PO.BCS01.15 · 生物信息与计算
利用体细胞突变与多态性种系变异评估等位基因表达差异
Assessing allelic expression variation using somatic mutations vs. polymorphic germline variants
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
体细胞突变的等位基因特异性表达（ASE）可由突变等位基因的顺式激活或野生型等位基因的沉默所致。以往研究通过检测RNA相对于DNA中突变等位基因的富集程度来考察这一现象，该方法可校正因体细胞拷贝数改变而导致的等位基因表达增加。在此我们表明，这种基于突变的方法可能受到肿瘤细胞与正常细胞之间基因表达差异的混杂影响——多数大体肿瘤样本中二者共存，从而在无ASE的情况下也会出现突变等位基因表达富集。通过对所有相关协变量进行建模，我们表明这种混杂效应在肿瘤纯度较低时加剧，且对于可触发无义介导的mRNA降解（NMD）的突变，其效应取决于突变等位基因的剂量。我们利用The Cancer Genomics Atlas（TCGA）数据集中的体细胞插入缺失（indel）进行分析，发现表达升高的截短型indel等位基因在肿瘤抑制基因（TSGs）中比在癌症中不常突变的基因（非驱动基因）中更为普遍（7.69% 对 1.76%，Fisher精确检验 p < 2.2×10⁻¹⁶）。与模型一致，此类indel在肿瘤中与较高的基因表达相关（相较于正常组织），并且对于TSGs中对NMD敏感的indel还与杂合性缺失（LOH）相关。相比之下，体细胞突变的ASE事件可通过评估与该体细胞突变定相（phased）的种系杂合单核苷酸多态性（SNPs）的等位基因富集来更准确地表征。在这种基于SNP的方法中，肿瘤/正常组织的表达差异和肿瘤纯度不产生或仅产生极小的混杂效应，从而能够将由顺式调控改变引起的真正ASE事件与由混杂因素引起的事件区分开来。为进一步评估基于SNP的ASE分析，我们在B细胞急性淋巴细胞白血病（B-ALL）细胞系Nalm6中进行了全基因组单倍型定相和单细胞全转录组测序。我们表明，即使在细胞系模型中，ASE也是一个异质性过程，不同细胞亚群中等位基因表达偏倚程度各异，且这种转录异质性有可能在治疗压力下促进克隆演化。
查看英文原文 English abstract
Allele-specific expression (ASE) of somatic mutations can be caused by cis -activation of the mutant allele or silencing of the wildtype allele. It has been investigated by examining the enrichment of mutant allele in RNA relative to DNA which can account for increased allelic expression due to somatic copy number alteration. Here we show that this mutation-based approach can be confounded by gene expression differences in tumor and normal cells that co-exist in most bulk tumor samples resulting in enriched mutant allele expression without ASE. By modeling all the relevant co-factors, we show that this confounding effect is exacerbated with low tumor purity and is dependent on mutant allele dosage for mutations that can trigger nonsense-mediated decay (NMD). Our analysis using somatic indels in The Cancer Genomics Atlas (TCGA) dataset found that truncating indel alleles with elevated expression were more prevalent in tumor suppressor genes (TSGs) than in genes not frequently mutated in cancers (non-driver genes) (7.69% vs. 1.76%, Fisher exact p < 2.2×10 -16 ). Consistent with the model, such indels were associated with higher gene expressions in tumor compared to normal and with loss of heterozygosity (LOH) for NMD-sensitive indels in TSGs. By contrast, ASE events of somatic mutations can more accurately be characterized by assessing allelic enrichment of germline heterozygous single nucleotide polymorphisms (SNPs) phased to the somatic mutation. In this SNP-based approach, tumor/normal expression differences and tumor purity exhibit none or minimum confounding effects, discriminating true ASE events caused by cis -regulatory change from those caused by confounding factors. To further evaluate the SNP-based ASE analysis, we performed genome-wide haplotype phasing and single-cell full transcriptome sequencing in the B-cell acute lymphoblastic leukemia (B-ALL) cell line Nalm6. We show that that ASE is a heterogenous process with varying degrees of allele expression biases in different cellular subpopulations even in a cell line model and such transcriptional heterogeneity can potentially contribute to clonal evolution under treatments.
利益披露 Disclosure
K. Hagiwara, None..
B. Ju, None..
N. V. Terekhanova, None..
J. Easton, None..
J. Zhang, None.