Machine learning identifies a common signature for anti-SSA/Ro60 antibody expression across autoimmune diseases

Anti-Ro autoantibodies are among the most frequently detected extractable nuclear antigen autoantibodies, mainly associated with primary Sjögren's syndrome (pSS), systemic lupus erythematosus (SLE) and undifferentiated connective tissue disease (UCTD). Is there a common signature to all patients expressing anti-Ro60 autoantibodies regardless of their disease phenotype?Using high-throughput multi-omics data collected within the cross-sectional cohort from the PRECISESADS IMI project (genetic, epigenomic, transcriptomic, combined with flow cytometric data, multiplexed cytokines, classical serology and clinical data), we assessed by machine learning the integrated molecular profiling of 520 anti-Ro60-positive (anti-Ro60+ ) compared to 511 anti-Ro60-negative (anti-Ro60- ) patients with pSS, SLE and UCTD, and 279 healthy controls (HCs).The selected features for RNA-Seq, DNA methylation and GWAS data allowed a clear separation between anti-Ro60+ and anti-Ro60- patients. The different features selected by machine learning from the anti-Ro60+ patients constitute specific signatures when compared to anti-Ro60- patients and HCs. Remarkably, the transcript z-score of three genes (ATP10A, MX1 and PARP14), presenting an overexpression associated with a hypomethylation and genetic variation, and independently identified by the Boruta algorithm, was clearly higher in anti-Ro60+ patients compared to anti-Ro60- patients in all the diseases. We demonstrate that these signatures, enriched in interferon stimulated genes, were also found in anti-Ro60+ patients with rheumatoid arthritis and systemic sclerosis and remained stable over time and not influenced by treatment.Anti-Ro60+ patients present a specific inflammatory signature regardless of their disease suggesting that a dual therapeutic approach targeting both Ro-associated RNAs and anti-Ro60 autoantibodies should be considered

Genome-wide profiling of G protein-coupled receptors in cerebellar granule neurons using high-throughput, real-time PCR

<p>Abstract</p> <p>Background</p> <p>G protein-coupled receptors (GPCRs) are major players in cell communication, regulate a whole range of physiological functions during development and throughout adult life, are affected in numerous pathological situations, and constitute so far the largest class of drugable targets for human diseases. The corresponding genes are usually expressed at low levels, making accurate, genome-wide quantification of their expression levels a challenging task using microarrays.</p> <p>Results</p> <p>We first draw an inventory of all endo-GPCRs encoded in the murine genome. To profile GPCRs genome-wide accurately, sensitively, comprehensively, and cost-effectively, we designed and validated a collection of primers that we used in quantitative RT-PCR experiments. We experimentally validated a statistical approach to analyze genome-wide, real-time PCR data. To illustrate the usefulness of this approach, we determined the repertoire of GPCRs expressed in cerebellar granule neurons and neuroblasts during postnatal development.</p> <p>Conclusions</p> <p>We identified tens of GPCRs that were not detected previously in this cell type; these GPCRs represent novel candidate players in the development and survival of cerebellar granule neurons. The sequences of primers used in this study are freely available to those interested in quantifying GPCR expression comprehensively.</p

A new molecular classification to drive precision treatment strategies in primary Sjögren’s syndrome

There is currently no approved treatment for primary Sjögren's syndrome, a disease that primarily affects adult women. The difficulty in developing effective therapies is -in part- because of the heterogeneity in the clinical manifestation and pathophysiology of the disease. Finding common molecular signatures among patient subgroups could improve our understanding of disease etiology, and facilitate the development of targeted therapeutics. Here, we report, in a cross-sectional cohort, a molecular classification scheme for Sjögren's syndrome patients based on the multi-omic profiling of whole blood samples from a European cohort of over 300 patients, and a similar number of age and gender-matched healthy volunteers. Using transcriptomic, genomic, epigenetic, cytokine expression and flow cytometry data, combined with clinical parameters, we identify four groups of patients with distinct patterns of immune dysregulation. The biomarkers we identify can be used by machine learning classifiers to sort future patients into subgroups, allowing the re-evaluation of response to treatments in clinical trials

Human Endogenous Retrovirus Group E and Its Involvement in Diseases

Human endogenous retrovirus group E (HERV-E) elements are stably integrated into the human genome, transmitted vertically in a Mendelian manner, and are endowed with transcriptional activity as alternative promoters or enhancers. Such effects are under the control of the proviral long terminal repeats (LTR) that are organized into three HERV-E phylogenetic subgroups, namely LTR2, LTR2B, and LTR2C. Moreover, HERV-E expression is tissue-specific, and silenced by epigenetic constraints that may be disrupted in cancer, autoimmunity, and human placentation. Interest in HERV-E with regard to these conditions has been stimulated further by concerns regarding the capacity of HERV-E elements to modify the expression of neighboring genes and/or to produce retroviral proteins, including immunosuppressive env peptides, which in turn may induce (auto)-antibody (Ab) production. Finally, better understanding of HERV-E elements may have clinical applications for prevention, diagnosis, prognosis, and therapy

