Biology subjects

Charre, C.

Publications and source records attributed to Charre, C..

6 recordsLinked to original sources

bioRxiv2026

Modeling how memory CD8 T cells can elicit post-treatment control of HIV infection

While most people living with HIV suffer progressive disease following cessation of antiretroviral therapy, a small fraction elicits lasting post-treatment control. Understanding the mechanisms underlying this control is key to devising effective HIV remission strategies. Although recent studies implicate memory CD8 T cells, how these cells establish lasting viremic control remains unknown. Here, we combine mathematical modeling and analysis of data from SIV-infected non-human primates to elucidate the underlying mechanisms. We recognized that sustained antigenic stimulation leads to heritable epigenetic remodeling of the CD8 T cell pool, impairing memory cell survivability. Antiretroviral therapy rapidly suppresses viremia, thereby arresting antigenic stimulation and preserving memory potential. The greater this preservation is, the better would be the memory recall response following viral rebound post-treatment. Our mathematical model based on this hypothesis predicts that post-treatment control is an alternative steady state to progressive infection, realized by strong memory-driven recall responses. Our model fits longitudinal virological data spanning the pre-, during-, and post-antiretroviral treatment phases of infection, and recapitulates the outcomes of progressive disease and long-term remission realized, the latter predominantly with early treatment initiation. It shows, consistently with data, that memory CD8 T cells could drive post-treatment control independently of the size of the latent reservoir, explaining how such control may be realized more widely than estimated with prevalent hypotheses. Our model further explains the existence of a window of treatment initiation times that maximizes the chances of post-treatment control. Finally, model predictions inform interventions targeting memory CD8 T cells for HIV remission.

immunology↗

bioRxiv2026

Negative HIV serology in perinatally infected children after early treatment and viral suppression: an exploratory analysis of immune correlates

BackgroundUndetectable HIV-specific antibodies in early-treated children with confirmed infection correlate with low viral reservoir and may identify those eligible for future HIV remission strategies. The neonatal immune systems unique characteristics, combined with impairments resulting from exposure to maternal HIV and antiretroviral treatment (ART), may affect antibody responses to HIV. Yet immune competence remains understudied in the context of negative HIV serology. The ANRS-EP59-CLEAC study included 76 children and adolescents with HIV. We measured plasma HIV antibodies by enzyme immunoassay, other analytes by ELISA or multiplex assays, and blood cell phenotypes and functions by flow cytometry. We used Fishers and Mann-Whitneys tests and logistic regression to analyze variables associated with negative HIV serology. Nine participants tested negative for HIV-specific antibodies, eight children and one adolescent. Negative HIV serology occurred exclusively in participants who had initiated ART early and had HIV RNA < 50 copies/mL at evaluation. Among 17 early-treated children with sustained viral suppression, only 7 had negative HIV serology. In this subgroup, negative HIV serology associated with higher nadir CD4 counts, lower plasma IgM levels, higher frequencies of circulating follicular CD8 T lymphocytes, and higher expression of the costimulatory molecule CD86 on myeloid dendritic cells. We found no evidence of B or T lymphocyte deficits associated with negative HIV serology. Low antigenic exposure was necessary but insufficient to explain negative HIV serology. Beyond its association with low HIV reservoir, negative HIV serology correlated with less severe prior CD4 T-lymphocyte depletion and higher frequencies of follicular CD8 T lymphocytes. SummaryIn HIV-infected infants, starting antiretroviral therapy (ART) very early dramatically improves health outcomes. An important phenomenon observed in some of these children is that, despite being HIV-infected, they show no detectable antibodies against the virus -- a profile referred to as negative HIV serology. This feature could help identify patients most likely to benefit from future strategies aimed at achieving long-term virus control without treatment. To better understand this phenomenon, we studied HIV-infected children and adolescents enrolled in the ANRS-EP59-CLEAC trial, which compares the effects of ART initiated early (before 6 months of age) versus late (after 24 months). We showed that negative HIV serology is associated with early treatment, but also with a better-preserved immune system: less depletion of CD4 T cells, which are critical immune cells, and a higher abundance of specific T lymphocytes with potent antiviral activity. Importantly, we found no evidence of defects in the mechanisms responsible for antibody production. These findings suggest that negative HIV serology reflects a favorable immunological profile and could serve as a useful marker to select children as candidates for HIV remission trials.

immunology↗

bioRxiv2024

Helicases DDX5 and DDX17 promote Hepatitis B Virus transcription termination heterogeneity in infected human hepatocytes

