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DNA methylation is a key determinant of response to targeted and immune checkpoint therapies in metastatic renal cell carcinoma

Jeanneret, F.; Schoch, S.; Ballester, P.; Symeonides, S. N.; Laird, A.; Axelson, H.; Pflieger, D.; Battail, C.

2024-11-06 bioinformatics
10.1101/2024.11.05.622095 bioRxiv
Show abstract

The response to targeted therapies and immune checkpoint inhibitors for patients suffering from metastatic clear cell renal cell carcinoma (ccRCC) is heterogeneous and currently not predictable in clinic. In this work, a comprehensive integrated study of 700 ccRCCs profiled by DNA methylation and RNA sequencing showed that the hyper-methylated tumors exhibited a worse prognosis, a higher fraction of cycling tumor cells and a lower activity of homeobox transcription factors. To translate the use of DNA methylation information into a clinical setting, we developed a simple model accurately predicting the ccRCC methylation subtypes (AUC-ROCs of 0.91) from two gene expression ratios (IGF2BP3/PCCA, TNNT1/TMEM88). In addition, these methylation subtypes were significantly associated with the therapeutic outcome of patients to anti-PD-1, mTOR inhibitor or tyrosine kinase inhibitor therapies. Overall, our framework for predicting the ccRCC DNA methylation subtypes from targeted gene expression data is easy to translate in clinic and contributes to better personalization of ccRCC therapies.

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