Biology subjects

Bonnefond, A.

Publications and source records attributed to Bonnefond, A..

14 recordsLinked to original sources

bioRxiv2025

Flagellin-mediated TLR5 activation enhances innate immune responses in healthy and diseased human airway epithelium

Bacterial pneumonia poses a significant challenge to public health, often leading to antibiotic treatment failure. Enhancing innate immunity represents a promising adjunctive strategy to conventional antibiotic therapy. Bacterial flagellin, a Toll-like receptor 5 (TLR5) agonist, has been shown to stimulate innate immune defenses when delivered via the respiratory route, demonstrating efficacy in both preventing and treating bacterial pneumonia in murine models. This protective effect is primarily mediated through TLR5-driven activation of airway epithelial cells. This study aimed to characterize the immunomodulatory effects of flagellin on human primary respiratory epithelium. Using the MucilAir air-liquid interface model and RNA sequencing, we demonstrated that apical administration of flagellin induced robust immune responses in airway epithelium derived from healthy individuals, as well as patients with chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF). TLR5-mediated epithelial signaling triggered key immune-related pathways, including cytokine production, leukocyte chemotaxis, neutrophil recruitment, and antimicrobial defense, with strong commonalities across healthy and diseased airway epithelia. Furthermore, we demonstrated that flagellin effectively activated epithelial immune responses even in the presence of the bacteria Pseudomonas aeruginosa or Streptococcus pneumoniae. However, epithelial activation alone was insufficient to directly limit bacterial colonization or replication, highlighting the potential role of epithelial-immune cell interactions in achieving effective bacterial clearance. These findings support TLR5 activation as a promising therapeutic strategy to enhance host defense mechanisms and improve treatment outcomes for bacterial pneumonia in both healthy individuals and patients with COPD or CF.

immunology↗

bioRxiv2025

Deep learning models reading clinical data and liver omics strongly distinguish NASH from steatosis and suggest new genes involved in liver disease severity

Background & AimsMetabolic dysfunction-associated steatotic liver disease (MASLD, previously NAFLD) is a frequent co-morbidity of obesity and diabetes, with prevalence increasing worldwide in all age groups and both sexes. Only early stages of the disease are fully reversible. Recognising liver disease stages and elucidating the molecular underpinning of their progression are thus medically important. We developed a deep learning model to recognise simple steatosis from steatohepatitis combining liver transcriptomics, epigenetics, and clinical data. MethodsWe used clinical data, liver gene expression and liver DNA methylation gathered from 300 patients with obesity of the ABOS cohort (80 without NAFLD, 137 with simple steatosis, 83 with steatohepatitis). We selected non-redundant clinical variables, gene expressions and CpGs methylation levels most associated with severity using unsupervised approaches. We designed a multi-module, multi-layer perceptron to predict patients liver status. We trained five model instances on independent training/test sets and combined the predictions. ResultsWe used a score based on gene expression/DNA methylation and relevant principal component analysis (PCA) loadings to select 200 genes and 260 CpG methylations. Models trained on the three modalities reached an AUC of 0.945 overall on a validation set with accuracies above 81% for simple steatosis and 88% for NASH, outperforming any other machine learning model so far. We retrieved patient clusters previously found using clinical variables in the latent space of our clinical data module, but not in the gene expression and DNA methylation modules. While all three modules are needed to reach the best prediction accuracy in all classes, the gene expression module had the most impact on the decision. Independent models weighted gene expression inputs similarly, shining light on their importance. The most impactful genes were linked to immune responses and extracellular matrix. However, many of those genes were previously unassociated with steatotic liver disease onset or progression. ConclusionsA multi-omics deep-learning model can recognise steatohepatitis from simple liver steatosis with an AUC of 0.945 and identify new genes potentially involved in NAFLD progression. Gene expressions profiles predicting disease severity are largely different from those specific of clinical variable clusters. Impact and implicationsThis study suggests that clinical variables are not sufficient to recognise the severity of steatotic liver disease with high accuracy, but model efficiency increases when used together with liver epigenetics and transcriptomics.

molecular biology↗

bioRxiv2025

Effects of mind-wandering on cognitive and neural processes: Identifying specific impairments in adults with attention-deficit/hyperactivity disorder

Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder characterized by symptoms of inattention and/or impulsivity/hyperactivity. Although not a core symptom, excessive mind-wandering (MW) is commonly associated with the disorder and may contribute to symptoms as well as performance deficits observed in these patients. The main aim behind the present study is to better characterize MW and its impact on performance measures as well as on neural activity in adults with ADHD. Twenty-eight medication-naive ADHD patients and 28 healthy controls were matched on sex, age, and level of education; they completed a prolonged Go/No-Go sustained attention task including thought-probes to detect episodes of MW. Analysis of EEG data focused on P100, P3b, and CRN event-related potentials reflecting early visual, attention allocation, and performance monitoring processes, respectively. MW, particularly spontaneous MW, was more frequent in patients and linked to a more severe ADHD symptomatology. A differentiated negative impact of MW on performance was noted in both groups: speed and variability of patients reaction times and accuracy in controls were affected. If the same perceptual (P100) and attentional (P3b) impairments were evidenced in both groups during MW, then the impairment of the performance monitoring (CRN) process was exclusively highlighted in ADHD patients (as revealed by a state x group interaction).Taken together, these results extend the understanding of the cognitive and neural processes associated with increased MW in patients and suggest performance monitoring as a potential key mechanism underlying specific MW-related impairments in ADHD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/677328v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@23ed8forg.highwire.dtl.DTLVardef@c155b7org.highwire.dtl.DTLVardef@e2a057org.highwire.dtl.DTLVardef@8cc5c0_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

A systematic review and ALE meta-analysis of cognitive control, motivation and effort-based decision-making in schizophrenia and mood disorders: Implications for multidimensional apathy

BackgroundApathy is present in about 50% of patients suffering from schizophrenia (SZ) and mood disorders (MD). Even though these two disorders are different, in psychiatry, apathy refers typically to the same unidimensional clinical entity, sharing the same pathophysiological processes and symptoms regardless of the underlying diagnosis. Neurology proposes another perspective: three forms of apathy --emotional, executive, and initiative-- are related to a disturbance in motivational processing, cognitive control, and effort-based decision-making, respectively. We explored whether this latter model can be applied in psychiatry by identifying differences between SZ and MD through a PRISMA meta-analysis of imaging studies on motivational, cognitive control, and effort-based decision-making networks. MethodsWe searched the Sleuth BrainMap database for studies on SZ, MD, and/or healthy controls using tasks that explore motivation, cognitive control, and effort-based decision-making. Twenty-eight functional MRI studies were identified and included for a coordinate-based activation likelihood estimation analysis. ResultsIn SZ, hypoactivity in the motivational structures, a specific hyperactivity in the right cerebellar vermis that has previously been linked to emotional blunting and apathy, and a lack of activation during effort-based decision-making that could imply an impaired reward processing, suggest a dominant form of emotional apathy. In MD, hypoactivity in both cognitive control and motivational structures, which has previously been linked to the co-occurrence of executive difficulty and amotivation, suggests a dominant mix of emotional/executive apathy. ConclusionsDespite a small number of studies, our results could help target new individualized treatment strategies in precision psychiatry based on a multidimensional approach to apathy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/634295v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@12ad24dorg.highwire.dtl.DTLVardef@54e4cforg.highwire.dtl.DTLVardef@179ede6org.highwire.dtl.DTLVardef@1f1d86c_HPS_FORMAT_FIGEXP M_FIG C_FIG The results of this meta-analysis highlight different activation profiles in SZ and in MD during motivational, cognitive control, and effort-based decision-making tasks, suggesting a dominant form of emotional apathy in SZ and a dominant coexistence of emotional and executive apathy in MD.

neuroscience↗

bioRxiv2024

Objective Markers of Sustained Attention Fluctuate Independently of Mind-Wandering Reports

Sustained attention fluctuates between periods of good and poor attentional performance. Two major methodologies exist to study these fluctuations: an objective approach that identifies "in-the-zone" states of consistent response times (RTs) and "out-of-the-zone" states of erratic RTs and a subjective approach that asks participants whether they are on-task or mind wandering. Although both approaches effectively predict attentional lapses, it remains unclear whether they capture the same or distinct attentional fluctuations. We combined both approaches within a single sustained attention task requiring frequent responses and response inhibition to rare targets to explore their consistency (N=40). Behaviorally, both objective out-of-the-zone and subjective mind-wandering states were associated with more attentional lapses. However, the percentage of time spent out-of-the-zone did not differ between on-task and mind-wandering periods and both objective and subjective states independently predicted error-proneness, suggesting that the two methods do not capture the same type of attention fluctuations. Whereas attentional preparation before correct inhibitions was greater during out-of-the-zone compared to in-the-zone periods, preparation did not differ by subjective state. In contrast, post-error slowing differed by both objective and subjective states, but in opposite directions: slowing was observed when participants were objectively out-of-the-zone or subjectively on-task. Overall, our results provide evidence that objective and subjective approaches capture distinct attention fluctuations during sustained attention tasks. Integrating both objective and subjective measures is crucial for fully understanding the mechanisms underlying our ability to remain focused.

