title: PEST domain mutations in Notch receptors comprise an oncogenic driver segment in triple-negative breast cancer sensitive to a γ-secretase inhibitor.
abstract: OBJECTIVE
  To identify and characterize novel, activating mutations in Notch receptors in breast cancer and to determine response to the gamma secretase inhibitor (GSI) PF-03084014.
  
  
  METHODS
  We used several computational approaches, including novel algorithms, to analyze next-generation sequencing data and related omic datasets from The Cancer Genome Atlas (TCGA) breast cancer cohort. Patient-derived xenograft (PDX) models were sequenced, and Notch-mutant models were treated with PF-03084014. Gene-expression and functional analyses were performed to study the mechanism of activation through mutation and inhibition by PF-03084014.
  
  
  RESULTS
  We identified mutations within and upstream of the PEST domains of NOTCH1, NOTCH2, and NOTCH3 in the TCGA dataset. Mutations occurred via several genetic mechanisms and compromised the function of the PEST domain, a negative regulatory domain commonly mutated in other cancers. Focal amplifications of NOTCH2 and NOTCH3 were also observed, as were heterodimerization or extracellular domain mutations at lower incidence. Mutations and amplifications often activated the Notch pathway as evidenced by increased expression of canonical Notch target genes, and functional mutations were significantly enriched in the triple-negative breast cancer subtype (TNBC). PDX models were also identified that harbored PEST domain mutations, and these models were highly sensitive to PF-03084014.
  
  
  CONCLUSIONS
  This work suggests that Notch-altered breast cancer constitutes a bona fide oncogenic driver segment with the most common alteration being PEST domain mutations present in multiple Notch receptors. Importantly, functional studies suggest that this newly identified class can be targeted with Notch inhibitors, including GSIs.
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Danan
authors.initials: D
authors.lastname: Li
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Keith
authors.initials: K
authors.lastname: Ching
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Cathy
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Xianxian
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Mark
authors.initials: M
authors.lastname: Ozeck
authors.affiliation: External Research Solutions, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Shi
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Li
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: Paul
authors.initials: P
authors.lastname: Rejto
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California.
authors.forename: James
authors.initials: J
authors.lastname: Christensen
authors.affiliation: Oncology Research Unit, Pfizer Global Research and Development, La Jolla, San Diego, California. peter.olson@pfizer.com.
authors.forename: Peter
authors.initials: P
authors.lastname: Olson
mesh_terms: D000465:Algorithms; D053829:Amyloid Precursor Protein Secretases / Q000037:antagonists & inhibitors*; D000818:Animals; D001483:Base Sequence; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations / Q000235:genetics; D005260:Female; D018628:Gene Dosage / Q000235:genetics; D006801:Humans; D051379:Mice; D016513:Mice, SCID; D017434:Protein Structure, Tertiary / Q000235:genetics; D051881:Receptor, Notch1 / Q000235:genetics*; D051883:Receptor, Notch2 / Q000235:genetics*; D000071656:Receptor, Notch3; D051880:Receptors, Notch / Q000235:genetics*; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics; D013764:Tetrahydronaphthalenes / Q000494:pharmacology; D064726:Triple Negative Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics; D014633:Valine / Q000031:analogs & derivatives / Q000494:pharmacology; D023041:Xenograft Model Antitumor Assays
chemical_list: C497761:NOTCH1 protein, human; C497764:NOTCH2 protein, human; C499374:NOTCH3 protein, human; D051881:Receptor, Notch1; D051883:Receptor, Notch2; D000071656:Receptor, Notch3; D051880:Receptors, Notch; D013764:Tetrahydronaphthalenes; D053829:Amyloid Precursor Protein Secretases; D014633:Valine; C550722:nirogacestat