Global mapping of the macrophage-HIV-1 transcriptome reveals that productive infection induces remodeling of the host cell DNA and chromatin

It has been proposed that macrophages could serve as long-lived compartments for HIV-1 infection under in vivo situations because these cells are resistant to the virus-mediated cytopathic effect, produce progeny virus over extended periods of time and are localized in tissues that are often less accessible by treatment. Comprehensive experimental studies are thus needed to characterize the HIV-1-induced modulation of host genes in these myeloid lineage cells. To shed light on this important issue, we performed comparative analyses of mRNA expression levels of host genes in uninfected bystander and HIV-1-infected human macrophages using an infectious reporter virus construct coupled with a large-scale RNA sequencing approach. We observed a rapid differential expression of several host factors in the productively infected macrophage population including genes regulating DNA replication factors and chromatin remodeling. A siRNA-mediated screening study to functionally identify host determinants involved in HIV-1 biology has provided new information on the virus molecular regulation in macrophages. Overall design: Human monocytes from healthy donors were differentiated in MØ by adherence for 3 days in the presence of RPMI-1640 culture medium supplemented with M-CSF (25 ng/mL) and 10% human AB serum. Cells were maintained in culture medium in absence of M-CSF for an additional 3 days, treated with Accutase™ (Stem Cell Technologies) for 60 to 90 min, and detached with a soft cell scraper (Sarstedt). Cells were plated at 2.5 x 10exp5 cells/mL for 24 (cell-culture coated dishes) or 72 h (Ultra-Low attachment dishes). MØ were infected with replication-competent NL/Bal-HSA (see A. Deshiere et al., Scientific Reports 2017) with multiplicities of infection (MOI) ranging from 0.004 to 2.5. HSApos and HSAneg MØ were isolated using biotinylated anti-HSA (clone M1/69; eBiosciences) and anti-Biotin Magnetic Beads (Miltenyi) in a MS separation column (Miltenyi). Purified MØ populations (HSAneg and HSApos) were resuspended and frozen in QIAzol lysis buffer. Total RNA was isolated from sorted cell populations using the miRNeasy Kit from QIAGEN (Valencia, CA).