Abstract
Proteases in apoptosis have evolved as major drug targets in the past few decades. Development in this direction has been brought about by efficient design and refinement of the various platforms of protease assays. These can be broadly categorized into general assays, that characterize kinetics and biochemistry of apoptotic proteases, and the more specific assays devoted to discern proteases involved in apoptosis. Together, these two approaches comprise a flawless two-pronged approach to understand the role of proteases in apoptosis and their therapeutic applications. This chapter lays down a comprehensive account of different experimental procedures spanning the use of in vitro purified proteases to those that monitor enzyme activity and its apoptotic effect in fixed or live cells. In this regard, fluorescence based platforms are the workhorse of fast, accurate, easy-to-use and high throughput screening amenable procedures. Therefore, they form the majority of techniques, among others, covered in this chapter. Apart from the popular methods currently in use, this chapter also provides a bird’s eye view of the future of the protease assays with special mention of protease activatable prodrugs and protease engineering.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Bond JS, Butler PE (1987) Intracellular proteases. Annu Rev Biochem 56:333–364
Dixon M, Webb E (1979) Enzymes. Academic Press, New York
Thompson CB (1995) Apoptosis in the pathogenesis and treatment of disease. Science 267:1456–1462
Turk B (2006) Targeting proteases: successes, failures and future prospects. Nat Rev Drug Discov 5:785–799
Elmore S (2007) Apoptosis: A review of programmed cell death. Toxicol Pathol 35:495–516
Favaloro B, Allocati N, Graziano V, Di Ilio C, De Laurenzi V (2012) Role of apoptosis in disease. Aging (Albany NY) 4:330–349
Mattson MP (2000) Apoptosis in neurodegenarative disorders. Nat Rev 1:120–129
Wyllie AH (1997) Apoptosis and carcinogenesis. Eur J Cell Biol 73:189–197
Eguchi K (2001) Apoptosis in autoimmune diseases. Intern Med 40:275–284
Hayashi T, Faustman DL (2003) Role of defective apoptosis in type 1 diabetes and other autoimmune diseases. Recent Prog Horm Res 58:131–153
Ameisen JC, Capron A (1991) Cell dysfunction and depletion in AIDS: the programmed cell death hypothesis. Immunol Today 12:102–105
Lockshin RA, Zakeri Z (2001) Programmed cell death and apoptosis: origins of the theory. Nat Rev Mol Cell Biol 2:545–550
Alberts B, Johnson A, Lewis J et al (2002) Molecular biology of the cell, 4th edn. Garland Science, New York
Kaufmann SH, Mesner PW Jr, Samejima K, Tone S, Earnshaw WC (2000) Detection of DNA cleavage in apoptotic cells. Methods Enzymol 322:3–15
Steller H (1995) Mechanisms and genes of cellular suicide. Science 267:1445–1449
Kaufmann SH, Desnoyers S, Ottaviano Y, Davidson NE, Poirier GG (1993) Specific proteolytic cleavage of poly(ADP-ribose) polymerase: an early marker of chemotherapy-induced apoptosis. Cancer Res 53:3976–3985
Casciola-Rosen LA, Miller DK, Anhalt GJ, Rosen A (1994) Specific cleavage of the 70-kDa protein component of the U1 small nuclear ribonucleoprotein is a characteristic biochemical feature of apoptotic cell death. J Biol Chem 269:30757–30760
Hebert L, Pandey S, Wang E (1994) Commitment to cell death is signaled by the appearance of a terminin protein of 30 kDa. Exp Cell Res 210:10–18
Oberhammer FA, Hochegger K, Froschl G, Tiefenbacher R, Pavelka M (1994) Chromatin condensation during apoptosis is accompanied by degradation of lamin A+B, without enhanced activation of cdc2 kinase. J Cell Biol 126:827–837
Martin S, O’Brien CA, Nishioka W et al (1995) Proteolysis of fodrin (non-erythroid spectrin) during apoptosis. J Biol Chem 270:6425–6428
Bruno S, Del Bino G, Lassota P, Giaretti W, Darzynkiewicz Z (1992) Inhibitors of proteases prevent endonucleolysis accompanying apoptotic death of HL-60 leukemic cells and normal thymocytes. Leukemia 6:1113–1120
Sarin A, Adams DH, Henkart PA (1993) Protease inhibitors selectively block T cell receptor-triggered programmed cell death in a murine T cell hybridoma and activated peripheral T cells. J Exp Med 178:1693–1700
Ray CA, Black RA, Kronheim SR, Greenstreet TA, Sleath PR, Salvesen GS, Pickup DJ (1992) Viral inhibition of inflammation: cowpox virus encodes an inhibitor of the interleukin-1 beta converting enzyme. Cell 69:597–604
