Received on August 16, 2006
Accepted on January 16, 2007

Molecular Diagnostics and Genetics

Preanalytical mRNA Stabilization of Whole Bone Marrow Samples

¹ Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
² Qiagen GmbH, Hilden, Germany

^* To whom correspondence should be addressed. E-mail: claudia{at}langebrake.de.

Background: Gene expression profiling is a useful tool for diagnosis and basic research of cancer. A major limitation is that, even during short-term storage of native specimens of peripheral blood or bone marrow (BM) and/or RNA isolation, significant changes of gene expression pattern can occur because of gene induction, repression, and RNA degradation.

Methods: We investigated the effectiveness of a newly developed RNA stabilization and preparation system for BM specimens (PAXgene^TM Bone Marrow RNA System) over time. We analyzed 256 RNA samples, processed from 64 BM specimens.

Results: Although the overall RNA yield (normalized to 1 x 10⁷ leukocytes) was not different, the RNA preparation using unstabilized reference samples had an 3 times higher failure rate. With the PAXgene system, we observed significantly higher RNA integrity compared with the reference RNA preparation system (P <0.01). In the stabilized samples, we found very high pairwise correlation in gene expression (C_T 0.16-0.53) for the analyzed genes (GATA1, RUNX1, NCAM1, and SPI1) after 48-h storage compared with immediate preparation of RNA (2 h after BM collection). However, we found major differences in half of the analyzed genes using the reference RNA isolation procedure (C_T 1.07 and 1.32).

Conclusions: The PAXgene system is able to stabilize RNA from clinical BM samples and is suitable to isolate high-quality and -quantity RNA.