optimized-high-quality-dna-extraction-from-formalin-fixed-paraffin

Optimized High Quality DNA Extraction from Formalin-Fixed Paraffin-Embedded Human Atherosclerotic Lesions

Formalin-fixed paraffin-embedded (FFPE) tissues represent a valuable source for molecular analyses and clinical genomic studies. These tissues are often ...

Technical University Munich

Deutsches Zentrum für Herz-Kreislaufforschung (DZHK)

Collecting biological tissue samples in a biobank grants a unique opportunity to validate diagnostic and therapeutic strategies for translational and clinical research. In the present work, we provide our long-standing experience in establishing and maintaining a biobank of vascular tissue samples, including the evaluation of tissue quality, especially in formalin-fixed paraffin-embedded specimens (FFPE). Our Munich Vascular Biobank includes, thus far, vascular biomaterial from patients with high-grade carotid artery stenosis ( = 1567), peripheral arterial disease ( = 703), and abdominal aortic aneurysm ( = 481) from our Department of Vascular and Endovascular Surgery (January 2004⁻December 2018). Vascular tissue samples are continuously processed and characterized to assess tissue morphology, histological quality, cellular composition, inflammation, calcification, neovascularization, and the content of elastin and collagen fibers. Atherosclerotic plaques are further classified in accordance with the American Heart Association (AHA), and plaque stability is determined. In order to assess the quality of RNA from FFPE tissue samples over time (2009⁻2018), RNA integrity number (RIN) and the extent of RNA fragmentation were evaluated. Expression analysis was performed with two housekeeping genes-glyceraldehyde 3-phosphate dehydrogenase () and beta-actin ()-using TaqMan-based quantitative reverse-transcription polymerase chain reaction (qRT)-PCR. FFPE biospecimens demonstrated unaltered RNA stability over time for up to 10 years. Furthermore, we provide a protocol for processing tissue samples in our Munich Vascular Biobank. In this work, we demonstrate that biobanking is an important tool not only for scientific research but also for clinical usage and personalized medicine.

Sabine Bauer

Department for Vascular and Endovascular Surgery,
Klinikum rechts der Isar,
Department of Experimental Cardiology,
German Heart Centre,
Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar,
Department of Experimental Cardiology, German Heart Centre

Technical University Munich

Optimized High Quality DNA Extraction from Formalin-Fixed Paraffin-Embedded Human Atherosclerotic Lesions