Tumor heterogeneity and acquired drug resistance in FGFR2-fusion-positive cholangiocarcinoma through rapid research autopsy
- Melanie A. Krook1,7,
- Russell Bonneville1,2,7,
- Hui-Zi Chen1,3,
- Julie W. Reeser1,
- Michele R. Wing1,
- Dorrelyn M. Martin1,
- Amy M. Smith1,
- Thuy Dao1,
- Eric Samorodnitsky1,
- Anoosha Paruchuri1,
- Jharna Miya1,
- Kaitlin R. Baker1,
- Lianbo Yu4,
- Cynthia Timmers1,
- Kristin Dittmar5,
- Aharon G. Freud1,6,
- Patricia Allenby6 and
- Sameek Roychowdhury1,3
- 1Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA;
- 2Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA;
- 3Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA;
- 4Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA;
- 5Department of Radiology, The Ohio State University, Columbus, Ohio 43210, USA;
- 6Department of Pathology, The Ohio State University, Columbus, Ohio 43210, USA
- Corresponding author: Sameek.Roychowdhury{at}osumc.edu
-
↵7 These authors contributed equally to this work.
Abstract
Cholangiocarcinoma is a highly aggressive and lethal malignancy, with limited treatment options available. Recently, FGFR inhibitors have been developed and utilized in FGFR-mutant cholangiocarcinoma; however, resistance often develops and the genomic determinants of resistance are not fully characterized. We completed whole-exome sequencing (WES) of 11 unique tumor samples obtained from a rapid research autopsy on a patient with FGFR-fusion-positive cholangiocarcinoma who initially responded to the pan-FGFR inhibitor, INCB054828. In vitro studies were carried out to characterize the novel FGFR alteration and secondary FGFR2 mutation identified. Multisite WES and analysis of tumor heterogeneity through subclonal inference identified four genetically distinct cancer cell populations, two of which were only observed after treatment. Additionally, WES revealed an FGFR2 N549H mutation hypothesized to confer resistance to the FGFR inhibitor INCB054828 in a single tumor sample. This hypothesis was corroborated with in vitro cell-based studies in which cells expressing FGFR2–CLIP1 fusion were sensitive to INCB054828 (IC50 value of 10.16 nM), whereas cells with the addition of the N549H mutation were resistant to INCB054828 (IC50 value of 1527.57 nM). Furthermore, the FGFR2 N549H secondary mutation displayed cross-resistance to other selective FGFR inhibitors, but remained sensitive to the nonselective inhibitor, ponatinib. Rapid research autopsy has the potential to provide unprecedented insights into the clonal evolution of cancer throughout the course of the disease. In this study, we demonstrate the emergence of a drug resistance mutation and characterize the evolution of tumor subclones within a cholangiocarcinoma disease course.
Footnotes
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[Supplemental material is available for this article.]
- Received January 17, 2019.
- Accepted April 15, 2019.
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