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

Stingele S, Stoehr G, Peplowska K, Cox J, Mann M, Storchova Z - Mol. Syst. Biol. (2012)

Bottom Line: We found that whereas transcription levels reflect the chromosome copy number changes, the abundance of some proteins, such as subunits of protein complexes and protein kinases, is reduced toward diploid levels.For example, the DNA and RNA metabolism pathways were downregulated, whereas several pathways such as energy metabolism, membrane metabolism and lysosomal pathways were upregulated.In particular, we found that the p62-dependent selective autophagy is activated in the human trisomic and tetrasomic cells.

View Article: PubMed Central - PubMed

Affiliation: Group of Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany.

ABSTRACT
Extra chromosome copies markedly alter the physiology of eukaryotic cells, but the underlying reasons are not well understood. We created human trisomic and tetrasomic cell lines and determined the quantitative changes in their transcriptome and proteome in comparison with their diploid counterparts. We found that whereas transcription levels reflect the chromosome copy number changes, the abundance of some proteins, such as subunits of protein complexes and protein kinases, is reduced toward diploid levels. Furthermore, using the quantitative data we investigated the changes of cellular pathways in response to aneuploidy. This analysis revealed specific and uniform alterations in pathway regulation in cells with extra chromosomes. For example, the DNA and RNA metabolism pathways were downregulated, whereas several pathways such as energy metabolism, membrane metabolism and lysosomal pathways were upregulated. In particular, we found that the p62-dependent selective autophagy is activated in the human trisomic and tetrasomic cells. Our data present the first broad proteomic analysis of human cells with abnormal karyotypes and suggest a uniform cellular response to the presence of an extra chromosome.

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Characterization of HCT116 and its tri- and tetrasomic derivatives. (A) Chromosome paints of used tri- and tetrasomic cell lines. Bar—10 μm. (B) Growth curves of tri- and tetrasomic cell lines in comparison with their diploid counterparts. Each point represents the mean with standard deviation of three independent experiments. (C) Cell-cycle progression of HCT116 (left panel) and HCT116 5/4 (right panel) after release from thymidine block, analyzed by flow cytometry. The major delay occurs in the G1 and the S phase. The length of each cell-cycle phase is indicated above the graph. Population was considered to enter a specific phase of cell cycle if at least 50% of cells showed corresponding DNA content. See also Supplementary Figure S1. Source data is available for this figure in the Supplementary Information.
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f1: Characterization of HCT116 and its tri- and tetrasomic derivatives. (A) Chromosome paints of used tri- and tetrasomic cell lines. Bar—10 μm. (B) Growth curves of tri- and tetrasomic cell lines in comparison with their diploid counterparts. Each point represents the mean with standard deviation of three independent experiments. (C) Cell-cycle progression of HCT116 (left panel) and HCT116 5/4 (right panel) after release from thymidine block, analyzed by flow cytometry. The major delay occurs in the G1 and the S phase. The length of each cell-cycle phase is indicated above the graph. Population was considered to enter a specific phase of cell cycle if at least 50% of cells showed corresponding DNA content. See also Supplementary Figure S1. Source data is available for this figure in the Supplementary Information.

Mentions: A detailed analysis of aneuploidy in human cells is hampered by the lack of an appropriate model with matching diploid and aneuploid cells. To circumvent this limitation, chromosome transfer via micronuclei was used to add an extra chromosome into HCT116 (Haugen et al, 2008) or HCT116 stably expressing H2B-GFP (Supplementary Figure S1A). This approach generated cognate trisomic and tetrasomic derivatives that carry additional copies of chromosome 3 (labeled HCT116 3/3) or chromosome 5 (trisomy: HCT116 H2B-GFP 5/3, tetrasomy: HCT116 5/4 and HCT116 H2B-GFP 5/4). HCT116 is a transformed cell line with several previously identified chromosomal changes such as the chromosome Y loss and amplified regions of chromosomes 8, 10 and 17 (Masramon et al, 2000). These aberrancies are mostly present in the new aneuploid cell lines (Supplementary Figure 1B) and thus likely do not affect the results. Nevertheless, to strengthen our analysis and to overcome this possible drawback, we generated cell lines trisomic for chromosomes 5 and 12, and another cell line trisomic for chromosome 21, both derived from the diploid primary epithelial cell line RPE-1 that was immortalized by the expression of hTert and that lacks substantial chromosomal aberrancies. The successful chromosome transfer was verified by chromosome paints (Figure 1A), comparative genomic hybridization (CGH) and multicolor fluorescence in situ hybridization (Supplementary Figure S1B and C). The analysis confirmed that original cell lines and their derivatives differ only by copy number of a specific chromosome.


