Comparative Genomic Profiling of Matched Primary and Metastatic Tumors in Renal Cell Carcinoma

Abstract

Background: Next-generation sequencing (NGS) studies of matched pairs of primary and metastatic tumors in renal cell carcinoma (RCC) have been limited to small cohorts.

Objective: To evaluate the discordance in somatic mutations between matched primary and metastatic RCC tumors.

Design, setting, and participants: Primary tumor (P), metastasis (M), and germline DNA from 60 patients with RCC was subjected to NGS with a targeted exon capture-based assay of 341 cancer-associated genes. Somatic mutations were called using a validated pipeline.

Outcome measurements and statistical analysis: Mutations were classified as shared (S) or private (Pr) in relation to each other within individual P-M pairs. The concordance score was calculated as (S-Pr)/(S+Pr). To calculate enrichment of Pr/S mutations for a particular gene, we calculated a two-sided p value from a binomial model for each gene with at least ten somatic mutation events, and also implemented a separate permutation test procedure. We adjusted p values for multiple hypothesis testing using the Benjamini-Hochberg procedure. The mutation discordance was calculated using Mann-Whitney U tests according to gene mutations or metastatic sites.

Results and limitations: Twenty-one pairs (35%) showed Pr mutations in both P and M samples. Of the remaining 39 pairs (65%), 14 (23%) had Pr mutations specific to P samples, 12 (20%) had Pr mutations to M samples, and 13 (22%) had identical somatic mutations. No individual gene mutation was preferentially enriched in either P or M samples. P-M pairs with SETD2 mutations demonstrated higher discordance than pairs with wild-type SETD2. We observed that patients who received therapy before sampling of the P or M tissue had higher concordance of mutations for P-M pairs than patients who did not (Mann-Whitney p=0.088).

Conclusions: Our data show mutation discordance within matched P-M RCC tumor pairs. As most contemporary precision medicine trials do not differentiate mutations detected in P and M tumors, the prognostic and predictive value of mutations in P versus M tumors warrants further investigation.

Patient summary: In this study we evaluated the concordance of mutations between matched primary and metastatic tumors for 60 kidney cancer patients using a panel of 341 cancer genes. Forty-seven patients carried nonidentical cancer gene mutations within their matched primary-metastatic pair. The mutation profile of the primary tumor alone could compromise precision in selecting effective targeted therapies and result in suboptimal clinical outcomes.

Keywords: Convergent evolution; Discordance; Genomics; Metastasis; Next-generation sequencing; Primary-metastasis tumor pairs; Renal cell carcinoma; Spatiotemporal divergence.

Fig. 1

Distribution of mutations across the cohort for known cancer genes with prevalent mutations in renal cell carcinoma (RCC). For each gene, the top row represents a mutation in the primary tumor and the bottom row represents a mutation in the metastatic lesion.

Fig. 2

Discordance of mutation patterns between primary and metastatic tumors. Shared mutations are in gray and private mutations in the primary tumor and metastasis in red and blue, respectively. (A) Shared and private mutations among the paired primary and metastatic samples. Every column represents a patient and the overall height of the column depicts the number of mutations in that pair. (B) Most commonly mutated genes across our cohort and events as shared or private alterations.

Fig. 3

Cases with SETD2 mutations in primary and/or metastatic lesions had lower concordance than cases with a wild-type SETD2 pair. The concordance score for each pair, ranging from −1 (all mutations were private) to +1 (all mutations were shared for both samples), is shown. Every point represents a pair sorted by concordance. To the left of the figure, pairs have predominantly private mutations, while predominantly shared mutations are shown to the right.

Fig. 4

Three spatiotemporally distinct patterns of convergent evolution through loss of function on the same individual genes. Six primary tumor-metastasis pairs carry private mutations on the same individual gene in both the primary and metastatic samples (black). Nine pairs not only have shared mutations on the same individual genes but also carry private mutations in either the primary tumor (n = 6, blue) or the metastatic tumor (n = 3, red).