Gene-expression reversal of lncRNAs and associated mRNAs expression in active vs latent HIV infection

Abstract

Interplay between lncRNAs and mRNAs is rapidly emerging as a key epigenetic mechanism in controlling various cell functions. HIV can actively infect and/or can persist latently for years by manipulating host epigenetics; however, its molecular essence remains undiscovered in entirety. Here for the first time, we delineate the influence of HIV on global lncRNAs expression in monocytic cells lines. Our analysis revealed the expression modulation of nearly 1060 such lncRNAs which are associated with differentially expressed mRNAs in active and latent infection. This suggests a greater role of lncRNAs in regulating transcriptional and post-transcriptional gene expression during HIV infection. The differentially expressed mRNAs were involved in several different biological pathways where immunological networks were most enriched. Importantly, we discovered that HIV induces expression reversal of more than 150 lncRNAs between its active and latent infection. Also, hundreds of unique lncRNAs were identified in both infection conditions. The pathology specific "gene-expression reversal" and "on-and-off" switching of lncRNAs and associated mRNAs may lead to establish the relationship between active and HIV infection.

Figure 1

(A,B) Volcano plots of the two samples t-tests of lncRNAs expression fold change for active (A) and latent (B) HIV infections in macrophages in compare to uninfected control: It shows differentially expressed lncRNAs with statistical significance that passed Volcano Plot filtering (Fold Change >= 2.0 and P-value <= 0.05). The vertical yellow lines correspond to 2.0-fold up and down and the horizontal yellow line represents a P-value up to 0.05. So the red cubes in the plot represent the differentially expressed lncRNAs with statistical significance. (C,D) Venn diagram showing no of common downregulated (C) and upregulated (D) lncRNAs in active vs latent infection.

Figure 2

(A,B) Volcano plots of the two samples t-tests of mRNAs expression fold change for active (A) and latent (B) HIV infections in macrophages in compare to uninfected control: It shows differentially expressed lncRNAs with statistical significance that passed Volcano Plot filtering (Fold Change >= 2.0 and P-value <= 0.05). The vertical yellow lines correspond to 2.0-fold up and down and the horizontal yellow line represents a P-value up to 0.05. So the red cubes in the plot represent the differentially expressed mRNAs with statistical significance. (C,D) Venn diagram showing no of common downregulated (C) and upregulated (D) lncRNAs in active vs latent infection.

Figure 3. Pathway analyses of differentially expressed mRNAs were based on latest KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg) database.

Most enriched pathway of upregulated (A) and downregulated (B) mRNAs in active infection condition was dominated by immunological networks. Pathway corresponding to upregulated mRNAs in latent infection (C) also includes many immunological networks and pathway corresponding to downregulated mRNAs in latent infection (D) showed enrichment of replication associated pathways. These differentially expressed mRNAs are associated with 155 biological pathways (Supplementary figure 2), where nodes with red color denotes significant association.

Figure 4

Gene expression reversal: Venn analysis showing number of those lncRNAs (A,B) and mRNAs (C,D) which were both downregulated and upregulated in active vs latent infection and vice versa. It was found that 94 lncRNAs downregulated in active infection were also upregulated in latent infection (A) and 60 lncRNAs upregulated in active infection were also downregulated in latent infection (B). Similarly, 63 mRNAs downregulated in active infection were also upregulated in latent infection and 116 mRNAs upregulated in active infection were also downregulated in latent infection. Details of these lncRNAs and mRNAs are given in supplementary data 1 and 2, respectively.

Figure 5

Interplay between differentially expressed lncRNAs and their associated mRNAs: A1: Pairs of lncRNAs downregulated in active infection and mRNAs downregulated and upregulated in active infection; A2: Pairs of lncRNAs downregulated in active infection and mRNAs upregulated in latent infection; A3: Pairs of lncRNAs downregulated in active infection and mRNAs downregulated in latent infection.

Figure 6

A1: Pairs of lncRNAs upregulated in active infection and mRNAs downregulated and upregulated in active infection; A2: Pairs of lncRNAs upregulated in active infection and mRNAs downregulated in latent infection. A3: Pair of lncRNAs upregulated in active infection and mRNAs upregulated in latent infection.

Figure 7

A1: Pairs of lncRNAs downregulated in latent infection and mRNAs downregulated in active infection; A2: Pairs of lncRNAs downregulated in latent infection and mRNAs upregulated in active infection; A3: 1–4: Pairs of lncRNAs downregulated in latent infection and mRNAs downregulated in latent infection; A4: Pairs of lncRNAs downregulated in latent infection and mRNAs upregulated in latent infection.

Figure 8

A1: Pairs of lncRNAs upregulated in latent infection and mRNAs downregulated in active infection; A2: Pairs of lncRNAs upregulated in latent infection and mRNAs upregulated in active infection; A3: 1–2: Pairs of lncRNAs upregulated in latent infection and mRNAs downregulated in latent infection; A4: 1–5: Pairs of lncRNAs upregulated in latent infection and mRNAs upregulated in latent infection.