Biology subjects

Laurent, B.

Publications and source records attributed to Laurent, B..

16 recordsLinked to original sources

bioRxiv2025

Parkinson's disease risk factors are expressed at brain barriers.

Parkinsons disease (PD) is characterized by the selective loss of dopaminergic neurons in the substantia nigra pars compacta, but whether its etiology is cell autonomous remains unclear. Increasing evidence implicates the blood-central nervous system (CNS) barriers in disease development, highlighting the importance of identifying genetic risk factors linked to cells forming the cerebrovasculature to advance this emerging area of research. The objective of this study is to identify PD genetic risk factors associated with blood-brain (BBB) and blood-cerebrospinal fluid (BCSFB) barriers, and to validate protein localization in human tissue and experimental models. To do so, we integrated genome-wide association studies and single nuclei RNA-sequencing datasets from the human postmortem substantia nigra (SN), midbrain, or cortical samples from control and PD donors. An in-depth bioinformatics analysis identified genes enriched in cell types that form the multicellular architecture of brain barriers, including CAVIN2, ANXA1, ANO2, and LRP1B. We further validated whether corresponding proteins were present in cell types associated with the blood-CNS barriers in human and mouse post-mortem tissues, as well as in iPSC-differentiated cells and choroid plexus organoids. Results showed that quantifying the proportion of endothelial cells expressing PD-related genes was under-evaluated at the transcript level compared to immunofluorescence analyses. In addition, we observed that CAVIN2 and ANXA1 proteins were more abundant at the vasculature of the substantia nigra vs. cortex, and CAVIN2 protein levels were reduced in PD vs. control human postmortem tissues. In contrast, the investigation of mouse postmortem samples demonstrated that the CAVIN2 protein is only present in a subset of mouse blood vessels, compared to nearly all vessels in human tissue. Similarly, mouse ANXA1 protein localizes to dopaminergic neurons of the substantia nigra and not at the vasculature, as seen in human tissue. The primary outcome of this study is the identification of PD-relevant risk genes specifically expressed at brain barriers and enriched in PD-relevant brain regions. The secondary outcome is the demonstration of poor transcript-protein correlation in - at least - a subset of PD risk factors, and a low interspecies conservation of protein localization for the selected candidates. In conclusion, the BBB and BCSFB may represent understudied contributors to PD, endothelial-specific proteins appear differentially regulated compared to transcripts, and experimental models require comprehensive validation to ensure relevance to the human condition.

neuroscience↗

bioRxiv2025

The Fragile X mental retardation protein (FMRP) coordinates an epigenetic checkpoint in neural progenitor cells

Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by silencing of the FMR1 gene, which encodes the multifunctional RNA-binding protein FMRP. While FMRP is best known for its roles in RNA metabolism, it can also associate with chromatin through recognition of histone H3 lysine 79 di-methylation (H3K79me2), an epigenetic mark linked to transcriptionally active genes. However, the functional relevance of this FMRP-H3K79me2 interaction has remained largely unexplored in the context of FXS pathophysiology. We assessed H3K79me2 levels during the differentiation of induced pluripotent stem cells (iPSCs) generated from both healthy individuals and FXS patients and discovered a global increase in H3K79me2 levels specifically in FXS neural progenitor cells (NPCs). Altered H3K79me2 landscape drives widespread transcriptional dysregulation, characterized by reduced expression of neurogenesis-associated genes alongside aberrant activation of programs promoting proliferation and glial lineage commitment. Functionally, these changes result in enhanced NPCs proliferation and a biased differentiation trajectory. Notably, pharmacological reduction of global H3K79me2 levels in FXS NPCs using DOT1L inhibitors effectively mitigates these defects, restoring proliferation rate and rebalancing lineage specification, thereby rescuing key aspects of the pathological phenotype. Collectively, our findings identify an H3K79me2-dependent epigenetic barrier regulating NPC proliferation and lineage commitment and link its dysregulation to the neurodevelopmental defects associated with FXS.

