Journal Article

Opposing roles of CLK SR kinases in controlling HIV-1 gene expression and latency

Fernet-Brochu, Raphaële, Guvenc, Furkan, Cochrane, Alan, Bell, Brendan, Been, Terek, Ocando, Alonso Villasmil, Maldonado, Rebecca Kaddis, Branch, Donald, Boligan, Kayluz Frias, Rahman, Fariha, Chabot, Benoit, Parent, Leslie J., Balachandran, Ahalya, Poirier, Mikaël, Gray-Owen, Scott D., Clayton, Kiera, Shkreta, Lulzim, Dahal, Subha

2022

Overview

Background The generation of over 69 spliced HIV-1 mRNAs from one primary transcript by alternative RNA splicing emphasizes the central role that RNA processing plays in HIV-1 replication. Control is mediated in part through the action of host SR proteins whose activity is regulated by multiple SR kinases (CLK1-4, SRPKs). Methods Both shRNA depletion and small molecule inhibitors of host SR kinases were used in T cell lines and primary cells to evaluate the role of these factors in the regulation of HIV-1 gene expression. Effects on virus expression were assessed using western blotting, RT-qPCR, and immunofluorescence. Results The studies demonstrate that SR kinases play distinct roles; depletion of CLK1 enhanced HIV-1 gene expression, reduction of CLK2 or SRPK1 suppressed it, whereas CLK3 depletion had a modest impact. The opposing effects of CLK1 vs. CLK2 depletion were due to action at distinct steps; reduction of CLK1 increased HIV-1 promoter activity while depletion of CLK2 affected steps after transcript initiation. Reduced CLK1 expression also enhanced the response to several latency reversing agents, in part, by increasing the frequency of responding cells, consistent with a role in regulating provirus latency. To determine whether small molecule modulation of SR kinase function could be used to control HIV-1 replication, we screened a GSK library of protein kinase inhibitors (PKIS) and identified several pyrazolo[1,5-b] pyridazine derivatives that suppress HIV-1 gene expression/replication with an EC 50 ~ 50 nM. The compounds suppressed HIV-1 protein and viral RNA accumulation with minimal impact on cell viability, inhibiting CLK1 and CLK2 but not CLK3 function, thereby selectively altering the abundance of individual CLK and SR proteins in cells. Conclusions These findings demonstrate the unique roles played by individual SR kinases in regulating HIV-1 gene expression, validating the targeting of these functions to either enhance latency reversal, essential for “Kick-and-Kill” strategies, or to silence HIV protein expression for “Block-and-Lock” strategies. Plain Language Summary Identifying cellular factors that regulate HIV-1 RNA processing provides important insights into novel strategies to control this infection. Different members of the SR kinase family have distinct roles in regulating virus expression because they affect distinct steps of transcription/RNA processing. We identify inhibitors of these kinases that suppress HIV-1 gene expression and replication in multiple assay systems at nanomolar concentrations with limited or no cytotoxicity. Our results highlight the therapeutic potential of targeting the post-integration stage of the HIV-1 lifecycle to selectively enhance or reverse provirus latency. A greater understanding of the molecular mechanisms underlying the effects observed will facilitate the development of more targeted approaches to modulate HIV-1 latency on the path toward a “functional” cure for this infection.

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Alternative Splicing / Antibodies / Biomedical and Life Sciences / Biomedicine / Cancer Research / Control / Gene Expression / Genes / Genetic research / HIV (Viruses) / HIV-1 / HIV-1 - physiology / Infectious Diseases / Latency / Messenger RNA / Protein Kinase Inhibitors - pharmacology / Protein kinases / Protein Structure / RNA processing / RNA, Viral - genetics / SR kinases / T cells / Vaccine / Viral proteins / Virology / Virus Latency