Risk factors for RNA integrity in fresh-frozen renal cancer samples from routine practice (UroCCR 9)

High-quality biospecimens are essential for transcriptomic analyses in renal cell carcinoma (RCC), yet real-world determinants of RNA integrity in routine surgical settings remain insufficiently documented. This study aimed to evaluate RNA quantity and quality from cryopreserved RCC tissues and identify factors associated with RNA degradation.

We conducted a retrospective analysis of 160 patients who underwent surgery for clear cell RCC and included in the UroCCR network (2005-2012). Tumor and matched normal kidney tissues were prospectively collected during partial or radical nephrectomy and snap-frozen. RNA was extracted using an automated protocol. RNA concentration was measured by NanoDrop spectrophotometry, and RNA quality was assessed using the RNA Quality Score (RQS). Multivariate linear regression models with random intercepts were used to identify factors associated with RNA degradation.

RNA extraction was successful in 302 of 310 samples. RNA concentration exceeded 25ng/μL in 93% of samples, and 78.4% met both quantitative and qualitative criteria (RQS≥6). Mean RNA concentration was 128.8±104.4ng/μL, and mean RQS was 7.52±1.40. Tumor tissue showed higher RNA quality than matched healthy tissue (mean RQS: 8.33±1.02 vs. 6.66±1.30; P<0.001). Preoperative embolization was independently associated with lower RNA quality (P<0.001). Freezing delay (mean 30±25min) and duration of storage were not associated with RNA degradation.

High-quality RNA can be extracted from fresh-frozen RCC tissues under routine clinical conditions. RNA integrity is mainly influenced by tumour biology rather than procedural delays, supporting biologically informed biobanking strategies.