Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes

Cell death is essential for a plethora of physiological processes, and its deregulation characterizes numerous human diseases. Thus, the in-depth investigation of cell death and its mechanisms constitutes a formidable challenge for fundamental and applied biomedical research, and has tremendous implications for the development of novel therapeutic strategies. It is, therefore, of utmost importance to standardize the experimental procedures that identify dying and dead cells in cell cultures and/or in tissues, from model organisms and/or humans, in healthy and/or pathological scenarios. Thus far, dozens of methods have been proposed to quantify cell death-related parameters. However, no guidelines exist regarding their use and interpretation, and nobody has thoroughly annotated the experimental settings for which each of these techniques is most appropriate. Here, we provide a nonexhaustive comparison of methods to detect cell death with apoptotic or nonapoptotic morphologies, their advantages and pitfalls. These guidelines are intended for investigators who study cell death, as well as for reviewers who need to constructively critique scientific reports that deal with cellular demise. Given the difficulties in determining the exact number of cells that have passed the point-of-no-return of the signaling cascades leading to cell death, we emphasize the importance of performing multiple, methodologically unrelated assays to quantify dying and dead cells.

R A Knight | G Melino | G M Cohen | A Ciechanover | S. Lipton | A. Ciechanover | C. Borner | D. Andrews | D. Green | K. Blomgren | E. Alnemri | G. Cohen | P. Vandenabeele | J. Tschopp | L. Scorrano | M. Peter | D. Rubinsztein | D. Klionsky | E. Morselli | L. Galluzzi | O. Kepp | G. Kroemer | R. Knight | G. Melino | M. Hengartner | A. Kimchi | Junying Yuan | G. Rabinovich | I. Vitale | W. El-Deiry | B. Zhivotovsky | H. Gronemeyer | S. Fulda | D. Bredesen | J. Marine | H. Steller | R. Flavell | J. Cidlowski | J. Penninger | M. Oren | B. Dynlacht | P. Nicotera | K. Vousden | S. Aaronson | U. Moll | J. Abrams | V. Laurenzi | E. Baehrecke | M. Blagosklonny | P. Golstein | P. Mehlen | T. Rudel | G. Hajnóczky | R. Rizzuto | C. Garrido | J. Medema | H. Simon | M. Jäättelä | Y. Tsujimoto | H. Ichijo | S. Martin | H. Puthalakath | S. Pervaiz | S. Kornbluth | R. Youle | N. Bazan | M. Piacentini | J. Prehn | D. Nicholson | F. Madeo | J. Prehn | C. Rodrigues | W. Malorni | J. Tschopp | B. Levine | C. Brenner | M. Castedo | E. Lugli | M. Deshmukh | J. Hardwick | G. Núñez | N G Bazan | G Hajnóczky | H Steller | L Galluzzi | S A Aaronson | J Abrams | E S Alnemri | D W Andrews | E H Baehrecke | M V Blagosklonny | K Blomgren | C Borner | D E Bredesen | C Brenner | M Castedo | J A Cidlowski | V De Laurenzi | R De Maria | M Deshmukh | B D Dynlacht | W S El-Deiry | R A Flavell | S Fulda | C Garrido | P Golstein | M-L Gougeon | D R Green | H Gronemeyer | J M Hardwick | M O Hengartner | H Ichijo | M Jäättelä | O Kepp | A Kimchi | D J Klionsky | S Kornbluth | S Kumar | B Levine | S A Lipton | E Lugli | F Madeo | W Malorni | J-CW Marine | S J Martin | J P Medema | P Mehlen | U M Moll | E Morselli | S Nagata | D W Nicholson | P Nicotera | G Nuñez | M Oren | J Penninger | S Pervaiz | M E Peter | M Piacentini | J H M Prehn | H Puthalakath | G A Rabinovich | R Rizzuto | C M P Rodrigues | D C Rubinsztein | T Rudel | L Scorrano | H-U Simon | J Tschopp | Y Tsujimoto | P Vandenabeele | I Vitale | K H Vousden | R J Youle | J Yuan | B Zhivotovsky | G Kroemer | S. Kumar | M. Gougeon | S. Lipton | J. Yuan | R. Maria | D. Rubinsztein | J. Cidlowski | R. Flavell | D. Klionsky | Jeremy Marine | H-U Simon | S. Nagata | Stuart A. Aaronson | Shigekazu Nagata | Santosh Kumar | S. Martin | Rosario Rizzuto | Y. Tsujimoto | G. Núñez | C. Garrido | Rosario Rizzuto | P. Nicotera | Cecília M P Rodrigues | H. Gronemeyer | Cecília M. P. Rodrigues | Carmen Garrido | Junying Yuan | Gerry Melino | Richard A. Flavell | Dale E. Bredesen | David W. Andrews | Nicolas G. Bazan | Christoph Borner | Catherine Brenner | Gerald M. Cohen | R. D. Maria | Simone Fulda | D. R. Green | Richard A. Knight | Santosh Kumar | Beth Levine | Enrico Lugli | Ute M. Moll | Shigekazu Nagata | Marcus E. Peter | Hans-Uwe Simon | Hermann Steller

[1]  D. Taatjes,et al.  Simultaneous triple fluorescence detection of mRNA localization, nuclear DNA, and apoptosis in cultured cells using confocal scanning laser microscopy , 1997, Histochemistry and Cell Biology.

