APO-SYS Consortium

 

Apoptosis Systems Biology Applied to Cancer and AIDS

 

An integrated approach of experimental biology, data mining, mathematical modeling, biostatistics, system engineering and molecular medicine

Publications    2010  2009   2008   2007        

2010

  1. Aho T, Almusa H, Matilainen J, Larjo A, Ruusuvuori P, Aho KL, Wilhelm T, Lähdesmäki H, Beyer A, Harju M, Chowdhury S, Leinonen K, Roos C, Yli-Harja O. Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PLoS One. 2010 May 14;5(5).

  2. Aymeric L, Apetoh L, Ghiringhelli F, Tesniere A, Martins I, Kroemer G, Smyth MJ, Zitvogel L. Tumor cell death and ATP release prime dendritic cells and efficient anticancer immunity. Cancer Res. 2010 Feb 1;70(3):855-8. Epub 2010 Jan 19. Review.

  3. Bennetzen MV, Larsen DH, Bunkenborg J, Bartek J, Lukas J, Andersen JS. Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response. Mol Cell Proteomics. 2010 Feb 16.

  4. Bialik S, Zalckvar E, Ber Y, Rubinstein AD, Kimchi A. Systems biology analysis of programmed cell death. Trends Biochem Sci. 2010 May 28.

  5. Bialik S, Kimchi A. Lethal weapons: DAP-kinase, autophagy and cell death DAP-kinase regulates autophagy. Curr Opin Cell Biol. 2010, Apr 22.

  6. Borbone E, Berlingieri MT, De Bellis F, Nebbioso A, Chiappetta G, Mai A, Altucci L, Fusco A. Histone deacetylase inhibitors induce thyroid cancer-specific apoptosis through proteasome-dependent inhibition of TRAIL degradation. Oncogene. 2010 Jan 7;29(1):105-16.

  7. Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A. Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol. 2010 Mar 5;6(3).

  8. Carmona-Gutierrez D, Eisenberg T, Büttner S, Meisinger C, Kroemer G, Madeo F. Apoptosis in yeast: triggers, pathways, subroutines. Cell Death Differ. 2010 Jan 15.

  9. Carmona-Gutierrez D, Fröhlich KU, Kroemer G, Madeo F. Metacaspases are caspases. Doubt no more. Cell Death Differ. 2010 Mar;17(3):377-8. 

  10. Ciccosanti F, Corazzari M, Soldani F, Matarrese P, Pagliarini V, Iadevaia V, Tinari A, Zaccarelli M, Perfettini JL, Malorni W, Kroemer G, Antinori A, Fimia GM, Piacentini M. Proteomic analysis identifies prohibitin down-regulation as a crucial event in the mitochondrial damage observed in HIV-infected patients. Antivir Ther. 2010;15(3):377-90.

  11. Criollo A, Senovilla L, Authier H, Maiuri MC, Morselli E, Vitale I, Kepp O, Tasdemir E, Galluzzi L, Shen S, Tailler M, Delahaye N, Tesniere A, De Stefano D, Younes AB, Harper F, Pierron G, Lavandero S, Zitvogel L, Israel A, Baud V, Kroemer G. IKK connects autophagy to major stress pathways. Autophagy. 2010 Jan;6(1):189-91.

  12. De Petris L, Pernemalm M, Elmberger G, Bergman P, Orre L, Lewensohn R, Lehtio J. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants. Proteome Sci. 2010 Feb 26;8(1):9.

  13. Djavaheri-Mergny M, Maiuri MC, Kroemer G. Cross talk between apoptosis and autophagy by caspase-mediated cleavage of Beclin 1. Oncogene. 2010 Jan 25.

  14. Düssmann H, Rehm M, Concannon CG, Anguissola S, Würstle M, Kacmar S, Völler P, Huber HJ, Prehn JH. Single-cell quantification of Bax activation and mathematical modelling suggest pore formation on minimal mitochondrial Bax accumulation. Cell Death Differ. 2010 Feb;17(2):278-90.

  15. Eisenberg T, Carmona-Gutierrez D, Büttner S, Tavernarakis N, Madeo F. Necrosis in yeast. Apoptosis. 2010 Jan 13.

  16. Fenner BJ, Scannell M, Prehn JH. Expanding the substantial interactome of NEMO using protein microarrays. PLoS One. 2010 Jan 20;5(1):e8799.

