Abstract 4518: 4CSeq analysis of a breast cancer susceptibility locus on 6q25.1
Authors: van Huffel Sofie , Day Robert C. , Antony Jisha , Marsman Judith , Horsfield Julia A. , Dunbier Anita K. 
Published: July 2016

Single nucleotide polymorphisms within the genomic region immediately upstream of ESR1, a gene on 6q25.1 encoding the estrogen receptor α (ER), have been found to be associated with increased risk of breast cancer1,2. Three genes within this region, CCDC170, RMND1 and ARMT1 are co-expressed with ESR1 in ER+ve breast cancers and CCDC170 expression is inversely associated with proliferation and recurrence free survival in a tamoxifen-treated patient cohort3. In addition, gene fusions between ESR1 and CCDC170 have been associated with aggressive and endocrine-resistant luminal B tumours4. This study aimed to investigate chromatin structure within the 6q25.1 region using targeted chromatin confirmation capture (3C) and circularised chromatin confirmation capture analysis sequencing (4Cseq) to explore whether the spatial organisation of the chromatin might be associated with the regulation of genes and mutational patterns at this locus.

To carry out 4Cseq analysis, chromatin from MCF7 cells was cross-linked, enzymatically digested, ligated, re-digested, circularised and then amplified before the purified PCR products were sequenced on an Illumina HiSeq2500. After the sequence reads were trimmed and processed, FourSig software was used to identify cis and trans interactions from the nine anchor points used in the assay. For 3C analysis, chromatin was cross-linked, digested, ligated, and analysed by quantitative real-time PCR. Data was normalised to a synthetically generated fragment.

Analyses revealed that the ESR1 promoter region contacted a number of different upstream regions including the promoters of RMND1 and CCDC170. A high frequency of interactions was observed in the intergenic region between CCDC170 and ESR1 where a number of SNPs associated with breast cancer risk have been found. In addition, contact between the 3’ end of the ESR1 gene and the 3’ end of CCDC170 suggests that there may be a regulatory interaction in this region. Contacts were also observed within CCDC170, immediately adjacent to the point at which gene fusions between ESR1 and CCDC170 have previously been observed4. Overall, these data support the hypothesis that chromatin structure may drive the co-expression of the genes at this locus and suggests that some interactions within the region occur in areas where genomic rearrangements in metastatic breast cancers have been observed.

References:

1.

Turnbull C et al. Nature Genetics 2010;42:504-7.

2.

Zheng W et al. Nature Genetics 2009;41:324-8.

3.

Dunbier A et al. PLoS Genetics 2011;7:e1001382.

4.

Veeraraghavan J. et al., Nature Communications 2013;5:4577.

Citation Format: Sofie van Huffel, Robert C. Day, Jisha Antony, Judith Marsman, Julia A. Horsfield, Anita K. Dunbier. 4CSeq analysis of a breast cancer susceptibility locus on 6q25.1. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4518.