Search bioRxiv⌕ Search

Biology subjects

Moreau, P.

Publications and source records attributed to Moreau, P..

At least 19 recordsLinked to original sources

Expression profile of CASSIOPEIA patients refines prognostic value of MRD negativity in multiple myeloma

Long-term follow-up of the CASSIOPEIA trial (NCT02541383) demonstrated superior progression-free survival (PFS) with daratumumab, both in combination with bortezomib, thalidomide, and dexamethasone during induction and consolidation, and during maintenance therapy, in transplant- eligible patients newly diagnosed with multiple myeloma (MM). However, outcomes among CASSIOPEIA patients remain heterogeneous across treatment groups. Measurable residual disease (MRD) is a strong indicator of the depth and duration of therapeutic response and is independently associated with both PFS and overall survival (OS), but it does not fully capture the biological diversity of MM. We performed a risk prediction analysis based on transcriptomic subgroups in CASSIOPEIA patients. A subset of 628 patients was characterized using RNA sequencing and consensus clustering identified five transcriptomic subtypes of MM. Long-term follow-up allowed the definition of three transcriptomic risk categories, with estimated 72-month PFS rates of 70%, 51%, and 27% for low, intermediate, and high-risk groups, respectively, among patients who received daratumumab in at least one treatment phase. In these patients, MRD negativity rates after consolidation and six months later were significantly higher in the low and high-risk groups compared with the intermediate-risk group. In the high-risk group, MRD status was not associated with PFS or OS. This suggests that, although daratumumab administered during both the induction/consolidation and maintenance phases improves the clinical outcomes of patients with activation of NSD2 or overexpressing members of the MAF family, highly aggressive minor clones may rapidly expand. These findings emphasize the need for novel therapeutic strategies in this high-risk population.

cancer biology↗

The phytolongin AtPhyl2.1 is involved in cell plate formation and root development

SNAREs are critical elements of the membrane trafficking machinery with a wide variety of functionality across this family of proteins. Phytolongins are a recently identified subfamily of longins which possess the typical longin domain but lack a SNARE motif. Phytolongins have an ubiquitous tissue expression in Arabidopsis and are distributed throughout the secretory pathway. We focused on Phytolongin 2.1 (PHYL2.1) which localizes to the endoplasmic reticulum, and observed a strong root growth phenotype in the loss-of-function Atphyl2.1-1 mutant. We demonstrate that whilst cell elongation efficiency was not affected in the mutant, cell division was significantly reduced. The resulting decrease in root length in the Atphyl2.1-1 mutant is explained by a smaller number of cells which then elongate to enable root growth. Root apical meristem architecture of Atphyl2.1-1 and another mutant Atphyl2.1-2 was disturbed and distances from the root quiescent center to the transition zone and the first areas of mis-organized cells were affected in both mutants. Investigation of the SNARE AtKNOLLE revealed significant perturbation of Atphyl2.1-1 cell plate formation in the mis-organised areas. Our results provide a first characterization of the phytolongin AtPHYL2.1 which appears involved in root cell plate formation, root cell division and therefore root development. HighlightThe phytolongin AtPHYL2.1 significantly affects the efficiency of cell plate formation and root development in Arabidopsis thaliana.

plant biology↗

Chromosome-level genome assembly and annotation of the chaetognath Flaccisagitta enflata

Chaetognaths, a phylum of enigmatic marine predators, present a significant challenge to phylogenetic reconstruction due to their uncertain evolutionary placement. While transcriptome analyses have suggested affinities with the Gnathifera clade, genomic data for this group remain scarce, hindering a comprehensive understanding of their evolution. Here, we present the first chromosome-level genome assembly of Flaccisagitta enflata, a species within the Aphragmophora order. The genome assembly includes 9 chromosome candidates with a total size of 794 Mb and a BUSCO score of 91.3% against the Metazoa lineage. This high-quality genome assembly provides a crucial resource for comparative genomic analyses within Chaetognatha and the broader Gnathifera clade, and it will facilitate investigations into chaetognath evolution and their phylogenetic relationships, addressing long-standing questions regarding their placement within the animal kingdom.

