Institut Pasteur

Chronic hepatitis B (CHB) affects an estimated 254 million people globally. Historically, WHO and professional society guidelines have recommended treatment for individuals at high risk of disease progression, including those with hepatitis B virus (HBV) DNA concentrations >20 000 IU/mL. Whether individuals at lower risk, including those with HBV DNA <20 000 IU/mL and normal alanine aminotransferase concentrations, benefit from treatment remains uncertain. To inform 2024 WHO guidelines and the potential expansion of treatment threshold recommendations, we conducted two linked systematic reviews and meta-analyses; this analysis examines the incidence of clinical outcomes in untreated adults with non-cirrhotic CHB stratified by baseline HBV DNA and ALT concentrations. In this systematic review and meta-analysis, we searched PubMed, Embase, Web of Science, and the Cochrane Library for longitudinal prospective and retrospective cohort studies, randomised controlled trials, and non-randomised studies of interventions, published in any language, from Jan 1, 2000, to Feb 6, 2023. We also reviewed the reference lists of included studies and systematic reviews and consulted networks of experts to identify other data sources. Included studies followed up adults (≥18 years) with non-cirrhotic CHB who had no history of antiviral therapy at enrolment, had baseline HBV DNA quantification and ALT measurement, had a follow-up period of at least 48 weeks, and assessed one or more of six key clinical outcomes (hepatocellular carcinoma, cirrhosis, liver-related mortality, all-cause mortality, liver decompensation, and indication for liver transplantation) or six additional outcomes (advanced liver fibrosis, progression of liver fibrosis, becoming eligible for antiviral treatment, hepatitis flare, and HBsAg and HBeAg seroclearance). Outcomes were required to be stratified by HBV DNA concentrations (<200 IU/mL, <2000 IU/mL, 2000-19 999 IU/mL, 20 000-199 999 IU/mL, and ≥200 000 IU/mL) or ALT concentrations (less than the upper limit of normal [ULN], 1·0-1·9 × ULN, and ≥2·0 × ULN). We excluded studies that focused solely on individuals who were pregnant; were co-infected with HIV, hepatitis C virus, or hepatitis D virus; or had another underlying condition other than CHB. We extracted aggregate data and used random-effects meta-analysis to pool incidence rates per 100 person-years. This study was registered with PROSPERO (CRD42023431652). Of 13 231 studies screened, 71 met the inclusion criteria. A concentration-response relationship was observed between single baseline HBV DNA measurements and hepatocellular carcinoma incidence rates per 100 person-years: 0·131 (95% CI 0·097 to 0·177, I2=0%) for HBV DNA concentrations <200 IU/mL, 0·176 (0·117-0·266, I2=88%) for <2000 IU/mL, 0·311 (0·245-0·393, I2=13%) for 2000-19 999 IU/mL, 0·862 (0·725-1·026, I2=0%) for 20 000-199 999 IU/mL, and 0·941 (0·668-1·324, I2=58%) for ≥200 000 IU/mL (p<0·0001 for between-group difference). Similar concentration-response patterns were observed for development of cirrhosis (0·298 [95% CI 0·214-0·415], two studies, for <200 IU/mL; 0·300 [0·146-0·616], I2=88%, for <2000 IU/mL; 0·712 [0·624-0·814], I2=46%, for 2000-19 999 IU/mL; 1·436 [0·991-2·082], I2=76%, for 20 000-199 999 IU/mL; and 2·193 [1·690-2·846], I2=82%, for ≥200 000 IU/mL) and liver-related mortality (0·086 [95% CI 0·054-0·136], one study; 0·083 [0·015-0·451], I2=0%; 0·303 [0·228-0·402], I2=0%; 0·766 [0·591-0·993], one study; and 1·118 [0·951-1·314], two studies), but no concentration-response relationship was observed between a single baseline HBV DNA assessment and all-cause mortality or liver decompensation. Compared with ALT below the ULN, incidence rates of hepatocellular carcinoma, cirrhosis, and liver-related mortality were higher in individuals with baseline ALT concentrations 1·0-1·9 × ULN or ≥2·0 × ULN. A similar pattern was not found for all-cause mortality, and other outcomes were not meta-analysed due to small numbers. Within the HBV DNA strata of <2000 IU/mL, 2000-19 999 IU/mL, and ≥200 000 IU/mL, hepatocellular carcinoma incidence rates were 2-3 times higher in individuals with ALT 1·0-1·9 × ULN than in those with ALT concentrations less than the ULN. Individuals with persistently low HBV DNA concentrations (<2000 IU/mL) or persistently normal ALT concentrations across multiple assessments had slightly lower hepatocellular carcinoma incidence rates compared with those assessed by a single measurement. Our risk of bias assessment found 15 (21%) of 71 studies to be rated as good quality, 40 (56%) as fair quality, and 16 (23%) as poor quality. These findings, alongside the linked systematic review and meta-analysis of antiviral treatment efficacy, supported the 2024 WHO guidelines expansion of treatment criteria to include individuals with HBV DNA concentrations >2000 IU/mL and ALT concentrations above the ULN. For those with HBV DNA concentrations <2000 IU/mL and persistently normal ALT concentrations, treatment can be deferred. WHO.

