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      Itaconate-producing neutrophils regulate local and systemic inflammation following trauma

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          Abstract

          Modulation of the immune response to initiate and halt the inflammatory process occurs both at the site of injury as well as systemically. Due to the evolving role of cellular metabolism in regulating cell fate and function, tendon injuries that undergo normal and aberrant repair were evaluated by metabolic profiling to determine its impact on healing outcomes. Metabolomics revealed an increasing abundance of the immunomodulatory metabolite itaconate within the injury site. Subsequent single-cell RNA-Seq and molecular and metabolomic validation identified a highly mature neutrophil subtype, not macrophages, as the primary producers of itaconate following trauma. These mature itaconate-producing neutrophils were highly inflammatory, producing cytokines that promote local injury fibrosis before cycling back to the bone marrow. In the bone marrow, itaconate was shown to alter hematopoiesis, skewing progenitor cells down myeloid lineages, thereby regulating systemic inflammation. Therapeutically, exogenous itaconate was found to reduce injury-site inflammation, promoting tenogenic differentiation and impairing aberrant vascularization with disease-ameliorating effects. These results present an intriguing role for cycling neutrophils as a sensor of inflammation induced by injury — potentially regulating immune cell production in the bone marrow through delivery of endogenously produced itaconate — and demonstrate a therapeutic potential for exogenous itaconate following tendon injury

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          Integrated analysis of multimodal single-cell data

          Summary The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce “weighted-nearest neighbor” analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.
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            Inference and analysis of cell-cell communication using CellChat

            Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer (http://www.cellchat.org/) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues.
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              Itaconate is an anti-inflammatory metabolite that activates Nrf2 via alkylation of KEAP1

              The endogenous metabolite itaconate has recently emerged as a regulator of macrophage function, but its precise mechanism of action remains poorly understood. Here we show that itaconate is required for the activation of the anti-inflammatory transcription factor Nrf2 (also known as NFE2L2) by lipopolysaccharide in mouse and human macrophages. We find that itaconate directly modifies proteins via alkylation of cysteine residues. Itaconate alkylates cysteine residues 151, 257, 288, 273 and 297 on the protein KEAP1, enabling Nrf2 to increase the expression of downstream genes with anti-oxidant and anti-inflammatory capacities. The activation of Nrf2 is required for the anti-inflammatory action of itaconate. We describe the use of a new cell-permeable itaconate derivative, 4-octyl itaconate, which is protective against lipopolysaccharide-induced lethality in vivo and decreases cytokine production. We show that type I interferons boost the expression of Irg1 (also known as Acod1) and itaconate production. Furthermore, we find that itaconate production limits the type I interferon response, indicating a negative feedback loop that involves interferons and itaconate. Our findings demonstrate that itaconate is a crucial anti-inflammatory metabolite that acts via Nrf2 to limit inflammation and modulate type I interferons.
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                Author and article information

                Contributors
                Journal
                JCI Insight
                JCI Insight
                JCI Insight
                JCI Insight
                American Society for Clinical Investigation
                2379-3708
                23 October 2023
                23 October 2023
                23 October 2023
                : 8
                : 20
                : e169208
                Affiliations
                [1 ]Department of Surgery,
                [2 ]Children’s Research Institute and Department of Pediatrics,
                [3 ]Department of Pediatrics, and
                [4 ]Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas, USA.
                [5 ]Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA.
                Author notes
                Address correspondence to: Robert Tower, Center for Organogenesis and Trauma, Charles and Jane Pak Center for Mineral Metabolism, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. Email: Robert.Tower@ 123456UTSouthwestern.edu . Or to: Benjamin Levi, Lee-Hudson Professor and Division Chief of General Surgery, Director, Center for Organogenesis and Trauma, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. Email: Benjamin.Levi@ 123456UTSouthwestern.edu .

                Authorship note: RJT and BL are co–corresponding authors.

                Author information
                http://orcid.org/0000-0002-0202-4298
                http://orcid.org/0000-0001-5815-4457
                http://orcid.org/0000-0002-5568-0096
                http://orcid.org/0000-0001-6179-3583
                Article
                169208
                10.1172/jci.insight.169208
                10619500
                37707952
                b855c714-bf6c-45f9-bbc8-029429e205de
                © 2023 Crossley et al.

                This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 27 January 2023
                : 5 September 2023
                Funding
                Funded by: NIH
                Award ID: R01AR079863,R61AR078072
                Funded by: University of Texas Southwestern Medical Center, https://doi.org/10.13039/100007914;
                Award ID: Faculty of Surgery Pilot Award
                Funded by: U.S. Department of Defense, https://doi.org/10.13039/100000005;
                Award ID: PR221151
                Categories
                Research Article

                immunology,inflammation,neutrophils
                immunology, inflammation, neutrophils

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