Combined Genome, Transcriptome and Metabolome Analysis in the Diagnosis of Childhood Cerebellar Ataxia

Abstract

Ataxia in children is a common clinical sign of numerous neurological disorders consisting of impaired coordination of voluntary muscle movement. Its most common form, cerebellar ataxia, describes a heterogeneous array of neurologic conditions with uncountable causes broadly divided as acquired or genetic. Numerous genetic disorders are associated with chronic progressive ataxia, which complicates clinical management, particularly on the diagnostic stage. Advances in omics technologies enable improvements in clinical practice and research, so we proposed a multi-omics approach to aid in the genetic diagnosis and molecular elucidation of an undiagnosed infantile condition of chronic progressive cerebellar ataxia. Using whole-exome sequencing, RNA-seq, and untargeted metabolomics, we identified three clinically relevant mutations (rs141471029, rs191582628 and rs398124292) and an altered metabolic profile in our patient. Two POLR1C diagnostic variants already classified as pathogenic were found, and a diagnosis of hypomyelinating leukodystrophy was achieved. A mutation on the MMACHC gene, known to be associated with methylmalonic aciduria and homocystinuria cblC type, was also found. Additionally, preliminary metabolome analysis revealed alterations in our patient's amino acid, fatty acid and carbohydrate metabolism. Our findings provided a definitive genetic diagnosis reinforcing the association between POLR1C mutations and hypomyelinating leukodystrophy and highlighted the relevance of multi-omics approaches to the disease.

Keywords: POLR1C; cerebellar ataxia; diagnosis; genomics; hypomyelination; leukodystrophy; metabolomics; transcriptomics.

Figure 1

MRI findings in the patient. These images, obtained at the age of 7, show: (a) Hypomyelination process with diffuse hyperintensity of the supratentorial and cerebellar white matter on the T2-weighted images (red arrows); (b) T1 diffuse isointensity of the supratentorial white matter on the T1 sequences (blue arrows); (c) Cerebellar atrophy (green arrow), and a thinned corpus callosum (orange arrow).

Figure 2

RT–PCR analysis of mRNA expressions of POLR1C and MMACHC in the patient and the control. mRNA expression was determined by RT–PCR is calculated as a ratio relative to GAPDH and expressed relative to the controls. Error bars represent standard deviation (SD). ***, p < 0.0001; **, p < 0.01.

Figure 3

RT–PCR analysis of mRNA expressions of POLR1C in the patient and her unaffected family members. mRNA expression determined by RT–PCR is calculated as a ratio relative to HPRT1 and expressed relative to her parents and sibling. (E2), (E3), and (E7) indicate the different primers used to analyze expression of POLR1C. Error bars represent standard deviation (SD). ***, p < 0.0001; *, p < 0.05; ns, not significant.