Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages
Abstract Ras guanine nucleotide exchange factor member 1b (RasGEF1b) of the RasGEF/CDC25 domain-containing family is preferentially expressed by macrophages. However, information is lacking about its role in macrophage function. In this study, we generated mice with ubiquitous deletion of Rasgef1b a...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-47040-9 |
| _version_ | 1827764442823131136 |
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| author | Heliana B. Fernandes Isadora Mafra de Oliveira Thomas S. Postler Sérgio Q. Lima Cícera A. C. Santos Michaelle S. Oliveira Felipe B. Leão Sankar Ghosh Maria C. Souza Warrison Andrade Aristóbolo M. Silva |
| author_facet | Heliana B. Fernandes Isadora Mafra de Oliveira Thomas S. Postler Sérgio Q. Lima Cícera A. C. Santos Michaelle S. Oliveira Felipe B. Leão Sankar Ghosh Maria C. Souza Warrison Andrade Aristóbolo M. Silva |
| author_sort | Heliana B. Fernandes |
| collection | DOAJ |
| description | Abstract Ras guanine nucleotide exchange factor member 1b (RasGEF1b) of the RasGEF/CDC25 domain-containing family is preferentially expressed by macrophages. However, information is lacking about its role in macrophage function. In this study, we generated mice with ubiquitous deletion of Rasgef1b and used RNA-seq-based transcriptomics to compare the global gene expression in wild-type and knock-out primary bone-marrow-derived macrophages under basal conditions and after lipopolysaccharide (LPS) treatment. Transcriptional filtering identified several genes with significantly different transcript levels between wild-type and knock-out macrophages. In total, 49 and 37 differentially expressed genes were identified at baseline and in LPS-activated macrophages, respectively. Distinct biological processes were significantly linked to down-regulated genes at the basal condition only, and largely included chemotaxis, response to cytokines, and positive regulation of GTPase activity. Importantly, validation by RT-qPCR revealed that the expression of genes identified as down-regulated after LPS stimulation was also decreased in the knock-out cells under basal conditions. We used a luciferase-based reporter assay to showcase the capability of RasGEF1b in activating the Serpinb2 promoter. Notably, knockdown of RasGEF1b in RAW264.7 macrophages resulted in impaired transcriptional activation of the Serpinb2 promoter, both in constitutive and LPS-stimulated conditions. This study provides a small collection of genes that shows relative expression changes effected by the absence of RasGEF1b in macrophages. Thus, we present the first evidence that RasGEF1b mediates the regulation of both steady-state and signal-dependent expression of genes and propose that this GEF plays a role in the maintenance of the basal transcriptional level in macrophages. |
| first_indexed | 2024-03-11T11:05:32Z |
| format | Article |
| id | doaj.art-8dcddc11268f4d179e7961f809826ed1 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-11T11:05:32Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-8dcddc11268f4d179e7961f809826ed12023-11-12T12:16:03ZengNature PortfolioScientific Reports2045-23222023-11-0113111510.1038/s41598-023-47040-9Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophagesHeliana B. Fernandes0Isadora Mafra de Oliveira1Thomas S. Postler2Sérgio Q. Lima3Cícera A. C. Santos4Michaelle S. Oliveira5Felipe B. Leão6Sankar Ghosh7Maria C. Souza8Warrison Andrade9Aristóbolo M. Silva10Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG)Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG)Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical CenterLaboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG)Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG)Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG)Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical CenterDepartment of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical CenterFaculdade de Medicina de Ribeirão PretoFaculdade de Medicina de Ribeirão PretoLaboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG)Abstract Ras guanine nucleotide exchange factor member 1b (RasGEF1b) of the RasGEF/CDC25 domain-containing family is preferentially expressed by macrophages. However, information is lacking about its role in macrophage function. In this study, we generated mice with ubiquitous deletion of Rasgef1b and used RNA-seq-based transcriptomics to compare the global gene expression in wild-type and knock-out primary bone-marrow-derived macrophages under basal conditions and after lipopolysaccharide (LPS) treatment. Transcriptional filtering identified several genes with significantly different transcript levels between wild-type and knock-out macrophages. In total, 49 and 37 differentially expressed genes were identified at baseline and in LPS-activated macrophages, respectively. Distinct biological processes were significantly linked to down-regulated genes at the basal condition only, and largely included chemotaxis, response to cytokines, and positive regulation of GTPase activity. Importantly, validation by RT-qPCR revealed that the expression of genes identified as down-regulated after LPS stimulation was also decreased in the knock-out cells under basal conditions. We used a luciferase-based reporter assay to showcase the capability of RasGEF1b in activating the Serpinb2 promoter. Notably, knockdown of RasGEF1b in RAW264.7 macrophages resulted in impaired transcriptional activation of the Serpinb2 promoter, both in constitutive and LPS-stimulated conditions. This study provides a small collection of genes that shows relative expression changes effected by the absence of RasGEF1b in macrophages. Thus, we present the first evidence that RasGEF1b mediates the regulation of both steady-state and signal-dependent expression of genes and propose that this GEF plays a role in the maintenance of the basal transcriptional level in macrophages.https://doi.org/10.1038/s41598-023-47040-9 |
| spellingShingle | Heliana B. Fernandes Isadora Mafra de Oliveira Thomas S. Postler Sérgio Q. Lima Cícera A. C. Santos Michaelle S. Oliveira Felipe B. Leão Sankar Ghosh Maria C. Souza Warrison Andrade Aristóbolo M. Silva Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages Scientific Reports |
| title | Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages |
| title_full | Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages |
| title_fullStr | Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages |
| title_full_unstemmed | Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages |
| title_short | Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages |
| title_sort | transcriptomic analysis reveals that rasgef1b deletion alters basal and lps induced expression of genes involved in chemotaxis and cytokine responses in macrophages |
| url | https://doi.org/10.1038/s41598-023-47040-9 |
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