Apoptosis and cell death

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Archive for December, 2008

Apolist: december 2008

Posted by cris on December 31, 2008

Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009
G Kroemer, L Galluzzi, P Vandenabeele, J Abrams, E S Alnemri, E H Baehrecke, M V Blagosklonny, W S El-Deiry, P Golstein, D R Green, M Hengartner, R A Knight, S Kumar, S A Lipton, W Malorni, G Nuñez, M E Peter, J Tschopp, J Yuan, M Piacentini, B Zhivotovsky & G Melino
[comments below]

Necroptosis: A Specialized Pathway of Programmed Necrosis
L. Galluzzi and G. Kroemer

Does autophagy have a license to kill mammalian cells?
F Scarlatti, R Granata, A J Meijer & P Codogno

Autophagy in aging, disease and death: the true identity of a cell death impostor
B Levine & G Kroemer

Autophagic cell death: the story of a misnomer
Guido Kroemer & Beth Levine


BH3 / mitochondria

Mechanism of apoptosis induction by inhibition of the anti-apoptotic BCL-2 proteins
Jerry E. Chipuk, John C. Fisher, Christopher P. Dillon, Richard W. Kriwacki, Tomomi Kuwana, and Douglas R. Green

Membrane Binding by tBid Initiates an Ordered Series of Events Culminating in Membrane Permeabilization by Bax
J.F. Lovell, L.P. Billen, S. Bindner, A. Shamas-Din, C. Fradin, B. Leber, and D.W. Andrews

Colorectal cancer cells with the BRAFV600E mutation are addicted to the ERK1/2 pathway for growth factor-independent survival and repression of BIM
J A Wickenden, H Jin, M Johnson, A S Gillings, C Newson, M Austin, S D Chell, K Balmanno, C A Pritchard & S J Cook

Endophilin B1/Bif-1 stimulates BAX activation independently from its capacity to produce large-scale membrane morphological rearrangements
Aitor Etxebarria, Oihana Terrones, Hirohito Yamaguchi, Ane Landajuela, Olatz Landeta, Bruno Antonsson, Hong-Gang Wang, and Gorka Basañez

NF-k B1 and c-Rel cooperate to promote the survival of TLR4-activated B cells by neutralizing Bim via distinct mechanisms
Ashish Banerjee, Raelene Grumont, Raffi Gugasyan, Christine White, Andreas Strasser, and Steve Gerondakis
Blood 2008;112 5063-5073

Extrinsic pathway

Identification of a Molecular Signaling Network that Regulates a Cellular Necrotic Cell Death Pathway
J. Hitomi, D.E. Christofferson, A. Ng, J. Yao, A. Degterev, R.J. Xavier, and J. Yuan

Distinct requirements for activation-induced cell surface expression of preformed Fas/CD95 ligand and cytolytic granule markers in T cells
D Kassahn, U Nachbur, S Conus, O Micheau, P Schneider, H-U Simon and T Brunner

Identification of an antiapoptotic protein complex at death receptors
M Sun, L Song, Y Li, T Zhou and R S Jope

Genetic delineation of the pathways mediated by Bid and JNK in TNFalpha-induced liver injury in adult and embryonic mice
Hong-Min Ni, Xiaoyun Chen, Ying-Hong Shi, Yong Liao, Amer A. Beg, Jia Fan, and Xiao-Ming Yin
J. Biol. Chem. published 7 December 2008, 10.1074/jbc.M807259200

TRAF2 Phosphorylation Modulates Tumor Necrosis Factor Alpha-Induced Gene Expression and Cell Resistance to Apoptosis
Ken Blackwell, Laiqun Zhang, Gregory S. Thomas, Shujie Sun, Hiroyasu Nakano, and Hasem Habelhah

Prevention of Autoimmunity and Control of Recall Response to Exogenous Antigen by Fas Death Receptor Ligand Expression on T Cells
I. Mabrouk, S. Buart, M. Hasmim, C. Michiels, E. Connault, P. Opolon, G. Chiocchia, M. Lévi-Strauss, S. Chouaib, and S. Karray

NDR Kinase Is Activated by RASSF1A/MST1 in Response to Fas Receptor Stimulation and Promotes Apoptosis
A. Vichalkovski, E. Gresko, H. Cornils, A. Hergovich, D. Schmitz, and B.A. Hemmings

