Crosstalk in competing endogenous RNA networks reveals new circular RNAs involved in the pathogenesis of early HIV infection

Abstract

Background: The events in early HIV infection (EHI) are important determinants of disease severity and progression rate to AIDS, but the mechanisms of pathogenesis in EHI have not been fully understood. Circular RNAs (circRNAs) have been verified as "microRNA sponges" that regulate gene expression through competing endogenous RNA (ceRNA) networks, but circRNA expression profiles and their contribution to EHI pathogenesis are still unclear.

Methods: Two different libraries were constructed with RNA from human peripheral blood mononuclear cells from 3 HARRT-naive EHI patients and 3 healthy controls (HCs). The complete transcriptomes were sequenced with RNA sequencing (RNA-Seq) and miRNA sequencing (miRNA-Seq). The differentially expressed (DE) RNAs were validated with RT-qPCR. The circRNA profile and circRNA-associated-ceRNA network in EHI were analyzed with the integrated data of RNA-Seq and miRNA-Seq. Gene ontology (GO) analysis was used to annotate the circRNAs involved in the circRNA-associated-ceRNA networks.

Results: A total of 1365 circRNAs, 30 miRNAs, and 2049 mRNAs were differentially expressed between HARRT-naive EHI patients and HCs. A ceRNA network was constructed with 516 DE circRNAs and 903 DE mRNAs that shared miR response elements with 21 DE miRNAs. GO analysis demonstrated the multiple roles of the circRNAs enriched in EHI with circRNA-associated-ceRNA networks, such as immune response, inflammatory response and defense responses to virus, 67 circRNAs were revealed to be potentially involved in HIV-1 replication through regulating the expression of CCNK, CDKN1A and IL-15.

Conclusions: This study, for the first time, revealed a large circRNA profile and complex pathogenesis roles of circRNAs in EHI. A group of enriched circRNAs and associated circRNA-associated-ceRNA networks might contribute to HIV replication regulation and provide novel potential targets for both the pathogenesis of EHI and antiviral therapy.

Keywords: HIV-1; Viral replication; ceRNA; circRNA.

Fig. 1

The Profiling and Characteristics of mRNAs and circRNAs in EHI. a Circos plot showing the mRNAs and circRNAs on human chromosomes. From the outside in, the first layer of the Circos plot is a chromosome map of the human genome; black and white bars are chromosome cytobands, and red bars represent centromeres. The second layer shows the 20 most significantly up-regulated and 20 most significantly down-regulated mRNAs. All DE mRNAs and circRNAs are marked in red and blue in the third layer. The fourth and fifth layers show the fold change of all DE mRNAs and circRNAs. b The counts of DE circRNAs based on their categories. c The distribution of the DE circRNAs based on the length of nucleic acids

Fig. 2

RNA-Seq and miRNA-Seq validated by RT-qPCR. a Validation of four DE circRNAs. b Validation of four DE mRNAs. c Validation of four DE miRNAs

Fig. 3

circRNA-associated-ceRNA networks in EHI. The ceRNA networks were based on circRNA-miRNA and miRNA-mRNA interactions. Shape corresponds to molecule type (circRNAs as squares, mRNAs as triangles, miRNAs as circles), colour corresponds to dysregulation (red as up-regulated, green as down-regulated). a circRNA (up in EHI)-miRNA (down in EHI)-mRNA (up in EHI). b circRNA (down in EHI)-miRNA (up in EHI)-mRNA (down in EHI)

Fig. 4

Gene ontology classifcations of the predicted targeting mRNAs of the circRNA-associated-ceRNA networks. The 10 most significantly enriched GO terms of the predicted targeting mRNAs of the circRNA-associated-ceRNA networks. P < 0.05 was used as the threshold for GO analysis