Onset of many neurodegenerative and neuromuscular diseases usually starts in adulthood; however, recent advances point toward neurodevelopmental changes as drivers of late neurodegeneration. How early neuropathological features occur in these conditions remains unclear, which is critical for timely therapeutic intervention. Here, we provide evidence that neurodevelopmental axonal defects initiate a motor phenotype in a zebrafish model of spinocerebellar ataxia type 37 (SCA37), a degenerative hereditary condition caused by an ATTTC repeat in the DAB1 gene. We investigated neuronal defects triggered by the embryonic AUUUC repeat RNA and their effects later in life by transiently expressing this RNA in embryos and analyzing innervation and motor function. We found abnormalities in motor neuron axonal outgrowth and muscle innervation. We also discovered disrupted embryonic motor activity and reduced locomotor distance and velocity in late adult zebrafish, demonstrating motor impairment. Moreover, we showed that NOVA2 expression rescues axonal defects, indicating dysfunction of NOVA2-regulated neurodevelopmental processes. Overall, our results establish embryonic expression of the AUUUC repeat RNA as a driver of axonal and synaptic abnormalities, interfering with neuronal circuits and culminating in adult motor dysfunction.

Repeat expansions are a known cause of progressive myoclonic epilepsy (PME) and familial adult myoclonic epilepsy (FAME). We hypothesized that PME and FAME may have an overlapping phenotypic spectrum and searched for pathogenic repeat expansions in 18 individuals from 15 families with later-onset PME or FAME. We generated whole genome sequencing data by short-read sequencing and searched for known and novel repeat expansions. No known, pathogenic repeat expansions were identified. Instead, we discovered a novel TTGTA expansion in the gene MARCHF6 at the same location as the known, pathogenic FAME3 expansion in a PME family. Targeted long-read sequencing of this locus revealed a large, complex repeat structure harbouring an expansion of the pathogenic TTTCA repeat that causes FAME, surrounded by TTTTA and TTGTA expansions. Motivated by this discovery, we developed a new bioinformatic approach, mixSTR, to search for evidence of such complex expansions and discovered an additional novel configuration of the FAME3 expansion containing hidden pathogenic TTTCA expansions embedded within a TTTTA expansion in a second family clinically diagnosed with FAME. Both families had initially tested negative for the FAME3 expansion with standard RP-PCR and short-read genome sequencing analysis. We searched large epilepsy and population cohorts but did not identify any additional new individuals with complex FAME3 expansions. These findings have two important implications. Firstly, known repeat expansion loci with unusual repeat expansions, even if not known to be pathogenic, warrant further investigation as they may contain hidden pathogenic repeat expansions. Secondly, they provide molecular support for the clinical idea that PME and FAME have an overlapping phenotypic spectrum, and that the known FAME repeat expansions should be part of the diagnostic assessment of unsolved PMEs.

Benign adult familial myoclonus epilepsy (BAFME) is an autosomal dominantly inherited disease characterized by infrequent seizures and tremorous myoclonus. The disease is also called familial adult myoclonic epilepsy (FAME) or familial cortical myoclonic tremor with epilepsy (FCMTE). Although the causes of BAFME had been unknown for a long, we identified TTTCA and TTTTA repeat expansions in intron 4 of SAMD12 as a cause of BAFME type 1. We also found TTTCA and TTTTA repeat expansions in TNRC6A and RAPGEF2 also cause the disease (BAFME types 6 and 7, respectively), thus proposing a concept of repeat motif-phenotype correlation. After that, TTTCA and TTTTA repeat expansions in STARD7, MARCHF6, YEATS2, and RAI1 have been identified as causes of BAFME types 2, 3, 4, and 8. The findings further supported the concept. The involvement of RNA-mediated toxicity, particularly of UUUCA repeats, is assumed to be the pathomechanism of this disease. The next step will be understanding the molecular pathomechanism of BAFME and identifying molecular targets of more efficient therapeutic approaches.

Familial adult myoclonic epilepsy (FAME), an autosomal dominant disorder, is characterized by cortical myoclonus and occasional generalized tonic-clonic seizures. To date, intronic pentanucleotide repeat expansions in at least seven genes, including SAMD12, TNRC6A, YEATS2, MARCHF6, STARD7, RAPGEF2, and RAI1, have been reported as causative. Detecting these repeat expansions using conventional sequencing techniques (Sanger or short-read next-generation sequencing) is not feasible as they cannot reliably span or characterize long repetitive elements. Although genetic testing has been performed in some research laboratories, comprehensive long read-based panel is unavailable for clinical application. To address this gap, we developed a targeted long-read sequencing panel and applied it in a clinical diagnostic context for the first time. We designed a custom long-read sequencing panel targeting all seven known FAME-associated repeat loci using Oxford Nanopore Cas9-enrichment technology and applied it to a 47-year-old woman with familial cortical myoclonic tremor, clinically suspected to have FAME. The panel functioned as intended, providing robust on-target coverage across all loci, facilitating confident interrogation of each repeat region. At the SAMD12 locus, strand-aware histograms and read-level inspection demonstrated a clear pathogenic expansion, encompassing mixed TTTTA/TTTCA motifs with detectable TTTGA interruptions, consistent with FAME1. Using the crude allele prediction option of tandem-genotypes, the expanded allele contained approximately 689 additional repeats relative to the reference genome. The other six loci showed no pathogenic expansions. This targeted long-read panel enabled the first clinical molecular diagnosis of FAME using a comprehensive assay, yielding allele-resolved characterization of the pathogenic repeat and its motif composition. With further validation, this approach may serve as a clinically practical tool for reliable detection of FAME1 and for broader screening of other FAME subtypes, potentially reducing reliance on prolonged clinical observation or specialized electrophysiological testing.

Familial Adult Myoclonic Epilepsy type 3 (FAME3) is a rare autosomal dominant disorder characterized by cortical tremor and epilepsy, caused by a noncoding pentanucleotide repeat expansion (TTTTA/TTTCA)n in the MARCHF6 gene. Conventional genetic testing often fails to detect this expansion due to its repetitive structure and intronic location. We evaluated a 61-year-old woman with refractory myoclonic and generalized tonic-clonic seizures, whose prior genetic testing-including exome and genome sequencing-was non-diagnostic. Using PacBio HiFi long-read whole-genome sequencing and the tandem repeat genotyping tool TRGT, we identified a pathogenic MARCHF6 intronic expansion. The proband harbored one allele with 15 TTTTA repeats and a second allele with a compound expansion of 661 TTTTA and 12 TTTCA repeats. Three affected relatives shared similarly expanded alleles, but with increasing repeat size in the latter generations. Importantly, analysis using TRGT-instability revealed repeat mosaicism in all affected individuals, reflected by variability in motif counts across individual sequencing reads. This somatic heterogeneity may contribute to the phenotypic penetrance, variable expressivity and pleiotropism seen in FAME3 disease expression. To our knowledge, this is the first clinical diagnosis of FAME3 using a commercially available long-read sequencing platform, underscoring its diagnostic utility in resolving complex repeat expansion disorders and uncovering biologically relevant mosaicism.