Characterization and Impact of TERT Promoter Region Mutations on Clinical Outcome in Renal Cell Carcinoma

Abstract

Background

Mutations in the promoter region of the TERT gene have been detected in a variety of cancers. These mutations can potentially lead to unlimited cell divisions and result in poor clinical prognosis.

Objective

To determine the role and relevance of TERT promoter region mutations in both clear cell (ccRCC) and non–clear cell (nccRCC) renal cell carcinoma using ultra-deep and whole-genome sequencing methods on primary tumor samples.

Design, setting, and participants

DNA from 281 kidney tumors (147 ccRCC and 134 nccRCC) was sequenced between 2013 and 2015, and clinical outcomes for these patients from a single institution were retrospectively analyzed.

Outcome measurements and statistical analysis

Differences in patient characteristics and mutational status were tested using Fisher's exact test for categorical variables and the Wilcoxon rank sum test for continuous variables. Survival times were estimated using the Kaplan-Meier method and differences were tested using the log-rank test.

Results and limitations

TERT mutations occurred in 12.2% of ccRCC and 10.4% of nccRCC cases. In >80% of the cases, mutations were located at C228T and were found to co-occur only rarely with other relevant RCC driver genes. The median follow-up among survivors overall was 2.5 yr (range 0.1–18.3). TERT promoter mutations were significantly associated with cancer-specific survival in ccRCC (hazard ratio 2.68, 95% confidence interval 1.19–6.01; p = 0.013). In nccRCC, TERT mutations were significantly associated with larger tumors and metastatic development. Assessment of further relevant clinical associations was precluded in the nccRCC group by the heterogeneous and small sample size.

Conclusions

Our data suggests that TERT mutational status reflects a distinct pathogenesis with an aggressive disease course in RCC. Stratifying patients with this unique tumorigenesis that leads to poor clinical outcomes could be a putative target for novel therapeutics.

Patient summary

We show a previously unrecognized frequency of TERT promoter mutations in both clear cell and non–clear cell renal cell carcinoma. TERT promoter mutations were associated with some worse outcomes in patients with clear cell renal cell carcinoma.

Introduction

Renal cell carcinoma (RCC) represents a heterogeneous group of malignancies comprising multiple histopathologic entities associated with a different landscape of molecular alterations in each subtype. Clear cell RCC (ccRCC) is the most common subtype, accounting for approximately 75% of all RCCs. The remaining subtypes are often grouped together as non–clear cell RCC (nccRCC), consisting of papillary RCC (15%), chromophobe RCC (5–10%), unclassified RCC (5%), and other rare entities [1].

Despite advances in our understanding of the genomic underpinnings of RCC, the full spectrum of cancer drivers in different histological subgroups is not yet completely understood. We sought to characterize the prevalence of further relevant somatic mutations in RCC, and focused specifically on the TERT gene, located on chromosome 5p. Up to 90% of human cancers have high levels of TERT RNA expression, and consequently high TERT enzyme activity. The TERT enzyme is responsible for addition of telomeric repeats to chromosomal ends [2]. Telomeres, located at the end of every chromosome, function to protect chromosomes from recombination and degradation. Telomeres are gradually shortened after every cell division, which leads to senescence and apoptosis of cells after a given number of divisions [3]. Telomerases, with their core unit TERT, are expressed and active in proliferating cells, and are downregulated in differentiated cells [4], [5] because of transcriptional silencing [2].

The role of TERT in telomere and telomerase dynamics is the basis behind its oncogenic potential, whereny overactive TERT can maintain telomere length, enabling malignant cells to divide indefinitely and resulting in immortalization of cells [4], [6]. Cancer-specific TERT transcription is putatively caused by mutations upstream of the translational start site of TERT, in the TERT promoter region [7]. Mutations in this crucial regulatory element allow TERT expression, leading to the creation of a novel binding site for the ETS family of transcription factors, which ultimately increases TERT transcriptional activity.

Overexpression of the TERT gene, and consequently high TERT activity, has been described in many cancers including melanoma, glioblastoma, and thyroid and urothelial tumors [8], [9], [10], [11], [12], and TERT promoter region mutations have been associated with advanced disease course and poor outcome [9], [13], [14], [15].

It has previously been reported that the mutational status of the TERT promoter in RCC is only 6–10% [7], [16], [17], [18]. However, most groups studied only ccRCC and the results were limited by the detection methods used, namely polymerase chain reaction and Sanger sequencing [17], which may underestimate the prevalence of TERT promoter alterations. Furthermore, the largest genomic characterization of ccRCC, performed by the Cancer Genome Atlas network [19], did not include the TERT gene in their analysis. The only comprehensive study that used next-generation sequencing to detect TERT promoter and gene aberrations investigated chromophobe RCC [18]. While TERT promoter mutations were detected in <5% of the cases analyzed, a wide range of breakpoints were observed within the TERT promoter region and were associated with TERT upregulation; however, the association with clinical outcomes was not established.

The aim of this study was to use whole-genome and ultra-deep target sequencing methods to characterize the prevalence of TERT gene and promoter mutations in RCC from a large single-institutional cohort. In addition, we aimed to define the impact of TERT mutations on clinical outcomes, namely metastatic development, recurrence, and disease-specific survival, in affected patients.