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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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Uniform global response to presence of an extra chromosome. (A) Two-dimensional annotation enrichment analysis. Pathways altered in the cell line with chromosome 3 trisomy in comparison with the cell line with chromosome 5 trisomy are plotted (Benjamini-Hochberg FDR threshold 0.02). Each dot represents one category as defined in the KEGG and GO database, the colors mark groups of related pathways as described in the inset. Axis—position scores of the pathways; negative values indicate downregulation, positive values indicate upregulation. See Supplementary Information for further details. (B) Pathway alterations identified in HCT116 and RPE-1 cells show similar trends. (C, D) Box-plots of all proteins within representative categories identified as significantly altered by the two-dimensional annotation enrichment analysis. Examples of upregulated (lysosome, carbohydrate catabolic process) and downregulated (spliceosome, chromatin remodeling) pathways show uniform response among all cell lines with extra chromosomes. All differences between DNA and protein levels are statistically significant (unpaired T-test with Welch's correction, P<0.05). For more information, see also Supplementary Figure S4 and Supplementary Table S2.
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f4: Uniform global response to presence of an extra chromosome. (A) Two-dimensional annotation enrichment analysis. Pathways altered in the cell line with chromosome 3 trisomy in comparison with the cell line with chromosome 5 trisomy are plotted (Benjamini-Hochberg FDR threshold 0.02). Each dot represents one category as defined in the KEGG and GO database, the colors mark groups of related pathways as described in the inset. Axis—position scores of the pathways; negative values indicate downregulation, positive values indicate upregulation. See Supplementary Information for further details. (B) Pathway alterations identified in HCT116 and RPE-1 cells show similar trends. (C, D) Box-plots of all proteins within representative categories identified as significantly altered by the two-dimensional annotation enrichment analysis. Examples of upregulated (lysosome, carbohydrate catabolic process) and downregulated (spliceosome, chromatin remodeling) pathways show uniform response among all cell lines with extra chromosomes. All differences between DNA and protein levels are statistically significant (unpaired T-test with Welch's correction, P<0.05). For more information, see also Supplementary Figure S4 and Supplementary Table S2.

Mentions: Next, we asked how aneuploidy affects global pathway regulation. To this end, we used a recently developed software called ‘2-D annotation enrichment analysis' (see Supplementary Information). For each clone, we identified all significantly altered pathways (as defined by Gene Ontology categories, KEGG pathways and CORUM database) and ranked the relative abundance changes of proteins within the category compared with the complete measured data set. The resulting score is on the scale from −1 to +1, where the pathways close to −1 are most downregulated and pathways close to +1 are most upregulated (see Supplementary Information for further details). Plotting these calculated scores revealed remarkable similarities in pathway regulation among the analyzed aneuploid cell lines (Figure 4A and B). We found that pathways involved in DNA and RNA metabolism, such as replication, DNA repair, transcription and mRNA processing, were significantly downregulated (Figure 4A, B and D; Supplementary Figure S5A), which is consistent with the observed growth delay in the G1 and S phase (Figure 1C; Supplementary Figure S1D, E and H). Upregulated categories identified in all analyzed cell lines included pathways required for lipid and membrane biogenesis, endoplasmic reticulum, Golgi vesicles and lysosome functions as well as energy metabolic pathways such as mitochondrial respiratory metabolism and carbohydrate metabolism (Figure 4A–C; Supplementary Figure S5A). Remarkably, the 2-D enrichment analysis of the transcriptome data determined similar changes in the pathway regulation, suggesting that the pathway response cannot be caused by a bias in protein detection (Supplementary Figure S5B and C). The observed alterations in pathway regulation were not an artifact of the chromosome number changes, since excluding the proteins coded on chromosome 5 from the analysis did not affect the identified pathways (Supplementary Figure S5D). Additionally, we found a remarkable overlap in pathway alterations between all RPE-1- and HCT116-derived trisomic and tetrasomic cell lines (Figure 4B; Supplementary Figure S5A). Taken together, the uniformity of the response in different human trisomic and tetrasomic cells demonstrates that the presence of an extra chromosome itself, and not individual chromosome or cell types, is an important determinant of the general cellular response.