[2]  Ruedi Aebersold,et al.  Molecular characterization of mitochondrial apoptosis-inducing factor , 1999, Nature.

[3]  Takenori Yamamoto,et al.  Molecular basis of morphological changes in mitochondrial membrane accompanying induction of permeability transition, as revealed by immuno-electron microscopy. , 2005, Mitochondrion.

[4]  G. Kroemer,et al.  Chloromethyl-X-Rosamine is an aldehyde-fixable potential-sensitive fluorochrome for the detection of early apoptosis. , 1996, Cytometry.

[5]  Y. Tamura,et al.  The phosphorylation status and anti‐apoptotic activity of Bcl‐2 are regulated by ERK and protein phosphatase 2A on the mitochondria , 2004, FEBS letters.

[6]  G. Kroemer,et al.  Autophagic cell death: the story of a misnomer , 2008, Nature Reviews Molecular Cell Biology.

[7]  G. Kroemer,et al.  Mass spectrometric identification of proteins released from mitochondria undergoing permeability transition , 2000, Cell Death and Differentiation.

[8]  M. Prevost,et al.  Real-time flow cytometry analysis of permeability transition in isolated mitochondria. , 2004, Experimental cell research.

[9]  R A Knight,et al.  Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009 , 2005, Cell Death and Differentiation.

[10]  E. Jacotot,et al.  Pharmacological screening and enzymatic assays for apoptosis. , 2009, Frontiers in bioscience.

[11]  Olivier Hermine,et al.  Caspase Activation Is Required for Terminal Erythroid Differentiation , 2001, The Journal of experimental medicine.

[12]  George H. Patterson,et al.  A Photoactivatable GFP for Selective Photolabeling of Proteins and Cells , 2002, Science.

[13]  Lorenzo Galluzzi,et al.  Mitochondrial membrane permeabilization in cell death. , 2007, Physiological reviews.

[14]  G. Szilágyi,et al.  Visualization of mitochondrial membrane potential and reactive oxygen species via double staining , 2006, Neuroscience Letters.

[15]  David A Basiji,et al.  Distinguishing modes of cell death using the ImageStream® multispectral imaging flow cytometer , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[16]  I. Weissman,et al.  bcl-2 inhibits apoptosis of neutrophils but not their engulfment by macrophages , 1994, The Journal of experimental medicine.

[17]  P. Debré,et al.  Defective humoral responses and extensive intravascular apoptosis are associated with fatal outcome in Ebola virus-infected patients , 1999, Nature Medicine.

[18]  W. Bursch,et al.  Autophagic and apoptotic types of programmed cell death exhibit different fates of cytoskeletal filaments. , 2000, Journal of cell science.

[19]  J. Bourhis,et al.  Enhancement of radiation response in p53-deficient cancer cells by the Aurora-B kinase inhibitor AZD1152 , 2007, Oncogene.

[20]  L. Margaritis,et al.  Cell death during Drosophila melanogaster early oogenesis is mediated through autophagy , 2009, Autophagy.

[21]  T. Motyl,et al.  Colocalization of BAX with BID and VDAC-1 in nimesulide-induced apoptosis of human colon adenocarcinoma COLO 205 cells , 2002, Anti-cancer drugs.

[22]  Guido Kroemer,et al.  Self-eating and self-killing: crosstalk between autophagy and apoptosis , 2007, Nature Reviews Molecular Cell Biology.

[23]  Nektarios Tavernarakis,et al.  Regulation of autophagy by cytoplasmic p53 , 2008, Nature Cell Biology.

[24]  X M Wang,et al.  A new microcellular cytotoxicity test based on calcein AM release. , 1993, Human immunology.

[25]  Guido Kroemer,et al.  Lysosomes and autophagy in cell death control , 2005, Nature Reviews Cancer.

[26]  E. Baehrecke,et al.  Growth Arrest and Autophagy Are Required for Salivary Gland Cell Degradation in Drosophila , 2007, Cell.

[27]  H. M. Petrassi,et al.  Substrate optimization for monitoring cathepsin C activity in live cells. , 2009, Bioorganic & medicinal chemistry.

