Epigenomic signatures as circulating and predictive biomarkers in sarcomatoid renal cell carcinoma

El Zarif, T.; Semaan, K.; Eid, M.; Sep, J.-H.; Semaan, S. G.; Davidsohn, M. P.; Fortunato, B.; Canniff, J.; Nassar, A. H.; Abou Alaiwi, S.; Bakouny, Z.; Lakshmi, G.; Savigano, H.; Lyons, K.; Matar, S.; Ali, A.; Saad, E.; Saliby, R. M.; Cordeiro, P.; Zhang, Z.; El Ahmar, N.; Nabil Laimon, Y.; Labaki, C.; Shah, V.; Freeman, D.; O'Toole, J.; Lee, G.-S. M.; Hwang, J.; Pomerantz, M.; Signoretti, S.; Xie, W.; Berchuck, J. E.; Viswanathan, S. R.; Van Allen, E. M.; Braun, D. A.; Choueiri, T. K.; Freedman, M. L.; Baca, S. C.

doi:10.1101/2023.11.27.568827

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bioRxiv · 10.1101/2023.11.27.568827

Epigenomic signatures as circulating and predictive biomarkers in sarcomatoid renal cell carcinoma

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Abstract

Renal cell carcinoma with sarcomatoid differentiation (sRCC) is associated with poor survival and heightened response to immune checkpoint inhibitors (ICIs). Two major barriers to improving outcomes for sRCC are (1) a limited understanding of its gene regulatory programs and (2) difficulty identifying sarcomatoid differentiation on tumor biopsies due to spatial heterogeneity. To address these challenges, we characterized the epigenomic landscape of sRCC by profiling 107 epigenomic libraries in tissue and plasma samples from 50 patients with RCC and healthy volunteers. We identified highly recurrent epigenomic reprogramming, as assessed by histone modifications and DNA methylation, that distinguishes sRCC from non-sarcomatoid RCC. Computational analysis of RCC epigenomic profiles and CRISPRa experiments implicated the transcription factor FOSL1 in activating sRCC-associated gene regulatory programs. Analysis of two randomized clinical trials identified FOSL1 expression as a predictive biomarker of response to ICIs in RCC. Finally, we demonstrate that epigenomic signatures of sRCC are detectable in patient plasma, establishing an approach for blood-based diagnosis of this clinically important phenotype. These findings provide a framework for the discovery and non-invasive detection of epigenomic correlates of tumor histology via liquid biopsy.

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El Zarif, T., Semaan, K., Eid, M., Sep, J.-H., Semaan, S. G., Davidsohn, M. P., Fortunato, B., Canniff, J., Nassar, A. H., Abou Alaiwi, S., Bakouny, Z., Lakshmi, G., Savigano, H., Lyons, K., Matar, S., Ali, A., Saad, E., Saliby, R. M., Cordeiro, P., Zhang, Z., El Ahmar, N., Nabil Laimon, Y., Labaki, C., Shah, V., Freeman, D., O'Toole, J., Lee, G.-S. M., Hwang, J., Pomerantz, M., Signoretti, S., Xie, W., Berchuck, J. E., Viswanathan, S. R., Van Allen, E. M., Braun, D. A., Choueiri, T. K., Freedman, M. L., Baca, S. C.. 2023-11-28. Epigenomic signatures as circulating and predictive biomarkers in sarcomatoid renal cell carcinoma. https://doi.org/10.1101/2023.11.27.568827

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