Biology subjects

Rousset, F.

Publications and source records attributed to Rousset, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Deciphering auditory neuroprogenitor stemness for large-scale neuronal screening

Sensorineural hearing loss can arise from damage to sensory hair cells, auditory neurons or their synaptic connections, with auditory neuropathy and cochlear synaptopathy highlighting the importance of neural integrity for hearing. The mammalian cochlea has limited capacity to regenerate lost auditory neurons. Understanding the molecular programs that sustain cochlear progenitor expansion and neurogenic competence could support neuronal regeneration and provide renewable models for auditory drug discovery. We previously established that WNT activation combined with dual SMAD inhibition (CHIR-DS) supports scalable expansion and neuronal differentiation of mouse auditory neuroprogenitors (ANPGs). Here, we characterize the transcriptional, chromatin and metabolic changes associated with the induced state. RNA-seq and ATAC-seq identified reduced Id1 and Id2 expression and increased accessibility at proneural basic helix-loop-helix motifs, alongside transcriptional enrichment of translation, mTOR and glucose-metabolism programs. Compared with growth-factor controls, CHIR-DS-treated ANPGs showed slight increase in glycolysis at early passage. However, after long-term expansion, both glycolysis and mitochondrial respiration were markedly enhanced. Human fetal ANPGs also responded to CHIR-DS with increased sphere growth and retained neural differentiation capacity, providing proof of concept beyond the mouse system. Finally, neurons derived from stemness-induced ANPGs (siANs) supported a 384-well reporter assay and a 2,560-compound pilot screen that nominated candidate neurite-outgrowth enhancers. Together, these findings validate the pathway basis of ANPG stemness induction, characterize the resulting molecular and metabolic state, and demonstrate human feasibility and a neuronal screening application.

neuroscience↗

bioRxiv2026

LGR5 and SOX2 expressing progenitor cells in the adult and aged human and mouse inner ear have the potential to produce Myosin 7A positive cells in vitro

Hearing loss and deafness as a result of hair cell loss cannot be restored due to the incapacity of spontaneous regeneration of these cells. Compounds that manipulate key signaling pathways can potentially regenerate cochlear hair cells. In order to test different compounds that promote hair cell regeneration in vitro models can be used. Three-dimensional cultures have allowed the expansion and experimentation of human and mouse inner ear organoids. This is mainly performed in the embryonic or the early postnatal developmental stage. However, since the majority of patients with hearing loss are adult, it is crucial to understand the adult inner ear regenerative capacity. Here, we evaluated progenitor cell markers in the adult human and mouse inner ear and the generation, expansion and differentiation of cochlear organoids derived from the adult human and mouse inner ear. Cochlear and vestibular sensory epithelium from adult humans; and from adult and aged mice express the progenitor markers SOX2 and LGR5; and can generate organoids in vitro. By optimizing the culture conditions, organoids derived from the cochlea and vestibular organ from adult human and adult and aged mouse differentiated to Myosin 7A positive cells. This indicates that the adult inner ear has regenerative capacity. These findings are encouraging for future regenerative therapies to cure hair cell-related hearing loss and deafness.

neuroscience↗

bioRxiv2026

A widespread NADase domain links bacterial immunity with human TEP1

Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune systems therefore have the potential to illuminate fundamental biological mechanisms throughout the tree of life. Here, we report that DUF4062 domains - which we rename NIR (NADase in bacterial immunity and vault ribonucleoproteins) - function in bacterial immunity against phages. We first identified NIR as an effector of Avs defense proteins, where it depletes cellular NAD+ to block viral infection. We then show that NIR domains are recurrently found as effectors in diverse defense systems. We use this association to uncover Vulcan and Vesta, two defense systems which trigger NAD+ depletion upon sensing distinct viral signals. Remarkably, NIR domains are widespread in eukaryotes where they are embedded in multiple NLR-like proteins. In particular, we identified a NIR domain with conserved NADase activity in the human TEP1 protein, a component of the telomerase complex and vault ribonucleoproteins. Together, these findings reveal an enzymatic activity shared between bacterial immunity and enigmatic eukaryotic machineries.

