Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

Molecular Systems Biology

Volumn 8, Issue , 2012, Pages

  Stingele, Silvia ^a   Stoehr, Gabriele ^a   Peplowska, Karolina ^a   Cox, Jürgen ^a   Mann, Matthias ^a   Storchova, Zuzana ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

aneuploidy; autophagy; p62; pathway analysis; proteomics

Indexed keywords

CELL DNA; PROTEIN KINASE; PROTEIN P62; PROTEOME; RNA; TRANSCRIPTOME; DNA; MESSENGER RNA;

ANEUPLOIDY; ANIMAL CELL; ARTICLE; CELL MEMBRANE; CELL STRAIN HCT116; CONTROLLED STUDY; DIPLOIDY; DNA METABOLISM; DOWN REGULATION; ENERGY METABOLISM; GENE DOSAGE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HUMAN; HUMAN CELL; INTRACELLULAR SIGNALING; KARYOTYPE; LYSOSOME; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SUBUNIT; PROTEOMICS; QUANTITATIVE ANALYSIS; RNA METABOLISM; SELECTIVE AUTOPHAGY; SUPERNUMERARY CHROMOSOME; UPREGULATION; AUTOPHAGY; CELL LINE; GENETICS; GENOME; HUMAN CHROMOSOME; METABOLISM; TETRASOMY; TRISOMY;

EUKARYOTA;

ANEUPLOIDY; AUTOPHAGY; CELL LINE; CHROMOSOMES, HUMAN; DNA; GENOME; HUMANS; PROTEIN SUBUNITS; PROTEOME; RNA, MESSENGER; TETRASOMY; TRANSCRIPTOME; TRISOMY;

EID: 84868290476     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2012.40     Document Type: Article

References (35)

