Abstract 954: Integrated genomic analysis by whole exome and transcriptome sequencing of tumor samples from EGFR-mutant non-small-cell lung cancer patients with acquired resistance to erlotinib
Authors: Giannikopoulos Petros , John John St. , Hahner Nicholas , Parker Joel S. , Karachaliou Niki , Costa Carlota , Westesson Oscar , Parikh Urvish , Foo Catherine K. , Cauhlin Aleah F. , Lozano Maria D. , Viteri Santiago , Perez-Gracia Jose L. , Curioni Alessandra , Jantus-Lewintre Eloisa , Camps Carlos , Vergenegre Alain , Gervais Radj , Wellde Anne , Barry Jonathan , Wellde George W. , Bordoni Rodolfo , Stahel Rolf , Zorilla Andres Felipe Cardona , Polkinghorn William R. , Weissman Jonathan , Bivona Trever G. , Rosell Rafael 
Published: May 2015

Abstract
Background: NSCLC p with EGFR mutations initially respond to EGFR tyrosine kinase inhibitors (TKIs) but ultimately relapse. Sub-genomic molecular studies indicate that the EGFR T790M mutation and the activation of MET, PI3K, AXL, HER2 and MAPK can lead to acquired resistance to EGFR TKIs. To date, no integrated comprehensive genomic investigation of EGFR TKI resistance has been reported.
Methods: FFPE biopsies of erlotinib-sensitive and erlotinib-resistant tumors were obtained from 16 EGFR mutant NSCLC patients. The samples were analyzed by whole exome sequencing and whole transcriptome sequencing utilizing the Illumina HiSeq2500 platform. In addition, targeted gene sequencing was performed with the Illumina TruSeq Amplicon-Cancer Panel and run on the MiSeq system.
Results: Erlotinib resistant NSCLC specimens harbored known resistance drivers, including EGFR T790M mutations (6/16; 38%), MET amplification (2/16; 13%), and AXL upregulation (3/16; 19%). Differential expression analysis between resistant and pre-treatment states revealed enrichment in the post-resistant tumors of ERBB2, and FGFR signaling pathways. Biopsies from patients that developed an EGFR T790M mutation post resistance exhibited enrichment in pathways associated with cell cycle, meiosis, telomere maintenance and transcriptional regulation. Copy number analysis demonstrated amplifications in the post-resistance setting that correlated significantly with progression free survival, including regions containing NFKBIA, NKX2-1, and TSC-1. There was also strong correlation between the copy number changes observed and the expression mRNA levels of specific genes. Of note, each resistant tumor exhibited greater copy number similarity to the corresponding matched pre-treatment sample compared to other tumors within the resistance cohort.
Conclusions: We conducted the first ever comprehensive integrated genomic analysis of EGFR TKI resistant NSCLC patients, and identified both known and potentially novel drivers of EGFR TKI resistance. This study demonstrated the feasibility and utility of comprehensive genomic analysis in the clinical management of NSCLC receiving targeted therapy. Together, our data provide unprecedented insight into the molecular pathogenesis of escape from EGFR oncogene inhibition in NSCLC. We are now conducting a prospective observational study in additional NSCLC patients on targeted therapy.
Citation Format: Petros Giannikopoulos, John St. John, Nicholas Hahner, Joel S. Parker, Niki Karachaliou, Carlota Costa, Oscar Westesson, Urvish Parikh, Catherine K. Foo, Aleah F. Cauhlin, Maria D. Lozano, Santiago Viteri, Jose L. Perez-Gracia, Alessandra Curioni, Eloisa Jantus-Lewintre, Carlos Camps, Alain Vergenegre, Radj Gervais, Anne Wellde, Jonathan Barry, George W. Wellde, Rodolfo Bordoni, Rolf Stahel, Andres Felipe Cardona Zorilla, William R. Polkinghorn, Jonathan Weissman, Trever G. Bivona, Rafael Rosell. Integrated genomic analysis by whole exome and transcriptome sequencing of tumor samples from EGFR-mutant non-small-cell lung cancer patients with acquired resistance to erlotinib. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 954. doi:10.1158/1538-7445.AM2014-954