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DNA methylation and histone modifications regulate SOX11 expression in lymphoid and solid cancer cells.

Nordström L, Andersson E, Kuci V, Gustavsson E, Holm K, Ringnér M, Guldberg P, Ek S - BMC Cancer (2015)

Bottom Line: In contrast, SOX11 regulation in neoplastic tissues is more complex involving both DNA methylation and histone modifications.The possibility to re-express SOX11 in non-methylated tissue is of clinical relevance, and was successfully achieved in cell lines with low levels of SOX11 methylation.In breast cancer patients, methylation of the SOX11 promoter was shown to correlate with estrogen receptor status, suggesting that SOX11 may be functionally re-expressed during treatment with HDAC inhibitors in specific patient subgroups.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunotechnology, CREATE Health, Lund University, Lund, Sweden. lena.nordstrom@immun.lth.se.

ABSTRACT

Background: The neural transcription factor SOX11 is present at specific stages during embryo development with a very restricted expression in adult tissue, indicating precise regulation of transcription. SOX11 is strongly up-regulated in some malignancies and have a functional role in tumorgenesis. With the aim to explore differences in epigenetic regulation of SOX11 expression in normal versus neoplastic cells, we investigated methylation and histone modifications related to the SOX11 promoter and the possibility to induce re-expression using histone deacetylase (HDAC) or EZH2 inhibitors.

Methods: The epigenetic regulation of SOX11 was investigated in distinct non-malignant cell populations (n = 7) and neoplastic cell-lines (n = 42) of different cellular origins. DNA methylation was assessed using bisulfite sequencing, methylation-specific melting curve analysis, MethyLight and pyrosequencing. The presence of H3K27me3 was assessed using ChIP-qPCR. The HDAC inhibitors Vorinostat and trichostatin A were used to induce SOX11 in cell lines with no endogenous expression.

Results: The SOX11 promoter shows a low degree of methylation and strong enrichment of H3K27me3 in non-malignant differentiated cells, independent of cellular origin. Cancers of the B-cell lineage are strongly marked by de novo methylation at the SOX11 promoter in SOX11 non-expressing cells, while solid cancer entities display a more varying degree of SOX11 promoter methylation. The silencing mark H3K27me3 was generally present at the SOX11 promoter in non-expressing cells, and an increased enrichment was observed in cancer cells with a low degree of SOX11 methylation compared to cells with dense methylation. Finally, we demonstrate that the HDAC inhibitors (vorinostat and trichostatin A) induce SOX11 expression in cancer cells with low levels of SOX11 methylation.

Conclusions: We show that SOX11 is strongly marked by repressive histone marks in non-malignant cells. In contrast, SOX11 regulation in neoplastic tissues is more complex involving both DNA methylation and histone modifications. The possibility to re-express SOX11 in non-methylated tissue is of clinical relevance, and was successfully achieved in cell lines with low levels of SOX11 methylation. In breast cancer patients, methylation of the SOX11 promoter was shown to correlate with estrogen receptor status, suggesting that SOX11 may be functionally re-expressed during treatment with HDAC inhibitors in specific patient subgroups.

No MeSH data available.


Related in: MedlinePlus

SOX11 promoter methylation in tumor cell-lines. SOX11 promoter methylation status assessed with MethyLight and MS-MCA. The methylation levels analyzed by MethyLight are presented as percent methylated reference (PMR). PMR < 1 was considered as unmethylated promoter. SOX11 promoter methylation was investigated in lymphoma cell lines with (A) MethyLight and (B) MS-MCA. SOX11 promoter methylation was investigated in solid tumor cell lines with (C) MethyLight and (D) MS-MCA.
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Fig2: SOX11 promoter methylation in tumor cell-lines. SOX11 promoter methylation status assessed with MethyLight and MS-MCA. The methylation levels analyzed by MethyLight are presented as percent methylated reference (PMR). PMR < 1 was considered as unmethylated promoter. SOX11 promoter methylation was investigated in lymphoma cell lines with (A) MethyLight and (B) MS-MCA. SOX11 promoter methylation was investigated in solid tumor cell lines with (C) MethyLight and (D) MS-MCA.

Mentions: To explore the difference between non-malignant reference tissue and neoplastic cells, we further investigated the methylation status of SOX11 in 42 cell lines (Table 1) representing a wide range of human tumors with subgroups known to express SOX11, including lymphoid malignancies (n=19), ovarian cancer (n=5), breast cancer (n=8), lung cancer (n=3), brain cancers (n=5) and neuroblastoma (n=2). To determine DNA methylation by complementary methods, MethyLight and methylation-specific melting curve analysis (MS-MCA) were used. The MethyLight and MS-MCA assays covered 8/28 and 28/28 CpG sites previously investigated in non-malignant mature B-cells, respectively (see Additional file 2). Overall, a good agreement between MethyLight and MS-MCA was observed in our sample set (Figure 2A and B), although calculated PMR values were significantly lower compared to absolute values derived from bisulfite sequencing of the same cell lines [17]. In agreement with public data [8,17,29], we show that SOX11 is de novo methylated in all Burkitt’s lymphomas, follicular lymphomas and diffuse large B-cell lymphomas. In mantle cell lymphomas that express SOX11, the promoter is generally unmethylated (Figure 2A and B). Solid tumors show a much more diverse methylation pattern within the SOX11 promoter (Figure 2C and D), possibly reflecting clinical subtypes with an altered epigenetic regulation.Table 1


DNA methylation and histone modifications regulate SOX11 expression in lymphoid and solid cancer cells.

