Deep Insight Into Long Non-Coding RNA and mRNA Transcriptome Profiling in HepG2 Cells Expressing Genotype IV Swine Hepatitis E Virus ORF3

Abstract Background: Swine hepatitis E (SHE) is a new type of zoonotic infectious disease caused by swine hepatitis E virus (SHEV). Open reading frame 3 (ORF3) is an important virulent protein of SHEV but its function still is mainly unclear.Methods: In this study we generated adenoviruses ADV4-ORF3 and ADV4-NC which successfully mediated overexpression of EGFP-ORF3 and EGFP, respectively, in HepG2 cells. High throughput sequencing was used to screen for differentially expressed long non‑coding RNAs (lncRNAs) and mRNAs. The cis-target genes of lncRNAs were predicted, functional enrichment (Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)) was performed, and 12 lncRNAs with statistically significant different expression (p value ≤ 0.05 and q value ≤ 1) were selected for further quantitative real-time reverse transcription (qRT-PCR) validation.Results: In HepG2 cells, we identified 62 significantly differential expression genes (DEGs) (6,564 transcripts), and 319 lncRNAs (124 known lncRNAs and 195 novel lncRNAs) that were affected by ORF3, which were involved in systemic lupus erythematosus, staphylococcus aureus infection, signaling pathways regulating pluripotency of stem cells, the PPAR signaling pathway, and platinum drug resistance pathways. Cis-target gene prediction identified 45 lncRNAs corresponding to candidate mRNAs, among which 8 were validated by qRT-PCR: LINC02476 (two transcripts), RAP2C-AS1, AC016526, AL139099, and ZNF337-AS1 (3 transcripts). Conclusions: Our results revealed the lncRNA profile in host cells affected by ORF3, which will help to determine the function of ORF3, and the infection mechanism and treatment of SHE.

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Deep Insight Into Long Non-coding RNA and mRNA Transcriptome Profiling in HepG2 Cells Expressing Genotype IV Swine Hepatitis E Virus ORF3

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.625609 ◽

2021 ◽

Vol 8 ◽

Author(s):

Hanwei Jiao ◽

Xuehong Shuai ◽

Yichen Luo ◽

Zhixiong Zhou ◽

Yu Zhao ◽

...

Keyword(s):

Hepg2 Cells ◽

Hepatitis E Virus ◽

High Throughput Sequencing ◽

Fluorescent Protein ◽

Hepatitis E ◽

Functional Enrichment ◽

Host Cells ◽

Differentially Expressed ◽

Qrt Pcr ◽

Swine Hepatitis

Swine hepatitis E (swine HE) is a new type of zoonotic infectious disease caused by the swine hepatitis E virus (swine HEV). Open reading frame 3 (ORF3) is an important virulent protein of swine HEV, but its function still is mainly unclear. In this study, we generated adenoviruses ADV4-ORF3 and ADV4 negative control (ADV4-NC), which successfully mediated overexpression of enhanced green fluorescent protein (EGFP)-ORF3 and EGFP, respectively, in HepG2 cells. High-throughput sequencing was used to screen for differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs). The cis-target genes of lncRNAs were predicted, functional enrichment (Gene Ontology [GO] and Kyoto Encyclopedia of Genes and Genomes [KEGG]) was performed, and 12 lncRNAs with statistically significant different expressions (p ≤ 0.05 and q ≤ 1) were selected for further quantitative real-time reverse transcription (qRT-PCR) validation. In HepG2 cells, we identified 62 significantly differentially expressed genes (DEGs) (6,564 transcripts) and 319 lncRNAs (124 known lncRNAs and 195 novel lncRNAs) that were affected by ORF3, which were involved in systemic lupus erythematosus, Staphylococcus aureus infection, signaling pathways pluripotency regulation of stem cells, the peroxisome proliferator-activated receptor (PPAR) signaling pathway, and platinum drug resistance pathways. Cis-target gene prediction identified 45 lncRNAs corresponding to candidate mRNAs, among which eight were validated by qRT-PCR: LINC02476 (two transcripts), RAP2C-AS1, AC016526, AL139099, and ZNF337-AS1 (3 transcripts). Our results revealed that the lncRNA profile in host cells affected by ORF3, swine HEV ORF3, might affect the pentose and glucuronate interconversions and mediate the formation of obstructive jaundice by influencing bile secretion, which will help to determine the function of ORF3 and the infection mechanism and treatment of swine HE.

