Exploring the genomic landscape of platinum resistant and sensitive germ cell tumours

Testicular germ cell tumours (TGCTs) are the most common solid tumours affecting young men. These tumours are highly curable, even with advanced or metastatic disease. Successful treatment of TGCTs has largely been attributable to the exceptional sensitivity of this tumour type to platinum-based chemotherapies. Still, ~10% of patients are refractory to treatment and have a poorer prognosis. Whilst various cellular mechanisms have been touted as underpinning platinum resistance, the somatic determinants of treatment failure largely remain a mystery.

With the advent of Next Generation Sequencing, there have been a number of recent studies looking at the patterns of somatic mutations in TGCT. However, TGCT is a low frequency tumour and sample sizes have necessarily been modest.  As for many cancers, collection of fresh tissue is the exception and most of the larger studies of TGCT have reported clinical series based on analysis of formalin fixed tissue looking at only a limited clinical panel of genes.  Furthermore, on account of biases in ascertainment of the samples included in the series, results have often been contradictory. To explore the question further, we performed whole exome sequencing (WES) and copy number profiling of 40 tumours from 26 patients with platinum resistant disease, the largest WES series to date in resistant samples.  We then combined our data with that from five additional studies for a total of 664 tumours from 631 patients to provide a comprehensive look at the genetic profiles of platinum resistant and sensitive TGCTs.  Importantly, we undertook an adjusted analysis across these studies to correct for the potential confounding effects of differential inclusion by histology (seminoma/nonseminoma), site (gonadal/extra-gonadal), stage (localised/metastatic), platform (exome/panel) and tissue (fresh frozen/FFPE).

 We found interesting new clinicopathalogical associations relating to point mutations in particular genes.  KIT mutation is inversely associated with platinum resistance.  TP53 mutations is associated with tumour location (it is much more common in extra gonadal than gonadal tumours) and mutations in WNT signalling pathway genes are associated with development of metastatic disease.  Whilst TGCTs overall have a low rate of somatic point mutations, platinum resistant tumours have a higher rate compared to the platinum sensitive counterparts, suggesting that resistance may be linked to having a larger genetic substrate offering potential for rescue during treatment. 

 Whilst quiet on the small variant front, TGCT are characterised by dramatic genomic instability with a notably high level of somatic copy number alterations, such as deletions and duplications. They are also highly aneuploid and often polyploid too. These features combine to result in TGCTs having very highly chaotic genomic copy number profiles. To date these have only been looked at qualitatively or using crude categorical groupings.  In this paper, to look quantitatively for patterns in the chaos, we apply for the first time in TGCT analysis of copy number signatures.  We used a method recently developed in the Brenton lab, whereby each signature represents a different mechanism via which the copy number alterations arise. These analyses revealed for the first time association between small variant changes (namely those in mutations in KIT and RAS) and gains and losses of large segments of chromosome arms, alluding to a possible causative mechanism. This molecular association makes sense in light of cellular studies that have linked these genes to roles in cell cycle control and chromosome segregation.

 We demonstrate that platinum resistance cannot be accounted for by a single molecular entity but is likely to involve multiple mutational processes and add further to the evolving molecular characterisation of this fascinating tumour.