Komiyama T, Ray CA, Pickup DJ, Howard AD, Thornberry NA, Peterson EP, Salvesen G (1994) Inhibition of interleukin-1 beta converting enzyme by the cowpox virus serpin CrmA. An example of cross-class inhibition. J Biol Chem 269:19331–19337
Kuida K, Lippke JA, Ku G, Harding MW, Livingston DJ, Su MS, Flavell RA (1995) Altered cytokine export and apoptosis in mice deficient in interleukin-1 beta converting enzyme. Science 267:2000–2003
Izzo JL Jr, Weir MR (2011) Angiotensin-converting enzyme inhibitors. J Clin Hypertens (Greenwich) 13:667–675
Thompson MA, Aberg JA, Hoy JF, Telenti A, Benson C, Cahn P, Eron JJ, Gunthard HF, Hammer SM, Reiss P, Richman DD, Rizzardini G, Thomas DL, Jacobsen DM, Volberding PA (2012) Antiretroviral treatment of adult HIV infection: 2012 recommendations of the International Antiviral Society-USA panel. JAMA 308:387–402
Nachman S, Zheng N, Acosta EP, Teppler H, Homony B, Graham B, Fenton T, Xu X, Wenning L, Spector SA, Frenkel LM, Alvero C, Worrell C, Handelsman E, Wiznia A (2014) Pharmacokinetics, safety, and 48-week efficacy of oral raltegravir in HIV-1-infected children aged 2 through 18 years. Clin Infect Dis 58:413–422
He Y, King MS, Kempf DJ, Lu L, Lim HB, Krishnan P, Kati W, Middleton T, Molla A (2008) Relative replication capacity and selective advantage profiles of protease inhibitor-resistant hepatitis C virus (HCV) NS3 protease mutants in the HCV genotype 1b replicon system. Antimicrob Agents Chemother 52:1101–1110
Kawada T, Okada Y, Hoson M, Endo S, Yokoyama M, Kitanaka Y, Kimura K, Abe H, Yamate N (1999) Argatroban, an attractive anticoagulant, for left heart bypass with centrifugal pump for repair of traumatic aortic rupture. Jpn J Thorac Cardiovasc Surg 47:104–109
Matsuo T, Kario K, Matsuda S, Yamaguchi N, Kakishita E (1995) Effect of thrombin inhibition on patients with peripheral arterial obstructive disease: A multicenter clinical trial of argatroban. J Thromb Thrombolysis 2:131–136
Herman GA, Stevens C, Van Dyck K, Bergman A, Yi B, De Smet M, Snyder K, Hilliard D, Tanen M, Tanaka W, Wang AQ, Zeng W, Musson D, Winchell G, Davies MJ, Ramael S, Gottesdiener KM, Wagner JA (2005) Pharmacokinetics and pharmacodynamics of sitagliptin, an inhibitor of dipeptidyl peptidase IV, in healthy subjects: results from two randomized, double-blind, placebo-controlled studies with single oral doses. Clin Pharmacol Ther 78:675–688
Karasik A, Aschner P, Katzeff H, Davies MJ, Stein PP (2008) Sitagliptin, a DPP-4 inhibitor for the treatment of patients with type 2 diabetes: a review of recent clinical trials. Curr Med Res Opin 24:489–496
Wadhawan M, Singh N, Rathaur S (2014) Inhibition of cathepsin B by E-64 induces oxidative stress and apoptosis in filarial parasite. PLoS One 9, e93161
Saeki Y, Fukunaga K, Tanaka K (2010) Proteasome inhibitors. Nihon Rinsho 68:1818–1822
Marchi E, Paoluzzi L, Scotto L, Seshan VE, Zain JM, Zinzani PL, O'Connor OA (2010) Pralatrexate is synergistic with the proteasome inhibitor bortezomib in in vitro and in vivo models of T-cell lymphoid malignancies. Clin Cancer Res 16:3648–3658
von Schwarzenberg K, Held SA, Schaub A, Brauer KM, Bringmann A, Brossart P (2009) Proteasome inhibition overcomes the resistance of renal cell carcinoma cells against the PPARgamma ligand troglitazone. Cell Mol Life Sci 66:1295–1308
Carreno FLG (1992) Protease inhibition in theory and practice. Biotechnol Educ 3:145–150
Sharma R (2012) Enzyme inhibition: mechanisms and scope, enzyme inhibition and bioapplications. In: Sharma R (ed) InTech, pp 1–35. ISBN: 978-953-51-0585-5. doi:10.5772/39273. Available from: http://www.intechopen.com/books/enzyme-inhibition-and-bioapplications/enzyme-inhibition-mechanisms-and-scope
Berg JM, Tymoczko J, Stryer L (2002) Biochemistry, 5th edn. W H Freeman, New York
Cleland WW (1967) Enzyme kinetics. Annu Rev Biochem 36:77–112
Briggs G, Haldane J (1925) A note on the kinetics of enzyme action. Biochem J 19:338–339
Rogers A, Gibon Y (2009) Chapter 4: Enzyme kinetics: theory & practice. In: Schwender J (ed) Plant metabolic networks. Springer, Berlin/Heidelberg/New York, pp 71–103. ISBN 978-0-38-778744-2
Gubler H, Schopfer U, Jacoby E (2013) Theoretical and experimental relationships between percent inhibition and IC50 data observed in high-throughput screening. J Biomol Screen 18:1–13
