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Biology subjects

Dumas, S.

Publications and source records attributed to Dumas, S..

12 recordsLinked to original sources

Interconnected Macroporous GelMA Scaffolds for Cell Culture through Temperature Controlled Spinodal Decomposition

Developing biomaterials that faithfully recapitulate the complex architecture of native tissues is central to tissue engineering. Conventional hydrogels typically exhibit nanoscale porosity, which limits mass transport and cell migration and thereby constrains tissue development. Here, we exploit liquid-liquid phase separation (LLPS) to generate interconnected macroporous gelatin methacryloyl (GelMA) scaffolds with tunable pore sizes ranging from 2 to 50 m under physiological pH conditions. By mapping the GelMA/dextran phase diagram, we identify a composition range in which LLPS occurs through spinodal decomposition, resulting in a spontaneous bicontinuous, trabecular-like architecture. Pore size can be further tuned by varying polymer concentrations and temperature. We advantageously combined thermal gradients and photopatterning to enable spatial control over pore morphology to fabricate hierarchically structured materials. The biological relevance of these architectures is assessed using fibroblasts cultured within controlled porosity gradients. We show that pore size strongly influences cell infiltration, growth, and spatial organization, with larger pores providing sufficient space for cell migration while reducing the dependence on matrix degradation. Pore size of 7-15 m is identified for maximizing fibroblast growth. Overall, our approach provides a versatile platform for porosity screening, enabling the engineering of biomimetic hydrogels with optimized microarchitectures tailored to specific biological contexts for three-dimensional cell culture.

bioengineering↗

Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland

Single-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell. Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles--absent in reference populations--and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.

genomics↗

Beta2* Nicotinic Receptors Tune Prefrontal Behavior Through Distinct Neuronal Populations

Beta2 subunit-containing nicotinic acetylcholine receptors (beta2*nAChRs) are highly expressed in the prefrontal cortex (PFC) and critically regulate behavioral and cognitive domains that are disrupted in neuropsychiatric disorders. Despite their therapeutic potential, the cell-type- and circuit-specific functions of beta2* nAChRs remain poorly defined, partially due to the lack of selective pharmacological tools. Here, we delineate the cellular expression patterns and behavioral roles of beta2* nAChRs expressed in a general vs. highly specific neuronal populations of the mouse PFC. Using fluorescence in situ hybridization (FISH), we mapped beta2 nicotinic subunit expression across cortical layers and major neuronal classes. We then employed CRISPR-mediated knockdown (KD) to reduce beta2* nAChRs expression selectively in two distinct PFC neuronal populations and, for comparison, in a striatal population. The KD of beta2* nAChRs in a mixed population of excitatory and inhibitory neurons in deep PFC layers resulted in a mild impairment of social and exploratory behaviors. In contrast, KD in a highly selective population of superficial-layer interneurons expressing the serotonin receptor 5HT3a induced a robust hypersocial phenotype, accompanied by changes in exploratory behavior. Notably, KD of beta2* nAChRs in a rare NPY-expressing striatal population slightly affected similar behavioral domains, but in the opposite direction to PFC manipulations. Together, these findings reveal opposing, cell-type- and region-specific contributions of beta2* nAChRs to behavioral regulations, highlighting the necessity of circuit-resolved targeting strategies to improve the precision and efficacy of therapeutic intervention for neuropsychiatric disorders.

neuroscience↗

A single-nucleus multimodal framework reveals epigenomic priming of chemoresistant states in ovarian cancer

Non-genetic intratumor heterogeneity (ITH) drives therapeutic failure in cancer, yet its clinical monitoring remains challenging. We develop a multimodal single-nucleus framework that simultaneously profiles transcriptional and histone modification landscapes from frozen biopsies. Applied to longitudinal samples from 16 patients with high-grade serous ovarian cancer (HGSOC), this approach reveals reproducible tumor evolution under chemotherapy: proliferative and interferon-responsive states are lost, while those associated with TNF- and epithelial-mesenchymal transition (EMT) expand. Chromatin profiling shows that these chemoresistant programs are epigenetically primed through H3K4me1 marks before treatment and nominates transcription-factor drivers, including ZBTB7A. Non-genetic baseline tumor composition predicts survival, and fibroblast remodeling parallels malignant adaptation. These findings establish a clinically scalable strategy for mapping functional ITH and identify epigenomic priming as a determinant of therapeutic failure. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=181 HEIGHT=200 SRC="FIGDIR/small/692102v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@432524org.highwire.dtl.DTLVardef@3b7843org.highwire.dtl.DTLVardef@54a2eforg.highwire.dtl.DTLVardef@95273d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Shaping and probing living tissues with magnetic bioprinting