[28]  G. Kroemer,et al.  Cytofluorometric quantitation of apoptosis-driven inner mitochondrial membrane permeabilization , 2003, Apoptosis.

[29]  John L Cleveland,et al.  Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes , 2008, Autophagy.

[30]  Philippe Dessen,et al.  Inhibition of Macroautophagy Triggers Apoptosis , 2005, Molecular and Cellular Biology.

[31]  Eric H. Baehrecke,et al.  Autophagy: dual roles in life and death? , 2005, Nature Reviews Molecular Cell Biology.

[32]  Y. Hsu,et al.  Bax in Murine Thymus Is a Soluble Monomeric Protein That Displays Differential Detergent-induced Conformations* , 1998, The Journal of Biological Chemistry.

[33]  C. Brenner,et al.  p53 Activation by Knockdown Technologies , 2007, PLoS genetics.

[34]  Katharina D'Herde,et al.  Apoptosis and necrosis: detection, discrimination and phagocytosis. , 2008, Methods.

[35]  P. Henkart,et al.  Assessment of Caspase Activities in Intact Apoptotic Thymocytes Using Cell-Permeable Fluorogenic Caspase Substrates , 2000, The Journal of experimental medicine.

[36]  P. Petit,et al.  Alterations in mitochondrial structure and function are early events of dexamethasone-induced thymocyte apoptosis , 1995, The Journal of cell biology.

[37]  A. Wyllie Glucocorticoid-induced thymocyte apoptosis is associated with endogenous endonuclease activation , 1980, Nature.

[38]  Philippe Dessen,et al.  A novel epidermal growth factor receptor inhibitor promotes apoptosis in non-small cell lung cancer cells resistant to erlotinib. , 2007, Cancer research.

[39]  J. Roa,et al.  Histologic sectioning produces TUNEL reactivity. A potential cause of false-positive staining. , 1999, Archives of pathology & laboratory medicine.

[40]  L. Galluzzi,et al.  Nonapoptotic role for Apaf-1 in the DNA damage checkpoint. , 2007, Molecular cell.

[41]  L. Zitvogel,et al.  Calreticulin exposure dictates the immunogenicity of cancer cell death , 2007, Nature Medicine.

[42]  Elisa Nemes,et al.  Multiparametric analysis of cells with different mitochondrial membrane potential during apoptosis by polychromatic flow cytometry , 2007, Nature Protocols.

[43]  S. Chittaranjan,et al.  Effector caspase Dcp-1 and IAP protein Bruce regulate starvation-induced autophagy during Drosophila melanogaster oogenesis , 2008, The Journal of cell biology.

[44]  G. Bellot,et al.  Mitochondrial membrane permeabilization produced by PTP, Bax and apoptosis: a 1H-NMR relaxation study , 2006, Cell Death and Differentiation.

[45]  R. D. De Abreu,et al.  Bcl-2 prevents loss of mitochondria in CCCP-induced apoptosis. , 2004, Experimental cell research.

[46]  G. Kroemer,et al.  Caspases disrupt mitochondrial membrane barrier function , 1998, FEBS letters.

[47]  R A Knight,et al.  Classification of cell death: recommendations of the Nomenclature Committee on Cell Death , 2005, Cell Death and Differentiation.

[48]  J. Nylandsted,et al.  Vincristine induces dramatic lysosomal changes and sensitizes cancer cells to lysosome-destabilizing siramesine. , 2007, Cancer research.

[49]  L. Zitvogel,et al.  Apoptosis regulation in tetraploid cancer cells , 2006, The EMBO journal.

[50]  G. Kroemer,et al.  Quantitation of mitochondrial alterations associated with apoptosis. , 2002, Journal of immunological methods.

[51]  G. Salvesen,et al.  Caspase substrates , 2007, Cell Death and Differentiation.

[52]  Nektarios Tavernarakis,et al.  No death without life: vital functions of apoptotic effectors , 2008, Cell Death and Differentiation.

[53]  Gerard I. Evan,et al.  The coordinate release of cytochrome c during apoptosis is rapid, complete and kinetically invariant , 2000, Nature Cell Biology.

[54]  E. Morselli,et al.  Hierarchical involvement of Bak, VDAC1 and Bax in cisplatin-induced cell death , 2008, Oncogene.

[55]  Thomas Farkas,et al.  Effective tumor cell death by sigma-2 receptor ligand siramesine involves lysosomal leakage and oxidative stress. , 2005, Cancer research.

[56]  L. Galluzzi,et al.  Methods to dissect mitochondrial membrane permeabilization in the course of apoptosis. , 2008, Methods in enzymology.