microbiology↗

bioRxiv2026

Physical interactions between pollen and pistil tissues mediate cryptic female choice in Brassica rapa

Cryptic female choice - female-mediated bias in fertilization after mating - is well established in animals and can also occur in plants when multiple pollens compete on the same pistil. However, whether interactions between pollen and pistil tissues after pollen deposition contribute to this process remains unknown. Here, we experimentally test whether such interactions mediate cryptic female choice in the angiosperm Brassica rapa. We quantified fertilization success of pollen donors competing on the same pistil using paternity analyses, and in parallel, made semi-in vivo assays to measure pollen tubes trajectories emerging from the excised styles and growing toward unfertilized ovules for each donor-recipient pair. We show that pollen tube growth towards ovules predicts higher fertilization success under pollen competition. Thus, we document a previously unobserved mechanism of cryptic female choice based on physical interactions between male and female components of reproduction. In addition, different recipient plants favour different pollen donors, consistent with non-directional female choice. Plants with longer styles bias paternities more strongly towards the most successful pollen donor. Overall, our study demonstrates that interactions between pollen tubes and pistil tissues after pollen germination enable plants to bias paternity toward particular donors.

evolutionary biology↗

bioRxiv2026

Experimental evidence for female choice in an angiosperm

Female choice is a central process of sexual selection that has shaped numerous phenotypes in animals. It may operate broadly across sexually reproducing organisms, including plants, not only because sex differences in sexual selection arise from anisogamy, wich refers to the unequal investment in gametes between sexes, but also because it can emerge from simple variation in female reproductive morphology. Here, we provide the first empirical test of cryptic female choice in an angiosperm by examining whether pollen and pistil traits jointly influence paternal fertilization success. Using experimental pollen competition, paternity analyses, and trait measurements, we show that pistil traits can bias paternity toward pollen donors with specific pollen traits. These results demonstrate that cryptic female choice operates in plants, paralleling mechanisms described in animals.

evolutionary biology↗

bioRxiv2026

Widespread immune systems protect bacteria against conjugative plasmids

Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipients, they may also behave as genetic parasites. Bacteria would thus be expected to have evolved barriers to plasmid conjugation. However, the distribution of these barriers and their underlying mechanisms remain poorly understood. Here, we performed a large-scale analysis of 364 diverse strains of the opportunistic pathogen Acinetobacter baumannii as recipients of the broad-host-range conjugative plasmids R388 and RP4. Major variations in host susceptibilities to conjugation, with limited phylogenetic association, suggested multiple and fast-evolving plasmid-specific barriers. Functional genetic analyses revealed a role for core genes, pointing to epistasis or genetic background effects. This is illustrated by the previously unrecognized role of H-NS expression in alleviating conjugation barriers in a strain-dependent manner. Most importantly, we identified three novel immune systems protecting bacteria against conjugation by R388 and RP4. Their patchy distribution within the species, and that of their homologs across bacteria, indicate that they are part of a dynamic repertoire of immune systems against conjugation. While the Ishtar system promotes plasmid loss through putative HEPN nuclease domains, Namtar and Attar sense distinct components of the R388 type IV secretion system (T4SS) to trigger a non-proliferative, energetically depleted state, analogously to the abortive infection response of anti-phage defenses. Live imaging of conjugation showed Namtar halting cell division in Escherichia coli recipients, conferring population-level immunity against plasmid spread via horizontal and vertical transmission. The existence of immune systems specifically targeting T4SS components suggests that conjugative plasmids impose a selective disadvantage greater than previously thought. This work reveals an additional layer of bacterial immunity directed at a class of genetic elements driving dissemination of antibiotic resistance.

microbiology↗

bioRxiv2025

Introducing a translationally relevant mouse model of radiosurgery-induced unilateral hearing loss

