Using iPSC variation to define HIV-1 regulatory networks

The pathogenic retrovirus human immunodeficiency virus type 1 (HIV-1) has caused the worldwide acquired immunodeficiency syndrome (AIDS) pandemic. It is estimated that ~37 million people currently live with HIV-1, with ~1.8 million new cases of infection and ~1 million AIDS deaths occurring every year (2017 figures, source: http://www.unaids.org/en/ resources/fact-sheet). AIDS is currently considered a treatable disease as a battery of effective anti-viral drugs that target essential viral proteins have been developed. Critically, there is no vaccine to prevent new infections and, once a person is infected, there is no cure (treatment leading to viral eradication). Moreover, with the passage of time, drug-resistant strains are becoming an increasingly significant problem in the clinic. It is therefore necessary to develop new anti-HIV-1 therapeutic approaches. Despite many years of intense investigation, the understanding of the complexity of cell-encoded factors and pathways that regulate HIV-1 replication (both positively and negatively) remains significantly incomplete. The identification and definition of new viral regulatory factors will suggest novel targets for future therapeutic intervention which, in addition to helping control viral growth and HIV-1-associated disease, may also impact research programmes seeking HIV-1 cure and/or vaccination. The feasibility of therapeutically targeting a cellular protein to inhibit HIV-1 is demonstrated by Maraviroc, a small molecule inhibitor that binds the HIV-1 entry receptor CCR5 to block infection. In this programme, we will develop and exploit an innovative inter-disciplinary strategy to discover novel human cell factors and pathways that regulate HIV-1 replication. We will use the deeply characterised HipSci library (www.hipsci.org) of induced pluripotent stem cells (iPSCs), for which detailed genomic, transcriptomic and proteomic information already exists, and correlate variations in HIV-1 infection phenotypes with key molecular signatures that are intrinsic to each iPSC line. To complement this approach, we will also reprogramme blood samples from patients at high risk of HIV-1 infection, and with known disease outcomes (the Multicenter AIDS Cohort Study - MACS; http://aidscohortstudy.org/), into iPSCs. Co-ordinated characterisation of these lines will add a further dimension to our study by also enabling molecular signatures and infection data to be correlated with clinical outcomes. In depth bioinformatic interrogation of these orthogonal datasets will suggest candidate cell-encoded HIV-1 regulatory factors, which will then be tested for function using established laboratory models of HIV-1 infection. In sum, our experimental pipeline comprises: (i) screening iPSC cell lines from two sources to find extreme HIV-1 infection phenotypes, (ii) using bioinformatic tools and whole cell molecular signatures to discover new regulatory factors and (iii) validating our findings in cell culture systems and characterising the mechanisms of action of novel HIV-1 regulators at the molecular level. Our goal is to uncover novel human proteins and pathways controlling HIV-1 replication, and to inform initiatives aiming to devise fresh therapeutic strategies for overcoming HIV-1 infection. Finally, and importantly, we are committed to sharing the iPSC lines that we will derive from HIV-1 exposed individuals: these can serve as a unique resource to study HIV-1 biology since iPSCs are virtually inexhaustible and have the potential to be differentiated into any human cell type, including the natural cellular targets of HIV-1.