neuroscience↗

bioRxiv2025

Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two rapidly evolving accessory chromosomes

Diplodia sapinea (Dothideomycetes) is a latent fungal pathogen with a global distribution that predominantly infects Pinus species. The impact of the fungus is increasing due to climate-driven range expansion and thus wide-scale disease outbreaks. With the aim of developing high quality genome resources, we generated chromosome-level genome assemblies for three D. sapinea isolates and low-coverage Illumina genome data for six additional isolates. By comparing these genome assemblies, we identified 14 core chromosomes and two accessory chromosomes (ACs) in the pathogen. The ACs encode 80 and 155 proteins, respectively, while 11374 - 11609 genes were identified in the core chromosomes. Both ACs had lower gene density and higher proportions of transposable elements compared to the core chromosomes. Sequence analysis indicated that genes on the ACs are rapidly evolving, suggesting they serve as evolutionary hotspots in the species. Sequence homology analyses suggested that the ACs were likely acquired horizontally, probably from a species in the Dothideomycetes. We designed PCR-based assays to aid in the detection of the ACs and applied these on a set of 37 isolates from 14 countries. One of the ACs was detected in 33 isolates from 13 countries, while the other AC was absent in all isolates tested. Pathogenicity trials on Pinus patula seedlings showed no correlation between the presence of ACs and isolate aggressiveness. The high-quality genomes provided here offer important resources for future research on this globally important pathogen, including the biological roles of the ACs.

genomics↗

bioRxiv2025

Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers

Genes involved in the regulation of chromatin structure are frequently disrupted in cancer, contributing to an aberrant transcriptome and phenotypic plasticity. Yet, therapeutics targeting mutant forms of chromatin-modifying enzymes have yielded only modest clinical utility, underscoring the difficulty of targeting the epigenomic underpinnings of aberrant gene regulatory networks. Here, we sought to identify novel epigenetic vulnerabilities in diffuse large B-cell lymphoma (DLBCL). Through phenotypic screens and biochemical analysis, we demonstrated that inhibition of the H3K9 demethylases KDM4A and KDM4C elicits potent, subtype-agnostic cytotoxicity by antagonizing transcriptional networks associated with B-cell identity and epigenetically rewiring heterochromatin. KDM4 demethylases associated with the KRAB zinc finger ZNF587, and their enzymatic inhibition led to DNA replication stress and DNA damage-induced cGAS-STING activation. Broad surveys of transcriptional data from patients also revealed KDM4 family dysregulation in several other cancer types. To explore this potential therapeutic avenue, we performed high-throughput small molecule screens with H3K9me3 nucleosome substrates and identified novel KDM4 demethylase inhibitors. AI-guided protein-ligand binding predictions suggested diverse modes of action for various small molecule hits. Our findings underscore the relevance of targeting fundamental transcriptional and epigenetic mechanisms for anti-cancer therapy. HIGHLIGHTSO_LIPhenotypic screens identified JIB-04 as a potent anti-cancer agent for multiple subtypes of diffuse large B-cell lymphoma C_LIO_LIJIB-04 binds and inhibits KDM4 demethylases resulting in epigenomic rewiring of heterochromatin C_LIO_LIKDM4 demethylases cooperate with KRAB zinc fingers to limit DNA replication stress, and KDM4 inhibition instigates DNA-damage and cGAS-STING activation in several human cancers C_LIO_LIHigh-throughput small molecule screens with semi-synthetic nucleosome substrates and AI-guided molecular docking simulations identify novel KDM4 inhibitors C_LI