neuroscience↗

bioRxiv2023

Multiple genetic variants at the SLC30A8 locus affect a local super-enhancer cluster to influence pancreatic β-cell survival and function

Variants at the SLC30A8 locus are associated with type 2 diabetes (T2D) risk. The lead variant, rs13266634, encodes an amino acid change, Arg325Trp (R325W), at the C-terminus of the secretory granule-enriched zinc transporter, ZnT8. Although this protein-coding variant was previously thought to be the sole driver of T2D risk at this locus, recent studies have provided evidence for lowered expression of SLC30A8 mRNA in protective allele carriers. In the present study, combined allele-specific expression (cASE) analysis in human islets revealed multiple variants that influence SLC30A8 expression. Epigenomic mapping identified an islet-selective enhancer cluster at the SLC30A8 locus, hosting multiple T2D risk and cASE associations, which is spatially associated with the SLC30A8 promoter and additional neighbouring genes. Deletions of variant-bearing enhancer regions using CRISPR-Cas9 in human-derived EndoC-{beta}H3 cells lowered the expression of SLC30A8 and several neighbouring genes, and improved insulin secretion. Whilst down-regulation of SLC30A8 had no effect on beta cell survival, loss of UTP23, RAD21 or MED30 markedly reduced cell viability. Although eQTL or cASE analyses in human islets did not support the association between these additional genes and diabetes risk, the transcriptional regulator JQ1 lowered the expression of multiple genes at the SLC30A8 locus and enhanced stimulated insulin secretion.

cell biology↗

bioRxiv2023

Control of human pancreatic beta cell kinome by GLP-1R biased agonism

AimTo determine the kinase activity profiles of human pancreatic beta cells downstream of GLP-1R balanced versus biased agonist stimulations. Materials and methodsThis study analysed the kinomic profiles of human EndoC-{beta}h1 cells following vehicle and glucagon-like peptide-1 receptor (GLP-1R) stimulation with the pharmacological agonist exendin-4, as well as exendin-4-based biased derivatives exendin-phe1 and exendin-asp3 for acute (10-minute) versus sustained (120-minute) responses, using PamChip(R) protein tyrosine kinase (PTK) and serine/threonine kinase (STK) assays. The raw data were filtered and normalised using BioNavigator. The kinase analyses were conducted with R, mainly including kinase-substrate mapping and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. ResultsThe present analysis reveals that kinomic responses are distinct for acute versus sustained GLP-1R agonist (GLP-1RA) exposure, with individual responses associated with agonists presenting specific bias profiles. According to pathway analysis, several kinases, including JNKs, PKCs, INSR and LKB1, are important GLP-1R signalling mediators, constituting potential targets for further research on biased GLP-1R downstream signalling. ConclusionResults from this study suggest that differentially biased exendin-phe1 and exendin-asp3 can modulate distinct kinase interaction networks. Further understanding of these mechanisms will have important implications for the selection of appropriate anti-T2D therapies with optimised downstream kinomic profiles.

cell biology↗

bioRxiv2022

The HDAC inhibitor trichostatin A impairs pancreatic β-cell function through an epigenome-wide reprogramming

ObjectiveThe pancreatic islets of Langerhans contain distinct cell subtypes including insulin-producing {beta} cells. Although their cell-specific gene expression pattern defines their identity, the underlying molecular network driving this transcriptional specificity is not fully understood. Among the numerous transcriptional regulators, histone deacetylases (HDAC) enzymes are potent chromatin modifiers which directly regulate gene expression through deacetylation of lysine residues within specific histone proteins. The precise molecular mechanisms underlying HDAC effects on cellular plasticity and {beta}-cell identity are currently unknown. MethodsThe pharmacological inhibition of HDAC activity by trichostatin A (TSA) was studied in the mouse Min6 and human EndocBH1 cell lines, as well as primary mouse sorted {beta} cells and human pancreatic islets. The molecular and functional effects of treating these complementary {beta}-cell models with TSA was explored at the epigenomic and transcriptomic level through next-generation sequencing of chromatin immunoprecipitation (ChIP) assays (ChIP-seq) and RNA sequencing (RNA-seq) experiments, respectively. ResultsWe showed that TSA alters insulin secretion associated with {beta}-cell specific transcriptome programming in both mouse and human {beta}-cell lines, as well as on human pancreatic islets. We also demonstrated that this alternative {beta}-cell transcriptional program in response to HDAC inhibition is related to an epigenome-wide remodeling at both promoters and enhancers. ConclusionsTaken together, our data indicate that full HDAC activity is required to safeguard the epigenome, to protect against loss of {beta}-cell identity with unsuitable expression of genes associated with alternative cell fates.

genomics↗

bioRxiv2022

Epigenetic changes associated with hyperglycaemia exposure in the longitudinal D.E.S.I.R. cohort.