Krishna PN (2011) Enzyme technology : pacemaker of biotechnology. PHI Learning Pvt. Ltd., New Delhi
Shen P, Larter R (1994) Role of substrate inhibition kinetics in enzymatic chemical oscillations. Biophys J 67:1414–1428
Holt A (1999) On the measurement of enzymes and their inhibitors. In: Cell neurobiology techniques. Humana Press, Totowa, pp 131–194
Waley SG (1993) The kinetics of slow-binding and slow, tight-binding inhibition: the effects of substrate depletion. Biochem J 294(Pt 1):195–200
Brooks HB, Geeganage S, Kahl SD et al (2012) Basics of enzymatic assays for HTS. In: Sittampalam GS, C N, Nelson H et al (ed). Eli Lilly & Company/National Center for Advancing Translational Sciences, Bethesda
Kraut J (1977) Serine proteases: structure and mechanism of catalysis. Annu Rev Biochem 46:331–358
Baruch A, Jeffery DA, Bogyo M (2004) Enzyme activity–it’s all about image. Trends Cell Biol 14:29–35
Funovics M, Weissleder R, Tung CH (2003) Protease sensors for bioimaging. Anal Bioanal Chem 377:956–963
Lakowicz JR (1983) Principles of fluorescence spectroscopy. Springer Science+Business Media, New York
Royer CA, Scarlata SF (2008) Fluorescence approaches to quantifying biomolecular interactions. Methods Enzymol 450:79–106
Burns B, Mendz G, Hazell S (1998) Methods for the measurement of a bacterial enzyme activity in cell lysates and extracts. Biol Proced Online 1:17–26
Shaner NC, Steinbach PA, Tsien RY (2005) A guide to choosing fluorescent proteins. Nat Method 2:905–909
Combs CA (2010) Fluorescence microscopy: a concise guide to current imaging methods. Curr Protoc Neurosci, Chapter 2, Unit 2 1
Delgadillo RF, Parkhurst LJ (2010) Spectroscopic properties of fluorescein and rhodamine dyes attached to DNA. Photochem Photobiol 86:261–272
Sjoback R, Nygren J, Kubista M (1995) Absorption and fluorescence properties of fluorescein. Spectrochim Acta A Mol Biomol Spectrosc 51:L7–L21
Batchelor RH, Zhou M (2002 Jun 1) A resorufin-based fluorescent assay for quantifying NADH. Anal Biochem 305(1):118–9
Benson JR, Hare PE (1975) O-phthalaldehyde: fluorogenic detection of primary amines in the picomole range. Comparison with fluorescamine and ninhydrin. Proc Natl Acad Sci U S A 72:619–622
Kiernan JA (2007) Indigogenic substrates for detection and localization of enzymes. Biotechnic Histochem 82:73–103
Grant SK, Sklar JG, Cummings RT (2002) Development of novel assays for proteolytic enzymes using rhodamine-based fluorogenic substrates. J Biomol Screen 7:531–540
Cilenti L, Lee Y, Hess S, Srinivasula S, Park KM, Junqueira D, Davis H, Bonventre JV, Alnemri ES, Zervos AS (2003) Characterization of a novel and specific inhibitor for the pro-apoptotic protease Omi/HtrA2. J Biol Chem 278:11489–11494
Sittampalam GS (2012) Assay guidance manual [Internet]. In: GS Sittampalam, C N, Nelson H et al (ed) Protease assays. Eli Lilly & Company/National Center for Advancing Translational Sciences, Bethesda
Farmer WH, Yuan ZY (1991) A continuous fluorescent assay for measuring protease activity using natural protein substrate. Anal Biochem 197:347–352
Wickstrom C, Herzberg MC, Beighton D, Svensater G (2009) Proteolytic degradation of human salivary MUC5B by dental biofilms. Microbiology 155:2866–2872
Chaganti LK, Kuppili RR, Bose K (2013) Intricate structural coordination and domain plasticity regulate activity of serine protease HtrA2. FASEB J 27:3054–3066
Shi J, Dertouzos J, Gafni A, Steel D (2008) Application of single-molecule spectroscopy in studying enzyme kinetics and mechanism. Methods Enzymol 450:129–157
Selvin PR (2000) The renaissance of fluorescence resonance energy transfer. Nat Struct Biol 7:730–734
Wu P, Brand L (1994) Resonance energy transfer: methods and applications. Anal Biochem 218:1–13
Packard BZ, Komoriya A (2008) A method in enzymology for measuring hydrolytic activities in live cell environments. Methods Enzymol 450:1–19
Jares-Erijman EA, Jovin TM (2003) FRET imaging. Nat Biotechnol 21:1387–1395
Packard BZ, Komoriya A (2008) Chapter 1: A method in enzymology for measuring hydrolytic activities in live cell environments. In: Ludwig B, Michael LJ (ed) Methods in enzymology. Academic Press, New York, pp 1–19
Berney C, Danuser G (2003) FRET or no FRET: a quantitative comparison. Biophys J 84:3992–4010
Didenko VV (2001) DNA probes using fluorescence resonance energy transfer (FRET): designs and applications. Biotechniques 31:1106–1116, 1118, 1120–1101
