Individualized transcriptomic changes in malignant and benign prostate identify markers of disease recurrence

In this study, the transcriptome profiles from malignant and adjacent benign prostate tissue samples were compared in 41 patients who underwent radical prostatectomy. Hierarchical clustering clearly separated benign and malignant tissues and included expected transcriptional changes associated with carcinogenesis.

Using reproducibility-optimized statistical testing (ROTS), we identified 45 genes whose expression differed between paired malignant and benign prostate tissue from the same patient (FDR < 0.05) in patients with and without biochemical recurrence (BCR). Within this individualized approach, two interconnected regulatory pathways underlying the pathogenesis were identified: one centered on FOS, NR4A, and EGR family transcription factors, with strong involvement of TNFα signaling, and another, a less dense network, centered on IL6.