Modeling cellular response in large-scale radiogenomic databases to advance precision radiotherapy

Venkata S.K. Manem, Meghan Lambie, Ian Smith, Petr Smirnov, Victor Kofia, Mark Freeman, Marianne Koritzinsky, Mohamed E. Abazeed, Benjamin Haibe-Kains, Scott V. Bratman*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

Radiotherapy is integral to the care of a majority of patients with cancer. Despite differences in tumor responses to radiation (radioresponse), dose prescriptions are not currently tailored to individual patients. Recent large-scale cancer cell line databases hold the promise of unravelling the complex molecular arrangements underlying cellular response to radiation, which is critical for novel predictive biomarker discovery. Here, we present RadioGx, a computational platform for integrative analyses of radioresponse using radiogenomic databases. We fit the dose–response data within RadioGx to the linear-quadratic model. The imputed survival across a range of dose levels (AUC) was a robust radioresponse indicator that correlated with biological processes known to underpin the cellular response to radiation. Using AUC as a metric for further investigations, we found that radiation sensitivity was significantly associated with disruptive mutations in genes related to nonhomologous end joining. Next, by simulating the effects of different oxygen levels, we identified putative genes that may influence radioresponse specifically under hypoxic conditions. Furthermore, using transcriptomic data, we found evidence for tissue-specific determinants of radioresponse, suggesting that tumor type could influence the validity of putative predictive biomarkers of radioresponse. Finally, integrating radioresponse with drug response data, we found that drug classes impacting the cytoskeleton, DNA replication, and mitosis display similar therapeutic effects to ionizing radiation on cancer cell lines. In summary, RadioGx provides a unique computational toolbox for hypothesis generation to advance preclinical research for radiation oncology and precision medicine. Significance: The RadioGx computational platform enables integrative analyses of cellular response to radiation with drug responses and genome-wide molecular data.

Original languageEnglish (US)
Pages (from-to)6227-6237
Number of pages11
JournalCancer Research
Volume79
Issue number24
DOIs
StatePublished - Dec 15 2019

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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