Chronic kidney disease and its most severe complication, end-stage renal disease (ESRD), represents an estimated financial burden of €4.4billion in 2021 in France. Therapeutic patient education (TPE) improves ESRD management and health outcomes. This study explored whether providing access to an interactive web-based TPE platform with community features was cost-effective. A within-trial cost-utility analysis was carried out over an 18 months horizon, using data from the PIC-R (Plateforme Interactive Communautaire-dialyse et transplantation Rénale) trial. ESRD or post-transplant patients were randomized 1:1:1 to a control group with no specific TPE program (Control), an intervention group with online TPE (e-TPE) and an intervention group with online TPE coupled with community features such as a patient forum and a chatroom with both patients and health care professionals (e-TPE + chat). The outcome measure was the cost per quality-adjusted life-year (QALY) and per year of full capability (YFC). Both intention-to-treat (ITT) and per protocol (PP) analyses were conducted, and missing data were handled using multiple imputation and selection models. Sensitivity analyses were performed. Among the 815 patients assessed for eligibility across 12 French centres, a total of 549 patients were included in the economic analysis: 186 in the Control group, 189 in the e-TPE group and 174 in the e-TPE + chat group. The e-TPE group demonstrated cost savings and slightly higher QALYs compared to the control group, making e-TPE dominant. Conversely, the e-TPE + chat intervention resulted in higher costs without substantial effectiveness gains, making it not cost-effective. e-TPE was deemed cost-effective for ESRD patients, while e-TPE + chat was not. Web-based platforms improve ESRD management when targeted to likely users.

Tunneling nanotubes (TNTs) are thin, actin-based membrane bridges that establish direct cytoplasmic continuity between distant cells, enabling the transfer of diverse cargoes ranging from ions and proteins to organelles such as mitochondria. Since their discovery in 2004, TNTs have been identified in numerous cell types and linked to an expanding range of physiological and pathological functions. Yet, their molecular identity and mechanisms of formation remain elusive. The most defining and least understood step in TNT biogenesis is membrane fusion, the process by which TNTs achieve open-ended continuity between cells, and this represents a critical frontier in the field. This review integrates recent advances in TNT biology, emphasizing the interplay between actin cytoskeletal dynamics, plasma membrane composition, and cell adhesion during TNT formation. It also draws mechanistic parallels with established models of membrane fusion, highlighting fundamental principles and shared regulators across fusion systems, many of which have been implicated in TNT functionality. By combining molecular, biophysical, and imaging perspectives, this review proposes a conceptual framework for TNT formation and fusion, identifies major methodological gaps, and outlines future directions to unravel the mechanisms that underlie intercellular cytoplasmic continuity.

