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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Descriptive Comparative Transcriptomic Analysis of Genotype IV SHEV ORF3-Expressing HepG2 Cells.

Hanwei Jiao1, Chi Meng1, Fengyuan Jiao1

  • 1The College of Veterinary Medicine, Southwest University, Chongqing 402460, China.

Microorganisms
|February 26, 2025
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Summary

Swine hepatitis E virus (SHEV) ORF3 protein is a key virulence factor. This study identified differentially expressed genes and pathways in HepG2 cells, revealing potential mechanisms of SHEV pathogenesis.

Keywords:
HepG2ORF3SHEVmRNAtranscriptome

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Area of Science:

  • Virology
  • Molecular Biology
  • Genomics

Background:

  • Swine hepatitis E virus (SHEV) causes a zoonotic disease, with Open Reading Frame 3 (ORF3) identified as a critical virulence factor.
  • The precise function and pathogenic mechanisms of SHEV ORF3 are not fully understood, necessitating further investigation into its molecular interactions.
  • ORF3's known roles include viral particle release, host innate immune modulation, and regulation of cellular processes like autophagy and apoptosis.

Purpose of the Study:

  • To investigate the molecular mechanisms and pathogenic role of the SHEV ORF3 protein.
  • To identify host genes and pathways affected by SHEV ORF3 expression using transcriptomic analysis.
  • To provide a genetic basis for understanding the physiological functions of SHEV ORF3.

Main Methods:

  • Construction of adenoviruses (ADV4-ORF3 and ADV4-GFP) for overexpression of EGFP-ORF3 and EGFP in HepG2 cells.
  • High-throughput sequencing to identify differentially expressed messenger RNAs (mRNAs) in response to SHEV ORF3.
  • Functional enrichment analysis (Gene Ontology and KEGG) and quantitative real-time reverse transcription PCR (qRT-PCR) for gene verification.

Main Results:

  • Overexpression of EGFP-ORF3 in HepG2 cells led to the identification of 217 differentially expressed mRNAs.
  • Functional enrichment analysis highlighted six key pathways, including inflammatory response, cytokine activity, and TNF signaling.
  • Comparative analysis revealed overlapping transcripts and 3 mRNAs (GPX1, MDM4, CLDN) common to transcriptome and lncRNA sequencing, with 8 differential genes verified by qRT-PCR.

Conclusions:

  • The study successfully identified and verified key host genes and pathways modulated by SHEV ORF3.
  • The findings provide a genetic foundation for understanding the physiological functions and pathogenic mechanisms of SHEV ORF3.
  • This research contributes to the knowledge of SHEV pathogenesis and potential therapeutic targets.