1. Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma.
- Author
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Egan JB, Marks DL, Hogenson TL, Vrabel AM, Sigafoos AN, Tolosa EJ, Carr RM, Safgren SL, Hesles EE, Almada LL, Romecin-Duran PA, Iguchi E, Ala'Aldeen A, Kocher JA, Oliver GR, Prodduturi N, Mead DW, Hossain A, Huneke NE, Tagtow CM, Ailawadhi S, Ansell SM, Banck MS, Bryce AH, Carballido EM, Chanan-Khan AA, Curtis KK, Resnik E, Gawryletz CD, Go RS, Halfdanarson TR, Ho TH, Joseph RW, Kapoor P, Mansfield AS, Meurice N, Nageswara Rao AA, Nowakowski GS, Pardanani A, Parikh SA, Cheville JC, Feldman AL, Ramanathan RK, Robinson SI, Tibes R, Finnes HD, McCormick JB, McWilliams RR, Jatoi A, Patnaik MM, Silva AC, Wieben ED, McAllister TM, Rumilla KM, Kerr SE, Lazaridis KN, Farrugia G, Stewart AK, Clark KJ, Kennedy EJ, Klee EW, Borad MJ, and Fernandez-Zapico ME
- 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., Competing Interests: AUTHORS’ DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST The following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. Relation-ships may not relate to the subject matter of this manuscript. For more information about ASCO’s conflict of interest policy, please refer to www.asco.org/rwc or po.ascopubs.org/site/ifc. Jan B. Egan No relationship to disclose David L. Marks Stock and Other Ownership Interests: WebMD, Cardinal Health (I), Prothena (I), Perrigo (I) Tara L. Hogenson No relationship to disclose Anne M. Vrabel No relationship to disclose Ashley N. Sigafoos No relationship to disclose Ezequiel J. Tolosa No relationship to disclose Ryan M. Carr No relationship to disclose Stephanie L. Safgren No relationship to disclose Elisa Enriquez Hesles No relationship to disclose Luciana L. Almada No relationship to disclose Paola A. Romecin-Duran No relationship to disclose Eriko Iguchi No relationship to disclose Aryan Ala’Aldeen No relationship to disclose Jean-Pierre A. Kocher No relationship to disclose Gavin R. Oliver No relationship to disclose Naresh Prodduturi No relationship to disclose David W. Mead No relationship to disclose Asif Hossain No relationship to disclose Norine E. Huneke No relationship to disclose Colleen M. Tagtow No relationship to disclose Sikander Ailawadhi Consulting or Advisory Role: Amgen, Takeda Pharmaceuticals, Novartis Research Funding: Pharmacyclics (Inst) Travel, Accommodations, Expenses: Amgen, Takeda Pharmaceuticals, Novartis Stephen M. Ansell Honoraria: WebMD, Research To Practice Research Funding: Bristol-Myers Squibb (Inst), Celldex Therapeutics (Inst), Seattle Genetics (Inst), Merck (Inst), Affimed (Inst), Trillium Therapeutics (Inst) Michaela S. Banck No relationship to disclose Alan H. BryceNo relationship to disclose Estrella M. Carballido No relationship to disclose Asher A. Chanan-Khan No relationship to disclose Kelly K. Curtis Employment: INC Research Stock and Other Ownership Interests: INC Research Travel, Accommodations, Expenses: INC Research Ernesto ResnikNo relationship to disclose Chelsea D. Gawryletz No relationship to disclose Ronald S. Go Speakers’ Bureau: OnLive, Takeda Pharmaceuticals Thorvardur R. Halfdanarson Consulting or Advisory Role: Lexicon (Inst), Ipsen (Inst), Merrimack (Inst) Research Funding: Esanex (Inst), Ipsen (Inst), Boston Biomedical (Inst) Thai H. Ho No relationship to disclose Richard W. Joseph Consulting or Advisory Role: Bristol-Myers Squibb, Nektar, Genoptix, Eisai, Bristol-Myers Squibb Research Funding: Merck, Bristol-Meyers Squibb, Roche (Inst), Genentech (Inst), X4P Pharmaceuticals (Inst), Amgen (Inst) Prashant Kapoor Consulting or Advisory Role: Sanofi (Inst) Research Funding: Amgen (Inst), Takeda Pharmaceuticals (Inst) Aaron S. Mansfield Consulting or Advisory Role: TrovaGene (Inst), Genentech (Inst), Bristol-Myers Squibb (Inst) Travel, Accommodations, Expenses: Bristol-Myers Squibb