New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling.

RAS is the most frequently mutated gene across human cancers, but developing inhibitors of mutant RAS has proven to be challenging. Given the difficulties of targeting RAS directly, drugs that impact the other components of pathways where mutant RAS operates may potentially be effective. However, the system-level features, including different localizations of RAS isoforms, competition between downstream effectors, and interlocking feedback and feed-forward loops, must be understood to fully grasp the opportunities and limitations of inhibiting specific targets. Mathematical modeling can help us discern the system-level impacts of these features in normal and cancer cells. New technologies enable the acquisition of experimental data that will facilitate development of realistic models of oncogenic RAS behavior. In light of the wealth of empirical data accumulated over decades of study and the advancement of experimental methods for gathering new data, modelers now have the opportunity to advance progress toward realization of targeted treatment for mutant RAS-driven cancers.

[1]  D. Bar-Sagi,et al.  Identification of the mitogen-activated protein kinase phosphorylation sites on human Sos1 that regulate interaction with Grb2 , 1996, Molecular and cellular biology.

[2]  Jens Timmer,et al.  Systems-level interactions between insulin–EGF networks amplify mitogenic signaling , 2009, Molecular systems biology.

[3]  G. L. Hamilton,et al.  Farnesyltransferase-Mediated Delivery of a Covalent Inhibitor Overcomes Alternative Prenylation to Mislocalize K-Ras. , 2017, ACS chemical biology.

[4]  B. Kholodenko,et al.  Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses , 2014, Journal of The Royal Society Interface.

[5]  N. Socci,et al.  Optimization of Dosing for EGFR-Mutant Non–Small Cell Lung Cancer with Evolutionary Cancer Modeling , 2011, Science Translational Medicine.

[6]  D T Denhardt,et al.  Signal-transducing protein phosphorylation cascades mediated by Ras/Rho proteins in the mammalian cell: the potential for multiplex signalling. , 1996, The Biochemical journal.

[7]  J. Licht,et al.  Sprouty proteins: multifaceted negative-feedback regulators of receptor tyrosine kinase signaling. , 2006, Trends in cell biology.

[8]  M. Mann,et al.  Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins* , 2012, Molecular & Cellular Proteomics.

[9]  J. Pessin,et al.  Insulin and Epidermal Growth Factor Receptors Regulate Distinct Pools of Grb2-SOS in the Control of Ras Activation* , 1996, The Journal of Biological Chemistry.

[10]  William S. Hlavacek,et al.  Relaxation oscillations and hierarchy of feedbacks in MAPK signaling , 2017, Scientific Reports.

[11]  R. Joseph,et al.  Vemurafenib: an evidence-based review of its clinical utility in the treatment of metastatic melanoma , 2014, Drug design, development and therapy.

[12]  Alfred Wittinghofer,et al.  GEFs and GAPs: Critical Elements in the Control of Small G Proteins , 2007, Cell.

[13]  Dave Trinel,et al.  Optimization of ERK Activity Biosensors for both Ratiometric and Lifetime FRET Measurements , 2014, Sensors.

[14]  James S. Duncan,et al.  Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast Cancer by Targeting BET Family Bromodomains. , 2015, Cell reports.

[15]  J. Pessin,et al.  SOS Phosphorylation and Disassociation of the Grb2-SOS Complex by the ERK and JNK Signaling Pathways (*) , 1996, The Journal of Biological Chemistry.

[16]  A. Gingras,et al.  The RhoGEF GEF-H1 is required for oncogenic RAS signaling via KSR-1. , 2014, Cancer cell.

[17]  E. Lander,et al.  Genetic Screens in Human Cells Using the CRISPR-Cas9 System , 2013, Science.

[18]  Jürg Zimmermann,et al.  Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr–Abl positive cells , 1996, Nature Medicine.

[19]  M. Clausen,et al.  Small-molecule kinase inhibitors: an analysis of FDA-approved drugs. , 2016, Drug discovery today.