Mechanical and geometric cues play a crucial role in vivo, regulating both morphogenetic processes and proper tissue function. This is particularly evident in skeletal muscle, where aligned architecture is essential for myogenesis and functional force generation. However, precisely engineering tissue geometry at both macroscopic and microscopic scales while simultaneously controlling internal mechanical forces remains a significant challenge. In this study, we introduce a magnetic tissue engineering platform based on a magnetic bioprinting technique, enabling precise control of biophysical cues that guide in vitro tissue morphogenesis. Applied here to skeletal muscle, this approach allows for the rapid fabrication of cohesive tissues in any desired shape using cells labeled with magnetic nanoparticles. Additionally, multiple cell types can be incorporated and spatially organized within the same construct through magnetic segregation. Optimizing tissue geometry further enables magnetic actuation, including the ability to trap and maintain tissue shape over time. Furthermore, this magnetic platform facilitates the investigation of how tissue architecture influences mechanical properties, such as resistance to rupture. Overall, this study highlights the significant potential of magnetic bioprinting and stimulation for controlling tissue morphology and advancing biomechanical research.

bioengineering↗

Spatio-molecular analysis of primate subthalamus defines anatomical domains relevant to Parkinson disease and neuropsychiatry

The subthalamic nucleus (STN) is a deep brain stimulation (DBS) treatment target for several disorders of vastly different symptoms, including Parkinsons disease (PD) and obsessive compulsive disorder (OCD). The STN is located in close proximity to the superolateral branch of the medial forebrain bundle (slMFB), a recent DBS target for treatment-resistant depression. Despite clinical application, spatio-molecular understanding of the STN and slMFB has remained elusive. To help solving this, transcriptome data generated in mice was here implemented in comparative analysis with macaque and human. Fluorescent in situ hybridization (FISH) analysis was performed on multiple serial brain sections covering the whole STN area in mice and macaque. Selected markers were further analysed in human sections and in whole mouse brains to allow spatial 3D analysis by light-sheet microscopy. Contrary to available brain atlases, we can now show that the hypothalamic structure known as the para-STN, a critical hub for interoception and emotional regulation, aligns with the STN, and is partly embedded within the MFB. Thus, para-STN occupies considerable space around several major DBS sites. Spatio-molecular data expose STN, MFB and para-STN as highly heterogeneous, including gradients of serotonin receptor subtype 2C (HTR2C). Molecularly reinforced anatomical maps of STN, para-STN, and MFB reveal unexpected details, and may inform spatial precision in neuromodulation strategies while also providing openings for molecular drug discovery.

neuroscience↗

A subset of dorsal raphe dopamine neurons is critical for survival-oriented vigilance.

