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Genetic Variants in the 53BP1 Gene and Skin Cancer Risk

  • Chunyan He
    Affiliations
    Department of Public Health, School of Medicine, Indiana University, Indianapolis, Indiana, USA

    Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana, USA
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  • Hongmei Nan
    Affiliations
    Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA

    Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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  • Abrar A. Qureshi
    Affiliations
    Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Clinical Research Program, Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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  • Jiali Han
    Affiliations
    Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA

    Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Clinical Research Program, Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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      Abbreviations

      BCC
      basal cell carcinoma
      SCC
      squamous cell carcinoma
      SNP
      single nucleotide polymorphism
      TO THE EDITOR
      The conserved p53-binding protein 1 (53BP1) was initially identified as a nuclear protein that interacts with the DNA-binding domain of tumor suppressor p53 and enhances p53-mediated transcription activation (
      • Iwabuchi K.
      • Li B.
      • Massa H.F.
      • et al.
      Stimulation of p53-mediated transcriptional activation by the p53-binding proteins, 53BP1 and 53BP2.
      ). The interaction region of 53BP1, BRCT (BRCA1 C-terminus) repeats, are present in several proteins involved in DNA repair and cell cycle control, suggesting a direct role of 53BP1 in the cellular response to DNA damage and maintenance of genomic stability (
      • Rappold I.
      • Iwabuchi K.
      • Date T.
      • et al.
      Tumor suppressor p53 binding protein 1 (53BP1) is involved in DNA damage-signaling pathways.
      ;
      • Joo W.S.
      • Jeffrey P.D.
      • Cantor S.B.
      • et al.
      Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure.
      ). Recently, studies suggested that 53BP1 is a central mediator of the DNA damage checkpoint signaling (
      • Wang B.
      • Matsuoka S.
      • Carpenter P.B.
      • et al.
      53BP1, a mediator of the DNA damage checkpoint.
      ) and it directly participates in the repair for DNA double-strand breaks (
      • Huyen Y.
      • Zgheib O.
      • Ditullio Jr, R.A.
      • et al.
      Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks.
      ). 53BP1-deficient mice exhibit growth retardation, high-radiation sensitivity, and tumor development features that are indicative of a defective DNA damage response (
      • Ward I.M.
      • Minn K.
      • van Deursen J.
      • et al.
      p53 binding protein 53BP1 is required for DNA damage responses and tumor suppression in mice.
      ). 53BP1 has been shown to constitutively have an important role in the etiology of human cancer (
      • DiTullio Jr, R.A.
      • Mochan T.A.
      • Venere M.
      • et al.
      53BP1 functions in an ATM-dependent checkpoint pathway that is constitutively activated in human cancer.
      ). It is plausible that sequence variation in the regulatory and coding regions of the 53BP1 gene might affect its transcription and protein structure thus, its biological function in checkpoint signaling and DNA repair, leads to susceptibility to cancers.
      In this study, we hypothesized that that common genetic variants of 53BP1 were associated with risk of skin cancer. We comprehensively surveyed common genetic variation of the 53BP1 gene using two complementary approaches, including putatively functional single nucleotide polymorphisms (SNPs) and choosing tagging-SNPs in the 53BP1 gene locus (introns and exons as well as 20kb upstream and 20kb downstream of the coding region). We performed a skin cancer case-control study of Caucasians nested within the Nurses' Health Study to evaluate whether these common genetic variants are associated with the risks of non-melanoma skin cancers (squamous cell carcinoma (SCC) and basal cell carcinoma (BCC)) along with melanoma risk. We further investigated the association of these genetic variants with pigmentary phenotypes (hair color, skin color, tanning ability, and the number of moles). The nested case-control study consisted of 218 incident melanoma cases, 285 incident SCC cases, 300 incident BCC cases, and 870 age-matched controls. A detailed description of the selection and characteristics of cases and controls was published previously (
