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Genetic alterations of histone lysine methyltransferases and their significance in breast cancer.

Liu L, Kimball S, Liu H, Holowatyj A, Yang ZQ - Oncotarget (2015)

Bottom Line: We identified 12 HMTs with the highest frequency of genetic alterations, including 8 with high-level amplification, 2 with putative homozygous deletion, and 2 with somatic mutation.Integrative analysis identified 8 HMTs (SETDB1, SMYD3, ASH1L, SMYD2, WHSC1L1, SUV420H1, SETDB2, and KMT2C) that are dysregulated by genetic alterations, classifying them as candidate therapeutic targets.Together, our findings provide a strong foundation for further mechanistic research and therapeutic options using HMTs to treat breast cancer.

View Article: PubMed Central - PubMed

Affiliation: Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA.

ABSTRACT
Histone lysine methyltransferases (HMTs), a large class of enzymes that catalyze site-specific methylation of lysine residues on histones and other proteins, play critical roles in controlling transcription, chromatin architecture, and cellular differentiation. However, the genomic landscape and clinical significance of HMTs in breast cancer remain poorly characterized. Here, we conducted a meta-analysis of approximately 50 HMTs in breast cancer and identified associations among recurrent copy number alterations, mutations, gene expression, and clinical outcome. We identified 12 HMTs with the highest frequency of genetic alterations, including 8 with high-level amplification, 2 with putative homozygous deletion, and 2 with somatic mutation. Different subtypes of breast cancer have different patterns of copy number and expression for each HMT gene. In addition, chromosome 1q contains four HMTs that are concurrently or independently amplified or overexpressed in breast cancer. Copy number or mRNA expression of several HMTs was significantly associated with basal-like breast cancer and shorter patient survival. Integrative analysis identified 8 HMTs (SETDB1, SMYD3, ASH1L, SMYD2, WHSC1L1, SUV420H1, SETDB2, and KMT2C) that are dysregulated by genetic alterations, classifying them as candidate therapeutic targets. Together, our findings provide a strong foundation for further mechanistic research and therapeutic options using HMTs to treat breast cancer.

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mRNA expression levels of eight HMTs in a panel of 20 breast cancer cell lines measured by qRT-PCRmRNA expression levels in the MCF10A cells, an immortalized but non-tumorigenic breast epithelial cell line, were arbitrarily set as 1. Relative expression levels are shown as fold changes compared with that in MCF10A cells.
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Figure 5: mRNA expression levels of eight HMTs in a panel of 20 breast cancer cell lines measured by qRT-PCRmRNA expression levels in the MCF10A cells, an immortalized but non-tumorigenic breast epithelial cell line, were arbitrarily set as 1. Relative expression levels are shown as fold changes compared with that in MCF10A cells.

Mentions: Next, we performed quantitative RT-PCR (qRT-PCR) analysis to measure the mRNA expression level of eight HMTs (SETDB1, ASH1L, SMYD2, SMYD3, SETD1A, WHSC1L1, SUV420H1, and SETDB2) in 20 breast cancer cell lines. MCF10A, an immortalized but non-tumorigenic breast epithelial cell line, was used as the control. These eight HMTs were chosen because seven of them showed the highest frequency of amplification (>5%), and the eighth, SETDB2, exhibited homozygous deletion in more than 2% of breast cancers. Although PRDM14 and PRDM7 were also among the HMTs with the highest frequency of amplification or homozygous deletion, respectively, in breast cancer, they were excluded from the qRT-PCR analysis because their expression levels in breast cancer cells were too low for detection (data not shown). Figure 5 shows the relative expression of eight HMT genes in 20 breast cancer cell lines compared with MCF10A cells. We found that mRNA levels of SETDB1 were more than two-fold higher in 14 of 20 breast cancer cell lines. For ASH1L, 11 of 20 cell lines; for SMYD2, 14 of 20; and for SMYD3, 6 of 20 breast cancer cell lines had two-fold higher mRNA levels. Notably, Colo824 showed higher expression of four 1q HMTs, with the highest expression of SETDB1 among the 20 breast cancer cell lines. In contrast, MCF7 showed higher expression of SETDB1, but not ASH1L and SMYD2, which is consistent with amplification of SETDB1, but not ASH1L and SMYD2, in this breast cancer cell line (Figure 5). We also found that SMYD3 and WHSC1L1 were prevalently overexpressed in several Luminal breast cancer cell lines. Breast cancer cell lines with deletion of SETDB2, such as SUM229, SUM149, HCC170, and SUM190, showed dramatically lower mRNA levels than MCF10A cells (Figure 5). Similar results were observed in RNA sequencing (RNA-Seq) data from 42 breast cancer cell lines compared with five normal mammary epithelial cell lines (Supplementary Figure S3). These experiments demonstrated that breast cancer cell lines with HMT gene CNAs showed a correlated change in mRNA expression. Thus, these cell lines provide useful preclinical models in which to investigate the biological functions of HMTs and to explore novel inhibitors for targeting HMTs in breast cancer in the future.


