Identification of Cellular Genes Targeted by KSHV-Encoded MicroRNAs

Abstract

MicroRNAs (miRNAs) are 19 to 23 nucleotide–long RNAs that post-transcriptionally regulate gene expression. Human cells express several hundred miRNAs which regulate important biological pathways such as development, proliferation, and apoptosis. Recently, 12 miRNA genes have been identified within the genome of Kaposi sarcoma–associated herpesvirus; however, their functions are still unknown. To identify host cellular genes that may be targeted by these novel viral regulators, we performed gene expression profiling in cells stably expressing KSHV-encoded miRNAs. Data analysis revealed a set of 81 genes whose expression was significantly changed in the presence of miRNAs. While the majority of changes were below 2-fold, eight genes were down-regulated between 4- and 20-fold. We confirmed miRNA-dependent regulation for three of these genes and found that protein levels of thrombospondin 1 (THBS1) were decreased >10-fold. THBS1 has previously been reported to be down-regulated in Kaposi sarcoma lesions and has known activity as a strong tumor suppressor and anti-angiogenic factor, exerting its anti-angiogenic effect in part by activating the latent form of TGF-β. We show that reduced THBS1 expression in the presence of viral miRNAs translates into decreased TGF-β activity. These data suggest that KSHV-encoded miRNAs may contribute directly to pathogenesis by down-regulation of THBS1, a major regulator of cell adhesion, migration, and angiogenesis.

Human herpesvirus miRNAs statistically preferentially target host genes involved in cell signaling and adhesion/junction pathways

“…As shown in Supplementary information, Table S2, similar patterns were observed -cell signaling pathways and cell adhesion/junction pathways were statistically significantly preferentially targeted. Moreover, similar statistical enrichment of cell signaling and adhesion/junction pathways was also observed in the downregulated genes identified by a recently published microarray-based viral miRNA target identification experiment [7] (Supplementary information, Table S3). …”

“…The components of junctional complexes and other adhesion proteins could also be used by viruses as receptors for entering or exiting the host cell [12]. Recently, KSHV-encoded miRNAs were reported to suppress a major regulator of cell adhesion and migration [7]. Two receptors in the adherens junction pathways, Nectin and ErbB1/2, were reported to be downregulated in infected cells, but the exact mechanisms remained unclear [13,14].…”

MicroRNAs in the regulation of TLR and RIG-I pathways

“…miR-K12-11 is the most characterized miRNA and targets cellular proteins, derived from KSHV. 120 It has 100% seed sequence homology with the human miR-155, which is essential for B-cell development, while its overexpression leads to B-cell lymphoma. 121,122 Recently, miR-K12-11, the oncogenic miR-155 equivalent, has been shown to contribute to malignant viral transformation by downregulating tumor suppressor and anti-angiogenic factor thrombospondin 1 112 and a transcriptional repressor BACH-1.…”

“…121,122 Recently, miR-K12-11, the oncogenic miR-155 equivalent, has been shown to contribute to malignant viral transformation by downregulating tumor suppressor and anti-angiogenic factor thrombospondin 1 112 and a transcriptional repressor BACH-1. 120,123,124 Cellular miRNAs are highly induced or regulated by viral infection, and can affect both the viral replication and host anti-viral immunity. Repression of Dicer increases the replication of HIV-1, VSV and influenza A virus, [125][126][127] suggesting that cellular miRNAs play a role in the restriction of viral biology.…”

Viral epigenomes in human tumorigenesis

“…Finally, miRNAs encoded by KSHV are involved in epigenetic regulation and expression of oncogenes (Cai et al, 2006;Flanagan, 2007;Samols et al, 2007), hence their study should help us to better understand the molecular mechanisms of viral tumorigenesis.…”