进化选择确定了肺癌亚型中与免疫相关的关键基因。
Evolutionary selection identifies critical immune-relevant genes in lung cancer subtypes.
作者信息
Luddy Kimberly A, Teer Jamie K, Freischel Audrey, O'Farrelly Cliona, Gatenby Robert
机构信息
Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.
Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.
出版信息
Front Genet. 2022 Aug 24;13:921447. doi: 10.3389/fgene.2022.921447. eCollection 2022.
In an evolving population, proliferation is dependent on fitness so that a numerically dominant population typically possesses the most well adapted phenotype. In contrast, the evolutionary "losers" typically disappear from the population so that their genetic record is lost. Historically, cancer research has focused on observed genetic mutations in the dominant tumor cell populations which presumably increase fitness. Negative selection, i.e., removal of deleterious mutations from a population, is not observable but can provide critical information regarding genes involved in essential cellular processes. Similar to immunoediting, "evolutionary triage" eliminates mutations in tumor cells that increase susceptibility to the host immune response while mutations that shield them from immune attack increase proliferation and are readily observable (e.g., B2M mutations). These dynamics permit an "inverse problem" analysis linking the fitness consequences of a mutation to its prevalence in a tumor cohort. This is evident in "driver mutations" but, equally important, can identify essential genes in which mutations are seen significantly less than expected by chance. Here we utilized this new approach to investigate evolutionary triage in immune-related genes from TCGA lung adenocarcinoma cohorts. Negative selection differs between the two cohorts and is observed in endoplasmic reticulum aminopeptidase genes, ERAP1 and ERAP2 genes, and DNAM-1/TIGIT ligands. Targeting genes or molecular pathways under positive or negative evolutionary selection may permit new treatment options and increase the efficacy of current immunotherapy.
在不断进化的群体中,增殖取决于适应性,因此数量上占优势的群体通常拥有最适应环境的表型。相比之下,进化上的“失败者”通常会从群体中消失,从而使其遗传记录丢失。从历史上看,癌症研究一直集中在占主导地位的肿瘤细胞群体中观察到的基因突变上,这些突变可能会提高适应性。负选择,即从群体中去除有害突变,是不可观察到的,但可以提供有关参与基本细胞过程的基因的关键信息。与免疫编辑类似,“进化筛选”消除了肿瘤细胞中增加对宿主免疫反应易感性的突变,而那些使其免受免疫攻击的突变则会增加增殖,并且很容易观察到(例如,B2M突变)。这些动态变化允许进行“反问题”分析,将突变的适应性后果与其在肿瘤队列中的流行程度联系起来。这在“驱动突变”中很明显,但同样重要的是,它可以识别出其中突变出现的频率明显低于偶然预期的必需基因。在这里,我们利用这种新方法来研究来自TCGA肺腺癌队列的免疫相关基因中的进化筛选。两个队列中的负选择有所不同,在内质网氨肽酶基因、ERAP1和ERAP2基因以及DNAM-1/TIGIT配体中观察到了负选择。针对处于正选择或负选择下的基因或分子途径可能会带来新的治疗选择,并提高当前免疫疗法的疗效。