EURURO Vol. 72 No. 4

545 656

1. Introduction
Neoadjuvant cisplatin-based chemotherapy (NAC) is the
standard treatment in muscle-invasive bladder cancer
(MIBC) prior to radical cystectomy . Although NAC
improves pathological downstaging and[5_TD$DIFF] patient survival,
only approximately 40% of patients experience a major
response, defined as absence of muscle-invasive disease and
lymph node metastasis (<pT2 and pN0) . Nonresponding
patients are unlikely to derive clinical benefit, are exposed to
substantial toxicity, and experience a delay in definitive local
therapy . Identification of molecular markers of non-
responsiveness is essential for more precise delivery of care.
Recent analyses suggest that specific mutations, especially in
ERCC2, ERBB2, and DNA repair genes, may predict response
to NAC Here we aimed to use RNA expression analysis
for the development of predictive biomarkers.
Recent identification of molecular gene expression
subtypes and prior work highlighting the clinical
impact of basal MIBC have advanced our understanding
of the biology of bladder cancer. Molecular classification
provides a framework for further study and has potential
implications for the clinical management of MIBC. Four
different molecular subtyping schemes have been described
. Each was developed in different patient popula-
tions using unique genomic platforms, and only one was
based on integrative multiplatform genomic analysis
. Despite these differences, each identifies molecular
phenotypes that share many similarities. They represent a
division into basal and luminal tumors at a higher level, with
different subclassifications that are specific to each system.
Choi et al first introduced the concept that
molecular subtypes may predict response to NAC. In three
cohorts with a total of 100 patients, a subset classified as
having ‘‘p53-like’’ tumors demonstrated a lower response
rate to cisplatin-based combination chemotherapy. This
finding has not been validated in additional larger patient
cohorts and has not been investigated with the other
subtyping methods. Furthermore, none of the four subtyp-
ing models is suitable for clinical implementation because
each requires classification of an entire patient cohort in
order to assign an individual patient sample to a subtype.
In this study, we aimed to correlate large multi-
institutional patient cohort outcomes after NAC with
molecular subtyping of pre-NAC specimens according to
four published classification methods: University of North
Carolina (UNC), MD Anderson Cancer Center (MDA), The
Cancer Genome Atlas (TCGA), and Lund University
. Moreover, we aimed to develop a single-patient
assay based on transcriptomic analysis of transurethral
resection (TUR) specimens that would be suitable for use in
a clinical laboratory setting.
2. Patients and methods
2.1. Patient populations
For the discovery NAC cohort, 250 consecutive patients from five
institutions were compiled. MIBC (cT2-4aN0-3M0) was diagnosed by
TUR prior to receiving at least three cycles of NAC. For the validation NAC
cohort, 93 consecutive patients with MIBC from two institutions were
selected, whose characteristics were similar to those of the discovery set.
2.2. Tissue sampling and gene expression profiling
Whole transcriptome analysis was performed on formalin-fixed,
paraffin-embedded tumor tissue with [18_TD$DIFF]GeneChip1 [19_TD$DIFF]Human Exon 1.0 ST
Array (Affymetrix) in a Clinical Laboratory Improvement Amendments
(CLIA)-certified laboratory . In total, 223/250 (89%) and 82/93 (88%)
of the discovery and validation NAC cohorts, respectively, passed quality
control (Supplementary Table 1). Microarray data were normalized and
genes summarized using single-channel array normalization
2.3. Datasets from the public domain
For investigation of the prognostic impact of the published methods for
molecular subtyping, the 397 patients without chemotherapy prior to
sample collection from the TCGA bladder urothelial carcinoma were
Outcome measurements and statistical analysis: Receiver-operating characteristics were
used to determine the accuracy of GSC. The effect of GSC on survival was estimated by Cox
proportional hazard regression models.
Results and limitations: The models generated subtype calls in expected ratios with high
concordance across subtyping methods. GSC was able to predict four consensus molecular
subtypes with high accuracy (73%), and clinical significance of the predicted consensus
subtypes could be validated in independent NAC and non-NAC datasets. Luminal tumors
had the best OS with and without NAC. Claudin-low tumors were associated with poor OS
irrespective of treatment regimen. Basal tumors showed the most improvement in OS with
NAC compared with surgery alone. The main limitations of our study are its retrospective
design and comparison across [14_TD$DIFF]datasets.
Conclusions: Molecular subtyping may have an impact on patient benefit to NAC. If
validated in additional studies, our results suggest that patients with basal tumors should
be prioritized for NAC. We discovered the first single-sample classifier to subtype MIBC,
which may be suitable for integration into routine clinical practice.
Patient summary: Different molecular subtypes can be identified in muscle-invasive
bladder cancer. Although cisplatin-based neoadjuvant chemotherapy improves patient
outcomes, we identified that the benefit is highest in patients with basal tumors. Our
newly discovered classifier can identify these molecular subtypes in a single patient and
could be integrated into routine clinical practice after further validation.
# 2017 European Association of Urology. Published by Elsevier B.V. All rights reserved.
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