High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic.
Identifieur interne : 000B53 ( PubMed/Corpus ); précédent : 000B52; suivant : 000B54High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic.
Auteurs : Yong-Li Xiao ; John C. Kash ; Stephen B. Beres ; Zong-Mei Sheng ; James M. Musser ; Jeffery K. TaubenbergerSource :
- The Journal of pathology [ 1096-9896 ] ; 2013.
English descriptors
- KwdEn :
- Epithelial Cells (virology), Female, Formaldehyde, Gene Library, Genome, Viral (genetics), High-Throughput Nucleotide Sequencing (methods), Humans, Influenza A virus (genetics), Influenza A virus (isolation & purification), Influenza, Human (virology), Lung (microbiology), Lung (pathology), Lung (virology), Male, Middle Aged, Molecular Sequence Annotation, Pandemics, Paraffin Embedding, RNA (genetics), RNA Stability, Sequence Analysis, RNA, Young Adult.
- MESH :
- chemical , genetics : RNA.
- chemical : Formaldehyde.
- genetics : Genome, Viral, Influenza A virus.
- isolation & purification : Influenza A virus.
- methods : High-Throughput Nucleotide Sequencing.
- microbiology : Lung.
- pathology : Lung.
- virology : Epithelial Cells, Influenza, Human, Lung.
- Female, Gene Library, Humans, Male, Middle Aged, Molecular Sequence Annotation, Pandemics, Paraffin Embedding, RNA Stability, Sequence Analysis, RNA, Young Adult.
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.
DOI: 10.1002/path.4145
PubMed: 23180419
Links to Exploration step
pubmed:23180419Le document en format XML
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Beres</name></author><author><name sortKey="Sheng, Zong Mei" sort="Sheng, Zong Mei" uniqKey="Sheng Z" first="Zong-Mei" last="Sheng">Zong-Mei Sheng</name></author><author><name sortKey="Musser, James M" sort="Musser, James M" uniqKey="Musser J" first="James M" last="Musser">James M. Musser</name></author><author><name sortKey="Taubenberger, Jeffery K" sort="Taubenberger, Jeffery K" uniqKey="Taubenberger J" first="Jeffery K" last="Taubenberger">Jeffery K. 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Kash</name></author><author><name sortKey="Beres, Stephen B" sort="Beres, Stephen B" uniqKey="Beres S" first="Stephen B" last="Beres">Stephen B. Beres</name></author><author><name sortKey="Sheng, Zong Mei" sort="Sheng, Zong Mei" uniqKey="Sheng Z" first="Zong-Mei" last="Sheng">Zong-Mei Sheng</name></author><author><name sortKey="Musser, James M" sort="Musser, James M" uniqKey="Musser J" first="James M" last="Musser">James M. Musser</name></author><author><name sortKey="Taubenberger, Jeffery K" sort="Taubenberger, Jeffery K" uniqKey="Taubenberger J" first="Jeffery K" last="Taubenberger">Jeffery K. Taubenberger</name></author></analytic><series><title level="j">The Journal of pathology</title><idno type="eISSN">1096-9896</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Epithelial Cells (virology)</term><term>Female</term><term>Formaldehyde</term><term>Gene Library</term><term>Genome, Viral (genetics)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Humans</term><term>Influenza A virus (genetics)</term><term>Influenza A virus (isolation & purification)</term><term>Influenza, Human (virology)</term><term>Lung (microbiology)</term><term>Lung (pathology)</term><term>Lung (virology)</term><term>Male</term><term>Middle Aged</term><term>Molecular Sequence Annotation</term><term>Pandemics</term><term>Paraffin Embedding</term><term>RNA (genetics)</term><term>RNA Stability</term><term>Sequence Analysis, RNA</term><term>Young Adult</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Formaldehyde</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Viral</term><term>Influenza A virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Influenza A virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Lung</term></keywords><keywords scheme="MESH" qualifier="pathology" xml:lang="en"><term>Lung</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Epithelial Cells</term><term>Influenza, Human</term><term>Lung</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Female</term><term>Gene Library</term><term>Humans</term><term>Male</term><term>Middle Aged</term><term>Molecular Sequence Annotation</term><term>Pandemics</term><term>Paraffin Embedding</term><term>RNA Stability</term><term>Sequence Analysis, RNA</term><term>Young Adult</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23180419</PMID><DateCompleted><Year>2013</Year><Month>04</Month><Day>23</Day></DateCompleted><DateRevised><Year>2019</Year><Month>10</Month><Day>08</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1096-9896</ISSN><JournalIssue CitedMedium="Internet"><Volume>229</Volume><Issue>4</Issue><PubDate><Year>2013</Year><Month>Mar</Month></PubDate></JournalIssue><Title>The Journal of pathology</Title><ISOAbbreviation>J. Pathol.</ISOAbbreviation></Journal><ArticleTitle>High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic.</ArticleTitle><Pagination><MedlinePgn>535-45</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/path.4145</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>Copyright © 2012 Pathological Society of Great Britain and Ireland. 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