Epigenetic field defect discriminates normal tissues from healthy and tumor-bearing kidneys

Abstract Background: The detection of alterations in DNA methylation (DNAm) in normal human tissues may provide molecular insights for cancer development, the estimation of personal cancer risk, and a basis for early diagnosis of malignancies to reduce cancer lethality. Thus, whether DNAm allows discrimination between healthy normal and normal tumor-adjacent renal tissues is an important question. Methods: DNAm of loci in the LINE1 repetitive sequence and ANKRD34B, NHLH2, TBR1, and ZIC1 was measured in a total of 493 tissue samples representing 342 normal autopsy and 151 histopathological normal tumor-adjacent renal tissues by pyro-sequencing a total of 22 CpG sites. Results: Unsupervised k-means clustering demonstrated a significant imbalance of tissue samples in three stable tissue clusters. Random forest classification demonstrated discrimination of normal and normal tumor-adjacent renal tissues with a median area under the ROC curve of 0.81 (p=2.7x10-9, diagnostic odds ratio 10.4). Variable importance analysis revealed CpG sites in LINE1 and ANKRD34B as the most important model contributors. Conclusions: DNAm alterations in normal tissues allow detection of renal cancer with high diagnostic efficiency, defining a DNAm field effect in the kidney. The methylation signature may serve as a basis for an epigenetic DNAm clock permitting estimation of individual renal cancer risk. ### Competing Interest Statement The authors have declared no competing interest.