[20]  T. Meyer,et al.  Reversible intracellular translocation of KRas but not HRas in hippocampal neurons regulated by Ca2+/calmodulin , 2005, The Journal of cell biology.

[21]  Boris N Kholodenko,et al.  Scaffolding Protein Grb2-associated Binder 1 Sustains Epidermal Growth Factor-induced Mitogenic and Survival Signaling by Multiple Positive Feedback Loops* , 2006, Journal of Biological Chemistry.

[22]  Nils Blüthgen,et al.  Effects of sequestration on signal transduction cascades , 2006, The FEBS journal.

[23]  B. Kholodenko,et al.  The topology design principles that determine the spatiotemporal dynamics of G-protein cascades. , 2012, Molecular Biosystems.

[24]  Eric Legius,et al.  Mutation analysis in Costello syndrome: functional and structural characterization of the HRAS p.Lys117Arg mutation , 2008, Human mutation.

[25]  Malte Schmick,et al.  KRas Localizes to the Plasma Membrane by Spatial Cycles of Solubilization, Trapping and Vesicular Transport , 2014, Cell.

[26]  C. Der,et al.  The RalGEF-Ral Effector Signaling Network: The Road Less Traveled for Anti-Ras Drug Discovery. , 2011, Genes & cancer.

[27]  Holger Sondermann,et al.  Regulation of Ras Signaling Dynamics by Sos-Mediated Positive Feedback , 2006, Current Biology.

[28]  John G. Albeck,et al.  Frequency-modulated pulses of ERK activity transmit quantitative proliferation signals. , 2013, Molecular cell.

[29]  Renaud Vincentelli,et al.  Quantifying domain-ligand affinities and specificities by high-throughput holdup assay , 2015, Nature Methods.

[30]  Yi Liu,et al.  Selective Inhibition of Oncogenic KRAS Output with Small Molecules Targeting the Inactive State. , 2016, Cancer discovery.

[31]  John C. Hunter,et al.  Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations , 2015, Molecular Cancer Research.

[32]  Hans Clevers,et al.  Targeting mutant RAS in patient-derived colorectal cancer organoids by combinatorial drug screening , 2016, eLife.

[33]  Stefan Wetzel,et al.  Small-molecule inhibition of APT1 affects Ras localization and signaling. , 2010, Nature chemical biology.

[34]  Martin Kircher,et al.  Deep proteome and transcriptome mapping of a human cancer cell line , 2011, Molecular systems biology.

[35]  Walter Kolch,et al.  Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients , 2015, Science Signaling.

[36]  B. Kholodenko Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects. , 2015, Cell reports.

[37]  M. Lythgoe,et al.  An MRAS, SHOC2, and SCRIB complex coordinates ERK pathway activation with polarity and tumorigenic growth. , 2013, Molecular cell.

[38]  M. Selbach,et al.  Global quantification of mammalian gene expression control , 2011, Nature.

[39]  Ruedi Aebersold,et al.  Mass-spectrometric exploration of proteome structure and function , 2016, Nature.

[40]  Boris N. Kholodenko,et al.  Bimodal Protein Distributions in Heterogeneous Oscillating Systems , 2012, CMSB.

[41]  Eric S. Lander,et al.  Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras , 2017, Cell.

[42]  D. Morrison,et al.  Impact of Feedback Phosphorylation and Raf Heterodimerization on Normal and Mutant B-Raf Signaling , 2009, Molecular and Cellular Biology.

[43]  K. Flaherty,et al.  Inhibition of mutated, activated BRAF in metastatic melanoma. , 2010, The New England journal of medicine.

[44]  R. Gillies,et al.  Exploiting evolutionary principles to prolong tumor control in preclinical models of breast cancer , 2016, Science Translational Medicine.

[45]  Philipp Selenko,et al.  Cell signaling, post-translational protein modifications and NMR spectroscopy , 2012, Journal of biomolecular NMR.

