美国哈佛医学院Vamsi K. Mootha研究组发现，单细胞分析揭示mtDNA的环境依赖性细胞级选择。2024年4月24日，《自然》杂志在线发表了这项成果。

研究人员通过将精确的线粒体DNA（mtDNA）碱基编辑（DdCBE）与一种新方法SCI-LITE（利用单细胞组合索引询问靶向表达）相结合，研究了分裂细胞中的异质性动态。研究人员设计了具有同义或非同义复合物I mtDNA突变的细胞，发现细胞群在标准培养条件下会清除非同义的mtDNA变体，而同义变体则得以保留。这表明，在形成群体异质性方面，选择比简单漂移更重要。研究人员同时追踪了单细胞mtDNA的异质性和祖先，发现虽然群体异质性发生了变化，但单个细胞系的异质性保持稳定，这表明选择作用于分裂细胞的细胞适应性水平。

利用这些见解，研究人员证明了其可以通过将细胞置于生化复合物I活性丧失的环境中，迫使细胞积累高水平的截短复合物I mtDNA异质性，据报道，在这种环境中，生化复合物I活性丧失有利于细胞的适应性。研究人员认为，在分裂细胞中，特定的非同义mtDNA异源体可能对细胞活力有害、中性甚至有益，但影响的“标记”完全取决于环境。

据了解，当野生型和突变型mtDNA分子在单个细胞中共存时，就会出现异源DNA。异源DNA水平在发育、疾病和衰老过程中会发生动态变化，但目前还不清楚这些变化是由选择还是漂移引起的，也不清楚它们是在细胞水平还是在细胞内发生的。

附：英文原文

Title: Single-cell analysis reveals context-dependent, cell-level selection of mtDNA

Author: Kotrys, Anna V., Durham, Timothy J., Guo, Xiaoyan A., Vantaku, Venkata R., Parangi, Sareh, Mootha, Vamsi K.

Issue&Volume: 2024-04-24

Abstract: Heteroplasmy occurs when wild-type and mutant mitochondrial DNA (mtDNA) molecules co-exist in single cells1. Heteroplasmy levels change dynamically in development, disease and ageing2,3, but it is unclear whether these shifts are caused by selection or drift, and whether they occur at the level of cells or intracellularly. Here we investigate heteroplasmy dynamics in dividing cells by combining precise mtDNA base editing (DdCBE)4 with a new method, SCI-LITE (single-cell combinatorial indexing leveraged to interrogate targeted expression), which tracks single-cell heteroplasmy with ultra-high throughput. We engineered cells to have synonymous or nonsynonymous complex I mtDNA mutations and found that cell populations in standard culture conditions purge nonsynonymous mtDNA variants, whereas synonymous variants are maintained. This suggests that selection dominates over simple drift in shaping population heteroplasmy. We simultaneously tracked single-cell mtDNA heteroplasmy and ancestry, and found that, although the population heteroplasmy shifts, the heteroplasmy of individual cell lineages remains stable, arguing that selection acts at the level of cell fitness in dividing cells. Using these insights, we show that we can force cells to accumulate high levels of truncating complex I mtDNA heteroplasmy by placing them in environments where loss of biochemical complex I activity has been reported to benefit cell fitness. We conclude that in dividing cells, a given nonsynonymous mtDNA heteroplasmy can be harmful, neutral or even beneficial to cell fitness, but that the ‘sign’ of the effect is wholly dependent on the environment. A new method for tracking single-cell heteroplasmy, called SCI-LITE, is combined with mitochondrial DNA base editing to reveal principles of heteroplasmy dynamics in dividing cells.

DOI: 10.1038/s41586-024-07332-0

Source: https://www.nature.com/articles/s41586-024-07332-0