Genomic analysis from BLASST-1 (Bladder Cancer Signal Seeking Trial) of nivolumab, gemcitabine, and cisplatin in patients with MIBC undergoing cystectomy.
Authors: Gupta Shilpa , Makarov Vladimir , Sonpavde Guru P. , Gibb Ewan , Gupta Sumati , Maughan Benjamin L. , Agarwal Neeraj , Mossanen Matthew , Thyagarajan Bharat , Diaz-Montero C. Marcela , Bangalore Prerana Parthasarathy , Konety Badrinath R. 
Published: March 2023

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Background: BLASST-1 is multi-center phase II trial evaluating neoadjuvant nivolumab (N) with gemcitabine-cisplatin (GC) for patients (pts) with MIBC undergoing radical cystectomy (RC) (NCT03294304). 41 pts with MIBC (cT2-T4a, N≤1, M0) were enrolled between Feb 2018 and June 2019; (cT2N0 90%, cT3N0 7%, cT4N1 3%). Pts received C (70mg/m2) IV on D1, G (1000mg/m2) on D1, D8 and N (360 mg) IV on D8 every 21 days for 4 cycles followed by RC within 8 wks. Primary endpoint was pathologic down staging (PaR; ≤pT1N0). Safety, Relapse-free survival (RFS), Progression-free survival (PFS) and biomarker analyses were secondary endpoints. PaR rate was 65.8%, pCR (≤pT is N0) rate was 49% and there were no safety concerns or delays to RC. At a median follow-up of 15.8 mos, 12-month RFS rate was 85.4% and PFS including death from any cause was 83%. We now report correlation of PaR with tumor mutation patterns of responders (R) and non-responders (NR) using Whole Genome Sequencing (WGS). Methods: DNA was extracted from pre-treatment tumor samples and sequenced to an average depth of 150X and DNA extracted from matched normal tissue (peripheral blood) to a mean depth of 50X. We analyzed 32 Tumor/Normal pairs and 6 Tumor only Whole Genome Samples; 26 pts were classified as (R) and 12 as (NR). Raw sequencing data samples were aligned to hg38 genome build using Burrows-Wheeler Aligner (BWA) followed by duplicate-read removal and base-quality score recalibration using the Genome Analysis Toolkit (GATK). Somatic SNV and INDELS were called by combination of 5 callers (Mutect2, Strelka, VarScan, Platypus and SomaticSniper) for Tumor/Normal pairs and Mutect2 for Tumor only samples following the guidelines of GDC DNA-Seq analysis pipeline. Set of genes known to be significantly mutated in MIBC and shown to impact response/resistance to chemotherapy/immunotherapy respectively were selected. Samples were grouped by response status. Results: Median tumor mutational burden (TMB) for the dataset closely matches with TCGA results. Genes ERCC2, ARID1A, DSP, HMCN1, ERBB2, ERBB3, STAG2, BRCA2 present in (R) only, whereas VHL, ERCC4, PALB2, CDKN2A and CSMD3 present in (NR) only. We also grouped genes based on their biological processes by known Oncogenic Signaling Pathways and the 3 most common pathways are Genome Integrity, RTK Signaling and Transcription Factor with the latter two primarily enriched in (R). We identified a SNP rs2853669 in 5 (NR) and 14 (R). Conclusions: The genomic analysis suggests ERCC2, ARID1A, DSP, HMCN1, ERBB2, ERBB3,STAG2, BRCA2 correlated with PaR and VHL, ERCC4, PALB2, CDKN2A and CSMD3 correlated with lack of response. In addition, RTK Signaling and Transcription Factor were primarily enriched in (R). This genomic correlation of response/resistance to neoadjuvant chemo-immunotherapy in MIBC can help guide future biomarker-driven studies. Clinical trial information: NCT03294304 .