[46]  A. Hauschild,et al.  Improved overall survival in melanoma with combined dabrafenib and trametinib. , 2015, The New England journal of medicine.

[47]  Mohammad Reza Ahmadian,et al.  Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders , 2011, Human mutation.

[48]  L. Kay,et al.  NMR spectroscopy brings invisible protein states into focus. , 2009, Nature chemical biology.

[49]  B. Kholodenko,et al.  Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. , 2000, European journal of biochemistry.

[50]  D. Bar-Sagi,et al.  Ras effectors and their role in mitogenesis and oncogenesis , 1997, Journal of Molecular Medicine.

[51]  Carla Mattos,et al.  A comprehensive survey of Ras mutations in cancer. , 2012, Cancer research.

[52]  S. Khozin,et al.  U.S. Food and Drug Administration approval summary: Erlotinib for the first-line treatment of metastatic non-small cell lung cancer with epidermal growth factor receptor exon 19 deletions or exon 21 (L858R) substitution mutations. , 2014, The oncologist.

[53]  M. Clausen,et al.  FDA-approved small-molecule kinase inhibitors. , 2015, Trends in pharmacological sciences.

[54]  J. Schlessinger,et al.  Cell Signaling by Receptor Tyrosine Kinases , 2000, Cell.

[55]  Ozlem Keskin,et al.  GTP-Dependent K-Ras Dimerization. , 2015, Structure.

[56]  Ronald J. Moore,et al.  Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum , 2012, Proceedings of the National Academy of Sciences.

[57]  T Aittokallio,et al.  Cancer stem cell drugs target K-ras signaling in a stemness context , 2016, Oncogene.

[58]  B. Kholodenko,et al.  Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor* , 1999, The Journal of Biological Chemistry.

[59]  Matthew S. Creamer,et al.  Use of mechanistic models to integrate and analyze multiple proteomic datasets. , 2015, Biophysical journal.

[60]  R. Wilson,et al.  Inactivation of RASA1 promotes melanoma tumorigenesis via R-Ras activation , 2016, Oncotarget.

[61]  A. Aplin,et al.  Targeting mutant NRAS signaling pathways in melanoma. , 2016, Pharmacological research.

[62]  David Cameron,et al.  2-year follow-up of trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer: a randomised controlled trial , 2007, The Lancet.

[63]  Mohammad Reza Ahmadian,et al.  Diverging gain-of-function mechanisms of two novel KRAS mutations associated with Noonan and cardio-facio-cutaneous syndromes. , 2013, Human molecular genetics.

[64]  D. Morrison,et al.  C-TAK1 regulates Ras signaling by phosphorylating the MAPK scaffold, KSR1. , 2001, Molecular cell.

[65]  S. Marqusee,et al.  A Ras-induced conformational switch in the Ras activator Son of sevenless , 2006, Proceedings of the National Academy of Sciences.

[66]  Steven P Gygi,et al.  Akt–RSK–S6 Kinase Signaling Networks Activated by Oncogenic Receptor Tyrosine Kinases , 2010, Science Signaling.

[67]  Franziska Michor,et al.  Pharmacokinetics and Drug Interactions Determine Optimum Combination Strategies in Computational Models of Cancer Evolution. , 2017, Cancer research.

[68]  Noo Li Jeon,et al.  Molecular Systems Biology Peer Review Process File Frequency Modulation of Erk Activation Dynamics Rewires Cell Fate Transaction Report , 2022 .

[69]  Jayajit Das,et al.  Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells , 2009, Cell.

[70]  Levi A Garraway,et al.  Circumventing cancer drug resistance in the era of personalized medicine. , 2012, Cancer discovery.

[71]  J. Colicelli,et al.  Human RAS Superfamily Proteins and Related GTPases , 2004, Science's STKE.

[72]  Mohammad Reza Ahmadian,et al.  Confirmation of the arginine-finger hypothesis for the GAP-stimulated GTP-hydrolysis reaction of Ras , 1997, Nature Structural Biology.

