCF4dysregulation, irrespective of CTG18.1 expansions, could cause FECD we also interrogated exome data generated from a large (n=141) genetically refined cohort of CTG18.1 expansion-negative FECD cases. We identify four rare and predicted deleterious (minor allele frequency <0.005; CADD>15)TCF4variants all encompassed by only a small fraction (10/93) of totalTCF4transcripts suggesting that, in rare instances, disruption of a specific subset of TCF4 isoforms may also confer CEC-specific disease independent of CTG18.1 expansions. In summary, our study supports the hypothesis that at least two distinct pathogenic mechanisms, RNA toxicity andTCF4isoform-specific dysregulation, underpin the pathophysiology of FECD. We anticipate these data will inform and guide the development of translational interventions for this common triplet-repeat mediated disease.

Name of the disease (synonyms) CUGC for posterior polymorphous corneal dystrophy (PPCD). OMIM# of the disease 122000; 609141; 618031. Name of the analysed genes or DNA/chromosome segments OVOL2 (PPCD1); ZEB1 (PPCD3); GRHL2 (PPCD4). OMIM# of the gene(s) 616441; 189909; 608576. Review of the analytical and clinical validity as well as of the clinical utility of DNA-based testing for variants in the OVOL2, ZEB1 and GRHL2 gene(s) in a diagnostic setting, predictive and parental settings and for risk assesment in relatives.

Keratoconus (KC) is characterised by thinning and ectasia of the cornea that leads to irregular myopic astigmatism and reduced vision. The onset is usually in childhood or early adulthood, with progression at a variable rate until stabilisation in most cases by 35 years (Gomes et al., 2015;Tur et al., 2017). It is a common cause of visual disability in young people with a prevalence as high as 1.2% in some populations (Chan et al., 2021;Davidson et al., 2014). Previously, 10% to 15% of patients required corneal transplantation (Gordon et al., 2006;Kennedy et al., 1986;Pearson et al., 2000), although this figure will likely reduce following the widespread introduction of corneal crosslinking (CXL) (Godefrooij et al., 2016;Sandvik et al., 2015). The aetiology of KC is complex. A recent genome-wide association study (GWAS) comprising 4669 cases reported 36 genetic loci that have implicated both dysregulation of corneal collagen matrix integrity and cell differentiation pathways