Intratumour Heterogeneity in Urologic Cancers: From Molecular Evidence to Clinical Implications

Abstract

Context

Intratumour heterogeneity (ITH) can impair the precise molecular analysis of tumours and may contribute to difficulties encountered in cancer biomarker qualification and treatment personalisation.

Objective

This review summarises the evidence for genetic ITH in renal, bladder, and prostate carcinomas and potential strategies to address the clinical and translational research challenges arising from ITH.

Evidence acquisition

Publications that assessed ITH in the relevant urologic cancers were identified in a literature review.

Evidence synthesis

ITH with functionally distinct tumour subclones has been identified in all three tumour types. Heterogeneity of actionable genetic changes and of prognostic biomarkers between different tumour regions in the same patient suggests limitations of single biopsy–based molecular analyses for precision medicine approaches. Evolutionary constraints may differ between patients and may allow the prediction of specific evolutionary trajectories.

Conclusions

Assessment of multiple tumour regions for precision medicine purposes, monitoring of subclonal dynamics over time, and the preferential targeting of genetic alterations located on the trunk of the phylogenetic tree of individual cancers may accelerate the development of personalised medicine strategies and improve our understanding of treatment failure.

Patient summary

Genetic alterations can be heterogeneous within urologic tumours, complicating their use as biomarkers for treatment personalisation. We present novel strategies to address these challenges.

Introduction

Intertumour heterogeneity of genetic driver aberrations has been identified in each of the most common urologic cancer types [1], [2], [3]. This is thought to be a major reason for the variability of outcomes even between patients with tumours of the same histologic type, stage, and grade. These and similar observations in other cancer types have led to the concept of personalised cancer therapy that aims to identify the optimal treatment for each individual patient based on molecular or pathologic biomarkers. Personalised therapy has successfully improved therapeutic outcomes and eliminated side effects from unnecessary treatment in some cancer types, for example in non–small cell lung cancer, where the effectiveness of epidermal growth factor receptor (EGFR) inhibitors is restricted to patients whose tumours harbour an activating EGFR mutation [4]. However, attempts to personalise therapy in urologic cancers through prognostic or predictive biomarkers have largely been unsuccessful to date.

The molecular characteristics of tumours can also vary within individual patients. Whereas intertumour heterogeneity provides a theoretical basis for treatment personalisation, intratumour heterogeneity (ITH) can complicate the precise molecular profiling and the identification of the optimal therapy for cancers harbouring several functionally distinct tumour subclones. This review summarises current insights into ITH and its potential implications for personalised cancer medicine approaches in the most common urologic cancers. It also outlines novel approaches to address ITH in the clinic.

Most cancers originate from a single cell that has been transformed through a small number of cancer driver mutations [5]. However, additional mutations can be acquired during the subsequent expansion of the cancer population, leading to genetic heterogeneity between the cells of a tumour. Although most new mutations are likely to be neutral (passenger mutations) or deleterious, advantageous mutations (driver mutations) occasionally occur and can lead to the expansion of intratumoural subclones with new functional characteristics. The heterogeneous nature of tumours was recognised by Nowell, who described cancer as an evolutionary process that can readily adapt to new environments such as those encountered during cancer drug therapy [6]. Genomic instability frequently occurs in malignant tumours [7] and can increase the genetic variability of cancer cell populations. Thus aggressive or drug-resistant tumour subclones may develop more rapidly in genomically unstable cancers.

This review focuses on genetic ITH in urologic cancers. However, ITH can also result from nongenetic molecular alterations [8]. Epigenetic DNA methylation can promote evolutionary adaptation similar to genetic alterations. Different functional states such as quiescent and proliferative states and cancer stem cell differentiation but also the heterogeneity of the tumour microenvironment add additional layers of complexity that may have an impact on therapeutic success.

Early studies into genetic ITH mainly relied on conventional Sanger DNA sequencing of spatially or temporally separated tumour samples. Many heterogeneous genetic alterations may have remained undetected with this low-throughput technology that restricts analysis to a small number of genes and lacks sensitivity for the detection of subclonal mutations present at low frequency. Today, next-generation sequencing (NGS) technologies permit nucleotide resolution analysis of all protein-coding DNA regions (exome sequencing) or of the entire genome. Through deeper NGS coverage, the subclonal mutations present in a small percentage of cells can be detected, and the subclonal structures present within a sample can be inferred [9]. Thus NGS technology has dramatically increased the ability to detect and characterise ITH (Fig. 1A and 1B). Emerging sequencing technologies will provide an even clearer picture of the heterogeneity at the single-cell level [10], [11].

Thus sequencing technology is no longer a limiting factor for the study of ITH. The new challenge is to develop sampling technologies to analyse somatic genetic alterations across different primary tumour regions and associated metastases and the dynamic changes of cancer genomes over time.

NGS applied to circulating tumour cells (CTCs) [12] or circulating cell-free DNA (cfDNA) from tumour [13] has shown that cancer-specific genomic alterations can be detected and tracked in the blood of cancer patients. These minimally invasive technologies may circumvent the limited availability of tumour samples, but further work will be necessary to reveal whether sufficient CTCs or cfDNA can be derived from most patients with a specific tumour type, whether these technologies are sufficiently sensitive for the analysis of early stage disease, and whether the clinically relevant subclones in heterogeneous cancers are represented.