Integrated analysis of whole-genome ChIP-Seq and RNA-Seq data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks

Dylan Z. Kelley, Emily L. Flam, Evgeny Izumchenko, Ludmila V. Danilova, Hildegard A. Wulf, Theresa Guo, Dzov A. Singman, Bahman Afsari, Alyza M. Skaist, Michael Considine, Jane A. Welch, Elena Stavrovskaya, Justin A. Bishop, William H. Westra, Zubair Khan, Wayne M. Koch, David Sidransky, Sarah J. Wheelan, Joseph A. Califano, Alexander V. FavorovElana J. Fertig, Daria A. Gaykalova

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus–related (HPVþ) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis.

Original languageEnglish (US)
Pages (from-to)6538-6550
Number of pages13
JournalCancer research
Volume77
Issue number23
DOIs
StatePublished - Dec 1 2017

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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    Kelley, D. Z., Flam, E. L., Izumchenko, E., Danilova, L. V., Wulf, H. A., Guo, T., Singman, D. A., Afsari, B., Skaist, A. M., Considine, M., Welch, J. A., Stavrovskaya, E., Bishop, J. A., Westra, W. H., Khan, Z., Koch, W. M., Sidransky, D., Wheelan, S. J., Califano, J. A., ... Gaykalova, D. A. (2017). Integrated analysis of whole-genome ChIP-Seq and RNA-Seq data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks. Cancer research, 77(23), 6538-6550. https://doi.org/10.1158/0008-5472.CAN-17-0833