Nordström L, Andersson E, Kuci V, Gustavsson E, Holm K, Ringnér M, Guldberg P, Ek S - BMC Cancer (2015)

SOX11 promoter methylation in tumor cell-lines. SOX11 promoter methylation status assessed with MethyLight and MS-MCA. The methylation levels analyzed by MethyLight are presented as percent methylated reference (PMR). PMR < 1 was considered as unmethylated promoter. SOX11 promoter methylation was investigated in lymphoma cell lines with (A) MethyLight and (B) MS-MCA. SOX11 promoter methylation was investigated in solid tumor cell lines with (C) MethyLight and (D) MS-MCA.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4403777&req=5

Fig2: SOX11 promoter methylation in tumor cell-lines. SOX11 promoter methylation status assessed with MethyLight and MS-MCA. The methylation levels analyzed by MethyLight are presented as percent methylated reference (PMR). PMR < 1 was considered as unmethylated promoter. SOX11 promoter methylation was investigated in lymphoma cell lines with (A) MethyLight and (B) MS-MCA. SOX11 promoter methylation was investigated in solid tumor cell lines with (C) MethyLight and (D) MS-MCA.
Mentions: To explore the difference between non-malignant reference tissue and neoplastic cells, we further investigated the methylation status of SOX11 in 42 cell lines (Table 1) representing a wide range of human tumors with subgroups known to express SOX11, including lymphoid malignancies (n=19), ovarian cancer (n=5), breast cancer (n=8), lung cancer (n=3), brain cancers (n=5) and neuroblastoma (n=2). To determine DNA methylation by complementary methods, MethyLight and methylation-specific melting curve analysis (MS-MCA) were used. The MethyLight and MS-MCA assays covered 8/28 and 28/28 CpG sites previously investigated in non-malignant mature B-cells, respectively (see Additional file 2). Overall, a good agreement between MethyLight and MS-MCA was observed in our sample set (Figure 2A and B), although calculated PMR values were significantly lower compared to absolute values derived from bisulfite sequencing of the same cell lines [17]. In agreement with public data [8,17,29], we show that SOX11 is de novo methylated in all Burkitt’s lymphomas, follicular lymphomas and diffuse large B-cell lymphomas. In mantle cell lymphomas that express SOX11, the promoter is generally unmethylated (Figure 2A and B). Solid tumors show a much more diverse methylation pattern within the SOX11 promoter (Figure 2C and D), possibly reflecting clinical subtypes with an altered epigenetic regulation.Table 1

Bottom Line: In contrast, SOX11 regulation in neoplastic tissues is more complex involving both DNA methylation and histone modifications.The possibility to re-express SOX11 in non-methylated tissue is of clinical relevance, and was successfully achieved in cell lines with low levels of SOX11 methylation.In breast cancer patients, methylation of the SOX11 promoter was shown to correlate with estrogen receptor status, suggesting that SOX11 may be functionally re-expressed during treatment with HDAC inhibitors in specific patient subgroups.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunotechnology, CREATE Health, Lund University, Lund, Sweden. lena.nordstrom@immun.lth.se.

ABSTRACT

Background: The neural transcription factor SOX11 is present at specific stages during embryo development with a very restricted expression in adult tissue, indicating precise regulation of transcription. SOX11 is strongly up-regulated in some malignancies and have a functional role in tumorgenesis. With the aim to explore differences in epigenetic regulation of SOX11 expression in normal versus neoplastic cells, we investigated methylation and histone modifications related to the SOX11 promoter and the possibility to induce re-expression using histone deacetylase (HDAC) or EZH2 inhibitors.

Methods: The epigenetic regulation of SOX11 was investigated in distinct non-malignant cell populations (n = 7) and neoplastic cell-lines (n = 42) of different cellular origins. DNA methylation was assessed using bisulfite sequencing, methylation-specific melting curve analysis, MethyLight and pyrosequencing. The presence of H3K27me3 was assessed using ChIP-qPCR. The HDAC inhibitors Vorinostat and trichostatin A were used to induce SOX11 in cell lines with no endogenous expression.

Results: The SOX11 promoter shows a low degree of methylation and strong enrichment of H3K27me3 in non-malignant differentiated cells, independent of cellular origin. Cancers of the B-cell lineage are strongly marked by de novo methylation at the SOX11 promoter in SOX11 non-expressing cells, while solid cancer entities display a more varying degree of SOX11 promoter methylation. The silencing mark H3K27me3 was generally present at the SOX11 promoter in non-expressing cells, and an increased enrichment was observed in cancer cells with a low degree of SOX11 methylation compared to cells with dense methylation. Finally, we demonstrate that the HDAC inhibitors (vorinostat and trichostatin A) induce SOX11 expression in cancer cells with low levels of SOX11 methylation.

Conclusions: We show that SOX11 is strongly marked by repressive histone marks in non-malignant cells. In contrast, SOX11 regulation in neoplastic tissues is more complex involving both DNA methylation and histone modifications. The possibility to re-express SOX11 in non-methylated tissue is of clinical relevance, and was successfully achieved in cell lines with low levels of SOX11 methylation. In breast cancer patients, methylation of the SOX11 promoter was shown to correlate with estrogen receptor status, suggesting that SOX11 may be functionally re-expressed during treatment with HDAC inhibitors in specific patient subgroups.

No MeSH data available.


Related in: MedlinePlus