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Improving Ribosomal RNA Integrity in Surgically Resected Human Brain Tumor Biopsies
Xavier Castells Domingo1,2, Laura Ferrer-Font2,3,4, Myriam Davila3
11 Servei de Genòmica i Bioinformàtica, Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Spain .
Background:
Biopsies extracted from brain cancer patients often display degraded ribosomal RNA, which makes them unusable in transcriptomic experiments. This has not been properly documented in previous works aimed at refining the molecular classification of brain cancer.
Objective:
To determine RNA integrity in a large cohort of human brain cancer biopsies and to evaluate different factors that may influence RNA integrity in both a murine model of glioblastoma and in additional subsets of patient biopsies.
Methods:
Total RNA was isolated from 255 biopsies of various human brain tumors (HBTs) and processed on a Bioanalyzer. Correct RNA integrity was considered for samples showing either the ribosomal 28S/18S peak ratio ≥ 1.2 or RNA integrity number ≥ 6. The time-dependent effect of ex vivo ischemia was evaluated in a murine model, whose results were tested in a new collection of 27 human biopsies. Multiple biopsy sampling was considered in a further set comprising 32 biopsies.
Results:
The 255 human biopsies revealed a substantial percentage of samples displaying degraded RNA (27.5%). The murine model confirmed the known relevance of ex vivo ischemia time in increased RNA degradation. Human biopsies extracted immediately after cauterization showed a trend toward less RNA degradation. Combining snap freezing and multiple sampling of biopsies, the percentage of patients with degraded RNA was reduced by twofold (15.6%).
Conclusions:
We provide a first concise study of factors influencing RNA degradation in HBT biopsies. Immediate biopsy removal after cauterization of the tumor area, snap freezing, and multiple sampling improve RNA quality.
Insights
Degraded ribosomal RNA (rRNA) in brain cancer biopsies hinders transcriptomic analysis. Immediate removal post-cauterization, snap freezing, and multiple sampling significantly improve RNA integrity in human brain tumor biopsies.
Area of Science:
- Neuro-oncology
- Molecular Biology
- Biotechnology
Background:
- Degraded ribosomal RNA (rRNA) is a common issue in human brain tumor (HBT) biopsies, limiting their utility in transcriptomic studies.
- Previous research has not adequately documented factors affecting RNA integrity in these samples, impacting molecular classification efforts.
Purpose of the Study:
- To assess RNA integrity across a large cohort of HBT biopsies.
- To identify key factors influencing RNA degradation in brain tumors, using both murine models and human samples.
Main Methods:
- RNA integrity was analyzed in 255 HBT biopsies using a Bioanalyzer, with integrity defined by 28S/18S rRNA peak ratio (≥ 1.2) or RNA integrity number (≥ 6).
- Ex vivo ischemia effects were studied in a murine glioblastoma model and validated in human biopsies.
- The impact of multiple biopsy sampling was evaluated in a separate cohort.
Main Results:
- A significant proportion (27.5%) of the 255 HBT biopsies exhibited degraded RNA.
- Murine models confirmed that ex vivo ischemia time directly correlates with increased RNA degradation.
- Immediate biopsy retrieval post-cauterization showed a trend towards reduced degradation.
- Implementing snap freezing and multiple sampling reduced the incidence of degraded RNA by 50% (to 15.6%).
Conclusions:
- This study provides initial insights into critical factors affecting RNA degradation in HBT biopsies.
- Optimizing biopsy handling—including immediate post-cauterization removal, snap freezing, and multiple sampling—enhances RNA quality for downstream analyses.
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