Abstract 25: Whole genome sequencing and quantitative proteomics reveal HPV integration and HER2 overexpression in a patient with cervical cancer: Comprehensive omics analysis driving clinical treatment decisions
Authors: Benz Stephen , Sanborn J Zackary , Hensley Nicole S. , Hembrough Todd , Vaske Charles J. , Burrows Jon , Rabizadeh Shahrooz , Royston Ivor , Soon-Shiong Patrick 
Published: May 2016

Abstract
Introduction: Selection of drugs to treat patients with cancer is typically based on the anatomical site in which the tumor is located. Here we report a treatment decision for a patient with relapsed, advanced cervical cancer that was based on a comprehensive omics analysis using whole genome sequencing (WGS) combined with quantitative proteomics.
Methods: The patient was a 44-year-old female whose disease had progressed following surgery and more than 4 lines of chemotherapy. WGS was performed on the patient's formalin-fixed, paraffin-embedded (FFPE) metastatic tumor sample and a matched-normal reference sample. Quantitative proteomics was performed on the FFPE tumor sample by Selected Reaction Monitoring Mass Spectrometry and was quantitated at the atomolar level.
Results: WGS found somatic mutations and rearrangements and reads mapping to human papillomavirus type 18 (HPV 18). Mutations more commonly found in breast cancer (ERBB2, CDH1, and CLTCL1) were noted. The HPV 18 genome was integrated into chromosome 17 in close proximity to a 7-fold amplification of the ERBB2 gene. Proteomic analysis of the FFPE tumor validated and quantitated overexpression of HER2 protein resulting from ERBB2 gene amplification, with 11,322 amol/μg of tissue protein. Clinically observed ranges for breast or gastric cancer are 150-500 amol/μg, with levels above 750 amol/μg correlating with FISH-positive amplification and clinical efficacy of trastuzumab (unpublished observation). Based on these comprehensive omic findings, trastuzumab, a therapy approved for breast and gastric cancer, was administered. The patient experienced a reduction in the size of her tumor (by CT/PET) and stabilization of her disease for 5 months.
Conclusion: WGS and proteomic profiling of this patient's disease identified, confirmed, and quantitated an appropriate target for pharmaceutical intervention. The patient presented with cervical cancer; however, the WGS analysis pointed towards a potentially causative integration of the HPV 18 genome resulting in ERBB2 amplification along with genomic mutations more commonly found in breast cancer. Proteomic analysis further validated and quantitated the HER2 expression resulting from ERBB2 gene amplification, leading to the patient's treatment with trastuzumab. Our findings argue for the use of comprehensive omics analysis to guide decision support for personalized management of cancer care with therapies determined based on a quantitative proteomic signature, independent of anatomical tumor type.
Citation Format: Stephen Benz, J Zackary Sanborn, Nicole S. Hensley, Todd Hembrough, Charles J. Vaske, Jon Burrows, Shahrooz Rabizadeh, Ivor Royston, Patrick Soon-Shiong. Whole genome sequencing and quantitative proteomics reveal HPV integration and HER2 overexpression in a patient with cervical cancer: Comprehensive omics analysis driving clinical treatment decisions. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 25.