Influenza A Virus Infection Reactivates Human Endogenous Retroviruses Associated with Modulation of Antiviral Immunity

Abstract

Human endogenous retrovirus (HERVs), normally silenced by methylation or mutations, can be reactivated by multiple environmental factors, including infections with exogenous viruses. In this work, we investigated the transcriptional activity of HERVs in human A549 cells infected by two wild-type (PR8M, SC35M) and one mutated (SC35MΔNS1) strains of Influenza A virus (IAVs). We found that the majority of differentially expressed HERVs (DEHERVS) and genes (DEGs) were up-regulated in the infected cells, with the most significantly enriched biological processes associated with the genes differentially expressed exclusively in SC35MΔNS1 being linked to the immune system. Most DEHERVs in PR8M and SC35M are mammalian apparent LTR retrotransposons, while in SC35MΔNS1, more HERV loci from the HERVW9 group were differentially expressed. Furthermore, up-regulated pairs of HERVs and genes in close chromosomal proximity to each other tended to be associated with immune responses, which implies that specific HERV groups might have the potential to trigger specific gene networks and influence host immunological pathways.

Keywords: expression analysis; functional annotation; gene regulation; genome analysis; immune response; virus-host interactions.

Figure A1

Principal component analysis (PCA) plots of the gene matrix (A,B) and HERV loci matrix (C,D) of second technical replicates. (A,C) PCA plots with all samples included. (B,D) PCA plots with the control sample 1 removed.

Figure A2

Principal component analysis (PCA) plots of the gene matrix (A,B) and HERV loci matrix (C,D) of third technical replicates. (A,C) PCA plots with all samples included. (B,D) PCA plots with the control sample 1 removed.

Figure A3

Top 10 most significantly enriched biological process GO terms associated with the genes exclusively differentially expressed in (A) PR8M infected cells, (B) SC35M infected cells, (C) SC35MΔNS1 infected cells. The terms are ranked according to the p-value.

Figure 1

Principal component analysis (PCA) plots of the gene matrix (A,B) and HERV loci matrix (C,D). (A,C) PCA plots with all samples included. (B,D) PCA plots with the control sample 1 removed. Only one technical replicate is shown in all plots. See Appendix A (Figure A1 and Figure A2) for the gene matrices of the other two technical replicates.

Figure 2

Volcano plots illustrating the differential expression of genes and HERV loci in all three cell lines compared to the mock control. (A,B) Differential expression genes and HERV loci in PR8M. (C,D) Differential expression of genes and HERV loci in SC35M. (E,F) Differential expression genes and HERV loci in SC35MΔNS1. DESeq2 converts very small s-values to 0, which leads to 580 genes in PR8M, 343 in genes in SC35M, and 75 genes in SC35MΔNS1 all having the same -Log10 (s-value) and appearing at the top.

Figure 3

(A–C) Percentage of DEHERVs in each HERV superfamily in the cells infected by PR8M (A), SC35M (B), and SC35MΔNS1 (C). (D,E) Venn diagrams showing the overlap between the differentially expressed genes (D) and HERV loci (E) in the three infected cells (SC35M, SC35MΔNS1, and PR8M) relative to mock control.

Figure 4

(A) Distribution of distances between DEGs and DEHERVs within DEHERV-G pairs. Zero distances correspond to overlapping DEGs and DEHERVs. (B,C) Overlaps between DEHERV-G pairs (B) and genes involved in DEHERV-G pairs (C) among the three IAV infected conditions vs. mock.

Figure 5

Top 10 most significantly enriched biological process GO terms associated with the protein-coding genes of the G+H+ DEHERV-G pairs. Terms are ranked according to the p-value. (A) PR8M infected cells, (B) SC35M infected cells, and (C) SC35MΔNS1 infected cells. Go terms related to immune or inflammation processes are shown in blue color.

Figure 6

Top 10 most significantly enriched KEGG pathways associated with the protein-coding genes of the G+H+ DEHERV-G pairs. Terms are ranked according to the p-value and bars filled in blue means their p-value lower than 0.05 while Benjamini–Hochberg corrected p-values larger than 0.05. (A) PR8M infected cells, (B) SC35M infected cells, (C) SC35MΔNS1 infected cells.