Biology subjects

Andre, M.

Publications and source records attributed to Andre, M..

12 recordsLinked to original sources

bioRxiv2026

Peripheral anatomy of the dolphin ear and associated nervous structures: insights from macroscopic dissection, DICE-{micro}CT, histology, and confocal microscopy

The peripheral auditory system of dolphins comprises specialised bony, fatty, vascular, and neural structures adapted for underwater hearing and diving physiology. These include the external ear canal, acoustic fat bodies, sinuses, and associated neurovascular networks, which together support sound conduction, protection, and possibly sensory functions. Despite advances in gross anatomical description, the detailed integration of these tissues, particularly the innervation, neurovascular organisation, and their functional implications, remains poorly understood. Previous studies have described the presence of sensory nerve formations and vascular plexuses, but their arrangement, connectivity, and relation to each other are unresolved. Here, we combine macroscopic dissection, DICE-{micro}CT, histology, and high-resolution confocal microscopy to characterise several neurovascular and sensory components of the dolphin peripheral auditory system in several delphinid species. Macroscopic dissection and DICE-{micro}CT revealed the traditional acoustic fat body distribution with detailed morphology of the posterolateral extension that is not well-known. The cranial nerve distribution, and specifically the mandibular nerve branching patterns, are described in detail. Confocal microscopy uncovered a stratified neurovascular plexus around the external ear canal with a complex sensory system comprising lamellar corpuscles, Merkel cell-neurite complexes, and intraepithelial nerve fibres. Notably, the lamellar corpuscles formed a continuous, three-dimensional neural network with frequent merging and splitting of axonal bundles, shared perineuria, and vascular integration, features not observed in previous studies. Our findings demonstrate that the dolphin external ear canal and surrounding structures form a sophisticated, multimodal somatosensory organ, integrating structural, vascular, and neural specialisations likely adapted for proprioceptive mechanosensation in the aquatic environment. This study provides insights into the integration of the various components of the peripheral hearing apparatus. Future studies integrating anatomical, electrophysiological, and biomechanical approaches are needed to fully elucidate these adaptations.

neuroscience↗

bioRxiv2025

Imputed transcriptional patterns in ancient genomes reveal molecular targets of selection

The genetically regulated component of molecular traits can be imputed from ancient genomes, though low genotyping quality and genetic drift may impair accurate expression prediction and results interpretation. We developed tissue-specific gene expression and alternative splicing prediction models and applied them to over a thousand imputed ancient genomes spanning 10,000 years of Western Eurasian history. We revealed gene regulatory patterns diverging with time, space and genomic ancestry by fitting predicted transcriptional profiles onto multivariable models including these factors. By interpreting associations with time as recent natural selection we identify hits mediated by transcriptional changes. Finally, we fine-mapped these selection signals to tissue-specific transcriptional traits, explicitly accounting for prediction uncertainty. Among others, we elucidate the spatial patterns and the regulatory features promoting selection at LCT, FADS1, SLC22A5/P4HA2, ACAD10/OAS3 and find novel signals of selection at TBIMB6, SORD2P and AC012370.3.

genomics↗

bioRxiv2025

Mobilizable adipose stromal cells fuel regenerative adipogenesis in injured muscle

Skeletal muscle regeneration is a highly orchestrated process involving the dynamic interplay of multiple cell types. Among these, fibro-adipogenic progenitors (FAPs), a population of resident mesenchymal stromal cells (MSCs), are essential for creating a supportive microenvironment that promotes satellite cell differentiation and modulates immune responses. Our recent work revealed that adipose stromal cells (ASCs) from subcutaneous adipose tissue (ScAT) infiltrate the injured muscle within the first 24h post-injury, contributing significantly to the regenerative process. Consequently, the FAP population in the regenerating muscle comprises both resident FAPs and infiltrated ASCs. In the present study, using single cell RNA-seq in a mouse model with trackable KikGR+ ASCs and bioinformatics analyses, we identify Limch1+/Prg4+ ASCs as the primary Mobilizable ASCs (Mob-ASCs) that migrate to and infiltrate the injury site. Notably, this migration is detectable as early as 14 hours post-injury. We demonstrate that these cells are pre-activated within the ScAT, primed to initiate both migratory and regenerative programs. Intriguingly, bioinformatic inference of key activated transcription factors suggested that adipogenesis is also activated in these cells. Leveraging supervised machine learning, we tracked the fate of Mob-ASCs within the regenerating muscle post-injury, where they continue to execute these programs. Importantly, these cells lineage is cued towards a fate of adipogenesis. In vivo, we observed transient generation of adipocytes with a peak at 7-9 days post-injury to which infiltrated ASCs contributed. In vitro, conditioned media assays further revealed that adipocytes derived from ASCs--but not those from FAPs--enhance myoblasts fusion. Collectively, our findings establish Limch1+/Prg4+ ASCs as the Mobilizable ASC population and suggest that their transient adipogenic differentiation is beneficial for muscle regeneration.

