Biology subjects

Dos Santos, M.

Publications and source records attributed to Dos Santos, M..

16 recordsLinked to original sources

bioRxiv2026

The evolution of family reputation extends indirect reciprocity

Reputation plays a major role in supporting cooperation among unrelated individuals through indirect reciprocity. By helping others, individuals build a good personal reputation and receive greater benefits from future partners. Most models of indirect reciprocity assume that a person's reputation reflects only their own behaviour. Yet in many societies, people are also judged by their family's reputation. How family reputation affects the evolution of cooperation, and whether reliance on it can itself evolve, remain unclear. Here we show that reputation inheritance expands the conditions under which indirect reciprocity favours cooperation, increasing helping and favouring greater reciprocity. Greater reciprocity in turn favours stronger reliance on inherited reputation, creating a positive feedback that stabilises cooperation, especially when interactions are infrequent or personal behaviour is difficult to observe. This feedback arises because cooperation generates future benefits both for the individual, through their personal reputation, and for their descendants, through inherited reputation. Reputation inheritance thereby provides a route via which kin selection and reciprocity, often treated as alternative explanations for cooperation, can reinforce one another. Our model helps explain why family-based reputation occurs across diverse human societies and provides an evolutionary framework for studying phenomena organised around family standing, including kin-based institutions, feuds between families and honour-based violence within them.

evolutionary biology↗

bioRxiv2026

Identification of a new population of myonuclei during skeletal muscle hypertrophy

BackgroundSkeletal muscle represents around 40% of total human body weight and exhibits remarkable plasticity. It can hypertrophy, atrophy, or regenerate in response to changes in activity, nutrient availability, or injury. The main component of striated muscle, the myofiber, is a post-mitotic, multinucleated cell that contains the muscles contractile unit, the sarcomere. The myonuclei within these fibers are specialized and differ in terms of gene expression and localization. Adult muscles also contain various other cell types, including adult muscle stem cells (MuSCs), macrophages, fibro-adipogenic progenitors (FAPs), and endothelial cells. MuSCs are central to muscle plasticity, and are capable of activation, proliferation, differentiation, and fusion to form new myofibers during regeneration, or to fuse with existing myofibers during hypertrophy. Muscle hypertrophy and myofibers enlargement involve increased protein synthesis and reduced protein degradation, as well as myonuclear accretion following satellite cell activation. Multiple signaling pathways, such as the mTOR pathway and the RhoA/SRF mechanotransduction pathway, are involved in these processes. MethodsWe performed single-nucleus RNA sequencing (snRNA-seq) on plantaris muscles of adult mice, comparing samples 7 days after hypertrophy induction (overload, 7OV) to non-hypertrophied controls (Ctl). RNAscope experiments on isolated myofibers identified the heterogeneity of myonuclei along the myofiber. ResultsSnRNA-seq analysis revealed a previously unknown population of myonuclei (UM). UM-Ctl, which is present only in the Ctl condition, and UM-7OV, only in the 7OV condition. These myonuclei are localised at the tips of myofibres. Furthermore, we determined that UM-7OV are not newly fused myonuclei from activated satellite cells. Trajectory analyses suggest that UM-Ctl transition into UM-7OV during hypertrophy, returning to a near-basal homeostatic state after 21 days of overload (21OV). Gene expression analysis showed that UM-Ctl and UM-7OV have distinct gene expression profiles compared to other myonuclei and respond differently to hypertrophy. ConclusionOur findings suggest the existence of a specific population of myonuclei with unique localization and gene expression profiles, which play distinct roles at baseline and during hypertrophy. These results highlight the differential properties of myonuclei in the myofiber and their potential specific functions in muscle homeostasis and adaptation.

molecular biology↗

bioRxiv2026

Postnatal Pax7-expressing limb cells are multipotent and generate non-myogenic lineages that persist into adulthood.

