Identification of HPV Integration and Gene Mutation in HeLa Cell Line by Integrated Analysis of RNA-Seq and MS/MS Data

HeLa
cell line, which was derived from cervical carcinoma, provides
an idea platform to study both the integration of human papillomavirus
and the massive mutations occurring on the cancer cell genome. Proteogenomics
is a field with the intersection of proteomics and genomics to perform
gene annotation and identify gene mutation. In this work, we first
identified the SNV/INDEL, structural variation (SV), and virus infection/integration
events from RNA-Seq data of HeLa cell line; then, by applying proteogenomics
strategy, we were able to detect some of the genomic events with the
tandem mass spectrometry (MS/MS) data from the same sample. Furthermore,
some of the mutated peptides were experimentally validated using multiple
reaction monitoring technology. The integrated analysis of the RNA-Seq
and MS/MS data not only renders the discovery of HeLa cell genome
variations more credible but also illustrates a practical workflow
for protein-coding mutation discovery in cancer-related studies.

HeLa细胞系（HeLa cell line）源自宫颈癌组织，是研究人乳头瘤病毒（human papillomavirus）整合以及癌细胞基因组大规模突变的理想平台。蛋白质基因组学（proteogenomics）是蛋白质组学与基因组学的交叉研究领域，旨在完成基因注释与基因突变识别。本研究首先从HeLa细胞系的RNA测序（RNA-Seq）数据中鉴定出单核苷酸变异/插入缺失变异（SNV/INDEL）、结构变异（SV）以及病毒感染与整合事件；随后，通过应用蛋白质基因组学策略，我们利用同一样本的串联质谱（MS/MS）数据检测到了部分基因组变异事件。此外，部分突变肽段通过多反应监测技术（multiple reaction monitoring technology）完成了实验验证。对RNA测序与串联质谱数据的整合分析，不仅使HeLa细胞基因组变异的发现更具可信度，同时也为癌症相关研究中的蛋白质编码突变发现提供了一套实用的工作流程。