Vaccinia Virus Transcriptome Analysis by RNA Sequencing

Key genes involved in nonalcoholic steatohepatitis improvement after bariatric surgery

Background

Nonalcoholic steatohepatitis (NASH) is the advanced stage of nonalcoholic fatty liver disease (NAFLD), one of the most prevalent chronic liver diseases. The effectiveness of bariatric surgery in treating NASH and preventing or even reversing liver fibrosis has been demonstrated in numerous clinical studies, but the underlying mechanisms and crucial variables remain unknown.

Methods

Using the GSE135251 dataset, we examined the gene expression levels of NASH and healthy livers. Then, the differentially expressed genes (DEGs) of patients with NASH, at baseline and one year after bariatric surgery, were identified in GSE83452. We overlapped the hub genes performed by protein-protein interaction (PPI) networks and DEGs with different expression trends in both datasets to obtain key genes. Genomic enrichment analysis (GSEA) and genomic variation analysis (GSVA) were performed to search for signaling pathways of key genes. Meanwhile, key molecules that regulate the key genes are found through the construction of the ceRNA network. NASH mice were induced by a high-fat diet (HFD) and underwent sleeve gastrectomy (SG). We then cross-linked the DEGs in clinical and animal samples using quantitative polymerase chain reaction (qPCR) and validated the key genes.

Results

Seven key genes (FASN, SCD, CD68, HMGCS1, SQLE, CXCL10, IGF1) with different expression trends in GSE135251 and GSE83452 were obtained with the top 30 hub genes selected by PPI. The expression of seven key genes in mice after SG was validated by qPCR. Combined with the qPCR results from NASH mice, the four genes FASN, SCD, HMGCS1, and CXCL10 are consistent with the biological analysis. The GSEA results showed that the 'cholesterol homeostasis' pathway was enriched in the FASN, SCD, HMGCS1, and SQLE high-expression groups. The high-expression groups of CD68 and CXCL10 were extremely enriched in inflammation-related pathways. The construction of the ceRNA network obtained microRNAs and ceRNAs that can regulate seven key genes expression.

Conclusion

In summary, this study contributes to our understanding of the mechanisms by which bariatric surgery improves NASH, and to the development of potential biomarkers for the treatment of NASH.

The transcriptome of the parapoxvirus Orf virus reveals novel promoters for heterologous gene expression by poxvirus vectors

Orf virus (ORFV) has been used as a vaccine delivery vector for multiple animal species. Several strategies are being used to improve the immunogenicity and efficacy of ORFV vectors, including the use of poxviral promoter(s) with strong early and late activity capable of driving the expression of the heterologous genes for a prolonged time and eliciting a potent immune response. Here, we used RNA-sequencing (RNA-Seq) approach to analyze the transcriptome of ORFV during infection in primary ovine cells. Based on the transcriptional profile of individual ORFV genes, we identified ORFV promoters with strong early and late activity and have shown that they can be used to express heterologous genes in ORFV vectors. Our results show that the intergenic regulatory sequence containing core promoter sequences present upstream of ORF112 (p112) and ORF116 (p116) lead to markedly higher transgene expression than conventional poxviral promoters. Thus, these promoters are valuable alternatives to express transgenes in poxviral vectors.

Exploration of the core gene signatures and mechanisms between NAFLD and sarcopenia through transcriptomic level

INTRODUCTION

The increased prevalence of non-alcoholic fatty liver disease (NAFLD) and sarcopenia among the elderly are facing a significant challenge to the world's health systems. Our study aims to identify the coexpressed genes in NAFLD and sarcopenia patients.

METHODS

We downloaded the transcriptome data of NAFLD tissue from patients, as well as muscle tissues from sarcopenia patients, from the GEO database in order to investigate the shared transcriptional regulation mechanisms between these two diseases. Then, focusing on the genes that were frequently expressed in these diseases, together with GSVA and WGCNA, we utilized a range of analysis methods to identify the main co-expressed genes in both diseases by taking intersections. We investigated these changes after learning that they mostly affected lipid metabolism and oxidative stress injury pathways.

RESULTS

By analyzing these genes and their interactions with transcription factors and proteins, we were able to identify 8 genes that share common patterns. From these 8 genes, we were possible to forecast potential future medicines. Our research raises the possibility of NAFLD and sarcopenia transcriptome regulatory pathways in aging populations.

DISCUSSION

In conclusion, a complete transcription pattern mapping was carried out in order to identify the core genes, underlying biological mechanisms, and possible therapeutic targets that regulate aging in NAFLD and sarcopenia patients. It provides novel insights and proof in favor of decreasing the increased prevalence of sarcopenia in the elderly caused by NAFLD.

Poxvirus-encoded decapping enzymes promote selective translation of viral mRNAs

Cellular decapping enzymes negatively regulate gene expression by removing the methylguanosine cap at the 5’ end of eukaryotic mRNA, rendering mRNA susceptible to degradation and repressing mRNA translation. Vaccinia virus (VACV), the prototype poxvirus, encodes two decapping enzymes, D9 and D10, that induce the degradation of both cellular and viral mRNAs. Using a genome-wide survey of translation efficiency, we analyzed vaccinia virus mRNAs in cells infected with wild type VACV and mutant VACVs with inactivated decapping enzymes. We found that VACV decapping enzymes are required for selective translation of viral post-replicative mRNAs (transcribed after viral DNA replication) independent of PKR- and RNase L-mediated translation repression. Further molecular characterization demonstrated that VACV decapping enzymes are necessary for efficient translation of mRNA with a 5'-poly(A) leader, which are present in all viral post-replicative mRNAs. Inactivation of D10 alone in VACV significantly impairs poly(A)-leader-mediated translation. Remarkably, D10 stimulates mRNA translation in the absence of VACV infection with a preference for RNA containing a 5’-poly(A) leader. We further revealed that VACV decapping enzymes are needed for 5’-poly(A) leader-mediated cap-independent translation enhancement during infection. Our findings identified a mechanism by which VACV mRNAs are selectively translated through subverting viral decapping enzymes to stimulate 5’-poly(A) leader-mediated translation.

Decapping enzymes are encoded in eukaryotic cells and some viruses. Previous studies indicated that decapping enzymes are negative gene expression regulators by accelerating mRNA degradation and repressing translation. Surprisingly however, in this study we found that vaccinia virus (VACV) encoded-decapping enzymes, D9 and D10, are required to promote selective synthesis of viral proteins, although they are known to promote both cellular and viral mRNA degradation. We further showed that the unusual 5'-UTR of VACV mRNA, the 5'-poly(A) leader, confers an advantage to mRNA translation promoted by the decapping enzymes during vaccinia virus infection. Moreover, D9 and D10 are necessary for stimulating poly(A)-leader-mediated cap-independent translation enhancement during VACV infection. In the absence of VACV infection, D10 alone stimulates mRNA translation in a decapping activity-dependent manner, with a preference for mRNA that contains a poly(A) leader. The stimulation of mRNA translation by D10 is unique among decapping enzymes. Therefore, we identified a new mechanism to selectively synthesize VACV proteins through a coordination of viral mRNA 5’-UTR and virus-encoded decapping enzymes.