Abstract
Posttranslational modification (PTM) enzymes are important modulators of protein structure and function. They typically act by chemically modifying amino acids, often on side chain functional groups, to change the physiochemical landscape of the protein and thus its biophysical behavior. In particular, protein kinases are enzymes that transfer phosphate from ATP to serine, threonine, or tyrosine in protein substrates. They are key regulators of vital cellular pathways such as survival, proliferation, and apoptosis, and their dysregulation in the context of cancer has been widely investigated for the purpose of development of anticancer drugs. However, several critical questions pertaining to their physiology, such as heterogeneity of kinase signaling within and between cells, and other factors that may play into the mechanisms of drug resistance, remain unanswered. Many of the current strategies to measure kinase activity lack the scope, subcellular resolution, and real-time monitoring ability needed to obtain the type of information needed about their dynamics and localization in cells. While FRET-based biosensors are capable of dynamic single cell imaging, their applications can be limited by difficulties in multiplexing and the inherent inadequacies of steady state measurements. In this chapter, we describe our fluorescence lifetime imaging microscopy (FLIM) probe technology in which peptide kinase substrates, linked to cell-penetrating peptides and labeled with small molecule fluorophores, are used to report kinase activity through time-resolved fluorescence imaging to visualize and quantify changes to the probe’s fluorescence lifetime. These can be multiplexed for more than one kinase at a time, and interpretation is not affected by differences in local intensity due to probe uptake and distribution or photobleaching. With careful choice of peptide substrate(s), fluorophore label, and imaging set-up, high specificity and spatiotemporal resolution can be achieved. Due to the mechanism by which the lifetime change occurs, this approach is compatible with other PTMs (such as acetylation, methylation), and so the considerations for kinase FLIM probe design described in this chapter should be broadly applicable for other PTMs as well.
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References
Bartram CR, Kleihauer E, de Klein A, Grosveld G, Teyssier JR, Heisterkamp N, Groffen J (1985) C-abl and bcr are rearranged in a Ph1-negative CML patient. EMBO J 4(3):683–686
Hernández SE, Krishnaswami M, Miller AL, Koleske AJ (2004) How do Abl family kinases regulate cell shape and movement? Trends Cell Biol 14(1):36–44
Roskoski R Jr (2019) Properties of FDA-approved small molecule protein kinase inhibitors: a 2020 update. Pharmacol Res 152:104609. https://doi.org/10.1016/j.phrs.2019.104609
Gross S, Rahal R, Stransky N, Lengauer C, Hoeflich KP (2015) Targeting cancer with kinase inhibitors. J Clin Invest 125(5):1780–1789. https://doi.org/10.1172/JCI76094
Levitzki A, Klein S (2019) My journey from tyrosine phosphorylation inhibitors to targeted immune therapy as strategies to combat cancer. Proc Natl Acad Sci U S A 116(24):11579–11586. https://doi.org/10.1073/pnas.1816012116
Klein S, Levitzki A (2007) Targeted cancer therapy: promise and reality. Adv Cancer Res 97:295–319. https://doi.org/10.1016/S0065-230X(06)97013-4
Kruk M, Widstrom N, Jena S, Wolter NL, Blankenhorn JF, Abdalla I, Yang T-Y, Parker LL (2019) Assays for tyrosine phosphorylation in human cells. Methods Enzymol 626:375–406
Chen C, Turk BE Analysis of serine-threonine kinase specificity using arrayed positional scanning peptide libraries. Curr Protoc Mol Biol. Chapter 18:Unit 18 4
Miller ML, Jensen LJ, Diella F, Jorgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R (2008) Linear motif atlas for phosphorylation-dependent signaling. Sci Signal 1(35):ra2. https://doi.org/10.1126/scisignal.1159433
