Integrative bulk and single-cell transcriptome profiling analysis reveals IFI27 as a novel interferon-stimulated gene in dengue

J Med Virol. 2023 Apr;95(4):e28706. doi: 10.1002/jmv.28706.

Abstract

The dengue virus (DENV) is a public health threat to humans. Increased vascular permeability, coagulopathy, and hemorrhagic diathesis are the pathophysiological hallmarks of severe dengue. However, although the interferon (IFN)-mediated innate immune response forms the backbone of cell-autonomous defense against pathogens, the exact IFN-stimulated genes (ISGs) involved in DENV infection remain to be determined. The present study collected transcriptomic data sets of peripheral blood mononuclear cells from DENV patients and healthy volunteers from public data repositories. Also, lentivirus and plasmid were used to overexpress and knockdown IFI27. Initially, differentially expressed genes were filtered, and gene set enrichment analysis (GSEA) was performed to assess related pathways. Subsequently, the least absolute shrinkage and selection operator regression and support vector machine-recursive feature elimination algorithms were used to screen crucial genes. The receiver operating characteristic curve analysis was then employed to test diagnostic efficacy. Next, CIBERSORT was used to analyze immune infiltration in 22 immune cell subsets. Additionally, to dissect high-resolution molecular phenotypes directly from individual cells and the cellular interactions between immune cell subpopulations, single-cell RNA sequencing (scRNA-seq) was performed. We found that the IFN-stimulated gene IFN-α-inducible protein 27 (IFI27) was highly expressed in dengue patients by leveraging bioinformatics analysis and machine learning algorithms. This finding was further validated in two independent published databases. In addition, IFI27 overexpression positively regulated DENV-2 infection, whereas IFI27 knockdown has the opposite effect. Consistently, scRNA-seq analysis supported this conclusion, along with further dissection of increased IFI27 expression mainly concentrated in monocytes and plasmacytoid dendritic cells. We also demonstrated that IFI27 inhibited dengue infection. Moreover, IFI27 was positively correlated with monocytes, M1 macrophages, activated dendritic cells, plasma cells, and resting mast cells and negatively correlated with CD8 T cells, γδ T cells, and naïve B cells. GSEA revealed that IFI27 was primarily enriched in the innate immune response, regulation of the viral life cycle, and JAK-STAT signaling pathway. Notably, the interactions between LGALS9 and its receptor CD47 were markedly increased in dengue patients compared to healthy controls, based on cell-cell communication analysis. Our findings reveal, for the first time, that IFI27 is a key ISG in DENV infection. Given that the innate immune system plays a significant role in antagonizing DENV invasion, while ISGs are the ultimate antiviral effectors, IFI27 may serve as a potential diagnostic marker and therapeutic target in dengue, although further validation is warranted.

Keywords: IFI27; dengue virus; interferon-stimulated genes; transcriptome profiling analysis.

MeSH terms

  • Dengue Virus*
  • Dengue*
  • Gene Expression Profiling
  • Humans
  • Interferons / genetics
  • Leukocytes, Mononuclear / metabolism
  • Membrane Proteins / genetics

Substances

  • Interferons
  • IFI27 protein, human
  • Membrane Proteins