Alu-specific microhomology-mediated deletion of the final exon of SPAST in three unrelated subjects with hereditary spastic paraplegia

Abstract

Purpose Autosomal dominant spastic paraplegia, type 4 (SPG4), a debilitating disorder of progressive spasticity and weakness of the lower limbs, results from heterozygous mutations in the SPAST gene. The full spectrum of SPAST mutations causing SPG4 and their mechanisms of formation remain to be determined. Methods We used multiplex ligation-dependent probe amplification, locus-specific array comparative genomic hybridization, and breakpoint DNA sequencing to identify and describe genomic rearrangements in three patients with a clinical presentation of hereditary spastic paraplegia. Results We describe three SPG4 patients with intragenic rearrangements in SPAST; all specifically delete the final exon, exon 17. Breakpoint sequence analyses provide evidence for Alu-specific microhomology-mediated deletion as the mechanism of exon loss; one complex rearrangement apparently occurred by multiple Alu-facilitated template switches. Conclusion We hypothesize that the high concentration of Alu family members in the introns and flanking sequence of SPAST may predispose to intragenic rearrangements. Thus, Alu-specific microhomology-mediated intragenic rearrangements in SPAST may be a common cause of SPG4. Furthermore, we propose that genomic deletions encompassing the final exon of SPAST may affect expression of SLC30A6, the most proximal downstream locus and a gene that has been implicated in the pathogenesis of Alzheimer disease, potentially explaining recent reports of dementia in selected SPG4 patients.

Mutational spectrum of the SPAST and ATL1 genes in Korean patients with hereditary spastic paraplegia

“…A relatively high density of Alu elements was found in the SPAST gene (36.6% compared with the overall genomic average of~10%) [23]; thus, exonic deletion and duplication events occur more frequently in SPAST than in other genes, especially in the last exon [22,24]. In a previous study, a low alu density was reported for the ATL1 gene, which was associated with a low number of exonic deletion and duplication events [24]. These exonic variations were likely pathogenic due to haploinsufficiency, as they should either create a pre-terminal stop codon (thus making the transcript susceptible to nonsense-mediated decay, even though the remaining exons may have been properly spliced), or they would remove large parts of the functionally important AAA domain [22].…”

“…Various percentages (2.5-5%) of exonic deletion cases have been reported [3,6,7,[20][21][22]. A relatively high density of Alu elements was found in the SPAST gene (36.6% compared with the overall genomic average of~10%) [23]; thus, exonic deletion and duplication events occur more frequently in SPAST than in other genes, especially in the last exon [22,24]. In a previous study, a low alu density was reported for the ATL1 gene, which was associated with a low number of exonic deletion and duplication events [24].…”

A common X-linked inborn error of carnitine biosynthesis may be a risk factor for nondysmorphic autism

“…Sequencing of the breakpoints of many deletions showed that almost all junctions occurred in long interspersed elements and short interspersed elements in the introns flanking exon 2 ( Fig. 2B and Table S2), as has been seen in other loci (23). For all SSC samples (probands, heterozygous mothers, and healthy fathers), the deletions were present in both DNA extracted directly from blood and DNA extracted from lymphoblastoid cell lines (LCLs).…”

Mechanisms underlying structural variant formation in genomic disorders

“…Structural variant formation events using homeologous sequences mostly generate nonrecurrent rearrangements that can be important contributors to genomic disorders 43,44,71–73 . For example, recombination between retroelements, such as short non-autonomous ~300 bp Alu elements, leading to CNVs is a predominant event in some genomic disorders 74 , such as autosomal-dominant spastic paraplegia 4 (SPG4; OMIM 182601 ) 43,72 and alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV; OMIM 265380 ) 44 . Alu - Alu -mediated rearrangement events have been historically attributed to NAHR; however, the low nucleotide sequence identity shared between the Alu family members, which can be as low as 75%, suggests that alternative recombination mechanisms also take place 43 .…”