[73]  F. McCormick,et al.  A cytoplasmic protein stimulates normal N-ras p21 GTPase, but does not affect oncogenic mutants. , 1987, Science.

[74]  E. Gilles,et al.  Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors , 2002, Nature Biotechnology.

[75]  L. Kay,et al.  Observing biological dynamics at atomic resolution using NMR. , 2009, Trends in biochemical sciences.

[76]  A. Wittinghofer,et al.  Kinetic analysis by fluorescence of the interaction between Ras and the catalytic domain of the guanine nucleotide exchange factor Cdc25Mm. , 1998, Biochemistry.

[77]  E. Stites,et al.  A computational panel of pathological RAS mutants with implications for personalized medicine and genetic medicine , 2017, bioRxiv.

[78]  Nicolas André,et al.  Mathematical Modeling of Cancer Immunotherapy and Its Synergy with Radiotherapy. , 2016, Cancer research.

[79]  P. Bastiaens,et al.  Small molecule inhibition of the KRAS–PDEδ interaction impairs oncogenic KRAS signalling , 2013, Nature.

[80]  D. Warburton,et al.  mSprouty2 inhibits FGF10-activated MAP kinase by differentially binding to upstream target proteins. , 2002, American journal of physiology. Lung cellular and molecular physiology.

[81]  Boris N. Kholodenko,et al.  Signalling ballet in space and time , 2010, Nature Reviews Molecular Cell Biology.

[82]  Edward C Stites,et al.  Network Analysis of Oncogenic Ras Activation in Cancer , 2007, Science.

[83]  W. Hsu,et al.  Phosphoproteomics Identifies Oncogenic Ras Signaling Targets and Their Involvement in Lung Adenocarcinomas , 2011, PloS one.

[84]  G. Ladds,et al.  Feedback activation of neurofibromin terminates growth factor-induced Ras activation , 2016, Cell Communication and Signaling.

[85]  The developing story of Sprouty and cancer , 2014, Cancer and Metastasis Reviews.

[86]  Holger Sondermann,et al.  Structural Analysis of Autoinhibition in the Ras Activator Son of Sevenless , 2004, Cell.

[87]  Boris N Kholodenko,et al.  Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades , 2006, Molecular systems biology.

[88]  Kevan M. Shokat,et al.  K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions , 2013, Nature.

[89]  David R. Gilbert,et al.  Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway , 2009, BMC Systems Biology.

[90]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[91]  A. Nicholson,et al.  Mutations of the BRAF gene in human cancer , 2002, Nature.

[92]  Marc Vidal,et al.  COT/MAP3K8 drives resistance to RAF inhibition through MAP kinase pathway reactivation , 2010, Nature.

[93]  B. Weber,et al.  SPRY2 Is an Inhibitor of the Ras/Extracellular Signal-Regulated Kinase Pathway in Melanocytes and Melanoma Cells with Wild-Type BRAF but Not with the V599E Mutant , 2004, Cancer Research.

[94]  Yiling Lu,et al.  Identification of optimal drug combinations targeting cellular networks: integrating phospho-proteomics and computational network analysis. , 2010, Cancer research.

[95]  Mitsuhiko Ikura,et al.  Integrated RAS signaling defined by parallel NMR detection of effectors and regulators. , 2014, Nature chemical biology.

[96]  I. Verlaan,et al.  Regulating c-Ras function cholesterol depletion affects caveolin association, GTP loading, and signaling , 2001, Current Biology.

[97]  Oliver E. Sturm,et al.  Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. , 2005, The Biochemical journal.

[98]  J. Cherfils,et al.  Ras superfamily GEFs and GAPs: validated and tractable targets for cancer therapy? , 2010, Nature Reviews Cancer.

[99]  K. Guan,et al.  Desensitization of Ras Activation by a Feedback Disassociation of the SOS-Grb2 Complex (*) , 1995, The Journal of Biological Chemistry.

