Breast Cancer Research and Treatment

, Volume 112, Issue 2, pp 229–236

Use of expression data and the CGEMS genome-wide breast cancer association study to identify genes that may modify risk in BRCA1/2 mutation carriers

  • Logan C. Walker
  • Nic Waddell
  • Anette Ten Haaf
  • kConFab Investigators
  • Sean Grimmond
  • Amanda B. Spurdle
Preclinical Study


Germline mutations in BRCA1 or BRCA2 confer an increased lifetime risk of developing breast or ovarian cancer, but variable penetrance suggests that cancer susceptibility is influenced in part by modifier genes. Microarray expression profiling was conducted for 69 irradiated lymphoblastoid cell lines derived from healthy controls, or from cancer-affected women with a strong family history of breast and ovarian cancer carrying pathogenic mutations in BRCA1 or BRCA2, or with no BRCA1/2 mutations (BRCAX). Genes discriminating between BRCA1, BRCA2 or BRCAX and controls were stratified based on irradiation response and/or cell cycle involvement. Gene lists were aligned against genes tagged with single nucleotide polymorphisms (SNPs) determined by the Cancer Genetic Markers of Susceptibility (CGEMS) Breast Cancer Whole Genome Association Scan to be nominally associated with breast cancer risk. Irradiation responsive genes whose expression correlated with BRCA1 and/or BRCA2 mutation status were more likely to be tagged by risk-associated SNPs in the CGEMS dataset (BRCA1, P = 0.0005; BRCA2, P = 0.01). In contrast, irradiation responsive genes correlating with BRCAX status were not enriched in the CGEMS dataset. Classification of expression data by involvement in cell cycle processes did not enrich for genes tagged by risk-associated SNPs, for BRCA1, BRCA2 or BRCAX groups. Using a novel combinatorial approach, we have identified a subset of irradiation responsive genes as high priority candidate BRCA1/2 modifier genes. Similar approaches may be used to identify genes and underlying genetic risk factors that interact with exogenous stimulants to cause or modify any disease, without a priori knowledge of the pathways involved.


BRCA1 BRCA2 BRCAX Breast cancer Cell cycle Cancer Genetic Markers of Susceptibilty (CGEMS) Irradiation Microarray Modifier genes 

