Determining signalling nodes for apoptosis by a genetic high-throughput screen

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Lin, Bevan ^a   Huntley, Derek ^a   AbuAli, Ghada ^a   Langley, Sarah R ^a   Sindelar, George ^a,b   Petretto, Enrico ^a   Butcher, Sarah ^a   Grimm, Stefan ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b Chemgineering Business Design GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GREEN FLUORESCENT PROTEIN;

APOPTOSIS; ARTICLE; BIOINFORMATICS; CELL ORGANELLE; CONTROLLED STUDY; DNA DETERMINATION; GENE CONTROL; GENE SEQUENCE; GENETIC SCREENING; GENETIC TRANSFECTION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; MICROTITER PLATE ASSAY; MOLECULAR CLONING; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SUICIDE GENE; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CELL FRACTIONATION; CELL STRAIN HEK293; DNA MICROARRAY; ENZYME LINKED IMMUNOSORBENT ASSAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; METABOLISM; METHODOLOGY; MOUSE; ROBOTICS;

ANIMALS; APOPTOSIS; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; ENZYME-LINKED IMMUNOSORBENT ASSAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; GREEN FLUORESCENT PROTEINS; HEK293 CELLS; HUMANS; MICE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ROBOTICS; SIGNAL TRANSDUCTION; SUBCELLULAR FRACTIONS;

EID: 80053054630     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025023     Document Type: Article

References (69)