[100]  Edward C. Stites,et al.  Differences in sensitivity to EGFR inhibitors could be explained by described biochemical differences between oncogenic Ras mutants , 2014, bioRxiv.

[101]  Kwang-Hyun Cho,et al.  Positive- and negative-feedback regulations coordinate the dynamic behavior of the Ras-Raf-MEK-ERK signal transduction pathway , 2009, Journal of Cell Science.

[102]  P. Johnston,et al.  Cancer drug resistance: an evolving paradigm , 2013, Nature Reviews Cancer.

[103]  J. Hancock,et al.  Ras trafficking, localization and compartmentalized signalling. , 2012, Seminars in cell & developmental biology.

[104]  J. Eccleston,et al.  Fluorescence approaches to the study of the p21ras GTPase mechanism. , 1991, Biochemical Society transactions.

[105]  D. Matallanas,et al.  Distinct Utilization of Effectors and Biological Outcomes Resulting from Site-Specific Ras Activation: Ras Functions in Lipid Rafts and Golgi Complex Are Dispensable for Proliferation and Transformation , 2006, Molecular and Cellular Biology.

[106]  Robert A Gatenby,et al.  Spatial heterogeneity and evolutionary dynamics modulate time to recurrence in continuous and adaptive cancer therapies , 2017, bioRxiv.

[107]  R. Pazdur,et al.  FDA drug approval summary: gefitinib (ZD1839) (Iressa) tablets. , 2003, The oncologist.

[108]  F. McCormick,et al.  Biochemical Characterization of a Novel KRAS Insertion Mutation from a Human Leukemia* , 1996, The Journal of Biological Chemistry.

[109]  Peter K. Sorger,et al.  Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway , 2016, Science Signaling.

[110]  A. Brunet,et al.  Growth factor‐stimulated MAP kinase induces rapid retrophosphorylation and inhibition of MAP kinase kinase (MEK1) , 1994, FEBS letters.

[111]  H. Varmus,et al.  Acquired Resistance of Lung Adenocarcinomas to Gefitinib or Erlotinib Is Associated with a Second Mutation in the EGFR Kinase Domain , 2005, PLoS medicine.

[112]  A. Aplin,et al.  Mechanisms of resistance to RAF inhibitors in melanoma , 2011, The Journal of investigative dermatology.

[113]  Boris N Kholodenko,et al.  Spatially distributed cell signalling , 2009, FEBS letters.

[114]  B. Kholodenko,et al.  The dynamic control of signal transduction networks in cancer cells , 2015, Nature Reviews Cancer.

[115]  M. Mann,et al.  Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells , 2014, Nature Methods.

[116]  B. Kholodenko,et al.  Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades , 2004, The Journal of cell biology.

[117]  Jungho Kim,et al.  Kinetic mechanisms of mutation-dependent Harvey Ras activation and their relevance for the development of Costello syndrome. , 2013, Biochemistry.

[118]  Ronald J. Hause,et al.  Comprehensive Binary Interaction Mapping of SH2 Domains via Fluorescence Polarization Reveals Novel Functional Diversification of ErbB Receptors , 2012, PloS one.

[119]  P. Bastiaens,et al.  Identification of pyrazolopyridazinones as PDEδ inhibitors , 2016, Nature Communications.

[120]  E. Castellano,et al.  Functional specificity of ras isoforms: so similar but so different. , 2011, Genes & cancer.

[121]  Gavin MacBeath,et al.  Quantifying protein–protein interactions in high throughput using protein domain microarrays , 2010, Nature Protocols.

[122]  Larry Rubinstein,et al.  The National Cancer Institute ALMANAC: A Comprehensive Screening Resource for the Detection of Anticancer Drug Pairs with Enhanced Therapeutic Activity. , 2017, Cancer research.

[123]  Neville E. Sanjana,et al.  Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells , 2014, Science.

[124]  Thierry Mora,et al.  Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves , 2016, bioRxiv.

