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miRNA expression profiling of 51 human breast cancer cell lines reveals subtype and driver mutation-specific miRNAs.

Riaz M, van Jaarsveld MT, Hollestelle A, Prager-van der Smissen WJ, Heine AA, Boersma AW, Liu J, Helmijr J, Ozturk B, Smid M, Wiemer EA, Foekens JA, Martens JW - Breast Cancer Res. (2013)

Bottom Line: Thirty miRNAs were associated with p16INK4 status while only a few miRNAs were associated with BRCA1, PIK3CA/PTEN and TP53 mutation status.Twelve miRNAs were associated with DNA copy number variation of the respective locus.Specific sets of miRNAs were associated with ERBB2 overexpression, p16INK4a or E-cadherin mutation or E-cadherin methylation status, which implies that these miRNAs may contribute to the driver role of these genetic aberrations.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Introduction: Breast cancer is a genetically and phenotypically complex disease. To understand the role of miRNAs in this molecular complexity, we performed miRNA expression analysis in a cohort of molecularly well-characterized human breast cancer cell lines to identify miRNAs associated with the most common molecular subtypes and the most frequent genetic aberrations.

Methods: Using a microarray carrying LNA™ modified oligonucleotide capture probes), expression levels of 725 human miRNAs were measured in 51 breast cancer cell lines. Differential miRNA expression was explored by unsupervised cluster analysis and was then associated with the molecular subtypes and genetic aberrations commonly present in breast cancer.

Results: Unsupervised cluster analysis using the most variably expressed miRNAs divided the 51 breast cancer cell lines into a major and a minor cluster predominantly mirroring the luminal and basal intrinsic subdivision of breast cancer cell lines. One hundred and thirteen miRNAs were differentially expressed between these two main clusters. Forty miRNAs were differentially expressed between basal-like and normal-like/claudin-low cell lines. Within the luminal-group, 39 miRNAs were associated with ERBB2 overexpression and 24 with E-cadherin gene mutations, which are frequent in this subtype of breast cancer cell lines. In contrast, 31 miRNAs were associated with E-cadherin promoter hypermethylation, which, contrary to E-cadherin mutation, is exclusively observed in breast cancer cell lines that are not of luminal origin. Thirty miRNAs were associated with p16INK4 status while only a few miRNAs were associated with BRCA1, PIK3CA/PTEN and TP53 mutation status. Twelve miRNAs were associated with DNA copy number variation of the respective locus.

Conclusion: Luminal-basal and epithelial-mesenchymal associated miRNAs determine the subdivision of miRNA transcriptome of breast cancer cell lines. Specific sets of miRNAs were associated with ERBB2 overexpression, p16INK4a or E-cadherin mutation or E-cadherin methylation status, which implies that these miRNAs may contribute to the driver role of these genetic aberrations. Additionally, miRNAs, which are located in a genomic region showing recurrent genetic aberrations, may themselves play a driver role in breast carcinogenesis or contribute to a driver gene in their vicinity. In short, our study provides detailed molecular miRNA portraits of breast cancer cell lines, which can be exploited for functional studies of clinically important miRNAs.

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Differential expression of miRNAs with respect to E-cadherin status. Differentially expressed miRNAs (A) between E-cadherin mutant and wild-type breast cancer cell lines in the luminal-group, and (B) between E-cadherin promoter hypermethylated and wild-type breast cancer cell lines in the estrogen receptor-negative/basal group. Cell lines HCC1806, SK-BR-7, SUM102PT, SUM149PT, and SUM229PE, which show partial promoter hypermethylation, were not included in the analysis since we were not sure to which extent partial promoter methylation will affect E-cadherin expression levels in these cell lines. Yellow and blue, high and low overall similarity of samples in miRNA expression, respectively.
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Figure 4: Differential expression of miRNAs with respect to E-cadherin status. Differentially expressed miRNAs (A) between E-cadherin mutant and wild-type breast cancer cell lines in the luminal-group, and (B) between E-cadherin promoter hypermethylated and wild-type breast cancer cell lines in the estrogen receptor-negative/basal group. Cell lines HCC1806, SK-BR-7, SUM102PT, SUM149PT, and SUM229PE, which show partial promoter hypermethylation, were not included in the analysis since we were not sure to which extent partial promoter methylation will affect E-cadherin expression levels in these cell lines. Yellow and blue, high and low overall similarity of samples in miRNA expression, respectively.

Mentions: E-cadherin elicits a growth suppressive effect in mammary epithelial cells and its expression is frequently lost in human breast tumors [30]. Loss of E-cadherin expression occurs either by gene mutation or by gene promoter hypermethylation. In this cohort of cell lines and in clinical specimens, E-cadherin is preferentially mutated in luminal/ER-positive cell lines while it is frequently inactivated by promoter hypermethylation in basal/ER-negative cell lines [21]. To determine whether loss of E-cadherin expression in human breast cancer cell lines is associated with differential expression of miRNAs, we compared 10 E-cadherin mutant cell lines with 17 wild-type cell lines within the luminal-group of cell lines (Figure 4A) and compared nine E-cadherin promoter hypermethylated cell lines with eight nonmethylated cell lines within the ER-negative/basal-group (Figure 4B). Our comparison revealed signatures of 24 and 31 differentially expressed miRNAs associated with E-cadherin mutant and wild type cell lines and with cell lines having E-cadherin promoter hypermethylation or not, respectively (P < 0.05) (Figure 4A, B; in see Tables S10 and S11 in Additional file 1). Interestingly, both E-cadherin signatures had no miRNAs in common showing similar behavior.


miRNA expression profiling of 51 human breast cancer cell lines reveals subtype and driver mutation-specific miRNAs.