1. Grimm S, (2004) The art and design of genetic screens: mammalian culture cells. Nat Rev Genet 5: 179-189.
2. Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL, et al. (2003) Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol Cell 12: 627-637.
3. Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, et al. (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428: 431-437.
4. Grimm S, Leder P, (1997) An apoptosis-inducing isoform of neu differentiation factor (NDF) identified using a novel screen for dominant, apoptosis-inducing genes. J Exp Med 185: 1137-1142.
5. Albayrak T, Scherhammer V, Schoenfeld N, Braziulis E, Mund T, et al. (2003) The Tumor Suppressor cybL, a Component of the Respiratory Chain, Mediates Apoptosis Induction. Mol Biol Cell 14: 3082-3096.
6. Neudecker F, Grimm S, (2000) High-throughput method for isolating plasmid DNA with reduced lipopolysaccharide content. Biotechniques 28: 107-109.
7. Schoenfeld N, Bauer MK, Grimm S, (2004) The metastasis suppressor gene C33/CD82/KAI1 induces apoptosis through reactive oxygen intermediates. Faseb J 18: 158-160.
8. Gewies A, Grimm S, (2003) Cathepsin-B and cathepsin-L expression levels do not correlate with sensitivity of tumour cells to TNF-alpha-mediated apoptosis. Br J Cancer 89: 1574-1580.
9. Bauer MKA, Schubert A, Rocks O, Grimm S, (1999) Adenine nucleotide translocase-1, a component of the permeability transition pore, can dominantly induce apoptosis. J Cell Biol 147: 1493-1502.
10. Mund T, Gewies A, Schoenfeld N, Bauer MK, Grimm S, (2003) Spike, a novel BH3-only protein, regulates apoptosis at the endoplasmic reticulum. Faseb J 17: 696-698.
11. Schubert A, Grimm S, (2004) Cyclophilin D, a Component of the Permeability Transition (PT)-Pore, Is an Apoptosis Repressor. Cancer Res 64: 85-93.
12. Irshad S, Mahul-Mellier AL, Kassouf N, Lemarie A, Grimm S, (2009) Isolation of ORCTL3 in a novel genetic screen for tumor-specific apoptosis inducers. Cell Death Differ 16: 890-898.
13. Lemarie A, Huc L, Pazarentzos E, Mahul-Mellier AL, Grimm S, (2010) Specific disintegration of complex II succinate:ubiquinone oxidoreductase links pH changes to oxidative stress for apoptosis induction. Cell Death Differ.
14. Iwasawa R, Mahul-Mellier AL, Datler C, Pazarentzos E, Grimm S, (2011) Fis1 and Bap31 bridge the mitochondria-ER interface to establish a platform for apoptosis induction. EMBO J 30: 556-568.
15. Grimm S, Kachel V, (2002) Robotic high-throughput assay for isolating apoptosis-inducing genes. Biotechniques 32: 670-677.
16. Kachel V, Sindelar G, Grimm S, (2006) High-throughput isolation of ultra-pure plasmid DNA by a robotic system. BMC Biotechnol 6: 9.
17. Nicholson DW, Ali A, Thornberry NA, Vaillancourt JP, Ding CK, et al. (1995) Identification and inhibition of the ICE/CED-3 protease necessary for mammalian apoptosis. Nature 376: 37-43.
18. Xu X, Shi YC, Gao W, Mao G, Zhao G, et al. (2002) The novel presenilin-1-associated protein is a proapoptotic mitochondrial protein. J Biol Chem 277: 48913-48922 Epub 42002 Oct 48910.
19. Kirkegaard T, Jaattela M, (2009) Lysosomal involvement in cell death and cancer. Biochim Biophys Acta 1793: 746-754 Epub 2008 Oct 2002.
20. Fu Y, Sies H, Lei XG, (2001) Opposite roles of selenium-dependent glutathione peroxidase-1 in superoxide generator diquat- and peroxynitrite-induced apoptosis and signaling. J Biol Chem 276: 43004-43009 Epub 42001 Sep 43018.
21. Prendergast GC, (2001) Actin' up: RhoB in cancer and apoptosis. Nat Rev Cancer 1: 162-168.
22. Fleischer A, Ayllon V, Rebollo A, (2002) ITM2BS regulates apoptosis by inducing loss of mitochondrial membrane potential. Eur J Immunol 32: 3498-3505.
23. Lv BF, Yu CF, Chen YY, Lu Y, Guo JH, et al. (2006) Protein tyrosine phosphatase interacting protein 51 (PTPIP51) is a novel mitochondria protein with an N-terminal mitochondrial targeting sequence and induces apoptosis. Apoptosis 11: 1489-1501.
24. James DI, Parone PA, Mattenberger Y, Martinou JC, (2003) hFis 1, a novel component of the mammalian mitochondrial fission machinery. J Biol Chem 278: 36373-36379 Epub 32003 Jun 36373.
25. Fleischer A, Rebollo A, (2004) Induction of p53-independent apoptosis by the BH3-only protein ITM2Bs. FEBS Lett 557: 283-287.
26. Stenzinger A, Schreiner D, Koch P, Hofer HW, Wimmer M, (2009) Cell and molecular biology of the novel protein tyrosine-phosphatase-interacting protein 51. Int Rev Cell Mol Biol 275: 183-246.
27. Suen DF, Norris KL, Youle RJ, (2008) Mitochondrial dynamics and apoptosis. Genes Dev 22: 1577-1590.
28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
29. Smedley D, Haider S, Ballester B, Holland R, London D, et al. (2009) BioMart-biological queries made easy. BMC Genomics 10: 22.
30. Ferri KF, Kroemer G, (2001) Organelle-specific initiation of cell death pathways. Nat Cell Biol 3: E255-263.
31. Bratton SB, Cohen GM, (2001) Apoptotic death sensor: an organelle's alter ego? Trends Pharmacol Sci 22: 306-315.
32. Hicks SW, Machamer CE, (2005) Golgi structure in stress sensing and apoptosis. Biochim Biophys Acta 1744: 406-414 Epub 2005 Mar 2022.
33. Vidal R, Frangione B, Rostagno A, Mead S, Revesz T, et al. (1999) A stop-codon mutation in the BRI gene associated with familial British dementia. Nature 399: 776-781.
