Defining solute carrier transporter signatures of murine immune cell subsets
Solute carrier (SLC) transporters are membrane-bound proteins that facilitate nutrient transport, and the movement across cellular membranes of various substrates ranging from ions to amino acids, metabolites and drugs. Recently, SLCs have gained increased attention due to their functional linkage t...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1276196/full |
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| author | Tania Løve Aaes Tania Løve Aaes Javier Burgoa Cardás Javier Burgoa Cardás Kodi S. Ravichandran Kodi S. Ravichandran Kodi S. Ravichandran Kodi S. Ravichandran |
| author_facet | Tania Løve Aaes Tania Løve Aaes Javier Burgoa Cardás Javier Burgoa Cardás Kodi S. Ravichandran Kodi S. Ravichandran Kodi S. Ravichandran Kodi S. Ravichandran |
| author_sort | Tania Løve Aaes |
| collection | DOAJ |
| description | Solute carrier (SLC) transporters are membrane-bound proteins that facilitate nutrient transport, and the movement across cellular membranes of various substrates ranging from ions to amino acids, metabolites and drugs. Recently, SLCs have gained increased attention due to their functional linkage to innate immunological processes such as the clearance of dead cells and anti-microbial defense. Further, the druggable nature of these transporters provides unique opportunities for improving outcomes in different immunological diseases. Although the SLCs represent the largest group of transporters and are often identified as significant hits in omics data sets, their role in immunology has been insufficiently explored. This is partly due to the absence of tools that allow identification of SLC expression in particular immune cell types and enable their comparison before embarking on functional studies. In this study, we used publicly available RNA-Seq data sets to analyze the transcriptome in adaptive and innate immune cells, focusing on differentially and highly expressed SLCs. This revealed several new insights: first, we identify differentially expressed SLC transcripts in phagocytes (macrophages, dendritic cells, and neutrophils) compared to adaptive immune cells; second, we identify new potential immune cell markers based on SLC expression; and third, we provide user-friendly online tools for researchers to explore SLC genes of interest (and the rest of the genes as well), in three-way comparative dot plots among immune cells. We expect this work to facilitate SLC research and comparative transcriptomic studies across different immune cells. |
| first_indexed | 2024-03-09T17:53:21Z |
| format | Article |
| id | doaj.art-746cfc38a126455f8d29b46e36a3865a |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-03-09T17:53:21Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-746cfc38a126455f8d29b46e36a3865a2023-11-24T10:32:02ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-11-011410.3389/fimmu.2023.12761961276196Defining solute carrier transporter signatures of murine immune cell subsetsTania Løve Aaes0Tania Løve Aaes1Javier Burgoa Cardás2Javier Burgoa Cardás3Kodi S. Ravichandran4Kodi S. Ravichandran5Kodi S. Ravichandran6Kodi S. Ravichandran7Department of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, BelgiumUnit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research, Ghent, BelgiumDepartment of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, BelgiumUnit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research, Ghent, BelgiumDepartment of Biomedical Molecular Biology, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, BelgiumUnit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research, Ghent, BelgiumDepartment of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, United StatesDivision of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United StatesSolute carrier (SLC) transporters are membrane-bound proteins that facilitate nutrient transport, and the movement across cellular membranes of various substrates ranging from ions to amino acids, metabolites and drugs. Recently, SLCs have gained increased attention due to their functional linkage to innate immunological processes such as the clearance of dead cells and anti-microbial defense. Further, the druggable nature of these transporters provides unique opportunities for improving outcomes in different immunological diseases. Although the SLCs represent the largest group of transporters and are often identified as significant hits in omics data sets, their role in immunology has been insufficiently explored. This is partly due to the absence of tools that allow identification of SLC expression in particular immune cell types and enable their comparison before embarking on functional studies. In this study, we used publicly available RNA-Seq data sets to analyze the transcriptome in adaptive and innate immune cells, focusing on differentially and highly expressed SLCs. This revealed several new insights: first, we identify differentially expressed SLC transcripts in phagocytes (macrophages, dendritic cells, and neutrophils) compared to adaptive immune cells; second, we identify new potential immune cell markers based on SLC expression; and third, we provide user-friendly online tools for researchers to explore SLC genes of interest (and the rest of the genes as well), in three-way comparative dot plots among immune cells. We expect this work to facilitate SLC research and comparative transcriptomic studies across different immune cells.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1276196/fullsolute carriers (SLCs)membrane transportertranscriptome (RNA-seq)phagocytesinnate immunityTriwise (R) |
| spellingShingle | Tania Løve Aaes Tania Løve Aaes Javier Burgoa Cardás Javier Burgoa Cardás Kodi S. Ravichandran Kodi S. Ravichandran Kodi S. Ravichandran Kodi S. Ravichandran Defining solute carrier transporter signatures of murine immune cell subsets Frontiers in Immunology solute carriers (SLCs) membrane transporter transcriptome (RNA-seq) phagocytes innate immunity Triwise (R) |
| title | Defining solute carrier transporter signatures of murine immune cell subsets |
| title_full | Defining solute carrier transporter signatures of murine immune cell subsets |
| title_fullStr | Defining solute carrier transporter signatures of murine immune cell subsets |
| title_full_unstemmed | Defining solute carrier transporter signatures of murine immune cell subsets |
| title_short | Defining solute carrier transporter signatures of murine immune cell subsets |
| title_sort | defining solute carrier transporter signatures of murine immune cell subsets |
| topic | solute carriers (SLCs) membrane transporter transcriptome (RNA-seq) phagocytes innate immunity Triwise (R) |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1276196/full |
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