Related Experiment Video
Updated: Nov 11, 2025
Patient-Derived Tumor Explants As a "Live" Preclinical Platform for Predicting Drug Resistance in Patients
Published on: February 7, 2021
Molecular Characterization of Residual Bladder Cancer after Neoadjuvant Pembrolizumab
Andrea Necchi1, Joep J de Jong2, Daniele Raggi3
1Vita-Salute San Raffaele University, Milan, Italy; Department of Medical Oncology, IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy.
Background:
In patients with muscle-invasive urothelial bladder cancer (MIBC), molecular alterations in immunotherapy-resistant tumors found at radical cystectomy (RC) remain largely unstudied.
Objective:
To investigate the biology of pembrolizumab-resistant tumors in comparison to an RC cohort treated without any systemic therapy and a cohort of neoadjuvant chemotherapy (NAC)-treated tumors.
Design, Setting, And Participants:
Transcriptome-wide expression profiling was performed on 26 RC samples from patients with ypT2-4 disease after pembrolizumab treatment, of which 22 had matched pretherapy samples. Unsupervised consensus clustering (CC) was performed to compare 26 post-pembrolizumab samples with 94 RC samples without neoadjuvant treatment and 21 samples collected from the former tumor bed of NAC-treated patients (scar tissue). Clusters were investigated for their biological and clinical characteristics and were compared to a cohort of post-NAC tumors (n = 133).
Outcome Measurements And Statistical Analysis:
Patient and tumor characteristics were compared between subgroups using χ2 tests and two-sided Wilcoxon rank-sum tests. The primary endpoint was recurrence-free survival.
Results And Limitations:
Molecular subtyping of pre- and post-pembrolizumab samples revealed significant differences: only 36% of samples had a concordant subtype according to the consensus classifier. Unsupervised CC revealed three distinct post-pembrolizumab clusters (basal, luminal, and scar-like). A scar-like subtype was present in 50% of the post-pembrolizumab cases (n = 13) and expressed genes associated with wound healing/scarring. This subtype had higher luminal marker expression in the post-pembrolizumab setting compared to CC scar-like tumors from the other cohorts. Patients with the scar-like subtype showed favorable prognosis after systemic therapy, but not in the RC-only setting. The small numbers in each subgroup represents the major study limitation.
Conclusions:
This study expands our understanding of the biology of pembrolizumab-resistant MIBC and provides a framework for defining molecular subtypes after treatment. The results further support the hypothesis that luminal-type tumors may be resistant to immunotherapy or that this treatment may select for, or induce, a luminal phenotype.
Patient Summary:
We carried out genetic analysis for bladder cancer tumors from patients who had received an immunotherapy agent called pembrolizumab and compared them to tumors treated with standard chemotherapy or just bladder removal. We found differences in gene expression between the treatment types and between tumor tissue from the same patient before and after treatment. These results may be helpful in personalizing therapy strategies for patients with bladder cancer.
Insights
Molecular subtypes of immunotherapy-resistant bladder cancer were identified. A scar-like subtype emerged post-pembrolizumab treatment, suggesting potential resistance mechanisms and informing personalized therapy for muscle-invasive urothelial carcinoma.
Area of Science:
- Oncology
- Genomics
- Immunotherapy
Background:
- Muscle-invasive urothelial bladder cancer (MIBC) presents challenges with immunotherapy resistance.
- Molecular characteristics of tumors resistant to pembrolizumab after radical cystectomy (RC) are not well understood.
Purpose of the Study:
- To investigate the molecular biology of pembrolizumab-resistant tumors.
- To compare these tumors with cohorts treated with neoadjuvant chemotherapy (NAC) or no systemic therapy prior to RC.
Main Methods:
- Transcriptome-wide expression profiling of 26 post-pembrolizumab RC samples (with 22 matched pre-therapy samples).
- Unsupervised consensus clustering (CC) to compare post-pembrolizumab tumors with RC and post-NAC tumor cohorts.
- Analysis of molecular subtypes, biological characteristics, and clinical outcomes.
Main Results:
- Significant molecular subtype differences were observed between pre- and post-pembrolizumab samples (only 36% concordance).
- Three distinct post-pembrolizumab clusters were identified: basal, luminal, and scar-like.
- A scar-like subtype (50% of post-pembrolizumab cases) showed wound healing gene expression and favorable prognosis post-systemic therapy, but not in the RC-only setting.
Conclusions:
- This study defines molecular subtypes in pembrolizumab-resistant MIBC, offering a framework for post-treatment classification.
- Results support the hypothesis that luminal-type tumors may be inherently resistant to immunotherapy or that treatment induces a luminal phenotype.
