title: Absolute quantitation of Met using mass spectrometry for clinical application: assay precision, stability, and correlation with MET gene amplification in FFPE tumor tissue.
abstract: BACKGROUND
  Overexpression of Met tyrosine kinase receptor is associated with poor prognosis. Overexpression, and particularly MET amplification, are predictive of response to Met-specific therapy in preclinical models. Immunohistochemistry (IHC) of formalin-fixed paraffin-embedded (FFPE) tissues is currently used to select for 'high Met' expressing tumors for Met inhibitor trials. IHC suffers from antibody non-specificity, lack of quantitative resolution, and, when quantifying multiple proteins, inefficient use of scarce tissue.
  
  
  METHODS
  After describing the development of the Liquid-Tissue-Selected Reaction Monitoring-mass spectrometry (LT-SRM-MS) Met assay, we evaluated the expression level of Met in 130 FFPE gastroesophageal cancer (GEC) tissues. We assessed the correlation of SRM Met expression to IHC and mean MET gene copy number (GCN)/nucleus or MET/CEP7 ratio by fluorescence in situ hybridization (FISH).
  
  
  RESULTS
  Proteomic mapping of recombinant Met identified 418TEFTTALQR426 as the optimal SRM peptide. Limits of detection (LOD) and quantitation (LOQ) for this peptide were 150 and 200 amol/µg tumor protein, respectively. The assay demonstrated excellent precision and temporal stability of measurements in serial sections analyzed one year apart. Expression levels of 130 GEC tissues ranged (<150 amol/µg to 4669.5 amol/µg. High correlation was observed between SRM Met expression and both MET GCN and MET/CEP7 ratio as determined by FISH (n = 30; R2 = 0.898). IHC did not correlate well with SRM (n = 44; R2 = 0.537) nor FISH GCN (n = 31; R2 = 0.509). A Met SRM level of ≥1500 amol/µg was 100% sensitive (95% CI 0.69-1) and 100% specific (95% CI 0.92-1) for MET amplification.
  
  
  CONCLUSIONS
  The Met SRM assay measured the absolute Met levels in clinical tissues with high precision. Compared to IHC, SRM provided a quantitative and linear measurement of Met expression, reliably distinguishing between non-amplified and amplified MET tumors. These results demonstrate a novel clinical tool for efficient tumor expression profiling, potentially leading to better informed therapeutic decisions for patients with GEC.
authors.affiliation: Department of Medicine, Section of Hematology & Oncology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Daniel V T
authors.initials: DV
authors.lastname: Catenacci
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: Wei-Li
authors.initials: WL
authors.lastname: Liao
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: Sheeno
authors.initials: S
authors.lastname: Thyparambil
authors.affiliation: Department of Medicine, Section of Hematology & Oncology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Les
authors.initials: L
authors.lastname: Henderson
authors.affiliation: Department of Medicine, Section of Hematology & Oncology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
authors.affiliation: Department of Pathology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Department of Medicine, Section of Hematology & Oncology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Brittany
authors.initials: B
authors.lastname: Rambo
authors.affiliation: Department of Pathology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: John
authors.initials: J
authors.lastname: Hart
authors.affiliation: Department of Pathology, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Shu-Yuan
authors.initials: SY
authors.lastname: Xiao
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Bengali
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: Jamar
authors.initials: J
authors.lastname: Uzzell
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: Marlene
authors.initials: M
authors.lastname: Darfler
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: David B
authors.initials: DB
authors.lastname: Krizman
authors.affiliation: Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
authors.forename: Fabiola
authors.initials: F
authors.lastname: Cecchi
authors.affiliation: Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
authors.forename: Donald P
authors.initials: DP
authors.lastname: Bottaro
authors.affiliation: Department of Health Studies, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Theodore
authors.initials: T
authors.lastname: Karrison
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Veenstra
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: Todd
authors.initials: T
authors.lastname: Hembrough
authors.affiliation: OncoPlex Diagnostics Inc., Rockville, Maryland, United States of America.
authors.forename: Jon
authors.initials: J
authors.lastname: Burrows
mesh_terms: D004938:Esophageal Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D005260:Female; D005784:Gene Amplification; D006801:Humans; D007150:Immunohistochemistry / Q000379:methods; D008297:Male; D013058:Mass Spectrometry / Q000379:methods*; D019859:Proto-Oncogene Proteins c-met / Q000235:genetics / Q000378:metabolism; D013274:Stomach Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology
chemical_list: C491743:MET protein, human; D019859:Proto-Oncogene Proteins c-met