Caractérisation de la présence d'anticorps anti-mitochondriaux associés au lupus érythémateux disséminé

Les mitochondries sont des organelles intracellulaires impliquées dans de nombreuses voies biologiques. Suite à la mort ou l’activation de certains types cellulaires, elles peuvent être relarguées dans le milieu extracellulaire où, elles sont reconnues comme des signaux de danger (DAMPS), générant une réponse pro-inflammatoire par le système immunitaire inné. Les interactions entre les mitochondries et l’immunité adaptative sont encore méconnues. Neuf classes d’anticorps anti mitochondriaux (AMA M1 à M9) ont été décrits différentes pathologies telles que la syphilis, la cirrhose biliaire primitive (CBP), le lupus érythémateux disséminé (LED) ou le syndrome des anti phospholipides (APS), sans que leur association avec l’expression clinique de ces maladies n’ait jamais été étudiée. Dans la présente étude, nous avons développé des méthodes de détection des AMA et anti-ADN mitochondrial (AMtDNA) puis étudié des corrélations entre la présence de ces anticorps et les caractéristiques de la maladie exprimées par des patients lupiques. Nous avons mis en évidence une association protectrice des AMA envers les évènements thrombotiques ainsi qu’une corrélation entre les niveaux d’AMtDNA et une élévation de l’index d’activité de la maladie (SLEDAI) en lien avec un accroissement des anticorps ciblant l’ADN double-brins (DsDNA).Mitochondria are intracellular organelles that are involved in a vast number of biological pathways. They may be released in the extracellular milieu upon cell death or the activation of several types of cells where they will be recognized as danger signals (DAMPs), eliciting a pro-inflammatory response by the innate immune system. To this day, interplays between mitochondria and the adaptive branch of the immunity are poorly defined. Nine classes of anti mitochondrial antibodies (AMA M1 to M9) were reported in diseases such as syphilis, primary biliary cirrhosis (PBS), systemic lupus erythematosus (SLE) or the anti-phospholipid syndrome (APS) but their association to the clinical manifestations of these diseases have never been studied. In the present study, we developed methods for the detection of AMA and anti-mitochondrial DNA antibodies (AMtDNA) then studied correlations between the presence of these antibodies and clinical features expressed by lupus patients. We found a protective association of AMA towards thrombotic events and that AMtDNA levels correlates with an increase of the SLE disease activity index (SLEDAI) linked to an increase of the antibodies targeting double-stranded DNA (DsDNA)

Identification des cibles antigéniques d'origine mitochondriale, reconnues par les autoanticorps dans le lupus érythémateux disséminé

