Unexpected complexity in the molecular diagnosis of spastic paraplegia 11

Abstract

Background: Spastic paraplegia 11 (SPG11) is the most prevalent form of autosomal recessive hereditary spastic paraplegia, resulting from biallelic pathogenic variants in the SPG11 gene (MIM *610844).

Methods: The proband is a 36-year-old female referred for genetic evaluation due to cognitive dysfunction, gait impairment, and corpus callosum atrophy (brain MRI was normal at 25-years-old). Diagnostic approaches included CGH array, next-generation sequencing, and whole transcriptome sequencing.

Results: CGH array revealed a 180 kb deletion located upstream of SPG11. Sequencing of SPG11 uncovered two rare single nucleotide variants: the novel variant c.3143C>T in exon 17 (in cis with the deletion), and the previously reported pathogenic variant c.6409C>T in exon 34 (in trans). Whole transcriptome sequencing revealed that the variant c.3143C>T caused exon 17 skipping.

Conclusion: We report a novel sequence variant in the SPG11 gene resulting in exon 17 skipping, which, along with a nonsense variant, causes Spastic Paraplegia 11 in our proband. In addition, a deletion upstream of SPG11 was identified in the patient, whose implication in the phenotype remains uncertain. Nonetheless, the deletion apparently affects cis-regulatory elements of the gene, suggesting a potential new pathogenic mechanism underlying the disease in a subset of undiagnosed patients. Our findings further support the hypothesis that the origin of thin corpus callosum in patients with SPG11 is of progressive nature.

Keywords: SPG11; cis‐regulatory elements; genetic diagnosis; spastic paraplegia 11; whole transcriptome sequencing.

FIGURE 1

(a) Brain MRI of the 36‐year‐old patient showing atrophy of the corpus callosum, bilateral temporal atrophy, and mild frontal atrophy (left: sagittal cut; right: axial cut). (b) Three‐generation pedigree of the family, indicating the genetic variants identified in the SPG11 gene for each individual (NM_025137.4). NT, not tested; WT, wild‐type.

FIGURE 2

Rey‐Osterrieth complex figure test (copy and memory) (a) and Behavioral Rating Inventory of Executive Function (BRIEF) (b) results in the patient at different ages. BRI, behavioral rating index; MCI, metacognition index.

FIGURE 3

(a) CGH array of the proband showing the deletion on chromosome 15q21.1 (chr15:44,960,975‐45,140,413; GRCh37/hg19), located very close to the 5′ end of the SPG11 gene. (b) NGS results showing the two point variants identified in the proband in the SPG11 gene: c.3143C>T (exon 17) and c.6409C>T (exon 34) (NM_025137.4). (c) Schematic representation of proband's spliced transcripts configuration generated using the Ballgown R software package on the transcriptome data, showing the expression of a normal transcript and an aberrant transcript with skipping of exon 17. (d) On the left, results of agarose gel electrophoresis showing cDNA amplicons of SPG11 (using a forward primer in exon 16 and a reverse primer in exon 18) from the patient (lane #4), the healthy daughter (#1), three controls (#2, #3, and #5), and a blank (#6). On the right, results of Sanger sequencing (reverse strand) of both bands in the proband, with the shorter band confirming skipping of exon 17.

FIGURE 4

Genomic map of the deletion identified in the patient, located upstream of the SPG11 gene. The presented data include: the minimal and maximal deletion size; gene content of the region; DNase I hypersensitivity clusters with signal in >20/125 ENCODE sources; H3K27ac, H3K4me1, and H3K4me3 histone marks on 7 cell lines from ENCODE; transcription factor binding sites; and GeneHancer analysis showing promoters and enhancers and their inferred target genes.