Effects of depeltion of Tim-4 on gene expression in Peritoneal macrophages (PEMs)
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE274504 | GEO | 2025/12/02
REPOSITORIES: GEO
Similar Datasets
Project description:T-cell immunoglobulin and mucin domain containing 4 (Tim-4) is known to suppress macrophage inflammatory responses in various diseases, but its role and underlying mechanism in peritoneal macrophage (PEMs) with LPS stimulation are unknown. PEMs were isolated from Tim-4fl/fl mice and LysM-Cre; Tim-4fl/fl mice, followed by stimulation with 100 ng/mL LPS for 24 hours. After validating the successful knockout of Tim-4 in macrophages, mass spectrometry was employed to identify differentially expressed proteins in PEMs.
2025-07-14 | PXD066149 |
Project description:Tumor-associated macrophages (TAMs) affect cancer progression and therapy. Ovarian carcinoma often metastasizes to the peritoneal cavity. Here, we found two peritoneal macrophage subsets in mice bearing ID8 ovarian cancer based on the Tim-4 (T-cell immunoglobulin and mucin domain containing 4) expression. Tim-4+ TAMs were embryonically originated and locally sustained while Tim-4- TAMs were replenished from circulating monocytes. Tim-4+ TAMs, but not Tim-4- TAMs, promoted tumor growth in vivo. Relative to Tim-4- TAMs, Tim-4+ TAMs manifested high oxidative phosphorylation and adapted mitophagy to alleviate oxidative stress. High levels of arginase-1 in Tim-4+ TAMs contributed to potent mitophagy activities via weakened mTORC1 activation due to low arginine resultant from arginase-1-mediated metabolism. Furthermore, genetic deficiency of autophagy element FIP200 resulted in Tim-4+ TAM loss via ROS-mediated apoptosis, and elevated T cell-immunity and ID8 tumor inhibition in vivo. Moreover, human ovarian cancer-associated CRIg (complement receptor of the Immunoglobulin superfamily) positive macrophages were transcriptionally, metabolically, and functionally similar to murine Tim-4+ TAMs. Thus, targeting CRIg+ (Tim-4+) TAMs may potentially treat ovarian cancer patients with peritoneal metastasis.
2020-09-09 | GSE157673 | GEO
Project description:Mucin-domain glycoproteins are densely O-glycosylated and play key roles in a host of biological functions. In particular, the T-cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, 3, 4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans, which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamic (MD) simulations of TIM-3 and 4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.
2023-09-27 | PXD039583 | Pride
Project description:T cell immunoglobulin and mucin-containing molecule 3 (TIM-3) exhibits unique, cell type- and context-dependent characteristics and functions. Here, we report that TIM-3 on myeloid cells plays essential roles in modulating lung inflammation. We found that myeloid cell-specific TIM-3 knock-in (FSF-TIM3/LysM-Cre+) mice have lower body weight and shorter lifespan than WT mice. Intriguingly, the lungs of FSF-TIM3/LysM-Cre+ mice display excessive inflammation and features of disease-associated pathology. We further revealed that galectin-3 levels are notably elevated in TIM-3-overexpressing lung-derived myeloid cells. Furthermore, both TIM-3 blockade and GB1107, a galectin-3 inhibitor, ameliorated lung inflammation in FSF-TIM3/LysM-Cre+/- mice. Using an LPS-induced lung inflammation model with myeloid cell-specific TIM-3 knock-out mice, we demonstrated the association of TIM-3 with both lung inflammation and galectin-3. Collectively, our findings suggest that myeloid TIM-3 is an important regulator in the lungs and that modulation of TIM-3 and galectin-3 could offer therapeutic benefits for inflammation-associated lung diseases.
2024-07-29 | GSE268660 | GEO
Project description:Allergic asthma is driven by type 2 inflammation involving cytokines such as IL-4, IL-5, and IL-13, with group 2 innate lymphoid cells (ILC2s) playing a key pathogenic role. Here, we identify T cell immunoglobulin and mucin domain-containing protein 3 (Tim-3) as a negative regulator of ILC2 function. Tim-3 expression was upregulated in activated pulmonary ILC2s, and engagement with Tim-3 agonists inhibited ILC2 activation, proliferation, and type 2 cytokine production via the NLK signaling pathway and suppression of mitochondrial metabolism. In vivo, Tim-3 agonists alleviated airway hyperreactivity (AHR) and inflammation in both IL-33- and Alternaria alternata-induced AHR models, while ILC2-specific Tim-3 deletion exacerbated AHR. These results were confirmed in human ILC2s and humanized mice, supporting the translational relevance. Our findings establish Tim-3 as an inhibitory checkpoint for ILC2s and suggest its potential as a therapeutic target in allergic asthma and other ILC2-mediated diseases.
