Cisneros Luis, Bussey Kimberly J, Orr Adam J, Miočević Milica, Lineweaver Charles H, Davies Paul
NantOmics, Tempe, Arizona, United States of America.
BEYOND Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, United States of America.
PLoS One. 2017 Apr 25;12(4):e0176258. doi: 10.1371/journal.pone.0176258. eCollection 2017.
Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes. In order to investigate these hypotheses we estimated the evolutionary ages of all human genes and then studied the probability of mutation and their biological function in relation to their age and genomic location for both normal germline and cancer contexts. We observed that under a model of uniform random mutation across the genome, controlled for gene size, genes less than 500 MY were more frequently mutated in both cases. Paradoxically, causal genes, defined in the COSMIC Cancer Gene Census, were depleted in this age group. When we used functional enrichment analysis to explain this unexpected result we discovered that COSMIC genes with recessive disease phenotypes were enriched for DNA repair and cell cycle control. The non-mutated genes in these pathways are orthologous to those underlying stress-induced mutation in bacteria, which results in the clustering of single nucleotide variations. COSMIC genes were less common in regions where the probability of observing mutational clusters is high, although they are approximately 2-fold more likely to harbor mutational clusters compared to other human genes. Our results suggest this ancient mutational response to stress that evolved among prokaryotes was co-opted to maintain diversity in the germline and immune system, while the original phenotype is restored in cancer. Reversion to a stress-induced mutational response is a hallmark of cancer that allows for effectively searching "protected" genome space where genes causally implicated in cancer are located and underlies the high adaptive potential and concomitant therapeutic resistance that is characteristic of cancer.
癌症有时被描述为在适应多细胞聚集生活的细胞中向单细胞行为的逆转。如果是这样的话,人们会预期癌症中的突变会破坏抑制对多细胞性有害的细胞水平特征的功能机制。这种机制应该是随着多细胞性的出现或在其出现之后进化而来的。这导致了两个相关但不同的假设:1)癌症中的体细胞突变将发生在比多细胞性出现(10亿年[MY])更年轻的基因中;2)在癌症中频繁突变且其突变对癌症表型的出现具有功能重要性的基因是在过去10亿年内进化而来的,因此将呈现出偏向年轻基因的年龄分布。为了研究这些假设,我们估计了所有人类基因的进化年龄,然后研究了正常生殖系和癌症背景下突变的概率及其与年龄和基因组位置相关的生物学功能。我们观察到,在控制基因大小的全基因组均匀随机突变模型下,两种情况下小于5亿年的基因更频繁地发生突变。矛盾的是,在COSMIC癌症基因普查中定义的致病基因在这个年龄组中却减少了。当我们使用功能富集分析来解释这个意外结果时,我们发现具有隐性疾病表型的COSMIC基因在DNA修复和细胞周期控制方面富集。这些途径中的未突变基因与细菌中应激诱导突变的基础基因是直系同源的,这导致了单核苷酸变异的聚集。COSMIC基因在观察到突变簇概率高的区域不太常见,尽管它们比其他人类基因携带突变簇的可能性大约高2倍。我们的结果表明,这种在原核生物中进化而来的对压力的古老突变反应被用于维持生殖系和免疫系统的多样性,而在癌症中恢复了原始表型。向应激诱导突变反应的逆转是癌症的一个标志,它允许有效地搜索“受保护”的基因组空间,其中与癌症有因果关系的基因位于该空间,并且是癌症所特有的高适应潜力和伴随的治疗抗性的基础。