Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma

Adrian D. Schubert, Esther Channah Broner, Nishant Agrawal, Nyall London, Alexander Pearson, Anuj Gupta, Neha Wali, Tanguy Y. Seiwert, Sarah Wheelan, Mark Lingen, Kay Macleod, Hailey Allen, Aditi Chatterjee, Saloura Vassiliki, Daria Gaykalova, Mohammad O. Hoque, David Sidransky, Karthik Suresh, Evgeny Izumchenko

Research output: Contribution to journalArticle

Abstract

Mutations in mitochondrial DNA (mtDNA) have been linked to risk, progression, and treatment response of head and neck squamous cell carcinoma (HNSCC). Due to their clonal nature and high copy number, mitochondrial mutations could serve as powerful molecular markers for detection of cancer cells in bodily fluids, surgical margins, biopsies and lymph node (LN) metastasis, especially at sites where tumor involvement is not histologically apparent. Despite a pressing need for high-throughput, cost-effective mtDNA mutation profiling system, current methods for library preparation are still imperfect for detection of low prevalence heteroplasmic mutations. To this end, we have designed an ultra-deep amplicon-based sequencing library preparation approach that covers the entire mitochondrial genome. We sequenced mtDNA in 28 HNSCCs, matched LNs, surgical margins and bodily fluids, and applied multiregional sequencing approach on 14 primary tumors. Our results demonstrate that this quick, sensitive and cost-efficient method allows obtaining a snapshot on the mitochondrial heterogeneity, and can be used for detection of low frequency tumor-associated mtDNA mutations in LNs, sputum and serum specimens. These findings provide the foundation for using mitochondrial sequencing for risk assessment, early detection, and tumor surveillance.

Original languageEnglish (US)
Pages (from-to)49-60
Number of pages12
JournalCancer Letters
Volume471
DOIs
StatePublished - Feb 28 2020

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Keywords

  • Cancer
  • Head and neck squamous cell carcinoma (HNSCC)
  • Mitochondrial DNA (mtDNA)
  • Mutations
  • Sequencing

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Schubert, A. D., Channah Broner, E., Agrawal, N., London, N., Pearson, A., Gupta, A., Wali, N., Seiwert, T. Y., Wheelan, S., Lingen, M., Macleod, K., Allen, H., Chatterjee, A., Vassiliki, S., Gaykalova, D., Hoque, M. O., Sidransky, D., Suresh, K., & Izumchenko, E. (2020). Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma. Cancer Letters, 471, 49-60. https://doi.org/10.1016/j.canlet.2019.12.006