Biology subjects

Furlan, A.

Publications and source records attributed to Furlan, A..

11 recordsLinked to original sources

bioRxiv2026

Experimental and mathematical models reveal that AMPK modulates circadian clock gene expression and period through NAD+-dependent regulation of Bmal1

The circadian clock allows living systems to anticipate environmental daily variations by scheduling cellular mechanisms according to the time of the day. The reciprocal interplay between metabolism and circadian clock is essential for energy homeostasis, and the disruption of metabolic clock inputs contributes to dysfunction of clocks in peripheral tissues. However, the molecular mechanisms through which the feeding/fasting cycle entrains peripheral clocks remain incompletely understood. Here, we investigate experimentally and theoretically the role of AMP-dependent kinase (AMPK), a key fasting sensor, in metabolic regulation of the circadian clock. Using a luciferase reporter driven by the Bmal1 promoter to monitor molecular clock activity in human U2OS cells, and thanks to a signal processing method based on the Hilbert transform to retrieve the instantaneous phase and period of circadian signals, we show that pharmacological activation of AMPK by AICAR significantly elevates Bmal1 promoter activity and markedly lengthens the clock period in a dose-dependent manner. Conversely, the clock period is shortened by the pharmacological inhibition by SR18292 of Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1-alpha). Importantly, the action of AICAR is abolished by FK866, a nicotinamide phosphoribosyltransferase (NAMPT) inhibitor, demonstrating that AMPK-dependent modulation of Bmal1 promoter activity requires NAD+ availability. These experimental results are recapitulated by numerical simulations of our previously published mathematical model, where PGC-1-alpha plays a key role in mediating AMPK activity to the clock. Moreover, the comparison of experimentally measured and theoretically predicted phase response curves, following AMPK activation at different circadian phases, provides an additional validation of the model. By integrating biological experiments with mathematical modeling, our results identify a key mechanism through which metabolic factors can entrain and regulate the circadian clock via NAD+-dependent AMPK-mediated regulation of Bmal1 promoter activity.

cell biology↗

bioRxiv2026

Mapping Enteric Neural Circuits by Anterograde Transsynaptic Tracing

The diverse functions of the enteric nervous system (ENS) arise from communication between molecularly distinct neuronal populations organized into complete circuits. While recent single-cell transcriptomic studies have resolved the molecular identity of enteric neuron classes, methods for defining their synaptic connectivity remain limited. Here, we describe the implementation of mWmC, an anterograde monosynaptic tracer based on a fusion of wheat germ agglutinin (WGA) and mCherry, as a non-toxic, single-component viral tool for mapping neuronal circuits within and beyond the ENS. Following adeno-associated virus (AAV)-mediated expression in enteric neurons, mWmC was efficiently expressed and transmitted selectively to postsynaptic neurons, with no detectable transfer to enteric glia, interstitial cells of Cajal, blood vessels or other mesenchymal cell types. The method also identified postsynaptic neurons in the celiac-superior mesenteric ganglia following tracing of intestinofugal enteric neurons, demonstrating its utility for mapping inter-organ circuits. As proof of principle, we applied mWmC to two genetically defined myenteric interneuron populations and identified preferential postsynaptic targets, revealing selective connectivity with distinct enteric neuron classes. Time-course experiments showed that transsynaptic labeling occurred between 4 and 10 days and reached a plateau thereafter, consistent with monosynaptic transfer. Finally, we developed a dual-reporter version of the system that simultaneously distinguishes input and target neurons within the same tissue. Together, mWmC provides a robust approach for defining circuit architecture in the ENS, linking molecular cell atlases with neuronal connectivity and paving the way for deeper insights into the circuit mechanisms underlying gut physiology. Graphical AbstractSchematics illustrating the implementation and applications of the anterograde monosynaptic tracer mWmC for mapping enteric neuronal circuits. Parts of schematics are generated with Biorender. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=36 SRC="FIGDIR/small/741165v2_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@19635bborg.highwire.dtl.DTLVardef@a18ffborg.highwire.dtl.DTLVardef@f3d011org.highwire.dtl.DTLVardef@e1359c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Targeting Neuromuscular Junction Regeneration is a Therapeutic Strategy in ALS

