High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic

Yong Li Xiao, John C. Kash, Stephen B. Beres, Zong Mei Sheng, James M. Musser, Jeffery K. Taubenberger

Research output: Contribution to journalArticle

36 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)535-545
Number of pages11
JournalJournal of Pathology
Volume229
Issue number4
DOIs
StatePublished - Mar 2013

Keywords

  • 1918 influenza virus
  • formalin-fixed, paraffin-embedded tissue
  • influenza A virus
  • NGS
  • pandemic

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

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