BackgroundStereotactic radiosurgery (SRS) is widely used to treat vestibular schwannomas but may cause irreversible hearing loss due to cochlear toxicity. The underlying mechanisms are not fully understood, and no effective otoprotective therapies exist. We aimed to establish a mouse model that replicates the clinical pattern of radiation-induced hearing loss. MethodsC57BL/6J mice (n=31) received 8 Gy (n=3), 16 Gy (n=5), 24 Gy (n=8), or 32 Gy (n=15) using the Leksell Gamma Knife ICON system. Targeting was based on the built-in cone-beam CT, co-registered with MRI and CT-based mouse atlases, to guide unilateral cochlea targeting. A single isocenter was placed lateral to the right cochlea, with the 80% isodose line traversing its medial edge. Auditory brainstem response (ABR) was measured at baseline and at 1 and 4 weeks post-SRS. A 32 Gy subgroup (n=7) was evaluated at 16 weeks. Histological analysis of cochleae was performed at 4 weeks in all groups and at 16 weeks in the long-term 32 Gy group. ResultsSRS was well tolerated, and the contralateral cochlea received a very low radiation dose. No ABR shifts were observed at 8 or 16 Gy, with only minimal histological changes. At 32 Gy, ABR threshold shifts at 22.6 and 32 kHz were evident by week 1 and worsened by week 4. Similar but milder effects occurred at 24 Gy. In the 32 Gy long-term subgroup, hearing loss progressed across all frequencies, most severely at high frequencies, alongside a sustained wave I amplitude decline. At 32 Gy, outer hair cells were reduced by 14% and 44% at 32 and 45.2 kHz, respectively, at 4 weeks, and by 38% and 80% at 16 weeks. Ribbon synapses were mildly reduced at 4 weeks and more markedly at 16 weeks in corresponding high-frequency regions. Spiral ganglion neuron density was mildly reduced at the basal and middle turns. All reported changes were statistically significant when compared to the contralateral ear. ConclusionsThis new model reproduces key features of SRS-induced cochlear toxicity, including unilateral, dose-dependent, and progressive hearing loss. It thus provides a valuable platform for investigating mechanisms and testing otoprotective strategies.

neuroscience↗

bioRxiv2025

Pollinator abundance shapes sexual selection in an angiosperm

Sexual selection is a cornerstone of evolutionary biology potentially operating in all sexually-reproducing organisms. Modern developments in the field revealed that this selective force extends beyond Darwins initial focus on access to mates in terms of competition for access to gametes of the other sex. Despite its presumed universality, sexual selection theory remains largely untested in plants compared to animals. This gap may partly stem from challenges in quantifying sexual selection using approaches that account for a critical plant-specific factor: the reliance on pollinators as third-party agents for accessing mates. Here, we quantified sexual selection along consecutive episodes of selection in the hermaphroditic plant Brassica rapa by integrating the monitoring of pollinator movements with genetic paternity analyses in experimental populations. Our approach identifies pollen competition for ovules as the primary arena for sexual selection in B. rapa. Darwinian competition for access to mates constitutes a secondary force, and was stronger in the male compared to the female sex function, as predicted by classic theory. Importantly, experimentally induced variation in pollinator abundance modulated the balance between pre- and post-pollination sexual selection. Under reduced pollinator abundance, the opportunity for selection on mate acquisition increased. Crucially, we demonstrate that ignoring pollinator movements among plants leads to erroneous quantification of pre-pollination sexual selection. We argue that a unifying theory of sexual selection requires a more comprehensive quantification of pre- and post-pollination episodes of selection, taking into account the specificities of gamete transfer in plants.

evolutionary biology↗

bioRxiv2025

Systematic discovery of TIR-based immune signaling systems in bacteria

Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immunity as well as in a family of bacterial defense systems called Thoeris. Here, we systematically scanned bacterial defense islands to identify anti-phage defense systems involving TIR-mediated signaling. We detected numerous configurations of such systems in bacterial genomes, involving [~]30 different protein effectors predicted to respond to TIR-produced immune signals. We experimentally verified 15 new TIR-containing systems, showing that they provide defense against phages through effector protein domains not previously known as associated with immunity. Further biochemical analyses revealed bacterial Thoeris systems that generate 2'cADPR, an immune signaling molecule central to plant immunity. We also discover multiple types of Thoeris that drive antiphage defense via canonical cADPR, a signaling molecule known to mediate human innate immunity. Our studies show that TIR-based immune signaling systems exist in at least 8% of bacterial genomes, and suggest conservation of TIR-derived immune signals across the tree of life.