Supplementary material

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10549_2007_9848_MOESM3_ESM.xls (142 kb)
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  1. 1.
    Oldenburg RA, Meijers-Heijboer H, Cornelisse CJ et al (2007) Genetic susceptibility for breast cancer: how many more genes to be found? Crit Rev Oncol Hematol 63(2):125–149PubMedCrossRefGoogle Scholar
  2. 2.
    Antoniou A, Pharoah PD, Narod S et al (2003) Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case Series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet 72(5):1117–1130PubMedCrossRefGoogle Scholar
  3. 3.
    Simchoni S, Friedman E, Kaufman B et al (2006) Familial clustering of site-specific cancer risks associated with BRCA1 and BRCA2 mutations in the Ashkenazi Jewish population. Proc Natl Acad Sci USA 103(10):3770–3774PubMedCrossRefGoogle Scholar
  4. 4.
    Smith A, Moran A, Boyd MC et al (2007) Phenocopies in BRCA1 and BRCA2 families: evidence for modifier genes and implications for screening. J Med Genet 44(1):10–15PubMedCrossRefGoogle Scholar
  5. 5.
    Antoniou AC, Sinilnikova OM, Simard J et al (2007) RAD51 135G>C modifies breast cancer risk among BRCA2 mutation carriers: results from a combined analysis of 19 studies. Am J Hum Genet 81(6):1186–1200PubMedCrossRefGoogle Scholar
  6. 6.
    Osorio A, Martinez-Delgado B, Pollan M et al (2006) A haplotype containing the p53 polymorphisms Ins16bp and Arg72Pro modifies cancer risk in BRCA2 mutation carriers. Hum Mutat 27(3):242–248PubMedCrossRefGoogle Scholar
  7. 7.
    Rebbeck TR, Kantoff PW, Krithivas K et al (1999) Modification of BRCA1-associated breast cancer risk by the polymorphic androgen-receptor CAG repeat. Am J Hum Genet 64(5):1371–1377PubMedCrossRefGoogle Scholar
  8. 8.
    Rebbeck TR, Wang Y, Kantoff PW et al (2001) Modification of BRCA1- and BRCA2-associated breast cancer risk by AIB1 genotype and reproductive history. Cancer Res 61(14):5420–5424PubMedGoogle Scholar
  9. 9.
    Spurdle AB, Antoniou AC, Duffy DL et al (2005) The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers. Breast Cancer Res 7(2):R176–R183PubMedCrossRefGoogle Scholar
  10. 10.
    Spurdle AB, Antoniou AC, Kelemen L et al (2006) The AIB1 polyglutamine repeat does not modify breast cancer risk in BRCA1 and BRCA2 mutation carriers. Cancer Epidemiol Biomarkers Prev 15(1):76–79PubMedCrossRefGoogle Scholar
  11. 11.
    Karran P (2000) DNA double strand break repair in mammalian cells. Curr Opin Genet Dev 10(2):144–150PubMedCrossRefGoogle Scholar
  12. 12.
    Shivji MK, Davies OR, Savill JM et al (2006) A region of human BRCA2 containing multiple BRC repeats promotes RAD51-mediated strand exchange. Nucleic Acids Res 34(14):4000–4011PubMedCrossRefGoogle Scholar
  13. 13.
    Broeks A, Braaf LM, Huseinovic A et al (2007) Identification of women with an increased risk of developing radiation-induced breast cancer: a case only study. Breast Cancer Res 9(2):R26PubMedCrossRefGoogle Scholar
  14. 14.
    Mullan PB, Quinn JE, Harkin DP (2006) The role of BRCA1 in transcriptional regulation and cell cycle control. Oncogene 25(43):5854–5863PubMedCrossRefGoogle Scholar
  15. 15.
    Marmorstein LY, Kinev AV, Chan GK et al (2001) A human BRCA2 complex containing a structural DNA binding component influences cell cycle progression. Cell 104(2):247–257PubMedCrossRefGoogle Scholar
  16. 16.
    Mann GJ, Thorne H, Balleine RL et al (2006) Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource. Breast Cancer Res 8(1):R12PubMedCrossRefGoogle Scholar
  17. 17.
    Marsh A, Healey S, Lewis A et al (2007) Mutation analysis of five candidate genes in familial breast cancer. Breast Cancer Res Treat 105(3):377–389PubMedCrossRefGoogle Scholar
  18. 18.
    Chenevix-Trench G, Healey S, Lakhani S et al (2006) Genetic and histopathologic evaluation of BRCA1 and BRCA2 DNA sequence variants of unknown clinical significance. Cancer Res 66(4):2019–2027PubMedCrossRefGoogle Scholar
  19. 19.
    Jen KY, Cheung VG (2003) Transcriptional response of lymphoblastoid cells to ionizing radiation. Genome Res 13(9):2092–2100PubMedCrossRefGoogle Scholar
  20. 20.
    Eberle MA, Ng PC, Kuhn K et al (2007) Power to detect risk alleles using genome-wide tag SNP panels. PLoS Genet 3(10):1827–1837PubMedCrossRefGoogle Scholar
  21. 21.
