A comprehensive molecular analysis of muscle-invasive bladder cancer (MIBC) tumors has uncovered specific protein isoforms and signaling pathways associated with resistance to standard cisplatin-based chemotherapy, offering new potential strategies to guide treatment and improve patient outcomes. The study, published in Cell Reports Medicine by researchers at Baylor College of Medicine, identified cell signaling pathways that drive chemotherapy resistance, suggesting potential new methods for treating MIBC.
“One of our goals was to identify molecular markers in patient tumors that would help us predict which patients were most likely to benefit from chemotherapy and which ones might not,” said first co-author, Matthew V. Holt, PhD, a laboratory director at Baylor College of Medicine.
Cisplatin-based neoadjuvant chemotherapy (NAC) is a standard of care for non-metastatic MIBC, but only about one-quarter of patients derive any benefit from this treatment. Recent research has sought to find ways to predict which people will respond and which people won’t. This research has largely focused on gene expression or mutations in DNA damage repair genes but has not been sufficient to explain the variability in response. The Baylor team took a broader, multiomics approach that integrated genomics, transcriptomics, proteomics, and phosphoproteomics.
For this research, the team analyzed 60 tumors—46 pre-treatment and 14 post-treatment—to generate detailed molecular profiles for each. “By computationally analyzing the vast information generated by the multiomics approach, we produced a molecular profile for each tumor sample and hoped to uncover patterns linked to resistance to chemotherapy,” said co-first author Yongchao Dou, PhD, an assistant professor at Baylor.
The study revealed that tumors resistant to chemotherapy were enriched for activity in the Wnt signaling and JAK/STAT pathways, particularly involving the kinase GSK3B and the transcription factor protein STAT3. “We also identified molecular pathways linked to resistance,” Dou said. “Wnt signaling, involving a protein called GSK3B, was more active in resistant tumors. The JAK/STAT pathway, especially the protein STAT3, was also more active in resistant cases. These data reveal these pathways as potential therapeutic targets to overcome chemoresistance.”
An important finding was that protein isoforms, rather than gene or RNA expression alone, were strong indicators of treatment response. “We investigated protein isoforms, which refers to slightly different forms of the same protein, which can behave differently. We found that certain isoforms—especially of proteins like ATAD1 and the RAF family—were more common in tumors that responded well to chemotherapy. These isoforms weren’t detectable by looking at genes or RNA alone,” Holt noted.
The researchers used a tool called SEPepQuant, a computational method that identifies protein isoforms, to analyze domain-level features of proteins. They found that peptides from conserved regions of RAF family proteins (ARAF, BRAF, RAF1) correlated strongly with chemotherapy sensitivity. “These peptides are common to all known ARAF, BRAF, and RAF1 isoforms,” the researchers wrote. “It may indicate that the abundance of core enzymatic domain of the RAF family is more important than abundances of specific RAF isoforms in the response to chemotherapy.”
The team also observed post-treatment changes in tumor subtypes and metabolism. Some tumors showed subtype switching after chemotherapy, which was previously suggested by RNA expression profiling. Chemotherapy also induced expression of MYC and lysosomal ATP pumps, possibly contributing to treatment survival mechanisms.
To evaluate potential combination therapies to address MIBC treatment resistance, the researchers examined targets of antibody-drug conjugates (ADCs) such as PD-L1, TROP2, and NECTIN-4. These proteins were differentially expressed across tumor subtypes but did not correlate with chemotherapy sensitivity. The data suggest, however, that a combination of chemotherapy plus ADCs or an immunotherapy could be more effective if tailored to tumor subtype.
This new proteogenomic for identifying and understanding molecular features that influence chemotherapy response could be leveraged for developing novel therapeutic approaches as well as complementary diagnostics.
“This study identified specific proteins and pathways linked to treatment resistance, as well as potential new ways to treat resistant tumors,” said senior author Seth P. Lerner, MD, professor of urology at Baylor. “This is important because it provides insights that can help expand the population that can be treated effectively and improve overall patient outcomes.”
While the findings are preliminary and included a small sample size of pre-treatment tumors, the team will now look to develop patient-derived xenograft models and organoids from incoming patients to validate the molecular mechanisms identified and test new therapeutic combinations.