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)

Uniform global response to presence of an extra chromosome. (A) Two-dimensional annotation enrichment analysis. Pathways altered in the cell line with chromosome 3 trisomy in comparison with the cell line with chromosome 5 trisomy are plotted (Benjamini-Hochberg FDR threshold 0.02). Each dot represents one category as defined in the KEGG and GO database, the colors mark groups of related pathways as described in the inset. Axis—position scores of the pathways; negative values indicate downregulation, positive values indicate upregulation. See Supplementary Information for further details. (B) Pathway alterations identified in HCT116 and RPE-1 cells show similar trends. (C, D) Box-plots of all proteins within representative categories identified as significantly altered by the two-dimensional annotation enrichment analysis. Examples of upregulated (lysosome, carbohydrate catabolic process) and downregulated (spliceosome, chromatin remodeling) pathways show uniform response among all cell lines with extra chromosomes. All differences between DNA and protein levels are statistically significant (unpaired T-test with Welch's correction, P<0.05). For more information, see also Supplementary Figure S4 and Supplementary Table S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Uniform global response to presence of an extra chromosome. (A) Two-dimensional annotation enrichment analysis. Pathways altered in the cell line with chromosome 3 trisomy in comparison with the cell line with chromosome 5 trisomy are plotted (Benjamini-Hochberg FDR threshold 0.02). Each dot represents one category as defined in the KEGG and GO database, the colors mark groups of related pathways as described in the inset. Axis—position scores of the pathways; negative values indicate downregulation, positive values indicate upregulation. See Supplementary Information for further details. (B) Pathway alterations identified in HCT116 and RPE-1 cells show similar trends. (C, D) Box-plots of all proteins within representative categories identified as significantly altered by the two-dimensional annotation enrichment analysis. Examples of upregulated (lysosome, carbohydrate catabolic process) and downregulated (spliceosome, chromatin remodeling) pathways show uniform response among all cell lines with extra chromosomes. All differences between DNA and protein levels are statistically significant (unpaired T-test with Welch's correction, P<0.05). For more information, see also Supplementary Figure S4 and Supplementary Table S2.
Mentions: Next, we asked how aneuploidy affects global pathway regulation. To this end, we used a recently developed software called ‘2-D annotation enrichment analysis' (see Supplementary Information). For each clone, we identified all significantly altered pathways (as defined by Gene Ontology categories, KEGG pathways and CORUM database) and ranked the relative abundance changes of proteins within the category compared with the complete measured data set. The resulting score is on the scale from −1 to +1, where the pathways close to −1 are most downregulated and pathways close to +1 are most upregulated (see Supplementary Information for further details). Plotting these calculated scores revealed remarkable similarities in pathway regulation among the analyzed aneuploid cell lines (Figure 4A and B). We found that pathways involved in DNA and RNA metabolism, such as replication, DNA repair, transcription and mRNA processing, were significantly downregulated (Figure 4A, B and D; Supplementary Figure S5A), which is consistent with the observed growth delay in the G1 and S phase (Figure 1C; Supplementary Figure S1D, E and H). Upregulated categories identified in all analyzed cell lines included pathways required for lipid and membrane biogenesis, endoplasmic reticulum, Golgi vesicles and lysosome functions as well as energy metabolic pathways such as mitochondrial respiratory metabolism and carbohydrate metabolism (Figure 4A–C; Supplementary Figure S5A). Remarkably, the 2-D enrichment analysis of the transcriptome data determined similar changes in the pathway regulation, suggesting that the pathway response cannot be caused by a bias in protein detection (Supplementary Figure S5B and C). The observed alterations in pathway regulation were not an artifact of the chromosome number changes, since excluding the proteins coded on chromosome 5 from the analysis did not affect the identified pathways (Supplementary Figure S5D). Additionally, we found a remarkable overlap in pathway alterations between all RPE-1- and HCT116-derived trisomic and tetrasomic cell lines (Figure 4B; Supplementary Figure S5A). Taken together, the uniformity of the response in different human trisomic and tetrasomic cells demonstrates that the presence of an extra chromosome itself, and not individual chromosome or cell types, is an important determinant of the general cellular response.

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