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Identifying Circular RNAs in HepG2 Expressing Genotype IV Swine Hepatitis E Virus ORF3 Via Whole Genome Sequencing

Cell Transplantation ◽

10.1177/09636897211055042 ◽

2021 ◽

Vol 30 ◽

pp. 096368972110550

Author(s):

Hanwei Jiao ◽

Yu Zhao ◽

Zhixiong Zhou ◽

Wenjie Li ◽

Bowen Li ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Hepg2 Cells ◽

Hepatitis E Virus ◽

Enrichment Analysis ◽

Hepatitis E ◽

Differentially Expressed ◽

Circular Rnas ◽

Whole Genome ◽

Swine Hepatitis

Swine hepatitis E (SHE) is a new type of zoonotic infectious disease caused by swine hepatitis E virus (SHEV). Open reading frame 3 (ORF3) is a key regulatory and virulent protein of SHEV. Circular RNAs (circRNAs) are a special kind of non-coding RNA molecule, which has a closed ring structure. In this study, to identify the circRNA profile in host cells affected by SHEV ORF3, adenovirus ADV4-ORF3 mediated the overexpression of ORF3 in HepG2 cells, whole genome sequencing was used to investigate the differentially expressed circRNAs, GO and KEGG were performed to enrichment analyze of differentially expressed circRNA-hosting gene, and Targetscan and miRanda softwares were used to analyze the interaction between circRNA and miRNA. The results showed adenovirus successfully mediated the overexpression of ORF3 in HepG2 cells, 1,105 up-regulation circRNAs and 1,556 down-regulation circRNAs were identified in ADV4-ORF3 infection group compared with the control. GO function enrichment analysis of differentially expressed circRNAs-hosting genes classified three main categories (cellular component, biological process and molecular function). KEGG pathway enrichment analysis scatter plot showed the pathway term of top20. The circRNAs with top10 number of BS sites for qRT-PCR validation were selected to confirmed, the results indicated that the up-regulated hsa_circ_0001423 and hsa_circ_0006404, and down-regulated of hsa_circ_0004833 and hsa_circ_0007444 were consistent with the sequencing data. Our findings first preliminarily found that ORF3 protein may affect triglyceride activation (GO:0006642) and riboflavin metabolism (ko00740) in HepG2 cells, which provides a scientific basis for further elucidating the effect of ORF3 on host lipid metabolism and the mechanism of SHEV infection.

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Transcriptome Analysis of HepG2 Cells Expressing ORF3 from Swine Hepatitis E Virus to Determine the Effects of ORF3 on Host Cells

BioMed Research International ◽

10.1155/2016/1648030 ◽

2016 ◽

Vol 2016 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Kailian Xu ◽

Shiyu Guo ◽

Tianjing Zhao ◽

Huapei Zhu ◽

Hanwei Jiao ◽

...

Keyword(s):

Lipid Metabolism ◽

Basement Membrane ◽

Membrane Protein ◽

Differentially Expressed Genes ◽

Hepg2 Cells ◽

Hepatitis E Virus ◽

Hepatitis E ◽

Integral Membrane Protein ◽

Host Cells ◽

Mrna Levels

Hepatitis E virus- (HEV-) mediated hepatitis has become a global public health problem. An important regulatory protein of HEV, ORF3, influences multiple signal pathways in host cells. In this study, to investigate the function of ORF3 from the swine form of HEV (SHEV), high-throughput RNA-Seq-based screening was performed to identify the differentially expressed genes in ORF3-expressing HepG2 cells. The results were validated with quantitative real-time PCR and gene ontology was employed to assign differentially expressed genes to functional categories. The results indicated that, in the established ORF3-expressing HepG2 cells, the mRNA levels of CLDN6, YLPM1, APOC3, NLRP1, SCARA3, FGA, FGG, FGB, and FREM1 were upregulated, whereas the mRNA levels of SLC2A3, DKK1, BPIFB2, and PTGR1 were downregulated. The deregulated expression of CLDN6 and FREM1 might contribute to changes in integral membrane protein and basement membrane protein expression, expression changes for NLRP1 might affect the apoptosis of HepG2 cells, and the altered expression of APOC3, SCARA3, and DKK1 may affect lipid metabolism in HepG2 cells. In conclusion, ORF3 plays a functional role in virus-cell interactions by affecting the expression of integral membrane protein and basement membrane proteins and by altering the process of apoptosis and lipid metabolism in host cells. These findings provide important insight into the pathogenic mechanism of HEV.

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Advances in Hepatitis E Virus Biology and Pathogenesis

Viruses ◽

10.3390/v13020267 ◽

2021 ◽

Vol 13 (2) ◽

pp. 267

Author(s):

Shaoli Lin ◽

Yan-Jin Zhang

Keyword(s):

