Abstract
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered “unfit” for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules. We conducted a systematic examination of nucleic acids and proteins co-extracted from 118 FFPE blocks sampled from the AIDS and Cancer Specimen Resource (ACSR) at The George Washington University after stratification by storage duration and the three most common tumor tissue types at the ACSR (adenocarcinoma, squamous cell carcinoma, and papillary carcinoma). DNA, RNA, miRNA, and protein could be co-extracted from 98% of the FFPE blocks sampled, with DNA and miRNA “fit” for diverse genomic purposes including sequencing. While RNA was the most labile of the FFPE derivatives, especially when assessed by RNA integrity number (RIN), it was still “fit” for genomic methods that use smaller sequence lengths, e.g., quantitative PCR. While more than half of the protein derivatives were fit for proteomic purposes, our analyses indicated a significant interaction effect on the absorbance values for proteins derived from FFPE, implying that storage duration may affect protein derivatives differently by tumor tissue type. The mean absorbance value for proteins derived from more recently stored FFPE was greater than protein derived from older FFPE, with the exception of adenocarcinoma tissue. Finally, the fitness of one type of derivative was weakly associated with the fitness of derivatives co-extracted from the same FFPE block. The current study used several novel quality assurance approaches and metrics to show that archival FFPE tissue blocks are a valuable resource for contemporary genomic and proteomic platforms.
Highlights
The demand for high-quality molecular derivatives from archived formalin-fixed paraffinembedded (FFPE) tissue from biorepositories has greatly increased in recent years due to the low cost, high-throughput, and accessibility of contemporary genomic and proteomic platforms [1, 2]
While previous studies have reported on the fitness of individual nucleic acids or protein extracted from FFPE tissue blocks for genomic and proteomic analyses [1, 2, 5,6,7,8, 14,15,16,17,18,19,20], the current study is unique in its systematic assessment of the fitness of nucleic acids and protein co-extracted from the same FFPE block
A critical tool in the current study was stratified random sampling. While this method is common in population-based studies, it is seldom used for quality assurance studies in biorepositories, despite the fact that biorepositories are amenable to stratified random sampling for two reasons: (1) the attributes of each sampling unit are readily available and (2) the numbers of sampling units falling into each strata are known and do not need to be estimated
Summary
The demand for high-quality molecular derivatives from archived formalin-fixed paraffinembedded (FFPE) tissue from biorepositories has greatly increased in recent years due to the low cost, high-throughput, and accessibility of contemporary genomic and proteomic platforms [1, 2]. A fit-for-purpose approach was used to assess the "fitness" of DNA, RNA, miRNA, and protein derivatives co-extracted from FFPE blocks archived in the AIDS and Cancer Specimen Resource (ACSR) at The George Washington University (GWU) The objective of this Fit For Purpose (FFP) study was to provide biobanks with a framework to apply in similar studies to assess nucleic acids and protein derivatives from FFPE tissue blocks [3, 9] and to produce evidence for the critical role of biorepositories as partners in cancer research
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