  17. Fulda S. Exploiting mitochondrial apoptosis for the treatment of cancer. Mitochondrion. 2010 May 16.

  18. Fulda S. Modulation of Apoptosis by Natural Products for Cancer Therapy. Planta Med. 2010 May 19.

  19. Fulda S. Evasion of apoptosis as a cellular stress response in cancer. Int J Cell Biol. 2010;2010:370835.

  20. Fulda S, Gorman AM, Hori O, Samali A. Cellular stress responses: cell survival and cell death. Int J Cell Biol. 2010;2010:214074.

  21. Galluzzi L, Kepp O, Morselli E, Vitale I, Senovilla L, Pinti M, Zitvogel L, Kroemer G. Viral strategies for the evasion of immunogenic cell death. J Intern Med. 2010 May;267(5):526-42.

  22. Galluzzi L, Morselli E, Kepp O, Maiuri MC, Kroemer G. Defective autophagy control by the p53 rheostat in cancer. Cell Cycle. 2010 Jan 2;9(2).

  23. Galluzzi L, Morselli E, Vitale I, Kepp O, Senovilla L, Criollo A, Servant N, Paccard C, Hupé P, Robert T, Ripoche H, Lazar V, Harel-Bellan A, Dessen P, Barillot E, Kroemer G. miR-181a and miR-630 regulate cisplatin-induced cancer cell death. Cancer Res. 2010 Mar 1;70(5):1793-803.

  24. Gogvadze V, Norberg E, Orrenius S, Zhivotovsky B. Involvement of Ca(2+) and ROS in alpha-tocopheryl succinate-induced mitochondrial permeabilization. Int J Cancer. 2010 Jan 26.

  25. Groth-Pedersen L, Jäättelä M. Combating apoptosis and multidrug resistant cancers by targeting lysosomes. Cancer Lett. 2010 Jun 30.

  26. Hellwig CT, Ludwig-Galezowska AH, Concannon CG, Litchfield DW, Prehn JH, Rehm M. Activity of protein kinase CK2 uncouples Bid cleavage from caspase-8 activation. J Cell Sci. 2010 May 1;123(Pt 9):1401-6

  27. Hangen E, Blomgren K, Bénit P, Kroemer G, Modjtahedi N. Life with or without AIF. Trends Biochem Sci. 2010 Feb 5.

  28. Hangen E, De Zio D, Bordi M, Zhu C, Dessen P, Caffin F, Lachkar S, Perfettini JL, Lazar V, Benard J, Fimia GM, Piacentini M, Harper F, Pierron G, Vicencio JM, Bénit P, de Andrade A, Höglinger G, Culmsee C, Rustin P, Blomgren K, Cecconi F, Kroemer G, Modjtahedi N.  A brain-specific isoform of mitochondrial apoptosis-inducing factor: AIF2. Cell Death Differ. 2010 Jan 29.

  29. Hellwig CT, Ludwig-Galezowska AH, Concannon CG, Litchfield DW, Prehn JH, Rehm M. Activity of protein kinase CK2 uncouples Bid cleavage from caspase-8 activation. J Cell Sci. 2010 May 1;123(Pt 9):1401-6.

  30. Hiscutt EL, Hill DS, Martin S, Kerr R, Harbottle A, Birch-Machin M, Redfern CP, Fulda S, Armstrong JL, Lovat PE. Targeting X-Linked Inhibitor of Apoptosis Protein to Increase the Efficacy of Endoplasmic Reticulum Stress-Induced Apoptosis for Melanoma Therapy. J Invest Dermatol. 2010 Jun 3.

  31. Huber HJ, Laussmann MA, Prehn JH, Rehm M. Diffusion is capable of translating anisotropic apoptosis initiation into a homogeneous execution of cell death. BMC Syst Biol. 2010 Feb 4;4:9.

  32. Høyer-Hansen M, Nordbrandt SP, Jäättelä M. Autophagy as a basis for the health-promoting effects of vitamin D. Trends Mol Med. 2010 May 18.

  33. Jiménez-Lara AM, Aranda A, Gronemeyer H. Retinoic acid protects human breast cancer cells against etoposide-induced apoptosis by NF-kappaB-dependent but cIAP2-independent mechanisms. Mol Cancer. 2010 Jan 26;9:15.

  34. Kaminskyy V, Zhivotovsky B. To kill or be killed: how viruses interact with the cell death machinery. J Intern Med. 2010 May;267(5):473-82.