microbiology↗

bioRxiv2025

Ancient convergence with prokaryote defense and recent adaptations to lentiviruses in primates characterize the ancestral immune factors SAMD9s

Human SAMD9 and SAMD9L are duplicated genes that encode innate immune proteins restricting poxviruses and lentiviruses, such as HIV, and implicated in life-threatening genetic diseases and cancer. Here, we combined structural similarity searches, phylogenetics and population genomics with experimental assays of SAMD9/9L functions to resolve the evolutionary and functional dynamics of these immune proteins, spanning from prokaryotes to primates. We discovered structural analogs of SAMD9/9L in the anti-bacteriophage defense system Avs, resulting from convergent evolution. Further, the predicted nuclease active site was conserved in bacterial analogs and was essential for cell death functions, suggesting a fundamental role in defense across different life kingdoms. Despite this ancestral immunity, we identified genomic signatures of evolutionary arms-races in mammals, with remarkable gene copy number variations targeted by natural selection. We further unveiled that the absence of SAMD9 in bonobos corresponds to a recent gene loss still segregating in the population. Finally, we found that chimp and bonobo SAMD9Ls have enhanced anti-HIV-1 functions, and that bonobo-specific SAMD9L polymorphisms confer increased anti-HIV-1 activity to human SAMD9L without compromising its effect on cell translation. These SAMD9/9L adaptations likely resulted from strong viral selective pressures, including by primate lentiviruses, and could contribute to lentiviral resistance in bonobos. Altogether, this study elucidates the interplay between ancient immune convergence across kingdoms and species-specific adaptations within the Avs9 and SAMD9/9L antiviral shared immunity. Significance statementThe SAMD9 gene family encodes antiviral factors of poxviruses and lentiviruses/HIV and is implicated in genetic diseases. Here, we found strong structural similarity with proteins from the Avs anti-bacteriophage system and uncovered ancient functional convergence in immune strategies between prokaryotes and metazoans. Within mammals, and more importantly in primates, we describe a highly dynamic evolutionary history of the SAMD9 gene family that underwent adaptive episodic gene losses. Unlike humans and chimps, some bonobos lack the SAMD9 gene entirely. Bonobos and chimps also possess unique variants of SAMD9L enhancing anti-HIV-1 activity without compromising cell functions, suggesting super-restrictors. This could also participate in shaping SIVcpz evolution and contribute to the absence of lentivirus-infected bonobos. Overall, the seeming dichotomy between the ancient evolutionary convergence in different kingdoms and recent functional adaptation within primates highlights the arms-races between key immune defense systems and viruses. This study paves the way for evolutionary medicine, where evolutionary-based discoveries may have application to human health, providing a deeper understanding of how the immune system adapts to fight viral infections over billion years of evolution.

evolutionary biology↗

bioRxiv2024

Better confidence intervals in simulation-based inference

Simulation-based methods such as approximate Bayesian computation (ABC) are widely used to infer the evolutionary history of populations from molecular genetic data. We describe and evaluate a new iterative method of statistical inference about model parameters, which revisits the idea of inferring a likelihood surface using simulation when the likelihood function cannot be evaluated. It is based on combining the random forest machine learning method, and multivariate Gaussian mixture (MGM) models, in an effective inference workflow, here used to fit models with up to 15 variable parameters. In addition to the traditional assessment of precision in terms of bias and mean square error, we also evaluate the coverage of confidence intervals. The method is compared with approximate Bayesian computation using random forests (ABC-RF), a non-iterative method sharing some technical features with the proposed approach, across scenarios of historical demographic inference from population genetic data. It is also compared to another iterative method, sequential neural likelihood estimation (SNLE). These comparisons highlight the importance of an iterative workflow for exploring the parameter space efficiently. For equivalent simulation effort of the data-generating process, the new summary-likelihood method provides intervals whose coverage is better controlled than the marginal coverage of intervals provided by ABC with random forests, and than generally reported for ABC methods. The iterative workflow can also yield greater improvements in estimator precision when larger datasets are used.