genomics↗

bioRxiv2025

Proof-of-principle of NF1 Gene Therapy in plexiform neurofibroma mice models

Neurofibromatosis type I is a rare neurocutaneous syndrome characterized by the development of disfiguring neurofibroma tumors with unmet clinical needs. As Neurofibromatosis Type I is a monogenic disease, the development of gene therapy is highly attractive, but it is currently unknown if rescuing the NF1 gene in established neurofibroma is sufficient for tumor regression. Here, we test this hypothesis by building two novel NF1 mouse models with reversible NF1 expression. In the first model, the human NF1 -/- Schwann cells named ipNF95.11b were genetically modified with a doxycycline-inducible full-length mouse Nf1 gene. One month after cells implantation in the sciatic nerve, mice were split into 2 groups. Strikingly, all sciatic nerves from mice allowed to drink doxycycline water for one month display complete normalization of the sciatic nerve histologically (n=6 sciatic nerves) whereas 83% (5 out of 6 sciatic nerves) develop or maintain a neurofibroma when drinking regular water. In the second model, the human NF1 +/- Schwann cells named ipNF95.11c were genetically modified with a doxycycline-inducible potent shRNA against the NF1 mRNA transcript. Strikingly, doxycycline withdrawal after neurofibroma establishment allowed complete normalization (n=4 sciatic nerves), whereas all sciatic nerves showed evidence of neurofibroma when kept on doxycycline (n=4 sciatic nerves). Thus, we proof-of-principle NF1 Gene Therapy in plexiform neurofibroma mice models.

cancer biology↗

bioRxiv2023

A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A

How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associated PHF21A missense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing of PHF21A-n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.

molecular biology↗

bioRxiv2023

Tracking the progression of Alzheimer's disease with peripheral blood monocytes

BackgroundAlzheimers disease (AD) is the most common form of dementia with the symptoms gradually worsening over the years. However, the driving pathological processes occur well before the appearance of symptoms. AD patients display signs of systemic inflammation, suggesting that it could precede the well-established AD hallmarks. We recently showed that the innate immune response in the form of monocyte activation is detectable at the pre-clinical stage. ObjectivesOur goal here is to characterize changes of gene expression in peripheral blood monocytes from patients at different stages of AD progression and validate potential biomarkers for a better prognosis and diagnosis of AD clinical spectrum. ResultsWe performed a whole transcriptome analysis on monocytes purified from healthy subjects, Mild Cognitive Impairment (MCI) and AD patients, and established the list of genes differentially expressed in monocytes during the disease evolution. We observed that, in the top 500 genes differentially expressed, a majority of these genes were upregulated (65%) during AD progression. These genes are mainly involved in chemokine/cytokine-mediated signaling pathways. We further confirmed several biomarkers by quantitative PCR and immunoblotting and showed that they are often deregulated at pre-clinical stages of the disease (MCI stage), supporting the hyperactivation of monocytes in MCI patients. PerspectivesOur findings provide evidence that the pre-clinical stage of AD can be detected in monocytes using a specific set of biomarkers, highlighting the importance to study the early innate immune response in AD. Our results open the possibility to use these biomarkers with different diagnostic methodologies to better predict and efficiently treat AD.

neuroscience↗

bioRxiv2023

Impact of in vivo cyclic reprogramming on the choroid plexus

In vivo reprogramming using the transient expression of Oct3/4, Sox2, Klf4 and c{square}Myc (OSKM) transcription factors can be used to induce tissue regeneration. A cyclic regime for short{square}term OSKM expression has been shown to promote regeneration of several organs however its impact on the brain remains largely unknown. We investigated the effects of a cyclic short-term OSKM expression on the choroid plexus (CP), a highly vascularized tissue found within the brain ventricles which is responsible for producing the cerebrospinal fluid (CSF). Transient reprogramming was done on 8-week-old mice carrying the polycistronic OSKM cassette under tetracycline operator (tetO) and confirmed the successful transient reprogramming. We then performed the analysis of the CP at cellular and molecular levels. The CP tissue exhibited minor morphological changes in height and area of epithelial cells. We did not observe any significant differences in the integrity of the brain-CSF barrier but noticed an increase of NKCC1 expression, a protein involved in CSF production. A whole transcriptome analysis (RNA-seq) was also carried on the tissue and showed no difference in gene expression after the transient reprogramming, at the exception of blood-related genes. Our results indicate that surprisingly the CP mainly remains insensible to in vivo transient reprogramming as only morphological and protein changes were observed in the tissue, suggesting that translational changes might be at stake during the reprogramming process but are not present at the transcriptomic level. Our results also highlight that more tailored strategies need to be developed for exploring the potential of CP reprogramming in regenerative medicine.