      • Han J.
      • Colditz G.A.
      • Liu J.S.
      • et al.
      Genetic variation in XPD, sun exposure, and risk of skin cancer.
      ).
      We included four putatively functional SNPs that have been identified in the promoter and coding regions of 53BP1 (http://egp.gs.washington.edu): rs1869258, rs560191, rs689647, and rs2602141. Using genotype data from the 90 CEU samples in the HapMap project, we further selected four tagging-SNPs by the Tagger program (r2>0.8): rs3862138, rs17782975, rs2242069, and rs999047 (Supplementary Figure S1 online and Supplementary Table S1 online). We genotyped the eight SNPs by the 5′ nuclease assay (TaqMan) in 384-well format, using the ABI PRISM 7900HT Sequence Detection System (Applied Biosystems, Foster City, CA). The distributions of genotypes for the eight SNPs were in Hardy–Weinberg equilibrium among controls. Because the three SNPs (rs1869258, rs560191, and rs2602141) are in high linkage disequilibrium (each pair-wise r2>0.9, Supplementary Table S2 online), we anticipated that these three SNPs would show similar effects on pigmentary phenotypes and skin cancer risk.
      We evaluated the main effect of the selected polymorphisms across the three types of skin cancer using unconditional logistic regression (Table 1). In the analyses controlling for the age, we found that three SNPs (rs689647, rs2242069, and rs999047) were consistently associated with a significantly decreased risk of BCC (additive odds ratio and 95% confidence interval: 0.69 (0.50–0.95), 0.68 (0.51–0.90), and 0.66 (0.48–0.91), respectively). These three SNPs are in moderate linkage disequilibrium (pair-wise r2 between 0.27 and 0.70, Supplementary Table S2 online). The non-synonymous SNP, rs689647 (G412S), has been investigated in a case-control study of breast cancer but found no association with breast cancer risk (
      • Frank B.
      • Hemminki K.
      • Bermejo J.L.
      • et al.
      TP53-binding protein variants and breast cancer risk: a case-control study.
      ). We did not observe significant association between three putatively functional SNPs (rs1869258, rs560191, and rs2602141) and any type of skin cancer, which was consistent with previous studies (
      • Frank B.
      • Hemminki K.
      • Bermejo J.L.
      • et al.
      TP53-binding protein variants and breast cancer risk: a case-control study.
      ;
      • Ma H.
      • Hu Z.
      • Zhai X.
      • et al.
      Joint effects of single nucleotide polymorphisms in P53BP1 and p53 on breast cancer risk in a Chinese population.
      ;
      • Rapakko K.
      • Heikkinen K.
      • Karppinen S.M.
      • et al.
      Germline alterations in the 53BP1 gene in breast and ovarian cancer families.
      ). We further evaluated haplotypes based on the four SNPs (rs689647, rs2602141, rs2242069, and rs999047) that modified the risk of the cancer subtypes (Table 1). We found that the variant allele of rs689647 was often inherited together with that of the other three SNPs and formed a haplotype in 11% of the population. This haplotype was significantly associated with a decreased risk of BCC (odds ratio, 0.66; 95% confidence interval, 0.45–0.96), suggesting a protective effect on BCC compared with the most frequent haplotype carrying all wild-type alleles in approximately 60% of the population. However, the haplotype carrying only the variant allele of rs2242066 or rs999047 was not significantly associated with BCC risk as suggested in single-SNP analysis, though the latter showed a non-significant decreased risk of BCC. Of note, the last haplotype carrying only the variant allele of rs999047 was associated with a non-significant increased risk of melanoma (odds ratio, 1.97; 95% confidence interval, 0.96–4.07), which was stronger than the association of single-SNP analysis (odds ratio, 1.23; 95% confidence interval, 0.90–1.68). These associations did not change substantially after additional adjustment for potential risk factors including pigmentary phenotypes, family history of skin cancer, geographic region, accumulative sun exposure, sunburns, and sunlamp use or tanning salon attendance. We did not observe any statistically significant interaction between pigmentary phenotypes and genetic variants on skin cancer risk.