Mitochondria are intracellular organelles in control of numerous biological functions (e.g.,from energy supply to steroidogenesis and programmed cell death by apoptosis). Evolutively, mitochondria are considered as derived from the endosymbiosis between an α-proteobacterium and a primitive eukaryotic cell. Due to its origin, the organelle displays prokaryotic motifs such as a circular double-stranded hypomethylated DNA (i.e., mtDNA) and N-formylated peptides. Intact or damaged mitochondria, as well as mitochondrial components may be extruded in the extracellular space upon cell activation or death. These features, as well as several biomolecules localized within the mitochondrion (e.g.,ATP, cytochrome C) are able to be recognized by the innate immune system as mitochondrial damage-associated molecular patterns, thus eliciting a proinflammatory response. A humoral immune response comprising anti-mitochondrial antibodies (AMA) is also described in various autoimmune conditions, such as AMA-M2 in primary biliary cirrhosis (i.e., PBC). Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the alternance of flares and phases of remission, due to the deposition of antibody-antigen scaffolds (i.e., immune complexes) within tissues, leading to various clinical manifestations (e.g., neuropsychiatric, hematological or dermatological disorders). The antiphospholipid syndrome (i.e., APS) is an autoimmune disease, with thromboembolic and/or obstetrical manifestations, that can either be found alone or along with SLE. While the immunogenicity of cardiolipin (i.e., a phospholipid uniquely synthetized by mitochondria In humans) is well described in SLE and APS (i.e., anticardiolipins), mitochondrial proteins targeted by autoantibodies are still poorly known. The present doctoral thesis follows my masters' project during which I developed ELISAs allowing for the detection of AMA targeting intact mitochondria (i.e., AwMA) or mtDNA (i.e., AmtDNA)¹. The present project aims aims to characterize the mitochondrial immunogenicity in SLE and APS. The University of Toronto Lupus Clinic cohort comprise sera from patients with SLE or APS (n=175 and n=12 respectively). AwMA and AmtDNA levels were assessed in these samples, as well as in sera from healthy volunteers (n=43) or patients with PBC (n=12). I observed that all patients had increased AwMA, compared to healthy individuals. AmtDNA were only increased in SLE patients and were associated with increased past reports of lupus nephritis (p=0.01). These results were published in March 2019 in Scientific Reports². During the acquisition of these data, I observed that patients' sera also presented immunoreactivity against mitochondrial RNA (i.e., mtRNA). I thus adapted my assays to detect autoantibodies against mtRNA (i.e., AmtRNA), and assessed their levels in sera from patients includes in the systemic autoimmune rheumatic disease biobank and data repository (i.e., SARD-BDB. Healthy:n=30, SLE:n=87). AmtRNA were significantly elevated in SLE (IgG: p<0.0001, IgM:p=0.0493). Surprisingly, AmtRNA-IgG were associated with decreased reports of past lupus nephritis (p=0.03) and carotid plaque (p=0.04). This study was published in Frontiers in Immunology in May 2019³. As each AMA assessed displayed biostatistical associations with antiphospholipids, I replicated these protocols, using sera from patients with APS, included in the SARD-BDB (n=27). AmtRNA (IgG:p=0.0005, IgM:p=0.01) and AmtDNA-IgM were increased in APS (p=0.009). However, only AmtDNA-IgM were associated with reports of arterial thromboses (p=0.047). This pilot study was published in Lupus in August 2020⁴. In a a recent study, accepted in Arthritis & Rheumatology in January 2022⁵, we identified by mass spectrometry 1345 proteins associated with AwMA, 431 of with were assigned to the mitochondrial proteome. These results allowed to identify two candidates: C1qBP and Mfn-1. IgGs to C1qBP were increased in (p=0.0167) and associated with positivity to the lupus anticoagulant (p=0.049) in SLE. IgGs against Mfn-1 are interesting candidates for the prediction of the disease (p=0.0052) and are associated with positivity to antiphospholipids (p=0.011) and antibodies against double-stranded DNA (p = 0.0005). These results highlight the immunogenicity of the organelle in SLE and APS. Mitochondrial antigens are interesting candidates for the development of novel clinical assays allowing improved prognosis, diagnosis, or disease stratification, ultimately contributing to the improvement of medical care for people with autoimmune conditions.Les mitochondries sont des organelles intracellulaires considérées comme issues de l'endosymbiose entre une α-protéobactérie et une cellule eucaryote primitive. L'organelle exprime ainsi des motifs moléculaires en lien avec son origine procaryote tels qu'un ADN hypométhylés (i.e., mtDNA) ou des peptides N-formylés. Des mitochondries ou bien des composantes mitochondriales pourront être libérées dans le milieu extracellulaire lors de différents évènements d'activation ou de mort cellulaire. Ces caractéristiques ainsi que certaines biomolécules, spécifiquement localisées dans la mitochondrie (e.g.,ATP, cytochrome C) auront la capacité d'être reconnues comme des motifs de dangers et de stimuler une réponse proinflammatoire de la part des cellules du système immunitaire inné. Une réponse humorale constituée d'anticorps anti-mitochondriaux (AMA) est connue dans différents troubles auto-immuns tels que les AMA-M2 dans la cirrhose biliaire primitive (PBC). Le lupus érythémateux disséminé (SLE) est une maladie auto-immune caractérisée par une succession de phases d'exacerbation et de rémission dues au dépôt d'enchevêtrements d'autoanticorps et de leurs antigènes dans les tissus, aboutissant à une grande variété de manifestations cliniques (e.g.,manifestations neuropsychiatriques, hématologiques, dermatologiques). Le syndrome des antiphospholipides (APS) est une maladie qui peut être distincte ou associée au SLE et présente des manifestations thromboemboliques et/ou obstétriques. Bien que l'immunogénicité de la cardiolipine (i.e., phospholipide uniquement synthétisée dans la mitochondrie chez l'humain) soit connue dans le cadre du SLE et de l'APS (i.e., anticardiolipines), l'antigénicité des protéines mitochondriales reste encore méconnue. Cette thèse de doctorat fait suite à mes travaux de maîtrise au cours desquels, j'ai développé des ELISAs permettant de mesurer des niveaux des IgGs dirigés contre les mitochondries intactes (i.e., AwMA) et le mtDNA (i.e., AmtDNA)¹. Mon projet de thèse vise à caractériser l'immunogénicité mitochondriale dans l'auto-immunité. La cohorte de la University of Toronto Lupus Clinic regroupe des échantillons d'échantillons de séra de patients souffrant de SLE ou d'APS (n=175 et n=12, respectivement). Les AwMA, et AmtDNA ont été mesurés au sein de ces échantillons ainsi que d'échantillons de volontaires sains (n=43) et de donneurs souffrant de PBC (n=12). Les patients souffrant des trois conditions présentaient une augmentation significative des AwMA par rapport aux contrôles sains. Les AmtDNA, uniquement augmentés chez les patients SLE (p=0.0004) ont été associés à des antécédents accrus de néphrite lupique (p=0.01). Ces résultats ont été publiés en mars 2019 dans le journal Scientific Reports² . Durant ces mesures, j'ai observé que les séra de patients présentaient aussi une immunoréactivité dirigée contre l'ARN mitochondrial (mtRNA). J'ai, par la suite, adapté mes tests pour détecter les AMA dirigés contre le mtRNA (i.e., AmtRNA) et les ai mesurés à l'aide de séra inclus dans la cohorte des maladies rhumatismales auto-immunes systémiques (MRAS. Sains:n=30, SLE:n=87). Les d'AmtRNA sont significativement élevés dans le SLE (IgG:p<0.0001 , IgM:p=0.0493). De façon surprenante, les AmtRNA-IgG sont associés avec des historiques réduits de néphrite lupique (p=0.03) et de plaque carotidienne (p=0.04). Ces travaux ont été publiés dans le journal Frontiers in Immunology en mai 2019³. L'ensemble des AMA mesurés présentant des associations biostatistiques avec différents anticorps antiphospholipides. J'ai répliqué mon protocole sur des échantillons de patients souffrant d'APS, inclus dans la cohorte MRAS (n=27). Les AmtRNA (IgG:p=0.0005, IgM:p=0.01) et les AmtDNA-IgM sont augmentés dans l'APS (p=0.009). Seuls les AmtRNA-IgM sont associées avec une diminution des antécédents de thromboses artérielles (p=0.047). Ce projet a fait l'objet d'un article, publié dans Lupus en aout 2020⁴. Dans une autre étude, acceptée dans le journal Arthritis & Rheumatology en janvier 2022⁵, nous avons identifié, par spectrométrie de masse, 1345 protéines associées aux AwMA dont 431 sont associées avec le protéome mitochondrial. Ces résultats m'ont permis d'identifier deux candidats d'intérêts : C1qBP et Mfn-1. Les anti-C1qBP sont significativement augmentés chez les patients lupiques (p=0.0167) et sont associés avec la positivité pour l'anticoagulant lupique (p=0.049). Les anti-Mfn1 constituent de potentiels candidats pour prédire la maladie (p=0.0052). Ils sont, par ailleurs, associés avec la positivité aux antiphospholipides (p=0.011) et aux anti-ADN double brins (p=0.0005). Ces résultats soulignent l'immunogénicité de la mitochondrie dans le SLE et l'APS. Les AMA et leurs cibles constituent de nouvelles avenues d'intérêt dans la mise au point de nouveaux tests cliniques permettant le diagnostic, le pronostic ou la classification de la maladie afin d'améliorer la prise en charge des patients lupiques

