IBCN 2023: Proteogenomic Characterization of Chemotherapy Response in Muscle Invasive Bladder Cancer

(UroToday.com) To further understand the underlying mechanisms of neoadjuvant chemotherapy resistance and identify alternative treatments for neoadjuvant chemotherapy-resistant MIBCs, they performed comprehensive proteogenomic profiling of pre- and post-neoadjuvant chemotherapy tumors with carefully curated response information.

They processed OCT-embedded and flash frozen tissue samples from 143 patients and samples containing >45% tumor, <10% muscle, and >2,000 protein identifications in a single-shot QC assay were selected for deep-scale proteomic and phosphoproteomic profiling. A final cohort of 58 tumors (44 pre-treatment and 14 post-treatment) were multiplexed using tandem mass tags (TMT-11), fractionated by basic reverse phase chromatography, and analyzed by liquid chromatography and tandem mass spectrometry (LC-MS/MS). Complimentary WES, RNASeq, and SureQuant targeted proteomics were performed with from the same samples. Fragpipe, Skyline and SEPepQuant were used to identify and quantify peptides, protein isoforms and gene abundance.

Over 12,000 proteins and 28,729 phospho-sites were identified, with 8,353 proteins in all samples, including 425 kinases and 77 targets of FDA approved therapies. Despite a median correlation of 0.48 between RNA and Protein abundances, subtyping assignments were mostly in agreement (81%) with an over-representation of neuronal subtypes. Multi-omics subtyping with NMF resulted in 4 clusters which are largely representative of previous subtypes. Resistant tumors had upregulated KRT20 protein while immune related proteins were elevated in sensitive tumors. GSK3B-S9 phosphorylation, which inhibits GSK3B activity, was significantly elevated in the sensitive group while the GSK3B protein abundance showed no difference. SEPepQuant identified specific isoforms which were differential between sensitive and resistant tumors while the gene level quantification was not associated with resistance, suggesting alternative splicing as a potential resistance mechanism. Integrating human tumor data with genetic screen data in bladder cancer cell lines identified druggable protein targets significantly associated with subtypes and resistance.

In summary, this analysis identified multiple avenues for therapeutic engagement for which additional studies are required.

Presented by: Mathew V Holt, PhD, Baylor College of Medicine

Written by: Stephen B. Williams, MD, MBA, MS @SWilliams_MD on Twitter during the International Bladder Cancer Network (IBCN) Annual Meeting, September 29-30, 2023, Montreal, Canada