Molecular modeling and functional analysis of exome sequencing-derived variants of unknown significance identify a novel, constitutively active FGFR2 mutant in cholangiocarcinoma

Jan B. Egan, David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala'Aldeen, Jean Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. TagtowSikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Alan H. Bryce, Estrella M. Carballido, Asher A. Chanan-Khan, Kelly K. Curtis, Ernesto Resnik, Chelsea D. Gawryletz, Ronald S. Go, Thorvardur R. Halfdanarson, Thai H. Ho, Richard W. Joseph, Prashant Kapoor, Aaron S. Mansfield, Nathalie Meurice, Amulya A.Nageswara Rao, Grzegorz S. Nowakowski, Animesh Pardanani, Sameer A. Parikh, John C. Cheville, Andrew L. Feldman, Ramesh K. Ramanathan, Steven I. Robinson, Raoul Tibes, Heidi D. Finnes, Jennifer B. McCormick, Robert R. McWilliams, Aminah Jatoi, Mrinal M. Patnaik, Alvin C. Silva, Eric D. Wieben, Tammy M. McAllister, Kandelaria M. Rumilla, Sarah E. Kerr, Konstantinos N. Lazaridis, Gianrico Farrugia, A. Keith Stewart, Karl J. Clark, Eileen J. Kennedy, Eric W. Klee, Mitesh J. Borad, Martin E. Fernandez-Zapico

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Purpose Genomic testing has increased the quantity of information available to oncologists. Unfortunately, many identified sequence alterations are variants of unknown significance (VUSs), which thus limit the clinician's ability to use these findings to inform treatment. We applied a combination of in silico prediction and molecular modeling tools and laboratory techniques to rapidly define actionable VUSs. Materials and Methods Exome sequencing was conducted on 308 tumors from various origins. Most single nucleotide alterations within gene coding regions were VUSs. These VUSs were filtered to identify a subset of therapeutically targetable genes that were predicted with in silico tools to be altered in function by their variant sequence. A subset of receptor tyrosine kinase VUSs was characterized by laboratory comparison of each VUS versus its wild-type counterpart in terms of expression and signaling activity. Results The study identified 4,327 point mutations of which 3,833 were VUSs. Filtering for mutations in genes that were therapeutically targetable and predicted to affect protein function reduced these to522VUSsof interest, including a largenumberof kinases.Tenreceptor tyrosine kinase VUSs were selected to explore in the laboratory. Of these, seven were found to be functionally altered. Three VUSs (FGFR2 F276C, FGFR4 R78H, and KDR G539R) showed increased basal or ligand-stimulated ERK phosphorylation compared with their wild-type counterparts, which suggests that they support transformation. Treatment of a patient who carried FGFR2 F276C with an FGFR inhibitor resulted in significant and sustained tumor response with clinical benefit. Conclusion The findings demonstrate the feasibility of rapid identification of the biologic relevance of somatic mutations, which thus advances clinicians' ability to make informed treatment decisions.

Original languageEnglish (US)
Pages (from-to)1-13
Number of pages13
JournalJCO Precision Oncology
Volume2017
Issue number1
DOIs
StatePublished - Jan 1 2017

    Fingerprint

All Science Journal Classification (ASJC) codes

  • Cancer Research
  • Oncology

Cite this

Egan, J. B., Marks, D. L., Hogenson, T. L., Vrabel, A. M., Sigafoos, A. N., Tolosa, E. J., Carr, R. M., Safgren, S. L., Hesles, E. E., Almada, L. L., Romecin-Duran, P. A., Iguchi, E., Ala'Aldeen, A., Kocher, J. P. A., Oliver, G. R., Prodduturi, N., Mead, D. W., Hossain, A., Huneke, N. E., ... Fernandez-Zapico, M. E. (2017). Molecular modeling and functional analysis of exome sequencing-derived variants of unknown significance identify a novel, constitutively active FGFR2 mutant in cholangiocarcinoma. JCO Precision Oncology, 2017(1), 1-13. https://doi.org/10.1200/PO.17.00018