Comprehensive Genomic Analysis of Translocation Renal Cell Carcinoma Reveals Copy-Number Variations as Drivers of Disease Progression

Abstract

Purpose: Translocation renal cell carcinoma (tRCC) is a rare, aggressive renal cell carcinoma (RCC) subtype. There is currently limited understanding on the role of molecular alterations in the pathogenesis and progression of these tumors. We investigated the association between somatic alterations and clinical outcomes in two independent cohorts profiled using DNA sequencing.

Experimental design: Twenty-two tRCCs underwent targeted sequencing [Memorial Sloan Kettering Cancer Center (MSK)-IMPACT]; a subset was profiled using exome-sequencing and combined with exome data from The Cancer Genome Atlas (TCGA) for analysis. The prognostic value of specific somatic aberrations, tumor mutation burden (TMB), and fraction of copy-number-altered genome (FCNAg) was explored. In TCGA cases, neoantigen prediction and immune cell deconvolution were performed using RNA-sequencing and exome data. Overall survival estimates were computed using the Kaplan-Meier method; time-on-treatment was calculated for 14 MSK-IMPACT patients who underwent systemic therapy. Associations between molecular features and outcomes were evaluated using nonparametric testing.

Results: Copy-number aberrant tRCCs were associated with poor overall survival (P = 0.03). Pediatric patients had tumors with lower FCNAg (P = 0.01). In one adult case with two chronologically distinct tumor samples sequenced, we confirmed that copy-number events occurred early during evolution. TERT promoter mutations were found exclusively in high-stage tumors. We found that tRCCs displayed distinct angiogenesis and PD-L1 gene expression profiles compared with other RCC subtypes.

Conclusions: Tumors molecularly defined by increased copy-number variations were associated with aggressive disease in tRCC. A higher burden of genomic events in adults compared with pediatric cases likely reflects a more aggressive clinical course. The unique immunophenotypic characteristics of tRCC merit further exploration.

Figure 1:

(A) Oncoprint displaying recurrent somatic mutations (genes mutated in >1 sample) and frequent copy number variants (CNVs) in the MSK-IMPACT cohort. Copy number variants (CNVs) CNVs are mostly found in cases with a high AJCC stage. The most frequent MiTF fusion gene was TFE3. (B) TMB in merged MSK-TCGA exomes compared to other TCGA-RCC cohorts. (C) Tumor mutation burden of tRCC is centered around a median value of 0.8 non-synonymous mutations per megabase, with two outlier cases. Mann-Whitney U tests were used for pairwise TMB comparisons between RCC subtypes.

Figure 2.

Association of FCNAg with AJCC stage and 9p loss. The broad line of the boxplots illustrate the median FCNAg, upper and lower hinges showing the interquartile ranges (IQR, 25% and 75% of values) and the whiskers illustrating values within 1.5x the IQR in the MSK (A) and TCGA (B) cohorts. Loss of chromosome 9p was found to be associated with higher FCNAg in the MSK (C) and TCGA cohorts (D).

Figure 3:

Proportion of patients with 9p loss and 17q gain in the MSK (A) and TCGA cohorts (B). Kaplan-Meier analysis of overall survival for patients with copy number-aberrant tumors (i.e. 9p loss, 17q gain, or high FCNAg [>within-cohort median]) in the MSK-IMPACT (C) and TCGA cohorts (D). Log-rank test results from both cohorts were combined in a meta-analysis using Fisher’s method (Chi-squared [4d.f]=10.52, p=0.03).

Figure 4:

Temporal evolution of tRCC in a single patient. (A) Private and shared copy number alterations and somatic mutations in two tRCCs tumors from a single patient. (B) Clinical course of tRCC patient from which tumor samples were derived. (C) Putative model for tRCC evolution in this case. Early loss of 9p and other copy number alterations was followed by large-scale whole genome duplication. The majority of somatic mutations were acquired in the period following the appearance of the most recent common ancestor (MRCA), which bore a high-burden of CNVs.

Figure 5:

(A) Swimmer plot displaying a heterogeneous pattern of substances and response, a few cases showing an exceptionally prolonged time on treatment, (B) Molecular features identified in patients with TOT >12 months.

Figure 6:

Three panels with pediatric cases in our MSK-IMPACT cohort displaying a favorable disease course after surgery as the only intervention (Created with BioRender.com).