Deng Y, Alicea-Velazquez NL, Bannwarth L, Lehtonen SI, Boggon TJ, Cheng HC, Hytonen VP, Turk BE (2014) Global analysis of human nonreceptor tyrosine kinase specificity using high-density Peptide microarrays. J Proteome Res 13(10):4339–4346. https://doi.org/10.1021/pr500503q
Songyang Z, Blechner S, Hoagland N, Hoekstra MF, Piwnica-Worms H, Cantley LC (1994) Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr Biol 4(11):973–982
Kettenbach AN, Wang T, Faherty BK, Madden DR, Knapp S, Bailey-Kellogg C, Gerber SA (2012) Rapid determination of multiple linear kinase substrate motifs by mass spectrometry. Chem Biol 19(5):608–618. https://doi.org/10.1016/j.chembiol.2012.04.011
Perez M, Blankenhorn J, Murray KJ, Parker LL (2019) High-throughput Identification of FLT3 wild-type and mutant kinase substrate preferences and application to design of sensitive in vitro kinase assay substrates. Mol Cell Proteomics 18(3):477–489. https://doi.org/10.1074/mcp.RA118.001111
Ross BL, Tenner B, Markwardt ML, Zviman A, Shi G, Kerr JP, Snell NE, McFarland JJ, Mauban JR, Ward CW, Rizzo MA, Zhang J (2018) Single-color, ratiometric biosensors for detecting signaling activities in live cells. eLife 7. https://doi.org/10.7554/eLife.35458
Lin W, Mehta S, Zhang J (2019) Genetically encoded fluorescent biosensors illuminate kinase signaling in cancer. J Biol Chem 294(40):14814–14822. https://doi.org/10.1074/jbc.REV119.006177
Greenwald EC, Mehta S, Zhang J (2018) Genetically encoded fluorescent biosensors illuminate the spatiotemporal regulation of signaling networks. Chem Rev 118(24):11707–11794. https://doi.org/10.1021/acs.chemrev.8b00333
González-Vera JA, Morris MC (2015) Fluorescent reporters and biosensors for probing the dynamic behavior of protein kinases. Proteomes 3(4):369–410
Damayanti NP, Parker LL, Irudayaraj JM (2013) Fluorescence lifetime imaging of biosensor peptide phosphorylation in single live cells. Angew Chem Int Ed Engl 52(14):3931–3934. https://doi.org/10.1002/anie.201209303
Damayanti NP, Jena S, Irudayaraj J, Parker LL. Multiplexable fluorescence lifetime imaging (FLIM) probes for Syk and Src-family kinases. bioRxiv [Internet]. 2019
Ravasco JM, Faustino H, Trindade A, Gois PM (2019) Bioconjugation with Maleimides: a useful tool for chemical biology. Chem Eur J 25(1):43–59
Fontaine SD, Reid R, Robinson L, Ashley GW, Santi DV (2014) Long-term stabilization of maleimide–thiol conjugates. Bioconjug Chem 26(1):145–152
Christie RJ, Fleming R, Bezabeh B, Woods R, Mao S, Harper J, Joseph A, Wang Q, Xu Z-Q, Wu H (2015) Stabilization of cysteine-linked antibody drug conjugates with N-aryl maleimides. J Control Release 220:660–670
Maawy AA, Hiroshima Y, Kaushal S, Luiken GA, Hoffman RM, Bouvet M (2013) Comparison of a chimeric anti-carcinoembryonic antigen antibody conjugated with visible or near-infrared fluorescent dyes for imaging pancreatic cancer in orthotopic nude mouse models. J Biomed Opt 18(12):126016
O'Connor D (2012) Time-correlated single photon counting. Academic Press, Cambridge, Massachusetts
Won Y, Moon S, Yang W, Kim D, Han W-T, Kim DY (2011) High-speed confocal fluorescence lifetime imaging microscopy (FLIM) with the analog mean delay (AMD) method. Opt Express 19(4):3396–3405
Kim DY, Hwang W, Kim DE, Won Y, Moon S, Lee SY, Kang MG, Han WS (2019) Analog mean-delay method: a new time-domain super-resolution technique for accurate fluorescence lifetime measurement. Single Molecule Spectroscopy and Superresolution Imaging XII. International Society for Optics and Photonics, Bellingham, Washington
Lakowicz JR (1999) Frequency-domain lifetime measurements. In: Principles of fluorescence spectroscopy. Springer, New York, pp 141–184
Wahl M (2014) Time-correlated single photon counting. Technical Note, pp 1–14, PicoQuant Website, URL: https://www.picoquant.com/images/uploads/page/files/7253/technote_tcspc.pdf