Sapsford KE, Berti L, Medintz IL (2006) Materials for fluorescence resonance energy transfer analysis: beyond traditional donorБ─⌠acceptor combinations. Angew Chem Int Ed 45:4562–4589
Piston DW, Kremers GJ (2007) Fluorescent protein FRET: the good, the bad and the ugly. Trends Biochem Sci 32:407–414
Szollosi J, Damjanovich S, Matyus L (1998) Application of fluorescence resonance energy transfer in the clinical laboratory: routine and research. Cytometry 34:159–179
Tian H, Ip L, Luo H, Chang DC, Luo KQ (2007) A high throughput drug screen based on fluorescence resonance energy transfer (FRET) for anticancer activity of compounds from herbal medicine. Br J Pharmacol 150:321–334
Stryer L (1978) Fluorescence energy transfer as a spectroscopic ruler. Annu Rev Biochem 47:819–846
Stojanovic MN, de Prada P, Landry DW (2000) Homogeneous assays based on deoxyribozyme catalysis. Nucleic Acids Res 28:2915–2918
van der Krogt GNM, Ogink J, Ponsioen B, Jalink K (2008) A comparison of donor-acceptor pairs for genetically encoded FRET sensors: application to the epac cAMP sensor as an example. PLoS One 3, e1916
Woehler A, Wlodarczyk J, Neher E (2010) Signal/noise analysis of FRET-based sensors. Biophys J 99:2344–2354
Okamura Y, Kondo S, Sase I, Suga T, Mise K, Furusawa I, Kawakami S, Watanabe Y (2000) Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization. Nucleic Acids Res 28, E107
Le Reste L, Hohlbein J, Gryte K, Kapanidis AN (2012) Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET. Biophys J 102:2658–2668
Tatham MH, Hay RT (2009) FRET-based in vitro assays for the analysis of SUMO protease activities. Methods Mol Biol 497:253–268
Cummings RT, Salowe SP, Cunningham BR, Wiltsie J, Park YW, Sonatore LM, Wisniewski D, Douglas CM, Hermes JD, Scolnick EM (2002) A peptide-based fluorescence resonance energy transfer assay for Bacillus anthracis lethal factor protease. Proc Natl Acad Sci U S A 99:6603–6606
Lea WA, Simeonov A (2011) Fluorescence polarization assays in small molecule screening. Expert Opin Drug Discov 6:17–32
Inglese J, Shamu CE, Guy RK (2007) Reporting data from high-throughput screening of small-molecule libraries. Nat Chem Biol 3:438–441
Owicki JC (2000) Fluorescence polarization and anisotropy in high throughput screening: perspectives and primer. J Biomol Screen 5:297–306
Pu Y, Wang W, Dorshow RB, Das BB, Alfano RR (2013) Review of ultrafast fluorescence polarization spectroscopy [Invited]. Appl Opt 52:917–929
Jameson DM, Croney JC (2003) Fluorescence polarization: past, present and future. Comb Chem High Throughput Screen 6:167–176
Halfman CJ, Schneider AS (1982) Direct measurement of fluorescence polarization or anisotropy. Anal Chem 54:2009–2011
Popelka SR, Miller DM, Holen JT, Kelso DM (1981) Fluorescence polarization immunoassay. II. Analyzer for rapid, precise measurement of fluorescence polarization with use of disposable cuvettes. Clin Chem 27:1198–1201
Brinkley M (1992) A brief survey of methods for preparing protein conjugates with dyes, haptens, and cross-linking reagents. Bioconjug Chem 3:2–13
Wessendorf MW, Brelje TC (1992) Which fluorophore is brightest? A comparison of the staining obtained using fluorescein, tetramethylrhodamine, lissamine rhodamine, Texas red, and cyanine 3.18. Histochemistry 98:81–85
Wood EJ (1994) Molecular probes: handbook of fluorescent probes and research chemicals: by R P Haugland, pp 390. Interchim (Molecular Probes Inc, PO Box 22010 Eugene, OR 97402–0414, USA, or 15 rue des Champs, 92600 Asnieres, Paris). 1992–1994. $15. Biochem Educ 22:83–83
Nasir MS, Jolley ME (1999) Fluorescence polarization: an analytical tool for immunoassay and drug discovery. Comb Chem High Throughput Screen 2:177–190
Levine LM, Michener ML, Toth MV, Holwerda BC (1997) Measurement of specific protease activity utilizing fluorescence polarization. Anal Biochem 247:83–88
Roehrl MH, Wang JY, Wagner G (2004) A general framework for development and data analysis of competitive high-throughput screens for small-molecule inhibitors of protein-protein interactions by fluorescence polarization. Biochemistry 43:16056–16066
Schade SZ, Jolley ME, Sarauer BJ, Simonson LG (1996) BODIPY-alpha-casein, a pH-independent protein substrate for protease assays using fluorescence polarization. Anal Biochem 243:1–7