  35. Karlebach G, Shamir R. Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case. BMC Syst Biol. 2010 Feb 25;4(1):15

  36. Kepp O, Galluzzi L, Zitvogel L, Kroemer G. Pyroptosis - a cell death modality of its kind? Eur J Immunol. 2010 Mar 3;40(3):627-630.

  37. Kirkegaard T, Rothe A, Petersen NHT, Mahalka AK, Olsen OD, Moilander I, Zylicz A, Knudsen J, Sandhoff K, Kinnunen PKJ, Nylandsted J, Jäättelä M. Hsp70 stabilizes lysosomes and reverts Niemann-Pick disease-associated lysosomal pathology. Nature 463:549-553,. 2010

  38. Koren I, Reem E, Kimchi A. DAP1, a Novel Substrate of mTOR, Negatively Regulates Autophagy. Curr Biol. 2010 May 26.

  39. Madeo F, Eisenberg T, Büttner S, Ruckenstuhl C, Kroemer G. Spermidine: a novel autophagy inducer and longevity elixir. Autophagy. 2010 Jan;6(1):160-2.

  40. Mader I, Wabitsch M, Debatin KM, Fischer-Posovszky P, Fulda S. Identification of a novel proapoptotic function of resveratrol in fat cells: SIRT1-independent sensitization to TRAIL-induced apoptosis. FASEB J. 2010 Jan 22.

  41. Maiuri MC, Criollo A, Kroemer G. Crosstalk between apoptosis and autophagy within the Beclin 1 interactome. EMBO J. 2010 Feb 3;29(3):515-6.

  42. Matic I, Sacchi A, Rinaldi A, Melino G, Khosla C, Falasca L, Piacentini M. Characterization of transglutaminase type II role in dendritic cell differentiation and function. J Leukoc Biol. 2010 Apr 6.

  43. Morselli E, Maiuri MC, Markaki M, Megalou E, Pasparaki A, Palikaras K, Criollo A, Galluzzi L, Malik SA, Vitale I, Michaud M, Madeo F, Tavernarakis N, Kroemer G. The life span-prolonging effect of sirtuin-1 is mediated by autophagy. Autophagy. 2010 Jan 2;6(1).

  44. Norberg E, Orrenius S, Zhivotovsky B. Mitochondrial regulation of cell death: processing of apoptosis-inducing factor (AIF). Biochem Biophys Res Commun. 2010 May 21;396(1):95-100.

  45. Norberg E, Gogvadze V, Vakifahmetoglu H, Orrenius S, Zhivotovsky B. Oxidative modification sensitizes mitochondrial apoptosis-inducing factor to calpain-mediated processing. Free Radic Biol Med. 2010 Mar 15;48(6):791-7.

  46. Pavet V, Beyrath J, Pardin C, Morizot A, Lechner MC, Briand JP, Wendland M, Maison W, Fournel S, Micheau O, Guichard G, Gronemeyer H. Multivalent DR5 Peptides Activate the TRAIL Death Pathway and Exert Tumoricidal Activity. Cancer Res. 2010 Jan 26.

  47. Perfettini JL, Nardacci R, Séror C, Raza SQ, Sepe S, Saïdi H, Brottes F, Amendola A, Subra F, Del Nonno F, Chessa L, D'Incecco A, Gougeon ML, Piacentini M, Kroemer G. 53BP1 represses mitotic catastrophe in syncytia elicited by the HIV-1 envelope. Cell Death Differ. 2010 May;17(5):811-20

  48. Petersen NH, Kirkegaard T, Olsen OD, Jäättelä M. Connecting Hsp70, sphingolipid metabolism and lysosomal stability. Cell Cycle. 2010 Jun 8;9(12).

  49. Prasad RB, Hosking FJ, Vijayakrishnan J, Papaemmanuil E, Koehler R, Greaves M, Sheridan E, Gast A, Kinsey SE, Lightfoot T, Roman E, Taylor M, Pritchard-Jones K, Stanulla M, Schrappe M, Bartram CR, Houlston RS, Kumar R, Hemminki K. Verification of the susceptibility loci on 7p12.2, 10q21.2, and 14q11.2 in precursor B-cell acute lymphoblastic leukemia of childhood. Blood. 2010 Mar 4;115(9):1765-7.

  50. Schroder K, Tschopp J. The inflammasomes. Cell. 2010 Mar 19;140(6):821-32. Review.

  51. Schroder K, Zhou R, Tschopp J. The NLRP3 inflammasome: a sensor for metabolic danger? Science. 2010 Jan 15;327(5963):296-300.

