title: Whole-exome tumor sequencing study in biliary cancer patients with a response to MEK inhibitors.
abstract: We previously conducted a phase-II study with selumetinib (AZD6244), a small molecule inhibitor of MEK1/2, in advanced biliary tract cancers (BTC), where the primary endpoint was response rate. Several patients experienced objective response. These findings were confirmed with MEK162 in a similar patient population. To assess for tumor-specific genetic variants that mediate sensitivity to MEK inhibition in BTC, we performed whole-exome sequencing in patients with an objective response to selumetinib. Normal and tumor DNA from FFPE tissue from two patients who experienced an objective response underwent whole-exome sequencing. Raw sequence reads were processed with GATK workflow and tumor specific variants were identified using MuTect and VarScan2. Ensemble Variant Effect Predictor was used to determine functional consequences of these variants. Copy number changes and potential gene fusion events were also screened. Findings were compared to assess for any commonality between the two tumor samples, and whether the identified variants were intrinsic to the MAPK pathway. 1169 and 628 tumor-specific variants were identified in the two samples. Further analysis demonstrated 60 and 53 functional and novel variants, respectively. Of the identified tumor-specific variants, fusion events or copy number changes, no commonality was seen. Several variants in genes associated with ERK signaling were present in each tumor sample. Although there were no common tumor-specific variants in the two patients who exhibited an objective response to selumetinib, several genes associated with ERK signaling were identified. Confirmatory studies investigating the role of the identified genes and other potential tumor independent factors need further investigation.
authors.affiliation: Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Ahn
authors.affiliation: Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA.
authors.forename: Hatice Gulcin
authors.initials: HG
authors.lastname: Ozer
authors.affiliation: Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA.
authors.forename: Baris
authors.initials: B
authors.lastname: Hancioglu
authors.affiliation: Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Lesinski
authors.affiliation: Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Timmers
authors.affiliation: Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
authors.forename: Tanios
authors.initials: T
authors.lastname: Bekaii-Saab
mesh_terms: D001661:Biliary Tract Neoplasms / Q000235:genetics* / Q000473:pathology; D005260:Female; D014644:Genetic Variation; D006801:Humans; D048369:MAP Kinase Kinase 1 / Q000037:antagonists & inhibitors*; D008297:Male; D009154:Mutation; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D048369:MAP Kinase Kinase 1
keywords: MEK inhibition; biliary cancer; whole-exome sequencing