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Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.

Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, Carr JM, Khrebtukova I, Luo S, Zhang L, Schroth GP, Perez EA, Thompson EA - PLoS ONE (2011)

Bottom Line: Gene expression in cell lines was dominated by ER-associated genes.In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines.The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.

View Article: PubMed Central - PubMed

Affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.

ABSTRACT
We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A), and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER- cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER- cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5 kb of the 5' end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER- breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.

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There is an inverse correlation between methylation status of promoter-proximal CpG islands and mRNA abundance.Panel A: A scatter plot and trend line between fold change of gene expression and mean difference of methylation between ER+ and ER− cell lines. The Pearson correlation coefficient R is −0.75 [95%CI: −0.81, −0.68] with p-value<2.2e-16. Panel B: The distance from the start of each of the CpG islands that exhibited inverse correlation with mRNA abundance, illustrated in Figure A, to the start of the corresponding gene plotted against log2 gene expression fold change between ER+ and ER− cell lines. Panel C: A histogram representing the distribution of differentially methylated CpG islands in 149 differentially expressed genes.
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pone-0017490-g004: There is an inverse correlation between methylation status of promoter-proximal CpG islands and mRNA abundance.Panel A: A scatter plot and trend line between fold change of gene expression and mean difference of methylation between ER+ and ER− cell lines. The Pearson correlation coefficient R is −0.75 [95%CI: −0.81, −0.68] with p-value<2.2e-16. Panel B: The distance from the start of each of the CpG islands that exhibited inverse correlation with mRNA abundance, illustrated in Figure A, to the start of the corresponding gene plotted against log2 gene expression fold change between ER+ and ER− cell lines. Panel C: A histogram representing the distribution of differentially methylated CpG islands in 149 differentially expressed genes.

Mentions: Of the 444 CpG islands that were differentially methylated in ER+ and ER− cell lines, 164 islands were located within 5 kb of the promoters of 162 differentially expressed genes. The relationship between the mean methylation difference and the log2 fold change for those 162 genes is shown in Figure 4A (Pearson correlation coefficient = −0.75 with 95% confidence interval: −0.81 to −0.68 and regression p-value<2.2e-16). A strong negative correlation was observed between methylation status and expression for most of these genes, although there were a number of outliers (13 genes) in which methylation status appeared to be unrelated to expression. We observed a strong inverse correlation between methylation status of 151 CpG islands and expression of 149 associated genes.


Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.

Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, Carr JM, Khrebtukova I, Luo S, Zhang L, Schroth GP, Perez EA, Thompson EA - PLoS ONE (2011)

There is an inverse correlation between methylation status of promoter-proximal CpG islands and mRNA abundance.Panel A: A scatter plot and trend line between fold change of gene expression and mean difference of methylation between ER+ and ER− cell lines. The Pearson correlation coefficient R is −0.75 [95%CI: −0.81, −0.68] with p-value<2.2e-16. Panel B: The distance from the start of each of the CpG islands that exhibited inverse correlation with mRNA abundance, illustrated in Figure A, to the start of the corresponding gene plotted against log2 gene expression fold change between ER+ and ER− cell lines. Panel C: A histogram representing the distribution of differentially methylated CpG islands in 149 differentially expressed genes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3045451&req=5

pone-0017490-g004: There is an inverse correlation between methylation status of promoter-proximal CpG islands and mRNA abundance.Panel A: A scatter plot and trend line between fold change of gene expression and mean difference of methylation between ER+ and ER− cell lines. The Pearson correlation coefficient R is −0.75 [95%CI: −0.81, −0.68] with p-value<2.2e-16. Panel B: The distance from the start of each of the CpG islands that exhibited inverse correlation with mRNA abundance, illustrated in Figure A, to the start of the corresponding gene plotted against log2 gene expression fold change between ER+ and ER− cell lines. Panel C: A histogram representing the distribution of differentially methylated CpG islands in 149 differentially expressed genes.
Mentions: Of the 444 CpG islands that were differentially methylated in ER+ and ER− cell lines, 164 islands were located within 5 kb of the promoters of 162 differentially expressed genes. The relationship between the mean methylation difference and the log2 fold change for those 162 genes is shown in Figure 4A (Pearson correlation coefficient = −0.75 with 95% confidence interval: −0.81 to −0.68 and regression p-value<2.2e-16). A strong negative correlation was observed between methylation status and expression for most of these genes, although there were a number of outliers (13 genes) in which methylation status appeared to be unrelated to expression. We observed a strong inverse correlation between methylation status of 151 CpG islands and expression of 149 associated genes.

Bottom Line: Gene expression in cell lines was dominated by ER-associated genes.In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines.The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.

View Article: PubMed Central - PubMed

Affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.

ABSTRACT
We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A), and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER- cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER- cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5 kb of the 5' end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER- breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.

Show MeSH
Related in: MedlinePlus