NIH, National Cancer Institute, Division of Cancer Treatment and Diagnosis (DCTD) NIH - National Institutes of Health National Cancer Institute DCTD - Division of Cancer Treatment and Diagnosis

Fit for genomic and proteomic purposes: Sampling the fitness of nucleic acid and protein derivatives from formalin fixed paraffin embedded tissue.

Author(s): Yakovleva A, Plieskatt JL, Jensen S, Humeida R, Lang J, Li G, Bracci P, Silver S, Bethony JM

Publication: PLoS One, 2017, Vol. 12, Page e0181756

PubMed ID: 28742856 PubMed Review Paper? No

Purpose of Paper

This paper investigated whether the duration of formalin-fixed paraffin-embedded (FFPE) tissue block storage affects the yield and quality of isolated DNA, RNA, microRNA (miRNA), and protein.

Conclusion of Paper

Significant differences in total RNA quality (determined by the ratio of absorbance at 260 nm to 280 nm) occurred when FFPE specimens were stratified by cancer tissue type (p<0.04) and in miRNA quality when stratified by FFPE block storage duration (p<0.03).  miRNA isolated from blocks stored for less than 1 y had a modestly higher mean absorbance ratio than those stored for more than 11 years. FFPE tumor specimens did not differ from one another when specimens were stratified by FFPE block storage duration or tumor tissue type for DNA concentration or purity (A260/280), protein purity (A280), total RNA concentration, or miRNA concentration. RIN was not associated with FFPE block storage duration or tumor tissue type when samples were grouped by RIN (< 2, 2-3, or >3).

Studies

  1. Study Purpose

    This study investigated whether the duration of formalin-fixed paraffin-embedded (FFPE) tissue block storage affects the yield and quality of isolated DNA, RNA, miRNA, and protein.  FFPE specimens from papillary, adenocarcinoma, and squamous tumor types that represented 120 cases from diverse geographic locations were analyzed.  Details on formalin fixation and paraffin processing of specimens was not provided. FFPE blocks were stored under temperature controlled conditions at 21-23°C for < 11 y (60 cases) or > 11 y (60 cases) prior to block facing (the first two 5 µm-thick sections were discarded) and sectioning. Each sample consisted of a single 10 µm-thick section that was stored in an Eppendorf tube at -20°C prior to analyte extraction and analysis.  Genomic DNA was extracted from each sample with the QIAamp DNA FFPE Tissue kit, miRNA was extracted with the miRNeasy FFPE kit, total RNA was extracted with the RNeasy FFPE kit, and protein was isolated with the Qproteome FFPE Tissue kit. All isolated analytes were stored at -70°C until analysis for concentration and purity by spectrophotometry (for absorbance at 230, 260, and 280 nm) using the SpectraDrop Micro-Volume Microplate. RNA integrity was also measured by RNA Integrity Number (RIN) with a bioanalyzer.

    Summary of Findings:

    Significant differences in total RNA quality (determined by the ratio of absorbance at  260 nm to 280 nm) occurred when FFPE specimens were stratified by cancer tissue type (p<0.04) and in miRNA quality when stratified by FFPE block storage duration (p<0.03). miRNA isolated from blocks stored for less than 11 years had a mean absorbance ratio that was 1.082 times higher than observed for blocks stored for more than 11 years. No differences in DNA, RNA or miRNA concentration;  or DNA purity (A260/280) and protein purity (A280) were observed when specimens were stratified by FFPE block storage duration or tumor tissue type.  FFPE block storage and tumor tissue type were not associated with DNA, RNA, or miRNA concentration.  No association was present between RIN and the duration of FFPE block storage or tumor tissue type when samples were grouped by RIN (< 2, 2-3, or >3).

    Biospecimens
    Preservative Types
    • Formalin
    Diagnoses:
    • Neoplastic - Carcinoma
    Platform:
    AnalyteTechnology Platform
    DNA Spectrophotometry
    Protein Spectrophotometry
    RNA Automated electrophoresis/Bioanalyzer
    RNA Spectrophotometry
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Preaquisition Diagnosis/ patient condition Papillary tumor
    Adenocarcinoma tumor
    Squamous tumor
    Storage Storage duration < 11 y
    > 11 y

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