Abstract: FR-PO972

Integrity and Expression of Low-Input, Degraded Renal mRNA for Precision Medicine Applications

Session Information

Category: Bioengineering and Informatics

  • 101 Bioengineering and Informatics

Authors

  • Eadon, Michael T., Indiana University Division of Nephrology, Indianapolis, Indiana, United States
  • Dagher, Pierre C., Indiana University, Indianapolis, Indiana, United States
  • El-Achkar, Tarek M., Indiana University, Indianapolis, Indiana, United States
  • Cheng, Yinghua, Indiana University School of Medicine, Greenwood, Indiana, United States
  • Dunn, Ken, Indiana University, Indianapolis, Indiana, United States
  • Parikh, Samir V., Ohio State University Medical Center, Columbus, Ohio, United States
  • Rovin, Brad H., Ohio State University Wexner Medical Center, Columbus, Ohio, United States
  • Winfree, Seth, Indiana University School of Medicine, Greenwood, Indiana, United States
  • Kelly, Katherine J., Indiana University, Indianapolis, Indiana, United States
  • Sutton, Timothy A., Indiana University School of Medicine, Greenwood, Indiana, United States
Background

Personalized medicine initiatives may entail the performance of molecular diagnostics on existing pathology samples from biological repositories. Technologies continue to evolve to define molecular signatures from low amounts of highly degraded RNA. We sought to understand the effect of differential tissue preservation and RNA degradation on renal expression using two different transcript expression platforms.

Methods

Kidneys from c57Bl/6 mice were subjected to one of five preservation conditions and RNA integrity was measured: frozen immediately (RIN 7.4 ± 0.2), stored 6 h in Michels solution (6.8 ± 0.6), stored 24 h in Michels solution (6.6 ± 0.3), stored 6 h in BE70 solution (3.3 ± 0.2), or formalin fixed (2.63 ± 0.2). In preparation for laser micro-dissection, tissue was subjected to immunofluorescence for the frozen (RIN 3.4 ± 0.2 post-stain) and formalin fixed (RIN 2.2 ± 0.1) conditions. Gene expression was measured using RNA sequencing and a microarray.

Results

Both platforms revealed a strong correlation between RNA from fresh frozen samples and highly degraded RNA from frozen stained (RNAseq: R = 0.922, Microarray: 0.964) or stained formalin fixed samples (RNAseq: R = 0.920, Microarray: 0.916). The inter-platform correlation ranged from R of 0.700 to 0.821. As compared to the microarray, both the dynamic range and coefficient of variation for RNAseq expression was larger.

Conclusion

Both the RNA sequencing and microarray platforms appear adequate to measure renal gene expression in highly degraded low-input RNA.

Funding

  • NIDDK Support