Abstract
This chapter describes how mathematical models can be used to investigate the possible range of behaviors for mutant forms of a protein. A mathematical model of the RAS signaling network that has previously been developed and applied to specific RAS mutants will be adapted for the process of computational random mutagenesis. By using this model to computationally investigate the range of RAS signaling outputs that would be anticipated over a wide range of the relevant parameter space, one can gain intuition about the types of behaviors that would be demonstrated by biological RAS mutants.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Mendiratta G, Ke E, Aziz M, Liarakos D, Tong M, Stites EC (2021) Cancer gene mutation frequencies for the U.S. population. Nat Commun 12(1):5961. https://doi.org/10.1038/s41467-021-26213-y
Moore AR, Rosenberg SC, McCormick F, Malek S (2020) RAS-targeted therapies: is the undruggable drugged? Nat Rev Drug Discov 19(8):533–552. https://doi.org/10.1038/s41573-020-0068-6
Westcott PM, Halliwill KD, To MD, Rashid M, Rust AG, Keane TM, Delrosario R, Jen KY, Gurley KE, Kemp CJ, Fredlund E, Quigley DA, Adams DJ, Balmain A (2015) The mutational landscapes of genetic and chemical models of Kras-driven lung cancer. Nature 517(7535):489–492. https://doi.org/10.1038/nature13898
Pershing NL, Lampson BL, Belsky JA, Kaltenbrun E, MacAlpine DM, Counter CM (2015) Rare codons capacitate Kras-driven de novo tumorigenesis. J Clin Invest 125(1):222–233. https://doi.org/10.1172/JCI77627
Krengel U, Schlichting I, Scherer A, Schumann R, Frech M, John J, Kabsch W, Pai EF, Wittinghofer A (1990) Three-dimensional structures of H-ras p21 mutants: molecular basis for their inability to function as signal switch molecules. Cell 62(3):539–548. https://doi.org/10.1016/0092-8674(90)90018-a
Hunter JC, Manandhar A, Carrasco MA, Gurbani D, Gondi S, Westover KD (2015) Biochemical and structural analysis of common cancer-associated KRAS mutations. Mol Cancer Res 13(9):1325–1335. https://doi.org/10.1158/1541-7786.MCR-15-0203
Gremer L, Merbitz-Zahradnik T, Dvorsky R, Cirstea IC, Kratz CP, Zenker M, Wittinghofer A, Ahmadian MR (2011) Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders. Hum Mutat 32(1):33–43. https://doi.org/10.1002/humu.21377
De Roock W, Jonker DJ, Di Nicolantonio F, Sartore-Bianchi A, Tu D, Siena S, Lamba S, Arena S, Frattini M, Piessevaux H, Van Cutsem E, O'Callaghan CJ, Khambata-Ford S, Zalcberg JR, Simes J, Karapetis CS, Bardelli A, Tejpar S (2010) Association of KRAS p.G13D mutation with outcome in patients with chemotherapy-refractory metastatic colorectal cancer treated with cetuximab. JAMA 304(16):1812–1820. https://doi.org/10.1001/jama.2010.1535
Hood FE, Klinger B, Newlaczyl AU, Sieber A, Dorel M, Oliver SP, Coulson JM, Bluthgen N, Prior IA (2019) Isoform-specific Ras signaling is growth factor dependent. Mol Biol Cell 30(9):1108–1117. https://doi.org/10.1091/mbc.E18-10-0676
Mageean CJ, Griffiths JR, Smith DL, Clague MJ, Prior IA (2015) Absolute quantification of endogenous Ras isoform abundance. PLoS One 10(11):e0142674. https://doi.org/10.1371/journal.pone.0142674
McFall T, Diedrich JK, Mengistu M, Littlechild SL, Paskvan KV, Sisk-Hackworth L, Moresco JJ, Shaw AS, Stites EC (2019) A systems mechanism for KRAS mutant allele-specific responses to targeted therapy. Sci Signal 12(600). https://doi.org/10.1126/scisignal.aaw8288
McFall T, Stites EC (2021) Identification of RAS mutant biomarkers for EGFR inhibitor sensitivity using a systems biochemical approach. Cell Rep 37(11):110096. https://doi.org/10.1016/j.celrep.2021.110096
Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J (2017) Deconstruction of the Ras switching cycle through saturation mutagenesis. elife 6. https://doi.org/10.7554/eLife.27810
