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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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Abundance of subunits of protein complexes and kinases in the tetrasomic cell line. (A) Density plots of subunits of protein complexes (as defined in the CORUM database) encoded on all disomic chromosomes compared with non-CORUM proteins (left panel); the same for proteins encoded on the tetrasomic chromosome 5 (right panel). The differences between CORUM and non-CORUM populations of chromosome 5 are statistically significant (Wilcoxon rank sum test). Dashed lines indicate medians of the populations. (B) Examples of protein complexes with at least one subunit coded on the tetrasomic chromosome 5. Each dot represents abundance changes of one gene (black), its corresponding mRNA (blue) and protein (red). Subunits coded on chromosome 5 are indicated with an arrow and number. (C) The abundance of DNA, mRNA and proteins of kinases coded on chromosome 5. See also Supplementary Figure S3. Source data is available for this figure in the Supplementary Information.
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f3: Abundance of subunits of protein complexes and kinases in the tetrasomic cell line. (A) Density plots of subunits of protein complexes (as defined in the CORUM database) encoded on all disomic chromosomes compared with non-CORUM proteins (left panel); the same for proteins encoded on the tetrasomic chromosome 5 (right panel). The differences between CORUM and non-CORUM populations of chromosome 5 are statistically significant (Wilcoxon rank sum test). Dashed lines indicate medians of the populations. (B) Examples of protein complexes with at least one subunit coded on the tetrasomic chromosome 5. Each dot represents abundance changes of one gene (black), its corresponding mRNA (blue) and protein (red). Subunits coded on chromosome 5 are indicated with an arrow and number. (C) The abundance of DNA, mRNA and proteins of kinases coded on chromosome 5. See also Supplementary Figure S3. Source data is available for this figure in the Supplementary Information.

Mentions: The fact that most proteins coded on the extra chromosomes are more abundant than proteins from diploid chromosomes indicates that there is no general efficient mechanism for ‘gene dosage compensation' of the analyzed tri- or tetrasomies. Nevertheless, a remarkable proportion of these proteins are present at levels lower than expected according to the gene and mRNA copy numbers, suggesting that some proteins or protein categories might be adjusted to normal abundance. A long standing hypothesis posits that free subunits of multimolecular complexes may be degraded in cells (see e.g., Goldberg and Dice, 1974 and Guialis et al, 1979). Analysis of our data confirmed that the abundances of subunits of protein complexes (as annotated in the CORUM database; Ruepp et al, 2010) that are encoded on the tetrasomic chromosome are lower than expected based on the gene copy number, and more similar to the protein abundances observed in the parental cell line HCT116; the median of proteins of CORUM complexes coded on chromosome 5 is shifted down to 0.43 (Figure 3A). A similar shift toward the diploid levels for the CORUM-annotated proteins can be detected in all analyzed cell lines (Supplementary Figure S4A). We examined 14 different macromolecular complexes with at least one subunit coded on the tetrasomic chromosome and found that 8 of them (57%) maintain stoichiometry by decreasing the protein abundance close to the normal, disomic levels, while the mRNA levels vary (Figure 3B; Supplementary Figure S4B; Supplementary Table S3).


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)

Abundance of subunits of protein complexes and kinases in the tetrasomic cell line. (A) Density plots of subunits of protein complexes (as defined in the CORUM database) encoded on all disomic chromosomes compared with non-CORUM proteins (left panel); the same for proteins encoded on the tetrasomic chromosome 5 (right panel). The differences between CORUM and non-CORUM populations of chromosome 5 are statistically significant (Wilcoxon rank sum test). Dashed lines indicate medians of the populations. (B) Examples of protein complexes with at least one subunit coded on the tetrasomic chromosome 5. Each dot represents abundance changes of one gene (black), its corresponding mRNA (blue) and protein (red). Subunits coded on chromosome 5 are indicated with an arrow and number. (C) The abundance of DNA, mRNA and proteins of kinases coded on chromosome 5. See also Supplementary Figure S3. 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

f3: Abundance of subunits of protein complexes and kinases in the tetrasomic cell line. (A) Density plots of subunits of protein complexes (as defined in the CORUM database) encoded on all disomic chromosomes compared with non-CORUM proteins (left panel); the same for proteins encoded on the tetrasomic chromosome 5 (right panel). The differences between CORUM and non-CORUM populations of chromosome 5 are statistically significant (Wilcoxon rank sum test). Dashed lines indicate medians of the populations. (B) Examples of protein complexes with at least one subunit coded on the tetrasomic chromosome 5. Each dot represents abundance changes of one gene (black), its corresponding mRNA (blue) and protein (red). Subunits coded on chromosome 5 are indicated with an arrow and number. (C) The abundance of DNA, mRNA and proteins of kinases coded on chromosome 5. See also Supplementary Figure S3. Source data is available for this figure in the Supplementary Information.
Mentions: The fact that most proteins coded on the extra chromosomes are more abundant than proteins from diploid chromosomes indicates that there is no general efficient mechanism for ‘gene dosage compensation' of the analyzed tri- or tetrasomies. Nevertheless, a remarkable proportion of these proteins are present at levels lower than expected according to the gene and mRNA copy numbers, suggesting that some proteins or protein categories might be adjusted to normal abundance. A long standing hypothesis posits that free subunits of multimolecular complexes may be degraded in cells (see e.g., Goldberg and Dice, 1974 and Guialis et al, 1979). Analysis of our data confirmed that the abundances of subunits of protein complexes (as annotated in the CORUM database; Ruepp et al, 2010) that are encoded on the tetrasomic chromosome are lower than expected based on the gene copy number, and more similar to the protein abundances observed in the parental cell line HCT116; the median of proteins of CORUM complexes coded on chromosome 5 is shifted down to 0.43 (Figure 3A). A similar shift toward the diploid levels for the CORUM-annotated proteins can be detected in all analyzed cell lines (Supplementary Figure S4A). We examined 14 different macromolecular complexes with at least one subunit coded on the tetrasomic chromosome and found that 8 of them (57%) maintain stoichiometry by decreasing the protein abundance close to the normal, disomic levels, while the mRNA levels vary (Figure 3B; Supplementary Figure S4B; Supplementary Table S3).

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