Abstract 86: Time course analysis of gene expression and epigenetic interactions in acquired cetuximab resistance in head and neck squamous cell carcinoma
Authors: Kagohara Luciane T. , Stein-O'Brien Genevieve , Li Sijia , Thakar Manjusha , Ranaweera Ruchira , Considine Michael , Califano Joseph A. , Chung Christine H. , Gaykalova Daria , Fertig Elana J. 
Published: July 2017

Abstract
The current study performs time course genomics and epigenomics profiling to determine the complex dynamics of interactions between gene expression and epigenetic changes that alter cellular signaling and drive acquired therapeutic resistance. Targeted therapeutic agents block the activity of specific molecules critical for tumor progression. Cetuximab is a monoclonal antibody against EGFR currently used in the treatment of head and neck squamous cell carcinoma (HNSCC) and metastatic colorectal cancers. Similar to many targeted therapeutics, cetuximab improves survival for a brief period of two years, after which most patients acquire resistance resulting in tumor progression or recurrence. The mechanisms that alter cellular signaling pathways and cause resistance are poorly understood. We hypothesize that the molecular alterations that precede the resistance phenotype are more likely to be responsible for the resistance than the widespread alterations observed once the resistance is established. To test this hypothesis, we develop a novel time course experimental and bioinformatics model of acquired resistance. Specifically, this protocol enables weekly profiling of RNA, DNA, and proliferation as cetuximab resistance developed in vitro. We apply the CoGAPS bioinformatics algorithm to perform integrated analysis of gene expression and DNA methylation. This analysis distinguishes signatures of sustained activation of cellular pathways in response to treatment from signatures of clonal expansion associated with acquired cetuximab resistance. Despite identifying massive changes in gene expression driven by therapeutic response, only the expression changes associated with the acquired resistance, and not response to treatment, have corresponding epigenetic signatures. The genomic signature associated with acquired resistance is enriched for gene targets of the AP-2 family of transcription factors. In a previous study, we found that these gene targets were overexpressed after short-term treatment in cetuximab sensitive cell lines and HNSCC tumors. Our data suggest that this family of transcription factors serves as a feedback mechanism to maintain homeostasis to growth factors receptor signaling. As a result, AP-2 transcription factors serve as a natural mechanism to cause subsequent therapeutic resistance without addition of genetic alterations. Further investigation is needed to determine the role of AP-2 transcription factors in acquired cetuximab resistance.
Citation Format: Luciane T. Kagohara, Genevieve Stein-O'Brien, Sijia Li, Manjusha Thakar, Ruchira Ranaweera, Michael Considine, Joseph A. Califano, Christine H. Chung, Daria Gaykalova, Elana J. Fertig. Time course analysis of gene expression and epigenetic interactions in acquired cetuximab resistance in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 86. doi:10.1158/1538-7445.AM2017-86