Biology subjects

Dupont, L.

Publications and source records attributed to Dupont, L..

10 recordsLinked to original sources

bioRxiv2023

Genome-wide CRISPR/Cas9 screen identifies MAT2A as a critical host factor for BK Polyomavirus

BK polyomavirus (BKPyV) is a ubiquitous human pathogen that causes major complications for renal transplant patients (polyomavirus-associated nephropathy) and hematopoietic stem cell transplant patients (haemorrhagic cystitis). There are currently no effective antivirals available against BKPyV. As polyomaviruses are small DNA viruses that express very few proteins and utilise host DNA polymerases for their replication, there is limited possibility of targeting viral proteins for therapeutic intervention. As such, there is increasing interest in targeting host pathways to inhibit these viruses. To identify host genes required for BKPyV infection we have conducted the first genome-wide CRISPR/Cas9 screen in BKPyV infected cells. This led to the identification of methionine adenosyltransferase 2A (MAT2A), which we have validated as a host dependency factor for BKPyV infection. MAT2A is a druggable host enzyme that synthesises S-adenosylmethionine, the principal co-factor and methyl donor within cells. We have found that a small molecule inhibitor of MAT2A is a potent antiviral drug inhibiting BKPyV replication, offering a new therapeutic option for treatment of BKPyV diseases.

microbiology↗

bioRxiv2023

A Multi-omic Analysis of the Human Lung Reveals Distinct Cell Specific Aging and Senescence Molecular Programs

Age is a major risk factor for lung disease. To understand the mechanisms underlying this association, we characterized the changing cellular, genomic, transcriptional, and epigenetic landscape of lung aging using bulk and single-cell RNAseq (scRNAseq) data. Our analysis revealed age-associated gene networks that reflected hallmarks of aging, including mitochondrial dysfunction, inflammation, and cellular senescence. Cell type deconvolution revealed age-associated changes in the cellular composition of the lung: decreased alveolar epithelial cells and increased fibroblasts and endothelial cells. In the alveolar microenvironment, aging is characterized by decreased AT2B cells and reduced surfactant production, a finding that was validated by scRNAseq and IHC. We showed that a previously reported senescence signature, SenMayo, captures cells expressing canonical senescence markers. SenMayo signature also identified cell-type specific senescence-associated co-expression modules that have distinct molecular functions, including ECM regulation, cell signaling, and damage response pathways. Analysis of somatic mutations showed that burden was highest in lymphocytes and endothelial cells and was associated with high expression of senescence signature. Finally, aging and senescence gene expression modules were associated with differentially methylated regions, with inflammatory markers such as IL1B, IL6R, and TNF being significantly regulated with age. Our findings provide new insights into the mechanisms underlying lung aging and may have implications for the development of interventions to prevent or treat age-related lung diseases.

genomics↗

bioRxiv2022

Reputation risk during dishonest social decision-making modulates anterior insular and cingulate cortex activity and connectivity

To explore the neural underpinnings of (dis)honest decision making under quasi-ecological conditions, we used an fMRI adapted version of a card game in which deceptive or truthful decisions are made to an opponent, with or without the risk of getting caught by them. Dishonest decisions were associated to increased activity in a cortico-subcortical circuit including the bilateral anterior cingulate cortex (ACC), anterior insula (AI), left dorsolateral prefrontal cortex, supplementary motor area, and right caudate. Crucially, deceptive immoral decisions under reputation risk enhanced activity of - and functional connectivity between - the bilateral ACC and left AI, suggesting the need for heightened emotional processing and cognitive control when making immoral decisions under reputation risk. Tellingly, more manipulative individuals required less involvement of the ACC during risky self-gain lies but more involvement during other-gain truths, pointing to the need of cognitive control only when going against ones own moral code.

neuroscience↗

bioRxiv2022

Wolbachia genomics support a tripartite nutritional symbiosis in blood-sucking Triatomine bugs