bioinformatics↗

bioRxiv2024

Performance evaluation of adaptive introgression classification methods

Introgression, the incorporation of foreign variants through hybridization and repeated backcross, is increasingly being studied for its potential evolutionary consequences, one of which is adaptive introgression (AI). In recent years, several statistical methods have been proposed for the detection of loci that have undergone adaptive introgression. Most of these methods have been tested and developed to infer the presence of Neanderthal or Denisovan AI in humans. Currently, the behaviour of these methods when faced with genomic datasets from evolutionary scenarios other than the human lineage remains unknown. This study therefore focuses on testing the performance of the methods using test data sets simulated under various evolutionary scenarios inspired by the evolutionary history of human, wall lizard (Podarcis) and bear (Ursus) lineages. These lineages were chosen to represent different combinations of divergence and migration times. We study the impact of these parameters, as well as migration rate, population size, selection coefficient and presence of recombination hotspots, on the performance of three methods (VolcanoFinder, Genomatnn and MaLAdapt) and a standalone summary statistic (Q95(w, y)). Furthermore, the hitchhiking effect of an adaptively introgressed mutation can have a strong impact on the flanking regions, and therefore on the discrimination between the genomic windows classes (i.e. AI/non-AI). For this reason, three different types of non-AI windows are taken into account in our analyses: independently simulated neutral introgression windows, windows adjacent to the window under AI, and windows coming from a second neutral chromosome unlinked to the chromosome under AI. Our results highlight the importance of taking into account adjacent windows in the training data in order to correctly identify the window with the mutation under AI. Finally, our tests show that methods based on Q95 seem to be the most efficient for an exploratory study of AI.

evolutionary biology↗

bioRxiv2024

Phages reconstitute NAD+ to counter bacterial immunity

Bacteria defend against phage infection via a variety of antiphage defense systems. Many defense systems were recently shown to deplete cellular nicotinamide adenine dinucleotide (NAD+) in response to infection, by breaking NAD+ to ADP-ribose (ADPR) and nicotinamide. It was demonstrated that NAD+ depletion during infection deprives the phage from this essential molecule and impedes phage replication. Here we show that a substantial fraction of phages possess enzymatic pathways allowing reconstitution of NAD+ from its degradation products in infected cells. We describe NAD+ reconstitution pathway 1 (NARP1), a two-step pathway in which one enzyme phosphorylates ADPR to generate ADPR-pyrophosphate (ADPR-PP), and the second enzyme conjugates ADPR- PP and nicotinamide to generate NAD+. Phages encoding the NARP1 pathway can overcome a diverse set of defense systems, including Thoeris, DSR1, DSR2, SIR2-HerA, and SEFIR, all of which deplete NAD+ as part of their defensive mechanism. Phylogenetic analyses show that NARP1 is primarily encoded on phage genomes, suggesting a phage- specific function in countering bacterial defenses. A second pathway, NARP2, allows phages to overcome bacterial defenses by building NAD+ via metabolites different than ADPR-PP. Our findings report a unique immune evasion strategy where viruses rebuild molecules depleted by defense systems, thus overcoming host immunity.

microbiology↗

bioRxiv2023

A conserved family of immune effectors cleaves cellular ATP upon viral infection

During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. In this study, we report a family of immune effectors in bacteria which, in response to phage infection, degrade cellular ATP and dATP by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems including CBASS, prokaryotic argonautes and NLR-like proteins, and we show that degradation of (d)ATP during infection halts phage propagation and aborts infection. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a new family of bacterial defense systems with a two-component phosphotransfer signaling architecture. The immune ATP nucleosidase domain is also encoded within a diverse set of eukaryotic proteins that have immune-like architectures, and we show biochemically that these eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.