neuroscience↗

bioRxiv2022

Functional characterization of a PHF8 processed pseudogene in the mouse genome

The majority of pseudogenes are generated when an RNA transcript is reverse-transcribed and integrated into the genome at a new location. Pseudogenes are often considered as an imperfect and silent copy of a functional gene because of the accumulation of numerous mutations in their sequence. Here we report the presence of PHF8-ps, a PHF8 retrotransposed pseudogene in the mouse genome, which has no disruptions in its coding sequence. We showed that this pseudogene was specifically transcribed in testis and can produce a Phf8-ps protein in vivo. As Phf8-ps protein has a well-conserved JmjC domain, we characterized its enzymatic activity and showed that Phf8-ps did not have the intrinsic capability to demethylate H3K9me2 in vitro compared to the parental Phf8 protein. Surprisingly, Phf8-ps did not localize in the nucleus like Phf8 but rather was mostly located at the cytoplasm. Finally, our proteomic analysis of Phf8-ps associated proteins revealed that Phf8-ps interacted with mitochondrial proteins but also with prefoldin subunits (PFDN proteins) that deliver unfolded proteins to the cytosolic chaperonin complex implicated the folding of cytosolic proteins. Together, our findings highlighted Phf8-ps as a new pseudogene-derived protein with distinct molecular functions from Phf8.

biochemistry↗

bioRxiv2022

Decoupling of mRNA and protein expression in aging brains reveals the age-dependent adaptation of specific gene subsets

During aging, changes in gene expression are associated with decline in physical and cognitive abilities. Here, we investigated the connection between changes of mRNA and protein expression in the brain by comparing the transcriptome and proteome of the mouse cortex during aging. Our transcriptomic analysis revealed that aging mainly triggers gene activation in the cortex. We showed that increase of mRNA expression correlates with protein expression, specifically in the anterior cingulate cortex where we also observed an increase of cortical thickness during aging. Genes exhibiting an aging-dependent increase of mRNA and protein levels are involved in sensory perception and immune functions. Our proteomic analysis also identified changes in protein abundance in the aging cortex and highlighted a subset of proteins that were differentially enriched but exhibited stable mRNA levels during aging, implying the contribution of aging-related post transcriptional and post-translational mechanisms. These specific genes were associated with general biological processes such as translation, ribosome assembly and protein degradation, but also important brain functions related to neuroplasticity. By decoupling mRNA and protein expression, we have thus characterized distinct subsets of genes that differentially adjust to cellular aging in the cerebral cortex.

biochemistry↗

bioRxiv2022

Interaction mechanism between the HSV-1 glycoprotein B and the antimicrobial peptide Amyloid-β

Unravelling the mystery of Alzheimers Disease (AD) requires urgent resolution given the worldwide increase of the aging population. There is a growing concern that the current leading AD hypothesis, the amyloid cascade hypothesis, does not stand up to validation with respect to emerging new data. Indeed, several paradoxes are being discussed in the literature, for instance, both the deposition of the Amyloid-Beta peptide (A{beta}) and the intracellular neurofibrillary tangles (NFTs) could occur within the brain without any cognitive pathology. Thus, these paradoxes suggest that something more fundamental is at play in the onset of the disease and other key and related pathomechanisms have to be investigated. The present study follows our previous investigations on the infectious hypothesis, which posits that some pathogens are linked to late onset AD. Our studies also build upon the shattering finding that A{beta} is a powerful antimicrobial agent capable of inhibiting pathogens as observed in in vitro experiments. Herein, we ask what are the molecular mechanisms in play when A{beta} neutralizes infectious pathogens? To answer this question, we probed at nanoscale lengths with FRET (Forster Resonance Energy Transfer), the interaction between A{beta} peptides and glycoprotein B (responsible of virus-cell binding) within the HSV-1 virion. We concluded that there is indeed a close interaction, likely nonspecific or semi-specific, between the two types of molecules, which participate in virus neutralization.

