30 years of repeat expansion disorders: What have we learned and what are the remaining challenges?

Abstract

Tandem repeats represent one of the most abundant class of variations in human genomes, which are polymorphic by nature and become highly unstable in a length-dependent manner. The expansion of repeat length across generations is a well-established process that results in human disorders mainly affecting the central nervous system. At least 50 disorders associated with expansion loci have been described to date, with half recognized only in the last ten years, as prior methodological difficulties limited their identification. These limitations still apply to the current widely used molecular diagnostic methods (exome or gene panels) and thus result in missed diagnosis detrimental to affected individuals and their families, especially for disorders that are very rare and/or clinically not recognizable. Most of these disorders have been identified through family-driven approaches and many others likely remain to be identified. The recent development of long-read technologies provides a unique opportunity to systematically investigate the contribution of tandem repeats and repeat expansions to the genetic architecture of human disorders. In this review, we summarize the current and most recent knowledge about the genetics of repeat expansion disorders and the diversity of their pathophysiological mechanisms and outline the perspectives of developing personalized treatments in the future.

Figure 1

Timeline of repeat expansion discovery in human disorders During the first twenty years, linkage analyses were the gold standard allowing to map the genomic region containing repeat expansions. The development of next-generation sequencing, and more particularly long-read sequencing, has marked a new milestone, making their identification at a genome-wide scale possible, and has allowed a new wave of repeat expansion discovery.

Figure 2

Location of repeat expansions within genes Repeat expansions may affect coding regions (mainly encoding polyglutamine or polyalanine tracts) or noncoding regions of genes. Noncoding repeat expansions are mainly located in promoters or 5′ untranslated regions (UTRs) or introns. Noncoding repeats in 5′ regions are often GC-rich and their expansion usually affects gene expression through methylation of other epigenetic processes. Intronic expansions and expansions affecting 3′ UTRs more often lead to RNA toxicity or polypeptide synthesis via repeat-associated non-AUG (RAN) translation and subsequent formation of cellular/nuclear aggregates. BCCD, brachydactyly and cleidocranial dysplasia; BSS, Baratela-Scott syndrome; CANVAS, cerebellar ataxia, neuropathy and vestibular areflexia syndrome; CCHS, congenital central hypoventilation syndrome; DM1, myotonic dystrophy type 1; DM2, myotonic dystrophy type 2; DRPLA, dentatorubral-pallidoluysian atrophy; EIEE1, early infantile epileptic encephalopathy type 1; EPM1, progressive myoclonus epilepsy type 1 (Unverricht-Lundborg disease); FAME, familial adult myoclonic epilepsy; FECD3, Fuchs endothelial corneal dystrophy type 3; FRAXE, fragile XE syndrome; FRDA, Friedreich ataxia; FTD/ALS, frontotemporal dementia / amyotrophic lateral sclerosis; FXS, fragile X syndrome; FXTAS, fragile X-associated tremor ataxia syndrome; GDPAG, global developmental delay, progressive ataxia, and elevated glutamine; HD, Huntington disease; HDL2, Huntington disease-like 2; HFGS, hand-foot-genital syndrome; HPE5, holoprosencephaly type 5; MRGH, mental retardation with isolated growth hormone deficiency; OPMD, oculopharyngeal muscular dystrophy; NIID, neuronal intranuclear inclusion disease; OPDM1, oculopharyngodistal myopathy type 1; OPDM2, oculopharyngeal muscular dystrophy type 2; OPML1, oculopharyngeal myopathy with leukoencephalopathy type 1; SBMA, spinal and bulbar muscular atrophy; SPD1, synpolydactyly type 1; SCA, spinocerebellar ataxia; SVA, SINE-VNTR-Alu retrotransposon; XDP, X-linked dystonia parkinsonism.

Figure 3

Main mechanisms associated with repeat expansions (A) Epigenetic gene silencing. Large, usually GC-rich expansions located in promoters and/or 5′ UTRs are frequently associated with DNA hypermethylation at CpG sites. Methylated expanded alleles are locked in a chromatin configuration preventing gene expression, and therefore leading to a loss-of-function of the expanded allele. Examples of this mechanisms include full expansions in FMR1 (fragile X syndrome) and expansions in XYLT1 (Scott-Baratela syndrome). (B) Sequestration of RNA-binding splicing factors. Specific expanded repeats within RNA molecules are able to form stable secondary structures such as hairpins, which can bind specific RNA-binding splicing factors (e.g., muscleblind-like proteins) with high affinity. These RNA molecules accumulate to form inclusions in the nucleus and sequester bound RNA-binding splicing factors, resulting in misplicing of a subset of transcripts requiring these factors. The illustration of this mechanism is provided by CTG/CAG expansions in DMPK. (C) Protein misfolding and aggregation. Coding expansions, particularly those encoding polyQ stretches, lead to neuronal intranuclear protein inclusions. This mechanism results from the ability of abnormally long polyQ chains to form β sheet structures prone to form insoluble fibrillar aggregates. (D) Repeat-associated non-AUG (RAN) translation. RAN translation is a non-canonical protein synthesis process in which peptide synthesis is initiated at the site of the expanded repeats in absence of an AUG codon. This process can theoretically occur in all reading frames on both sense and antisense DNA strands, resulting in up to six different polypeptides, although only some of these peptides are toxic and/or preferentially expressed. For example, intermediate CGG expansions (ranging from 55 to 200 repeats) associated with FXTAS mainly lead to synthesis of polyglycine peptides that are able to accumulate and form protein aggregates. The list of repeat expansion disorders associated with RAN occurs is rapidly increasing and so far includes DM2, FXTAS, FXPOI, HD, C9ORF72-FTD/ALS, SCA8, and SCA31.