The nutritional symbiosis promoted by bacteria is a key determinant for adaptation and evolution of many insect lineages. A complex form of nutritional mutualism that arose in blood-sucking insects critically depends on diverse bacterial symbionts that supplement the diet of their nutrient-poor hosts with B vitamins. For instance, the triatomine bug Rhodnius prolixus, one of the main vectors of the Chagas disease in humans, is known to maintain a nutritional symbiosis with the gut symbionts Rhodococcus rhodnii. In this study, we show that Wolbachia symbionts are also widely distributed in the Rhodnius genus. We have screened a large set of Rhodnius blood-sucking bugs samples belonging to 17 different species and to the three phylogenetic groups, prolixus, pallescens and pictipes. We assembled 13 genomes of Wolbachia infecting eight Rhodnius species from prolixus and pictipes groups. We demonstrate that these Wolbachia belong to supergroup F and are closely related to Wolbachia infecting the bedbug Cimex lectularius (wCle). Although bedbugs and triatomines are very distantly related hemipteran bugs, the genomes of their respective Wolbachia were highly similar, suggesting recent horizontal host switches. We also show that Rhodnius Wolbachia genomes infecting the prolixus group encode intact biotin operon, the hallmark of nutritional symbiosis in bedbugs. This operon is lacking from all the other Wolbachia infecting R. pictipes. Finally, host genome analyses provide evidence of massive Wolbachia-to-Rhodnius gene transfers in almost samples, providing footprints of past infections that support a widespread and probably ancient symbiotic association between Wolbachia and triatomine bugs. Our results suggest that both Wolbachia and R. rhodnii gut symbionts and their Rhodnius host maintain a highly prevalent symbiotic relationship, in which the vertically-inherited Wolbachia has the metabolic potantial to ensure or complement, the nutritional mutualism provided by the gut symbionts. Specific loss of the biotin operon in some symbiont genomes suggests that the boundaries between obligatory mutualism, facultative mutualism and parasitism in Wolbachia are transient and fluid, supporting a dynamic process of transition and reversion from one state to another.

evolutionary biology↗

bioRxiv2022

Reproductive strategies in a complex of simultaneously hermaphroditic species, the Allolobophora chlorotica case study

An in-depth knowledge of reproductive strategies is essential to understand the evolutionary history of species and their resulting patterns of taxonomic diversity. In particular, the study of life history traits related to reproduction could help to resolve the speciation patterns in the cryptic species complexes recently found in earthworms. Here, we carried out a parentage analysis in such a complex, the Allolobophora chlorotica aggregate. Using four nuclear microsatellite markers and a fragment of the cytochrome c oxidase subunit I mitochondrial gene we investigated (i) the mating strategies between individuals belonging to two divergent mitochondrial lineages (L2 and L3) that cannot be distinguished with nuclear markers and (ii) the reproductive isolation between lineages that are differentiated both at the mitochondrial and nuclear level (L2/L3 and L1). Among the 157 field collected individuals, 66 adults were used in cross-breeding experiments to form 22 trios based on their assignment to a mitochondrial lineage, and 453 obtained juveniles were genotyped. We showed that adults that mated with both their potential mates in the trio produced significantly more juveniles. In L2 and L3 crosses, a sex-specific pattern of reproduction characteristic to each lineage was observed, suggesting a possible conflict of interest between mating partners. In L2/L3 and L1 crosses, a high production of cocoons was counterbalanced by a low hatching rate, suggesting a post-zygotic reproductive isolation. Reproductive strategies are thus likely to contributed to the diversification of this complex of species and we advocate further studies on sexual selection and sex allocation in earthworms.

evolutionary biology↗

bioRxiv2021

INTEGUMENT-SPECIFIC TRANSCRIPTIONAL REGULATION IN THE MID- STAGE OF FLAX SEED DEVELOPMENT INFLUENCES THE RELEASE OF MUCILAGE AND THE SEED OIL CONTENT

