title: Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues.
abstract: Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for transcriptomic research. However, use of FFPE samples in genomic studies has been limited by technical challenges resulting from nucleic acid degradation. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues preserved in formalin for different amounts of time using 2 DNA microarray protocols and 2 whole-transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other methods by having the highest correlations of differentially expressed genes (DEGs), and best overlap of pathways, between FRO and FFPE groups. The effect of sample time in formalin (18 h or 3 weeks) on gene expression profiles indicated that test article treatment, not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18 h and 3 week FFPE samples compared with FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of time in paraffin on genomic profiles. Ribo-depletion RNA-seq analysis of 8-, 19-, and 26-year-old control blocks resulted in comparable quality metrics, including expected distributions of mapped reads to exonic, untranslated region, intronic, and ribosomal fractions of the transcriptome. Overall, our results indicate that FFPE samples are appropriate for use in genomic studies in which frozen samples are not available, and that ribo-depletion RNA-seq is the preferred method for this type of analysis in archival and long-aged FFPE samples.
authors.affiliation: *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa K1S 5B6, Canada;
authors.forename: A Francina
authors.initials: AF
authors.lastname: Webster
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065;
authors.forename: Paul
authors.initials: P
authors.lastname: Zumbo
authors.affiliation: National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709;
authors.forename: Jennifer
authors.initials: J
authors.lastname: Fostel
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065;
authors.forename: Jorge
authors.initials: J
authors.lastname: Gandara
authors.affiliation: Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, North Carolina 27709;
authors.forename: Susan D
authors.initials: SD
authors.lastname: Hester
authors.affiliation: ILS, Inc., PO Box 13501, Research Triangle Park, North Carolina 27709;
authors.forename: Leslie
authors.initials: L
authors.lastname: Recio
authors.affiliation: *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada;
authors.forename: Andrew
authors.initials: A
authors.lastname: Williams
authors.affiliation: Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, North Carolina 27709;
authors.forename: Charles E
authors.initials: CE
authors.lastname: Wood
authors.affiliation: *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada; Carole.Yauk@hc-sc.gc.ca chm2042@med.cornell.edu.
authors.forename: Carole L
authors.initials: CL
authors.lastname: Yauk
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065; The Feil Family Brain and Mind Research Institute (BMRI), 413 East 69th Street, New York, New York 10021; and The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 1305 York Avenue, New York, New York 10065 Carole.Yauk@hc-sc.gc.ca chm2042@med.cornell.edu.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
mesh_terms: D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D005260:Female; D005404:Fixatives; D005557:Formaldehyde; D005629:Frozen Sections; D005663:Furans / Q000633:toxicity*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000187:drug effects*; D053263:Gene Regulatory Networks; D008099:Liver / Q000187:drug effects* / Q000378:metabolism; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics*; D051381:Rats; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D013997:Time Factors; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D005404:Fixatives; D005663:Furans; D012333:RNA, Messenger; D005557:Formaldehyde; C039281:furan
keywords: FFPE; RNA-seq; archival RNA; biorepositories; microarray; toxicogenomics