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      NAD + metabolism drives astrocyte proinflammatory reprogramming in central nervous system autoimmunity

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          Significance

          NAD + has emerged as an important cofactor that can rewire metabolism and link energy status with cellular immune response reprogramming, raising the possibility that an improved understanding of NAD + immunometabolic function in neuroinflammation could be exploited therapeutically. We have now identified the enzymes NAMPT, CD38, and the transcription factor NFATC3 as critical nodes in regulating astrocyte pathogenicity and controlling experimental neuroinflammation. Importantly, we have corroborated these murine findings in human astrocytes and analysis of MS brain samples. Overall, our results describe the role of NAD + metabolism in the local immune response in the CNS and reveal targetable mechanistic insights into how NAD + immunometabolic signaling controls astrocyte activation and promotes CNS autoimmunity.

          Abstract

          Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). Astrocytes are the most abundant glial cells in the CNS, and their dysfunction contributes to the pathogenesis of MS and its animal model, experimental autoimmune encephalomyelitis (EAE). Recent advances highlight the pivotal role of cellular metabolism in programming immune responses. However, the underlying immunometabolic mechanisms that drive astrocyte pathogenicity remain elusive. Nicotinamide adenine dinucleotide (NAD +) is a vital coenzyme involved in cellular redox reactions and a substrate for NAD +-dependent enzymes. Cellular NAD + levels are dynamically controlled by synthesis and degradation, and dysregulation of this balance has been associated with inflammation and disease. Here, we demonstrate that cell-autonomous generation of NAD + via the salvage pathway regulates astrocyte immune function. Inhibition of nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme in the salvage pathway, results in depletion of NAD +, inhibits oxidative phosphorylation, and limits astrocyte inflammatory potential. We identified CD38 as the main NADase up-regulated in reactive mouse and human astrocytes in models of neuroinflammation and MS. Genetic or pharmacological blockade of astrocyte CD38 activity augmented NAD + levels, suppressed proinflammatory transcriptional reprogramming, impaired chemotactic potential to inflammatory monocytes, and ameliorated EAE. We found that CD38 activity is mediated via calcineurin/NFAT signaling in mouse and human reactive astrocytes. Thus, NAMPT–NAD +–CD38 circuitry in astrocytes controls their ability to meet their energy demands and drives the expression of proinflammatory transcriptional modules, contributing to CNS pathology in EAE and, potentially, MS. Our results identify candidate therapeutic targets in MS.

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          Most cited references84

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            STAR: ultrafast universal RNA-seq aligner.

            Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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              Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

              Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
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                Author and article information

                Journal
                Proc Natl Acad Sci U S A
                Proc Natl Acad Sci U S A
                pnas
                PNAS
                Proceedings of the National Academy of Sciences of the United States of America
                National Academy of Sciences
                0027-8424
                1091-6490
                22 August 2022
                30 August 2022
                22 February 2023
                : 119
                : 35
                : e2211310119
                Affiliations
                [1] aSagol School of Neuroscience, Tel Aviv University , Tel Aviv 69978, Israel;
                [2] bShmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel;
                [3] cDepartment of Neurology and Neurological Sciences, Beckman Center for Molecular Medicine, Stanford University School of Medicine , Stanford, CA 94305-5316
                Author notes
                2To whom correspondence may be addressed. Email: liormayo@ 123456tauex.tau.ac.il .

                Edited by Harvey Cantor, Dana-Farber Cancer Institute, Boston, MA; received July 1, 2022; accepted July 28, 2022

                Author contributions: L.S. and L.M. designed research; T.M., D.S., S.Y., A.T., T.C., A.G.-Y., R.P., N.B.-H., and L.M. performed research; T.M., D.S., S.Y., G.Y., A.T., R.P., L.S., and L.M. analyzed data; and L.S. and L.M. wrote the paper.

                1T.M. and D.S. contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-2472-8501
                https://orcid.org/0000-0002-2437-2250
                https://orcid.org/0000-0002-1296-6692
                Article
                202211310
                10.1073/pnas.2211310119
                9436380
                35994674
                fb77f906-33f3-4061-bc78-963d420cd6a5
                Copyright © 2022 the Author(s). Published by PNAS.

                This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

                History
                : 28 July 2022
                Page count
                Pages: 12
                Funding
                Funded by: Israel Science Foundation (ISF) 501100003977
                Award ID: 963/16
                Award ID: 293/17
                Award ID: and 1564/20
                Award Recipient : Lior Mayo
                Funded by: National Multiple Sclerosis Society (NMSS) 100000890
                Award ID: RG1611-26083. RG1702-27015
                Award Recipient : Lior Mayo
                Categories
                420
                Biological Sciences
                Immunology and Inflammation

                astrocyte,tryptophan catabolism,neuroinflammation,multiple sclerosis,nicotinamide adenine dinucleotide

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