AimUnderstanding DNA methylation dynamics associated with progressive hyperglycaemia exposure could provide early diagnostic biomarkers and an avenue for delaying type 2 diabetes (T2D) disease. We aimed to identify DNA methylation changes during a 6-year period associated with early hyperglycaemia exposure using the longitudinal D.E.S.I.R. cohort. MethodsWe selected individuals with progressive hyperglycaemia exposure based on T2D diagnostic criteria: 27 with long-term exposure, 34 with short-term exposure and 34 normoglycaemic controls. DNA from blood at inclusion and at the 6-years visit was subjected to methylation analysis using 850K methylation-EPIC arrays. A linear mixed model was used to perform an epigenome-wide association study (EWAS) and identify methylated changes associated with hyperglycaemia exposure during 6-year time-period. ResultsWe did not identify differentially methylated sites that reached FDR-significance in our cohort. Based on EWAS, we focused our analysis on methylation sites that had a constant effect during the 6-years across the hyperglycaemia groups compared to controls and found the most statistically significant site was the reported cg19693031 probe (TXNIP). We also performed an EWAS with HbA1c, using the inclusion and the 6-years methylation data and did not identify any FDR-significant CpGs. ConclusionsOur study reveals that DNA methylation changes are not robustly associated with hyperglycaemia exposure or HbA1c during a short-term period, however, our top loci indicate potential interest and should be replicated in larger cohorts.

genomics↗

bioRxiv2022

BIN1 regulates electrical activity and network synchronization in hiPSC-derived neurons

BackgroundBridging Integrator 1 (BIN1) is the second most important Alzheimers disease (AD) risk gene, but its physiological roles in neurons and its contribution to brain pathology remain largely elusive. In this work, we show that BIN1 plays a critical role in the regulation of calcium homeostasis, electrical activity, and gene expression of glutamatergic neurons. MethodsWe generated 3D cerebral organoids and 2D enriched neuronal cell cultures from isogenic BIN1 wild-type (WT), heterozygous (HET) and homozygous knockout (KO) human-induced pluripotent stem cells (hiPSCs). Using single-cell RNA-sequencing, biochemical assays, immunocytochemistry and multi-electrode array(MEA) electrophysiology, we characterized the molecular and functional consequences of reduced BIN1 expression in different neural cell types. ResultsWe show that BIN1 is mainly expressed by oligodendrocytes and glutamatergic neurons of cerebral organoids, like in the human brain. Both BIN1 HET and KO cerebral organoids show specific transcriptional alterations, mainly associated with ion transport and synapses in glutamatergic neurons. We then demonstrate that BIN1 cell-autonomously regulates gene expression in glutamatergic neurons by using a novel protocol to generate pure culture of human-derived induced neurons (hiNs). Using this system, we also show that BIN1 plays a key role in the regulation of neuronal calcium transients and electrical activity via its interaction with the L-type voltage-gated calcium channel Cav1.2. BIN1 KO hiNs show reduced activity-dependent internalization and higher Cav1.2 expression compared to WT hiNs. Pharmacological treatment with clinically relevant doses of nifedipine, a calcium channel blocker, partly rescues neuronal electrical and gene expression alterations in BIN1 KO glutamatergic neurons. Further, we show that transcriptional alterations in BIN1 KO hiNs affecting biological processes related to calcium homeostasis are also present in glutamatergic neurons of the human brain at late stages of AD pathology. ConclusionsTogether, our findings suggest that BIN1-dependent alterations in neuronal properties could contribute to AD pathophysiology and that treatment with low doses of clinically approved calcium blockers should be considered as an option to dampen disease onset and progression.

neuroscience↗

bioRxiv2021

Excessive fetal growth affects HSC quiescence maintenance through epigenetic programming of EGR1 transcriptional network

Excessive fetal growth is associated with DNA methylation alterations in human hematopoietic stem and progenitor cells (HSPC), but their functional impact remains elusive. We implemented an integrative analysis combining single-cell epigenomics, single-cell transcriptomics, and in vitro analyses to functionally link DNA methylation changes to putative alterations of HSPC functions. We showed in hematopoietic stem cells (HSC) from large for gestational age neonates that both DNA hypermethylation and chromatin rearrangement target a specific network of transcription factors known to sustain stem cell quiescence. In parallel, we found a decrease expression of key genes regulating HSC differentiation including EGR1, KLF2, SOCS3, and JUNB. Our functional analyses showed that this epigenetic programming was associated with a decreased ability for HSCs to stay quiescent. Taken together, our multimodal approach using single-cell (epi)genomics showed that human fetal overgrowth affects hematopoietic stem cells quiescence maintenance via epigenetic programming.