Defensive behaviors are essential for survival, with risk assessment enabling organisms to evaluate and respond to potential threats. The dorsal raphe nucleus (DRN), a key neuromodulatory center, is crucial for encoding motivational salience and regulating arousal and sleep-wake states through its diverse neuronal populations, including dopaminergic neurons (DRNDA). While the roles of DRNDA neurons have been studied, their specific contributions to threat evaluation are less understood. Recent research identifies a distinct subset of DRNDA neurons that express vasoactive intestinal peptide (VIP) and project to the central amygdala (CeA) and the oval nucleus of the bed nucleus of the stria terminalis (ovBNST). Together, these two regions comprise the central extended amygdala, a key network regulating adaptive responses to threats. We hypothesized that distinct DRNDA subpopulations exert diverging effects on sleep-wake regulation and that DRNVIP neurons play a pivotal role in coordinating activity between the CeA and ovBNST, thereby influencing risk assessment and defensive response. To test this hypothesis, we used a combination of in situ hybridization, immunochemistry, whole-brain mapping, electrophysiology, and cell-specific genetic tools in mice and non-human primates. Our findings reveal that DRNVIP neurons form a key DRNDA neuronal subset, uniquely positioned to regulate the central extended amygdala through a feedback loop. These neurons receive inputs from Protein Kinase C delta (PKC-{delta}) neurons in the ovBNST and CeA and send glutamate-releasing projections back to these regions, modulating PKC-{delta} neuron excitability. Selective ablation of DRNVIP neurons increases activity in both the BNST and CeA, disrupting active-phase sleep architecture and impairing risk assessment and defensive behaviors. Together, these findings suggest DRNVIP neurons control specific phases of sleep and orchestrate the central extended amygdalas role in risk assessment and defensive responses. HIGHLIGHTSO_LIDRNVIP neurons form a subset of DRNDA neurons in mice and non-human primates. C_LIO_LIDRNVIP receive inputs from Protein Kinase C delta (PKC-{delta}) neurons in the ovBNST and CeA and project back to both. C_LIO_LIBy releasing glutamate, DRNVIP neurons regulate PKC-{delta} neuron excitability in the ovBNST and CeA. C_LIO_LIAblating DRNVIP neurons increases BNST and CeA activity, disrupts active-phase sleep architecture, and impairs threat responses. C_LI IN BRIEFDRNVIP neurons, a key subset of DRNDA neurons in mice and primates, are strategically positioned to influence the central extended amygdala via feedback loops. They regulate PKC-{delta} neuron excitability in the ovBNST and CeA through glutamate release, with their ablation heightening activity in these regions and altering active-phase sleep architecture, risk assessment and defensive behaviors.

neuroscience↗

Magnetic printing and actuation of stretchable muscle tissue

While the link between tissue organization, stimulation, and function is now acknowledged as crucial for tissue development, engineering tissues with precise, long-lasting shapes and the capability for mechanical stimulation remains challenging. This study addresses this challenge by developing a next-generation magnetic bioprinting approach to create anisotropic, shape-controlled, scaffold-free, and stretchable skeletal muscle constructs. Murine skeletal muscle cells and human induced pluripotent stem cell-derived skeletal muscle cells, labeled with iron oxide nanoparticles, were magnetically bioprinted into wrench-shaped tissues. Their magnetic properties allowed these tissues to be clipped onto magnetic needles, preserving their shape over two weeks of culture while promoting anisotropic differentiation and myoblast fusion. Additionally, the magnetic tissues could be stretched by up to 100%, enhancing their anisotropy and improving muscle maturation. This magnetic toolbox demonstrates significant advancements in muscle tissue engineering, as evidenced by enhanced indicators of myoblast differentiation, including cell fusion, increased myogenic maturation and contractility. These findings highlight the potential of magnetic-based techniques for developing advanced muscle-on-chip systems and other complex tissue constructs.

bioengineering↗

Genetic liability underlying reward-related comorbidity in psychiatric disorders involves the coincident functions of autism-linked ADGRL1 and hevin

Comorbidity between psychiatric traits is thought to involve overlapping pleiotropic effects from sets of genes. Notably, substance abuse is a shared comorbid condition among various neurodevelopmental disorders with externalizing symptoms such as autism spectrum disorder and attention-deficit hyperactivity disorder, thus hinting at the nucleus accumbens (NAc) as a site for predisposition underlying convergence of genetic influences in reward-related comorbidity. Here, we identify the autism-related gene encoding the adhesion G protein-coupled receptor (aGPCR) Latrophilin-1/ADGRL1 as an essential transducer of reward mechanisms in the NAc. We found that ADGRL1 mRNA is ubiquitously expressed throughout major NAc neuronal populations in mice. A mouse model of pan-neuronal Adgrl1 deficiency in the NAc displayed cocaine-seeking impairments in adult individuals denoting its role in drug-induced reinforcement and reward. Connecting molecular pathways of cocaine-induced learning, we uncover that ADGRL1 constitutes a functional receptor for autism-related cocaine effector molecule hevin/SPARCL1. Indeed, hevin interacts with membrane-expressed ADGRL1 and induces its internalization while stabilizing its uncleaved fraction. Moreover, hevin alters the formation of intercellular adhesion contacts mediated by ADGRL1 and Neurexin-1. Importantly, the functional constitutive coupling between ADGRL1 and various G protein pathways is selectively modulated by hevin stimulation with a bias toward Gi3, Gs, and G13 proteins. These findings unveil the dual role of ADGRL1 and hevin as genetic risk factors for both psychiatric disorders and substance abuse to define the molecular etiology of comorbidity.