Overwiew of the latest technologies in methylation studies

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Interest of the CD5 / CD6 couple in human B lymphocytes

Issues d'un gène ancestral commun, les molécules CD5 et CD6 sont présentes à la surface de tous les lymphocytes T (LT) matures ainsi qu'à la surface de certains lymphocytes B (LB). Ces deux protéines font partie de la famille des « Scavenger Receptor Cystein Rich » (SRCR) protéines mais la régulation, l'expression et les fonctions de ces deux molécules ne sont pas totalement résolues. Ainsi, CD5 est impliquée dans la régulation du récepteur à l’antigène des LB et des LT, dans la tolérance des LB et elle est présente à la surface des LB régulateurs. A l’opposé, CD6 possède un rôle dans la prolifération des lymphocytes, la survie, la migration et l’adhésion cellulaire. Les expressions de CD5 et CD6 diffèrent au sein des LB normaux ainsi qu'en pathologie. Dans le cadre du lupus érythémateux systémique (LES), le nombre de molécules CD5 à la surface des LB CD5+ est réduit. Dans une autre maladie auto-immune (MAI), le Syndrome de Gougerot Sjögren (SGS), l'expression de CD6 à la membrane des LB n'est pas affectée mais la distribution des LB mémoires CD6+, mais pas des LB naïfs, est modifiée par rapport aux témoins sains. En effet, les LB CD6+ sont sous représentés dans le sang périphérique et ce, en raison de leur délocalisation dans les glandes salivaires (GS) des patients. Cette délocalisation est liée à la surexpression d’ALCAM, le ligand naturel de CD6, par les cellules épithéliales au cours du SGS. L'étude de la diminution de l'expression de CD5 à la surface des LB de patients atteints de LES a permis de montrer qu'il existait un défaut dans le processus de la méthylation de l'ADN chez ces patients. Ce même défaut a été retrouvé dans les GS de patients atteints de SGS. Enfin, les LB de patients atteints de leucémie lymphoïde chronique (LLC) sont porteurs des deux molécules à leur membrane. Nous avons testé l'effet in vitro et in vivo d'un l'anticorps monoclonal (Acm) humanisé anti-CD6, T1H, dans la LLC. De façon intéressante, il s’avère que cet Acm favorise la lyse des LB de LLC et ceci, de façon équivalente au rituximab dans un modèle murin in vivo. T1H est internalisé par les LT et est donc inefficace sur ces cellules. Ces résultats nous permettent de conclure que même si les molécules CD5 et CD6 sont proches phylogénétiquement, elles possèdent des fonctions et des modes de régulation différents entre les LB et les LT mais aussi au sein des différentes populations de LB. Une meilleure compréhension des fonctions et des modes d'actions de ces deux protéines ouvre des perspectives thérapeutiques dans le traitement des MAI et de la LLC.Derived from a common ancestral gene, CD5 and CD6 molecules are present on the surface of all mature T lymphocytes (LT) and some B lymphocytes (LB). These two proteins are members of the "Scavenger Receptor Cystein Rich" family proteins (SRCR) but the regulation, the expression and the function of these molecules is not totally resolved. CD5 is involved in the regulation of antigen receptor in LB and in LT, in the LB tolerance and is present on the surface of regulator B cells. In contrast, CD6 plays a role in lymphocyte proliferation, survival, migration, and cell adhesion. Expressions of CD5 and CD6 differ within normal LB and and LB present in different in pathologies. In the context of systemic lupus erythematosus (LES), the number of CD5 molecules on the surface of CD5+ LB is reduced. In another autoimmune disease (MAI), the Sjogren Syndrome (SS), the expression of CD6 at the membrane of B cells is not affected but the distribution of CD6 + memory LB but not naive LB is changed compared to healthy controls. Indeed, LB CD6 + are underrepresented in the peripheral blood and, it’s due to their relocation in the salivary glands (GS) of patients. This relocation is related to overexpression of ALCAM, the natural ligand of CD6, by epithelial cells in SS. The study of the decreased expression of CD5 on the surface of LB SLE patients has shown that there was a defect in the process of DNA methylation in these patients. The same defect was found in the GS of SS patients. Finally, B cells from chronic lymphocytic leukemia patients (CLL) are holders of the two molecules on their membrane. We tested the effect in vitro and in vivo of a humanized monoclonal antibody (mAb) anti-CD6, T1H, in the CLL. Interestingly, it appears that this mAb promotes lysis of CLL LB and this effect is equivalent to the one that rituximab was shown to have in an in vivo mouse model. T1H is internalized by LT and is therefore ineffective on these cells. These results allow us to conclude that even if the CD5 and CD6 molecules are phylogenetically close, they have different functions and modes of regulation between LB and LT but also within different populations of LB. A better understanding of their functions and action pathway of these two proteins opens up therapeutic perspectives for the treatment of MAI and CLL

Epigenétique et autoimmunité

International audienc

Epigenomic revolution in autoimmune diseases

International audienc

Epigenomic revolution in autoimmune diseases

International audienc

Human Endogenous Retrovirus Group E and Its Involvement in Diseases

International audienc