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      Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF

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      1 , 2 , 3 , , 1 , 2 , 4 , 5 , 6 , 1 , 7 , 8 , 1 , 9 , 2 , 3 , 10 , 1 , 11 , 1 , 6 , 6 , 1 , 1 , 12 , 13 , 1 , 1 , 1 , 14 , 15 , 16 , 17 , 16 , 17 , 1 , 18 , 1 , 1 , 4 , 19 , 20 , 21 , 8 , 22 , 23 , 3 , 10 , 21 , 4 , 24 , 6 , 4 , 24 , 1 , 2 , 25 , 1 ,
      Nature Communications
      Nature Publishing Group UK
      Mucosal immunology, Monocytes and macrophages

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          Abstract

          Stromal cells support epithelial cell and immune cell homeostasis and play an important role in inflammatory bowel disease (IBD) pathogenesis. Here, we quantify the stromal response to inflammation in pediatric IBD and reveal subset-specific inflammatory responses across colon segments and intestinal layers. Using data from a murine dynamic gut injury model and human ex vivo transcriptomic, protein and spatial analyses, we report that PDGFRA +CD142 /low fibroblasts and monocytes/macrophages co-localize in the intestine. In primary human fibroblast-monocyte co-cultures, intestinal PDGFRA +CD142 /low fibroblasts foster monocyte transition to CCR2 +CD206 + macrophages through granulocyte-macrophage colony-stimulating factor (GM-CSF). Monocyte-derived CCR2 +CD206 + cells from co-cultures have a phenotype similar to intestinal CCR2 +CD206 + macrophages from newly diagnosed pediatric IBD patients, with high levels of PD-L1 and low levels of GM-CSF receptor. The study describes subset-specific changes in stromal responses to inflammation and suggests that the intestinal stroma guides intestinal macrophage differentiation.

          Abstract

          Stromal cells are key players in immune cell homeostasis. Here, the authors decipher subset-specific human stromal responses in inflammatory bowel disease and suggest that intestinal PDGFRA +CD142 /low fibroblasts guide monocyte transition to macrophages in human gut through GM-CSF.

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          Most cited references71

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          Comprehensive Integration of Single-Cell Data

          Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
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            Fast, sensitive, and accurate integration of single cell data with Harmony

            The emerging diversity of single cell RNAseq datasets allows for the full transcriptional characterization of cell types across a wide variety of biological and clinical conditions. However, it is challenging to analyze them together, particularly when datasets are assayed with different technologies. Here, real biological differences are interspersed with technical differences. We present Harmony, an algorithm that projects cells into a shared embedding in which cells group by cell type rather than dataset-specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. In six analyses, we demonstrate the superior performance of Harmony to previously published algorithms. We show that Harmony requires dramatically fewer computational resources. It is the only currently available algorithm that makes the integration of ~106 cells feasible on a personal computer. We apply Harmony to PBMCs from datasets with large experimental differences, 5 studies of pancreatic islet cells, mouse embryogenesis datasets, and cross-modality spatial integration.
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              UMAP: Uniform Manifold Approximation and Projection

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                Author and article information