Organs are composed of a complex arrangement of diverse cell types that can originate from independent cell lineages or shared progenitors. Skeletal muscle is derived from mesodermal Pax7+ stem/progenitor cells that can differentiate into myoblasts to form muscle fibers. During embryogenesis, however, somitic Pax7+ cells can also give rise to non-muscle cell types, including dermis and adipocytes. Here, we asked whether Pax7+ cells retain such multipotency during early postnatal growth of limb muscles. Using lineage tracing, we uncovered unexpected plasticity at early postnatal days, leading to the generation of multiple non-myogenic lineages, including a previously unrecognized Pax7-derived subpopulation of fibro-adipogenic progenitors that we termed Pax7FAPs and further investigated. Using mouse models, we further show that Notch signaling primes neonatal Pax7+ cells toward a fibrogenic molecular identity at the expense of myogenic differentiation, thereby biasing their trajectory toward a fibrogenic fate. In the adult muscle, long-term tracing revealed that neonatally produced Pax7FAPs persist into adulthood. In addition, injury in adult muscle triggered de novo generation of Pax7FAPs, which displayed higher proliferative capacity than resident stromal cells. This newfound multipotency of postnatal Pax7+ cells adds a new dimension to our understanding of cellular contributions during postnatal muscle development and regeneration.

developmental biology↗

bioRxiv2026

c-MAF transduces motor neuron firing to sustain fast-glycolytic myofibers and neuromuscular junctions

This study examined how motoneuron activity influences transcription factor binding in mouse fast glycolytic Myh4+ muscle fibers. Single nucleus multiomics of innervated versus denervated tibialis anterior muscles revealed altered chromatin accessibility: SIX and c-MAF binding sites decreased while JUN, FOS, and RUNX1 sites increased in denervated Myh4+ myonuclei. c-MAF showed strong nuclear enrichment after 100 Hz stimulation and periods of increased motoneuron activity but was absent following denervation, establishing it as a primary readout of fast motoneuron firing. Genome-wide analysis demonstrated that c-MAF binding site spacing encodes functionally distinct muscle gene programs. Analysis of constitutive and inducible skeletal muscle-specific c-Maf mutants revealed that c-MAF loss caused region-specific MYH4+ fiber atrophy, MYH1/MYH2 fiber type shifts resembling ALS G93A mouse phenotypes, and progressive neuromuscular junction fragmentation with increased motoneuron terminal sprouting and ectopic reinnervation. These findings establish c-MAF as a critical mediator linking motoneuron activity to muscle gene regulation, fiber integrity, and neuromuscular junction maintenance in fast glycolytic fibers.

physiology↗

bioRxiv2026

SIX1-dependent myofiber typology and metabolism controls muscle hypertrophy

The different types of muscle fibres respond in a specific way to hypertrophy or atrophy. The mechanisms underlying these heterogeneous adaptations remain poorly understood. Using single-nucleus RNA sequencing, we propose that fast glycolytic fibres show genetic limitations to hypertrophy induced by mechanical overload. We show that a prior fibre transition, achieved by reducing SIX1 protein expression (hypomorphism), enhances and accelerates overload-induced hypertrophy, bypassing the genetic limitations of fast glycolytic fibres. In contrast and unexpectedly, Six1 knockout in myofibers abolished overload-induced hypertrophy and instead caused atrophy of IIb/IIx fibers, despite the induction of a strong slow oxidative phenotype. In particular, Six1 deletion leads to metabolic defects caused by inhibition of glycolysis, AMPK and mitochondrial biogenesis. Our findings highlight the critical role of SIX1/AMPK/glycolysis-dependent aerobic metabolism in muscle growth and suggest that fibre type transitions, coupled with preserved metabolic function, may optimise hypertrophic responses.

