Maintenance of proteostasis in human aneuploid cell lines

• Applicant: Professorin Dr. Zuzana Storchova
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry ; Cell Biology
• Term: from 2012 to 2016
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 209937551

• Final Report Year: 2018

Final Report Abstract

What are the cellular consequences of abnormal chromosome numbers? Although up to 80 % of tumors contain non-diploid chromosome numbers, little is known about how cells react to this imbalance. To study consequences of aneuploidy, we have developed a model system where we transfer individual chromosomes to a diploid cell to construct aneuploid cells with defined karyotypic changes. By using this approach, we were able to directly compare isogenic cells that differ only by the presence of a single extra chromosome and to identify novel and previously unappreciated consequences of abnormal chromosome numbers. First, presence of extra chromosome markedly deregulated the gene expression. We found that not only the expression of genes encoded on the aneuploid chromosome was altered, but also genome-wide changes were readily identified. The latter changes are uniform regardless the identity of the extra chromosome and consist of on one hand overexpression of the genes required for lysosomal pathways and autophagy, endoplasmic reticulum, inflammatory response, membrane metabolism and glycolysis and, on the other hand, downregulation of genes required for cell cycle and growth, DNA replication, transcription and translation. Similar pathway deregulation was observed when proteome was analyzed. Moreover, this response to aneuploidy is highly conserved among various eukaryotic species. Further analysis of the phenotypical consequences of downregulation of DNA replication pathway revealed marked replication defects in aneuploid cells. Second, we found that the increased expression of the genes encoded on the extra chromosomes leads to imbalance in protein stoichiometry and subsequently to proteotoxic stress. This is reflected by upregulation of autophagy and lysosomal pathways, impaired protein folding and increased sensitivity to inhibitors of protein folding. Maintenance of protein homeostasis is critical for cellular processes, particular when considering balance among subunits of macromolecular protein complexes. Close analysis of the kinetics of protein stability revealed that proteasome-mediated degradation is essential to alleviate the consequences of imbalance among subunits of macromolecule complexes and this general phenomenon is of critical importance in aneuploid cells. Finally, autophagy seems to play an important role in cellular response to aneuploidy. We found that, in aneuploid cells, specifically the pathway of selective autophagy is active, which contributes to intracellular homeostasis by mediating the degradation of unwanted cytoplasmic material such as aggregated proteins, damaged or overabundant organelles and invading pathogens. Our data suggest that the transcription factor TFEB is critical to activation of this pathway in aneuploid cells. Further research will be required to fully understand the mechanisms of autophagy activation in response to abnormal chromosome numbers and its function in aneuploid cells. Taken together, using a novel model of defined aneuploidy in human cells, we have made a significant progress towards understanding the complex cellular changes triggered by abnormal chromosome numbers. Since aneuploidy is a common pathological factor, we believe that by defining the key aspects of the cellular stresses triggered by aneuploidy we will be able to determine novel and previously underappreciated therapeutical opportunities.

Publications

• (2012) Global analysis of genome, transcriptome and proteome reveals cellular response to aneuploidy, Molecular Systems Biology 8: 608
  Stingele S, Stoehr G, Peplowska K, Cox J, Mann M, Storchová Z
  
• (2013) Activation of autophagy in cells with abnormal karyotype, Autophagy 9:246-248
  Stingele S, Stoehr G, Storchová Z
  
• (2014) Dynamic karyotype, dynamic proteome: Buffering the effects of aneuploidy. Biochim Biophys Acta.1843:473-81
  Donnelly N, Storchová Z
  
• (2014) HSF1 deficiency and impaired HSP90-dependent protein folding are hallmarks of aneuploid human cells, EMBO Journal 33:2374-87
  Donnelly N, Passerini V, Dürrbaum M, Stingele S, Storchová Z
  
• (2014) Unique features of the transcriptional response to model aneuploidy in human cells. BMC Genomics 15:139-52
  Dürrbaum M, Kuznetsova AY, Passerini V, Stingele S, Stoehr G, Storchová Z
  
• (2015) Aneuploidy and proteotoxic stress in cancer, Molecular & Cellular Oncology, 2: e976491
  Donnelly N, Storchová Z
  
• (2015) Causes and consequences of protein folding stress in aneuploid cells, Cell Cycle, 14:4, 495-501
  Donnelly N, Storchová Z
  
• (2015) Effects of aneuploidy on gene expression: implications for cancer, FEBS J. 283: 791-802
  Dürrbaum M, Storchová Z
  
• (2016) Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation. Cell 167:803-815
  McShane E, Sin C, Zauber H, Wells J, Donnelly N, Wang X, Hou Y, Chen W, Storchová Z, Marsh J, Valeriani A and Selbach M
  
• (2016) The presence of extra chromosomes leads to genomic instability, Nat Commun. 7:10754
  Passerini V, Ozeri-Galai E, de Pagter MS, Donnelly N, Schmalbrock S, Kloosterman WP, Kerem B, Storchová Z
  
• (2016) Too much to handle - how gaining chromosomes destabilizes the genome. Cell Cycle. 16:1-8
  Passerini V, Storchová Z
  
• (2018) The deregulated microRNAome contributes to the cellular response to aneuploidy. BMC Genomics 19:197
  Dürrbaum M, Kruse C, Nieken KJ, Habermann B, Storchová Z