RNA quality assessment of long-term storage biobank samples from colorectal cancer patients for sequencing and profiling

Abstract

Samples from patients with colorectal cancer (CRC) are valuable tools for understanding the development, progression, and treatment of the disease. However, to date, the integrity of long-term preserved human specimens in biobanks has not been well understood. In this study, we investigated the RNA quality of 12-year-stored specimens, including frozen and formalin-fixed, paraffin-embedded (FFPE) tumor tissues from CRC patients at the Siriraj Biobank. We assessed the RNA quality of 12-year and 2-year storage samples using three technologies: next-generation sequencing (NGS), Nanostring nCounter® platform, and GeoMx® digital spatial profiling (DSP). We found that the RNA quality of 12-year storage frozen tissues was consistent with the criteria for RNA sequencing. Although RNA in long-term storage FFPE tissues was degraded, the normalized counts of RNA from the 12-year-stored FFPE samples were comparable to those from the 2-year-stored FFPE samples in the Nanostring nCounter® gene expression assay. For histological staining, clear tissue microanatomy was observed in the FFPE blocks stored for 12 years. In GeoMx® DSP, there was no statistically significant difference in the normalized counts of RNA from the 12- and 2-year stored FFPE samples. Our results suggest the potential utilization of long-term storage biobank specimens from patients with CRC for NGS, Nanostring nCounter® gene expression analysis, and GeoMx® DSP.