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HIV persistence in tissues on dolutegravir-based therapy is not associated with resistance mutations to dolutegravir
No full textInternational audienceBackgroundRelatively few studies have investigated HIV-1 persistence in tissues, especially in healthy people-living-with-HIV-1 (PLWH) on a successful antiretroviral regimen containing second generation integrase inhibitors.MethodsIn the ANRS EP64 DOLUVOIR, we explore HIV-1 persistence in five accessible anatomical sites in 20 PLWH on an efficient first-line ART regimen containing dolutegravir with virological load <50 copies/mL: PBMCs, rectum, adipose tissue, lymph node and sperm. We quantify total HIV-DNA and cell-associated HIV-1 RNA in different compartments. We sequence HIV-1 DNA for searching drug resistance mutations (DRM) (in RT and INT) and for studying HIV diversity within tissues (ENV). Intact proviral DNA is estimated in PBMCs with an adapted IPDA assay.ResultsBroad ranges of total HIV-DNA and transcripts levels are detected in lymph nodes, PBMCs, adipose tissue and rectum with the highest levels being found in lymph nodes (2.77 log copies HIV-1-DNA/106 cells and 1.50 log copies of HIV-1 cell-associated-RNA/µg RNA). HIV-1 DNA is undetected in all sperm samples (n = 19) except for one (1.52 log copies HIV-1-DNA/106 cells). No difference is noted between the diversity in the four compartments. DRMs to the current regimen are found archived in compartments of six participants. Only two major DRMs to dolutegravir (G118R and R263K) are found archived in two participants. They are the results of APOBEC hypermutations.ConclusionsDespite ongoing transcriptional activity, persistence of HIV-1 in deep tissues is not associated with the selection of DRMs to dolutegravir on intact proviruses. Our results suggest that the detectable transcriptional activity stems predominantly from defective proviral DNA
Single-cell spatially resolved transcriptomic characterization of the developing mouse cochlea
No full textThe cochlea, the sensory organ of hearing, functions as a frequency analyzer, analogous to a musical instrument. During development, while the medio-lateral axis supports differentiation of sensory cells and their surrounding supporting cells, the longitudinal axis underlies frequency-dependent properties of the cochlea. The combination of these two gene expression gradients defines unique physiological attributes of each cell intimately linked to its position within the cochlea. To determine which cochlear cell-types have a transcriptomic signature sensitive to these two gradients and identify the underlying gene regulatory networks, we took advantage of the advent of spatial single cell transcriptomics methodologies. We therefore generated a spatial transcriptomic atlas reaching single cell resolution based on the Visium HD technique, a sequencing-based technology that employ arrays of spatially barcoded probes to capture RNA molecules unbiasedly from histological tissue sections. Spatial transcriptional changes during embryonic stages, E14 and E16, as well as during postnatal development, P1 and P8, were investigated. Based on this dataset, not only cell-type assignment in single cell RNA-seq experiments could be validated, but the classification for some cell-types could be refined. Gradients of gene expression along the medio-lateral and longitudinal axes in multiple cell-types together with their temporal dynamics across development were also uncovered. Altogether, this atlas paves the way for deciphering gene regulatory networks controlling gene expression as a function of position in the cochlear cell types, providing a valuable resource for the design of efficient, robust and safe gene therapy strategies
La biochimie des interactions conservées de la levure à l'homme pour la voie NMD
No full textNonsense-mediated mRNA decay (NMD) is one of the most extensively studied pathways of cytoplasmic mRNA degradation. It plays a critical role in diverse cellular processes by eliminating aberrant transcripts containing premature stop codons and by regulating the stability of physiological mRNAs. NMD factors were initially identified through genetic screens in S. cerevisiae (UPF1, 2, 3) and C. elegans (SMG-1, SMG5-7). Subsequent biochemical studies revealed the composition of NMD complexes and identified additional factors. A major protein hub for NMD is Upf1, an ATP-dependent RNA helicase that is part of two mutually exclusive NMD assemblies, the Upf1-Upf2-Upf3 complex and the Upf1-decapping complex, which contains the decapping enzyme and its co-factors. Here, we discuss recent findings, primarily from budding yeast, on the protein-protein interactions driving NMD complex dynamics and their similarities to human NMD. Together, the N-terminal cysteine and histidine rich (CH) and helicase domains (HD) of Upf1 act as a hub for binding multiple partners. Upf1 is required for binding to NMD substrates and for the initiation of RNA degradation through decapping (yeast) or endonucleolytic hydrolysis (humans). We focus on the interplay between Upf2, Dcp2 and Nmd4 (yeast SMG6), which ensures the mutually exclusive formation of Upf1-bound subcomplexes modulating Upf1's affinity for RNA. Thus, the study of NMD factors interactions in different organisms sheds new light on the remarkable conservation of NMD molecular mechanisms
Cell size heterogeneity controls crystallization of the developing fruit fly wing