Croessmann S, Sheehan JH, Lee K-M, Sliwoski G, He J, Nagy R, Riddle D, Mayer IA, Balko JM, Lanman R (2018) PIK3CA C2 domain deletions hyperactivate phosphoinositide 3-kinase (PI3K), generate oncogene dependence, and are exquisitely sensitive to PI3Kα inhibitors. Clin Cancer Res 24(6):1426–1435
Smith I, Greenside PG, Natoli T, Lahr DL, Wadden D, Tirosh I, Narayan R, Root DE, Golub TR, Subramanian A (2017) Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the connectivity map. PLoS Biol 15(11):e2003213
Graf BW, Boppart SA (2010) Imaging and analysis of three-dimensional cell culture models. In: Live cell imaging. Springer, New York, pp 211–227
Lindgren M, Hällbrink M, Prochiantz A, Langel Ü (2000) Cell-penetrating peptides. Trends Pharmacol Sci 21(3):99–103
Ossum CG, Wulff T, Hoffmann EK (2006) Regulation of the mitogen-activated protein kinase p44 ERK activity during anoxia/recovery in rainbow trout hypodermal fibroblasts. J Exp Biol 209(9):1765–1776
Hubbard SR, Miller WT (2007) Receptor tyrosine kinases: mechanisms of activation and signaling. Curr Opin Cell Biol 19(2):117–123
Gocek E, Moulas AN, Studzinski GP (2014) Non-receptor protein tyrosine kinases signaling pathways in normal and cancer cells. Crit Rev Clin Lab Sci 51(3):125–137
Keshvara LM, Isaacson C, Harrison ML, Geahlen RL (1997) Syk activation and dissociation from the B-cell antigen receptor is mediated by phosphorylation of tyrosine 130. J Biol Chem 272(16):10377–10381
Gerritsen H, Asselbergs M, Agronskaia A, Van Sark W (2002) Fluorescence lifetime imaging in scanning microscopes: acquisition speed, photon economy and lifetime resolution. J Microsc 206(3):218–224
Kim D, Hwang W, Won Y, Moon S, Kim DY (2018) Enhancement of measurement speed and photon economy in multiphoton detected fluorescence lifetime imaging microscopy. In: Multiphoton Microscopy in the Biomedical Sciences XVIII. International Society for Optics and Photonics, Bellingham, Washington
Schneckenburger H, Wagner M, Weber P, Strauss WS, Sailer R (2004) Autofluorescence lifetime imaging of cultivated cells using a UV picosecond laser diode. J Fluoresc 14(5):649–654
Chacko JV, Eliceiri KW (2019) Autofluorescence lifetime imaging of cellular metabolism: sensitivity toward cell density, pH, intracellular, and intercellular heterogeneity. Cytometry A 95(1):56–69
Zheng Q, Jockusch S, Zhou Z, Blanchard SC (2014) The contribution of reactive oxygen species to the photobleaching of organic fluorophores. Photochem Photobiol 90(2):448–454
Bogdanov AM, Kudryavtseva EI, Lukyanov KA (2012) Anti-fading media for live cell GFP imaging. PLoS One 7(12):e53004
Keshava N, Mustard JF (2002) Spectral unmixing. IEEE Signal Process Mag 19(1):44–57
Gómez CA, Sutin J, Wu W, Fu B, Uhlirova H, Devor A, Boas DA, Sakadžić S, Yaseen MA (2018) Phasor analysis of NADH FLIM identifies pharmacological disruptions to mitochondrial metabolic processes in the rodent cerebral cortex. PLoS One 13(3):e0194578
Lakner P, Möller Y, Olayioye M, Brucker S, Schenke-Layland K, Monaghan M (2016) A phasor approach analysis of multiphoton FLIM measurements of three-dimensional cell culture models. In: Multiphoton Microscopy in the Biomedical Sciences XVI. International Society for Optics and Photonics, Bellingham, Washington
Eichorst JP, Teng KW, Clegg RM (2014) Polar plot representation of time-resolved fluorescence. In: Fluorescence Spectroscopy and Microscopy. Springer, New York, pp 97–112
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Jena, S., Parker, L.L. (2022). Fluorescence Lifetime Imaging Probes for Cell-Based Measurements of Enzyme Activity. In: Rasooly, A., Baker, H., Ossandon, M.R. (eds) Biomedical Engineering Technologies. Methods in Molecular Biology, vol 2394. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1811-0_9
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