Age at cancer onset in germline TP53 mutation carriers: association with polymorphisms in predicted G-quadruplex structures

Abstract

Germline TP53 mutations predispose to multiple cancers defining Li-Fraumeni/Li-Fraumeni-like syndrome (LFS/LFL), a disease with large individual disparities in cancer profiles and age of onset. G-quadruplexes (G4s) are secondary structural motifs occurring in guanine tracks, with regulatory effects on DNA and RNA. We analyzed 85 polymorphisms within or near five predicted G4s in TP53 in search of modifiers of penetrance of LFS/LFL in Brazilian cancer families with (n = 35) or without (n = 110) TP53 mutations. Statistical analyses stratified on family structure showed that cancer tended to occur ~15 years later in mutation carriers who also carried the variant alleles of two polymorphisms within predicted G4-forming regions, rs17878362 (TP53 PIN3, 16 bp duplication in intron 3; P = 0.082) and rs17880560 (6 bp duplication in 3' flanking region; P = 0.067). Haplotype analysis showed that this inverse association was driven by the polymorphic status of the remaining wild-type (WT) haplotype in mutation carriers: in carriers with a WT haplotype containing at least one variant allele of rs17878362 or rs17880560, cancer occurred ~15 years later than in carriers with other WT haplotypes (P = 0.019). No effect on age of cancer onset was observed in subjects without a TP53 mutation. The G4 in intron 3 has been shown to regulate alternative p53 messenger RNA splicing, whereas the biological roles of predicted G4s in the 3' flanking region remain to be elucidated. In conclusion, this study demonstrates that G4 polymorphisms in haplotypes of the WT TP53 allele have an impact on LFS/LFL penetrance in germline TP53 mutation carriers.

Figures

Fig. 1.

Predicted localization of G4s and associated polymorphisms in TP53. (A) Schematic representation of G4 localization and polymorphisms at the TP53 locus. G1 to G5: position of G4 motifs predicted using the QGRS mapper software set at its default parameters (see Materials and methods). A to G: position of polymorphisms within or near these G4. S1: sequence 1 encompassing G3; S2: sequence 2 encompassing G5. (B) Sequence of S1 region, from intron 2 to intron 3 (small letters), encompassing exon 3 (capital letters). Two G-tract domains forming putative G4 are shown in bold. The position of polymorphisms B in intron 2 (G/C, rs1642785) and C in intron 3 (16bp duplication, rs17878362) are underlined. (C) Sequence of S2 region encompassing the 3′ flanking region of TP53 after cleavage site. Bold letters: G-tracts forming putative G4. The position of polymorphisms F (6bp duplication, rs17880560) and G (C/T, rs1614984) are underlined.

Fig. 2.

Genotype-dependent Kaplan–Meier disease-free probability estimates in LFL/LFS family members with or without TP53 mutations. Kaplan–Meier probability is shown for rs17878362 (A), rs17880560 (B) and rs1042522 (C). In each panel, the left panel corresponds to subjects of the MUT group (TP53 mutation carriers) and the right panel to subjects of the WT2 group (families with no mutation detected). The tables under the graphs show disease-free probability estimates at different ages (10, 30, 50 and 65 years) according to genotype. Only probabilities up to 65 years are shown. *: G corresponds to the arginine and C to the proline variants of rs1042522.

Fig. 3.

Kaplan–Meier disease-free probability estimates based on the haplotype of the WT allele. Kaplan–Meier probabilities in MUT (TP53 mutation carriers in LFL/LFS family members) (A) and WT2 groups (LFL/LFS families with no mutation detected) (B) are shown. In the MUT group, the TP53 mutation is present on a haplotype defined as A1A1 (non-duplicated variant for both polymorphisms; rs17878362 andrs17880560), and the remaining WT haplotype is shown. In the WT2 group, in which subjects carry two WT alleles, one of the alleles has been ‘fixed’ as the A1A1 haplotype and the effect of the other haplotype is shown. Tables under the graphs show disease-free probability estimates at different ages (10, 30, 50 and 65 years) according to haplotypes (A1A1: non-duplicated for both polymorphisms; A1A2: non-duplicated for rs17878362 and duplicated for rs17880560; A2A1: duplicated for rs17878362 and non-duplicated for rs17880560). Only probabilities up to 65 years are shown.

Fig. 4.

Effect of different WT haplotypes in TP53 mutation carriers: a model. TP53 alleles are represented as rods. Left, mutant allele occurring on a haplotype carrying A1 variants of both rs17878362 and rs17880560 (A1A1). Right, different types of WT haplotypes. The WT haplotype defined by A1A1 is considered as a ‘weak’ haplotype (associated with early cancer, indicative low capacity to compensate the loss of p53 function of the mutant allele). The WT haplotypes defined by A1A2 or A2A1 are considered as ‘strong haplotype’ (associated with later cancer onset, thus providing at least partial compensation for the loss of function of the mutant allele). Of note, our data do not predict the effect of WT A2A2 haplotypes, or the effects of these haplotypes when the mutation occurs on another haplotype than A1A1.