No full textA fundamental question in Biology is to understand how patterns and shapes emerge from the collective interplay of large numbers of cells. Cells forming two-dimensional epithelial tissues behave as active materials that undergo remodeling and spontaneous shape changes. Focussing on the fly wing as a model system, we find that the cellular packing in the wing epithelium transitions from a disordered packing to an ordered, crystalline packing. We investigate biophysical mechanisms controlling this crystallization process. While previous studies propose a role of tissue shear flow in establishing the ordered cell packing in the fly wing, we reveal a role of cell size heterogeneity. Indeed, we find that even if tissue shear have been inhibited, cell packings in the fruit fly wing epithelium transition from disordered to an ordered packing. We propose that the transition is controlled by the cell size heterogeneity, which is quantified by the cell size polydispersity. We use the vertex model of epithelial tissues to show that there is a critical value of cell size polydispersity above which cellular packings are disordered and below which they form a crystalline packing. By analyzing experimental data we find that cell size polydispersity decreases during fly wing development. The observed dynamics of tissue crystallisation is consistent with the slow ordering kinetics we observe in the vertex model. Therefore, although tissue shear does not control the transition, it significantly enhances the rate of tissue scale ordering by facilitating alingment of locally ordered crystallites
Slap restricts oncogenic Src-family kinase signaling to maintain colonic epithelial homeostasis
No full textSrc-family kinases (SFKs) regulate proliferation in colonic epithelial cells (CECs), but the mechanisms that restrain their activity remain poorly defined. We identify Src-like adaptor protein (SLAP), a negative regulator of receptor tyrosine kinase signaling, as a key suppressor of SFK activity in the colon. Constitutive and inducible epithelial-specific Slap deletion using a villin-CreERT2 model increases CEC proliferation and accelerates tumorigenesis in the azoxymethane/dextran sodium sulfate (AOM/DSS) model. Slap deficiency also enhances SFK-dependent expansion of normal and tumor-derived colonic organoids. Mechanistically, we identify the receptor tyrosine kinase EphB2, an upstream activator of SFKs and CEC proliferation, as an additional SLAP-regulated target. Together, these findings reveal a non-genetic mechanism by which SFKs drive colonic transformation and establish SLAP as a tumor suppressor that constrains oncogenic SFK signaling in the colonic epithelium
The microbiota affects energy production, nitrogen excretion and sterol metabolism in mosquito larvae
No full textPosted December 18, 2025 on bioRxiv.Mosquito larvae rely on a living microbiota for normal development because the microbiota supplies essential nutrients, particularly vitamins. Beyond vitamin provision, transcriptomic data suggest that the microbiota also supports other key nutritional processes. Here, we explored these roles by conducting a metabolomics analysis on Aedes aegypti third instar larvae following microbiota depletion. We sampled larvae and dissected guts 12- and 20-hours post-decolonization and analysed methanol-soluble metabolites using untargeted gas chromatography–mass spectrometry. Our findings reveal a pronounced impact of gut microbial presence on several metabolites involved in the tricarboxylic acid cycle and the uricolytic pathway. Germ-free larvae also had a lower quantity of cholesterol in guts and their long-chain fatty acid profile was altered in guts and whole larvae. Sterols, including cholesterol, are essential precursors for the production of the moulting hormone 20-hydroxyecdysone. We therefore tested how supplementing exogenous cholesterol affects the development of germ-free larvae. The effects proved to be highly concentration-dependent, ranging from a marginally significant increase in successful development to adulthood at low concentrations to a pronounced developmental impairment at higher concentrations. Moreover, bacteria deficient in fatty acids beta-oxidation had a significantly lower ability to support larval development. Together, the observed alterations suggest that microbiota-deprived larvae exhibit a downregulation of metabolic processes related to energy production, nitrogen excretion and sterol metabolism, likely due to the absence of microbiota-derived vitamins essential for these central metabolic functions.ImportanceMosquito larvae depend on gut microbiota for normal growth because microbes supply essential nutrients, particularly B vitamins. To explore microbial roles beyond vitamin provision, we analysed metabolic changes in Aedes aegypti larvae after microbiota removal using gas chromatography-mass spectrometry. Germ-free larvae exhibited decreased metabolites associated with the tricarboxylic acid cycle and uricolytic pathway, indicating a general slowdown in metabolic activity and nitrogen waste processing. Additionally, the absence of a microbiota affected cholesterol and fatty acid metabolism. To validate these findings, we found that supplementing germ-free larvae with low levels of cholesterol modestly improved their development. In contrast, larvae colonized with bacteria deficient in fatty acid metabolism exhibited significantly reduced developmental success. Overall, the findings show that removing the microbiota downregulates key metabolic pathways related to energy production, nitrogen excretion, and sterol metabolism, highlighting that bacterial vitamins and fatty acid degradation are vital for mosquito larval development and successful transformation into adults