Reliability of mantle tomography models assessed by spectral element simulation

Global tomographic models collected in the Seismic wave Propagation and Imaging in Complex (SPICE media: a European network) model library (http://www.spicertn.org/research/planetaryscale/tomography/) share a similar pattern of long, spatial wavelength heterogeneity, but are not consistent at shorter spatial wavelengths. Here, we assess the performance of global tomographic models by comparing how well they fit seismic waveform observations, in particular Love and Rayleigh wave overtones and fundamental modes. We first used the coupled spectral element method (CSEM) to calculate long-period (>100 s) synthetic seismograms for different global tomography models. The CSEM can incorporate the effect of three-dimensional (3-D) variations in velocity, anisotropy, density and attenuation with very little numerical dispersion. We then compared quantitatively synthetic seismograms and real data. To restrict ourselves to high-quality overtone data, and to minimize the effects of the finite extent of seismic sources and of crustal heterogeneity, we favour deep (>500 km) earthquakes of intermediate magnitude (Mw ∼ 7). Our comparisons reveal that: (1) The 3-D global tomographic models explain the data much better than the one-dimensional (1-D) anisotropic Preliminary Reference Earth Model (PREM). The current 3-D tomographic models have captured the large-scale features of upper-mantle heterogeneities, but there is still some room for the improvement of large-scale features of global tomographic models. (2) The average correlation coefficients for deep events are higher than those for shallow events, because crustal structure is too complex to be completely incorporated into CSEM simulations. (3) The average correlation coefficient (or the time lag) for the major-arc wave trains is lower (or higher) than that for the minor-arc wave trains. Therefore, the current tomographic models could be much improved by including the major-arc wave trains in the inversion. (4) The shallow-layer crustal correction has more effects on the fundamental surface waves than on the overtone

