Functional characterization of variants of unknown significance in a spinocerebellar ataxia patient using an unsupervised machine learning pipeline

• Published in: Human genome variation Vol. 9; no. 1; p. 10
• Main Authors: Nath, Siddharth, Caron, Nicholas S., May, Linda, Gluscencova, Oxana B., Kolesar, Jill, Brady, Lauren, Kaufman, Brett A., Boulianne, Gabrielle L., Rodriguez, Amadeo R., Tarnopolsky, Mark A., Truant, Ray
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14-04-2022; Springer Nature B.V; Nature Publishing Group
• Subjects: 631/1647/245/2225; 692/699/375/365; Ataxia; Ataxin; Biomedical and Life Sciences; Biomedicine; Cerebellar ataxia; Cerebellum; Cytoskeleton; DNA topoisomerase; Dystrophy; Fidelity; Gene Expression; Gene Function; Gene Therapy; Genetic diversity; Genomes; Human Genetics; Image processing; Localization; Microscopy; Mitochondria; Molecular Medicine; Mutation; Neurodegenerative diseases; Pathogenesis; Polyglutamine; Spinocerebellar ataxia; Trinucleotide repeat diseases; Trinucleotide repeats; Whole genome sequencing
• ISSN: 2054-345X; 2054-345X
• DOI: 10.1038/s41439-022-00188-8

CAG-expanded
ATXN7
has been previously defined in the pathogenesis of spinocerebellar ataxia type 7 (SCA7), a polyglutamine expansion autosomal dominant cerebellar ataxia. Pathology in SCA7 occurs as a result of a CAG triplet repeat expansion in excess of 37 in the first exon of
ATXN7
, which encodes ataxin-7. SCA7 presents clinically with spinocerebellar ataxia and cone-rod dystrophy. Here, we present a novel spinocerebellar ataxia variant occurring in a patient with mutations in both
ATXN7
and
TOP1MT
, which encodes mitochondrial topoisomerase I (top1mt). Using machine-guided, unbiased microscopy image analysis, we demonstrate alterations in ataxin-7 subcellular localization, and through high-fidelity measurements of cellular respiration, bioenergetic defects in association with top1mt mutations. We identify ataxin-7 Q35P and top1mt R111W as deleterious mutations, potentially contributing to disease states. We recapitulate our mutations through
Drosophila
genetic models. Our work provides important insight into the cellular biology of ataxin-7 and top1mt and offers insight into the pathogenesis of spinocerebellar ataxia applicable to multiple subtypes of the illness. Moreover, our study demonstrates an effective pipeline for the characterization of previously unreported genetic variants at the level of cell biology.
Neurodegenerative disease: Finding new mutations associated with ataxia
Two genetic mutations combine to cause a novel variant of spinocerebellar ataxia (SCA), a rare neurodegenerative disease. SCA affects the cerebellum, a brain region that controls movement, causing progressive coordination problems. Presented with a patient with an atypical form of SCA, Ray Truant at McMaster University in Hamilton, Canada, and co-workers used whole-genome sequencing to identify mutations in two genes:
ATXN7
, involved in cytoskeleton maintenance, and
TOP1MT
, in mitochondria, the cellular powerhouses. Unable to see differences in the affected tissues using routine microscopy, the researchers used computer-guided microscopy image analysis to determine that the altered ATXN7 protein was mis-located in cells. High-fidelity measurements of cell metabolism showed that mitochondria with altered
TOP1MT
produced insufficient energy. These results clarify the genetics of ataxia, and offer new ways to identify the effects of rare mutations.