      Table 1Associations between selected SNPs in 53BP1 region and skin cancer risk
      MelanomaSCCBCC
      Controls (%)Cases (%)Multivariate OR
      Unconditional logistic regression adjusted for age;
      Cases (%)Multivariate OR
      Unconditional logistic regression adjusted for age;
      Cases (%)Multivariate OR
      Unconditional logistic regression adjusted for age;
      5′ UTR
       rs3862138
       CC503 (62.9)132 (63.5)1.00 (ref)173 (66.3)1.00 (ref)179 (65.1)1.00 (ref)
       CT+TT297 (37.1)76 (36.5)0.99 (0.72-1.36)88 (33.7)0.85 (0.63–1.14)96 (34.9)0.90 (0.68-1.21)
       Per copy of T0.93 (0.71-1.24)0.95 (0.74–1.21)0.98 (0.77-1.24)
      P for trend0.640.660.86
      Coding region
       rs17782975
       TT670 (81.8)168 (82.4)1.00 (ref)222 (81.0)1.00 (ref)227 (82.8)1.00 (ref)
       TC+CC149 (18.2)36 (17.6)0.96 (0.64-1.44)52 (19.0)1.05 (0.74–1.49)47 (17.2)0.92 (0.64-1.33)
       Per copy of C1.00 (0.68-1.48)1.10 (0.79–1.52)0.92 (0.65-1.30)
      P for trend0.990.580.62
       rs689647 (G412S)
       CC635 (76.5)155 (75.2)1.00 (ref)225 (82.1)1.00 (ref)243 (82.9)1.00 (ref)
       CT+TT195 (23.5)51 (24.8)1.08 (0.76-1.55)49 (17.9)0.71 (0.50–1.01)50 (17.1)0.68 (0.48-0.95)
       Per copy of T1.05 (0.76–1.46)0.74 (0.53–1.02)0.69 (0.50-0.95)
      P for trend0.770.070.02
       rs2602141 (K1136Q)
      The two SNPs (rs1869258 and rs560191) that are in high linkage disequilibrium with rs2602141 (each pair-wise r2>0.9) showed similar associations with the risk of melanoma, SCC and BCC.
       TT389 (46.4)86 (41.0)1.00 (ref)143 (52.4)1.00 (ref)154 (52.0)1.00 (ref)
       TG+GG449 (53.6)124 (59.0)1.27 (0.93–1.72)130 (47.6)0.78 (0.60–1.03)142 (48.0)0.80 (0.61-1.05)
       Per copy of G1.05 (0.83–1.34)0.85 (0.69–1.06)0.86 (0.70-1.06)
      P for trend0.670.140.15
       rs2242069
       TT545 (67.0)132 (65.3)1.00 (ref)194 (72.9)1.00 (ref)212 (76.3)1.00 (ref)
       TG+GG269 (33.0)70 (34.7)1.09 (0.79–1.52)72 (27.1)0.75 (0.55–1.02)66 (23.7)0.63 (0.46-0.86)
       Per copy of G1.13 (0.85–1.50)0.83 (0.63–1.09)0.68 (0.51-0.90)
      P for trend0.410.180.01
      3′ UTR
       rs999047
       AA597 (74.5)136 (69.7)1.00 (ref)220 (80.3)1.00 (ref)226 (81.9)1.00 (ref)
       AG+GG204 (25.5)59 (30.3)1.29 (0.91–1.82)54 (19.7)0.72 (0.51–1.00)50 (18.1)0.65 (0.46-0.91)
       Per copy of G1.23 (0.90–1.68)0.82 (0.60–1.10)0.66 (0.48-0.91)
      P for trend0.20.180.01
      Haplotype (ABCD)
      Haplotype based on the four SNPs A: rs689647; B: rs2602141; C:rs2242069; D: rs999047; 0, wild-type allele; 1, variant allele.
       0 0 0 0863 (61.1)203 (59.3)1.00288 (61.5)1.00326 (65.3)1.00
       0 1 0 0279 (19.8)63 (18.5)0.97 (0.70–1.35)92 (19.7)0.99 (0.75–1.30)98 (19.5)0.92 (0.71-1.21)
       1 1 1 1160 (11.3)40 (11.7)1.08 (0.73–1.60)42 (9.0)0.78 (0.54–1.13)40 (8.0)0.66 (0.45-0.96)
       0 0 1 073 (5.2)21 (6.2)1.28 (0.76–2.17)27 (5.7)1.12 (0.69–1.82)26 (5.2)0.89 (0.55-1.43)
       0 0 0 124 (1.7)11 (3.2)1.97 (0.96–4.07)11 (2.4)1.40 (0.68–2.87)5 (1.1)0.59 (0.22-1.61)
       Rare<1% combined12 (0.9)4 (1.2)1.42 (0.45–4.54)8 (1.8)1.92 (0.80–4.63)4 (0.9)0.89 (0.29-2.75)
      P for global test0.520.400.31
      Abbreviations: BCC, basal cell carcinoma; OR, odds ratio; SCC, squamous cell carcinoma; SNP, single nucleotide polymorphism; UTR, untranslated region; 53BP1, p53-binding protein 1.
      1 Unconditional logistic regression adjusted for age;
      2 The two SNPs (rs1869258 and rs560191) that are in high linkage disequilibrium with rs2602141 (each pair-wise r2>0.9) showed similar associations with the risk of melanoma, SCC and BCC.
      3 Haplotype based on the four SNPs A: rs689647; B: rs2602141; C:rs2242069; D: rs999047; 0, wild-type allele; 1, variant allele.
