Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression

Abstract

Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease.

Figure 1.

Results of TERT fine-mapping analysis. (A) Regional association plot of the imputed iCOGS genotype data. Typed SNPs are indicated in red and imputed SNPs in grey. Diamonds denote SNPs significantly associated with PrCa after multiple LR analyses. The 20 kb interval is denoted by the shaded region that is expanded below. Forty-four SNPs were associated with PrCa risk at P < 10⁻⁵ (indicated by the red line). (B) Expanded detail for the 20 kb interval. The positions of 42 SNPs located within this window significant at P < 10⁻⁵ are marked (42 SNPs P < 10⁻⁵), as are the 4 SNPs independently significant after multiple LR model and SNPs that overlap with ENCODE annotations (ENCODE intersect), including DNase I hypersensitivity (DNase Clusters) and TFBS ChIP signals. The positions of TERT gene transcripts from Ensembl 65 (TERT), CpG island regions (CpG), segmental duplications (SegDup) and ENCODE chromatin state (Broad ChromHmm) are also indicated. The light grey rectangle (Broad ChrommHmm) denotes a region of heterochromatin, the yellow rectangle a weak enhancer and the dark grey rectangle a polycomb-repressed region. All tracks were generated using the Hg19 build of the UCSC genome browser. The locations of regions 1–4 are indicated as coloured rectangles and numbered. (C) LD plot for the 20 kb interval. r² values are derived from imputed data for the UKGPCS subset of iCOGS samples. Triangles indicate the boundaries of regions 1–4. MLR, multiple LR.

Figure 2.

mRNA expression levels in benign prostate tissue for three SNPs in region 1 of the TERT locus. A significant increase in TERT expression was observed for the minor (protective) alleles of (A) rs10069690, (C) rs2242652 and (D) rs7725218. No effect on expression of the CLPTM1L gene was observed, data are shown only for (B) rs10069690.