A Two-Color Haploid Genetic Screen Identifies Novel Host Factors Involved in HIV-1 Latency

Michael Röling, Mahsa Mollapour Sisakht, Enrico Ne, Panagiotis Moulos, Raquel Crespo, Mateusz Stoszko, Elisa de Crignis, Helen Bodmer, Tsung Wai Kan, Maryam Akbarzadeh, Vaggelis Harokopos, Pantelis Hatzis, Robert Jan Palstra*, Tokameh Mahmoudi

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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To identify novel host factors as putative targets to reverse HIV-1 latency, we performed an insertional mutagenesis genetic screen in a latent HIV-1 infected pseudohaploid KBM7 cell line (Hap-Lat). Following mutagenesis, insertions were mapped to the genome, and bioinformatic analysis resulted in the identification of 69 candidate host genes involved in maintaining HIV-1 latency. A select set of candidate genes was functionally validated using short hairpin RNA (shRNA)-mediated depletion in latent HIV-1 infected J-Lat A2 and 11.1 T cell lines. We confirmed ADK, CHD9, CMSS1, EVI2B, EXOSC8, FAM19A, GRIK5, IRF2BP2, NF1, and USP15 as novel host factors involved in the maintenance of HIV-1 latency. Chromatin immunoprecipitation assays indicated that CHD9, a chromodomain helicase DNA-binding protein, maintains HIV-1 latency via direct association with the HIV-1 59 long terminal repeat (LTR), and its depletion results in increased histone acetylation at the HIV-1 promoter, concomitant with HIV-1 latency reversal. FDA-approved inhibitors 5-iodotubercidin, trametinib, and topiramate, targeting ADK, NF1, and GRIK5, respectively, were characterized for their latency reversal potential. While 5-iodotubercidin exhibited significant cytotoxicity in both J-Lat and primary CD41 T cells, trametinib reversed latency in J-Lat cells but not in latent HIV-1 infected primary CD41 T cells. Importantly, topiramate reversed latency in cell line models, in latently infected primary CD41 T cells, and crucially in CD41 T cells from three people living with HIV-1 (PLWH) under suppressive antiretroviral therapy, without inducing T cell activation or significant toxicity. Thus, using an adaptation of a haploid forward genetic screen, we identified novel and druggable host factors contributing to HIV-1 latency. IMPORTANCE A reservoir of latent HIV-1 infected cells persists in the presence of combination antiretroviral therapy (cART), representing a major obstacle for viral eradication. Reactivation of the latent HIV-1 provirus is part of curative strategies which aim to promote clearance of the infected cells. Using a two-color haploid screen, we identified 69 candidate genes as latency-maintaining host factors and functionally validated a subset of 10 of those in additional T-cell-based cell line models of HIV-1 latency. We further demonstrated that CHD9 is associated with HIV-1’s promoter, the 59 LTR, while this association is lost upon reactivation. Additionally, we characterized the latency reversal potential of FDA compounds targeting ADK, NF1, and GRIK5 and identify the GRIK5 inhibitor topiramate as a viable latency reversal agent with clinical potential.

Original languageEnglish
Article numbere02980-21
Issue number6
Publication statusPublished - 7 Dec 2021

Bibliographical note

Funding Information:
T.M. received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP/2007-2013)/ERC STG 337116 Trxn-PURGE, Dutch AIDS Fonds grant 2014021, Erasmus MC mRACE research grant, Health Holland/Aidsfonds grant LSHM19100-SGF ICD-ICK4HIVCure, and ZonMW/Aidsfonds grant 446002508. R.-J.P. received funding from Dutch AIDS Fonds grant 2016014. R.C. received funding from Dutch Aidsfonds Small Grant 2020. We thank Thijn Brummelkamp for providing materials and expertise. We declare no conflict of interest.

Publisher Copyright:
Copyright © 2021 Röling et al.


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