Abstract C059: Optimization of DNA extraction methods from FFPE prostate tumor tissues of Black men to identify DNA methylation biomarkers

Abstract

Abstract Prostate cancer is the second leading cause of cancer related deaths among men in the United States, and health disparities in those diagnosed with prostate cancer are observed between those of African and European ancestry. Our approach to understand the mechanisms underlying these differences is to compare DNA methylation profiles between samples using formalin-fixed parafin-embedded (FFPE) prostate tumor tissues. To profile DNA methylation from FFPE prostate tumor tissues, we tested magnetic bead and column based DNA extraction methods, and evaluated them on their total DNA yield. Additionally, we assessed the relationship between DNA yield and clinical features. Prostate specimens for this study were obtained from the University of Florida in the form of FFPE tissue slides. Both tumor and normal tissue regions were outlined on an H&E reference slide and the respective regions were macro-dissected from unstained slides of the same block. The areas of macro-dissected regions were measured using ImageJ, and the number of slides were taken to further normalize DNA yield. Magnetic bead and column based FFPE DNA extraction kits were used to isolate DNA, and the relative amounts of the isolated DNA per tissue size were evaluated. In addition, various clinical features of the samples were compared to determine if their presence influences DNA yield. Preliminary data suggests that total DNA extracted from both bead and column based methods are relatively comparable, but bead based methods yielded better quality of DNA. We observed minimal correlation between DNA yield and grade group. We detected a potential association between cribriform pattern and DNA yield. We are in the process of profiling DNA methylation using the isolated DNA. Successful completion of this study will identify DNA methylation biomarkers and further develop diagnostic and therapeutic tools for prostate cancer patients from African ancestry. Citation Format: Colton Stensrud, Claire Stevens, Leonardo Gonzalez-Smith, Huan Cao, Sarah Buxbaum, Sara Falzarano, Suhn Rhie. Optimization of DNA extraction methods from FFPE prostate tumor tissues of Black men to identify DNA methylation biomarkers [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C059.