Defining the microenvironment landscape of bladder cancer using highly multiplexed spatial genomic and proteomic analysis

Reeves, J.; Zhang, Z.; Norgaard, Z. K.; Zhou, D. M.; Gong, J.; Liang, Y.; Das, S.; Warren, S. E.; Korpal, M.; Hoang, M. L.; Beechem, J. M.; Kumar, P.; Rimkunas, V.

doi:10.1101/675926

bioRxiv · 10.1101/675926

Defining the microenvironment landscape of bladder cancer using highly multiplexed spatial genomic and proteomic analysis

Reeves, J.·Zhang, Z.·Norgaard, Z. K.·Zhou, D. M.·Gong, J.·Liang, Y.·Das, S.·Warren, S. E.·Korpal, M.·Hoang, M. L.·Beechem, J. M.·Kumar, P.·Rimkunas, V.

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Abstract

Muscle-invasive bladder cancer (MIBC) is an aggressive disease with limited therapeutic options. PD-1 pathway targeting immunotherapies have been approved to treat advanced bladder cancer, but most patients exhibit primary resistance, suggesting that immune evasion mechanisms exist. The PPAR{gamma} pathway has been identified as a potential therapeutic target in MIBC that is associated with reduced CD8+ T-cell infiltration and increased resistance to immunotherapies. We comprehensively profiled the tumor microenvironment (TME) in formalin-fixed, paraffin-embedded (FFPE) tissues from a cohort of PPAR{gamma}high (n=13) and PPRAR{gamma}low (n=12) MIBC, integrating bulk gene expression, targeted mutation sequencing, immunohistochemistry and multiplex spatial profiling of RNA and protein expression on the GeoMx Digital Spatial Profiling (DSP) platform. Molecular subtyping was consistent between traditional methods and GeoMx profiling, and, in this cohort, we observed little evidence of spatial heterogeneity in tumor subtyping. The previously characterized T-cell exclusion phenotype of PPAR{gamma}high MIBC was recapitulated on the GeoMx platform and was further extended to show that this is a general phenomenon across immune cell types, supporting potential combination of PPAR{gamma} inhibition with ICIs. Furthermore, we found that while immune cells were excluded from PPAR{gamma}high tumors, the stromal compartment from these tumors was not significantly different than those PPAR{gamma}low tumors. By preserving spatial relationships during the GeoMx analysis, we also identify a novel association between lower immune cell expression in the tumors and higher expression of {beta}-catenin in the stroma, and differential expression of other WNT pathway members associated with PPAR{gamma} activity.\n\nOne Sentence SummaryA new method for capturing tumor-immune signaling in FFPE tissues explores how the PPARG signaling axis is associated with immune cell exclusion in bladder cancer.

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Reeves, J., Zhang, Z., Norgaard, Z. K., Zhou, D. M., Gong, J., Liang, Y., Das, S., Warren, S. E., Korpal, M., Hoang, M. L., Beechem, J. M., Kumar, P., Rimkunas, V.. 2019-06-21. Defining the microenvironment landscape of bladder cancer using highly multiplexed spatial genomic and proteomic analysis. https://doi.org/10.1101/675926

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