First evidence of human borreliosis local transmission in Cambodia
No full textInternational audienceWe report the first cases of confirmed human local transmission of borreliosis in Cambodia. Four patients, including cases with no travel history, presented typical clinical signs and tested positive for Borrelia burgdorferi antibodies. These findings confirm the presence, circulation, and local transmission of Borrelia in Cambodia. These results are important to convince for the need and the development of surveillance of tick-borne diseases in Southeast Asia
Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)
No full textInternational audienceThe 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequently ratified by the ICTV membership. An additional 9 error correction proposals were also approved in August 2025. This article lists the taxonomy proposals that have now been incorporated into release 40 version v2 of the Master Species List (https://ictv.global/msl), the Virus Metadata Resource (https://ictv.global/vmr), and associated ICTV databases. In addition to the assignments of 1,563 new virus species, 243genera, 55 families, 11 orders, and 8 classes, there were substantial additions to higher taxonomic ranks. These include the creation of a new realm (Singelaviria), which is based on the recognition of a separate evolutionary origin for the hallmark capsid genes of members of the kingdom Helvetiavirae. These express capsid proteins forming a single jelly-roll fold that is structurally and evolutionarily distinct from those of members of the family Bamfordvirae , assigned to the realm Varidnaviria . Furthermore, the realm Varidnaviria underwent a major reorganization, including the addition of a new kingdom, Abadenavirae . Another notable change was the classification of the vertebrate-infecting single-stranded DNA anellovirids into a new phylum Commensaviricota (kingdom Shotokuvirae , realm Monodnaviria). Archaeal viruses infecting the hyperthermophilic Archaeoglobi were assigned to a new phylum Calorviricota, in the kingdom Trapavirae (realm Monodnaviria ), whereas RNA viruses infecting hyperthermophilic bacteria were classified into a new phylum Artimaviricota (realm Riboviria). In recognition of his extensive and valuable contributions to virus taxonomic developments in Study Groups and over the period of his EC membership, Stuart Siddell was honoured as a new life member of the ICTV. The ICTV has created a new strategy for disseminating information on taxonomy advances through annual open-access publication of citeable taxonomy proposal summaries from each ICTV Subcommittee. A collective total of 354 co-authors of the seven summaries were drawn from members of each Subcommittee, the EC, and a very large number of contributors from the wider virology community
Immune control of brain physiology
No full textInternational audienceThe peripheral immune system communicates with the brain through complex anatomical routes involving the skull, the brain borders, circumventricular organs and peripheral nerves. These immune-brain communication pathways were classically considered to be dormant under physiological conditions and active only in cases of infection or damage. Yet, peripheral immune cells and signals are key in brain development, function and maintenance. In this Perspective, we propose an alternative framework for understanding the mechanisms of immune-brain communication. During brain development and in homeostasis, these anatomical structures allow selected elements of the peripheral immune system to affect the brain directly or indirectly, within physiological limits. By contrast, in ageing and pathological settings, detrimental peripheral immune signals hijack the existing communication routes or alter their structure. We discuss why a diversity of communication channels is needed and how they work in relation to one another to maintain homeostasis of the brain
Replication Stress is an Actionable Genetic Vulnerability in Desmoplastic Small Round Cell Tumors
No full textInternational audienceDesmoplastic small round cell tumor (DSRCT) is an aggressive sarcoma subtype that is driven by the EWS-WT1 chimeric transcription factor. The prognosis for DSRCT is poor, and major advances in treating DSCRT have not occurred for over two decades. To identify effective therapeutic approaches to target DSRCT, we conducted a high-throughput drug sensitivity screen in a DSRCT cell line assessing chemosensitivity profiles for 79 small-molecule inhibitors. DSRCT cells were sensitive to PARP and ATR inhibitors (PARPi, ATRi), as monotherapies and in combination. These effects were recapitulated using multiple clinical PARPi and ATRi in three biologically distinct, clinically-relevant models of DSRCT, including cell lines, a patient-derived xenograft (PDX)-derived organoid model, and a cell line-derived xenograft mouse model. Mechanistically, exposure to a combination of PARPi and ATRi caused increased DNA damage, G2/M checkpoint activation, micronuclei accumulation, replication stress, and R-loop formation. EWS-WT1 silencing abrogated these phenotypes and was epistatic with exogenous expression of the R-loop resolution enzyme RNase H1 in reversing the sensitivity to PARPi and ATRi monotherapies. The combination of PARPi and ATRi also induced EWS-WT1-dependent cell-autonomous activation of the cGAS/STING innate immune pathway and cell surface expression of PD-L1. Taken together, these findings point towards a role for EWS-WT1 in generating R-loop-dependent replication stress that leads to a targetable vulnerability, providing a rationale for the clinical assessment of PARPi and ATRi in DSRCT