Caspase-8 mediates mitochondrial release of pro-apoptotic proteins in a manner independent of its proteolytic activity in apoptosis induced by the protein synthesis inhibitor acetoxycycloheximide in human leukemia Jurkat cells
Kimiko Kadohara, Michiko Nagumo, Shun Asami, Yoshinori Tsukumo, Hikaru Sugimoto, Masayuki Igarashi, Kazuo Nagai, and Takao Kataoka

Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death
John G. Albeck, John M. Burke, Sabrina L. Spencer, Douglas A. Lauffenburger, and Peter K. Sorger

Other stuff

Nucleophosmin is cleaved and inactivated by the cytotoxic granule protease granzyme M during NK cell-mediated killing.
Sean P. Cullen, Inna S. Afonina, Roberta Donadini, Alexander U. Luthi, Jan Paul Medema, Phillip I. Bird, and Seamus J. Martin

Glucose metabolism inhibits apoptosis in neurons and cancer cells by redox inactivation of cytochrome c
Allyson E. Vaughn and Mohanish Deshmukh

Regulation of the Drosophila apoptosome through feedback inhibition
Peter J. Shapiro, Hans H. Hsu, Heekyung Jung, Edith S. Robbins and Hyung Don Ryoo

The Protein Kinase DYRK1A Regulates Caspase-9-Mediated Apoptosis during Retina Development
Ariadna Laguna1, 2, Sergi Aranda1, 2, María José Barallobre, Rima Barhoum3, Eduardo Fernández4, Vassiliki Fotaki1, 7, Jean Maurice Delabar5, Susana de la Luna1, 2, 6, Pedro de la Villa3 and Maria L. Arbonés

Crystal structure of procaspase-1 zymogen domain reveals insight into inflammatory caspase autoactivation
J. Michael Elliott, Lionel Rouge, Christian Wiesmann, and Justin M. Scheer
J. Biol. Chem. published 30 December 2008, 10.1074/jbc.M806121200

X-linked and cellular IAPs modulate the stability of C-RAF kinase and cell motility
Taner Dogan, Gregory S. Harms, Mirko Hekman, Christiaan Karreman, Tripat Kaur Oberoi, Emad S. Alnemri, Ulf R. Rapp and Krishnaraj Rajalingam

Chemotherapy Induces Tumor Clearance Independent of Apoptosis
Jennifer L. Guerriero, Dara Ditsworth, Yongjun Fan, Fangping Zhao, Howard C. Crawford, and Wei-Xing Zong
Cancer Res 2008;68 9595-9600


Special issue of CDD on autophagy

Bcl-2 Proteins and Apoptosis: Choose Your Partner
G.C. Shore and M. Nguyen

Staying alive: apoptosome feedback inhibition
Hermann Steller

Cell death: DIAP1 puts ubiquitin on drICE

Transcriptional inhibitors, p53 and apoptosis
Andrei L. Gartel

Holiday reads
A biomolecular carol I – resolutions
A biomolecular carol II – scared Dickens-less

About the recommendations of the “Nomenclature Committee on Cell Death”

I think this is a much better job than the previous recommendations. Still, I can’t see clear definitions of cell death modes, which I think should have been the aim of this article.

Apoptosis is defined in the text by morphological criteria, and these morphological changes are consequences of caspase activity. Then, I think it makes kind of sense to define apoptosis as ‘caspase-dependent cell death’. In this sense, it is quite confusing to mention CICD (caspase independent, MOMP-dependent, Bcl-2-like-regulated cell death) as if it was “apoptosis without most morphological signs of apoptosis”. Then, what is apoptosis?  Should it be a morphological or a biochemical definition?  I miss a clear definition of apoptosis and CICD in the text.

Also, in my opinion, necroptosis (RIPK1-dependent cell death) deserves to be separated from the ‘default’ term ‘necrosis’, especially now that we’re getting a lot of information about its regulation.

And my main concern. ‘Autophagic cell death’. I interpret that the text tries to say that in most cases the term “autophagic cell death” is being used incorrectly to describe “apoptosis with autophagy” (which is apoptosis). Perhaps even cases of necroptosis are being described as “autophagic cell death” in the literature. And still, a biochemical definition is missing in the paragraph. It is described as cell death with “massive” autophagy and without chromatin condensation. So, what is it if caspase inhibitors block death? This experiment is missing in a huge proportion of articles describing “autophagic cell death”.
Moreover, “autophagy” (not even ‘autophagic cell death’) is included as a mode of cell death in the tables (tables 2 and 3). This is extremely confusing. I would like to suggest the editor and members of the committee who read this to please be even more aggressive/clear next time and make sure that people start using the term “cell death with autophagy” instead of “autophagic cell death” when appropriate.