      We evaluated the associations between the selected SNPs and pigmentary phenotypes among controls using linear regression models (Table 2). We found the three highly correlated putatively functional SNPs (rs1869258, rs560191, and rs2602141) were associated with lighter hair color (P for trend, 0.04, 0.07, and 0.03, respectively) and more moles (P for trend, 0.02, 0.003, and 0.003, respectively). We also found one intronic SNP in 5′ terminus, rs17782975, was significantly associated with more moles (P for trend, 0.01). No statistically significant associations between genetic variants and skin color or tanning ability were observed. To our knowledge, this is the first report that 53BP1 is associated with pigmentary phenotypes in Caucasians, although this gene has shown clear evidence of adaptive skin pigmentation selection in Africans (
      • Izagirre N.
      • Garcia I.
      • Junquera C.
      • et al.
      A scan for signatures of positive selection in candidate loci for skin pigmentation in humans.
      ). Two other genes involved in DNA repair, p53 and MDM2, have been reported to be associated with pigmentary phenotypes (
      • Cui R.
      • Widlund H.R.
      • Feige E.
      • et al.
      Central role of p53 in the suntan response and pathologic hyperpigmentation.
      ;
      • Nan H.
      • Qureshi A.A.
      • Hunter D.J.
      • et al.
      A functional SNP in the MDM2 promoter, pigmentary phenotypes, and risk of skin cancer.
      ).
      Table 2Associations between selected SNPs in 53BP1 region and hair color and moles among controls
      Hair colorMoles
      SNPβ1SEP-valueβ
      The regression parameter β refers to the mean change in scoring in hair color (black to blonde) and number of moles per copy of the SNP minor allele. We regressed an ordinal coding for hair color (1=black; 2=dark brown; 3=light brown; 4=blonde; and 5=red) or number of moles (1: none; 2: 1–2; 3: 3-5; 4: 6-9; 5: 10-14 and 5: 15+) on an ordinal coding for genotype (0, 1, or 2 copies of SNP minor allele). β>0 means that the SNP is associated with lighter hair color and more moles.
      SEP-value
      rs38621380.140.120.230.200.120.11
      rs17782975-0.010.160.960.450.180.01
      rs6896470.220.150.130.190.150.22
      rs2602141
      The two SNPs (rs1869258 and rs560191) that are in high linkage disequilibrium with rs2602141 (each pair-wise r2>0.9) showed similar associations with hair color (P-value, 0.04 and 0.07, respectively) and moles (P-value, 0.02 and 0.003, respectively).
      0.220.100.030.310.110.003
      rs22420690.210.130.100.100.130.44
      rs9990470.200.140.16-0.080.140.57
      Abbreviations: SNP, single nucleotide polymorphism; 53BP1, p53-binding protein 1.
      1 The regression parameter β refers to the mean change in scoring in hair color (black to blonde) and number of moles per copy of the SNP minor allele. We regressed an ordinal coding for hair color (1=black; 2=dark brown; 3=light brown; 4=blonde; and 5=red) or number of moles (1: none; 2: 1–2; 3: 3-5; 4: 6-9; 5: 10-14 and 5: 15+) on an ordinal coding for genotype (0, 1, or 2 copies of SNP minor allele). β>0 means that the SNP is associated with lighter hair color and more moles.
      2 The two SNPs (rs1869258 and rs560191) that are in high linkage disequilibrium with rs2602141 (each pair-wise r2>0.9) showed similar associations with hair color (P-value, 0.04 and 0.07, respectively) and moles (P-value, 0.02 and 0.003, respectively).
      In summary, we systematically evaluated the common genetic variants of the 53BP1 gene and the risk of skin cancer. We found three SNPs (rs689647, rs2242069, and rs999047) were significantly associated with a decreased risk of BCC. These findings may lead to further replication and functional studies that will elucidate the underlying mechanisms of skin cancer development associated with these genetic variants.

      ACKNOWLEDGMENTS

      We thank Dr Hardeep Ranu and Ms Pati Soule for their laboratory assistance, and Ms Carolyn Guo for her programming support. We are indebted to the participants in the Nurses' Health Study for their dedication and commitment. Grant sponsor: NIH Grants CA122838 and CA128080.

      SUPPLEMENTARY MATERIAL

      Supplementary material is linked to the online version of the paper at http://www.nature.com/jid

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