[57]  K. Blomgren,et al.  Failure to complete apoptosis following neonatal hypoxia–ischemia manifests as “continuum” phenotype of cell death and occurs with multiple manifestations of mitochondrial dysfunction in rodent forebrain , 2007, Neuroscience.

[58]  H. Ischiropoulos,et al.  Evaluation of the probe 2',7'-dichlorofluorescin as an indicator of reactive oxygen species formation and oxidative stress. , 1992, Chemical research in toxicology.

[59]  S. Srinivasula,et al.  Negative regulation of erythropoiesis by caspase-mediated cleavage of GATA-1 , 1999, Nature.

[60]  D. Green,et al.  Early redistribution of plasma membrane phosphatidylserine is a general feature of apoptosis regardless of the initiating stimulus: inhibition by overexpression of Bcl-2 and Abl , 1995, The Journal of experimental medicine.

[61]  H. Steller,et al.  Detection of apoptosis by terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling and acridine orange in Drosophila embryos and adult male gonads , 2006, Nature Protocols.

[62]  J. Lemasters,et al.  Screening assays for the mitochondrial permeability transition using a fluorescence multiwell plate reader. , 2001, Analytical biochemistry.

[63]  Qihua Sun,et al.  Autophagy Gene-Dependent Clearance of Apoptotic Cells during Embryonic Development , 2007, Cell.

[64]  Sudhir V. Shah,et al.  p53-dependent Caspase-2 Activation in Mitochondrial Release of Apoptosis-inducing Factor and Its Role in Renal Tubular Epithelial Cell Injury* , 2005, Journal of Biological Chemistry.

[65]  G. Kroemer,et al.  An Anti-apoptotic Viral Protein That Recruits Bax to Mitochondria* , 2004, Journal of Biological Chemistry.

[66]  T D Simmons,et al.  Measurement of the ADP:ATP ratio in human leukaemic cell lines can be used as an indicator of cell viability, necrosis and apoptosis. , 2000, Journal of immunological methods.

[67]  D. Green,et al.  The Release of Cytochrome c from Mitochondria: A Primary Site for Bcl-2 Regulation of Apoptosis , 1997, Science.

[68]  J. Roa,et al.  Histologic Sectioning Produces TUNEL Reactivity , 2009 .

[69]  L. Galluzzi,et al.  Methods for the assessment of mitochondrial membrane permeabilization in apoptosis , 2007, Apoptosis.

[70]  S. Ben‐Sasson,et al.  Identification of programmed cell death in situ via specific labeling of nuclear DNA fragmentation , 1992, The Journal of cell biology.

[71]  L. Galluzzi,et al.  Mitochondrial control of cell death induced by hyperosmotic stress , 2006, Apoptosis.

[72]  S. Lipton,et al.  Apoptosis and necrosis: two distinct events induced, respectively, by mild and intense insults with N-methyl-D-aspartate or nitric oxide/superoxide in cortical cell cultures. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[73]  Lorenzo Galluzzi,et al.  To die or not to die: that is the autophagic question. , 2008, Current molecular medicine.

[74]  G. Miotto,et al.  Transient and long-lasting openings of the mitochondrial permeability transition pore can be monitored directly in intact cells by changes in mitochondrial calcein fluorescence. , 1999, Biophysical journal.

[75]  B. Reed,et al.  Autophagy promotes caspase-dependent cell death during Drosophila development , 2009, Autophagy.

[76]  K. Nave,et al.  Bcl-xL increases mitochondrial fission, fusion, and biomass in neurons , 2009, The Journal of cell biology.

[77]  L. Galluzzi,et al.  Inhibition of Chk1 Kills Tetraploid Tumor Cells through a p53-Dependent Pathway , 2007, PloS one.

[78]  E. Crouser,et al.  Quantitation of cytochrome c release from rat liver mitochondria. , 2003, Analytical biochemistry.

[79]  James E. Goldman,et al.  Protection against Fatal Sindbis Virus Encephalitis by Beclin, a Novel Bcl-2-Interacting Protein , 1998, Journal of Virology.

[80]  M. Prevost,et al.  Mitochondrial Release of Caspase-2 and -9 during the Apoptotic Process , 1999, The Journal of experimental medicine.

[81]  T. Vanden Berghe,et al.  Methods for distinguishing apoptotic from necrotic cells and measuring their clearance. , 2008, Methods in enzymology.

[82]  H. Steller,et al.  Programmed cell death during Drosophila embryogenesis. , 1993, Development.

[83]  Yi-Te Hsu,et al.  Movement of Bax from the Cytosol to Mitochondria during Apoptosis , 1997, The Journal of cell biology.

[84]  K. Schulze-Osthoff,et al.  The dark side of a tumor suppressor: anti-apoptotic p53 , 2008, Cell Death and Differentiation.