Genomic heterogeneity as a barrier to precision oncology in urothelial cancer

Abstract

Precision oncology relies on the accurate molecular characterization of individual patients with cancer at the time of treatment initiation. However, tumor molecular profiles are not static, and cancers continually evolve because of ongoing mutagenesis and clonal selection. Here, we performed genomic analyses of primary tumors, metastases, and plasma collected from individual patients to define the concordance of actionable genomic alterations and to identify drivers of metastatic disease progression. We observed a high degree of discordance of actionable genomic alterations, with 23% discordant between primary and metastatic disease sites. Among chromatin-modifying genes, ARID1A mutations, when discordant, were exclusive to the metastatic tumor samples. Our findings indicate that the high degree of lesion-to-lesion genomic heterogeneity may be a barrier to precision oncology approaches for bladder cancer and that circulating tumor DNA profiling may be preferred to tumor sequencing for a subset of patients.

Keywords: ARID1A; CP: Cancer; FGFR3; bladder cancer; cell-free DNA; genomic heterogeneity; metastasis; urothelial carcinoma.

Figure 1.. Clinical characteristics of prospectively sequenced urothelial carcinomas

(A) Clinical and tumor features of the prospective Memorial Sloan Kettering Cancer Center (MSK) and retrospective The Cancer Genome Atlas (TCGA) bladder urothelial carcinoma cohorts. (B) Distribution of the biopsied metastatic disease sites in the MSK urothelial carcinoma study cohort. (C) Frequency of alterations in frequently mutated oncogenes in the MSK urothelial cancer cohort stratified by disease state (low-grade primary tumors, non-invasive and invasive high-grade [HG] primary tumors, and metastatic sites). Significant values are labeled as adjusted p value (q value): *q < 0.05, **q < 0.01, ***q < 0.001. Adjustment for multiple comparisons using the false discovery method demonstrated no loss in significance of the highlighted genes but a loss of significance for KDM6A and ARID1A (p = 0.03, q = 0.06). See also Figure S1 and Tables 1 and S1.

Figure 2.. Whole-exome sequencing of 22 paired primary and metastatic urothelial cancers

(A) OncoPrint of whole-exome sequencing data from 22 primary-metastasis urothelial cancer pairs. Tumor mutational burden (mutations/megabase [MB]) and select recurrently mutated genes are shown. Each column represents an individual patient with the mutational status of the primary tumor on the left and the metastatic specimen on the right. (B) Mutational concordance and discordance between primary and metastatic tumor samples shown as the fraction of mutations that were shared, exclusive to the primary tumor or to the metastasis. (C and D) Phylogenic analysis of the primary and metastatic tumors from two representative patients. Shown are the mutation matrix colored as trunk (dark green) or exclusive (light green) for the respective phylogeny, fraction of tumor cells mutated (cancer cell fractions, shades of blue) and inferred evolutionary relationship. Numbers indicate shared or private mutation counts. See also Figure S2.

Figure 3.. Frequent discordance of actionable genomic alterations in primary and metastatic urothelial carcinomas

(A) Targeted sequencing of 119 paired primary and metastatic urothelial cancer samples. Each column represents an individual patient with the mutational status of the primary tumor on the left and the metastatic specimen on the right. Only oncogenic and likely oncogenic mutations, fusions, and ERBB2 amplifications were included in the OncoPrint. (B) Comparison of tumor mutational burden (TMB) in primary and metastatic tumor sites. (C) Mutational concordance of select frequently mutated genes including targetable kinases and chromatin-modifying genes. Percentages reflect only patients with a mutation in the designated gene in either the primary or metastasis or both. See also Figure S3.

Figure 4.. Concordance of oncogenic mutations between tumor and cell-free DNA (cfDNA) in patients with metastatic urothelial cancer

(A) Concordance between primary and metastatic tumor sites and plasma-derived cfDNA in 45 patients with metastatic urothelial cancer stratified by all mutations, oncogenic/likely oncogenic mutations only, and actionable mutations only as defined by OncoKB levels 1–4. (B) OncoPrint of select actionable/oncogenic genes in patient-matched primary, metastatic, and cfDNA samples. (C) Paired comparison of tumor and cfDNA samples from 123 patients with metastatic urothelial cancer. (D) Patient P-0033799 presented with localized bladder cancer and was treated with neoadjuvant chemotherapy followed by radical cystectomy. The patient later developed multiple lung metastases and was treated with pembrolizumab. Upon further progression, a biopsy of a lung metastasis identified an actionable FGFR3 mutation (S371C) not present in the primary tumor sample. Plasma collected for cfDNA analysis prior to initiation of erdafitinib identified two additional actionable FGFR3 mutations (R248C and S249C) and a FGFR3-TACC3 fusion. While on therapy, cfDNA analyses identified 4 additional FGFR3 mutations, a subset of which have been previously been shown to confer resistance to FGFR-directed therapy. Numbers correspond to the interval in months between each specimen collection. See also Figures S4 and S5.