Opinions welcome.


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glycolist: july-november

Posted by cris on December 22, 2008

Glucose metabolism attenuates p53 and puma-dependent cell death upon growth factor deprivation
Yuxing Zhao, Jonathan L. Coloff, Emily C. Ferguson, Sarah R. Jacobs, Kai Cui, and Jeffrey C. Rathmell
J. Biol. Chem. published 6 November 2008, 10.1074/jbc.M803580200

Ceramide starves cells to death by downregulating nutrient transporter proteins
Garret G. Guenther, Eigen R. Peralta, Kimberly Romero Rosales, Susan Y. Wong, Leah J. Siskind, and Aimee L. Edinger

FKBP36 is an inherent multi-functional glyceraldehyde-3-phosphate dehydrogenase inhibitor
Franziska Jarczowski, Günther Jahreis, Frank Erdmann, Angelika Schierhorn, Gunter Fischer, and Frank Edlich
J. Biol. Chem. published 10 November 2008, 10.1074/jbc.M709779200

Rapamycin differentially inhibits S6Ks and 4E-BP1 to mediate cell-type-specific repression of mRNA translation
Andrew Y. Choo, Sang-Oh Yoon, Sang Gyun Kim, Philippe P. Roux, and John Blenis

Peptide combinatorial libraries Identify TSC2 as a DAPK death domain binding protein and reveal a stimulatory role for DAPK in mTORC1 signalling
Craig Stevens, Yao Lin, Ben Harrison, Lindsay Burch, Rachel A. Ridgway, Owen Sansom, and Ted Hupp

A novel inhibitor of glucose uptake sensitizes cells to FAS-induced cell death
Wood, T. E., Dalili, S., Simpson, C. D., Hurren, R., Mao, X., Saiz, F. S., Gronda, M., Eberhard, Y., Minden, M. D., Bilan, P. J., Klip, A., Batey, R. A., Schimmer, A. D.

Regulation of TORC1 by Rag GTPases in nutrient response
Eunjung Kim, Pankuri Goraksha-Hicks, Li Li, Thomas P. Neufeld and Kun-Liang Guan

Glucose controls CREB activity in islet cells via regulated phosphorylation of TORC2
Deidre Jansson, Andy Cheuk-Him Ng, Accalia Fu, Chantal Depatie, Mufida Al Azzabi, and Robert A. Screaton

Hypoxia signals autophagy in tumor cells via AMPK activity, independent of HIF-1, BNIP3, and BNIP3L
I Papandreou, A L Lim, K Laderoute & N C Denko

Inactivation of the CYLD Deubiquitinase by HPV E6 Mediates Hypoxia-Induced NF-κB Activation
J. An, D. Mo, H. Liu, M.S. Veena, E.S. Srivatsan, R. Massoumi, and M.B. Rettig

A769662, a novel activator of AMP-activated protein kinase, inhibits non-proteolytic components of the 26S proteasome by an AMPK-independent mechanism
Daniel Moreno, Erwin Knecht, Benoit Viollet and Pascual Sanz

AMP-Activated Protein Kinase Signaling Results in Cytoplasmic Sequestration of p27
John D. Short, Kevin D. Houston, Ruhee Dere, Sheng-Li Cai, Jinhee Kim, Charles L. Johnson, Russell R. Broaddus, Jianjun Shen, Susie Miyamoto, Fuyuhiko Tamanoi, David Kwiatkowski, Gordon B. Mills, and Cheryl Lyn Walker

SREBP Activity Is Regulated by mTORC1 and Contributes to Akt-Dependent Cell Growth
T. Porstmann, C.R. Santos, B. Griffiths, M. Cully, M. Wu, S. Leevers, J.R. Griffiths, Y.-L. Chung, and A. Schulze

Inhibition of fatty acid synthase induces caspase 8-mediated tumor cell apoptosis by Up-regulating DDIT4
Lynn M. Knowles, Chen Yang, Andrei Osterman, and Jeffrey W. Smith

Akt inhibition promotes autophagy and sensitizes PTEN-null tumors to lysosomotropic agents
Michael Degtyarev, Ann De Mazière, Christine Orr, Jie Lin, Brian B. Lee, Janet Y. Tien, Wei W. Prior, Suzanne van Dijk, Hong Wu, Daniel C. Gray, David P. Davis, Howard M. Stern, Lesley J. Murray, Klaus P. Hoeflich, Judith Klumperman, Lori S. Friedman, and Kui Lin