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

Stingele S, Stoehr G, Peplowska K, Cox J, Mann M, Storchova Z - Mol. Syst. Biol. (2012)

Characterization of HCT116 and its tri- and tetrasomic derivatives. (A) Chromosome paints of used tri- and tetrasomic cell lines. Bar—10 μm. (B) Growth curves of tri- and tetrasomic cell lines in comparison with their diploid counterparts. Each point represents the mean with standard deviation of three independent experiments. (C) Cell-cycle progression of HCT116 (left panel) and HCT116 5/4 (right panel) after release from thymidine block, analyzed by flow cytometry. The major delay occurs in the G1 and the S phase. The length of each cell-cycle phase is indicated above the graph. Population was considered to enter a specific phase of cell cycle if at least 50% of cells showed corresponding DNA content. See also Supplementary Figure S1. Source data is available for this figure in the Supplementary Information.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472693&req=5

f1: Characterization of HCT116 and its tri- and tetrasomic derivatives. (A) Chromosome paints of used tri- and tetrasomic cell lines. Bar—10 μm. (B) Growth curves of tri- and tetrasomic cell lines in comparison with their diploid counterparts. Each point represents the mean with standard deviation of three independent experiments. (C) Cell-cycle progression of HCT116 (left panel) and HCT116 5/4 (right panel) after release from thymidine block, analyzed by flow cytometry. The major delay occurs in the G1 and the S phase. The length of each cell-cycle phase is indicated above the graph. Population was considered to enter a specific phase of cell cycle if at least 50% of cells showed corresponding DNA content. See also Supplementary Figure S1. Source data is available for this figure in the Supplementary Information.
Mentions: A detailed analysis of aneuploidy in human cells is hampered by the lack of an appropriate model with matching diploid and aneuploid cells. To circumvent this limitation, chromosome transfer via micronuclei was used to add an extra chromosome into HCT116 (Haugen et al, 2008) or HCT116 stably expressing H2B-GFP (Supplementary Figure S1A). This approach generated cognate trisomic and tetrasomic derivatives that carry additional copies of chromosome 3 (labeled HCT116 3/3) or chromosome 5 (trisomy: HCT116 H2B-GFP 5/3, tetrasomy: HCT116 5/4 and HCT116 H2B-GFP 5/4). HCT116 is a transformed cell line with several previously identified chromosomal changes such as the chromosome Y loss and amplified regions of chromosomes 8, 10 and 17 (Masramon et al, 2000). These aberrancies are mostly present in the new aneuploid cell lines (Supplementary Figure 1B) and thus likely do not affect the results. Nevertheless, to strengthen our analysis and to overcome this possible drawback, we generated cell lines trisomic for chromosomes 5 and 12, and another cell line trisomic for chromosome 21, both derived from the diploid primary epithelial cell line RPE-1 that was immortalized by the expression of hTert and that lacks substantial chromosomal aberrancies. The successful chromosome transfer was verified by chromosome paints (Figure 1A), comparative genomic hybridization (CGH) and multicolor fluorescence in situ hybridization (Supplementary Figure S1B and C). The analysis confirmed that original cell lines and their derivatives differ only by copy number of a specific chromosome.

Bottom Line: We found that whereas transcription levels reflect the chromosome copy number changes, the abundance of some proteins, such as subunits of protein complexes and protein kinases, is reduced toward diploid levels.For example, the DNA and RNA metabolism pathways were downregulated, whereas several pathways such as energy metabolism, membrane metabolism and lysosomal pathways were upregulated.In particular, we found that the p62-dependent selective autophagy is activated in the human trisomic and tetrasomic cells.

View Article: PubMed Central - PubMed

Affiliation: Group of Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany.

ABSTRACT
Extra chromosome copies markedly alter the physiology of eukaryotic cells, but the underlying reasons are not well understood. We created human trisomic and tetrasomic cell lines and determined the quantitative changes in their transcriptome and proteome in comparison with their diploid counterparts. We found that whereas transcription levels reflect the chromosome copy number changes, the abundance of some proteins, such as subunits of protein complexes and protein kinases, is reduced toward diploid levels. Furthermore, using the quantitative data we investigated the changes of cellular pathways in response to aneuploidy. This analysis revealed specific and uniform alterations in pathway regulation in cells with extra chromosomes. For example, the DNA and RNA metabolism pathways were downregulated, whereas several pathways such as energy metabolism, membrane metabolism and lysosomal pathways were upregulated. In particular, we found that the p62-dependent selective autophagy is activated in the human trisomic and tetrasomic cells. Our data present the first broad proteomic analysis of human cells with abnormal karyotypes and suggest a uniform cellular response to the presence of an extra chromosome.

Show MeSH
Related in: MedlinePlus