1. Academic Validation
  2. Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma

Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma

  • JCO Precis Oncol. 2017:2017. doi: 10.1200/PO.17.00018.
Jan B Egan 1 David L Marks 1 Tara L Hogenson 1 Anne M Vrabel 1 Ashley N Sigafoos 1 Ezequiel J Tolosa 1 Ryan M Carr 1 Stephanie L Safgren 1 Elisa Enriquez Hesles 1 Luciana L Almada 1 Paola A Romecin-Duran 1 Eriko Iguchi 1 Aryan Ala'Aldeen 1 Jean-Pierre A Kocher 1 Gavin R Oliver 1 Naresh Prodduturi 1 David W Mead 1 Asif Hossain 1 Norine E Huneke 1 Colleen M Tagtow 1 Sikander Ailawadhi 1 Stephen M Ansell 1 Michaela S Banck 1 Alan H Bryce 1 Estrella M Carballido 1 Asher A Chanan-Khan 1 Kelly K Curtis 1 Ernesto Resnik 1 Chelsea D Gawryletz 1 Ronald S Go 1 Thorvardur R Halfdanarson 1 Thai H Ho 1 Richard W Joseph 1 Prashant Kapoor 1 Aaron S Mansfield 1 Nathalie Meurice 1 Amulya A Nageswara Rao 1 Grzegorz S Nowakowski 1 Animesh Pardanani 1 Sameer A Parikh 1 John C Cheville 1 Andrew L Feldman 1 Ramesh K Ramanathan 1 Steven I Robinson 1 Raoul Tibes 1 Heidi D Finnes 1 Jennifer B McCormick 1 Robert R McWilliams 1 Aminah Jatoi 1 Mrinal M Patnaik 1 Alvin C Silva 1 Eric D Wieben 1 Tammy M McAllister 1 Kandelaria M Rumilla 1 Sarah E Kerr 1 Konstantinos N Lazaridis 1 Gianrico Farrugia 1 A Keith Stewart 1 Karl J Clark 1 Eileen J Kennedy 1 Eric W Klee 1 Mitesh J Borad 1 Martin E Fernandez-Zapico 1
Affiliations

Affiliation

  • 1 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. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor, Aaron S. Mansfield, Amulya A. Nageswara Rao, Grzegorz S. Nowakowski, Animesh Pardanani, Sameer A. Parikh, John C. Cheville, Andrew L. Feldman, Ramesh K. Ramanathan, Steven I. Robinson, Heidi D. Finnes, Jennifer B. McCormick, Robert R. McWilliams, Aminah Jatoi, Mrinal M. Patnaik, Eric D. Wieben, Tammy M. McAllister, Kandelaria M. Rumilla, Sarah E. Kerr, Konstantinos N. Lazaridis, Gianrico Farrugia, Karl J. Clark, Eric W. Klee, and Martin E. Fernandez-Zapico, Mayo Clinic, Rochester; Ernesto Resnik, Bio-Techne, Minneapolis, MN; Sikander Ailawadhi, Asher A. Chanan-Khan, and Richard W. Joseph, Mayo Clinic, Jacksonville, FL; Jan B. Egan, Alan H. Bryce, Estrella M. Carballido, KellyK. Curtis, Chelsea D. Gawryletz, Thai H. Ho,Nathalie Meurice, Ramesh K. Ramanathan, Raoul Tibes, Alvin C. Silva, A. Keith Stewart, and Mitesh J. Borad, Mayo Clinic, Phoenix, AZ; and Eileen J. Kennedy, University of Georgia, Athens, GA.
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 to 522VUSs of interest, including a large number of kinases. Ten receptortyrosine 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.

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