                Contributors
                egle.kvedaraite@ki.se
                mattias.svensson@ki.se
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                26 February 2024
                26 February 2024
                2024
                : 15
                : 1752
                Affiliations
                [1 ]GRID grid.24381.3c, ISNI 0000 0000 9241 5705, Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, , Karolinska University Hospital, ; Stockholm, Sweden
                [2 ]Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [3 ]Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, ( https://ror.org/00m8d6786) Stockholm, Sweden
                [4 ]Pediatric Gastroenterology, Hepatology and Nutrition Unit, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, ( https://ror.org/00m8d6786) Stockholm, Sweden
                [5 ]Department of Medicine Solna, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [6 ]GRID grid.59409.31, ISNI 0000 0004 0552 5033, Miltenyi Biotec B.V. & Co. KG, ; Bergisch Gladbach, Germany
                [7 ]Dermatology and Venereology Section, Department of Medicine Solna, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [8 ]Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [9 ]GRID grid.10548.38, ISNI 0000 0004 1936 9377, Science for Life Laboratory, Department of Biochemistry and Biophysics and National Bioinformatics Infrastructure Sweden, , Stockholm University, ; Solna, Sweden
                [10 ]Department of Oncology-Pathology, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [11 ]Bioinformatics and Expression Analysis Core Facility, Department of Biosciences and Nutrition, Karolinska Institutet, ( https://ror.org/056d84691) Huddinge, Sweden
                [12 ]Tech Watch, Flanders Institute for Biotechnology, ( https://ror.org/03xrhmk39) Ghent, Belgium
                [13 ]GRID grid.4714.6, ISNI 0000 0004 1937 0626, Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, , Karolinska Institutet, ; Huddinge, Sweden
                [14 ]Department of Transplantation Surgery, Karolinska University Hospital, ( https://ror.org/00m8d6786) Stockholm, Sweden
                [15 ]Department of Clinical Science, Intervention and Technology, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [16 ]Department of Molecular Medicine and Surgery, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [17 ]Department of Pelvic Cancer, GI Oncology and Colorectal Surgery Unit, Karolinska University Hospital, ( https://ror.org/00m8d6786) Stockholm, Sweden
                [18 ]GRID grid.5037.1, ISNI 0000000121581746, Science for Life Laboratory, Dept. of Applied Physics, , Royal Institute of Technology, ; Solna, Sweden
                [19 ]GRID grid.11486.3a, ISNI 0000000104788040, VIB Single Cell Core, VIB, ; Ghent, Belgium
                [20 ]VIB-UGent Center for Inflammation Research, ( https://ror.org/04q4ydz28) 9052 Ghent, Belgium
                [21 ]Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institutet and University Hospital, ( https://ror.org/056d84691) Stockholm, Sweden
                [22 ]GRID grid.4714.6, ISNI 0000 0004 1937 0626, Department of Clinical Science and Education, , Södersjukhuset, Karolinska Institutet, ; Stockholm, Sweden
                [23 ]GRID grid.416648.9, ISNI 0000 0000 8986 2221, Sachs’ Children and Youth Hospital, Department of Gastroenterology, , Södersjukhuset, ; Stockholm, Sweden
                [24 ]Department of Women’s and Children’s Health, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [25 ]Theme of Children’s Health, Karolinska University Hospital, ( https://ror.org/00m8d6786) Stockholm, Sweden
                Author information
                http://orcid.org/0000-0001-5308-092X
                http://orcid.org/0000-0003-3155-1123
                http://orcid.org/0000-0002-4347-7648
                http://orcid.org/0000-0002-2513-5927
                http://orcid.org/0000-0001-5016-5960
                http://orcid.org/0000-0003-2685-2052
                http://orcid.org/0000-0003-0633-1719
                http://orcid.org/0000-0001-7727-8113
                http://orcid.org/0000-0002-4162-0973
                http://orcid.org/0000-0002-6803-8377
                http://orcid.org/0000-0001-6915-0339
                http://orcid.org/0000-0001-9522-9729
                http://orcid.org/0000-0002-1119-0976
                http://orcid.org/0000-0002-0629-2126
                http://orcid.org/0000-0003-1695-7934
                Article
                46076
                10.1038/s41467-024-46076-3
                10897309
                38409190
                9f5385a3-8d12-432d-b8a8-0119edc5e55b
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 20 April 2023
                : 9 February 2024
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100006313, Barncancerfonden (Swedish Childhood Cancer Foundation);
                Award ID: 2021
                Award Recipient :
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                © Springer Nature Limited 2024

                Uncategorized
                mucosal immunology,monocytes and macrophages
                Uncategorized
                mucosal immunology, monocytes and macrophages

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