1. Äit Yahya-Graison E, Aubert J, Dauphinot L, Rivals I, Prieur M, Golfier G, Rossier J, Personnaz L, Créau N, Bléhaut H, Robin S, Delabar JM, Potier MC (2007) Classificationofhuman chromosome 21 gene-expression variations in Down syndrome: impact on disease phenotypes. Am J Hum Genet 81: 475-491 (Pubitemid 47330207)
2. Birchler JA, Riddle NC, Auger DL, Veitia RA (2005) Dosage balance in gene regulation: biological implications. Trends Genet 21: 219-226 (Pubitemid 40387899)
3. Chen G, Bradford WD, Seidel CW, Li R (2012) Hsp90 stress potentiates rapid cellular adaptation through induction of aneuploidy. Nature 482: 246-250
4. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210 (Pubitemid 34679544)
5. Fournier RE (1981) A general high-efficiency procedure for production of microcell hybrids. Proc Natl Acad Sci USA 78: 6349-6353 (Pubitemid 12179709)
6. Gidalevitz T, Ben-Zvi A, Ho KH, Brignull HR, Morimoto RI (2006) Progressive disruption of cellular protein folding in models of polyglutamine diseases. Science 311: 1471-1474 (Pubitemid 43376703)
7. Goldberg AL, Dice JF (1974) Intracellular protein degradation in mammalian and bacterial cells. Annu Rev Biochem 43: 835-869
8. Guialis A, Morrison KE, Ingles CJ (1979) Regulated synthesis of RNA polymerase II polypeptides in Chinese hamster ovary cell lines. J Biol Chem 254: 4171-4176
9. Guo M, Birchler JA (1994) Trans-acting dosage effects on the expression of model gene systems in maize aneuploids. Science 266: 1999-2002
10. Hassold T, Hall H, Hunt P (2007) The origin of human aneuploidy: where we have been, where we are going. Hum Mol Genet 16: R203-R208
11. Haugen AC, Goel A, Yamada K, Marra G, Nguyen TP, Nagasaka T, Kanazawa S, Koike J, Kikuchi Y, Zhong X, Arita M, Shibuya K, Oshimura M, Hemmi H, Boland CR, Koi M (2008) Genetic instability caused by loss of MutS homologue 3 in human colorectal cancer. Cancer Res 68: 8465-8472
12. He C, Klionsky DJ (2009) Regulation mechanisms and signaling pathways of autophagy. Annu Rev Genet 43: 67-93
13. Huettel B, Kreil DP, Matzke M, Matzke AJ (2008) Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana. PLoS Genet 4: e1000226
14. Kabeya Y, Mizushima N, Ueno T, Yamamoto A, Kirisako T, Noda T, Kominami E, Ohsumi Y, Yoshimori T (2000) LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J 19: 5720-5728
15. Kimura S, Noda T, Yoshimori T (2007) Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy 3: 452-460 (Pubitemid 47293726)
16. Klionsky DJ, Abeliovich H, Agostinis P, Agrawal DK, Aliev G, Askew DS, Baba M, Baehrecke EH, Bahr BA, Ballabio A, Bamber BA, Bassham DC, Bergamini E, Bi X, Biard-Piechaczyk M, Blum JS, Bredesen DE, Brodsky JL, Brumell JH, Brunk UT et al (2008) Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 4: 151-175 (Pubitemid 351231180)
17. Kvitek DJ, Will JL, Gasch AP (2008) Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet 4: e1000223
18. Lamark T, Johansen T (2009) Autophagy: links with the proteasome. Curr Opin Cell Biol 22: 192-198
19. Makarevitch I, Phillips RL, Springer NM (2008) Profiling expression changes caused by a segmental aneuploid in maize. BMC Genomics 9: 7-16
20. Masramon L, Ribas M, Cifuentes P, Arribas R, Garćia F, Egozcue J, Peinado MA, Miró R (2000) Cytogenetic characterization of two colon cell lines by using conventional G-banding, comparative genomic hybridization, and whole chromosome painting. Cancer Genet Cytogenet 121: 17-21 (Pubitemid 30665735)
21. Niwa O, Tange Y, Kurabayashi A (2006) Growth arrest and chromosome instability in aneuploid yeast. Yeast 23: 937-950 (Pubitemid 44794855)
22. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1: 376-386
23. Pankiv S, Clausen TH, Lamark T, Brech A, Bruun JA, Outzen H, Overvatn A, Bjorkoy G, Johansen T (2007) p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem 282: 24131-24145 (Pubitemid 47328003)
24. Pavelka N, Rancati G, Zhu J, Bradford WD, Saraf A, Florens L, Sanderson BW, Hattem GL, Li R (2010) Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature 468: 321-325
25. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW (2010) CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res 38: D497-D501
26. Segal DJ, McCoy EE (1974) Studies on Down's syndrome in tissue culture. I. Growth rates and protein contents of fibroblast cultures. J Cell Physiol 83: 85-90
27. Selmecki A, Forche A, Berman J (2006) Aneuploidy and isochromo-some formation in drug-resistant Candida albicans. Science 313: 367-370 (Pubitemid 44480964)
28. Sheltzer JM, Blank HM, Pfau SJ, Tange Y, George BM, Humpton TJ, Brito IL, Hiraoka Y, Niwa O, Amon A (2011) Aneuploidy drives genomic instability in yeast. Science 333: 1026-1030
29. Stenberg P, Lundberg LE, Johansson A-M, Rydén P, Svensson MJ, Larsson J (2009) Buffering of Segmental and Chromosomal Aneuploidies in Drosophila melanogaster. PLoS Genet 5: e1000465
30. Storchova Z, Pellman D (2004) From polyploidy to aneuploidy, genome instability and cancer. Nat Rev Mol Cell Biol 5: 45-54 (Pubitemid 38089840)
31. Tang YC, Williams BR, Siegel JJ, Amon A (2011) Identification of aneuploidy-selective antiproliferation compounds. Cell 144: 499-512
32. Torres EM, Dephoure N, Panneerselvam A, Tucker CM, Whittaker CA, Gygi SP, Dunham MJ, Amon A (2010) Identification of aneuploidy-tolerating mutations. Cell 143: 71-83
33. Torres EM, Sokolsky T, Tucker CM, Chan LY, Boselli M, Dunham MJ, Amon A (2007) Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science 317: 916-924 (Pubitemid 47301313)
34. Upender MB, Habermann JK, McShane LM, Korn EL, Barrett JC, Difilippantonio MJ, Ried T (2004) Chromosome transfer induced aneuploidy results in complex dysregulation of the cellular transcriptome in immortalized and cancer cells. Cancer Res 64: 6941-6949 (Pubitemid 39331003)
35. Williams BR, Prabhu VR, Hunter KE, Glazier CM, Whittaker CA, Housman DE, Amon A (2008) Aneuploidy affects proliferation and spontaneous immortalization in mammalian cells. Science 322: 703-709