  52. Shen S, Kepp O, Martins I, Vitale I, Souquère S, Castedo M, Pierron G, Kroemer G. Defective autophagy associated with LC3 puncta in epothilone-resistant cancer cells Cell Cycle. 2010 Jan 29;9(2).

  53. Sherborne AL, Hosking FJ, Prasad RB, Kumar R, Koehler R, Vijayakrishnan J, Papaemmanuil E, Bartram CR, Stanulla M, Schrappe M, Gast A, Dobbins SE, Ma Y, Sheridan E, Taylor M, Kinsey SE, Lightfoot T, Roman E, Irving JA, Allan JM, Moorman AV, Harrison CJ, Tomlinson IP, Richards S, Zimmermann M, Szalai C, Semsei AF, Erdelyi DJ, Krajinovic M, Sinnett D, Healy J, Neira AG, Kawamata N, Ogawa S, Koeffler HP, Hemminki K, Greaves M, Houlston RS. Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk. Nat Genet. 2010 Jun;42(6):492-4.

  54. Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R. Expander: from expression microarrays to networks and functions. Nat Protoc. 2010;5(2):303-22

  55. Vaculova A, Kaminskyy V, Jalalvand E, Surova O, Zhivotovsky B. Doxorubicin and etoposide sensitize small cell lung carcinoma cells expressing caspase-8 to TRAIL. Mol Cancer. 2010 Apr 23;9(1):87.

  56. Vakifahmetoglu-Norberg H, Zhivotovsky B. The unpredictable caspase-2: what can it do? Trends Cell Biol. 2010 Jan 8.

  57. Van Herreweghe F, Festjens N, Declercq W, Vandenabeele P. Tumor necrosis factor-mediated cell death: to break or to burst, that's the question. Cell Mol Life Sci. 2010 Mar 4.

  58. Vande Walle L, Wirawan E, Lamkanfi M, Festjens N, Verspurten J, Saelens X, Vanden Berghe T, Vandenabeele P. The mitochondrial serine protease HtrA2/Omi cleaves RIP1 during apoptosis of Ba/F3 cells induced by growth factor withdrawal. Cell Res. 2010 Feb 2.

  59. Vitale I, Senovilla L, Jemaà M, Michaud M, Galluzzi L, Kepp O, Nanty L, Criollo A, Rello-Varona S, Manic G, Métivier D, Vivet S, Tajeddine N, Joza N, Valent A, Castedo M, Kroemer G. Multipolar mitosis of tetraploid cells: inhibition by p53 and dependency on Mos. EMBO J. 2010 Feb 25.

  60. Zalckvar E, Yosef N, Reef S, Ber Y, Rubinstein AD, Mor I, Sharan R, Ruppin E, Kimchi A. A systems level strategy for analyzing the cell death network: implication in exploring the apoptosis/autophagy connection. Cell Death Differ. 2010 Feb 12.

  61. Zhivotovsky B, Orrenius S. Cell death mechanisms: Cross-talk and role in disease. Exp Cell Res. 2010 Mar 5.

  62. Zitvogel L, Kepp O, Kroemer G. Decoding Cell Death Signals in Inflammation and Immunity. Cell. 2010 Mar 19;140(6):798-804.

  63. Wickström M, Viktorsson K, Lundholm L, Aesoy R, Nygren H, Sooman L, Fryknäs M, Vogel LK, Lewensohn R, Larsson R, Gullbo J. The alkylating prodrug J1 can be activated by aminopeptidase N, leading to a possible target directed release of melphalan. Biochem Pharmacol. 2010 Jan 11.

  64. Wolkenhauer O, Auffray C, Baltrusch S, Blüthgen N, Byrne H, Cascante M, Ciliberto A, Dale T, Drasdo D, Fell D, Ferrell JE Jr, Gallahan D, Gatenby R, Günther U, Harms BD, Herzel H, Junghanss C, Kunz M, van Leeuwen I, Lenormand P, Levi F, Linnebacher M, Lowengrub J, Maini PK, Malik A, Rateitschak K, Sansom O, Schäfer R, Schürrle K, Sers C, Schnell S, Shibata D, Tyson J, Vera J, White M, Zhivotovsky B, Jaster R. Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res. 2010 Jan 1;70(1):12-3.

  65. Yazdi AS, Drexler SK, Tschopp J. The Role of the Inflammasome in Nonmyeloid Cells. J Clin Immunol. 2010 Jun 27.