BACKGROUND: RNA analysis of surgical specimens is one of the most useful methods for exploring biomarkers of advanced cancer. The most readily available source for RNA is formalin-fixed, paraffin-embedded (FFPE) specimens, but RNA isolated from FFPE tissue is of limited use. The PAXgene Tissue (PAX) system is a formalin-free system designed to improve the quality of molecular analysis without diminishing the quality of histopathological analysis. In this human colorectal cancer tissue study, we aimed to evaluate whether surgical specimens fixed with PAX can preserve high-quality RNA in comparison with FFPE and fresh-frozen tissue specimens. METHODS: Ten consecutive advanced colorectal cancer patients undergoing colectomy were examined. Each specimen was processed in three ways: as frozen tissue, as PAX-fixed tissue, and as formalin-fixed tissue. RNA integrity numbers (RINs) were assessed using an Agilent Bioanalyzer. RNA transcript levels and stability were investigated by quantitative real-time PCR. We also evaluated the immunohistochemical intensity of Ki-67, CEA, and EGFR in the PAX samples. RESULTS: The average RINs of RNA extracted from frozen and PAX samples were significantly higher than those from FFPE samples (p < 0.001). The cycle threshold (Ct) values were similar in PAX and frozen samples, but significantly increased in FFPE samples (p < 0.001). Most of the ΔCt values in the PAX samples did not differ significantly from those in the matched frozen samples. On the other hand, most of the ΔCt values in the FFPE samples differed significantly from those in the matched frozen samples. The immunohistochemical intensity in the PAX samples was well preserved. CONCLUSIONS: The quality of RNA extracted from PAX samples may be slightly inferior to that from frozen samples, but is greatly superior to that from FFPE samples.
BACKGROUND: RNA analysis of surgical specimens is one of the most useful methods for exploring biomarkers of advanced cancer. The most readily available source for RNA is formalin-fixed, paraffin-embedded (FFPE) specimens, but RNA isolated from FFPE tissue is of limited use. The PAXgene Tissue (PAX) system is a formalin-free system designed to improve the quality of molecular analysis without diminishing the quality of histopathological analysis. In this humancolorectal cancer tissue study, we aimed to evaluate whether surgical specimens fixed with PAX can preserve high-quality RNA in comparison with FFPE and fresh-frozen tissue specimens. METHODS: Ten consecutive advanced colorectal cancerpatients undergoing colectomy were examined. Each specimen was processed in three ways: as frozen tissue, as PAX-fixed tissue, and as formalin-fixed tissue. RNA integrity numbers (RINs) were assessed using an Agilent Bioanalyzer. RNA transcript levels and stability were investigated by quantitative real-time PCR. We also evaluated the immunohistochemical intensity of Ki-67, CEA, and EGFR in the PAX samples. RESULTS: The average RINs of RNA extracted from frozen and PAX samples were significantly higher than those from FFPE samples (p < 0.001). The cycle threshold (Ct) values were similar in PAX and frozen samples, but significantly increased in FFPE samples (p < 0.001). Most of the ΔCt values in the PAX samples did not differ significantly from those in the matched frozen samples. On the other hand, most of the ΔCt values in the FFPE samples differed significantly from those in the matched frozen samples. The immunohistochemical intensity in the PAX samples was well preserved. CONCLUSIONS: The quality of RNA extracted from PAX samples may be slightly inferior to that from frozen samples, but is greatly superior to that from FFPE samples.
Authors: Arthur Morley-Bunker; John Pearson; Margaret J Currie; Helen Morrin; Martin R Whitehead; Tim Eglinton; Logan C Walker Journal: Oncotarget Date: 2019-02-15
Authors: Ryan DeCoste; Yutaka Amemiya; Sarah Nersesian; Lauren Westhaver; Stacey N Lee; Michael D Carter; Heidi L Sapp; Ashley E Stueck; Thomas Arnason; Jeanette Boudreau; Arun Seth; Weei-Yuarn Huang Journal: J Clin Med Date: 2022-07-21 Impact factor: 4.964