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Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer.

Rafique S, Thomas JS, Sproul D, Bickmore WA - Genome Biol. (2015)

Bottom Line: This occurs not only at individual genes, but also over larger chromosomal domains.For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus.In MCF7 cells, we show that this depends on the presence of estrogen.

View Article: PubMed Central - PubMed

Affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. sehrishrafique@hotmail.com.

ABSTRACT

Background: Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers.

Results: We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen.

Conclusions: Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells.

No MeSH data available.


Related in: MedlinePlus

Chromatin compaction at subregion 2 of the 16p11.2 RER region in breast cancer cell lines, in normal breast tissue and in primary breast tumors. a Box plots comparing the distribution of normalized FISH interprobe distances (d2/r2) measured across subregion 2 of the 16p11.2 RER region in a normal breast cell line (HMLE) and in ER+ (MCF7, LY2, MDAMB361) and ER− (MDAMB231 and MDAMB468) breast cancer cell lines. n = 45–60 cells. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). b Box plots showing the distribution of normalized FISH interprobe distances (d2/r2) measured across subregion 2 of the 16p11.2 RER region in normal breast tissue and in ER+ and ER− tumor tissues. n = 250–300 alleles. Distances in the ER+ tumor were significantly greater than in normal tissue (p < 0.0001) or in the ER− tumor (p = 0.004). Differences between normal and ER− tumor tissue were not significant (p = 0.24). c Example FISH images using probe pairs (red and green) that delineate subregion 2 in normal breast tissue and in ER+ and ER− tumor tissue. DNA is stained with DAPI (blue). Scale bar = 5 μm
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Fig6: Chromatin compaction at subregion 2 of the 16p11.2 RER region in breast cancer cell lines, in normal breast tissue and in primary breast tumors. a Box plots comparing the distribution of normalized FISH interprobe distances (d2/r2) measured across subregion 2 of the 16p11.2 RER region in a normal breast cell line (HMLE) and in ER+ (MCF7, LY2, MDAMB361) and ER− (MDAMB231 and MDAMB468) breast cancer cell lines. n = 45–60 cells. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). b Box plots showing the distribution of normalized FISH interprobe distances (d2/r2) measured across subregion 2 of the 16p11.2 RER region in normal breast tissue and in ER+ and ER− tumor tissues. n = 250–300 alleles. Distances in the ER+ tumor were significantly greater than in normal tissue (p < 0.0001) or in the ER− tumor (p = 0.004). Differences between normal and ER− tumor tissue were not significant (p = 0.24). c Example FISH images using probe pairs (red and green) that delineate subregion 2 in normal breast tissue and in ER+ and ER− tumor tissue. DNA is stained with DAPI (blue). Scale bar = 5 μm

Mentions: To determine the chromatin compaction status at subregion 2 in a normal breast cell line, FISH was also carried out on the non-transformed immortalized human mammary epithelial cell line HMLE [36]. The chromatin state of this region in HMLE was more compact than in MCF7 and LY2 cells, but not significantly different to that in the ER− cell lines MDAMB231 and MDAMB468 (Fig. 6a). A second independent ER+ breast cancer cell line, MDAMB361, showed a trend to being more de-compact than HMLE but this difference was not significant (Fig. 6a). This lesser de-compaction correlates with the expression level of genes in subregion 2 in MDAMB361, which was lower than in MCF7s and LY2 (Fig. 5c). We also note that unlike MCF7s and LY2 cells, MDAMB361 cells are HER2+ due to copy number amplification of the ERBB2 oncogene [20]. Our analysis of RER gene expression demonstrates that the breast tumors of the ERBB2 subtype have lower expression levels of cluster 1 RER regions (Fig. 3b). This suggests that the expression of ERBB2 oncogene lessens RER region expression and chromatin decompaction phenotype of cluster 1 RER regions, such as the 16p11.2 region.Fig. 6


Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer.

Rafique S, Thomas JS, Sproul D, Bickmore WA - Genome Biol. (2015)

Chromatin compaction at subregion 2 of the 16p11.2 RER region in breast cancer cell lines, in normal breast tissue and in primary breast tumors. a Box plots comparing the distribution of normalized FISH interprobe distances (d2/r2) measured across subregion 2 of the 16p11.2 RER region in a normal breast cell line (HMLE) and in ER+ (MCF7, LY2, MDAMB361) and ER− (MDAMB231 and MDAMB468) breast cancer cell lines. n = 45–60 cells. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). b Box plots showing the distribution of normalized FISH interprobe distances (d2/r2) measured across subregion 2 of the 16p11.2 RER region in normal breast tissue and in ER+ and ER− tumor tissues. n = 250–300 alleles. Distances in the ER+ tumor were significantly greater than in normal tissue (p < 0.0001) or in the ER− tumor (p = 0.004). Differences between normal and ER− tumor tissue were not significant (p = 0.24). c Example FISH images using probe pairs (red and green) that delineate subregion 2 in normal breast tissue and in ER+ and ER− tumor tissue. DNA is stained with DAPI (blue). Scale bar = 5 μm
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Fig6: Chromatin compaction at subregion 2 of the 16p11.2 RER region in breast cancer cell lines, in normal breast tissue and in primary breast tumors. a Box plots comparing the distribution of normalized FISH interprobe distances (d2/r2) measured across subregion 2 of the 16p11.2 RER region in a normal breast cell line (HMLE) and in ER+ (MCF7, LY2, MDAMB361) and ER− (MDAMB231 and MDAMB468) breast cancer cell lines. n = 45–60 cells. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). b Box plots showing the distribution of normalized FISH interprobe distances (d2/r2) measured across subregion 2 of the 16p11.2 RER region in normal breast tissue and in ER+ and ER− tumor tissues. n = 250–300 alleles. Distances in the ER+ tumor were significantly greater than in normal tissue (p < 0.0001) or in the ER− tumor (p = 0.004). Differences between normal and ER− tumor tissue were not significant (p = 0.24). c Example FISH images using probe pairs (red and green) that delineate subregion 2 in normal breast tissue and in ER+ and ER− tumor tissue. DNA is stained with DAPI (blue). Scale bar = 5 μm
Mentions: To determine the chromatin compaction status at subregion 2 in a normal breast cell line, FISH was also carried out on the non-transformed immortalized human mammary epithelial cell line HMLE [36]. The chromatin state of this region in HMLE was more compact than in MCF7 and LY2 cells, but not significantly different to that in the ER− cell lines MDAMB231 and MDAMB468 (Fig. 6a). A second independent ER+ breast cancer cell line, MDAMB361, showed a trend to being more de-compact than HMLE but this difference was not significant (Fig. 6a). This lesser de-compaction correlates with the expression level of genes in subregion 2 in MDAMB361, which was lower than in MCF7s and LY2 (Fig. 5c). We also note that unlike MCF7s and LY2 cells, MDAMB361 cells are HER2+ due to copy number amplification of the ERBB2 oncogene [20]. Our analysis of RER gene expression demonstrates that the breast tumors of the ERBB2 subtype have lower expression levels of cluster 1 RER regions (Fig. 3b). This suggests that the expression of ERBB2 oncogene lessens RER region expression and chromatin decompaction phenotype of cluster 1 RER regions, such as the 16p11.2 region.Fig. 6

Bottom Line: This occurs not only at individual genes, but also over larger chromosomal domains.For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus.In MCF7 cells, we show that this depends on the presence of estrogen.

View Article: PubMed Central - PubMed

Affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. sehrishrafique@hotmail.com.

ABSTRACT

Background: Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers.

Results: We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen.

Conclusions: Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells.

No MeSH data available.


Related in: MedlinePlus