Patel T, Gores GJ, Kaufmann SH (1996) The role of proteases during apoptosis. FASEB J 10:587–597
Williams M, Henkart P (1994) Apoptotic cell death induced by intracellular proteolysis. J Irnmunol 153:4247–4255
Fernandes-Alnemri T, Litwack G, Alnemri ES (1995) Mch2, a new member of the apoptotic Ced-3/Ice cysteine protease gene family. Cancer Res 55:2737–2742
Fesus L, Davies PJ, Piacentini M (1991) Apoptosis: molecular mechanisms in programmed cell death. Eur J Cell Biol 56:170–177
Kim TK, Eberwine JH (2010) Mammalian cell transfection: the present and the future. Anal Bioanal Chem 397:3173–3178
Jiang JK, Ma X, Wu QY, Qian WB, Wang N, Shi SS, Han JL, Zhao JY, Jiang SY, Wan CH (2014) Upregulation of mitochondrial protease HtrA2/Omi contributes to manganese-induced neuronal apoptosis in rat brain striatum. Neuroscience 268:169–179
Saraste A, Pulkki K (2000) Morphologic and biochemical hallmarks of apoptosis. Cardiovasc Res 45:528–537
Michalet X, Kapanidis AN, Laurence T, Pinaud F, Doose S, Pflughoefft M, Weiss S (2003) The power and prospects of fluorescence microscopies and spectroscopies. Annu Rev Biophys Biomol Struct 32:161–182
Telford WG, King LE, Fraker PJ (1992) Comparative evaluation of several DNA binding dyes in the detection of apoptosis-associated chromatin degradation by flow cytometry. Cytometry 13:137–143
Whitaker JE, Haugland RP, Moore PL, Hewitt PC, Reese M (1991) Cascade blue derivatives: water soluble, reactive, blue emission dyes evaluated as fluorescent labels and tracers. Anal Biochem 198:119–130
Andree HA, Reutelingsperger CP, Hauptmann R, Hemker HC, Hermens WT, Willems GM (1990) Binding of vascular anticoagulant alpha (VAC alpha) to planar phospholipid bilayers. J Biol Chem 265:4923–4928
Fadok VA, Voelker DR, Campbell PA, Cohen JJ, Bratton DL, Henson PM (1992) Exposure of phosphatidylserine on the surface of apoptotic lymphocytes triggers specific recognition and removal by macrophages. J Immunol 148:2207–2216
Koopman G, Reutelingsperger CP, Kuijten GA, Keehnen RM, Pals ST, van Oers MH (1994) Annexin V for flow cytometric detection of phosphatidylserine expression on B cells undergoing apoptosis. Blood 84:1415–1420
Riccardi C, Nicoletti I (2006) Analysis of apoptosis by propidium iodide staining and flow cytometry. Nat Protoc 1:1458–1461
Rieger AM, Nelson KL, Konowalchuk JD, Barreda DR (2011) Modified annexin V/propidium iodide apoptosis assay for accurate assessment of cell death. J Vis Exp (50). pii: 2597. doi:10.3791/2597
Shapiro HM (2005) Practical flow cytometry. Wiley, New York
Hingorani R, Deng J, Elia J, McIntyre C, Mittar D (2011) Detection of apoptosis using the BD annexin V FITC assay on the BD FACSVerse™ system. BD Biosciences, San Jose, pp 1–12
Gavrieli Y, Sherman Y, Ben-Sasson SA (1992) Identification of programmed cell death in situ via specific labeling of nuclear DNA fragmentation. J Cell Biol 119:493–501
Ben-Sasson SA, Sherman Y, Gavrieli Y (1995) Identification of dying cells–in situ staining. Methods Cell Biol 46:29–39
Darzynkiewicz Z (1994) Flow cytometry. Methods Cell Biol 41:27–442
Li X, Traganos F, Melamed MR, Darzynkiewicz Z (1995) Single-step procedure for labeling DNA strand breaks with fluorescein- or BODIPY-conjugated deoxynucleotides: detection of apoptosis and bromodeoxyuridine incorporation. Cytometry 20:172–180
Loo DT (2002) TUNEL assay. An overview of techniques. Methods Mol Biol 203:21–30
Walker PR, Carson C, Leblanc J, Sikorska M (2002) Labeling DNA damage with terminal transferase. Applicability, specificity, and limitations. Methods Mol Biol 203:3–19
Suman S, Pandey A, Chandna S (2012) An improved non-enzymatic “DNA ladder assay” for more sensitive and early detection of apoptosis. Cytotechnology 64:9–14
Zhivotosky B, Orrenius S (2001) Assessment of apoptosis and necrosis by DNA fragmentation and morphological criteria. Curr Protoc Cell Biol, Chapter 18, Unit 18 13
Archana M, Yogesh TL, Kumaraswamy KL (2013) Various methods available for detection of apoptotic cells–a review. Indian J Cancer 50:274–283
Matassov D, Kagan T, Leblanc J, Sikorska M, Zakeri Z (2004) Measurement of apoptosis by DNA fragmentation. Methods Mol Biol 282:1–17
Kasibhatla S, Amarante-Mendes GP, Finucane D, Brunner T, Bossy-Wetzel E, Green DR (2006) Analysis of DNA fragmentation using agarose gel electrophoresis. CSH Protoc 2006
