Chromatin organisation in breast cancer

Epigenetic misregulation of gene expression is known to be an important feature in cancer. This has mainly been studied at the level of changes in DNA methylation and histone modifications at individual genes. In this thesis I have set out to investigate whether there are long-range changes in chromatin structure linked to altered gene expression in breast cancer. From large published datasets, I used a computational approach to identify large genomic regions which are coordinately misregulated in breast cancer independent of copy number aberrations (genomic effects). I found 26 regions of co-ordinate regulation of neighbouring genes that are consistent between breast tumours and breast cancer cell lines. These regions had different expression phenotypes (activation, repression, no change) compared to normal breast and also with tumour subtype (luminal vs basal and ER status). The regions of epigenetic regulation (RER) identified in breast cancer were mostly cancer type specific. I investigated the mechanism of long-range misregulation at one such region on chromosome 16p11.2 which is aberrantly activated in breast cancer. Interestingly, in estrogen-receptor positive (ER+ve) cells, genes in this region are upregulated relative to estrogen receptor negative (ER-ve) cells. Using fluorescence in situ hybridisation (FISH) I found that in ER+ve breast cancer cell lines and tumour tissue this region is in a more decondensed chromatin architecture than in ER-ve cell lines and tumour tissue. Furthermore this region was very compact in a normal breast epithelial cell line and breast tissue corresponding to what would be expected from the expression data. Estrogen was found to play a key role in maintaining the aberrant decondensation of chromatin at this locus on chr16p11.2, as shown by compaction of the region by starving ER+ve cells of estrogen and decompaction upon subsequent estrogen treatment. Interestingly there was also an estrogen mediated repositioning of the 16p11.2 RER domain away from the nuclear centre in hormone starved conditions and towards the centre upon estrogen stimulation. Together these results show that estrogen is key to regulating the changes in nuclear organisation and chromatin decompaction at this locus, which are associated with aberrant patterns of gene expression in ER+ve breast cancer

Activation of Estrogen-Responsive Genes Does Not Require Their Nuclear Co-Localization

The spatial organization of the genome in the nucleus plays a role in the regulation of gene expression. Whether co-regulated genes are subject to coordinated repositioning to a shared nuclear space is a matter of considerable interest and debate. We investigated the nuclear organization of estrogen receptor alpha (ERα) target genes in human breast epithelial and cancer cell lines, before and after transcriptional activation induced with estradiol. We find that, contrary to another report, the ERα target genes TFF1 and GREB1 are distributed in the nucleoplasm with no particular relationship to each other. The nuclear separation between these genes, as well as between the ERα target genes PGR and CTSD, was unchanged by hormone addition and transcriptional activation with no evidence for co-localization between alleles. Similarly, while the volume occupied by the chromosomes increased, the relative nuclear position of the respective chromosome territories was unaffected by hormone addition. Our results demonstrate that estradiol-induced ERα target genes are not required to co-localize in the nucleus

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

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0719-9) contains supplementary material, which is available to authorized users

Some General Fractional Integral Inequalities Involving LR–Bi-Convex Fuzzy Interval-Valued Functions

The main objective of this paper is to introduce a new class of convexity called left-right–bi-convex fuzzy interval-valued functions. We study this class from the perspective of fractional Hermite–Hadamard inequalities, involving a new fractional integral called the left-right–AB fractional integral. We discuss several special cases that demonstrate that our results are quite unifying. We provide non-trivial numerical examples regarding special means for positive real numbers in order to check the validity of our outcomes

Some General Fractional Integral Inequalities Involving LR–Bi-Convex Fuzzy Interval-Valued Functions

The main objective of this paper is to introduce a new class of convexity called left-right–bi-convex fuzzy interval-valued functions. We study this class from the perspective of fractional Hermite–Hadamard inequalities, involving a new fractional integral called the left-right–AB fractional integral. We discuss several special cases that demonstrate that our results are quite unifying. We provide non-trivial numerical examples regarding special means for positive real numbers in order to check the validity of our outcomes