Genetic alterations of histone lysine methyltransferases and their significance in breast cancer.

Liu L, Kimball S, Liu H, Holowatyj A, Yang ZQ - Oncotarget (2015)

mRNA expression levels of eight HMTs in a panel of 20 breast cancer cell lines measured by qRT-PCRmRNA expression levels in the MCF10A cells, an immortalized but non-tumorigenic breast epithelial cell line, were arbitrarily set as 1. Relative expression levels are shown as fold changes compared with that in MCF10A cells.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4385864&req=5

Figure 5: mRNA expression levels of eight HMTs in a panel of 20 breast cancer cell lines measured by qRT-PCRmRNA expression levels in the MCF10A cells, an immortalized but non-tumorigenic breast epithelial cell line, were arbitrarily set as 1. Relative expression levels are shown as fold changes compared with that in MCF10A cells.
Mentions: Next, we performed quantitative RT-PCR (qRT-PCR) analysis to measure the mRNA expression level of eight HMTs (SETDB1, ASH1L, SMYD2, SMYD3, SETD1A, WHSC1L1, SUV420H1, and SETDB2) in 20 breast cancer cell lines. MCF10A, an immortalized but non-tumorigenic breast epithelial cell line, was used as the control. These eight HMTs were chosen because seven of them showed the highest frequency of amplification (>5%), and the eighth, SETDB2, exhibited homozygous deletion in more than 2% of breast cancers. Although PRDM14 and PRDM7 were also among the HMTs with the highest frequency of amplification or homozygous deletion, respectively, in breast cancer, they were excluded from the qRT-PCR analysis because their expression levels in breast cancer cells were too low for detection (data not shown). Figure 5 shows the relative expression of eight HMT genes in 20 breast cancer cell lines compared with MCF10A cells. We found that mRNA levels of SETDB1 were more than two-fold higher in 14 of 20 breast cancer cell lines. For ASH1L, 11 of 20 cell lines; for SMYD2, 14 of 20; and for SMYD3, 6 of 20 breast cancer cell lines had two-fold higher mRNA levels. Notably, Colo824 showed higher expression of four 1q HMTs, with the highest expression of SETDB1 among the 20 breast cancer cell lines. In contrast, MCF7 showed higher expression of SETDB1, but not ASH1L and SMYD2, which is consistent with amplification of SETDB1, but not ASH1L and SMYD2, in this breast cancer cell line (Figure 5). We also found that SMYD3 and WHSC1L1 were prevalently overexpressed in several Luminal breast cancer cell lines. Breast cancer cell lines with deletion of SETDB2, such as SUM229, SUM149, HCC170, and SUM190, showed dramatically lower mRNA levels than MCF10A cells (Figure 5). Similar results were observed in RNA sequencing (RNA-Seq) data from 42 breast cancer cell lines compared with five normal mammary epithelial cell lines (Supplementary Figure S3). These experiments demonstrated that breast cancer cell lines with HMT gene CNAs showed a correlated change in mRNA expression. Thus, these cell lines provide useful preclinical models in which to investigate the biological functions of HMTs and to explore novel inhibitors for targeting HMTs in breast cancer in the future.

Bottom Line: We identified 12 HMTs with the highest frequency of genetic alterations, including 8 with high-level amplification, 2 with putative homozygous deletion, and 2 with somatic mutation.Integrative analysis identified 8 HMTs (SETDB1, SMYD3, ASH1L, SMYD2, WHSC1L1, SUV420H1, SETDB2, and KMT2C) that are dysregulated by genetic alterations, classifying them as candidate therapeutic targets.Together, our findings provide a strong foundation for further mechanistic research and therapeutic options using HMTs to treat breast cancer.

View Article: PubMed Central - PubMed

Affiliation: Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA.

ABSTRACT
Histone lysine methyltransferases (HMTs), a large class of enzymes that catalyze site-specific methylation of lysine residues on histones and other proteins, play critical roles in controlling transcription, chromatin architecture, and cellular differentiation. However, the genomic landscape and clinical significance of HMTs in breast cancer remain poorly characterized. Here, we conducted a meta-analysis of approximately 50 HMTs in breast cancer and identified associations among recurrent copy number alterations, mutations, gene expression, and clinical outcome. We identified 12 HMTs with the highest frequency of genetic alterations, including 8 with high-level amplification, 2 with putative homozygous deletion, and 2 with somatic mutation. Different subtypes of breast cancer have different patterns of copy number and expression for each HMT gene. In addition, chromosome 1q contains four HMTs that are concurrently or independently amplified or overexpressed in breast cancer. Copy number or mRNA expression of several HMTs was significantly associated with basal-like breast cancer and shorter patient survival. Integrative analysis identified 8 HMTs (SETDB1, SMYD3, ASH1L, SMYD2, WHSC1L1, SUV420H1, SETDB2, and KMT2C) that are dysregulated by genetic alterations, classifying them as candidate therapeutic targets. Together, our findings provide a strong foundation for further mechanistic research and therapeutic options using HMTs to treat breast cancer.

Show MeSH
Related in: MedlinePlus