Georgiou CD, Papapostolou I, Grintzalis K (2009) Protocol for the quantitative assessment of DNA concentration and damage (fragmentation and nicks). Nat Protocols 4:125–131
Belfield H, Chikh A, Ramadan S (2005) Apoptosis methods and protocols. Cell Death Differ 12:834–834
Darzynkiewicz Z, Huang X (2004) Analysis of cellular DNA content by flow cytometry. Curr Protoc Immunol, Chapter 5, Unit 5 7
Otto F (1990) DAPI staining of fixed cells for high-resolution flow cytometry of nuclear DNA. Methods Cell Biol 33:105–110
Wang ZB, Liu YQ, Cui YF (2005) Pathways to caspase activation. Cell Biol Int 29:489–496
Lu CX, Fan TJ, Hu GB, Cong RS (2003) Apoptosis-inducing factor and apoptosis. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 35:881–885
Fan TJ, Han LH, Cong RS, Liang J (2005) Caspase family proteases and apoptosis. Acta Biochim Biophys Sin (Shanghai) 37:719–727
Niles AL, Moravec RA, Riss TL (2008) Caspase activity assays. Methods Mol Biol 414:137–150
Scholz J, Broom DC, Youn DH, Mills CD, Kohno T, Suter MR, Moore KA, Decosterd I, Coggeshall RE, Woolf CJ (2005) Blocking caspase activity prevents transsynaptic neuronal apoptosis and the loss of inhibition in lamina II of the dorsal horn after peripheral nerve injury. J Neurosci 25:7317–7323
Callus BA, Vaux DL (2006) Caspase inhibitors: viral, cellular and chemical. Cell Death Differ 14:73–78
Amstad PA, Yu G, Johnson GL, Lee BW, Dhawan S, Phelps DJ (2001) Detection of caspase activation in situ by fluorochrome-labeled caspase inhibitors. Biotechniques 31:608–610, 612, 614, passim
Preaudat M, Ouled-Diaf J, Alpha-Bazin B, Mathis G, Mitsugi T, Aono Y, Takahashi K, Takemoto H (2002) A homogeneous caspase-3 activity assay using HTRF technology. J Biomol Screen 7:267–274
Butterick TA, Duffy CM, Lee RE, Billington CJ, Kotz CM, Nixon JP. Use of a caspase multiplexing assay to determine apoptosis in a hypothalamic cell model. J Vis Exp (86). doi:10.3791/51305
Porter AG, Janicke RU (1999) Emerging roles of caspase-3 in apoptosis. Cell Death Differ 6:99–104
Nestal de Moraes G, Carvalho E, Maia RC, Sternberg C (2011) Immunodetection of caspase-3 by Western blot using glutaraldehyde. Anal Biochem 415:203–205
Mandal D, Mazumder A, Das P, Kundu M, Basu J (2005) Fas-, caspase 8-, and caspase 3-dependent signaling regulates the activity of the aminophospholipid translocase and phosphatidylserine externalization in human erythrocytes. J Biol Chem 280:39460–39467
Bardet P-L, Kolahgar G, Mynett A, Miguel-Aliaga I, Briscoe J, Meier P, Vincent J-P (2008) A fluorescent reporter of caspase activity for live imaging. Proc Natl Acad Sci 105:13901–13905
Hug H, Los M, Hirt W, Debatin KM (1999) Rhodamine 110-linked amino acids and peptides as substrates to measure caspase activity upon apoptosis induction in intact cells. Biochemistry 38:13906–13911
Darzynkiewicz Z, Bedner E, Smolewski P, Lee BW, Johnson GL (2002) Detection of caspases activation in situ by fluorochrome-labeled inhibitors of caspases (FLICA). Methods Mol Biol 203:289–99
Nicholson DW, Ali A, Thornberry NA, Vaillancourt JP, Ding CK, Gallant M, Gareau Y, Griffin PR, Labelle M, Lazebnik YA et al (1995) Identification and inhibition of the ICE/CED-3 protease necessary for mammalian apoptosis. Nature 376:37–43
Reyland ME, Anderson SM, Matassa AA, Barzen KA, Quissell DO (1999) Protein kinase C delta is essential for etoposide-induced apoptosis in salivary gland acinar cells. J Biol Chem 274:19115–19123
Li L, Lorenzo PS, Bogi K, Blumberg PM, Yuspa SH (1999) Protein kinase Cdelta targets mitochondria, alters mitochondrial membrane potential, and induces apoptosis in normal and neoplastic keratinocytes when overexpressed by an adenoviral vector. Mol Cell Biol 19:8547–8558
Bellido T, Huening M, Raval-Pandya M, Manolagas SC, Christakos S (2000) Calbindin-D28k is expressed in osteoblastic cells and suppresses their apoptosis by inhibiting caspase-3 activity. J Biol Chem 275:26328–26332
Han H, Wang H, Long H, Nattel S, Wang Z (2001) Oxidative preconditioning and apoptosis in L-cells. Roles of protein kinase B and mitogen-activated protein kinases. J Biol Chem 276:26357–26364
Namura S, Zhu J, Fink K, Endres M, Srinivasan A, Tomaselli KJ, Yuan J, Moskowitz MA (1998) Activation and cleavage of caspase-3 in apoptosis induced by experimental cerebral ischemia. J Neurosci 18:3659–3668
Porn-Ares MI, Samali A, Orrenius S (1998) Cleavage of the calpain inhibitor, calpastatin, during apoptosis. Cell Death Differ 5:1028–1033