microbiology↗

bioRxiv2022

Genetic drivers of chromosomal integron stability

Integrons are adaptive bacterial devices that rearrange promoter less gene cassettes into variable ordered arrays under stress conditions, to sample combinatorial phenotypic diversity. Chromosomal integrons often carry hundreds of silent gene cassettes, with integrase-mediated recombination leading to rampant DNA excision and integration, posing a potential threat to genome integrity. How this activity is regulated and controlled, particularly through selective pressures, to maintain such large cassette arrays is unknown. Here we show a key role of promoter-containing toxin-antitoxin (TA) cassettes as abortive systems that kill the cell when the overall cassette excision rate is too high. These results highlight the importance of TA cassettes regulating the cassette recombination dynamics and provide insight into the evolution and success of integrons in bacterial genomes. TeaserThe accumulation of cassette functions in integrons is ensured by toxin-antitoxin systems which kill the cell when the cassette excision rate is too high.

genetics↗

bioRxiv2022

Primate mothers promote proximity between their offspring and infants who look like them

Behavioral discrimination of kin is a key process structuring social relationships in animals. In this study, we provide a first example of discrimination towards non-kin by third-parties through a mechanism of phenotype matching. In mandrills, we recently demonstrated increased facial resemblance among paternally-related juvenile and adult females indicating adaptive opportunities for paternal kin recognition. Here, we hypothesize that mothers use offsprings facial resemblance with other infants to guide offsprings social opportunities towards similarly-looking ones. Using deep learning for face recognition in 80 wild mandrill infants, we first show that infants born to the same father or conceived during the tenure of the same alpha male resemble each other the most, independently of their age, sex or maternal origin, extending previous results to the youngest age class. Using long-term behavioral observations on association patterns and controlling for matrilineal origin, maternal relatedness and infant age and sex, we then demonstrate that, as hypothesized, mothers are spatially closer to infants that resemble their own offspring more, thereby facilitating associations among similar-looking infants. Using theoretical modeling, we describe a plausible evolutionary process whereby mothers gain fitness benefits by promoting nepotism among paternally related infants. This mechanism, that we call "second-order kin selection", may extend beyond mother-infant interactions and has the potential to explain cooperative behaviors among non-kin in social species, including humans.

evolutionary biology↗

bioRxiv2021

Prophage-encoded hotspots of bacterial immune systems

The arms race between bacteria and phages led to the emergence of a variety of genetic systems used by bacteria to defend against viral infection, some of which were repurposed as powerful biotechnological tools. While numerous defense systems have been identified in genomic regions termed defense islands, it is believed that many more remain to be discovered. Here, we show that P2- like prophages and their P4-like satellites have genomic hotspots that represent a significant source of novel anti-phage systems. We validate the defense activity of 14 systems spanning various protein domains and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Immunity hotspots are present across prophages of distant bacterial species, highlighting their biological importance in the competition between bacteria and phages.

microbiology↗

bioRxiv2020

Outer membrane lipoprotein DolP interacts with the BAM complex and promotes fitness during envelope stress response

In Gram-negative bacteria, coordinated remodelling of the outer membrane (OM) and the peptidoglycan is crucial for envelope integrity. Envelope stress caused by unfolded OM proteins (OMPs) activates sigmaE ({sigma}E) in Enterobacteria. {sigma}E upregulates OMP biogenesis factors, including the {beta}-barrel assembly machinery (BAM) that catalyzes OMP-folding. Elevated {sigma}E activity, however, can be detrimental for OM integrity. Here we report that DolP (YraP), a {sigma}E-upregulated OM lipoprotein important for envelope integrity, is a novel interactor of BAM and we demonstrate that OM-assembled BamA is a critical determinant of the BAM-DolP complex. Mid-cell recruitment of DolP had been previously associated to activation of septal peptidoglycan remodelling during cell division, but its role during envelope stress was unknown. We now show that DolP promotes cell fitness upon stress-induced activation of {sigma}E and opposes a detrimental effect caused by the overaccumulation of BAM in the OM. During envelope stress, DolP loses its association with the mid-cell, thus suggesting a possible link between envelope stress caused by impaired OMP biogenesis and the regulation of a late step of cell division.

microbiology↗