[125]  B N Kholodenko,et al.  Signal processing at the Ras circuit: what shapes Ras activation patterns? , 2004, Systems biology.

[126]  D. Esposito,et al.  Dragging ras back in the ring. , 2014, Cancer cell.

[127]  Mohammad Reza Ahmadian,et al.  The RAS-Effector Interface: Isoform-Specific Differences in the Effector Binding Regions , 2016, PloS one.

[128]  B. Druker,et al.  Specific Targeted Therapy of Chronic Myelogenous Leukemia with Imatinib , 2003, Pharmacological Reviews.

[129]  Christina Kiel,et al.  Structure‐energy‐based predictions and network modelling of RASopathy and cancer missense mutations , 2014, Molecular systems biology.

[130]  D. Fell,et al.  Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells , 2000, FEBS letters.

[131]  K. Gerwert,et al.  Ras catalyzes GTP hydrolysis by shifting negative charges from gamma- to beta-phosphate as revealed by time-resolved FTIR difference spectroscopy. , 2001, Biochemistry.

[132]  Anne-Claude Gingras,et al.  Evolution of AF6-RAS association and its implications in mixed-lineage leukemia , 2017, Nature Communications.

[133]  Bernd Bodenmiller,et al.  Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry , 2017, Nature Biotechnology.

[134]  Andre Hoelz,et al.  Structural Evidence for Feedback Activation by Ras·GTP of the Ras-Specific Nucleotide Exchange Factor SOS , 2003, Cell.

[135]  Boris N. Kholodenko,et al.  Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise , 2012, BMC Systems Biology.

[136]  R. Goody,et al.  Kinetics of interaction of nucleotides with nucleotide-free H-ras p21. , 1990, Biochemistry.

[137]  Gideon Bollag,et al.  GTPase activating proteins: critical regulators of intracellular signaling. , 2002, Biochimica et biophysica acta.

[138]  M. Mann,et al.  The coming age of complete, accurate, and ubiquitous proteomes. , 2013, Molecular cell.

[139]  P. Sorger,et al.  Systems biology and combination therapy in the quest for clinical efficacy , 2006, Nature chemical biology.

[140]  Jonathan D. Licht,et al.  Mammalian Sprouty Proteins Inhibit Cell Growth and Differentiation by Preventing Ras Activation* , 2001, The Journal of Biological Chemistry.

[141]  Ultan McDermott,et al.  Elevated CRAF as a potential mechanism of acquired resistance to BRAF inhibition in melanoma. , 2008, Cancer research.

[142]  K. Svoboda,et al.  A genetically encoded fluorescent sensor of ERK activity , 2008, Proceedings of the National Academy of Sciences.

[143]  Jay T. Groves,et al.  Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics , 2014, Science.

[144]  R. Beroukhim,et al.  The RasGAP gene, RASAL2, is a tumor and metastasis suppressor. , 2013, Cancer cell.

[145]  S. Fesik,et al.  Drugging the undruggable RAS: Mission Possible? , 2014, Nature Reviews Drug Discovery.

[146]  Jared E. Toettcher,et al.  Using Optogenetics to Interrogate the Dynamic Control of Signal Transmission by the Ras/Erk Module , 2013, Cell.

[147]  Alexander R A Anderson,et al.  Phase i trials in melanoma: A framework to translate preclinical findings to the clinic. , 2016, European journal of cancer.

[148]  Timothy A. Whitehead,et al.  Determination of binding affinity upon mutation for type I dockerin–cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing , 2016, Proteins.

[149]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[150]  C. Mattos,et al.  Allosteric modulation of Ras positions Q61 for a direct role in catalysis , 2010, Proceedings of the National Academy of Sciences.

[151]  Ruedi Aebersold,et al.  Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins. , 2014, Journal of proteome research.

[152]  O. Carugo,et al.  A Mek1–Mek2 heterodimer determines the strength and duration of the Erk signal , 2009, Nature Structural &Molecular Biology.

