Identification of HPV integration and gene mutation in HeLa cell line by integrated analysis of RNA-Seq and MS/MS data

Han Sun, Chen Chen, Baofeng Lian, Menghuan Zhang, Xiaojing Wang, Bing Zhang, Yixue Li, Pengyuan Yang, Lu Xie

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1678-1686
Number of pages9
JournalJournal of Proteome Research
Volume14
Issue number4
DOIs
StatePublished - Apr 3 2015
Externally publishedYes

Keywords

  • HPV
  • HeLa
  • MRM
  • MS/MS
  • RNA-Seq
  • proteogenomics

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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