Molecular Profiling Of Post-Pembrolizumab Muscle-Invasive Bladder Cancer (Mibc) Reveals Unique Features That May Inspire New Seguential Therapies In Pathologically-Nonresponders

Introduction In the PURE-01 study, a proportion of patients (pts) with muscle-invasive bladder cancer (MIBC; T2-4N0M0) had residual invasive disease (ypT2-4) at radical cystectomy (RC) after neoadjuvant pembrolizumab (pembro). The pembro-induced alterations in immunotherapy-resistant tumors remain largely unstudied. We aimed to investigate the biological characteristics of pembro-resistant tumors in comparison to neoadjuvant chemotherapy (NAC)-resistant tumors. Methods Gene expression profiling was performed on 26 RC samples from pts with ypT2-4 disease post-pembro, of which 22 had matched pre-pembro transurethral resection of the bladder tumor (TURBT) samples. Matched cases were analyzed by differential gene expression, hallmark signatures, and molecular subtyping (Decipher Bladder, TCGA, Consensus and Lund classifiers). Unsupervised consensus clustering (CC) was used to compare the 26 post-pembro samples with 133 post-NAC samples and to 21 samples collected from the former tumor bed of NAC-treated patients (scar tissue), all derived from RC specimens. Results Molecular subtyping of the pre- and post-pembro samples revealed significant ‘subtype switching’ with only 41% of samples having concordant subtypes using the Decipher Bladder classifier. The post-pembro samples did not cluster with scar tissues on clustering but were highly associated with immune-infiltrated cases from the post-NAC cohort. Two major groups of post-pembro tumors were identified, the first defined by markedly higher immune, stromal, angiogenesis and epithelial-to-mesenchymal signature scores and the second by higher tumor purity, KRAS and reactive oxygen species signature scores. Checkpoint inhibitor genes (CD274, PDCD1LG2) were consistently expressed in both groups. Conclusions This study expands our knowledge of pembro-resistant tumors finding the molecular characteristics of these tumors is strikingly different from NAC-resistant tumors. Two distinct clusters of tumors were identified post-pembro, neither of which were characterized as having a scar-like character. A larger cohort will be required to further understand the clinical implications of these findings.