Riaz M, van Jaarsveld MT, Hollestelle A, Prager-van der Smissen WJ, Heine AA, Boersma AW, Liu J, Helmijr J, Ozturk B, Smid M, Wiemer EA, Foekens JA, Martens JW - Breast Cancer Res. (2013)

Differential expression of miRNAs with respect to E-cadherin status. Differentially expressed miRNAs (A) between E-cadherin mutant and wild-type breast cancer cell lines in the luminal-group, and (B) between E-cadherin promoter hypermethylated and wild-type breast cancer cell lines in the estrogen receptor-negative/basal group. Cell lines HCC1806, SK-BR-7, SUM102PT, SUM149PT, and SUM229PE, which show partial promoter hypermethylation, were not included in the analysis since we were not sure to which extent partial promoter methylation will affect E-cadherin expression levels in these cell lines. Yellow and blue, high and low overall similarity of samples in miRNA expression, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3672661&req=5

Figure 4: Differential expression of miRNAs with respect to E-cadherin status. Differentially expressed miRNAs (A) between E-cadherin mutant and wild-type breast cancer cell lines in the luminal-group, and (B) between E-cadherin promoter hypermethylated and wild-type breast cancer cell lines in the estrogen receptor-negative/basal group. Cell lines HCC1806, SK-BR-7, SUM102PT, SUM149PT, and SUM229PE, which show partial promoter hypermethylation, were not included in the analysis since we were not sure to which extent partial promoter methylation will affect E-cadherin expression levels in these cell lines. Yellow and blue, high and low overall similarity of samples in miRNA expression, respectively.
Mentions: E-cadherin elicits a growth suppressive effect in mammary epithelial cells and its expression is frequently lost in human breast tumors [30]. Loss of E-cadherin expression occurs either by gene mutation or by gene promoter hypermethylation. In this cohort of cell lines and in clinical specimens, E-cadherin is preferentially mutated in luminal/ER-positive cell lines while it is frequently inactivated by promoter hypermethylation in basal/ER-negative cell lines [21]. To determine whether loss of E-cadherin expression in human breast cancer cell lines is associated with differential expression of miRNAs, we compared 10 E-cadherin mutant cell lines with 17 wild-type cell lines within the luminal-group of cell lines (Figure 4A) and compared nine E-cadherin promoter hypermethylated cell lines with eight nonmethylated cell lines within the ER-negative/basal-group (Figure 4B). Our comparison revealed signatures of 24 and 31 differentially expressed miRNAs associated with E-cadherin mutant and wild type cell lines and with cell lines having E-cadherin promoter hypermethylation or not, respectively (P < 0.05) (Figure 4A, B; in see Tables S10 and S11 in Additional file 1). Interestingly, both E-cadherin signatures had no miRNAs in common showing similar behavior.

Bottom Line: Thirty miRNAs were associated with p16INK4 status while only a few miRNAs were associated with BRCA1, PIK3CA/PTEN and TP53 mutation status.Twelve miRNAs were associated with DNA copy number variation of the respective locus.Specific sets of miRNAs were associated with ERBB2 overexpression, p16INK4a or E-cadherin mutation or E-cadherin methylation status, which implies that these miRNAs may contribute to the driver role of these genetic aberrations.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Introduction: Breast cancer is a genetically and phenotypically complex disease. To understand the role of miRNAs in this molecular complexity, we performed miRNA expression analysis in a cohort of molecularly well-characterized human breast cancer cell lines to identify miRNAs associated with the most common molecular subtypes and the most frequent genetic aberrations.

Methods: Using a microarray carrying LNA™ modified oligonucleotide capture probes), expression levels of 725 human miRNAs were measured in 51 breast cancer cell lines. Differential miRNA expression was explored by unsupervised cluster analysis and was then associated with the molecular subtypes and genetic aberrations commonly present in breast cancer.

Results: Unsupervised cluster analysis using the most variably expressed miRNAs divided the 51 breast cancer cell lines into a major and a minor cluster predominantly mirroring the luminal and basal intrinsic subdivision of breast cancer cell lines. One hundred and thirteen miRNAs were differentially expressed between these two main clusters. Forty miRNAs were differentially expressed between basal-like and normal-like/claudin-low cell lines. Within the luminal-group, 39 miRNAs were associated with ERBB2 overexpression and 24 with E-cadherin gene mutations, which are frequent in this subtype of breast cancer cell lines. In contrast, 31 miRNAs were associated with E-cadherin promoter hypermethylation, which, contrary to E-cadherin mutation, is exclusively observed in breast cancer cell lines that are not of luminal origin. Thirty miRNAs were associated with p16INK4 status while only a few miRNAs were associated with BRCA1, PIK3CA/PTEN and TP53 mutation status. Twelve miRNAs were associated with DNA copy number variation of the respective locus.

Conclusion: Luminal-basal and epithelial-mesenchymal associated miRNAs determine the subdivision of miRNA transcriptome of breast cancer cell lines. Specific sets of miRNAs were associated with ERBB2 overexpression, p16INK4a or E-cadherin mutation or E-cadherin methylation status, which implies that these miRNAs may contribute to the driver role of these genetic aberrations. Additionally, miRNAs, which are located in a genomic region showing recurrent genetic aberrations, may themselves play a driver role in breast carcinogenesis or contribute to a driver gene in their vicinity. In short, our study provides detailed molecular miRNA portraits of breast cancer cell lines, which can be exploited for functional studies of clinically important miRNAs.

Show MeSH
Related in: MedlinePlus