A Single Nucleotide Polymorphism Within Molybdenum Cofactor Sulfurase Gene Is Associated With Neuropsychiatric Conditions

XDH genotypes through gene-gene interactions with NUDT15 affect azathioprine-induced leukopenia in Chinese patients

Aim: To investigate whether genotypes of XDH, GMPS and MOCOS were associated with azathioprine-induced adverse drug reaction (ADR) and had the gene-gene interactions with NUDT15 rs116855232 to induce leukopenia. Methods: Patients who had taken azathioprine were recruited. Genotyping of those gene was performed. Risk factor to ADR was analyzed by logistic regression. The generalized multifactor dimensionality reduction (GMDR) was assessed based on gene-gene interactions with ADR. Results: A total of 111 patients were included in this study, all of whom were Han Chinese. XDH rs2295475 was a risk factor of myelotoxicity (p = 0.022). NUDT15 rs116855232 was a risk factor of myelotoxicity, grade ≥2 leukopenia and drug treatment termination (p-values were <0.05). Rs2295475 and rs116855232 had a gene-gene interaction. The model was associated with grade ≥2 leukopenia (OR: 17.99; 95% CI: 4.11-78.81). Conclusion: Combined testing genotype for rs2295475 and rs116855232 could improve the prediction of azathioprine-induced leukopenia.

Classifying single nucleotide polymorphisms in humans

Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation amongst the human population and are key to personalized medicine. New tests are presented to distinguish pathogenic/malign (i.e., likely to contribute to or cause a disease) from nonpathogenic/benign SNPs, regardless of whether they occur in coding (exon) or noncoding (intron) regions in the human genome. The tests are based on the nearest neighbor (NN) model of Gibbs free energy landscapes of DNA hybridization and on deep structural properties of DNA revealed by an approximating metric (the h-distance) in DNA spaces of oligonucleotides of a common size. The quality assessments show that the newly defined PNPG test can classify a SNP with an accuracy about 73% for the required parameters. The best performance among machine learning models is a feed-forward neural network with fivefold cross-validation accuracy of at least 73%. These results may provide valuable tools to solve the SNP classification problem, where tools are lacking, to assess the likelihood of disease causing in unclassified SNPs. These tests highlight the significance of hybridization chemistry in SNPs. They can be applied to further the effectiveness of research in the areas of genomics and metabolomics.

Classical Xanthinuria in Nine Israeli Families and Two Isolated Cases from Germany: Molecular, Biochemical and Population Genetics Aspects

Classical xanthinuria is a rare autosomal recessive metabolic disorder caused by variants in the XDH (type I) or MOCOS (type II) genes. Thirteen Israeli kindred (five Jewish and eight Arab) and two isolated cases from Germany were studied between the years 1997 and 2013. Four and a branch of a fifth of these families were previously described. Here, we reported the demographic, clinical, molecular and biochemical characterizations of the remaining cases. Seven out of 20 affected individuals (35%) presented with xanthinuria-related symptoms of varied severity. Among the 10 distinct variants identified, six were novel: c.449G>T (p.(Cys150Phe)), c.1434G>A (p.(Trp478*)), c.1871C>G (p.(Ser624*)) and c.913del (p.(Leu305fs*1)) in the XDH gene and c.1046C>T (p.(Thr349Ileu)) and c.1771C>T (p.(Pro591Ser)) in the MOCOS gene. Heterologous protein expression studies revealed that the p.Cys150Phe variant within the Fe/S-I cluster-binding site impairs XDH biogenesis, the p.Thr349Ileu variant in the NifS-like domain of MOCOS affects protein stability and cysteine desulfurase activity, while the p.Pro591Ser and a previously described p.Arg776Cys variant in the C-terminal domain affect Molybdenum cofactor binding. Based on the results of haplotype analyses and historical genealogy findings, the potential dispersion of the identified variants is discussed. As far as we are aware, this is the largest cohort of xanthinuria cases described so far, substantially expanding the repertoire of pathogenic variants, characterizing structurally and functionally essential amino acid residues in the XDH and MOCOS proteins and addressing the population genetic aspects of classical xanthinuria.