neuroscience↗

bioRxiv2021

Functional and structural characterization of Serratia marcescens ExbB: determinants of the interaction with HasB/TonB

ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The opportunistic pathogen Serratia marcescens (Sm) possesses both TonB and a heme-specific TonB paralog, HasB. ExbBSm has a long periplasmic extension absent in other bacteria such as E. coli (Ec). Long ExbBs are found in several genera of Alphaproteobacteria, most often in correlation with a hasB gene. We investigated specificity determinants of ExbBSm and HasB. We determined the cryo-EM structures of ExbBSm and of the ExbB-ExbDSm complex from S. marcescens. ExbBSm alone is a stable pentamer, and its complex includes two ExbD monomers. We showed that ExbBSm extension interacts with HasB and is involved in heme acquisition and we identified key residues in the membrane domain of ExbBSm and ExbBEc, essential for function and likely involved in the interaction with TonB/HasB. Our results shed light on the new class of inner membrane energy machinery formed by ExbB,ExbD and HasB.

microbiology↗

bioRxiv2021

Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

AO_SCPLOWBSTRACTC_SCPLOWChromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in detail for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de novo whole-genome assembly obtained from a new method of DNA extraction and long-reads sequencing Nanopore technology obtained from a Japanese isolate sampled in the native area of the species. The comparison with a recently published reference genome revealed stable gene and transposable elements (TEs) repertoires. We also showed that the C. parasitica genome is lowly compartmentalized, with a poor association between TEs and genes, such as those potentially involved in host interactions (i.e., genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations in the invasive success of this fungal pathogen species.

genomics↗

bioRxiv2020

QTL mapping for aggressiveness variation in F. graminearum revealed one causal mutation in FgVe1 velvet protein

Fusarium graminearum is one of the most frequent causal agents of the Fusarium Head Blight in the world, a cereal disease spread throughout the world, reducing grain production and quality. F. graminearum isolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population, for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel of in planta and in vitro proxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a mutation was identified and functionally validated in the gene FgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.

microbiology↗

bioRxiv2020

MEIS-WNT5A axis regulates development of 4th ventricle choroid plexus

The choroid plexus (ChP) produces cerebrospinal fluid and forms a critical barrier between the brain and the circulation. While the ChP forms in each brain ventricle, it adopts a different shape in each one and remarkably little is known about the mechanisms underlying its development. Here, we show that epithelial WNT5A is critical for determining fourth ventricle (4V) ChP morphogenesis and size. Systemic Wnt5a knockout, or forced WNT5A overexpression beginning at E10.5, profoundly reduced the size and development of ChP in all ventricles. However, conditional deletion of Wnt5a expression in Foxj1-expressing epithelial cells affected only the branched, villous morphology of the 4V ChP. We found that WNT5A was enriched in epithelial cells localized to the distal tips of 4V ChP villi, where WNT5A acted locally to activate non-canonical Wnt signaling via Ror1/Ror2 receptors. During 4V ChP development, MEIS1 bound to the proximal Wnt5a promoter, and gain- and loss-of-function approaches demonstrated that MEIS1 regulated Wnt5a expression. Collectively, our findings demonstrate a dual function of WNT5A in ChP development and identify MEIS1 and MEIS2 as upstream regulators of Wnt5a in the 4V ChP epithelium.

developmental biology↗

bioRxiv2018

Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure

We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-the-art algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, ...), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores.

neuroscience↗