HIV Modifies the m6A and m5C Epitranscriptomic Landscape of the Host Cell

The study of RNA modifications, today known as epitranscriptomics, is of growing interest. The N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications are abundantly present on mRNA molecules, and impact RNA interactions with other proteins or molecules, thereby affecting cellular processes, such as RNA splicing, export, stability, and translation. Recently m6A and m5C marks were found to be present on human immunodeficiency (HIV) transcripts as well and affect viral replication. Therefore, the discovery of RNA methylation provides a new layer of regulation of HIV expression and replication, and thus offers novel array of opportunities to inhibit replication. However, no study has been performed to date to investigate the impact of HIV replication on the transcript methylation level in the infected cell. We used a productive HIV infection model, consisting of the CD4+ SupT1 T cell line infected with a VSV-G pseudotyped HIVeGFP-based vector, to explore the temporal landscape of m6A and m5C epitranscriptomic marks upon HIV infection, and to compare it to mock-treated cells. Cells were collected at 12, 24, and 36 h post-infection for mRNA extraction and FACS analysis. M6A RNA modifications were investigated by methylated RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-Seq). M5C RNA modifications were investigated using a bisulfite conversion approach followed by high-throughput sequencing (BS-Seq). Our data suggest that HIV infection impacted the methylation landscape of HIV-infected cells, inducing mostly increased methylation of cellular transcripts upon infection. Indeed, differential methylation (DM) analysis identified 59 m6A hypermethylated and only 2 hypomethylated transcripts and 14 m5C hypermethylated transcripts and 7 hypomethylated ones. All data and analyses are also freely accessible on an interactive web resource (http://sib-pc17.unil.ch/HIVmain.html). Furthermore, bothm6A andm5Cmethylations were detected on viral transcripts and viral particle RNA genomes, as previously described, but additional patterns were identified. This work used differential epitranscriptomic analysis to identify novel players involved in HIV life cycle, thereby providing innovative opportunities for HIV regulation

Rockfalls change the runout and frequency of debris flows at Punta Nera (Eastern Italian Alps)

In the Dolomitic region, many debris flow basins have headwaters characterized by extremely steep slopes of bare outcropping rock. Cliffs are commonly incised by multiple chutes which rapidly deliver runoff at their base where the channels incise scree deposits. Debris flows mobilize and transport sediment along such ephemeral channels following intense summer convective rainstorms. In the debris flow basin of Punta Nera, a series of rockfalls, which occurred in the upper part of the headwater between 2013 and 2016, caused dramatic changes in the debris flow dynamics. Starting from the summer of 2014, the runout of debris flow events increased so much that it reached the national road, which runs at the toe of the debris flow fan, attracting media attention and prompting the adoption of protective measures. Here, we use newspaper reports, direct observations, aerial and terrestrial photograph, monitoring data and topographic surveys to document the rockfalls and the debris flow activity. The sudden increase in sediment availability changed the magnitude of events, their runout and the critical conditions for debris-flow occurrence

Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro through Cell Activation Dynamics

Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men’s. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers’ expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure

Rockfalls change the runout and frequency of debris flows at Punta Nera (Eastern Italian Alps)

In the Dolomitic region, many debris flow basins have headwaters characterized by extremely steep slopes of bare outcropping rock. Cliffs are commonly incised by multiple chutes which rapidly deliver runoff at their base where the channels incise scree deposits. Debris flows mobilize and transport sediment along such ephemeral channels following intense summer convective rainstorms. In the debris flow basin of Punta Nera, a series of rockfalls, which occurred in the upper part of the headwater between 2013 and 2016, caused dramatic changes in the debris flow dynamics. Starting from the summer of 2014, the runout of debris flow events increased so much that it reached the national road, which runs at the toe of the debris flow fan, attracting media attention and prompting the adoption of protective measures. Here, we use newspaper reports, direct observations, aerial and terrestrial photograph, monitoring data and topographic surveys to document the rockfalls and the debris flow activity. The sudden increase in sediment availability changed the magnitude of events, their runout and the critical conditions for debris-flow occurrence

Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART

The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies