amda 2 13 a major update for automated cross platform microarray data analysis

Microarray platforms require analytical pipelines with modules for data pre-processing including data normalization, statistical analysis for identification of differentially expressed genes, cluster analysis, and functional annotation. We previously developed the Automated Microarray Data Analysis (AMDA, version 2.3.5) pipeline to process Affymetrix 3′ IVT GeneChips. The availability of newer technologies that demand open-source tools for microarray data analysis has impelled us to develop an updated multi-platform version, AMDA 2.13. It includes additional quality control metrics, annotation-driven (annotation grade of Affymetrix NetAffx) and signal-driven (Inter-Quartile Range) gene filtering, and approaches to experimental design. To enhance understanding of biological data, differentially expressed genes have been mapped into KEGG pathways. Finally, a more stable and user-friendly interface was designed to integrate the requirements for different platforms. AMDA 2.13 allows the analysis of Affymetrix..

Characterization of mouse spinal cord vascular network by means of synchrotron radiation X-ray phase contrast tomography

High resolution Synchrotron-based X-ray Phase Contrast Tomography (XPCT) allows the simultaneous detection of three dimensional neuronal and vascular networks without using contrast agents or invasive casting preparation. We show and discuss the different features observed in reconstructed XPCT volumes of the ex vivo mouse spinal cord in the lumbo-sacral region, including motor neurons and blood vessels. We report the application of an intensity-based segmentation method to detect and quantitatively characterize the modification in the vascular networks in terms of reduction in experimental visibility. In particular, we apply our approach to the case of the experimental autoimmune encephalomyelitis (EAE), i.e. human multiple sclerosis animal model

A New Thiopurine S-Methyltransferase Haplotype Associated With Intolerance to Azathioprine

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BBB-endothelial tight junction response to mesenchymal stem cells in a model of MOG EAE

Experimental autoimmune encephalomyelitis (EAE), an induced autoimmune disease of the central nervous system, simulates the main histopathological and clinical aspects of multiple sclerosis including the impairment of the blood-brain barrier (BBB). In several experimental models of human neurodegenerative diseases, the intravenous (iv) injection of bone marrow-derived mesenchymal stem cells (MSCs) ameliorates clinical symptoms and histopathological features [1,2]. On the basis of these data, we have analyzed the status of BBB tight junctions (TJs) of cerebral cortex microvessels in a model of MOG-EAE with iv injection of MSCs (EAE-MSC). The observations were carried out on EAE-MSC mice sacrificed at 6-24 hrs and 10 days after MSCs iv injection. The expression of endothelial TJ proteins, claudin-5 and occludin, was analyzed in healthy, EAE, and EAE-MSC mice by immunofluorescence confocal microscopy, together with the evaluation of barrier function by FITC-Dextran, as an exogenous permeability tracer. The results demonstrate that unlike EAE animals, characterized by an interrupted junctional staining and a barrier leakage, EAE-MSC mice show together with attenuate disease symptoms, a continuous, control- like claudin-5 and occludin junctional pattern and a functionally recovered barrier efficiency. Overall, these findings suggest that during EAE, the neuroprotective effect of the injected MSCs includes a reparative BBB response that in turn may contribute to the reduction of the inflammatory infiltrates and to the significant amelioration of the disease

Immunolocalization of CCL2-expressing cells in EAE and EAE-MSC cerebral cortex

The chemokine CCL2 has been considered as a mediator of inflammation in different diseases of the central nervous system, including experimental autoimmune encephalomyelitis (EAE), where the chemokine mediates extravasation of mononuclear leukocytes and loss of microvessel barrier function [1]. Previous studies have demonstrated that cellular sources of CCL2 during both EAE and multiple sclerosis (MS) are astrocytes and microvessel endothelial cells (ECs). Initially, we have demonstrated that in a MOG-induced model of EAE in C57BL/6 mice, 6 hrs after the intravenous treatment with bone marrow derived mesenchymal stem cells (MSCs) [2], the junctional staining patter of blood-brain barrier (BBB) microvessels and their functional effectiveness to permeability tracers seem to be restored. We have subsequently analysed, in the same experimental models, EAE and EAE-MSC mice, expression and immunolocalization of chemokine CCL2 by double immmunolabelling with cell-specific markers: endothelial PECAM-1 (CD31), OPCs (oligodendrocyte precursor cells) proteoglycan NG2, astrocytic GFAP, and Iba1 for microglia cells. Surprisingly, in the adopted model of cerebral cortex EAE, astrocytes and ECs do not show any detectable CCL2 expression, instead a strong staining is observed on activated parenchymal and perivascular microglia. Astrogliosis, microglia activation, and CCL2 overexpression appearing strongly reduced in EAE mice after MSC treatment. These observations identify microglia cells as the major source of CCL2 in EAE mice, whose barrier is damaged, and suggest the downregulation of the chemokine in perivascular microglia as a possible mechanism involved in BBB protection after MSC administration

Dysregulation of regulatory CD56bright NK cells/T cells interactions in multiple sclerosis

Recent evidence has shown that CD56bright NK cells, a subset of NK cells abundant in lymph nodes, may have an immunoregulatory function. In multiple sclerosis (MS), expansion of CD56bright NK cells has been associated to successful response to different treatments and to remission of disease during pregnancy; how whether they exert immunoregulation in physiologic conditions and whether this is impaired in MS is not known. We dissected the immunoregulatory role of CD56bright NK cells function in healthy subjects (HS) and compared it with that of untreated MS subjects or patients with clinically isolated syndrome suggestive of MS (CIS). We found that CD56bright NK cells from HS acquire, upon inflammatory cues, the capability of suppressing autologous CD4+T cell proliferation through direct cytotoxicity requiring engagement of natural cytotoxicity receptors (NCRs) and secretion of granzyme B. CD56bright NK cells from patients with MS/CIS did not differ in frequency and share a similar phenotype but displayed a significantly lower ability to inhibit autologous T cell proliferation. This impairment was not related to deficient expression of NCRs or granzyme B by CD56bright NK cells, but to increased HLA-E expression on T cells from MS/CIS subjects, which could enhance the inhibitory effect mediated by NKG2A that is homogeneously expressed on CD56bright NK cells. The defect in controlling autologous T cells by CD56bright NK cells in MS/CIS might contribute to the excess of autoimmune response that is associated to disease development

X-Ray Phase Contrast Tomography Reveals Early Vascular Alterations and Neuronal Loss in a Multiple Sclerosis Model

The degenerative effects of multiple sclerosis at the level of the vascular and neuronal networks in the central nervous system are currently the object of intensive investigation. Preclinical studies have demonstrated the efficacy of mesenchymal stem cell (MSC) therapy in experimental autoimmune encephalomyelitis (EAE), the animal model for multiple sclerosis, but the neuropathology of specific lesions in EAE and the effects of MSC treatment are under debate. Because conventional imaging techniques entail protocols that alter the tissues, limiting the reliability of the results, we have used non-invasive X-ray phase-contrast tomography to obtain an unprecedented direct 3D characterization of EAE lesions at micro-to-nano scales, with simultaneous imaging of the vascular and neuronal networks. We reveal EAE-mediated alterations down to the capillary network. Our findings shed light on how the disease and MSC treatment affect the tissues, and promote X-ray phase-contrast tomography as a powerful tool for studying neurovascular diseases and monitoring advanced therapies

‘Multi-Epitope-Targeted’ Immune-Specific Therapy for a Multiple Sclerosis-Like Disease via Engineered Multi-Epitope Protein Is Superior to Peptides

Antigen-induced peripheral tolerance is potentially one of the most efficient and specific therapeutic approaches for autoimmune diseases. Although highly effective in animal models, antigen-based strategies have not yet been translated into practicable human therapy, and several clinical trials using a single antigen or peptidic-epitope in multiple sclerosis (MS) yielded disappointing results. In these clinical trials, however, the apparent complexity and dynamics of the pathogenic autoimmunity associated with MS, which result from the multiplicity of potential target antigens and “epitope spread”, have not been sufficiently considered. Thus, targeting pathogenic T-cells reactive against a single antigen/epitope is unlikely to be sufficient; to be effective, immunospecific therapy to MS should logically neutralize concomitantly T-cells reactive against as many major target antigens/epitopes as possible. We investigated such “multi-epitope-targeting” approach in murine experimental autoimmune encephalomyelitis (EAE) associated with a single (“classical”) or multiple (“complex”) anti-myelin autoreactivities, using cocktail of different encephalitogenic peptides vis-a-vis artificial multi-epitope-protein (designated Y-MSPc) encompassing rationally selected MS-relevant epitopes of five major myelin antigens, as “multi-epitope-targeting” agents. Y-MSPc was superior to peptide(s) in concomitantly downregulating pathogenic T-cells reactive against multiple myelin antigens/epitopes, via inducing more effective, longer lasting peripheral regulatory mechanisms (cytokine shift, anergy, and Foxp3+ CTLA4+ regulatory T-cells). Y-MSPc was also consistently more effective than the disease-inducing single peptide or peptide cocktail, not only in suppressing the development of “classical” or “complex EAE” or ameliorating ongoing disease, but most importantly, in reversing chronic EAE. Overall, our data emphasize that a “multi-epitope-targeting” strategy is required for effective immune-specific therapy of organ-specific autoimmune diseases associated with complex and dynamic pathogenic autoimmunity, such as MS; our data further demonstrate that the “multi-epitope-targeting” approach to therapy is optimized through specifically designed multi-epitope-proteins, rather than myelin peptide cocktails, as “multi-epitope-targeting” agents. Such artificial multi-epitope proteins can be tailored to other organ-specific autoimmune diseases

Antibodies Against Human BLyS and APRIL Attenuate EAE Development in Marmoset Monkeys

B lymphocyte stimulator (BLyS, also indicated as BAFF (B-cell activating factor) and CD257), and A Proliferation Inducing Ligand (APRIL, CD256) are two members of the TNF superfamily with a central role in B cell survival. Antibodies against these factors have potential therapeutic relevance in autoimmune inflammatory disorders with a proven pathogenic contribution of B cells, such as multiple sclerosis (MS). In the current study we performed a multi-parameter efficacy comparison of monoclonal antibodies against human anti-BLyS and anti-APRIL in a common marmoset (Callithrix jacchus) model of experimental autoimmune encephalomyelitis (EAE). A MS-like disease was induced by immunization with recombinant human myelin/oligodendrocyte glycoprotein (rhMOG) in complete Freund's adjuvant. The results show that the anti-BLyS and anti-APRIL antibody cause significant depletion of circulating CD20+ B cells, but a small subset of CD20 + CD40highB cells was not depleted. Induction of CD20+ B cell depletion from lymph nodes was only observed in the anti-BLyS treated monkeys. Both antibodies had a significant inhibitory effect on disease development, but all monkeys developed clinically evident EAE. Anti-BLyS treated monkeys were sacrificed with the same clinical signs as saline-treated monkeys, but nevertheless displayed significantly reduced spinal cord demyelination. This effect was not observed in the anti-APRIL treated monkeys. The two antibodies had a different effect on T cell subset activation and the profiles of ex vivo released cytokines. In conclusion, treatment with anti-BLyS and anti-APRIL delays the development of neurological disease in a relevant preclinical model of MS. The two mAbs achieve this effect via different mechanisms