Poster Presentation 44th Lorne Genome Conference 2023

Unraveling the mechanisms involved in the co-regulation of breast cancer associated genes at the 6q25.1 locus (#244)

Amie Siemonek 1 , Sofie Van Huffle 1 , Rob Weeks 2 , Julia Horsfield 2 , Anita Dunbier 1
  1. Department of Biochemistry, Centre for Translational Cancer Research, University of Otago, Dunedin, New Zealand
  2. Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand

Oestrogen receptor positive breast cancer is the most commonly diagnosed cancer in women world-wide. Oestrogens promote growth, proliferation and differentiation in both healthy and malignant breast tissue1. However, normal ER signaling is frequently disrupted in breast cancer and reprogramming of the oestrogen regulated network appears to play an important role in neoplastic transformation2,3.

 Oestrogen receptor alpha (ERa) is encoded by the ESR1 gene on chromosome 6q. rs77275268 is a variant upstream of ESR1 which is present as C/T where the minor allele (T) is associated with breast cancer susceptibility4. This variant occurs within a putative binding site of the CCCTC binding factor (CTCF). CTCF is a methylation-sensitive transcription factor and is thought to play an important role in genome architecture. Variation at CTCF binding sites has the potential alter chromatin conformation and dysregulate gene expression.  In ER positive breast tumours the expression of ESR1 is highly correlated with the expression of three upstream genes, which encode RMND1, ARMT1 and CCDC1705. We hypothesised that the rs77275268 variant could alter the three-dimensional organization of these correlated genes, which may contribute to genetic breast cancer susceptibility.

To investigate if the C to T variant alters the binding of CTCF we performed targeted bisulphite sequencing in CRISPR-edited MCF7 cells. Results indicate that there is a complete loss of methylation at the SNP site. We subsequently performed Cut&Run sequencing to establish if the loss of methylation at this site results in a change in CTCF binding. Preliminary results support this hypothesis suggesting that the loss of CTCF binding within this region could affect local gene expression.

  1. Saha Roy, S., & Vadlamudi, R. K. (2012). Role of Estrogen Receptor Signaling in Breast Cancer Metastasis. International Journal of Breast Cancer, 2012, 1–8. https://doi.org/10.1155/2012/654698
  2. Chi, D., Singhal, H., Li, L., Xiao, T., Liu, W., Pun, M., Jeselsohn, R., He, H., Lim, E., Vadhi, R., Rao, P., Long, H., Garber, J., & Brown, M. (2019). Estrogen receptor signaling is reprogrammed during breast tumorigenesis. Proceedings of the National Academy of Sciences of the United States of America, 116(23), 11437–11443. https://doi.org/10.1073/pnas.1819155116
  3. Achinger-Kawecka, J., Valdes-Mora, F., Luu, P.-L., Giles, K. A., Caldon, C. E., Qu, W., Nair, S., Soto, S., Locke, W. J., Yeo-Teh, N. S., Gould, C. M., Du, Q., Smith, G. C., Ramos, I. R., Fernandez, K. F., Hoon, D. S., Gee, J. M. W., Stirzaker, C., & Clark, S. J. (2020). Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer. Nature Communications, 11(1), 320. https://doi.org/10.1038/s41467-019-14098-x
  4. Stacey, S. N., Sulem, P., Zanon, C., Gudjonsson, S. A., Thorleifsson, G., Helgason, A., Jonasdottir, A., Besenbacher, S., Kostic, J. P., & Fackenthal, J. D. (2010). Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus. PLoS Genetics, 6(7), e1001029.
  5. Dunbier, A. K., Anderson, H., Ghazoui, Z., Lopez-Knowles, E., Pancholi, S., Ribas, R., Drury, S., Sidhu, K., Leary, A., Martin, L. A., & Dowsett, M. (2011). ESR1 is co-expressed with closely adjacent uncharacterised genes spanning a breast cancer susceptibility locus at 6q25.1. PLoS Genetics, 7(4). https://doi.org/10.1371/journal.pgen.1001382