The life cycle of Leishmania infantum is maintained mainly in dogs in anthropogenic environments and in many other wild animals in the sylvatic cycle. The ecological plasticity of some wild canids facilitates their role as hosts for Leishmania spp. in different endemic regions. Although red foxes (Vulpes vulpes) frequently test positive for L. infantum in Europe, little is known about their clinical presentation, immune response, or treatment outcomes. This study investigated the prevalence, clinical, and immunological features of L. infantum infection in foxes from southern Italy, complemented by an in vitro evaluation of cytokine responses in fox macrophages. Wild foxes from a wildlife rehabilitation center in southern Italy were molecularly and serologically screened for L. infantum. One sick fox underwent a complete diagnostic confirmation, treatment, and follow-up through hematological, biochemical, cytological, and molecular evaluations. In addition, peripheral blood mononuclear cells (PBMCs) isolated from a healthy fox were differentiated into macrophages and experimentally infected with L. infantum to assess early host-parasite interactions and cytokine gene expression profiles at two time points (4h and 48h). Overall, 13 out of 54 foxes (24.1%) were molecularly positive for L. infantum, with a prevalence of 25% (5/20) in necropsied animals and 22% (9/41) in live animals. One individual tested seropositive for L. infantum and Ehrlichia sp. using the SNAP Leish 4Dx® test (2.4%, 1/41). The sick fox treated with meglumine antimoniate and allopurinol showed marked clinical and laboratory improvement. In the in vitro evaluation, the percentage of infected macrophages decreased from 32.8% at 4h (2.25 parasites/cell) to 21.5% at 48h (2 parasites/cell). Cytokine gene expression at 4h and 48h showed an increase in interleukin-6 (IL-6) (0.164-0.552) and IL-10 (0.828-4.245), stable IL-4 (0.505-0.708), a decrease in IL-12 (1.793-1.223) and IFN-γ (1.507-0.613), and consistently low TNF-α (0.377-0.411). The present study confirmed a high L. infantum prevalence of infection in red foxes from southern Italy. Serological findings herein and inthe literature, together with in vitro cytokine gene expression, suggested that most foxes may remain subclinically infected. The high molecular positivity and the synanthropic nature of red foxes reinforce their role as reservoirs of L. infantum in endemic areas.

Over the past 20 years, the limited efficacy of CD8⁺ T cell-based vaccines against viruses in clinical trials has shifted attention away from such strategies. However, recent findings have brought renewed appreciation for the central importance of CD8⁺ T cells in controlling both acute and chronic viral infections and in preventing severe or progressive disease. This work highlights shared features, such as effector functions and stemness properties, of effective CD8⁺ T cell responses against diverse viruses such as SARS-CoV-2 and HIV. A deeper understanding and simpler interpretation of the functional workings of CD8⁺ T cell-mediated immunity, combined with advances in immunological and biotechnological tools, are opening new avenues for eliciting optimal T cell responses, both for prophylactic and for therapeutic applications. Collectively, these developments revive optimism that vaccines and immunotherapies designed to harness robust CD8⁺ T cell responses could have a major role in combating emerging viral threats and in achieving long-term suppression of persistent infections such as HIV-1 to undetectable levels.

Essential nuclear processes require pairs of chromosomal loci to find each other in three-dimensional space. Polymer models of chromosome dynamics typically assume that the stochastic forces driving such locus motion are spatially uncorrelated, implying that relative diffusion follows directly from single-locus dynamics. Here we show that this assumption fails in living cells. Using live-cell imaging in fly embryos and mouse embryonic stem cells, we find that pairwise locus distances diffuse markedly slower than predicted for independent fluctuations. Combining stochastic trajectory analysis with polymer simulations, we demonstrate that this slowdown arises from non-equilibrium spatially correlated fluctuations (SCFs) in the nucleoplasm, which cause nearby loci to move coherently. We establish three experimentally testable signatures of SCFs: fluctuation amplitudes plateau at large distances, are independent of genomic separation, and show an anomalous temporal scaling. All three predictions are confirmed experimentally, including for loci on separate chromosomes. ATP depletion and disruption of cohesin-mediated loop extrusion reveal that both active processes and crosslinking contribute to correlation magnitudes. Because SCFs slow relative motion preferentially at short distances, they reduce encounter frequencies while prolonging encounter durations, generating a trade-off with direct implications for gene regulation. Our results identify spatially correlated fluctuations as a fundamental determinant of relative motion in confined active polymers.