Barreiro-Iglesias A, Shifman MI (2012) Use of fluorochrome-labeled inhibitors of caspases to detect neuronal apoptosis in the whole-mounted lamprey brain after spinal cord injury. Enzyme Res 2012:7
Kumar S, Baglioni C (1991) Protection from tumor necrosis factor-mediated cytolysis by overexpression of plasminogen activator inhibitor type-2. J Biol Chem 266:20960–20964
Miura M, Friedlander RM, Yuan J (1995) Tumor necrosis factor-induced apoptosis is mediated by a CrmA-sensitive cell death pathway. Proc Natl Acad Sci U S A 92:8318–8322
Strober W (2001) Trypan blue exclusion test of cell viability. Curr Protoc Immunol Appendix 3, Appendix 3B
Avelar-Freitas BA, Almeida VG, Pinto MC, Mourao FA, Massensini AR, Martins-Filho OA, Rocha-Vieira E, Brito-Melo GE (2014) Trypan blue exclusion assay by flow cytometry. Braz J Med Biol Res 47:307–315
Santiago Y, Chan E, Liu P-Q, Orlando S, Zhang L, Urnov FD, Holmes MC, Guschin D, Waite A, Miller JC, Rebar EJ, Gregory PD, Klug A, Collingwood TN (2008) Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci 105:5809–5814
Hertzog PJ, Kola I (2001) Overview. Gene knockouts. Methods Mol Biol 158:1–10
Wilson TJ, Kola I (2001) The LoxP/CRE system and genome modification. Methods Mol Biol 158:83–94
Szulc J, Aebischer P (2008) Conditional gene expression and knockdown using lentivirus vectors encoding shRNA. Methods Mol Biol 434:291–309
Hobel S, Aigner A (2010) Polyethylenimine (PEI)/siRNA-mediated gene knockdown in vitro and in vivo. Methods Mol Biol 623:283–297
Mocellin S, Provenzano M (2004) RNA interference: learning gene knock-down from cell physiology. J Transl Med 2:39
Hertzog PJ (2001) Isolation of embryonic fibroblasts and their use in the in vitro characterization of gene function. Methods Mol Biol 158:205–15
DeChiara TM (2001) Gene targeting in ES cells. Methods Mol Biol 158:19–45
Tessarollo L (2001) Manipulating mouse embryonic stem cells, pp 47–63
Moore CB, Guthrie EH, Huang MT, Taxman DJ (2010) Short hairpin RNA (shRNA): design, delivery, and assessment of gene knockdown. Methods Mol Biol 629:141–158
Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protocols 8:2281–2308
Deveau H, Garneau JE, Moineau S (2010) CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 64:475–493
Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9:467–477
Tiwari M, Lopez-Cruzan M, Morgan WW, Herman B (2011) Loss of caspase-2-dependent apoptosis induces autophagy after mitochondrial oxidative stress in primary cultures of young adult cortical neurons. J Biol Chem 286:8493–8506
Sawitzke JA, Thomason LC, Bubunenko M, Li X, Costantino N, Court DL (2013) Recombineering: using drug cassettes to knock out genes in vivo. Methods Enzymol 533:79–102
Malla RR, Gopinath S, Alapati K, Gorantla B, Gondi CS, Rao JS (2012) uPAR and cathepsin B inhibition enhanced radiation-induced apoptosis in gliomainitiating cells. Neuro Oncol 14:745–760
Zhou Y, Liang S, Williams LR (2002) Markers of poly (ADP-ribose) polymerase activity as correlates of DNA damage. Methods Mol Biol 203:247–55
Whitacre CM, Zborowska E, Willson JK, Berger NA (1999) Detection of poly(ADP-ribose) polymerase cleavage in response to treatment with topoisomerase I inhibitors: a potential surrogate end point to assess treatment effectiveness. Clin Cancer Res 5:665–672
Fischer U, Schulze-Osthoff K (2005) New approaches and therapeutics targeting apoptosis in disease. Pharmacol Rev 57:187–215
Oberholzer C, Oberholzer A, Clare-Salzler M, Moldawer LL (2001) Apoptosis in sepsis: a new target for therapeutic exploration. FASEB J 15:879–892
Cao Y, Mohamedali KA, Marks JW, Cheung LH, Hittelman WN, Rosenblum MG (2013) Construction and characterization of novel, completely human serine protease therapeutics targeting Her2/neu. Mol Cancer Ther 12:979–991
Drag M, Salvesen GS (2010) Emerging principles in protease-based drug discovery. Nat Rev Drug Discov 9:690–701
Lopez-Otin C, Bond JS (2008) Proteases: multifunctional enzymes in life and disease. J Biol Chem 283:30433–30437
Karikari CA, Roy I, Tryggestad E, Feldmann G, Pinilla C, Welsh K, Reed JC, Armour EP, Wong J, Herman J, Rakheja D, Maitra A (2007) Targeting the apoptotic machinery in pancreatic cancers using small-molecule antagonists of the X-linked inhibitor of apoptosis protein. Mol Cancer Ther 6:957–966