physiology↗

bioRxiv2025

Interaction dynamics between epithelial cysts captured by tissue rheology

Epithelial cysts are minimal structures involved in morphogenesis. They are fluid-filled cavities surrounded by an epithelial monolayer. Cysts grow during development and their interactions shape organs. While their growth dynamics as single structures are well characterised, the physical mechanisms underlying their interaction remain poorly understood. Here we design a minimal assay of interacting cyst doublets based on microfabrication, quantitative biology, and theory to show that Madin-Darby Canine Kidney (MDCK) cyst interactions are essentially determined by the rheological properties of their epithelial monolayers. We report two phases of interaction between epithelial cysts: coalescence of cellular monolayers and lumen fusion, with similar speeds of 0.3 {micro}m/h. We modulate the distribution of interaction phenotypes by reducing cell-cell adhesion using E-cadherin knock-out MDCK cells and we report that E-cadherin depletion promotes lumen fusion. Remarkably, the dynamics of coalescence and fusion are conserved between both cell lines. To understand the conserved speeds and the effect of cell-cell adhesion, we model the mechanical behavior of cyst doublets as a complex fluid to predict a speed determined by viscosity, a stretch-dependent monolayer tension, and the adhesion energy between cells. We measure these parameters through rheological experiments using micropipette aspiration and lumen drainage, which span the full range of stretch. A key insight from this analysis is that accounting for the tensions dependence on stretch is is essential to capture the different dynamics observed during cyst interaction. Using these rheological measurements, we successfully recapitulate the conserved speed. Altogether, our results open new perspectives to understand tissue dynamics during organogenesis through simple physical arguments. Significance StatementCysts are fluid-filled cavities sur-rounded by a cellular monolayer. Interactions between cysts are important during morphogenesis, yet their governing rules are poorly understood. Here we designed a doublet assay using microfabrication to control cyst geometry and characterized their interaction dynamics. We report that speeds of coalescence and fusion between epithelial cysts are conserved even for cell lines depleted in E-cadherin, a central adhesion protein. We measured their rheological parameters by two independent methods, micropipette aspiration and laser cutting. Using a simple model and scaling arguments, we demonstrate that these parameters are sufficient to explain interaction speeds. This study sheds light on the interplay between tissue dynamics and rheology and its implication in orchestrating morphogenetic events in vitro and in vivo.

biophysics↗

bioRxiv2025

Interplay between Rac1/RhoA and actin waves in giant epithelial cells : experiment and theory

The acto-myosin cytoskeleton is a key driver of cellular shape changes in vivo and in vitro. Acto-myosin organization results from actin assembly and interactions between actin and myosin, which are both regulated by small Rho GTPases like Rac1 and RhoA. To uncover principles governing cytoskeletal organization, we analyzed actin patterns using live microscopy and theory. In giant Madin-Darby Canine Kidney (MDCK) epithelial cells and REF52 fibroblasts, we observed acto-myosin stress fibres and propagating waves. Stress fibres were stationary and correlated with homogeneous distributions of Rac and RhoA activity. Waves propagated at {approx} 1m/min and were associated with density variations of actin, Rac and active RhoA. Some waves transported cellular components or generated protrusions at the cell edge. Essential features of wave propagation are captured by a polar reaction-diffusion system for actin and Rac. Notably, two colliding waves annihilate each other. In cells, myosin activity was not required for the emergence of waves, but tended to suppress them. Consistently, local activation of RhoA slowed down or stopped and broke waves. These results highlight how the coupling between acto-myosin and Rho GTPase generates a variety of cytoskeletal structures and dynamics. O_TEXTBOXSIGNIFICANCEThe cytoskeleton shapes cells in vitro and in vivo. Its molecular mechanisms have been extensively documented, but the mesoscopic structures resulting from the interplay between the activator and the motor activity have been poorly characterized. Here we show that two structures are conserved in two systems, stress fibres with RhoA activity and diffusion actin waves regulated by Rac1. The annihilation of waves and the alteration of the wave dynamics are reproduced by a minimal model based on a polar reaction-diffusion model. This approach could pave the way to a generic description of regulated active gels in cells with potential biological functions, such as stress generation for fibres and probing of space and homogenization of the cortex by actin waves. C_TEXTBOX

biophysics↗

bioRxiv2024

Resolving out of Africa event for Papua New Guinean population using neural network

