Findlay IJ, De Iuliis GN, Duchatel RJ, Jackson ER, Vitanza NA, Cain JE, Waszak SM, Dun MD. Pharmaco-proteogenomic profiling of pediatric diffuse midline glioma to inform future treatment strategies. Oncogene. 2022;41(4):461–75.

Article  CAS  Google Scholar 

Duchatel RJ, Jackson ER, Alvaro F, Nixon B, Hondermarck H, Dun MD. Signal transduction in diffuse intrinsic pontine glioma. Proteomics. 2019;19(21–22): e1800479.

Article  Google Scholar 

Staudt D, Murray HC, McLachlan T, Alvaro F, Enjeti AK, Verrills NM, Dun MD. Targeting oncogenic signaling in mutant FLT3 acute myeloid leukemia: the path to least resistance. Int J Mol Sci. 2018;19(10):3198.

Article  Google Scholar 

McLachlan T, Matthews WC, Jackson ER, Staudt D, Douglas AM, Findlay IJ, Persson ML, Duchatel RJ, Mannan A, Germon ZP, et al. B-cell lymphoma 6 (BCL6): from master regulator of humoral immunity to oncogenic driver in pediatric cancers. Mol Cancer Res. 2022;20(12):1711–23.

Article  Google Scholar 

Cicenas J, Zalyte E, Bairoch A, Gaudet P. Kinases and cancer. Cancers. 2018;10(3):63.

Article  Google Scholar 

Dun MD, Mannan A, Rigby CJ, Butler S, Toop HD, Beck D, Connerty P, Sillar J, Kahl RGS, Duchatel RJ, et al. Shwachman-Bodian-Diamond syndrome (SBDS) protein is a direct inhibitor of protein phosphatase 2A (PP2A) activity and overexpressed in acute myeloid leukaemia. Leukemia. 2020;34(12):3393–7.

Article  CAS  Google Scholar 

Smith AM, Dun MD, Lee EM, Harrison C, Kahl R, Flanagan H, Panicker N, Mashkani B, Don AS, Morris J, et al. Activation of protein phosphatase 2A in FLT3+ acute myeloid leukemia cells enhances the cytotoxicity of FLT3 tyrosine kinase inhibitors. Oncotarget. 2016;7(30):47465–78.

Article  Google Scholar 

Toop HD, Dun MD, Ross BK, Flanagan HM, Verrills NM, Morris JC. Development of novel PP2A activators for use in the treatment of acute myeloid leukaemia. Org Biomol Chem. 2016;14(20):4605–16.

Article  CAS  Google Scholar 

Cohen P, Cross D, Jänne PA. Kinase drug discovery 20 years after imatinib: progress and future directions. Nat Rev Drug Discov. 2021;20(7):551–69.

Article  CAS  Google Scholar 

Bhullar KS, Lagarón NO, McGowan EM, Parmar I, Jha A, Hubbard BP, Rupasinghe HPV. Kinase-targeted cancer therapies: progress, challenges and future directions. Mol Cancer. 2018;17(1):48.

Article  Google Scholar 

Dun MD, Chalkley RJ, Faulkner S, Keene S, Avery-Kiejda KA, Scott RJ, Falkenby LG, Cairns MJ, Larsen MR, Bradshaw RA, et al. Proteotranscriptomic profiling of 231-BR breast cancer cells: identification of potential biomarkers and therapeutic targets for brain metastasis*[S]. Mol Cell Proteom. 2015;14(9):2316–30.

Article  CAS  Google Scholar 

Degryse S, de Bock CE, Demeyer S, Govaerts I, Bornschein S, Verbeke D, Jacobs K, Binos S, Skerrett-Byrne DA, Murray HC, et al. Mutant JAK3 phosphoproteomic profiling predicts synergism between JAK3 inhibitors and MEK/BCL2 inhibitors for the treatment of T-cell acute lymphoblastic leukemia. Leukemia. 2018;32(3):788–800.

Article  CAS  Google Scholar 

Murray HC, Dun MD, Verrills NM. Harnessing the power of proteomics for identification of oncogenic, druggable signalling pathways in cancer. Expert Opin Drug Discov. 2017;12(5):431–47.

Article  CAS  Google Scholar 

Murray HC, Enjeti AK, Kahl RGS, Flanagan HM, Sillar J, Skerrett-Byrne DA, Al Mazi JG, Au GG, de Bock CE, Evans K, et al. Quantitative phosphoproteomics uncovers synergy between DNA-PK and FLT3 inhibitors in acute myeloid leukaemia. Leukemia. 2021;35(6):1782–7.

Article  CAS  Google Scholar 

Duchatel RJ, Mannan A, Jackson ER, Staudt D, Skerrett-Byrne DA, Jamaluddin MFB, Woldu AS, Douglas A, Hulleman E, Carcaboso AM, et al. DIPG-29. Phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) inhibition drives protein kinase c activation (PKC) in diffuse intrinsic pontine glioma (DIPG). NeuroOncology. 2020;22(Supplement_3):iii292–3.

Google Scholar 

Domon B, Aebersold R. Mass spectrometry and protein analysis. Science. 2006;312(5771):212–7.

Article  CAS  Google Scholar 

Ong SE, Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol. 2005;1(5):252–62.

Article  CAS  Google Scholar 

Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteom. 2002;1(5):376–86.

Article  CAS  Google Scholar 

Engholm-Keller K, Birck P, Størling J, Pociot F, Mandrup-Poulsen T, Larsen MR. TiSH—a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC. J Proteom. 2012;75(18):5749–61.

Article  CAS  Google Scholar 

Li J, Cai Z, Bomgarden RD, Pike I, Kuhn K, Rogers JC, Roberts TM, Gygi SP, Paulo JA. TMTpro-18plex: the expanded and complete set of TMTpro reagents for sample multiplexing. J Proteome Res. 2021;20(5):2964–72.