genomics↗

Enhanced Brain-Heart Connectivity as a Precursor of Reduced State Anxiety After Therapeutic Virtual Reality Immersion

State anxiety involves transient feelings of tension and nervousness in response to threats, which can escalate into anxiety disorders if persistent. Despite treatments, 30%-50% of individuals show limited improvement, and neurophysiological mechanisms of treatment responsiveness remain unclear, requiring the development of objective biomarkers. In this study, we monitored multimodal electrophysiological parameters: heart rate variability (high-frequency, low-frequency, LF/HF ratio), EEG beta and alpha relative power, and brain-to-heart connectivity in participants with real-life state anxiety. Participants underwent a therapeutic intervention combining virtual-reality immersion, hypnotic script, and a breath control exercise. Real-life state anxiety was captured using the STAI-Y1 scale before and after the intervention. We observed reduced anxiety immediately after the intervention in 16 out of 27 participants. While all participants, independently of their STAI-Y1 score, showed increased HRV low frequency power, only treatment-responders displayed increased overall autonomic tone (high and low frequency HRV), increased midline beta power and brain-to-heart connectivity. Notably, the LF/HF ratio showed a significant linear relationship with anxiety reduction, with higher ratios linked to greater therapeutic response. These findings suggest that increased cognitive regulation of brain-to-heart connectivity could serve as a biomarker for therapeutic efficacy, with elevated midline beta power facilitating improved cardiac tone in responders. Significance StatementElevated state anxiety can escalate into debilitating disorders, such as generalized anxiety disorder, yet treatment efficacy remains inconsistent, and reliable biomarkers predicting therapeutic outcomes are lacking. This study identifies key neural and physiological markers linked to effective anxiety reduction following a virtual reality-based non-pharmacological intervention in healthy participants with increased state anxiety. Anxiety reduction is associated with increased midline beta power, heightened heart rate variability (LF/HF ratio), and enhanced brain-to-heart connectivity. These findings highlight the role of brain-to-heart modulation and autonomic nervous system functioning in therapeutic response. By highlighting these biomarkers, this research aims at advancing our understanding of anxiety treatment mechanisms and offering insights into the development of biomarker-driven, scalable interventions.

neuroscience↗

Mechanism of homology search expansion during recombinational DNA break repair

Homology search catalyzed by a RecA/Rad51 nucleoprotein filament (NPF) is a central step of DNA double-strand break (DSB) repair by homologous recombination. How it operates in cells remains elusive. Here we developed a Hi-C-based methodology to map single-stranded DNA (ssDNA) contacts genome-wide in S. cerevisiae, which revealed two main homology search phases. Initial search conducted by short NPFs is confined in cis by cohesin-mediated chromatin loop folding. Progressive growth of stiff NPFs enables exploration of distant genomic sites. Long-range resection by Exo1 drives this transition from local to genome-wide search by providing ssDNA substrates for assembly of extensive NPFs. DSB end-tethering promotes coordinated homology search by NPFs formed on the two DSB ends. Finally, an autonomous genetic element on chromosome III engages the NPF and stimulates homology search in its vicinity. This work reveals the mechanism of the progressive and uneven expansion of homology search orchestrated by chromatin organizers, long-range resection, end-tethering, specialized genetic elements, and that exploits the stiff NPF structure conferred by Rad51 oligomerization. Highlights- Cohesin-mediated chromatin loops constrain homology search in cis for NPF regions close to the resection front - Stiffening of ssDNA by Rad51 enables genome-wide homology search by DSB-proximal sites - Exo1-mediated long-range resection promotes genome-wide homology search - DSB end-tethering promotes coordinated homology search by NPFs formed on both DSB ends - The recombination enhancer focuses homology search in its vicinity

genetics↗

An IL-1β driven neutrophil-stromal cell axis fosters a BAFF-rich microenvironment in multiple myeloma