physiology↗

bioRxiv2025

Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication

Coronaviruses, including SARS-CoV-2, can cause severe disease in humans, whereas reservoir hosts like Rhinolophus bats remain asymptomatic. To investigate how host-specific protein-protein interactions (PPIs) influence infection, we generated comparative PPI maps for SARS-CoV-2 and its bat-origin relative RaTG13 using affinity purification-mass spectrometry (AP-MS) in human and Rhinolophus ferrumequinum (RFe) bat cells. This approach identified both conserved and virus- and host-specific interactions that regulate infection dynamics. Notably, SARS-CoV-2 required a non-synonymous mutation in nucleocapsid to replicate in bat cells expressing human ACE2 and TMPRSS2. Analysis of the viral protein Orf9b revealed differential interactions with mitochondrial proteins Tom70 and MTARC2. A single residue difference in Orf9b between SARS-CoV-2 and RaTG13 functions as a molecular switch, weakening Tom70 binding and immune evasion in human cells while enhancing interaction with the bat-specific restriction factor MTARC2. These findings demonstrate how a single-residue substitution can reshape virus-host interactions and contribute to immune evasion and host adaptation.

systems biology↗

bioRxiv2025

Impairment of homeostatic structural plasticity caused by the autism and schizophrenia-associated 16p11.2 duplication

Homeostatic plasticity is essential for information processing and the stability of neuronal circuits, however its relevance to neuropsychiatric disorders remains unclear. The 16p11.2 duplication (BP4-BP5) is a genetic risk factor that strongly predisposes to a range of severe mental illnesses including autism, schizophrenia, intellectual disability, and epilepsy. The duplication consists of a 600 kb region on chromosome 16, including 27 protein-coding genes, with poorly defined effects on neuronal structure and function. Here, we used a mouse model of the 16p11.2 duplication to investigate the impact of this variant on synaptic structure and downstream homeostatic plasticity. We find that 16p11.2 duplication neurons exhibit overly branched dendritic arbors and excessive spine numbers, which host an overabundance of surface AMPA receptor subunit GluA1. Using a homeostatic plasticity paradigm, we show that 16p11.2 duplication neurons fail to undergo synaptic upscaling upon activity deprivation, consistent with disrupted structural plasticity. We also observe that the increased surface abundance of GluA1 occludes further insertion events, a critical mechanism for synaptic plasticity. Finally, we show that genetically correcting the dosage of 16p11.2-encoded Prrt2 to wild-type levels rescues structural spine phenotypes. Our work suggests that aberrant plasticity could contribute to the etiology of neuropsychiatric disorders.

neuroscience↗

bioRxiv2024

Pro-cognitive reshaping of neuronal dynamics by a human CSF-based factor

Neuronal connection dysfunction is a convergent cause of cognitive deficits in mental disorders. Cognitive processes are finely regulated at the synaptic level by membrane proteins, some of which are shed and detectable in patients cerebrospinal fluid (CSF). However, whether these soluble synaptic proteins can harnessed as innovative pro-cognitive factors to treat brain disorders remains unclear. Here, we use quantitative proteomics to identify shed synaptic proteins dysregulated in the CSF of subjects with schizophrenia (SCZ), a mental disorder characterized by cognitive and synaptic dysfunction. The level of a yet uncharacterized soluble form of the voltage-gated calcium channel auxiliary subunit, 2{delta}-1, is robustly reduced in SCZ CSF. Remarkably, soluble 2{delta}-1 is convergently downregulated across several brain disorder CSF proteomes. We show that the brain releases soluble 2{delta}-1 in an activity-dependent manner, which can reorganize neuronal network dynamics by binding to synaptic targets and promoting inhibitory neuron plasticity. A single brain injection of a synthetic soluble 2{delta}-1 improved interneuron and cognitive deficits in a mutant mouse model of SCZ and cortical dysfunction. These findings underscore the potential of shed synaptic proteins as novel therapeutic agents capable of enhancing brain function in diverse brain disorders characterized by cognitive impairment.

neuroscience↗

bioRxiv2024

Biologically grounded brain-on-chip model identifies selective topographic reorganization within hyperexcitable neural networks

