Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element

• Main Authors: Baxter, Joseph S., Johnson, Nichola, Tomczyk, Katarzyna, Gillespie, Andrea, Maguire, Sarah, Brough, Rachel, Fachal, Laura, Michailidou, Kyriaki, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Ahearn, Thomas U., Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Augustinsson, Annelie, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bogdanova, Natalia, Bojesen, Stig E., Brenner, Hermann, Brucker, Sara Y., Cai, Qiuyin, Campa, Daniele, Canzian, Federico, Castelao, Jose E., Chan, Tsun L., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Choi, Ji-Yeob, Clarke, Christine L., Collaborators, Nbcs, Colonna, Sarah, Conroy, Don M., Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doerk, Thilo, Dossus, Laure, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Engel, Christoph, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Gago-Dominguez, Manuela, Gao, Chi, Garcia-Closas, Montserrat, Garcia-Saenz, Jose A., Ghoussaini, Maya, Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Guenel, Pascal, Guendert, Melanie, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hall, Per, Hamann, Ute, Hartman, Mikael, Hatse, Sigrid, Hauke, Jan, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L., Hou, Ming-Feng, Ito, Hidemi, Iwasaki, Motoki, Jager, Agnes, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Joseph, Vijai, Jung, Audrey, Kaaks, Rudolf, Kang, Daehee, Keeman, Renske, Khusnutdinova, Elza, Kim, Sung-Won, Kosma, Veli-Matti, Kraft, Peter, Kristensen, Vessela N., Kubelka-Sabit, Katerina, Kurian, Allison W., Kwong, Ava, Lacey, James, Lambrechts, Diether, Larson, Nicole L., Larsson, Susanna C., Le Marchand, Loic, Lejbkowicz, Flavio, Li, Jingmei, Long, Jirong, Lophatananon, Artitaya, LubiNski, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Matsuo, Keitaro, Mavroudis, Dimitrios, Mayes, Rebecca, Menon, Usha, Milne, Roger L., Taib, Nur Aishah Mohd, Muir, Kenneth, Muranen, Taru A., Murphy, Rachel A., Nevanlinna, Heli, O'Brien, Katie M., Offit, Kenneth, Olson, Janet E., Olsson, Hakan, Park, Sue K., Park-Simon, Tjoung-Won, Patel, Alpa, Peterlongo, Paolo, Peto, Julian, Plaseska-Karanfilska, Dijana, Presneau, Nadege, Pylkas, Katri, Rack, Brigitte, Rennert, Gad, Romero, Atocha, Ruebner, Matthias, Ruediger, Thomas, Saloustros, Emmanouil, Sandler, Dale P., Sawyer, Elinor J., Schmidt, Marjanka K., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Shah, Mitul, Shen, Chen-Yang, Shu, Xiao-Ou, Simard, Jacques, Southey, Melissa C., Stone, Jennifer, Surowy, Harald, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teo, Soo Hwang, Teras, Lauren R., Terry, Mary Beth, Toland, Amanda E., Tomlinson, Ian, Truong, Therese, Tseng, Chiu-Chen, Untch, Michael, Vachon, Celine M., van den Ouweland, Ans M. W., Wang, Sophia S., Weinberg, Clarice R., Wendt, Camilla, Winham, Stacey J., Winqvist, Robert, Wolk, Alicja, Wu, Anna H., Yamaji, Taiki, Zheng, Wei, Ziogas, Argyrios, Pharoah, Paul D. P., Dunning, Alison M., Easton, Douglas F., Pettitt, Stephen J., Lord, Christopher J., Haider, Syed, Orr, Nick, Fletcher, Olivia, kConFab Investigators, I, Investigators, ABCTB
• Format: Article
• Published: Cell Press 2021
• Subjects: BF Psychology; QH426 Genetics
• Online Access: http://eprints.um.edu.my/34718/

A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30-to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 x 10(-31)).