title: High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic.
abstract: Most biopsy and autopsy tissues are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. The RNA genome of the 1918 pandemic influenza virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Here, the full genome of the 1918 virus at 3000× coverage was determined in one high-throughput sequencing run of a library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. Bacterial sequences associated with secondary bacterial pneumonias were also detected. Host transcripts were well represented in the library. Compared to a 2009 pandemic influenza virus FFPE post-mortem library, the 1918 sample showed significant enrichment for host defence and cell death response genes, concordant with prior animal studies. This methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of diseases.
authors.affiliation: Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Yong-Li
authors.initials: YL
authors.lastname: Xiao
authors.forename: John C
authors.initials: JC
authors.lastname: Kash
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Beres
authors.forename: Zong-Mei
authors.initials: ZM
authors.lastname: Sheng
authors.forename: James M
authors.initials: JM
authors.lastname: Musser
authors.forename: Jeffery K
authors.initials: JK
authors.lastname: Taubenberger
mesh_terms: D004847:Epithelial Cells / Q000821:virology; D005260:Female; D005557:Formaldehyde; D015723:Gene Library; D016679:Genome, Viral / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009980:Influenza A virus / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000821:virology*; D008168:Lung / Q000382:microbiology / Q000473:pathology / Q000821:virology*; D008297:Male; D008875:Middle Aged; D058977:Molecular Sequence Annotation; D058873:Pandemics; D016612:Paraffin Embedding; D012313:RNA / Q000235:genetics; D020871:RNA Stability; D017423:Sequence Analysis, RNA; D055815:Young Adult
chemical_list: D005557:Formaldehyde; D012313:RNA