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

Area of Science:

• Oncology
• Molecular Biology
• Biobanking

Background:

• High-quality biospecimens are crucial for transcriptomic analyses in renal cell carcinoma (RCC).
• Real-world factors influencing RNA integrity in routine surgical settings for RCC are not well-documented.
• This study evaluates RNA quantity and quality from cryopreserved RCC tissues and identifies degradation factors.

Purpose of the Study:

• To assess RNA quantity and quality in cryopreserved renal cell carcinoma (RCC) tissues.
• To identify factors influencing RNA degradation in routine surgical settings.
• To inform biobanking strategies for transcriptomic research in RCC.

Main Methods:

• Retrospective analysis of 160 clear cell RCC patients from the UroCCR network (2005-2012).
• Prospective collection and snap-freezing of tumor and matched normal kidney tissues.
• Automated RNA extraction, NanoDrop spectrophotometry for concentration, and RNA Quality Score (RQS) for quality assessment.
• Multivariate linear regression models with random intercepts were employed.

Main Results:

• Successful RNA extraction from 302 of 310 samples (97.4%).
• 93% of samples exceeded 25 ng/µL RNA concentration; 78.4% met quantitative and qualitative criteria (RQS ≥ 6).
• Tumor tissue exhibited significantly higher RNA quality (mean RQS 8.33) than matched normal tissue (mean RQS 6.66).
• Preoperative embolization was independently associated with lower RNA quality (p < 0.001).
• Freezing delay (mean 30 min) and storage duration did not correlate with RNA degradation.

Conclusions:

• High-quality RNA can be reliably extracted from fresh-frozen RCC tissues under standard clinical conditions.
• Tumor biology is a more significant determinant of RNA integrity than short procedural delays.
• Findings support the development of biologically informed biobanking strategies for RCC research.