Supplementary Material for: Large common mitochondrial DNA deletions are associated with a mitochondrial SNP T14798C near the 3' breakpoints

Introduction Large somatic deletions of mitochondrial DNA (mtDNA) accumulate with aging in metabolically active tissues such as the brain. We have cataloged the breakpoints and frequencies of large mtDNA deletions in the human brain. Methods We quantified 112 high-frequency mtDNA somatic deletions across four human brain regions with the Splice-Break2 pipeline. In addition, we utilized PLINK/Seq to test the association of mitochondrial genotypes with the abundance of these high-frequency mtDNA deletions. A conservative p-value threshold of 5E-08 was used to find the significant loci. Results One mtDNA SNP (T14798C) was significantly associated with mtDNA deletions in two brain regions, the dorsolateral prefrontal cortex (DLPFC) and the superior temporal gyrus (STG). Since the DLPFC showed the most robust association between T14798C and two deletion breakpoints (7816-14807 and 5462-14807), this association was tested in the DLPFC of a replication sample and validated the first results. Incorporating the C allele at 14798 bp increased the perfect/imperfect length of the repeat at the 3' breakpoint of the two associated deletions. Conclusion This is the first study to identify the association of mtDNA SNP with large mtDNA deletions in the human brain. The T14798C allele located in the MT-CYB gene is a common polymorphism that occurs in several mitochondrial haplogroups. We hypothesize that the T14798C association with two deletions occurs by extending the repeat length around the 3' deletion breakpoints. This simple mechanism suggests that mtDNA SNPs can affect the mitochondrial genome structure, especially in brain where high levels of reactive oxygen species (ROS) lead to deletion accumulation with aging.

研究背景：线粒体DNA（mitochondrial DNA）的大片段体细胞缺失会随衰老在代谢活跃的组织（如大脑）中累积。本研究对人类大脑中大片段mtDNA缺失的断裂位点与发生频率进行了编目。研究方法：本研究借助Splice-Break2流程，对四个人类脑区中的112种高频mtDNA体细胞缺失进行了定量分析。此外，本研究使用PLINK/Seq工具，探究线粒体基因型与这些高频mtDNA缺失丰度之间的关联。研究采用5E-08这一保守的P值阈值以筛选显著位点。研究结果：一种mtDNA单核苷酸多态性（Single Nucleotide Polymorphism，SNP）T14798C，在两个脑区——背外侧前额叶皮层（dorsolateral prefrontal cortex，DLPFC）和颞上回（superior temporal gyrus，STG）——中与mtDNA缺失存在显著关联。由于背外侧前额叶皮层中T14798C与两种缺失断裂位点（7816-14807和5462-14807）的关联最为显著，研究在重复样本的背外侧前额叶皮层中验证了该关联，证实了初始研究结果。在14798bp位点引入C等位基因，可延长两种相关缺失的3'断裂位点处的完美/非完美重复序列长度。研究结论：本研究是首个在人类大脑中证实mtDNA单核苷酸多态性与大片段mtDNA缺失存在关联的研究。位于MT-CYB基因中的T14798C等位基因是一种常见多态性，可在多个线粒体单倍群中出现。我们推测，T14798C与两种缺失的关联，是通过延长3'缺失断裂位点周边的重复序列长度实现的。这一简单机制表明，mtDNA单核苷酸多态性可影响线粒体基因组结构，尤其在大脑中——大脑内高水平的活性氧（reactive oxygen species，ROS）会随衰老促使缺失累积。