The demographic history of the Papua New Guinean population is a subject of significant interest due to its early settlement in New Guinea, at least 50 thousand years ago, and its relative isolation compared to other out of Africa populations. This isolation, combined with substantial Denisovan ancestry, contributes to the unique genetic makeup of the Papua New Guinean population. Previous research suggested the possibility of admixture with an early diverged modern human population, but the extent of this contribution remains debated. This study re-examines the demographic history of the Papua New Guinean population using newly published samples and advanced analytical methods. Our findings demonstrate that the observed shifts in relative cross coalescent rate curves are unlikely to result from technical artefacts or contributions from an earlier out of Africa population. Instead, they are likely due to a significant bottleneck and slower population growth rate within the Papua New Guinean population. Our analysis positions the Papua New Guinean population as a sister group to other Asian populations, challenging the notion of Papua New Guinean as an outgroup to both European and Asian populations. This study provides new insights into the complex demographic history of the Papua New Guinean population and underscores the importance of considering population-specific demographic events in interpreting relative cross coalescent rate curves.

evolutionary biology↗

bioRxiv2024

Contribution of the neuron-specific ATP1A3 to embryonic spinal circuit emergence

The early neurodevelopmental contributions of ion pumps remain poorly characterized. Combining analysis of public human embryo single-cell transcriptomic datasets and an embryonic chicken model, we found a conserved differentiation sequence whereby spinal cord neurons switch on neuron-specific alpha3 subunit (ATP1A3) of Na+/K+ ATPases. In the chicken model, ATP1A3 is distributed along axons and growth cones. Its knockdown alters axon pathfinding of dorsal interneurons (DIN) that wire spinocerebellar circuits. In mirror of reported electric field (EF)-driven cell migration, we found that DIN axons align in EFs, which was abolished by Na+/K+ ATPase inhibitor Ouabain and ATP1A3 knockdown. We recorded an embryonic trans-neural-epithelial potential generating EF whose pharmacological and surgical manipulation mimicked ATP1A3 knock-down-induced altered DIN axon pathfinding. Using DINs transplantation paradigm, we found that ATP1A3 is required cell-autonomously for EF-mediated long-range guidance. Finally, dominant-negative ATP1A3 mutation causing an early ATP1A3 childhood disease disrupts this fundamental developmental process, revealing unexpected pathogenic mechanisms.

developmental biology↗

bioRxiv2024

Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations

Neandertals and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 years, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that Denisovan-like haplotypes exhibit increased levels of population differentiation between PNG highlanders and lowlanders. The highly differentiated haplotypes, more common among highlanders, reside in genomic areas linked to brain development genes. Conversely, those more frequent in lowlanders overlap with genes enriched in immune response processes. Furthermore, Denisovan-like haplotypes displayed pronounced signatures of diversification within the major histocompatibility complex. Our findings suggest that Denisovan DNA has provided a valuable source of genetic variation to PNG genomes that facilitated adaptive responses to environmental challenges.

genomics↗

bioRxiv2023

DMRT1 is a Testis Determining Gene in Rabbits and is Also Essential for Female Fertility

DMRT1 is the testis-determining factor in several species of vertebrates, but its involvement in mammalian testes differentiation, where SRY is the testis-determining gene, remains ambiguous. So far, DMRT1 loss of function has been described in two mammalian species and induces different phenotypes: disorders of sex development (46, XY DSD) in men and male infertility in mice. We thus abolished DMRT1 expression by CRISPR/Cas9 in a third species of mammal, the rabbit. First, we observed that gonads from XY DMRT1-/- rabbit fetuses differentiated like ovaries, highlighting that DMRT1 is involved in testis determination. In addition to SRY, DMRT1 is required in the supporting cells to increase the expression of the SOX9 gene, which heads the testicular genetic cascade. Second, we highlighted another function of DMRT1 in the germline since XX and XY DMRT1-/- ovaries did not undergo meiosis and folliculogenesis. XX DMRT1-/- adult females were sterile, showing that DMRT1 is also crucial for female fertility. To conclude, these phenotypes indicate an evolutionary continuum between non-mammalian vertebrates such as birds and non-rodent mammals. Furthermore, our data support the potential involvement of DMRT1 mutations in different human pathologies, such as 46, XY DSD as well as male and female infertility.

