Gene Expression Profiling of FFPE Samples: A Titration Test

• Published in: Technology in cancer research & treatment Vol. 21; p. 15330338221129710
• Main Authors: Manjunath, Harshitha Shobha, Al Khulaifi, Moza, Sidahmed, Heba, Ammar, Adham, Vadakekolathu, Jayakumar, Rutella, Sergio, Al-Mohannadi, Muneera Jassim, Elawad, Mamoun, Mifsud, William, Charles, Adrian, Maccalli, Cristina, Tomei, Sara
• Format: Journal Article
• Language: English
• Published: Los Angeles, CA SAGE Publications 01.01.2022; Sage Publications Ltd; SAGE Publishing
• Subjects: Gene expression; Impact of Advances in Genomic Technologies in Cancer Research, Diagnostics and Therapy; Paraffin; Titration; titration; RNA; FFPE; gene expression; nCounter
• ISSN: 1533-0346; 1533-0338
• DOI: 10.1177/15330338221129710

The gene expression analysis of formalin-fixed paraffin-embedded (FFPE) tissues is often hampered by poor RNA quality, which results from the oxidation, cross-linking and other chemical modifications induced by the inclusion in paraffin. Yet, FFPE samples are a valuable source for molecular studies and can provide great insights into disease progression and prognosis. With the advancement of genomic technologies, new methods have been established that offer reliable and accurate gene expression workflows on samples of poor quality. NanoString is a probe-based technology that allows the direct counting of the mRNA transcripts and can be applied to degraded samples. Here, we have tested 2 RNA extraction methods for FFPE samples, and we have performed a titration experiment to evaluate the impact of RNA degradation and RNA input on the gene expression profiles assessed using the NanoString IO360 panel. We have selected FFPE samples of different DV200 values and assessed them on the nCounter platform with 2 different amounts of input RNA. This study concludes that the nCounter is a robust and reliable platform to assess the gene expression of RNA samples with DV200 > 30%; its robustness and ease of use could be of particular benefit to clinical settings.