Ursu O, Neal JT, Shea E, Thakore PI, Jerby-Arnon L, Nguyen L, Dionne D, Diaz C, Bauman J, Mosaad MM, Fagre C, Lo A, McSharry M, Giacomelli AO, Ly SH, Rozenblatt-Rosen O, Hahn WC, Aguirre AJ, Berger AH, Regev A, Boehm JS (2022) Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Nat Biotechnol. https://doi.org/10.1038/s41587-021-01160-7
Zafra MP, Parsons MJ, Kim J, Alonso-Curbelo D, Goswami S, Schatoff EM, Han T, Katti A, Fernandez MTC, Wilkinson JE, Piskounova E, Dow LE (2020) An in vivo Kras Allelic series reveals distinct phenotypes of common oncogenic variants. Cancer Discov 10(11):1654–1671. https://doi.org/10.1158/2159-8290.CD-20-0442
Burd CE, Liu W, Huynh MV, Waqas MA, Gillahan JE, Clark KS, Fu K, Martin BL, Jeck WR, Souroullas GP, Darr DB, Zedek DC, Miley MJ, Baguley BC, Campbell SL, Sharpless NE (2014) Mutation-specific RAS oncogenicity explains NRAS codon 61 selection in melanoma. Cancer Discov 4(12):1418–1429. https://doi.org/10.1158/2159-8290.CD-14-0729
Stites EC, Trampont PC, Ma Z, Ravichandran KS (2007) Network analysis of oncogenic Ras activation in cancer. Science 318(5849):463–467. https://doi.org/10.1126/science.1144642
Stites EC, Ravichandran KS (2012) Mathematical investigation of how oncogenic ras mutants promote ras signaling. Methods Mol Biol 880:69–85. https://doi.org/10.1007/978-1-61779-833-7_5
Stites EC (2021) Mathematical modeling to study KRAS mutant-specific responses to pathway inhibition. Methods Mol Biol 2262:311–321. https://doi.org/10.1007/978-1-0716-1190-6_19
Stites EC, Trampont PC, Haney LB, Walk SF, Ravichandran KS (2015) Cooperation between noncanonical Ras network mutations. Cell Rep 10(3):307–316. https://doi.org/10.1016/j.celrep.2014.12.035
Stites EC (2014) Differences in sensitivity to EGFR inhibitors could be explained by described biochemical differences between oncogenic Ras mutants. bioRxiv. https://doi.org/10.1101/005397
Stites EC, Shaw AS (2018) Quantitative systems pharmacology analysis of KRAS G12C covalent inhibitors. CPT Pharmacometrics Syst Pharmacol 7(5):342–351. https://doi.org/10.1002/psp4.12291
Donovan S, Shannon KM, Bollag G (2002) GTPase activating proteins: critical regulators of intracellular signaling. Biochim Biophys Acta 1602(1):23–45
Markevich NI, Moehren G, Demin OV, Kiyatkin A, Hoek JB, Kholodenko BN (2004) Signal processing at the Ras circuit: what shapes Ras activation patterns? Syst Biol (Stevenage) 1(1):104–113
Kiel C, Serrano L (2014) Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations. Mol Syst Biol 10:727. https://doi.org/10.1002/msb.20145092
Wolf J, Dronov S, Tobin F, Goryanin I (2007) The impact of the regulatory design on the response of epidermal growth factor receptor-mediated signal transduction towards oncogenic mutations. FEBS J 274(21):5505–5517. https://doi.org/10.1111/j.1742-4658.2007.06066.x
Wey M, Lee J, Jeong SS, Kim J, Heo J (2013) Kinetic mechanisms of mutation-dependent Harvey Ras activation and their relevance for the development of Costello syndrome. Biochemistry 52(47):8465–8479. https://doi.org/10.1021/bi400679q
Stites EC, Ravichandran KS (2012) Mechanistic modeling to investigate signaling by oncogenic Ras mutants. Wiley Interdiscip Rev Syst Biol Med 4(1):117–127. https://doi.org/10.1002/wsbm.156
Acknowledgments
This work was supported by NIH grant DP2 AT011327 and DoD grant W81XWH-20-10538.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Stites, E.C. (2023). Computational Random Mutagenesis to Investigate RAS Mutant Signaling. In: Nguyen, L.K. (eds) Computational Modeling of Signaling Networks. Methods in Molecular Biology, vol 2634. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3008-2_15
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3008-2_15
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3007-5
Online ISBN: 978-1-0716-3008-2
eBook Packages: Springer Protocols