Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan.
Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
Arthritis Res Ther. 2018 Jul 6;20(1):137. doi: 10.1186/s13075-018-1637-5.
Accumulating evidence implicates mitochondrial DNA (mtDNA) alleles, which are independent of the nuclear genome, in disease, especially in human metabolic diseases. However, this area of investigation has lagged behind in researching the nuclear alleles in complex traits, for example, in gout.
Next-generation sequencing was utilized to investigate the relationship between mtDNA alleles and phenotypic variations in 52 male patients with gout and 104 age-matched male non-gout controls from the Taiwan Biobank whole-genome sequencing samples. Differences from a reference sequence (GRCh38) were identified. The sequence kernel association test (SKAT) was applied to identify gout-associated alleles in mitochondrial genes. The tools Polymorphism Phenotyping, Sorting Intolerant From Tolerant (SIFT), Predict the pathology of Mutations (PMUT), Human Mitochondrial Genome Database (mtDB), Multiple Alignment using Fast Fourier Transform (MAFFT), and Mammalian Mitochondrial tRNA Genes (Mamit-tRNA) were used to evaluate pathogenicity of alleles. Validation of selected alleles by quantitative polymerase chain reaction of single nucleotide polymorphisms (qPCR SNPs) was also performed.
We identified 456 alleles in patients with gout and 640 alleles in non-gout controls with 274 alleles shared by both. Mitochondrial genes were associated with gout, with MT-CO3, MT-TA, MT-TC, and MT-TT containing potentially pathogenic gout-associated alleles and displaying evidence of gene-gene interactions. All heteroplasmy levels of potentially pathogenic alleles exceeded metabolic thresholds for pathogenicity. Validation assays confirmed the next-generation sequencing results of selected alleles. Among them, potentially pathogenic MT-CO3 alleles correlated with high-density lipoprotein (HDL) levels (P = 0.034).
This study provided two scientific insights. First, this was the most extensive mitochondrial genomic profiling associated with gout. Second, our results supported the roles of mitochondria in gout and HDL, and this comprehensive analysis framework can be applied to other diseases in which mitochondrial dysfunction has been implicated.
越来越多的证据表明，线粒体 DNA（mtDNA）等位基因与疾病有关，这些等位基因独立于核基因组，尤其是在人类代谢疾病中。然而，在研究复杂性状中的核等位基因方面，这一领域的研究一直滞后，例如在痛风中。
利用下一代测序技术，对来自台湾生物银行全基因组测序样本的 52 名男性痛风患者和 104 名年龄匹配的男性非痛风对照者的 mtDNA 等位基因与表型变异之间的关系进行了研究。与参考序列（GRCh38）的差异被识别出来。应用序列核关联测试（SKAT）来识别线粒体基因中与痛风相关的等位基因。使用 Polymorphism Phenotyping、Sorting Intolerant From Tolerant（SIFT）、Predict the pathology of Mutations（PMUT）、Human Mitochondrial Genome Database（mtDB）、Multiple Alignment using Fast Fourier Transform（MAFFT）和 Mammalian Mitochondrial tRNA Genes（Mamit-tRNA）等工具来评估等位基因的致病性。还通过单核苷酸多态性（SNP）的定量聚合酶链反应（qPCR）对选定的等位基因进行了验证。
我们在痛风患者中鉴定出 456 个等位基因，在非痛风对照组中鉴定出 640 个等位基因，其中 274 个等位基因在两组中均有发现。线粒体基因与痛风相关，MT-CO3、MT-TA、MT-TC 和 MT-TT 基因中含有潜在致病性的痛风相关等位基因，并显示出基因-基因相互作用的证据。所有潜在致病性等位基因的异质性水平均超过了致病性的代谢阈值。验证实验证实了选定等位基因的下一代测序结果。其中，潜在致病性的 MT-CO3 等位基因与高密度脂蛋白（HDL）水平相关（P=0.034）。
本研究提供了两个科学见解。首先，这是与痛风相关的最广泛的线粒体基因组分析。其次，我们的研究结果支持线粒体在痛风和高密度脂蛋白中的作用，并且这种全面的分析框架可以应用于其他涉及线粒体功能障碍的疾病。