neuroscience↗

Magnetic Microtweezers for High-Throughput Bioseparation in Sub-Nanoliter Droplets

Multiomics studies at single-cell level require small volume manipulation, high throughput analysis and multiplexed detection, characteristics that droplet microfluidics can tackle. However, the initial step of molecules bioseparation remains challenging. Here, we describe a unique magnetic device to trap and extract magnetic particles in sub-nanoliter droplets, for compartmentalisation of detection steps. Relying on electrodeposition of NiFe structures and microfluidic manipulation, this technology has allowed the purification of genetic material at single-cell scale and was able to reach an extraction rate of 72% for a sample of purified oligonucleotides.

bioengineering↗

Into the deep: The subthalamic and para-subthalamic nuclei in behavioral avoidance

The subthalamic nucleus (STN) is a key component of the brain network for movement control. However, the STN is strikingly heterogeneous and also intricately engaged in limbic and cognitive functions. The STN shows aberrant firing activity in several neurological and neuropsychiatric disorders, including Parkinso[n]s disease (PD). Deep brain stimulation (DBS) in the STN alleviates motor impairment in PD, but patients have reported altered mood as adverse side-effect. Recent observations suggest that optogenetic STN activation in mice induces flight behavior. We hypothesized that STN activation stand at risk of causing an aversive response with behavioral avoidance as consequence. The STN is directly adjoined with the para-STN (pSTN), a hypothalamic area correlated with appetitive and aversive behavior. STN-DBS aiming to correct STN might thereby also modulate pSTN. To dissociate the impact of STN and pSTN, we took advantage of selective promoters in mice, identified in our recent RNA- sequencing of the subthalamic area, to selectively direct optogenetic excitation. Acute photostimulation resulted in aversion via both the STN and pSTN, but only STN- stimulation-paired cues resulted in conditioned avoidance. Viral-genetic tracing coupled with electrophysiological recordings identified a polysynaptic pathway from the STN to the lateral habenula, a critical hub for aversion and associated with clinical depression. This study demonstrates that STN activation is directly correlated with aversion, and thereby contributes neurobiological underpinnings to emotional affect upon STN manipulation with implications for STN-targeted treatment outcome.

neuroscience↗

Unexpected inhibition of motor function by dopamine activation of D1/D2 co-expressing striatal neurons.

The central function of the striatum and its dopaminergic (DA) afferents in motor control and the integration of cognitive and emotional processes is commonly explained by the two striatal efferent pathways characterized by striatal projection neurons (SPNs) expressing DA D1 receptors and D2 receptors (D1-SPNs and D2-SPNs), without regard to SPNs coexpressing both receptors (D1/D2-SPNs). We developed an approach that enables the targeting of these hybrid SPNs and demonstrated that although these SPNs are less abundant, they play a major role in guiding the motor function of the other two main populations. D1/D2-SPNs project exclusively to the external globus pallidus (GPe) and have specific electrophysiological features with distinctive integration of DA signals. Optogenetic stimulation and loss-of-function experiments indicated that D1/D2-SPNs potentiate the prokinetic and antikinetic functions of D1-SPNs and D2-SPNs, respectively, and restrain the integrated motor response to psychostimulants. Overall, our findings demonstrate the essential role of this third unacknowledged population of D1/D2 coexpressing neurons, which orchestrates the fine-tuning of DA regulation in the thalamo-cortico-striatal loops. One-Sentence SummaryD1/D2 SPNs modulate the motor function of both D1- and D2-SPNs

neuroscience↗