Flax (Linum usitatissimum L.) seed oil, which accumulates in the embryo, and mucilage, which is synthesized in the seed coat, are of great economic importance for food, pharmaceutical as well as chemical industries. Theories on the link between oil and mucilage production in seeds consist in the spatio-temporal competition of both compounds for photosynthates during the very early stages of seed development. In this study, we demonstrate a positive relationship between seed oil production and seed coat mucilage extrusion in the agronomic model, flax. Three recombinant inbred lines were selected for low, medium and high mucilage and seed oil contents. Metabolite and transcript profiling (1H NMR and DNA oligo-microarrays) was performed on the seeds during seed development. These analyses showed main changes in the seed coat transcriptome during the mid-phase of seed development (25 Days Post-Anthesis), once the mucilage biosynthesis and modification processes are thought to be finished. These transcriptome changes comprised genes that are putatively involved in mucilage chemical modification and oil synthesis, as well as gibberellic acid (GA) metabolism. The results of these integrative biology approach, suggest that transcriptional regulations of seed oil and fatty acid (FA) metabolism could occur in the seed coat during the mid-stage of seed development, once the seed coat carbon supplies have been used for mucilage biosynthesis and mechanochemical properties of the mucilage secretory cells.

plant biology↗

bioRxiv2020

At each site its diversity: DNA barcoding reveals remarkable earthworm diversity in neotropical rainforests of French Guiana

Despite their recognized essential role in soil, earthworms in tropical environments are still understudied. The aim of this study was to re-evaluate the diversity at the regional scale, as well as to investigate the environmental and spatial drivers of earthworm communities. We sampled earthworm communities across a range of habitats at six locations in French Guiana using three different sampling methods. We generated 1675 DNA barcodes and combined them with data from a previous study. Together, all sequences clustered into 119 MOTUs which were used as proxy to assess species richness. Only two MOTUs were common between the six locations and 20.2 % were singletons, showing very high regional species richness and a high number of rare species. A canonical redundancy analysis was used to identify key drivers of the earthworm community composition. The RDA results and beta-diversity calculations both show strong species turnover and a strong spatial effect, resulting from dispersal limitations that are responsible for the current community composition. Sampling in different microhabitats allowed the discovery of 23 MOTUs that are exclusively found in decaying trunks and epiphytes, highlighting hidden diversity of earthworms outside of soil.

ecology↗

bioRxiv2020

Ecology and population genetics of the parasitoid Phobocampe confusa (Hymenoptera: Ichneumonidae) in relation to its hosts, Aglais species (Lepidoptera: Numphalidae).

The biology of parasitoids in natural ecosystems remain very poorly studied, while they are key species for their functioning. Here we focused on Phobocampe confusa, a vanessines specialist, responsible for high mortality rates in very emblematic butterfly species in Europe (genus Aglais). We studied its ecology and genetic structure in connection with those of its host butterflies in Sweden. To this aim, we gathered data from 428 P. confusa individuals reared from 6094 butterfly larvae (of A. urticae, A. io and in two occasions of Araschnia levana) collected over two years (2017 and 2018) and 19 sites distributed along a 500 km latitudinal gradient. We found that P. confusa is widely distributed along the latitudinal gradient. Its distribution is constrained over time by the phenology of its hosts. The large variation in climatic conditions between sampling years explains the decrease in phenological overlap between P. confusa and its hosts in 2018 and the 33.5% decrease in the number of butterfly larvae infected. At least in this study, P. confusa seems to favour A. urticae as host: while it parasitized nests of A. urticae and A. io equally, the proportion of larvae is significantly higher for A. urticae. At the landscape scale, P. confusa is almost exclusively found in vegetated open land and near deciduous forests, whereas artificial habitats are negatively correlated with the likelihood of a nest to be parasitized. The genetic analyses on 89 adult P. confusa and 87 adult A. urticae using COI and AFLP markers reveal a low genetic diversity in P. confusa and a lack of population genetic structure in both species, at the scale of our sampling. Further genetic studies using high-resolution genomics tools will be required to better understand the population genetic structure of P. confusa, its biotic interactions with its hosts, and ultimately the stability and the functioning of natural ecosystems.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

bioRxiv2020

(p)ppGpp and malonyl-CoA set the pace for Staphylococcus aureus adaptation to FASII antibiotics and provide a basis for bi-therapy inhibition

