What Urine Measures Is Not What Tissue Encodes: Compartment-Specific miRNA Coordination in Prostate Cancer

Background

Prostate cancer (PCa) diagnosis remains challenged by the limited specificity of prostate-specific antigen (PSA) testing, which cannot reliably distinguish malignancy from benign prostatic hyperplasia (BPH). MicroRNAs (miRNAs) are emerging candidates for liquid biopsy-based diagnostics, but most studies assess expression in isolation within a single compartment (biological source - Tissue, blood, serum, urine etc.), overlooking both compartment-specific behavior and the coordinated relationships among miRNAs.

Methods

We profiled four candidate miRNAs — miR-19b-3p, miR-21-5p, miR-101-3p and miR-375-3p, across four biological compartments (prostate tumor tissue, urine, serum, and blood) in 179 patients undergoing prostate biopsy for clinical suspicion of PCa (104 PCa, 75 BPH) using qRT-PCR. Urinary exosomal RNA was isolated with a commercial exosome isolation kit so from here onwards this compartment will be referred to as urine. Differential expression was quantified using Cohen’s d ; inter-miRNA coordination was assessed via Spearman correlation and differential correlation (Δ r ) analysis; and a compartment-level network rewiring score was derived as the sum of |Δ r | across miRNA pairs. Cross-compartment structural alignment was evaluated by comparing correlation patterns at the population level. Diagnostic models combining PSA, age, and urinary exosomal-miRNA features were evaluated using Logistic Regression, Elastic Net Logistic Regression and Naive Bayes classifiers under leave-one-out cross-validation (LOOCV).

Results

Effect sizes were largest and most consistent in urine, with miR-101-3p showing the strongest separation between PCa and BPH ( d = −1.01), followed by miR-21-5p ( d ≈ −0.72) and miR-19b-3p ( d ≈ −0.64). Two markers (miR-19b-3p, miR-375-3p) showed directional reversals across compartments, indicating that disease-associated signals are compartment-specific rather than uniformly conserved. In tumor tissue, PCa was associated with substantial reorganization of inter-miRNA coordination (network rewiring score = 2.46), including the emergence of a strong miR-21-5p–miR-375-3p co-regulatory axis (Δ r = +0.87) and decoupling of the miR-21-5p–miR-19b-3p relationship (Δ r = −0.64). Urine showed a structurally distinct coordination pattern (rewiring score = 1.77), dominated by a miR-101-3p–miR-19b-3p axis (Δ r = +0.56) absent from tissue; cross-compartment comparison showed concordance in only 1 of 6 miRNA pairs, indicating that urine’s architecture is largely independent of tissue’s.

For diagnostic translation, the conventional PSA cutoff (4 ng/mL) achieved 100% sensitivity but only 23.5% specificity. In urine, miR-101-3p performs better than other miRNAs, with AUC of 0.71 (95% CI: 0.56–0.85). Adding PSA and age to the urinary miR-101-3p further improved discrimination to an AUC of 0.91 (95% CI: 0.82–0.99), with 70.5% specificity at 92.8% sensitivity; this pattern was consistent across Elastic Net and Logistic Regression classifiers. Expanding the model to include all urinary miRNAs, age, and pair-derived coordination features did not improve on this result (AUC = 0.88), indicating that population-level coordination changes did not translate into additional individual-level diagnostic value in this cohort.

Conclusions

miRNA signals in extracellular compartments do not represent direct surrogates of tumor-level molecular architecture; each compartment harbors a distinct, transformed coordination structure reflecting its biological context. While these coordination-level changes are mechanistically informative, the most direct translational gain in this study came from a parsimonious model combining PSA, age with a single urinary marker, miR-101-3p, which improved AUC from 0.71 to 0.91, with specificity 70.5% at 90% sensitivity criteria. This combination represents a promising, interpretable candidate for reducing unnecessary prostate biopsies, pending validation in larger, independent cohorts.