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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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Transcriptome profiling of host-microbe interactions by differential display RT-PCR.

Leong Wai Fook1, Vincent T K Chow

  • 1Institute of Molecular and Cell Biology, Proteos, Singapore.

Methods in Molecular Biology (Clifton, N.J.)
|March 20, 2010
PubMed
Summary

Differential display RT-PCR reveals host-pathogen interactions by analyzing gene expression changes in rhabdomyosarcoma cells during enterovirus 71 infection. This method identified novel transcripts and alternative splicing, offering insights into viral pathogenesis.

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Area of Science:

  • Molecular Biology
  • Virology
  • Cell Biology

Background:

  • DNA microarray is popular for global gene expression analysis.
  • Differential display RT-PCR offers advantages for studying host-microbe interactions without pre-defined gene sets.
  • This technique allows simultaneous analysis of host and pathogen transcripts and discovery of novel transcripts or splicing variants.

Purpose of the Study:

  • To investigate the gene expression response of rhabdomyosarcoma cells to enterovirus 71 (EV71) infection.
  • To identify differentially expressed mRNAs during EV71 infection using differential display RT-PCR.

Main Methods:

  • Differential display RT-PCR was employed to compare gene expression profiles.
  • Rhabdomyosarcoma cells were infected with a neurovirulent strain of EV71 at various time points.
  • Uninfected cells served as controls.

Main Results:

  • Numerous mRNAs were found to be up- or down-regulated during EV71 infection.
  • Less than half of the identified clones corresponded to known genes involved in cellular processes like cytoskeleton, cell cycle, and protein translation.
  • Several novel genes were discovered, along with an alternative splicing form of TRIP7 that was down-regulated.

Conclusions:

  • Differential display RT-PCR is a valuable tool for elucidating transcriptomic profiles in host-microbe interactions.
  • This technique enhances understanding of microbial pathogenesis by revealing host responses.
  • The study identified specific molecular changes during EV71 infection, including novel gene expression and alternative splicing.