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DNA methylation status defines clinicopathological parameters including survival for patients with clear cell renal cell carcinoma (ccRCC)

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Tumor Biology

Abstract

Epigenetic alterations in the methylome have been associated with tumor development and progression in renal cell carcinoma (RCC). In this study, 45 tumor samples, 12 tumor-free kidney cortex tissues, and 24 peripheral blood samples from patients with clear cell RCC (ccRCC) were analyzed by genome-wide promoter-directed methylation arrays and related to clinicopathological parameters. Unsupervised hierarchical clustering separated the tumors into two distinct methylation groups (clusters A and B), where cluster B had higher average methylation and increased number of hypermethylated CpG sites (CpGs). Furthermore, tumors in cluster B had, compared with cluster A, a larger tumor diameter (p = 0.033), a higher morphologic grade (p < 0.001), a higher tumor-node-metastasis (TNM) stage (p < 0.001), and a worse prognosis (p = 0.005). Higher TNM stage was correlated to an increase in average methylation level (p = 0.003) and number of hypermethylated CpGs (p = 0.003), whereas a number of hypomethylated CpGs were mainly unchanged. However, the predicted age of the tumors based on methylation profile did not correlate with TNM stage, morphological grade, or methylation cluster. Differently methylated (DM) genes (n = 840) in ccRCC samples compared with tumor-free kidney cortex samples were predominantly hypermethylated and a high proportion were identified as polycomb target genes. The DM genes were overrepresented by transcription factors, ligands, and receptors, indicating functional alterations of significance for ccRCC progression. To conclude, increased number of hypermethylated genes was associated with increased TNM stage of the tumors. DNA methylation classification of ccRCC tumor samples at diagnosis can serve as a clinically applicable prognostic marker in ccRCC.

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Acknowledgments

This study was supported by grants from the Swedish Cancer Society (BL, GR), the Cancer Research Foundation in Umeå (BL, GR, SD), the Kempe Foundations (GR, SD), and the Västerbotten County Council (BL, GR).

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Authors and Affiliations

  1. Department of Medical Biosciences, Pathology, Umeå University, SE-90185, Umeå, Sweden

    Emma Andersson Evelönn, Sofie Degerman, Linda Köhn, Mattias Landfors & Göran Roos

  2. Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden

    Mattias Landfors

  3. Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden

    Börje Ljungberg

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  1. Emma Andersson Evelönn
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Correspondence to Göran Roos.

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Ethical approval

The study was approved by the regional ethical review board in Umeå (Dnr 2011-156-31M 110523).

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Informed consent was obtained from all participants included in the study.

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Supplementary Figure 1

Preprocessing of methylation data from Illumina Infinium HumanMeth27K arrays. CpG sites were excluded if ≤ 3 reported beads/array in any sample, if CpG sites had a detection p value equal to or greater than 0.05 and if CpG sites were located on sex chromosomes X and Y. (GIF 15 kb)

High resolution image (TIF 102 kb)

Supplementary Figure 2

Distribution of DM-CpGs, genomic aberrations and mutations in the VHL gene. White blocks represent unmethylated, black methylated, light gray wild type and dark gray deleted/mutated. (GIF 53 kb)

High resolution image (TIF 310 kb)

Supplementary Table 1

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Evelönn, E.A., Degerman, S., Köhn, L. et al. DNA methylation status defines clinicopathological parameters including survival for patients with clear cell renal cell carcinoma (ccRCC). Tumor Biol. 37, 10219–10228 (2016). https://doi.org/10.1007/s13277-016-4893-5

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  • DOI: https://doi.org/10.1007/s13277-016-4893-5

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