Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1.
Meyer KB., O'Reilly M., Michailidou K., Carlebur S., Edwards SL., French JD., Prathalingham R., Dennis J., Bolla MK., Wang Q., de Santiago I., Hopper JL., Tsimiklis H., Apicella C., Southey MC., Schmidt MK., Broeks A., Van 't Veer LJ., Hogervorst FB., Muir K., Lophatananon A., Stewart-Brown S., Siriwanarangsan P., Fasching PA., Lux MP., Ekici AB., Beckmann MW., Peto J., Dos Santos Silva I., Fletcher O., Johnson N., Sawyer EJ., Tomlinson I., Kerin MJ., Miller N., Marme F., Schneeweiss A., Sohn C., Burwinkel B., Guénel P., Truong T., Laurent-Puig P., Menegaux F., Bojesen SE., Nordestgaard BG., Nielsen SF., Flyger H., Milne RL., Zamora MP., Arias JI., Benitez J., Neuhausen S., Anton-Culver H., Ziogas A., Dur CC., Brenner H., Müller H., Arndt V., Stegmaier C., Meindl A., Schmutzler RK., Engel C., Ditsch N., Brauch H., Brüning T., Ko Y-D., GENICA Network None., Nevanlinna H., Muranen TA., Aittomäki K., Blomqvist C., Matsuo K., Ito H., Iwata H., Yatabe Y., Dörk T., Helbig S., Bogdanova NV., Lindblom A., Margolin S., Mannermaa A., Kataja V., Kosma V-M., Hartikainen JM., Chenevix-Trench G., kConFab Investigators None., Australian Ovarian Cancer Study Group None., Wu AH., Tseng C-C., Van Den Berg D., Stram DO., Lambrechts D., Thienpont B., Christiaens M-R., Smeets A., Chang-Claude J., Rudolph A., Seibold P., Flesch-Janys D., Radice P., Peterlongo P., Bonanni B., Bernard L., Couch FJ., Olson JE., Wang X., Purrington K., Giles GG., Severi G., Baglietto L., McLean C., Haiman CA., Henderson BE., Schumacher F., Le Marchand L., Simard J., Goldberg MS., Labrèche F., Dumont M., Teo S-H., Yip C-H., Phuah S-Y., Kristensen V., Grenaker Alnæs G., Børresen-Dale A-L., Zheng W., Deming-Halverson S., Shrubsole M., Long J., Winqvist R., Pylkäs K., Jukkola-Vuorinen A., Kauppila S., Andrulis IL., Knight JA., Glendon G., Tchatchou S., Devilee P., Tollenaar RAEM., Seynaeve CM., García-Closas M., Figueroa J., Chanock SJ., Lissowska J., Czene K., Darabi H., Eriksson K., Hooning MJ., Martens JWM., van den Ouweland AMW., van Deurzen CHM., Hall P., Li J., Liu J., Humphreys K., Shu X-O., Lu W., Gao Y-T., Cai H., Cox A., Reed MWR., Blot W., Signorello LB., Cai Q., Pharoah PDP., Ghoussaini M., Harrington P., Tyrer J., Kang D., Choi J-Y., Park SK., Noh D-Y., Hartman M., Hui M., Lim W-Y., Buhari SA., Hamann U., Försti A., Rüdiger T., Ulmer H-U., Jakubowska A., Lubinski J., Jaworska K., Durda K., Sangrajrang S., Gaborieau V., Brennan P., McKay J., Vachon C., Slager S., Fostira F., Pilarski R., Shen C-Y., Hsiung C-N., Wu P-E., Hou M-F., Swerdlow A., Ashworth A., Orr N., Schoemaker MJ., Ponder BAJ., Dunning AM., Easton DF.
The 10q26 locus in the second intron of FGFR2 is the locus most strongly associated with estrogen-receptor-positive breast cancer in genome-wide association studies. We conducted fine-scale mapping in case-control studies genotyped with a custom chip (iCOGS), comprising 41 studies (n = 89,050) of European ancestry, 9 Asian ancestry studies (n = 13,983), and 2 African ancestry studies (n = 2,028) from the Breast Cancer Association Consortium. We identified three statistically independent risk signals within the locus. Within risk signals 1 and 3, genetic analysis identified five and two variants, respectively, highly correlated with the most strongly associated SNPs. By using a combination of genetic fine mapping, data on DNase hypersensitivity, and electrophoretic mobility shift assays to study protein-DNA binding, we identified rs35054928, rs2981578, and rs45631563 as putative functional SNPs. Chromatin immunoprecipitation showed that FOXA1 preferentially bound to the risk-associated allele (C) of rs2981578 and was able to recruit ERα to this site in an allele-specific manner, whereas E2F1 preferentially bound the risk variant of rs35054928. The risk alleles were preferentially found in open chromatin and bound by Ser5 phosphorylated RNA polymerase II, suggesting that the risk alleles are associated with changes in transcription. Chromatin conformation capture demonstrated that the risk region was able to interact with the promoter of FGFR2, the likely target gene of this risk region. A role for FOXA1 in mediating breast cancer susceptibility at this locus is consistent with the finding that the FGFR2 risk locus primarily predisposes to estrogen-receptor-positive disease.