Article  CAS  Google Scholar 

Bantscheff M, Lemeer S, Savitski MM, Kuster B. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem. 2012;404(4):939–65.

Article  CAS  Google Scholar 

Li Z, Adams RM, Chourey K, Hurst GB, Hettich RL, Pan C. Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ orbitrap velos. J Proteome Res. 2012;11(3):1582–90.

Article  CAS  Google Scholar 

Čuklina J, Lee CH, Williams EG, Sajic T, Collins BC, Rodríguez Martínez M, Sharma VS, Wendt F, Goetze S, Keele GR, et al. Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial. Mol Syst Biol. 2021;17(8): e10240.

Article  Google Scholar 

Nixon B, Johnston SD, Skerrett-Byrne DA, Anderson AL, Stanger SJ, Bromfield EG, Martin JH, Hansbro PM, Dun MD. Modification of crocodile spermatozoa refutes the tenet that post-testicular sperm maturation is restricted to mammals. Mol Cell Proteom. 2019;18(Suppl 1):S58–76.

Article  Google Scholar 

Muehlbauer LK, Hebert AS, Westphall MS, Shishkova E, Coon JJ. Global phosphoproteome analysis using high-field asymmetric waveform ion mobility spectrometry on a hybrid orbitrap mass spectrometer. Anal Chem. 2020;92(24):15959–67.

Article  CAS  Google Scholar 

Hebert AS, Prasad S, Belford MW, Bailey DJ, McAlister GC, Abbatiello SE, Huguet R, Wouters ER, Dunyach J-J, Brademan DR, et al. Comprehensive single-shot proteomics with FAIMS on a hybrid orbitrap mass spectrometer. Anal Chem. 2018;90(15):9529–37.

Article  CAS  Google Scholar 

Almazi JG, Pockney P, Gedye C, Smith ND, Hondermarck H, Verrills NM, Dun MD. Cell-free DNA blood collection tubes are appropriate for clinical proteomics: a demonstration in colorectal cancer. Proteom Clin Appl. 2018;12(3): e1700121.

Article  Google Scholar 

Wiredja DD, Koyutürk M, Chance MR. The KSEA app: a web-based tool for kinase activity inference from quantitative phosphoproteomics. Bioinformatics. 2017;33(21):3489–91.

Article  CAS  Google Scholar 

Casado P, Rodriguez-Prados J-C, Cosulich SC, Guichard S, Vanhaesebroeck B, Joel S, Cutillas PR. Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. Sci Signal. 2013;6(268):rs6.

Article  Google Scholar 

Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2015;43(Database issue):D512–20.

Article  CAS  Google Scholar 

Wilhelm S, Carter C, Lynch M, Lowinger T, Dumas J, Smith RA, Schwartz B, Simantov R, Kelley S. Discovery and development of sorafenib: a multikinase inhibitor for treating cancer. Nat Rev Drug Discov. 2006;5(10):835–44.

Article  CAS  Google Scholar 

Golding SE, Rosenberg E, Valerie N, Hussaini I, Frigerio M, Cockcroft XF, Chong WY, Hummersone M, Rigoreau L, Menear KA, et al. Improved ATM kinase inhibitor KU-60019 radiosensitizes glioma cells, compromises insulin, AKT and ERK prosurvival signaling, and inhibits migration and invasion. Mol Cancer Ther. 2009;8(10):2894–902.

Article  CAS  Google Scholar 

Bliss CI. The toxicity of poisons applied jointly1. Ann Appl Biol. 1939;26(3):585–615.

Article  CAS  Google Scholar 

Heberle H, Meirelles GV, da Silva FR, Telles GP, Minghim R. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinform. 2015;16(1):169.

Article  Google Scholar 

Network CGAR. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368(22):2059–74.

Article  Google Scholar 

Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, et al. Genomic classification and prognosis in acute myeloid leukemia. N Engl J Med. 2016;374(23):2209–21.

Article  CAS  Google Scholar 

Smith CC, Lin K, Stecula A, Sali A, Shah NP. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia. 2015;29(12):2390–2.

Article  CAS  Google Scholar 

Alvarado Y, Kantarjian HM, Luthra R, Ravandi F, Borthakur G, Garcia-Manero G, Konopleva M, Estrov Z, Andreeff M, Cortes JE. Treatment with FLT3 inhibitor in patients with FLT3-mutated acute myeloid leukemia is associated with development of secondary FLT3–tyrosine kinase domain mutations. Cancer. 2014;120(14):2142–9.

Article  CAS  Google Scholar 

Keller DM, Zeng X, Wang Y, Zhang QH, Kapoor M, Shu H, Goodman R, Lozano G, Zhao Y, Lu H. A DNA damage-induced p53 serine 392 kinase complex contains CK2, hSpt16, and SSRP1. Mol Cell. 2001;7(2):283–92.

Article  CAS  Google Scholar 

Sayed M, Pelech S, Wong C, Marotta A, Salh B. Protein kinase CK2 is involved in G2 arrest and apoptosis following spindle damage in epithelial cells. Oncogene. 2001;20(48):6994–7005.

Article  CAS  Google Scholar 

Taira N, Yamamoto H, Yamaguchi T, Miki Y, Yoshida K. ATM augments nuclear stabilization of DYRK2 by inhibiting MDM2 in the apoptotic response to DNA damage. J Biol Chem. 2010;285(7):4909–19.

Article  CAS  Google Scholar 

Tian B, Yang Q, Mao Z. Phosphorylation of ATM by Cdk5 mediates DNA damage signalling and regulates neuronal death. Nat Cell Biol. 2009;11(2):211–8.