34. Wanders RJ, Ferdinandusse S, Brites P, Kemp S, (2010) Peroxisomes, lipid metabolism and lipotoxicity. Biochim Biophys Acta 1801: 272-280.
35. Calore F, Genisset C, Casellato A, Rossato M, Codolo G, et al. Endosome-mitochondria juxtaposition during apoptosis induced by H. pylori VacA. Cell Death Differ 17: 1707-1716 Epub 2010 Apr 1730.
36. Schulze-Osthoff K, Walczak H, Droge W, Krammer PH, (1994) Cell nucleus and DNA fragmentation are not required for apoptosis. J Cell Biol 127: 15-20.
37. Garrido C, Kroemer G, (2004) Life's smile, death's grin: vital functions of apoptosis-executing proteins. Curr Opin Cell Biol 16: 639-646.
38. Zhang S, Malmersjo S, Li J, Ando H, Aizman O, et al. (2006) Distinct role of the N-terminal tail of the Na,K-ATPase catalytic subunit as a signal transducer. J Biol Chem 281: 21954-21962 Epub 22006 May 21924.
39. Evan GI, Wyllie AH, Gilbert CS, Littlewood TD, Land H, et al. (1992) Induction of apoptosis in fibroblasts by c-myc protein. Cell 69: 119-128.
40. Kan Z, Jaiswal BS, Stinson J, Janakiraman V, Bhatt D, et al. Diverse somatic mutation patterns and pathway alterations in human cancers.
41. Zhang L, Zhang W, Chen K, (2010) Search for cancer risk factors with microarray-based genome-wide association studies. Technol 9: 107-121.
42. Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M, (2001) Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res 11: 1463-1468.
43. Reed JC, Doctor KS, Godzik A, (2004) The domains of apoptosis: a genomics perspective. Sci STKE 2004: re9.
44. Henry-Mowatt J, Dive C, Martinou JC, James D, (2004) Role of mitochondrial membrane permeabilization in apoptosis and cancer. Oncogene 23: 2850-2860.
45. Galluzzi L, Kroemer G, (2007) Mitochondrial apoptosis without VDAC. Nat Cell Biol 9: 487-489.
46. Bredesen DE, (2000) Apoptosis: overview and signal transduction pathways. J Neurotrauma 17: 801-810.
47. Vaux DL, (2002) Apoptosis and toxicology-what relevance? Toxicology 181-182: 3-7.
48. Sakahira H, Enari M, Nagata S, (1998) Cleavage of CAD inhibitor in CAD activation and DNA degradation during apoptosis. Nature 391: 96-99.
49. Lazebnik YA, Kaufmann SH, Desnoyers S, Poirier GG, Earnshaw WC, (1994) Cleavage of poly(ADP-ribose) polymerase by a proteinase with properties like ICE. Nature 371: 346-347.
50. Iwasawa R, Mahul-Mellier AL, Datler C, Pazarentzos E, Grimm S, (2010) Fis1 and Bap31 bridge the mitochondria-ER interface to establish a platform for apoptosis induction.
51. Cowin PA, Anglesio M, Etemadmoghadam D, Bowtell DD, (2010) Profiling the cancer genome. Annu 11: 133-159.
52. Brachat A, Pierrat B, Brungger A, Heim J, (2000) Comparative microarray analysis of gene expression during apoptosis-induction by growth factor deprivation or protein kinase C inhibition. Oncogene 19: 5073-5082.
53. Brachat A, Pierrat B, Xynos A, Brecht K, Simonen M, et al. (2002) A microarray-based, integrated approach to identify novel regulators of cancer drug response and apoptosis. Oncogene 21: 8361-8371.
54. Brecht K, Simonen M, Heim J, (2005) Upregulation of alpha globin promotes apoptotic cell death in the hematopoietic cell line FL5.12. Apoptosis 10: 1043-1062.
55. Albayrak T, Grimm S, (2003) A high-throughput screen for single gene activities: isolation of apoptosis inducers. Biochem Biophys Res Commun 304: 772-776.
56. Grimm S, Voss-Neudecker F, (2003) High-Purity Plasmid Isolation Using Silica Oxide. Methods Mol Biol 235: 83-88.
57. Grimm S, Lin B, (2009) Genetic cell culture screens reveal mitochondrial apoptosis control. Front Biosci 14: 1471-1478.
58. Koenig-Hoffmann K, Bonin-Debs AL, Boche I, Gawin B, Gnirke A, et al. (2005) High throughput functional genomics: identification of novel genes with tumor suppressor phenotypes. Int J Cancer 113: 434-439.
59. Park KM, Kang E, Jeon YJ, Kim N, Kim NS, et al. (2007) Identification of novel regulators of apoptosis using a high-throughput cell-based screen. Mol Cells 23: 170-174.
60. Alcala S, Klee M, Fernandez J, Fleischer A, Pimentel-Muinos FX, (2008) A high-throughput screening for mammalian cell death effectors identifies the mitochondrial phosphate carrier as a regulator of cytochrome c release. Oncogene 27: 44-54 Epub 2007 Jul 2009.
61. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, et al. (2009) Ensembl 2009. Nucleic Acids Res 37: D690-697 Epub 2008 Nov 2025.
62. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
63. Zdobnov EM, Apweiler R, (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
64. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, et al. (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13: 2129-2141.
65. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, et al. (2016) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res 38: D204-210 Epub 2009 Dec 2016.
66. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
67. Bolstad BM, Irizarry RA, Astrand M, Speed TP, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
68. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80 Epub 2004 Sep 2015.
69. Schwender H, Ickstadt K, (2008) Empirical Bayes analysis of single nucleotide polymorphisms. BMC Bioinformatics 9: 144.