Background & AimsTranscription termination fine tunes gene expression and contributes to specify the function of RNAs in eukaryotic cells. Transcription termination of hepatitis B virus (HBV) is subjected to the recognition of the canonical polyadenylation signal (cPAS) common to all viral transcripts. The regulation of the usage of this cPAS and its impact on viral gene expression and replication is currently unknown. Approach & ResultsTo unravel the regulation of HBV transcript termination, we implemented a 3 RACE-PCR assay coupled to single molecule sequencing both in in vitro infected hepatocytes and in chronically infected patients. The detection of a previously unidentified transcriptional readthrough indicated that the cPAS was not systematically recognized during HBV replication in vitro and in vivo. Gene expression downregulation experiments demonstrated a role for the RNA helicases DDX5 and DDX17 in promoting viral transcriptional readthrough, which was, in turn, associated to HBV RNA destabilization and decreased HBx protein expression. RNA and chromatin immunoprecipitation, together with mutation of cPAS sequence suggested a direct role of DDX5 and DDX17 in functionally linking cPAS recognition to transcriptional readthrough, HBV RNA stability and replication. ConclusionsOur findings identify DDX5 and DDX17 as crucial determinants for HBV transcriptional fidelity and as host restriction factors for HBV replication.

molecular biology↗

bioRxiv2022

Performance of the cobas(R) HBV RNA Automated Investigational Assay for the Detection and Quantification of Circulating HBV RNA in Chronic HBV Patients

BackgroundThe amount of HBV RNA in peripheral blood may reflect HBV covalently closed circular DNA (cccDNA) transcriptional activity within infected hepatocytes. Quantification of circulating HBV RNA (cirB-RNA) is thus a promising biomarker for monitoring antiviral treatment. ObjectivesWe evaluated the performance of an automated, prototype quantitative HBV RNA assay for use on the Roche cobas(R) 6800/8800 systems. Study DesignThe sensitivity, specificity, linearity, and potential interference by HBV DNA of the cobas(R) HBV RNA assay were assessed using synthetic HBV armored RNA and clinical specimens. Resultscobas(R) HBV RNA results were linear between 10 and 107 copies/mL in clinical samples of several HBV genotypes, and up to 109 copies/mL with synthetic RNA. Precision and reproducibility were excellent, with standard deviation below 0.15 log10 copies/mL and coefficients of variation below 5% throughout the linear range. The presence of HBV DNA had minimal (<0.3 log10 copies/mL) impact on HBV RNA quantification at DNA:RNA ratios of up to approximately one million. In a panel of 36 untreated patient samples, cirB-RNA concentrations were approximately 200-fold lower than HBV DNA. cirB-RNA was detected in all 13 HBeAg-positive patients (mean 6.0 log10 copies/mL), and in 20 of 23 HBeAg-negative patients (mean of quantifiable samples 2.2 log10 copies/mL). Finally, cirB-RNA was detected in 12 of 20 nucleoside analog-treated patients (mean of quantifiable samples 3.4 log10 copies/mL). ConclusionsThe cobas(R) 6800/8800 investigational HBV RNA assay is a high throughput, sensitive and inclusive assay to evaluate the clinical relevance of cirB-RNA quantification in patients with chronic hepatitis B.

microbiology↗

bioRxiv2020

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialized kits including a hybridization capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP) and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples, with mNGS and RVOP producing the most complete genomes. For mid viral loads, 2/8 and 1/8 genomes were incomplete (<99%) with mNGS and both CleanPlex and RVOP, respectively. For low viral loads (Ct [≥]25), amplicon-based enrichment methods were the most sensitive techniques yielding complete genomes for 7/8 samples. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in two samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34-nt deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a default of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer annealing or probe-hybridizing regions and would require regular updates of the technique according to SARS-CoV-2 evolution.

genomics↗

bioRxiv2019

Quantifying transmission dynamics of acute hepatitis C virus infections in men having sex with men using phylodynamics

Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with new and classical hosts, makes prevalence and incidence rates poorly informative. However, additional insights can be gained by analyzing virus phylogenies inferred from dated genetic sequence data. By combining a phylodynamics approach based on Approximate Bayesian Computation (ABC) and an original transmission model, we estimate key epidemiological parameters of an ongoing HCV epidemic among MSMs in Lyon (France). We show that this new epidemic is largely independent of the classical HCV epidemics and that its doubling time is ten times lower (0.44 years versus 4.37 years). These results have practical implications for HCV control and illustrate the additional information provided by virus genomics in public health.

evolutionary biology↗