Chapter Twenty-Two
Mechanisms and Methods in Glucose Metabolism and Cell Death
Yuxing Zhao, Heather L. Wieman, Sarah R. Jacobs, Jeffrey C. Rathmell


Hypoxia, HIF1 and glucose metabolism in the solid tumour
Nicholas C. Denko

Hypoxia signalling through mTOR and the unfolded protein response in cancer
Bradly G. Wouters & Marianne Koritzinsky

Nutrient sensing: TOR’s Ragtime
Alfred J. Meijer and Patrice Codogno

Cancer Cell Metabolism: Warburg and Beyond
P.P. Hsu and D.M. Sabatini

Autophagy inhibitors deliver a knock-out blow
Richard Robinson
J. Cell Biol. 2008;183 2-3, Published online Oct 6 2008, 10.1083/jcb.1831iti3.

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ApoList: November

Posted by cris on December 12, 2008

hi all,
here’s the list for papers published in november.

Inactivation of Effector Caspases through Nondegradative Polyubiquitylation
M. Ditzel, M. Broemer, T. Tenev, C. Bolduc, T.V. Lee, K.T.G. Rigbolt, R. Elliott, M. Zvelebil, B. Blagoev, A. Bergmann, and P. Meier

An intracellular wave of cytochrome c propagates and precedes Bax redistribution during apoptosis
Lydia Lartigue, Chantal Medina, Laura Schembri, Paul Chabert, Marion Zanese, Flora Tomasello, Renée Dalibart, Didier Thoraval, Marc Crouzet, François Ichas, and Francesca De Giorgi

IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-κB as well as cell survival and oncogenesis pp1309 – 1317
Mads Gyrd-Hansen, Maurice Darding, Maria Miasari, Massimo M. Santoro, Lars Zender, Wen Xue, Tencho Tenev, Paula C.A. da Fonseca, Marketa Zvelebil, Janusz M. Bujnicki, Scott Lowe, John Silke and Pascal Meier

Structure of transmembrane pore induced by Bax-derived peptide: Evidence for lipidic pores
Shuo Qian, Wangchen Wang, Lin Yang, and Huey W. Huang

Glucose metabolism attenuates p53 and puma-dependent cell death upon growth factor deprivation
Yuxing Zhao, Jonathan L. Coloff, Emily C. Ferguson, Sarah R. Jacobs, Kai Cui, and Jeffrey C. Rathmell
J. Biol. Chem. published 6 November 2008, 10.1074/jbc.M803580200

The BH3-only protein Bik/Blk/Nbk inhibits nuclear translocation of activated ERK1/2 to mediate IFN -induced cell death
Yohannes A. Mebratu, Burton F. Dickey, Chris Evans, and Yohannes Tesfaigzi

Apoptosis-based treatment of glioblastomas with ABT-737, a novel small molecule inhibitor of Bcl-2 family proteins
K E Tagscherer, A Fassl, B Campos, M Farhadi, A Kraemer, B C Böck, S Macher-Goeppinger, B Radlwimmer, O D Wiestler, C Herold-Mende & W Roth

Identification of the major phosphorylation site in Bcl-xL induced by microtubule inhibitors and analysis of its functional significance
Meenakshi Upreti, Elena N. Galitovskaya, Rong Chu, Alan J. Tackett, David T. Terrano, Susana Granell, and Timothy C. Chambers

Mcl-1 expression has in vitro and in vivo significance in chronic lymphocytic leukemia and is associated with other poor prognostic markers
Chris Pepper, Thet Thet Lin, Guy Pratt, Saman Hewamana, Paul Brennan, Louise Hiller, Robert Hills, Rachel Ward, Jane Starczynski, Belinda Austen, Laura Hooper, Tatjana Stankovic, and Chris Fegan

SM-164: A Novel, Bivalent Smac Mimetic That Induces Apoptosis and Tumor Regression by Concurrent Removal of the Blockade of cIAP-1/2 and XIAP
Jianfeng Lu, Longchuan Bai, Haiying Sun, Zaneta Nikolovska-Coleska, Donna McEachern, Su Qiu, Rebecca S. Miller, Han Yi, Sanjeev Shangary, Yi Sun, Jennifer L. Meagher, Jeanne A. Stuckey, and Shaomeng Wang
Cancer Res 2008;68 9384-9393