Pregnant Women ◽

Hepatitis E Virus ◽

Case Fatality ◽

Hepatitis E ◽

Host Cells ◽

High Rate ◽

Rapid Progression ◽

Genotype 1 ◽

Genotype 3 ◽

Zoonotic Infections

Hepatitis E virus (HEV) is one of the causative agents for liver inflammation across the world. HEV is a positive-sense single-stranded RNA virus. Human HEV strains mainly belong to four major genotypes in the genus Orthohepevirus A, family Hepeviridae. Among the four genotypes, genotype 1 and 2 are obligate human pathogens, and genotype 3 and 4 cause zoonotic infections. HEV infection with genotype 1 and 2 mainly presents as acute and self-limiting hepatitis in young adults. However, HEV infection of pregnant women with genotype 1 strains can be exacerbated to fulminant hepatitis, resulting in a high rate of case fatality. As pregnant women maintain the balance of maternal-fetal tolerance and effective immunity against invading pathogens, HEV infection with genotype 1 might dysregulate the balance and cause the adverse outcome. Furthermore, HEV infection with genotype 3 can be chronic in immunocompromised patients, with rapid progression, which has been a challenge since it was reported years ago. The virus has a complex interaction with the host cells in downregulating antiviral factors and recruiting elements to generate a conducive environment of replication. The virus-cell interactions at an early stage might determine the consequence of the infection. In this review, advances in HEV virology, viral life cycle, viral interference with the immune response, and the pathogenesis in pregnant women are discussed, and perspectives on these aspects are presented.

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Seasonal pattern of hepatitis E virus prevalence in swine in two different geographical areas of China

Epidemiology and Infection ◽

10.1017/s0950268813000113 ◽

2013 ◽

Vol 141 (11) ◽

pp. 2403-2409 ◽

Cited By ~ 8

Author(s):

Y. H. LU ◽

H. Z. QIAN ◽

A. Q. HU ◽

X. QIN ◽

Q. W. JIANG ◽

...

Keyword(s):

Hepatitis E Virus ◽

Seasonal Pattern ◽

Eastern China ◽

Geographical Area ◽

Hepatitis E ◽

Southwestern China ◽

Seasonal Patterns ◽

Virus Prevalence ◽

Swine Hepatitis ◽

A Minor

SUMMARYWe studied seasonal patterns of swine hepatitis E virus (HEV) infection in China. From 2008 to 2011, 4200 swine bile specimens were collected for the detection of HEV RNA. A total of 92/2400 (3·83%) specimens in eastern China and 47/1800 (2·61%) specimens in southwestern China were positive for HEV. Seasonal patterns differing by geographical area were suggested. In eastern China, the major peak of HEV RNA prevalence was during March–April, with a minor peak during September–October, and a dip during July–August. In southwestern China, the peak was during September–October and the dip during March–April. The majority of subtype 4a cases (63/82, 76·83%) were detected in the first half of the year, while the majority of subtype 4b cases (26/29, 89·66%) were concentrated in the second half of the year, suggesting that different subtypes contribute to different peaks. Our results indicate that the distribution of HEV subtypes is associated with seasonal patterns.

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Experimental infection of mongolian gerbils by a genotype 4 strain of swine hepatitis E virus

Journal of Medical Virology ◽

10.1002/jmv.21573 ◽

2009 ◽

Vol 81 (9) ◽

pp. 1591-1596 ◽

Cited By ~ 26

Author(s):

Wengui Li ◽

Quan Sun ◽

Ruiping She ◽

Decheng Wang ◽

Xinhui Duan ◽

...

Keyword(s):

Experimental Infection ◽

Hepatitis E Virus ◽

Hepatitis E ◽

Mongolian Gerbils ◽

Genotype 4 ◽

Swine Hepatitis

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Induction of antibody and interferon-γ production in mice immunized with virus-like particles of swine hepatitis E virus

Journal of Veterinary Science ◽

10.4142/jvs.2014.15.4.575 ◽

2014 ◽

Vol 15 (4) ◽

pp. 575 ◽

Cited By ~ 1

Author(s):

Young-Jo Song ◽

Woo-Jung Park ◽

Seul-Kee Lee ◽

Joong-Bok Lee ◽

Seung-Yong Park ◽

...

Keyword(s):

Hepatitis E Virus ◽

Hepatitis E ◽

Interferon Γ ◽

Virus Like Particles ◽

Swine Hepatitis

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Detection of Human Food-Borne and Zoonotic Viruses on Irrigated, Field-Grown Strawberries

Applied and Environmental Microbiology ◽

10.1128/aem.00251-12 ◽

2012 ◽

Vol 78 (10) ◽

pp. 3763-3766 ◽

Cited By ~ 110

Author(s):

Julie Brassard ◽

Marie-Josée Gagné ◽

Mylène Généreux ◽

Caroline Côté

Keyword(s):

Irrigation Water ◽

Hepatitis E Virus ◽

Hepatitis E ◽

Human Food ◽

Food Borne ◽

Zoonotic Viruses ◽

Swine Hepatitis

ABSTRACTThis study evaluated the presence of pathogenic human and zoonotic viruses on irrigated, field-grown strawberries. Norovirus genogroup I, rotavirus, and swine hepatitis E virus genogroup 3 were detected on strawberries, and irrigation water is suspected as the contamination origin.

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