genomics↗

bioRxiv2021

A crosstalk between E2F1 and GLP-1 signaling pathways modulates insulin secretion

Compromised {beta}-cell function contributes to type 2 diabetes (T2D) development. The glucagon like peptide 1 (Glp-1) has emerged as a hormone with broad pharmacological potential toward T2D treatment, notably by improving {beta}-cell functions. Recent data have shown that the transcription factor E2f1, besides its role as a cell cycle regulator, is involved in glucose homeostasis by modulating {beta}-cell mass, function and identity. Here, we demonstrate a crosstalk between the E2F1, phosphorylation of retinoblastoma protein (pRb) and Glp-1 signaling pathways. We found that {beta}-cell specific E2f1 deficient mice (E2f1{beta}-/-) presented with impaired glucose homeostasis and decreased glucose stimulated-insulin secretion mediated by exendin 4 (i.e., GLP1R agonist), which were associated with decreased expression of Glp1r encoding Glp-1 receptor (GLP1R) in E2f1{beta}-/- pancreatic islets. Decreasing E2F1 transcriptional activity with an E2F inhibitor in islets from nondiabetic humans decreased GLP1R levels and blunted the incretin effect of exendin 4 on insulin secretion. Conversely, overexpressing E2f1 in pancreatic {beta} cells increased Glp1r expression associated with enhanced insulin secretion mediated by GLP1R agonist. Interestingly, kinome analysis of mouse islets demonstrated that an acute treatment with exendin 4 increased pRb phosphorylation and subsequent E2f1 transcriptional activity. This study suggests a molecular crosstalk between the E2F1/pRb and GLP1R signaling pathways that modulates insulin secretion and glucose homeostasis.

physiology↗

bioRxiv2020

Pancreatic β-cell specific loss of E2f1 impairs insulin secretion and β-cell identity through the epigenetic repression of non β-cell programs

The loss of pancreatic {beta}-cell identity emerges as an important feature of type 2 diabetes development, but the molecular mechanisms are still elusive. Here, we explore the cell-autonomous role of the cell cycle regulator and transcription factor E2F1 in the maintenance of {beta}-cell identity and insulin secretion. We show that the {beta}-cell-specific loss of E2f1 function in mice triggers glucose intolerance associated with defective insulin secretion, an altered -to-{beta}-cell ratio, a downregulation of many {beta}-cell genes and a concomitant increase of non-{beta}-cell markers. Mechanistically, the epigenomic profiling of non-beta cell upregulated gene promoters identified an enrichment of bivalent H3K4me3/H3K27me3 or H3K27me3 marks. Conversely, downregulated genes were enriched in active chromatin H3K4me3 and H3K27ac histone marks. We find that histone deacetylase inhibitors modulate E2F1 transcriptional and epigenomic signatures associated with these {beta}-cell dysfunctions. Finally, the pharmacological inhibition of E2F transcriptional activity in human islets also impairs insulin secretion and the expression of {beta}-cell identity genes. Our data suggest that E2F1 is critical for maintaining {beta}-cell identity through a sustained repression of non {beta}-cell transcriptional programs.

physiology↗

bioRxiv2018

Performance - Based Clustering Enables The Study Of Physiological Features Supporting Sustained Attention Capacities

In the present study, we investigated different sustained attention performance profiles in the general adult population and if age is a determinant factor among these profiles. We also reported some specificities in terms of brain oscillations. The sustained attention to response task was applied combined with electrophysiological recordings in 59 adults, aged from 19 to 86 years. We used a hierarchical cluster analysis to group individuals based on similarity of levels and patterns of performance across variables of interest. We focused on the most common attentional-related variables, which allowed us to identify four distinct clusters showing specific sustained attention profiles. Furthermore, our analysis clearly revealed that age was not the determinant factor of these profiles. Finally, we highlighted specificities in terms of brain oscillations. Subjects from cluster 1- the \"high-performers\" - demonstrated a globally increased theta-gamma coupling maintained over time and an increase of theta activity at the FC6 and F8 electrodes. Subjects from cluster 2, who adopted a more cautious response strategy, presented a higher level of modulation exerted by the electrode FT7 over Oz and a higher theta-gamma coupling at the Oz. This result suggests that cluster-based method to useful in understanding specific mechanisms underlying sustained attention features.

neuroscience↗