Abstract Non-homologous end joining (NHEJ) repairs DNA double-strand breaks by synapsing and ligating DNA ends. In vertebrates, DNA-PKcs promotes end alignment and processing, yet several eukaryotes - including budding yeast - perform NHEJ without DNA-PKcs, and the underlying mechanism remains unclear. Here we report cryo-electron microscopy structures of reconstituted Saccharomyces cerevisiae NHEJ synaptic complexes assembled on DNA ends bearing either 4-bp terminal microhomologies or blunt termini. On the microhomology substrate with a single 5’-P, we capture a ligation-competent short-range complex in which a single Dnl4 catalytic core is fully ordered and engaged at the 5′-adenylated nick. When two 5’-P are present, we resolve two predominant, coexisting DNA-aligned protective states in which both Dnl4 DBD-NTD modules occupy the break region with reciprocal geometries, supporting an alternating engagement model for sequential sealing of the two strands while maintaining continuous end association. In contrast, blunt-ended substrates yield a non-aligned protective configuration in which two Dnl4 catalytic modules constrain the DNA ends ∼30 Å apart in a ligation-incompatible arrangement, providing a structural explanation for slow blunt-end joining in yeast. Together, these structures define architectural and mechanistic principles of DNA-PKcs-independent NHEJ.

Abstract In the context of viral epidemic surveillance, generating accurate consensus viral genomes from sequencing data is critical for tracking the emergence of mutations of concern, evaluating the genomic diversity of circulating viruses, and anticipating which viral strains could become most prevalent. However, this task is made difficult by the presence of Deletion-containing Viral Genomes (DelVGs), which contain truncated (or rearranged) and potentially mutated versions of the full length virus genome. Because these DelVGs can outnumber the full genome in terms of coverage, potential DelVG specific mutations may be erroneously incorporated into the final consensus, thereby compromising its accuracy. Automatic detection of these DelVGs and of the genomic positions that may harbor DelVG specific mutations is therefore crucial. Here, we present DIPScan, a new method able to (i) accurately and efficiently detect DelVGs in short read datasets, and (ii) mask or correct positions in the consensus genome that may be affected by DelVG-specific mutations. Using several hundreds of simulated and real patient-derived NGS datasets from the National Reference Center (NRC) for respiratory viruses at Institut Pasteur, we demonstrate the capacity of DIPScan to accurately and efficiently detect DelVGs and to correctly adjust the consensus sequences. DIPScan is implemented as a Nextflow workflow, making it highly flexible, scalable, and reproducible, and is now used routinely at the NRC.

Human leukocyte antigen-G (HLA-G) is an immunomodulatory molecule known to play a crucial role in immune tolerance and regulation. In the context of human African trypanosomiasis (HAT), higher soluble HLA-G levels were detected in the plasma of confirmed cases, representing a serological marker of T. b. gambiense infection. As trypanosomes also invade extravascular tissues, especially the skin, this study explored the potential role of HLA-G in the dermal immune response during T. b. gambiense infection. Blood and skin samples from 50 seronegative individuals, 45 seropositive suspects and 36 confirmed HAT cases, collected between 2018 and 2022 in endemic foci of Guinea and Côte d'Ivoire, were analyzed. Plasmatic and dermal levels of HLA-G proteins were quantified by ELISA and immuno-histochemistry, respectively, and compared to the trypanosome detection results in the same samples. The implication of soluble HLA-G plasma level as a biomarker of T. b. gambiense infection was confirmed. In the dermis, HLA-G isoforms were expressed either with a granular distribution or with in diffuse halos. Granular patterns of dermal HLA-G were directly associated with the presence of trypanosomes in the dermis. The presence of diffuse halos was correlated to higher sHLA-G levels in the plasma. In total, this study provides the first evidence of the involvement of HLA-G in the extravascular immune response against parasites, especially in the skin. It shows that HLA-G distribution in the extravascular compartment also represents a biomarker of trypanosome infection.

Genome integrity is essential for cellular survival and adaptation across diverse physiological states. The fission yeast Schizosaccharomyces pombe relies on conserved DNA repair pathways to maintain genome stability during proliferative growth and in the absence of cell division (quiescence/G0). Using 5-fluoroorotic acid (5-FOA) counter-selection, we examined spontaneous mutation accumulation in both conditions in a wild-type prototrophic strain. Unexpectedly, we identified in growing and quiescent cells a class of 5-FOA-resistant mutants that, unlike canonical ura4 or ura5 loss-of-function mutants, retain the ability to grow without uracil supplementation. Genetic analyses showed that this phenotype is stable and segregates as a single locus. Whole-genome sequencing of tetrads from independent crosses revealed multiple hypomorphic alleles of ura6, which encodes the essential uridylate kinase. These alleles, comprising non-synonymous substitutions and an in-frame duplication, cluster within conserved regions of the protein and likely reduce production of the toxic 5-FOA-derived metabolite while preserving sufficient uracil biosynthesis.