Connectomics has revolutionized our understanding of brain function by emphasizing the importance of neural networks and their topographical organization. Corticostriatal circuits, which play a critical role in cognition and emotion, follow a precise topographic architecture essential for integrating and processing cortical information within the basal ganglia. Disruptions to this connectivity are often implicated in neurodevelopmental and psychiatric disorders such as obsessive compulsive disorders, schizophrenia, epilepsy, and autism spectrum disorders. However, studying network disruptions in vivo presents significant challenges due to their intricate architecture and early developmental onset. To address this, we employed a brain-on-chip microfluidic platform to recreate a biologically relevant model of topographically organized corticostriatal networks. By mimicking the directional control of neuronal projections using Tesla valve-inspired microchannels, we demonstrate that genetic perturbations affecting neuronal excitability during development lead to selective alterations of local versus long-range network topology, resulting in the formation of new convergent nodes. This model offers critical insights into how early perturbations contribute to circuit-specific pathologies, providing a valuable tool for understanding neurodevelopmental disorders and advancing therapeutic strategies.

neuroscience↗

bioRxiv2024

Protocol for muscle fiber type and cross-sectional areaanalysis in cryosections of whole lower mouse hindlimbs

We outline a robust, simple, and cost-effective method to simultaneously visualize all mouse lower hindlimb skeletal muscles. We describe procedures for orientating the whole lower hindlimb in gum tragacanth prior to freezing, simplifying the proceeding experimental steps, and enhancing the clarity and comprehensiveness of characterizations. We then detail steps for quantifying muscle fiber size and fiber type characteristics in a single cryosection using immunofluorescence and histochemistry. This protocol can be applicable for commonly used histological and (immuno) histochemical evaluations such muscle degeneration/regeneration, fibrosis, immune cell infiltration, enzymatic activity and glycogen content. HighlightsO_LIEmbedding and orientating mouse lower hindlimb in tragacanth before freezing enhances clarity and simplifies steps. C_LIO_LISimultaneously visualizing myofibers in different muscle compartments enables efficient and comprehensive evaluations of morphology and physiological characteristics. C_LIO_LISingle cryosection analysis of myofiber size and types with immunofluorescence. C_LIO_LIApplicable for evaluating muscle degeneration, fibrosis, and immune infiltration. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/608909v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@9d3fe4org.highwire.dtl.DTLVardef@1cdcc85org.highwire.dtl.DTLVardef@2e494eorg.highwire.dtl.DTLVardef@cebfc6_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

Comparing cellular response to two radiation treatments based on key features visualization

MotivationIn modern treatment by radiotherapy, different irradiation modalities can be used, potentially producing different amounts of adverse effects. The differences between these modalities are often studied via two-sample time course in vitro experiments. The resulting data may be of high complexity, in which case simple methods are unadapted for extracting all the relevant information. MethodsIn this article we introduce network-based tools for the visualization of the key statistical features, extracted from the data. For the key features extraction we utilize a statistical framework performing estimation, clustering with alignment of temporal omic fold changes originating from two-sample time course data. ResultsThe approach was applied to real transcriptomic data obtained with two different types of irradiation. The results were analyzed using biological literature and enrichment analysis, thus validating the robustness of the proposed tools as well as achieving better understanding of the differences in the impact of the treatments in question. Availability and implementationPython package freely available here: https://github.com/parsenteva/scanofc. Contactpolina.arsenteva@u-bourgogne.fr

bioinformatics↗

bioRxiv2023

Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket

To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate binding pocket. Of 631 fragments soaked, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (2 hits) or at crystal packing interfaces (3 hits). Notably, two fragments with a pose sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. Our structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography. SynopsisAn X-ray crystallographic screen on SARS-CoV-2 3CL protease resulted in 29 fragment hits, including two isatin-based reversible covalent binders, and revealed a strong influence of the crystal form used for fragment soaking on the bound conformation of three additional reference fragments.