[153]  S. Dhanasekaran,et al.  KRAS Engages AGO2 to Enhance Cellular Transformation. , 2016, Cell reports.

[154]  B. Kholodenko,et al.  Signalling over a distance: gradient patterns and phosphorylation waves within single cells. , 2010, Biochemical Society transactions.

[155]  F. Gnad,et al.  Systems-wide Analysis of K-Ras, Cdc42, and PAK4 Signaling by Quantitative Phosphoproteomics* , 2013, Molecular & Cellular Proteomics.

[156]  G. Keating Afatinib: A Review of Its Use in the Treatment of Advanced Non-Small Cell Lung Cancer , 2014, Drugs.

[157]  K. Ravichandran,et al.  Cooperation between Noncanonical Ras Network Mutations. , 2015, Cell reports.

[158]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[159]  Yoon-Koo Kang,et al.  Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): a phase 3, open-label, randomised controlled trial , 2010, The Lancet.

[160]  R. Goody,et al.  Individual rate constants for the interaction of Ras proteins with GTPase-activating proteins determined by fluorescence spectroscopy. , 1997, Biochemistry.

[161]  Ming Zhou,et al.  Regulation of Raf-1 by direct feedback phosphorylation. , 2005, Molecular cell.

[162]  Marco Y. Hein,et al.  A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards* , 2014, Molecular & Cellular Proteomics.

[163]  G. Guy,et al.  Sprouty Proteins Are Targeted to Membrane Ruffles upon Growth Factor Receptor Tyrosine Kinase Activation , 2000, The Journal of Biological Chemistry.

[164]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[165]  Jacob J. Hughey,et al.  High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells , 2014, Cell.

[166]  Y. Yarden,et al.  Phosphorylation of Carboxyl-terminal Tyrosines Modulates the Specificity of Sprouty-2 Inhibition of Different Signaling Pathways* , 2005, Journal of Biological Chemistry.

[167]  M. Ahmadian,et al.  Duplication of Glu37 in the switch I region of HRAS impairs effector/GAP binding and underlies Costello syndrome by promoting enhanced growth factor-dependent MAPK and AKT activation. , 2010, Human molecular genetics.

[168]  John V Heymach,et al.  Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome. , 2012, Journal of the National Cancer Institute.

[169]  Pablo Rodriguez-Viciana,et al.  A phosphatase holoenzyme comprised of Shoc2/Sur8 and the catalytic subunit of PP1 functions as an M-Ras effector to modulate Raf activity. , 2006, Molecular cell.

[170]  Christopher A. Voigt,et al.  Spatiotemporal Control of Cell Signalling Using A Light-Switchable Protein Interaction , 2009, Nature.

[171]  I. Huvar,et al.  A decrease in the intracellular guanosine 5'-triphosphate concentration is necessary for granulocytic differentiation of HL-60 cells, but growth cessation and differentiation are not associated with a change in the activation state of Ras, the transforming principle of HL-60 cells. , 1997, Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research.

[172]  K. Ravichandran,et al.  Mechanistic modeling to investigate signaling by oncogenic Ras mutants , 2012, Wiley interdisciplinary reviews. Systems biology and medicine.

[173]  Mitsuhiko Ikura,et al.  NMR-based functional profiling of RASopathies and oncogenic RAS mutations , 2013, Proceedings of the National Academy of Sciences.

[174]  Karel Svoboda,et al.  The Spread of Ras Activity Triggered by Activation of a Single Dendritic Spine , 2008, Science.

[175]  M. Barbacid ras genes. , 1987, Annual review of biochemistry.

[176]  David A. Williams,et al.  Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease , 2016, American journal of hematology/oncology.

[177]  Kuen-Feng Chen,et al.  Lapatinib inhibits CIP2A/PP2A/p-Akt signaling and induces apoptosis in triple negative breast cancer cells , 2016, Oncotarget.

[178]  A. Wittinghofer,et al.  Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time , 2001, Proceedings of the National Academy of Sciences of the United States of America.