developmental biology↗

bioRxiv2022

Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels

Highlanders and lowlanders of Papua New Guinea (PNG) have faced distinct environmental conditions. These environmental differences lead to specific stress on PNG highlanders and lowlanders, such as hypoxia and environment-specific pathogen exposure, respectively. We hypothesise that these constraints induced specific selective pressures that shaped the genomes of both populations. In this study, we explored signatures of selection in newly sequenced whole genomes of 54 PNG highlanders and 74 PNG lowlanders. Based on multiple methods to detect selection, we investigated the 21 and 23 genomic top candidate regions for positive selection in PNG highlanders and PNG lowlanders, respectively. To identify the most likely candidate SNP driving selection in each of these regions, we computationally reconstructed allele frequency trajectories of variants in each of these regions and chose the SNP with the highest likelihood of being under selection with CLUES. We show that regions with signatures of positive selection in PNG highlanders genomes encompass genes associated with the hypoxia-inducible factors pathway, brain development, blood composition, and immunity, while selected genomic regions in PNG lowlanders contain genes related to immunity and blood composition. We found that several candidate driver SNPs are associated with haematological phenotypes in the UK biobank. Moreover, using phenotypes measured from the sequenced Papuans, we found that two candidate SNPs are significantly associated with altered heart rates in PNG highlanders and lowlanders. Furthermore, we found that 16 of the 44 selection candidate regions harboured archaic introgression. In four of these regions, the selection signal might be driven by the introgressed archaic haplotypes, suggesting a significant role of archaic admixture in local adaptation in PNG populations.

evolutionary biology↗

bioRxiv2022

Absence of estrogen leads to defects in spermatogenesis and increased semen abnormalities in male rabbits

Estrogens are steroid hormones produced by the aromatization of androgens by the aromatase enzyme, encoded by the CYP19A1 gene. Although generally referred to as "female sex hormones", estrogen is also produced in the adult testes of many mammals, including humans. To better understand the function of estrogens in the male, we used the rabbit model which is an important biomedical model. First, the expression of CYP19A1 was localized, demonstrating that testicular estrogens are produced by meiotic germ cells inside the seminiferous tubules. Next, the cells expressing ESR1 and ESR2 were identified, showing that estrogens could exert their function on post-meiotic germ cells in the tubules and play a role during sperm maturation, since ESR1 and ESR2 were detected in the cauda epididymis. Then, CRISPR/Cas9 CYP19A1-/- genetically modified rabbits were analyzed. CYP19A1-/- males showed decreased fertility with lower sperm count associated with hypo-spermatogenesis and lower spermatid number. Germ/sperm cell DNA methylation was unchanged, while sperm parameters were affected as CYP19A1-/- males exhibited reduced sperm motility associated with increased flagellar defects. In conclusion, testicular estrogens could be involved in the spermatocyte-spermatid transition in the testis, and in the acquisition of sperm motility in the epididymis.

molecular biology↗

bioRxiv2017

Inhibition of granulocyte ROS production by opioids prevents regeneration

Inhibition of regeneration and induction of healing are classic outcomes of tissue repair in adult mammals. Here, by using gain and loss of function experiments, we demonstrate that both endogenous and exogenous opioids prevent tissue regeneration in adults, by inhibiting the early reactive oxygen species (ROS) production occurring after lesion and required for regeneration. These effects can be overcome and regeneration induced by the use of an opioid antagonist. These results, obtained in both gold-standard adult zebrafish and a newly-developed model of regeneration in adult mammals, demonstrate that this mechanism can be considered as a general paradigm in vertebrates. In addition, we show that opioids act via signaling through peripheral mu-receptors expressed on granulocytes. This work clearly demonstrates the deleterious role of opioids on tissue regeneration through the control of ROS production in vertebrates and thus questions about opioid-based analgesia in perioperative care.

physiology↗