Instability and denervation of the neuromuscular junction (NMJ) are early events in Amyotrophic Lateral Sclerosis (ALS), likely reflecting a progressive decline in the regenerative capacity of motor neurons (MNs) and their environment. To investigate this, we evaluated NMJ regeneration throughout disease progression in SOD1G93A mice following reversible axon terminal degeneration induced by -Latrotoxin. In parallel, we monitored the expression of CXCR4, a GPCR upregulated during axonal regeneration, and tested whether its pharmacological activation could mitigate ALS- related functional decline. We found that NMJ regenerative capacity is largely preserved during pre- and early symptomatic stages, and remains active in subsets of NMJs even at later stages. CXCR4 is expressed at axon terminals from early disease stages, declining only at end stage. Its expression is conserved across ALS models, including SOD1G93A pigs, hiPSC-derived MN with ALS mutations, and biopsies from sporadic ALS patients. CXCR4 stimulation improved motor function, NMJ innervation, MN survival, and respiratory performance in ALS mice, and axon outgrowth in iPSC-derived MN. These findings identify the NMJ and CXCR4 as viable therapeutic targets in ALS.

neuroscience↗

bioRxiv2025

AI assisted design of ligands for Lipocalin-2

Lipocalin-2 (LCN2) is an acute-phase glycoprotein whose upregulation is linked to blood- brain-barrier breakdown and neuroinflammation, making it an attractive diagnostic and therapeutic target. We developed an end-to-end, AI-guided workflow to rapidly design de-novo miniproteins that bind LCN2. Backbone scaffolds were generated with RFdiffusion, sequences were optimized with ProteinMPNN, and candidates filtered in silico using a consensus of AlphaFold2 confidence metrics (mean interface pAE < 10) and binding free energy predicted by Prodigy. From an initial library of 10,000 designs, five were expressed and purified from E. coli. Using biolayer interferometry (BLI) we identified MiniP-2 as the lead construct, exhibiting a dissociation constant (Kd) of 4.2 nM. Structural modeling revealed that binding is primarily mediated by backbone hydrogen bonds along with a stabilizing salt bridge between Arg37 of MinP-2 and Asp97 of LCN2. These findings demonstrate that a fully computational generative workflow can yield nanomolar LCN2 binders in a single design-build-test cycle. MinP-2 represents a promising starting point for affinity maturation, structural studies, and in vivo evaluation as an imaging probe or antagonist of LCN2-mediated signaling. Specifically, SPR competition experiments showed that MinP-2 can inhibit LCN2 binding to MMP-9, suggesting its potential to mitigate the pathological effects of this interaction within the central nervous system.

biochemistry↗

bioRxiv2022

Bacterial aerobic methane cycling by the marine sponge-associated microbiome

BackgroundMethanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfate-depleted sediments. However, methane oxidizing bacteria from the candidate phylum Binatota have recently been described and shown to be present in oxic shallow-water marine sponges, where sources of methane remain undescribed. ResultsHere, using an integrative -omics approach, we provide evidence for sponge-hosted bacterial methanogenesis occurring in fully oxygenated shallow water habitats. Specifically, we suggest methanogenesis occurs via at least two independent pathways involving methylamine and methylphosphonate transformations that, concomitantly to aerobic methane production, generate bioavailable nitrogen and phosphate, respectively. Methylphosphonate may be sourced from seawater continuously filtered by the sponge host. Methylamines may also be externally sourced or, alternatively, generated by a multi-step metabolic process where carnitine, derived from sponge cell debris, is transformed to methylamine by different sponge-hosted microbial lineages. Finally, methanotrophs specialized in pigment production, affiliated to the phylum Binatota, may provide a photoprotective function, closing a previously undescribed C1-metabolic loop that involves both the sponge host and specific members of the associated microbial community. ConclusionGiven the global distribution of this ancient animal lineage and their remarkable water filtration activity, sponge hosted methane cycling may affect methane supersaturation in oxic coastal environments. Depending on the net balance between methanogenesis and methanotrophy, sponges may serve as marine sources or sinks of this potent greenhouse gas.

microbiology↗

bioRxiv2021

Neurotensin neurons in the central extended amygdala control energy balance

Overeating and a sedentary life style are major causes of obesity and related metabolic disorders. Identification of the neurobiological processes that regulate energy balance will facilitate development of interventions for these disorders. Here we show that the Neurotensin-expressing neurons in the mouse IPAC (IPACNts), a nucleus of the central extended amygdala, bidirectionally coordinate hedonic feeding and physical activity, thereby regulating energy balance, metabolic processes and bodyweight. IPACNts are preferentially activated by consumption of highly palatable food or exposure to its taste and smell. Activating IPACNts promotes food intake in a palatability-dependent manner and decreases locomotion. Conversely, inhibiting IPACNts selectively reduces palatable food intake and dramatically enhances physical activity and energy expenditure, and in parallel stimulates physiological responses that oppose diet-induced obesity and metabolic dysfunctions. Thus, a single neuronal population, Neurotensin-expressing neurons in the IPAC, acts to control obesogenic and leptogenic processes by synergistically coordinating energy intake and expenditure with metabolism.

