食管癌呼吸链编码核基因的体细胞突变模式及其自然选择信号研究

The formation of cancer was recognized as a process of somatic evolution driven by natural selection (Nowell 1976 Science 194:23-28), in which any genetic alterations that confer selective advantage to the fitness of the malignant cell would then be preferentially kept. Indeed, signature of positive selection has been detected on a number of cancer-related genes, opening a new avenue in understanding themolecularmechanism underling carcinogenesis (Crespi and Summers 2006 Biol Rev Camb Philos Soc 81:407-424)..Since the switch of energy metabolism (from oxidative phosphorylation to aerobic glycolysis), one of hallmarks of cancer (Hanahan and Weinberg 2011 Cell 144:646-674), has played crucial role in helping cancer cell to adapt its extreme micro-conditions (e.g. lack of oxygen) and meet the requirements of the rapid proliferation, it remains however unknown whether this switch has led to any genetic adaptive alternations in the energy metabolism related genes in cancer cells. Recently, our work on cancerous mitochondrial DNA (mtDNA) revealed that the observed somatic mutations on the molecule were likely the result of relaxed negative selection (Liu et al. 2012 Mol Biol Evol 29:1255-1261). This observation seems to be in agreement with the observation that aerobic glycolysis, instead of mitochondrial respiration, plays the key role in generating energy in cancer cells (Vander Heiden et al. 2009 Science 324:1029-1033). However, since mtDNA encodes only a few sub-units of the respiratory chain (RC), the coming question is: whether the signal of the relaxed selective constrains could also be detected in the nuclear genes encoding the most units of RC? To achieve this objective, our current project plans to recruit the 186 esophageal cancer tissue samples whose mitochondrial genomes have already been studied in our previous report (Liu et al. 2012 Mol Biol Evol 29:1255-1261). By re-sequencing all the RC-encoded nuclear genes in cancer tissues, screening the observed variants in the matched normal tissues (thus to distill the cancerous somatic mutations), and extensively studying their somatic mutation spectra and variation patterns, we aim to evaluate the signal of selective constraints on the RC-encoded nuclear genes and thus answer the question of "whether the relaxed selective constraints is a common pressure across all the RC-encoded genes". Addressing this issue could provide novel insights, from the angle of molecular evolution, in better understanding: whether the function of mitochondrial oxidative phosphorylation is declined or impaired with the switch of energy metabolism in cancer cells.

癌细胞产能方式的转换（有氧呼吸→糖酵解）被认为是其能有效适应缺氧微环境并满足快速增殖的关键原因之一，但迄今并不清楚在此过程中癌细胞能量代谢途径相关基因是否发生了相应的遗传变化？我们近期研究工作揭示，食管癌线粒体基因组上积累的体细胞突变模式呈现自然选择压力放松信号，这可能是由于癌细胞中呼吸链功能发生降低所致。但由于mtDNA仅编码了少数呼吸链亚基，而绝大部分亚基均由核基因编码，接下来面临的问题是：自然选择压力放松信号是否也存在于那些编码呼吸链蛋白的核基因上？鉴于此，本项目拟基于前期mtDNA研究工作中的93对食管癌组织及癌旁正常组织样本，通过详尽研究食管癌组织中编码呼吸链所有核基因的体细胞突变频谱及其变异模式，澄清呼吸链编码核基因是否也承受与mtDNA类似的自然选择压力。研究工作的开展将有助于从分子进化视角诠释，"伴随着癌产能方式的转变，呼吸链的作用是否发生了相应的降低"这一重要科学问题。

癌细胞产能方式的转换（有氧呼吸→糖酵解）被认为是其能有效适应缺氧微环境并满足快速增殖的关键原因之一，但迄今并不清楚在此过程中癌细胞能量代谢途径相关基因是否发生了相应的遗传变化。我们前期研究工作揭示，在这种产能发生改变的背景下，肿瘤细胞线粒体DNA（mtDNA）的体细胞突变，特别是食管癌呈现显著的自然选择压力放松信号。本项目研究继而深入研究，搜集了中国地区包括食管癌患者的共153个癌症患者，以及561个正常个体作为对照，发现mtDNA种系突变在单倍型类群的组成、突变模式以及突变的致病性潜力等方面，癌症患者和正常群体之间的种系突变模式均无显著差异。该发现进一步印证了肿瘤细胞产能方式发生了转变这一特征，原因是mtDNA突变虽能够影响呼吸链的氧化磷酸化水平，但对肿瘤细胞能量代谢的影响却非常有限。而另一方面，我们不但搜集了食管癌的全基因组数据，更加扩展搜集了10,648个癌症患者的全基因组突变分析，发现核基因编码的呼吸链基因与mtDNA类似，也呈现典型的自然选择压力放松的情况。除此之外，细胞功能实验也证实了肿瘤细胞呼吸链基因呈现选择压力放松的状态，并导致相关呼吸链蛋白功能的降低。除此之外，我们还大量搜集肿瘤细胞能量代谢转变的相关文章，全面深入的分析了肿瘤细胞发生这种转变的原因，并进一步证实癌细胞中能量代谢方式的转换并伴随着mtDNA和核基因编码的呼吸链亚基的自然选择压力放松的遗传机制，为研究癌症的发生发展提供了新的思路。

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