Role of host microRNAs in Kaposi’s sarcoma herpesvirus tumorigenesis and lytic reactivation

Abstract

Kaposi’s sarcoma herpesvirus (KSHV) is the etiological agent of Kaposi’s sarcoma (KS), a leading cause of morbidity and mortality in sub-Saharan Africa. KSHV-encoded microRNAs (miRNAs) are known to play a role in viral oncogenesis; however, the role of host miRNAs in KS tumorigenesis remains largely unknown. Here, high-throughput small-RNA sequencing of the cellular transcriptome in a KS xenograft model revealed miR-127 as one of the most significantly down-regulated miRNAs, which we validated in KS patient tissues. We show that restoration of miR-127 expression suppresses KSHV-driven cellular transformation and proliferation, and induces G1 cell cycle arrest by directly targeting the oncogene SKP2. This miR-127-induced G1 arrest is rescued by disrupting the miR-127 target site in SKP2 messenger RNA (mRNA) using gene editing. Mechanistically, miR-127-mediated SKP2 repression elevates cyclin-dependent kinase (CDK) inhibitor p21Cip1 and down-regulates cyclin E, cyclin A, and CDK2, leading to activation of the retinoblastoma (RB) tumor suppressor pathway and suppression of the transcriptional activities of E2F and Myc. Furthermore, miR-127 reconstitution in a KS xenograft mouse model suppresses KSHV-positive tumor growth by targeting SKP2 in vivo. These findings identify a previously unrecognized tumor suppressor function for miR-127 in KS and demonstrate that the miR-127/SKP2 axis is a viable therapeutic strategy for KS. KSHV exhibits two distinct life cycles: latency and lytic infection. The ability of KSHV to reactivate from latency and re-enter lytic infection is critical for viral persistence and consequently KS development. Leveraging high-throughput miRNA-mRNA transcriptomics and phenotypic analyses we identify cellular miR-31 as a suppressor of KSHV lytic reactivation from latency. We show that ectopic expression of miR-31 impairs lytic gene expression and subsequent virion production during KSHV reactivation. Mechanistic studies demonstrate that miR-31 restricts KSHV lytic reactivation by directly repressing the RNA-binding protein KHDRBS3, a key regulator of alternative splicing. Moreover, miR-31 down-regulates the main KSHV transcription factor, replication and transcription activator (RTA), required for the latent-to-lytic switch. These results reveal a previously unappreciated role of miR-31 in restricting KSHV lytic reactivation and suggest that modulating the miR-31/KHDRBS3 axis may lead to novel strategies to target the viral life cycle for the treatment of KSHV-associated cancer.