neuroscience↗

bioRxiv2020

Molecular architecture of the developing mouse brain

The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions, and intrinsic genetic programs that result in the generation of likely more than a thousand distinct cell types. Therefore, a complete understanding of mammalian brain development requires systematic mapping of cell states covering the entire relevant spatiotemporal range. Here we report a comprehensive single-cell transcriptome atlas of mouse brain development spanning from gastrulation to birth. We identified almost a thousand distinct cellular states, including the initial emergence of the neuroepithelium, a rich set of region-specific secondary organizers and a complete developmental program for the functional elements of the brain and its enclosing membranes. We used the atlas to directly test the hypothesis that human glioblastoma reflects a return to a developmental cell state. In agreement, most aneuploid tumor cells matched embryonic rather than adult types, while karyotypically normal cells predominantly matched adult immune cell types.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2020

A central amygdala-globus pallidus circuit conveys unconditioned stimulus information and controls fear learning

The central amygdala (CeA) is critically involved in a range of adaptive behaviors. In particular, the somatostatin-expressing (Sst+) neurons in the CeA are essential for classic fear conditioning. These neurons send long-range projections to several extra-amygdala targets, but the functions of these projections remain elusive. Here, we found in mice that a subset of Sst+ CeA neurons send projections to the globus pallidus external segment (GPe), and constitute essentially the entire GPe-projecting CeA population. Notably, chronic inhibition of GPe-projecting CeA neurons completely blocks auditory fear conditioning. These neurons are selectively excited by the unconditioned stimulus (US) during fear conditioning, and transient inactivation or activation of these neurons during US presentation impairs or promotes, respectively, fear learning. Our results suggest that a major function of Sst+ CeA neurons is to represent and convey US information through the CeA-GPe circuit, thereby instructing learning in fear conditioning.

neuroscience↗

bioRxiv2019

Opposing contributions of GABAergic and glutamatergic ventral pallidal neurons to motivational behaviours

The ventral pallidum (VP) is critical for invigorating reward seeking and is also involved in punishment avoidance, but how it contributes to such opposing behavioural actions remains unclear. Here we show that GABAergic and glutamatergic VP neurons selectively control behaviour in opposing motivational contexts. In vivo recording combined with optogenetics in mice revealed that these two populations oppositely encode positive and negative motivational value, are differentially modulated by animals internal state and determine the behavioural response during motivational conflict. Furthermore, GABAergic VP neurons are essential for movements towards reward in a positive motivational context, but suppress movements in an aversive context. In contrast, glutamatergic VP neurons are essential for movements to avoid a threat but suppress movements in an appetitive context. Our results indicate that GABAergic and glutamatergic VP neurons encode the drive for approach and avoidance, respectively, with the balance between their activities determining the type of motivational behaviour.

neuroscience↗

bioRxiv2018

Molecular architecture of the mouse nervous system

The mammalian nervous system executes complex behaviors controlled by specialised, precisely positioned and interacting cell types. Here, we used RNA sequencing of half a million single cells to create a detailed census of cell types in the mouse nervous system. We mapped cell types spatially and derived a hierarchical, data-driven taxonomy. Neurons were the most diverse, and were grouped by developmental anatomical units, and by the expression of neurotransmitters and neuropeptides. Neuronal diversity was driven by genes encoding cell identity, synaptic connectivity, neurotransmission and membrane conductance. We discovered several distinct, regionally restricted, astrocytes types, which obeyed developmental boundaries and correlated with the spatial distribution of key glutamate and glycine neurotransmitters. In contrast, oligodendrocytes showed a loss of regional identity, followed by a secondary diversification. The resource presented here lays a solid foundation for understanding the molecular architecture of the mammalian nervous system, and enables genetic manipulation of specific cell types.

neuroscience↗

bioRxiv2017

RNA velocity in single cells

RNA abundance is a powerful indicator of the state of individual cells, but does not directly reveal dynamic processes such as cellular differentiation. Here we show that RNA velocity--the time derivative of RNA abundance--can be estimated by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. We show that RNA velocity is a vector that predicts the future state of individual cells on a timescale of hours. We validate the accuracy of RNA velocity in the neural crest lineage, demonstrate its use on multiple technical platforms, reconstruct the branching lineage tree of the mouse hippocampus, and measure RNA kinetics in human embryonic brain. We expect RNA velocity to greatly aid the analysis of developmental lineages and cellular dynamics, particularly in humans.

genomics↗