A Prognostic Gene Expression Signature in the Molecular Classification of Chemotherapy-naïve Urothelial Cancer is Predictive of Clinical Outcomes from Neoadjuvant Chemotherapy: A Phase 2 Trial of Dose-dense Methotrexate, Vinblastine, Doxorubicin, and Cisplatin with Bevacizumab in Urothelial Cancer

Abstract

Background: Gene expression profiling (GEP) suggests there are three subtypes of muscle-invasive urothelial cancer (UC): basal, which has the worst prognosis; p53-like; and luminal. We hypothesized that GEP of transurethral resection (TUR) and cystectomy specimens would predict subtypes that could benefit from chemotherapy.

Objective: To explore clinical outcomes for patients treated with dose-dense (DD) methotrexate, vinblastine, doxorubicin, and cisplatin (MVAC) and bevacizumab (B) and the impact of UC subtype.

Design, setting, and participants: Sixty patients enrolled in a neoadjuvant trial of four cycles of DDMVAC + B between 2007 and 2010. TUR and cystectomy specimens for GEP were available from 38 and 23 patients, respectively, and from an additional confirmation cohort of 49 patients treated with perioperative MVAC.

Outcome measurements and statistical analysis: Relationships with outcomes were analyzed using multivariable Cox regression and log-rank tests.

Results and limitations: Chemotherapy was active, with pT0N0 and ≤pT1N0 downstaging rates of 38% and 53%, respectively, and 5-yr overall survival (OS) of 63%. Bevacizumab had no appreciable impact on outcomes. Basal tumors had improved survival compared to luminal and p53-like tumors (5-yr OS 91%, 73%, and 36%, log-rank p=0.015), with similar findings on multivariate analysis. Bone metastases within 2 yr were exclusively associated with the p53-like subtype (p53-like 100%, luminal 0%, basal 0%; p ≤ 0.001). Tumors enriched with the p53-like subtype at cystectomy suggested chemoresistance for this subtype. A separate cohort treated with perioperative MVAC confirmed the UC subtype survival benefit (5-yr OS 77% for basal, 56% for luminal, and 56% for p53-like; p=0.021). Limitations include the small number of pretreatment specimens with sufficient tissue for GEP.

Conclusion: GEP was predictive of clinical UC outcomes. The basal subtype was associated with better survival, and the p53-like subtype was associated with bone metastases and chemoresistant disease.

Patient summary: We can no longer think of urothelial cancer as a single disease. Gene expression profiling identifies subtypes of urothelial cancer that differ in their natural history and sensitivity to chemotherapy.

Keywords: Basal; Bevacizumab; Dose-dense methotrexate cisplatin; Gene expression profiling; Luminal; Neoadjuvant; Subtype; Urothelial cancer; p53.

Fig. 1

(A) Overall survival (OS) for all patients. The 5-yr OS and disease-specific survival (DSS) were 63% and 64%, respectively, for all patients treated with neoadjuvant chemotherapy with dose-dense methotrexate, vinblastine, doxorubicin, and cisplatin (DDMVAC) + bevacizumab (median follow-up 49 mo). (B) OS for patients with urothelial carcinoma of the bladder and upper tract. The 5-yr OS and DSS were both 72% in upper tract disease, and 60% and 61%, respectively, in bladder/urethral cancer. (C) OS by pathologic stage. Downstaging to ≤pT1N0 had a significant impact on 5-yr survival (OS and DSS 93%) compared to those who were not downstaged (OS and DSS 29%; log-rank p ≤ 0.0001). CI = confidence interval.

Fig. 1

(A) Overall survival (OS) for all patients. The 5-yr OS and disease-specific survival (DSS) were 63% and 64%, respectively, for all patients treated with neoadjuvant chemotherapy with dose-dense methotrexate, vinblastine, doxorubicin, and cisplatin (DDMVAC) + bevacizumab (median follow-up 49 mo). (B) OS for patients with urothelial carcinoma of the bladder and upper tract. The 5-yr OS and DSS were both 72% in upper tract disease, and 60% and 61%, respectively, in bladder/urethral cancer. (C) OS by pathologic stage. Downstaging to ≤pT1N0 had a significant impact on 5-yr survival (OS and DSS 93%) compared to those who were not downstaged (OS and DSS 29%; log-rank p ≤ 0.0001). CI = confidence interval.

Fig. 2

(A) Gene expression profiling in matched transurethral resection (TUR) and cystectomy specimens. Left: Chemotherapy induced the active p53 gene signature (log ratio cystectomy/TUR for matched tumors). Right: relative expression of the p53 gene signature in each pre- and post-treatment tumor arranged according to subtype membership. To visualize gene expression patterns, specific gene expression values adjusted to a median of zero were used. (B) Pathologic stage by subtype. (C) Overall survival (OS) by subtype. The basal subtype was associated with better survival after neoadjuvant chemotherapy compared to the p53-like and luminal subtypes (5-yr OS 91%, 73%, and 36%, respectively; p = 0.015). (D) Bone metastases (mets) by subtype. Bone metastases only occurred in the p53-like subtype (53%), with none in the basal and luminal subtypes. (E) Gene expression profile comparing TUR to cystectomy. Post-treatment tumors were enriched with an active p53 gene expression signature that was distinct from the p-53 like subtype at TUR. Owing to quantile normalization, the subtype membership of a few TUR tumors was changed when we combined TUR and cystectomy. CI = confidence interval.

Fig. 3

Survival in the confirmatory data set by subtype. Gene expression profiling of pretreatment tissue from patients treated in a clinical trial of perioperative methotrexate, vinblastine, doxorubicin, and cisplatin (MVAC) confirmed the survival advantage seen in the basal subtype. After chemotherapy the 5-yr overall survival (95% confidence interval) was 77% (59–100%) for the basal, 56% (37–87%) for the luminal, and 56% (37–87%) for the p53-like subtype (p = 0.021, log-rank test). OS = overall survival; CI = confidence interval.