The CoLiS Platform for the Analysis of Maintainer Scripts in Debian Software Packages

International audienceThe software packages of the Debian distribution include more than twenty-seven thousand maintainer scripts in total, almost all of them being written in the Posix shell language. These scripts are executed with root privileges at installation, update, and removal of a package, which makes them critical for system maintenance. While the Debian policy provides guidance for package maintainers producing the scripts, only few tools exist to check the compliance of a script to that policy. We present CoLiS, a software platform for discovering violations of non-trivial properties required by the Debian policy in maintainer scripts. We describe our methodology which is based on symbolic execution and feature tree constraints, and we give an overview of the toolchain. We obtain promising results: our toolchain is effective in analysing a large set of Debian maintainer scripts, and it has already detected over 150 policy violations that have lead to bug reports, more than two-third of them now being fixed

l(1)-regularized maximum likelihood estimation with focused-spot illumination quadruples the diffraction-limited resolution in fluorescence microscopy

Super-resolution fluorescence microscopy has proven to be a useful tool in biological studies. To achieve more than two-fold resolution improvement over the diffraction limit, existing methods require exploitation of the physical properties of the fluorophores. Recently, it has been demonstrated that achieving more than two-fold resolution improvement without such exploitation is possible using only a focused illumination spot and numerical post-processing. However, how the achievable resolution is affected by the processing step has not been thoroughly investigated. In this paper, we focus on the processing aspect of this emerging super-resolution microscopy technique. Based on a careful examination of the dominant noise source and the available prior information in the image, we find that if a processing scheme is appropriate for the dominant noise model in the image and can utilize the prior information in the form of sparsity, improved accuracy can be expected. Based on simulation results, we identify an improved processing scheme and apply it in a real-world experiment to super-resolve a known calibration sample. We show an improved super-resolution of 60nm, approximately four times beyond the conventional diffraction-limited resolution.</p

Achieving superresolution with illumination-enhanced sparsity.

Recent advances in superresolution fluorescence microscopy have been limited by a belief that surpassing two-fold resolution enhancement of the Rayleigh resolution limit requires stimulated emission or the fluorophore to undergo state transitions. Here we demonstrate a new superresolution method that requires only image acquisitions with a focused illumination spot and computational post-processing. The proposed method utilizes the focused illumination spot to effectively reduce the object size and enhance the object sparsity and consequently increases the resolution and accuracy through nonlinear image post-processing. This method clearly resolves 70nm resolution test objects emitting ~530nm light with a 1.4 numerical aperture (NA) objective, and, when imaging through a 0.5NA objective, exhibits high spatial frequencies comparable to a 1.4NA widefield image, both demonstrating a resolution enhancement above two-fold of the Rayleigh resolution limit. More importantly, we examine how the resolution increases with photon numbers, and show that the more-than-two-fold enhancement is achievable with realistic photon budgets

Interactive Parallelization of Embedded Real-Time Applications Starting from Open-Source Scilab & Xcos

International audienceIn this paper, we introduce the workflow of interactive parallelization for optimizing embedded real-time applications for multicore architectures. In our approach, the real-time applications are written in the Scilab high-level mathematical & scientific programming language or with a Scilab Xcos block-diagram ap-proach. By using code generation and code parallelization technol-ogy combined with an interactive GUI, the end user can map appli-cations to the multicore processor iteratively. The approach is eval-uated on two use cases: (1) an image processing application written in Scilab and (2) an avionic system modeled in Xcos. Using the workflow, an end-to-end model-based approach targeting multicore processors is enabled resulting in a significant reduction in devel-opment effort and high application speedup. The workflow de-scribed in this paper is developed and tested within the EU-funded ARGO project focused on WCET-Aware Parallelization of Model-Based Applications for Heterogeneous Parallel Systems