biophysics↗

bioRxiv2022

Rescue of neuropsychiatric phenotypes in a mouse model of 16p11.2 duplication syndrome by genetic correction of an epilepsy network hub

Neuropsychiatric disorders (NPDs) share genetic etiology and are frequently co-morbid with epilepsy, but the biological basis of this shared risk remains poorly understood. The 16p11.2 microduplication (16p11.2dup/+) is a highly pleiotropic copy number variant (CNV) conferring risk for multiple NPDs including autism spectrum disorder, schizophrenia and intellectual disability, and is associated with a high prevalence of seizures. We used a mouse model of the 16p11.2 duplication (16p11.2dup/+) to uncover molecular and circuit properties associated with this broad phenotypic spectrum, and examined genes within the locus capable of phenotype reversal. Quantitative proteomics of cortical membranes revealed alterations to synaptic protein networks and products of diverse NPD risk genes in 16p11.2dup/+ mice. Network analysis identified an epilepsy-associated protein subnetwork, which was dysregulated in 16p11.2dup/+ mice and proteomic datasets from human NPDs. We investigated circuit properties in 16p11.2dup/+ mice and found they exhibited hypersynchronous activity and enhanced network glutamate release, which increased susceptibility to seizures. We hypothesized that a regulator of the synaptic and epilepsy-associated protein network could have an important impact on pathophysiology. Human brain co-expression and interactome analysis revealed PRRT2 as a major hub in the dysregulated epilepsy subnetwork. Remarkably, restoring Prrt2 copy number to wild-type levels rescued aberrant circuit properties, seizure susceptibility and social interaction deficits in 16p11.2dup/+ mice. We show that proteomics and network biology can identify important disease hubs in multigenic CNVs, and reveal molecular and circuit phenotypes which may be relevant to the complex symptomatology of 16p11.2 duplication carriers.

neuroscience↗

bioRxiv2021

A fast Myh super enhancer dictates adult muscle fiber phenotype through competitive interactions with the fast Myh genes

The contractile properties of adult myofibers are shaped by their Myosin heavy chain (MYH) isoform content. We identify by snATAC-seq a 42kb super-enhancer (SE) at the locus regrouping the fast Myh (fMyh) genes. By 4C-seq we show that active fMyh promoters interact with the SE by DNA looping, leading to the activation of a single promoter per nucleus. A rainbow mouse transgenic model of the locus including the SE recapitulates the endogenous spatio-temporal expression of adult fMyh genes. In situ deletion of the SE by CRISPR/Cas9 editing demonstrates its major role in the control of associated fMyh genes, and deletion of two fMyh genes at the locus reveals an active competition of the promoters for the shared SE. Last, by disrupting the organization of fMyh, we uncover positional heterogeneity within limb skeletal muscles that may underlie selective muscle susceptibility to damage in certain myopathies.

cell biology↗

bioRxiv2020

Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers

Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. By snRNA-seq and snATAC-seq, we showed that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we showed that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential panel of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a unique mechanism of coordination of gene expression in a syncytium.

cell biology↗

bioRxiv2019

Towards an ″assayome″ for binary interactome mapping

Complementary assays are required to comprehensively map complex biological entities such as genomes, proteomes and interactome networks. However, how various assays can be optimally combined to approach completeness while maintaining high precision often remains unclear. Here, we propose the concept of an "assayome" for binary protein-protein interaction (PPI) mapping as an optimal combination of assays and/or assay versions that maximizes detection of true positive interactions, while avoiding detection of random protein pairs. We engineered a novel NanoLuc two-hybrid (N2H) system that integrates 12 different versions differing by protein expression systems and tagging configurations. The resulting N2H assayome recovers as many PPIs as 10 distinct assays combined. Thus, to further improve PPI mapping, developing alternative versions of existing assays might be as productive as designing completely new assays. Our assayome concept should be applicable to systematic mapping of other biological landscapes.

systems biology↗