Genomic and metabolic investigation of an unknown inborn error of leucine metabolism mimicking MCC deficiency

Abstract

This study revolves around a family in which 4 male members have metabolic profiles similar to that of atypical 3–methylcrotonyl–CoA carboxylase (MCC) deficiency, an inborn error of leucine catabolism. This profile consists of high urinary 3–hydroxyisovaleric acid (3–HIVA) and trace amounts of 3–methylcrotonylglycine. One of the individuals also had clinical symptoms of chronic fatigue and muscle weakness, symptoms also related to MCC–deficiency. Further investigation showed that these individuals were negative for MCC–deficiency. The inheritance pattern of the abnormal metabolic profile seemed to indicate a link to the X–chromosome. In this study the single nucleotide polymorphism (SNP) and copy number variation (CNV) profiles of the X–chromosomes of participating members of the family were investigated for a possible link to the abnormal metabolic profile, using SNP6 DNA microarrays. The data generated by the SNP6 arrays was of good quality. The small sample size available for this study necessitated an unorthodox method for analysing the SNP6 data. No clear link between the SNP6 data and the abnormal metabolic profile was found. Selected SNP calls made by the SNP6 arrays were verified by sequencing. The origin of the elevated 3–HIVA detected in the urine of the male family members was also investigated. This was done by culturing fibroblasts from case individuals in culture medium supplemented with deuterium labelled leucine. The culture medium was analysed using GC–MS after an organic acid extraction. The resulting data seems to indicate at least two sources of 3–HIVA formation by the cells, one originating from leucine and another from a source other than leucine. The mevalonate shunt is one possible source of 3–HIVA, which does not originate from leucine catabolism.