Nathalie Meurice No relationship to disclose Amulya A. Nageswara Rao No relationship to disclose Grzegorz S. Nowakowski Consulting or Advisory Role: Celgene (Inst), MorphoSys (Inst), Genentech (Inst) Research Funding: Celgene (Inst) Animesh Pardanani No relationship to disclose Sameer A. Parikh Research Funding: Pharmacyclics (Inst) John C. Cheville No relationship to disclose Andrew L. Feldman Consulting or Advisory Role: Infinity Pharmaceuticals Patents, Royalties, Other Intellectual Property: Inventor of technology for which the Mayo Clinic holds an unlicensed patent or has submitted a patent application (Inst) Ramesh K. Ramanathan Honoraria: Taiho Pharmaceutical, Cerulean Pharma, Pharmacyclics, Insys Therapeutics, Novocure Consulting or Advisory Role: Cerulean Pharma, Novocure, INSYS Therapeutics, Pharmacyclics Research Funding: AbbVie (Inst), Celgene (Inst), Merck (Inst), Schering Plough (Inst), Merrimack (Inst), Boston Biomedical (Inst), BERG (Inst), Superlab Far East (Inst) Steven I. Robinson Travel, Accommodations, Expenses: Tricon Pharmaceuticals Raoul Tibes Research Funding: Novartis (Inst), Merck (Inst), Seattle Genetics (Inst), Boehringer Ingelheim (Inst), Astellas Pharma (Inst), Astex Pharmaceuticals (Inst)Heidi D. Finnes Jennifer B. McCormick No relationship to disclose Robert R. McWilliams Consulting or Advisory Role: Merrimack (Inst) Research Funding: PRISM BioLab (Inst), Genentech (Inst), Novartis (Inst), NewLink Genetics (Inst), Eli Lilly (Inst), Aduro Biotech (Inst), Pfizer (Inst), Sanofi (Inst) Travel, Accommodations, Expenses: AstraZeneca Aminah Jatoi Research Funding: Entera Health, Boston Biologics Mrinal M. Patnaik No relationship to disclose Alvin C. Silva No relationship to disclose Eric D. Wieben Patents, Royalties, Other Intellectual Property: Champions Oncology–licensed IP-targeted therapy with abiraterone acetate ($0 received), WuXi AppTec–licensed IP-breast cancer xenografts ($12,737 to Mayo Clinic; Inst), Affymetrix-licensed IP on several variants in drug processing enzymes ($0 in past 2 years), Life Technologies–licensed IP on several variants in drug processing enzymes ($0 in past 2 years) Tammy M. McAllister No relationship to disclose Kandelaria M. Rumilla No relationship to disclose Sarah E. Kerr Research Funding: Abbott Molecular Konstantinos N. Lazaridis No relationship to disclose Gianrico Farrugia No relationship to disclose A. Keith Stewart Consulting or Advisory Role: Celgene, Bristol-Myers Squibb, Janssen Pharmaceuticals, Roche, Amgen Karl J. Clark Patents, Royalties, Other Intellectual Property: Inventor on patents associated with the Sleeping Beauty transposon system Eileen J. Kennedy Patents, Royalties, Other Intellectual Property: Patent on unrelated work (US patent 9,458,189) for “ligation of stapled polypeptides” issued October 4, 2016 Eric W. Klee Patents, Royalties, Other Intellectual Property: Royalties on software development Mitesh J. Borad Stock and Other Ownership Interests: GlaxoSmithKline, Gilead Sciences Consulting or Advisory Role: G1 Therapeutics, TD2, Fujifilm (Inst), Agios (Inst), INSYS Therapeutics (Inst), Novartis (Inst), ArQule (Inst), Celegene (Inst), Inspyr Therapeutics, Halozyme Therapeutics (Inst) Research Funding: Boston Biomedical (Inst), miRNA Therapeutics (Inst), Senhwa Biosciences (Inst), Medimmune (Inst), Bioline (Inst), Agios (Inst), Halozyme Therapeutics (Inst), Celgene (Inst), Threshold Pharmaceuticals (Inst), Toray (Inst), Dicerna Pharmaceuticals (Inst), Sillajen (Inst), Eisai (Inst), Taiho Pharmaceuticals (Inst), EMD Serono (Inst), Isis Pharmaceuticals (Inst), Incyte (Inst), Sun BioPharma (Inst), ARIAD Pharmaceuticals (Inst), ImClone Systems (Inst) Travel, Accommodations, Expenses: ArQule, Celgene, AstraZeneca Martin E. Fernandez-Zapico No relationship to disclose
- Published
- 2017
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