Mahato R, Tai W, Cheng K (2011) Prodrugs for improving tumor targetability and efficiency. Adv Drug Deliv Rev 63:659–670
Stella VJ (2004) Prodrugs as therapeutics. Expert Opin Ther Pat 14:277–280
Rautio J, Kumpulainen H, Heimbach T, Oliyai R, Oh D, Jarvinen T, Savolainen J (2008) Prodrugs: design and clinical applications. Nat Rev Drug Discov 7:255–270
Li C, Yu DF, Newman RA, Cabral F, Stephens LC, Hunter N, Milas L, Wallace S (1998) Complete regression of well-established tumors using a novel water-soluble poly(L-glutamic acid)-paclitaxel conjugate. Cancer Res 58:2404–2409
Roy S, Bayly CI, Gareau Y, Houtzager VM, Kargman S, Keen SL, Rowland K, Seiden IM, Thornberry NA, Nicholson DW (2001) Maintenance of caspase-3 proenzyme dormancy by an intrinsic “safety catch” regulatory tripeptide. Proc Natl Acad Sci U S A 98:6132–6137
Nguyen JT, Wells JA (2003) Direct activation of the apoptosis machinery as a mechanism to target cancer cells. Proc Natl Acad Sci U S A 100:7533–7538
Jiang X, Kim HE, Shu H, Zhao Y, Zhang H, Kofron J, Donnelly J, Burns D, Ng SC, Rosenberg S, Wang X (2003) Distinctive roles of PHAP proteins and prothymosin-alpha in a death regulatory pathway. Science 299:223–226
Vocero-Akbani AM, Heyden NV, Lissy NA, Ratner L, Dowdy SF (1999) Killing HIV-infected cells by transduction with an HIV protease-activated caspase-3 protein. Nat Med 5:29–33
Jang B, Choi Y (2012) Photosensitizer-conjugated gold nanorods for enzyme-activatable fluorescence imaging and photodynamic therapy. Theranostics 2:190–197
Kim GB, Kim YP (2012) Analysis of protease activity using quantum dots and resonance energy transfer. Theranostics 2:127–138
Yhee JY, Kim SA, Koo H, Son S, Ryu JH, Youn IC, Choi K, Kwon IC, Kim K (2012) Optical imaging of cancer-related proteases using near-infrared fluorescence matrix metalloproteinase-sensitive and cathepsin B-sensitive probes. Theranostics 2:179–189
Lee S, Kim K (2012) Protease activity: meeting its theranostic potential. Theranostics 2:125–126
Jokerst JV, Raamanathan A, Christodoulides N, Floriano PN, Pollard AA, Simmons GW, Wong J, Gage C, Furmaga WB, Redding SW, McDevitt JT (2009) Nano-bio-chips for high performance multiplexed protein detection: determinations of cancer biomarkers in serum and saliva using quantum dot bioconjugate labels. Biosens Bioelectron 24:3622–3629
Hu M, Yan J, He Y, Lu H, Weng L, Song S, Fan C, Wang L (2010) Ultrasensitive, multiplexed detection of cancer biomarkers directly in serum by using a quantum dot-based microfluidic protein chip. ACS Nano 4:488–494
Zajac A, Song D, Qian W, Zhukov T (2007) Protein microarrays and quantum dot probes for early cancer detection. Colloids Surf B: Biointerfaces 58:309–314
He H, Xie C, Ren J (2008) Nonbleaching fluorescence of gold nanoparticles and its applications in cancer cell imaging. Anal Chem 80:5951–5957
Swierczewska M, Lee S, Chen X (2011) The design and application of fluorophore-gold nanoparticle activatable probes. Phys Chem Chem Phys 13:9929–9941
Richard JA, Jean L, Schenkels C, Massonneau M, Romieu A, Renard PY (2009) Self-cleavable chemiluminescent probes suitable for protease sensing. Org Biomol Chem 7:2941–2957
Giron P, Dayon L, Turck N, Hoogland C, Sanchez JC (2011) Quantitative analysis of human cerebrospinal fluid proteins using a combination of cysteine tagging and amine-reactive isobaric labeling. J Proteome Res 10:249–258
Simon GM, Cravatt BF (2010) Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study. J Biol Chem 285:11051–11055
Berger AB, Vitorino PM, Bogyo M (2004) Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery. Am J Pharmacogenomics 4:371–381
Li Q, Yi L, Marek P, Iverson BL (2013) Commercial proteases: present and future. FEBS Lett 587:1155–1163
Pogson M, Georgiou G, Iverson BL (2009) Engineering next generation proteases. Curr Opin Biotechnol 20:390–397
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Acharya, S., Kuppili, R.R., Chaganti, L.K., Bose, K. (2015). Proteases in Apoptosis: Protocols and Methods. In: Bose, K. (eds) Proteases in Apoptosis: Pathways, Protocols and Translational Advances. Springer, Cham. https://doi.org/10.1007/978-3-319-19497-4_5
Download citation
DOI: https://doi.org/10.1007/978-3-319-19497-4_5
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-19496-7
Online ISBN: 978-3-319-19497-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)