The bone marrow permanently harbors high numbers of neutrophils, and a tumor-supportive bias of these cells could significantly impact bone marrow-confined malignancies. In multiple myeloma, the bone marrow is characterized by inflammatory stromal cells with the potential to influence neutrophils. We investigated myeloma-associated alterations in marrow neutrophils and the impact of stromal inflammation on neutrophil function. Mature neutrophils in myeloma marrow are activated and tumor-supportive, transcribing increased levels of IL-1{beta}, and myeloma cell survival factor BAFF. Interactions with inflammatory stromal cells can induce neutrophil activation, including BAFF secretion, in a STAT3-dependent manner and once activated, neutrophils gain the ability to reciprocally induce stromal activation. After first-line myeloid-depleting treatment, patient bone marrow retains residual stromal inflammation and newly-formed neutrophils are reactivated. Combined, we identify a neutrophil-stromal cell feed-forward loop driving tumor-supportive inflammation that persists after treatment and warrants novel strategies to target both stromal and immune microenvironments in multiple myeloma.

immunology↗

Force propagation between epithelial cells depends on active coupling and mechano-structural polarization

Cell-generated forces play a major role in coordinating the large-scale behavior of cell assemblies, in particular during development, wound healing and cancer. Mechanical signals propagate faster than biochemical signals, but can have similar effects, especially in epithelial tissues with strong cell-cell adhesion. However, a quantitative description of the transmission chain from force generation in a sender cell, force propagation across cell-cell boundaries, and the concomitant response of receiver cells is missing. For a quantitative analysis of this important situation, here we propose a minimal model system of two epithelial cells on an H-pattern ("cell doublet"). After optogenetically activating RhoA, a major regulator of cell contractility, in the sender cell, we measure the mechanical response of the receiver cell by traction force and monolayer stress microscopies. In general, we find that the receiver cells shows an active response so that the cell doublet forms a coherent unit. However, force propagation and response of the receiver cell also strongly depends on the mechano-structural polarization in the cell assembly, which is controlled by cell-matrix adhesion to the adhesive micropattern. We find that the response of the receiver cell is stronger when the mechano-structural polarization axis is oriented perpendicular to the direction of force propagation, reminiscent of the Poisson effect in passive materials. We finally show that the same effects are at work in small tissues. Our work demonstrates that cellular organization and active mechanical response of a tissue is key to maintain signal strength and leads to the emergence of elasticity, which means that signals are not dissipated like in a viscous system, but can propagate over large distances.

biophysics↗

Cell size and actin architecture determine force generation in optogenetically activated adherent cells

Adherent cells use actomyosin contractility to generate mechanical force and to sense the physical properties of their environment, with dramatic consequences for migration, division, differentiation and fate. However, the organization of the actomyosin system within cells is highly variable, with its assembly and function being controlled by small GTPases from the Rho-family. How activation of these regulators translates into cell-scale force generation and the corresponding sensing capabilities in the context of different physical environments is not understood. Here we probe this relationship combining recent advances in non-neuronal optogenetics with micropatterning and traction force microscopy on soft elastic substrates. We find that after whole-cell RhoA-activation by the CRY2/CIBN optogenetic system with a short pulse of 100 milliseconds, single cells contract before returning to their original tension setpoint with near perfect precision on a time scale of several minutes. To decouple the biochemical and mechanical elements of this response, we introduce a mathematical model that is parametrized by fits to the dynamics of the substrate deformation energy. We find that the RhoA-response builds up quickly on a time scale of 20 seconds, but decays slowly on a time scale of 50 seconds. The larger the cells and the more polarized their actin cytoskeleton, the more substrate deformation energy is generated. RhoA-activation starts to saturate if optogenetic pulse length exceeds 50 milliseconds, revealing the intrinsic limits of biochemical activation. Together our results suggest that adherent cells establish tensional homeostasis by the RhoA-system, but that the setpoint and the dynamics around it are strongly determined by cell size and the architecture of the actin cytoskeleton, which both are controlled by the extracellular environment.

biophysics↗

LILRB1 and LILRB2 expression in peripheral blood immune cells at 18 and 24 months of age in infants born from mothers with placental malaria