Switch in Fas-activated death signaling pathway as result of keratin 8/18-intermediate filament loss
Stéphane Gilbert, Alexandre Ruel, Anne Loranger, Normand Marceau

Bile acid-induced apoptosis in hepatocytes is caspase-6-dependent
Christian Rust, Nadine Wild, Carina Bernt, Timo Vennegeerts, Ralf Wimmer, and Ulrich Beuers
J. Biol. Chem. published 18 November 2008, 10.1074/jbc.M804585200

Structural basis for executioner caspase recognition of P5 position in substrates
Guoxing Fu, Alexander A. Chumanevich, Johnson Agniswamy, Bin Fang, Robert W. Harrison, Irene T. Weber

Spatial differences in active caspase-8 defines its role in T-cell activation versus cell death
A Koenig, J Q Russell, W A Rodgers & R C Budd

Caspase 8 promotes peripheral localization and activation of Rab5
Vicente A. Torres, Ainhoa Mielgo, Daniela Barilà, Deborah H. Anderson, and Dwayne Stupack
J. Biol. Chem. published 29 October 2008, 10.1074/jbc.M805878200

Cardiolipin provides an essential activating platform for caspase-8 on mitochondria
Francois Gonzalvez, Zachary T. Schug, Riekelt H. Houtkooper, Elaine D. MacKenzie, David G. Brooks, Ronald J.A. Wanders, Patrice X. Petit, Frédéric M. Vaz, and Eyal Gottlieb

Irene L. Ch’en, Daniel R. Beisner, Alexei Degterev, Candace Lynch, Junying Yuan, Alexander Hoffmann, and Stephen M. Hedrick
Antigen-mediated T cell expansion regulated by parallel pathways of death
[about caspase-8 and necroptosis]

IRF-5 is a mediator of the death receptor-induced apoptotic signaling pathway
Guodong Hu and Betsy J. Barnes
J. Biol. Chem. published 20 November 2008, 10.1074/jbc.M804744200

A non-apoptotic role for caspase-9 in muscle differentiation
Thomas V. A. Murray, Jill M. McMahon, Breege A. Howley, Alanna Stanley, Thomas Ritter, Andrea Mohr, Ralf Zwacka, and Howard O. Fearnhead

Caspase-mediated cleavage of importin-α increases its affinity for MCM and downregulates DNA synthesis by interrupting the binding of MCM to chromatin
Byung Ju Kim and Hoyun Lee

Role of the proteolytic hierarchy between cathepsin L, cathepsin D and caspase-3 in regulation of cellular susceptibility to apoptosis and autophagy
Xin Zheng, Fei Chu, Bernard L. Mirkin, Thangirala Sudha, Shaker A. Mousa and Abdelhadi Rebbaa

Motor Deficit in a Drosophila Model of Mucolipidosis Type IV due to Defective Clearance of Apoptotic Cells
K. Venkatachalam, A.A. Long, R. Elsaesser, D. Nikolaeva, K. Broadie, and C. Montell

The evolution of BIR domain and its containing proteins
Lihuan Cao, Zhenghan Wang, Xianmei Yang, Li Xie and Long Yu


Caspases and IAPs: A Dance of Death Ensures Cell Survival
S. Galbán, G.F. Brady, and C.S. Duckett

Radiotherapy: Worming your way to cell death

A new Aven-ue to DNA-damage checkpoints
Atan Gross

Caspase-9 muscles in

Apoptosis-induced compensatory proliferation. The Cell is dead. Long live the Cell!
Yun Fan and Andreas Bergmann

Phagosome maturation during the removal of apoptotic cells: receptors lead the way
Zheng Zhou and Xiaomeng Yu

Mcl-1: the 1 in CLL
Varsha Gandhi, Kumudha Balakrishnan, and Lisa S. Chen

Role of nuclear bodies in apoptosis signalling
Eva Krieghoff-Henning and Thomas G. Hofmann

Functional architecture of the cell nucleus: Towards comprehensive toponome reference maps of apoptosis
Walter Schubert, Manuela Friedenberger, Marcus Bode, Andreas Krusche and Reyk Hillert

A get-together for caspases
Mitch Leslie
J. Cell Biol. 2008;183 568, Published online Nov 10 2008, 10.1083/jcb.1834iti2.

Caspase-8 goes cardiolipin: a new platform to provide mitochondria with microdomains of apoptotic signals?
Luca Scorrano
J. Cell Biol. 2008;183 579-581, Published online Nov 10 2008, 10.1083/jcb.200810125.

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