Fatty acid biosynthesis (FASII) enzymes are considered valid targets for antimicrobial drug development against the human pathogen Staphylococcus aureus. However, incorporation of host fatty acids confers FASII antibiotic adaptation that compromises prospective treatments. S. aureus adapts to FASII inhibitors by a first non-replicative latency period followed by outgrowth. Here we used transcriptional fusions and direct metabolite measurements to investigate the factors that dictate the duration of latency prior to outgrowth. We show that stringent response induction leads to repression of FASII and phospholipid synthesis genes. (p)ppGpp induction inhibits synthesis of malonyl-CoA, a molecule that derepresses FapR, a key regulator of FASII and phospholipid synthesis. Anti-FASII treatment also triggers transient expression of (p)ppGpp-regulated genes during the anti-FASII latency phase, with concomitant repression of FapR regulon expression. These effects are reversed upon outgrowth. GTP depletion, a known consequence of stringent response, also occurs during FASII latency, and is proposed as the common signal linking these responses. We next show that anti-FASII treatment shifts malonyl-CoA distribution between its interactants FapR and FabD, towards FapR, increasing expression of phospholipid synthesis genes plsX and plsC during outgrowth. We conclude that components of the stringent response dictate malonyl-CoA availability in S. aureus FASII regulation, and contribute to latency prior to anti-FASII-adapted outgrowth. A combinatory approach, coupling a (p)ppGpp inducer and an anti-FASII, blocks S. aureus outgrowth, opening perspectives for bi-therapy treatment. ImportanceStaphylococcus aureus is a major human bacterial pathogen for which new inhibitors are urgently needed. Antibiotic development has centered on the fatty acid synthesis (FASII) pathway, which provides the building blocks for bacterial membrane phospholipids. However, S. aureus overcomes FASII inhibition and adapts to anti-FASII by using exogenous fatty acids that are abundant in host environments. This adaptation mechanism comprises a transient latency period, followed by bacterial outgrowth. Here we use metabolite sensors and promoter reporters to show that responses to stringent conditions and to FASII inhibition intersect: both involve GTP and malonyl-CoA. These two signaling molecules contribute to modulating the duration of latency prior to S. aureus adaptation outgrowth. We exploit these novel findings to propose a bi-therapy treatment against staphylococcal infections.

microbiology↗

bioRxiv2019

Permissive Fatty Acid Incorporation in Host Environments Promotes Staphylococcal Adaptation to FASII Antibiotics

Development of fatty acid synthesis pathway (FASII) inhibitors against the major human pathogen Staphylococcus aureus hinges on the accepted but unproven postulate that an endogenously synthesized branched chain fatty acid is required to complete membrane phospholipids. Evidence for anti-FASII efficacy in animal models supported this view. However, restricted test conditions used previously to show FASII antibiotic efficacy led us to investigate these questions in a broader, host-relevant context. We report that S. aureus rapidly adapts to FASII antibiotics without FASII mutations when exposed to host environments. Treatment with a lead FASII antibiotic upon signs of infection, rather than just after inoculation as commonly practiced, failed to eliminate S. aureus from infected organs in a septicemia model. In vitro, addition of serum facilitated rapid S. aureus FASII bypass by environmental fatty acid (eFA) replacement in phospholipids. Serum lowers membrane stress, leading to increased retention of the two substrates required for exogenous fatty acid (eFA) utilization. In these conditions, eFA occupy both phospholipid positions 1 and 2, regardless of anti-FASII selection. This study revises conclusions on S. aureus fatty acid requirements by disproving the postulate of fatty acid stringency, and reveals an Achilles heel for using FASII antibiotics to treat infection in monotherapy.\n\nSignificance statementAntibiotic discovery to overcome treatment failure has huge socio-medical and economic stakes. The fatty acid synthesis (FASII) pathway is considered an ideal druggable target against the human pathogen Staphylococcus aureus, based on evidence of anti-FASII efficacy in infection models, and the postulate that S. aureus synthesizes an irreplaceable fatty acid. We report that S. aureus alters its behavior in host-relevant conditions. Administering FASII antibiotics upon signs of infection, rather than just after inoculation as frequently practiced, failed to clear septicemic infections. In serum, S. aureus rapidly overcomes FASII antibiotics by incorporating alternative fatty acids. We conclude that previously, premature antibiotic treatments and experimental constraints masked S. aureus antibiotic adaptation capacity. These findings should help streamline future drug development programs.

microbiology↗