BackgroundPlacental malaria (PM) is associated with a higher susceptibility of infants to Plasmodium falciparum (Pf) malaria. A hypothesis of immune tolerance has been suggested but no clear explanation has been provided so far. Our goal was to investigate the involvement of inhibitory receptors LILRB1 and LILRB2, known to drive immune evasion upon ligation with pathogen and/or host ligands, in PM-induced immune tolerance. MethodsInfants of mothers with or without PM were enrolled in Allada, southern Benin, and followed-up for 24 months. Antibodies with specificity for five blood stage parasite antigens were quantified by ELISA, and the frequency of immune cell subsets was quantified by flow cytometry. LILRB1 or LILRB2 expression was assessed on cells collected at 18 and 24 months of age. ResultsInfants born to PM-mothers had a higher risk of developing clinical malaria than those born to mothers without PM (IRR=1.53, p=0.040), and such infants displayed a lower frequency of non-classical monocytes (OR=0.74, p=0.01) that overexpressed LILRB2 (OR=1.36, p=0.002). Moreover, infants born to PM-mothers had lower levels of cytophilic IgG and higher levels of IL-10 during active infection. ConclusionModulation of IgG and IL-10 levels could impair monocyte functions (opsonisation/phagocytosis) in infants born to PM-mothers, possibly contributing to their higher susceptibility to malaria. The long-lasting effect of PM on infants monocytes was notable, raising questions about the capacity of ligands such as Rifins or HLA-I molecules to bind to LILRB1 and LILRB2 and to modulate immune responses, and about the reprogramming of neonatal monocytes/macrophages. KEY POINTSInfants of mothers with placental malaria were more susceptible to clinical malaria than those born to mothers without placental malaria and they displayed a lower frequency of non-classical monocytes that overexpressed LILRB2.

immunology↗

Chromatin accessibility combined with enhancer clusters activation mediates heterogeneous response to dexamethasone in myeloma cells

Glucocorticoids (GC) effects occur through binding to the GC receptor (GR) which, once translocated to the nucleus, binds to GC response elements (GREs) to activate or repress target genes. Among GCs, dexamethasone (Dex) is widely used in treatment of multiple myeloma (MM), mainly in combination regimens. However, despite a definite benefit, all patients relapse. Moreover, while GC efficacy can be largely attributed to lymphocyte-specific apoptosis, its molecular basis remains elusive. To determine the functional role of GR binding in myeloma cells, we generated bulk and single cell multi-omic data and high-resolution contact maps of active enhancers and target genes. We show that a minority (6%) of GR binding sites are associated with enhancer activity gains and increased interaction loops. We find that enhancers contribute to regulate gene activity through combinatorial assembly of large stretches of enhancers and/or enhancer cliques. Furthermore, one enhancer, proximal to GR-responsive genes, is predominantly associated with increased chromatin accessibility and higher H3K27ac occupancy. Finally, we show that Dex exposure leads to co-accessibility changes between predominant enhancer and other regulatory regions of the interaction network. Notably, these epigenomic changes are associated with cell-to-cell transcriptional heterogeneity. As consequences, BIM critical for GR-induced apoptosis and CXCR4 protective from chemotherapy-induced apoptosis are rather upregulated in different cells. In summary, our work provides new insights into the molecular mechanisms involved in Dex escape.

cancer biology↗

Lyso-Phosphatidic Acid Acyl-Transferases: a link with intracellular protein transport in Arabidopsis root cells?

