title: Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state.
abstract: Treatment of BRAF-mutant melanomas with MAP kinase pathway inhibitors is paradigmatic of the promise of precision cancer therapy but also highlights problems with drug resistance that limit patient benefit. We use live-cell imaging, single-cell analysis, and molecular profiling to show that exposure of tumor cells to RAF/MEK inhibitors elicits a heterogeneous response in which some cells die, some arrest, and the remainder adapt to drug. Drug-adapted cells up-regulate markers of the neural crest (e.g., NGFR), a melanocyte precursor, and grow slowly. This phenotype is transiently stable, reverting to the drug-naïve state within 9 days of drug withdrawal. Transcriptional profiling of cell lines and human tumors implicates a c-Jun/ECM/FAK/Src cascade in de-differentiation in about one-third of cell lines studied; drug-induced changes in c-Jun and NGFR levels are also observed in xenograft and human tumors. Drugs targeting the c-Jun/ECM/FAK/Src cascade as well as BET bromodomain inhibitors increase the maximum effect (Emax) of RAF/MEK kinase inhibitors by promoting cell killing. Thus, analysis of reversible drug resistance at a single-cell level identifies signaling pathways and inhibitory drugs missed by assays that focus on cell populations.
authors.affiliation: Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA mohammad_fallahisichani@hms.harvard.edu peter_sorger@hms.harvard.edu.
authors.forename: Mohammad
authors.identifier: 0000-0003-0917-3525
authors.initials: M
authors.lastname: Fallahi-Sichani
authors.affiliation: Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA.
authors.forename: Verena
authors.initials: V
authors.lastname: Becker
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.|Broad Institute of Harvard and MIT, Cambridge, MA, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Izar
authors.affiliation: Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Baker
authors.affiliation: HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
authors.forename: Jia-Ren
authors.initials: JR
authors.lastname: Lin
authors.affiliation: Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA.
authors.forename: Sarah A
authors.identifier: 0000-0002-3118-3378
authors.initials: SA
authors.lastname: Boswell
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
authors.forename: Parin
authors.identifier: 0000-0002-7259-1810
authors.initials: P
authors.lastname: Shah
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
authors.forename: Asaf
authors.identifier: 0000-0002-6859-7435
authors.initials: A
authors.lastname: Rotem
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.|Broad Institute of Harvard and MIT, Cambridge, MA, USA.|Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
authors.forename: Levi A
authors.initials: LA
authors.lastname: Garraway
authors.affiliation: Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA mohammad_fallahisichani@hms.harvard.edu peter_sorger@hms.harvard.edu.|HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.|Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
authors.forename: Peter K
authors.identifier: 0000-0002-3364-1838
authors.initials: PK
authors.lastname: Sorger
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000187:drug effects; D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000187:drug effects; D002470:Cell Survival / Q000187:drug effects; D019008:Drug Resistance, Neoplasm / Q000187:drug effects; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D007211:Indoles / Q000008:administration & dosage* / Q000494:pharmacology; D020935:MAP Kinase Signaling System / Q000187:drug effects*; D008545:Melanoma / Q000188:drug therapy / Q000235:genetics*; D051379:Mice; D009154:Mutation; D009419:Nerve Tissue Proteins / Q000235:genetics*; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics*; D017475:Receptors, Nerve Growth Factor / Q000235:genetics*; D059010:Single-Cell Analysis; D013449:Sulfonamides / Q000008:administration & dosage* / Q000494:pharmacology; D000077484:Vemurafenib; D023041:Xenograft Model Antitumor Assays
chemical_list: D007211:Indoles; C484065:NGFR protein, human; D009419:Nerve Tissue Proteins; D017475:Receptors, Nerve Growth Factor; D013449:Sulfonamides; D000077484:Vemurafenib; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf
keywords: BRAFV600E melanomas; RAF and MEK inhibitors; adaptive and reversible drug resistance; de‐differentiated NGFRHigh state