    Easton DF, Pooley KA, Dunning AM et al (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447(7148):1087–1093PubMedCrossRefGoogle Scholar
  22. 22.
    Bussey KJ, Kane D, Sunshine M et al (2003) MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol 4(4):R27PubMedCrossRefGoogle Scholar
  23. 23.
    Smith P, McGuffog L, Easton DF et al (2006) A genome wide linkage search for breast cancer susceptibility genes. Genes Chromosomes Cancer 45(7):646–655PubMedCrossRefGoogle Scholar
  24. 24.
    Cox A, Dunning AM, Garcia-Closas M et al (2007) A common coding variant in CASP8 is associated with breast cancer risk. Nat Genet 39(3):352–358PubMedCrossRefGoogle Scholar
  25. 25.
    Rahman N, Seal S, Thompson D et al (2007) PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nat Genet 39(2):165–167PubMedCrossRefGoogle Scholar
  26. 26.
    Renwick A, Thompson D, Seal S et al (2006) ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nat Genet 38(8):873–875PubMedCrossRefGoogle Scholar
  27. 27.
    Seal S, Thompson D, Renwick A et al (2006) Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nat Genet 38(11):1239–1241PubMedCrossRefGoogle Scholar
  28. 28.
    Steffen J, Nowakowska D, Niwinska A et al (2006) Germline mutations 657del5 of the NBS1 gene contribute significantly to the incidence of breast cancer in Central Poland. Int J Cancer 119(2):472–475PubMedCrossRefGoogle Scholar
  29. 29.
    Dubrovska A, Kanamoto T, Lomnytska M et al (2005) TGFbeta1/Smad3 counteracts BRCA1-dependent repair of DNA damage. Oncogene 24(14):2289–2297PubMedCrossRefGoogle Scholar
  30. 30.
    Hu YF, Li R (2002) JunB potentiates function of BRCA1 activation domain 1 (AD1) through a coiled-coil-mediated interaction. Genes Dev 16(12):1509–1517PubMedCrossRefGoogle Scholar
  31. 31.
    Preobrazhenska O, Yakymovych M, Kanamoto T et al (2002) BRCA2 and Smad3 synergize in regulation of gene transcription. Oncogene 21(36):5660–5664PubMedCrossRefGoogle Scholar
  32. 32.
    Krendel M, Zenke FT, Bokoch GM (2002) Nucleotide exchange factor GEF-H1 mediates cross-talk between microtubules and the actin cytoskeleton. Nat Cell Biol 4(4):294–301PubMedCrossRefGoogle Scholar
  33. 33.
    Wozniak MA, Desai R, Solski PA et al (2003) ROCK-generated contractility regulates breast epithelial cell differentiation in response to the physical properties of a three-dimensional collagen matrix. J Cell Biol 163(3):583–595PubMedCrossRefGoogle Scholar
  34. 34.
    Gooch JL, Lee AV, Yee D (1998) Interleukin 4 inhibits growth and induces apoptosis in human breast cancer cells. Cancer Res 58(18):4199–4205PubMedGoogle Scholar
  35. 35.
    Balasubramanian SP, Azmy IA, Higham SE et al (2006) Interleukin gene polymorphisms and breast cancer: a case control study and systematic literature review. BMC Cancer 6:188PubMedCrossRefGoogle Scholar
  36. 36.
    Consortium TIH (2003) The international HapMap project. Nature 426(6968):789–796CrossRefGoogle Scholar
  37. 37.
    Papageorgio C, Brachmann R, Zeng J et al (2007) MAGED2: a novel p53-dissociator. Int J Oncol 31(5):1205–1211PubMedGoogle Scholar
  38. 38.
    Schuyer M, Berns EM (1999) Is TP53 dysfunction required for BRCA1-associated carcinogenesis? Mol Cell Endocrinol 155(1–2):143–152PubMedCrossRefGoogle Scholar
  39. 39.
    Welch PJ, Wang JY (1993) A C-terminal protein-binding domain in the retinoblastoma protein regulates nuclear c-Abl tyrosine kinase in the cell cycle. Cell 75(4):779–790PubMedCrossRefGoogle Scholar
  40. 40.
    Gery S, Komatsu N, Baldjyan L et al (2006) The circadian gene per1 plays an important role in cell growth and DNA damage control in human cancer cells. Mol Cell 22(3):375–382PubMedCrossRefGoogle Scholar
  41. 41.
    Winter SL, Bosnoyan-Collins L, Pinnaduwage D et al (2007) Expression of the circadian clock genes Per1 and Per2 in sporadic and familial breast tumors. Neoplasia 9(10):797–800PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC. 2007

Authors and Affiliations

  • Logan C. Walker
    • 1
  • Nic Waddell
    • 1
  • Anette Ten Haaf
    • 1
  • kConFab Investigators
    • 2
  • Sean Grimmond
    • 3
  • Amanda B. Spurdle
    • 1
  1. 1.Queensland Institute of Medical ResearchPO Royal Brisbane HospitalBrisbaneAustralia
  2. 2.Peter MacCallum Cancer CentreEast MelbourneAustralia
  3. 3.Institute for Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia

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