Phosphatidic acid (PA) and Lysophosphatidic acid acyltransferases (LPAATs) might be critical for the secretory pathway. Four extra-plastidial LPAATs (numbered 2,3,4 and 5) were identified in A. thaliana. These AtLPAATs, displaying an enzymatic activity specific for LPA to produce PA, are located in the endomembrane system. We focused on the putative role of the AtLPAATs 3, 4 and 5 in the secretory pathway of root cells through genetical (knock-out mutants), biochemical (activity inhibitor, lipid analyses) and imaging (live and immuno-confocal microscopies) approaches. Treating a lpaat4;lpaat5 double mutant with the LPAAT inhibitor CI976 showed a primary root growth decrease. The transport of the auxin transporter PIN2 was disturbed in this lpaat4;lpaat5 double mutant treated with CI976, but not that of H+-ATPases. The lpaat4;lpaat5 double mutant was sensitive to salt stress and the transport of the aquaporin PIP2;7 to the plasma membrane in the lpaat4;lpaat5 double mutant treated with CI976 was reduced. We measured the amounts of neo-synthesized PA in roots, and found a decrease in PA only in the lpaat4;lpaat5 double mutant treated with CI976, suggesting that the protein transport impairment was due to a critical PA concentration threshold. HighlightPhosphatidic acid produced by Lyso-Phosphatidic Acid Acyl-Transferases has an impact on the efficiency of the intracellular transport of some proteins in Arabidopsis thaliana root cells.

cell biology↗

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability

BackgroundCancer evolution depends on epigenetic and genetic diversity. Historically, in multiple myeloma (MM), subclonal diversity and tumor evolution have been investigated mostly from a genetic perspective. ResultsHere, we combined the notions of epipolymorphism and epiallele switching to analyze DNA methylation heterogeneity in MM patients. We show that MM is characterized by the continuous accumulation of stochastic methylation at the promoters of development-related genes. High entropy change is associated with poor outcomes and depends predominantly on partially methylated domains (PMDs). These PMDs, which represent the major source of inter- and intrapatient DNA methylation heterogeneity in MM, are linked to other key epigenetic aberrations, such as CpG island (CGI)/transcription start site (TSS) hypermethylation and H3K27me3 redistribution as well as 3D organization alterations. In addition, transcriptome analysis revealed that intratumor methylation heterogeneity was associated with low-level expression and high variability. ConclusionWe propose that disordered methylation in MM is responsible for high epigenetic and transcriptomic instability allowing tumor cells to adapt to environmental changes by tapping into a pool of evolutionary trajectories.

cancer biology↗

Sphingolipids mediate polar sorting of PIN2 through phosphoinositide consumption at the trans-Golgi Network

The lipid composition of organelles acts as a landmark to define membrane identity and specify subcellular function. Phosphoinositides are anionic lipids acting in protein sorting and trafficking at the trans-Golgi network (TGN). In animal cells, sphingolipids are known to control the turnover of phosphoinositides through lipid exchange mechanisms at endoplasmic reticulum/TGN contact sites. In this study, we discovered a completely new mechanism acting on sphingolipid-mediated phosphoinositides homeostasis at the TGN in plant cells. We used multi-approaches to show that a reduction of the acyl-chain length of sphingolipid results in increased level of phosphatidylinositol-4-phosphate (PI4P) at the TGN, independently from either lipid exchange induced by sphingolipid synthetic flux, or local PI4P synthesis. Instead, we found that sphingolipids mediate the consumption of PI4P through phosphoinositide-specific phospholipase C (PI-PLC) and this process impacts the sorting of the auxin efflux carrier PIN2 at the TGN. Together, our data identify a new mode of action of sphingolipids in lipid interplay at the TGN during protein sorting.

plant biology↗

Chromosight: A computer vision program for pattern detection in chromosome contact maps

Chromosomes of all species studied so far display a variety of higher order organizational features such as domains or loops often associated to biological functions and visible on Hi-C contact maps. We developed Chromosight, an algorithm inspired from computer vision that can detect patterns in Hi-C maps. Chromosight has greater sensitivity than existing methods, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Code and documentation: https://github.com/koszullab/chromosight

bioinformatics↗

Revealing the impact of recurrent and rare structural variants in multiple myeloma

The landscape of structural variants (SVs) in multiple myeloma remains poorly understood. Here, we performed comprehensive classification and analysis of SVs in multiple myeloma, interrogating a large cohort of 762 patients with whole genome and RNA sequencing. We identified 100 SV hotspots involving 31 new candidate driver genes, including drug targets BCMA (TNFRSF17) and SLAMF7. Complex SVs, including chromothripsis and templated insertions, were present in 61 % of patients and frequently resulted in the simultaneous acquisition of multiple drivers. After accounting for all recurrent events, 63 % of SVs remained unexplained. Intriguingly, these rare SVs were associated with up to 7-fold enrichment for outlier gene expression, indicating that many rare driver SVs remain unrecognized and are likely important in the biology of individual tumors.

genomics↗

DNA hydroxymethylation reveals transcription regulation networks and prognostic signatures in multiple myeloma

Multiple myeloma (MM) is a plasma cell malignancy that remains challenging to cure despite a substantially improving median survival. During the last decade, DNA copy number variation and gene expression studies have described the pathology and its heterogeneity among patients. Epigenetic modifications play important roles in MM, but they are rarely associated with clinical aspects of the disease. In this epigenomics study, we produced quantifications of genomic 5-methylcytosine (5mC) and of 5-hydroxymethylcytosine (5hmC) as well as genome-wide maps of hydroxymethylation to analyse myeloma cells taken from a cohort of 40 newly diagnosed and homogeneously treated patients. We found 5hmC to be globally depleted in MM compared to normal plasma cells, as well as being reduced in advanced clinical stages of the disease. From the hydroxymethylome data, we observed that remaining 5hmC is organised in large peak clusters and is associated with well-known disease-related genes. Based on their signal correlation, these 5hmC peak clusters can be gathered in 2 regulation networks involving core transcription factors such as IRF4, MYC, PRDM1 and TCF3. By performing paired hydroxymethylomes at diagnosis and at relapse, we found the disease progression to be heterogeneous and patient-specific. We found that the location of 5hmC at tumor suppressor TP53INP1 is associated with better outcome while global high level of 5hmC tends to be associated with better overall survival. Together, our study suggests that 5hmC provides new biological insights of the disease severity and progression, and can be used for retrospective studies.\n\nKey PointsO_LI5hmC is globally depleted in MM and even more in advanced stages of the disease.\nC_LIO_LI5hmC is locally detected at transcriptionally active regions of MM where its presence can be associated with survival.\nC_LI

cancer biology↗

In vivo phosphatidylserine variations steer Rho GTPase signaling in a cell-context dependent manner

AbstractRho GTPases are master regulators of cell signaling, but how they are regulated depending on the cellular context is unclear. Here, we show that the phospholipid phosphatidylserine acts as a developmentally-controlled lipid rheostat that tunes Rho GTPase signaling in Arabidopsis. Live super-resolution single molecule imaging revealed that RHO-OF-PLANT6 (ROP6) is stabilized by phosphatidylserine into plasma membrane (PM) nanodomains, which is required for auxin signaling. Furthermore, we uncovered that the PM phosphatidylserine content varies during plant root development and that the level of phosphatidylserine modulates the quantity of ROP6 nanoclusters induced by auxin and hence downstream signaling, including regulation of endocytosis and gravitropism. Our work reveals that variations in phosphatidylserine levels are a physiological process that may be leveraged to regulate small GTPase signaling during development.\n\nOne Sentence SummaryPhosphatidylserine acts as a developmentally-controlled lipid rheostat that regulates cellular auxin sensitivity and plant development.

plant biology↗

Genomic landscape and chronological reconstruction of driver events in multiple myeloma

Multiple myeloma (MM) has a heterogeneous genome, evolving through both pre-clinical and post-diagnosis phases. Here, using sequences from 67 MM genomes serially collected from 30 patients together with public datasets, we establish a hierarchy of driver lesions. Point mutations, structural variants and copy number aberrations define at least 7 genomic subgroups of MM, each with distinct sets of co-operating driver mutations. Complex structural events are major drivers of MM, including chromothripsis, chromoplexy and a replication-based mechanism of templated insertions: these typically occur early. Hyperdiploidy also occurs early, with individual chromosomes often gained in more than one chronological epoch of MM evolution, showing a preferred order of acquisition. Positively selected point mutations frequently occur in later phases of disease development, as do structural variants involving MYC. Thus, initiating driver events of MM, drawn from a limited repertoire of structural and numerical chromosomal changes, shape preferred trajectories of subsequent evolution.

cancer biology↗