2026-02-22 | GSE298909 | GEO
Project description:Bladder cancer (BC) is one of the most common cancers in the world. T-cell immunoglobulin and mucin domain 1 (TIM-1) are involved in the progression of multiple tumors. However the role of TIM-1 in BC progression is poorly understood. In this study, we searched the Gene Expression Profiling Interactive Analysis (GEPIA) database and performed immunohistochemistry (IHC) to assess TIM-1 protein expression in bladder cancer (BC) patients. The results demonstrated that BC with high TIM-1 expression was associated with longer overall survival (OS) and disease-specific survival (DSS) than BC with low TIM-1 expression. Overexpression of TIM-1 inhibits BC cell proliferation in both cell culture and animal experiments. RNA sequencing data indicated that interferon-induced protein with tetratricopeptide repeats (IFIT) genes induced by interferon-α (IFN-α) were significantly enriched among the genes upregulated by TIM-1 overexpression. Mechanistically, our data revealed that TIM-1 promotes IFN-α release and activates the IFIT2/p-STAT1 pathway, which is known to be related to tumor cell proliferation. Moreover, knockdown of IFIT2 in TIM-1-overexpressing BC cells hinders the tumor suppressive effect of TIM-1. Our results revealed that TIM-1 is a potential molecular marker for BC prognosis and indicate that high TIM-1 expression suppresses BC cell proliferation in an IFIT2/p-STAT1-dependent manner.
2023-03-08 | GSE226545 | GEO
Project description:Tim-3, or transmembrane immunoglobulin and mucin domain-3, is a type I membrane protein expressed by various immune cell types and which is best known as a negative regulator of anti-tumor immunity. However, Tim-3 also has a co-stimulatory role in T cells under some conditions, via enhancement of PI3K signaling. We hypothesize that Tim-3 signaling enhances CD8+ T cell activation during acute infection and contributes to enhanced CD8+ effector function. To test this hypothesis, we used LCMV-specific TCR transgenic (P14) mice expressing a truncated, non-signaling, allele of Tim-3 or CD8-specific deletion of Tim-3. CD8+ T cell effectors were analyzed by flow cytometry after acute infection with LCMV Armstrong. At the effector stage, endogenous Tim-3+ T cells had increased expression of effector CD8 markers, compared with Tim-3 negative cells. Tim-3 knockout mice also showed a significantly lower number of LCMV-specific T cells. Additionally, endogenous Tim-3+ T cells were also significantly better at cytokine production and had increased cytotoxicity. Tim-3 expression correlated with better cell survival in homeostatic conditions after the virus had been cleared. Bulk RNA sequencing and TCR sequencing revealed that Tim-3-expressing effector CD8+ T cells had a distinct pattern of effector gene upregulation, with increased expansion of a subset of TCR clones. Mechanistically, Tim-3 signals enhances phosphorylation of Foxo1, inhibiting its entry into the nucleus, conferring enhanced effector function. Thus, Tim-3 signaling contributes positively to an effective CD8+ T cell response during acute infection. These findings may lead to a better understanding of CD8+ T cell function in different settings, including in tumors.
2025-07-01 | GSE301002 | GEO
Project description:Tim-3, or transmembrane immunoglobulin and mucin domain-3, is a type I membrane protein expressed by various immune cell types and which is best known as a negative regulator of anti-tumor immunity. However, Tim-3 also has a co-stimulatory role in T cells under some conditions, via enhancement of PI3K signaling. We hypothesize that Tim-3 signaling enhances CD8+ T cell activation during acute infection and contributes to enhanced CD8+ effector function. To test this hypothesis, we used LCMV-specific TCR transgenic (P14) mice expressing a truncated, non-signaling, allele of Tim-3 or CD8-specific deletion of Tim-3. CD8+ T cell effectors were analyzed by flow cytometry after acute infection with LCMV Armstrong. At the effector stage, endogenous Tim-3+ T cells had increased expression of effector CD8 markers, compared with Tim-3 negative cells. Tim-3 knockout mice also showed a significantly lower number of LCMV-specific T cells. Additionally, endogenous Tim-3+ T cells were also significantly better at cytokine production and had increased cytotoxicity. Tim-3 expression correlated with better cell survival in homeostatic conditions after the virus had been cleared. Bulk RNA sequencing and TCR sequencing revealed that Tim-3-expressing effector CD8+ T cells had a distinct pattern of effector gene upregulation, with increased expansion of a subset of TCR clones. Mechanistically, Tim-3 signals enhances phosphorylation of Foxo1, inhibiting its entry into the nucleus, conferring enhanced effector function. Thus, Tim-3 signaling contributes positively to an effective CD8+ T cell response during acute infection. These findings may lead to a better understanding of CD8+ T cell function in different settings, including in tumors.
2025-07-01 | GSE300892 | GEO
Project description:Tim-3, or transmembrane immunoglobulin and mucin domain-3, is a type I membrane protein expressed by various immune cell types and which is best known as a negative regulator of anti-tumor immunity. However, Tim-3 also has a co-stimulatory role in T cells under some conditions, via enhancement of PI3K signaling. We hypothesize that Tim-3 signaling enhances CD8+ T cell activation during acute infection and contributes to enhanced CD8+ effector function. To test this hypothesis, we used LCMV-specific TCR transgenic (P14) mice expressing a truncated, non-signaling, allele of Tim-3 or CD8-specific deletion of Tim-3. CD8+ T cell effectors were analyzed by flow cytometry after acute infection with LCMV Armstrong. At the effector stage, endogenous Tim-3+ T cells had increased expression of effector CD8 markers, compared with Tim-3 negative cells. Tim-3 knockout mice also showed a significantly lower number of LCMV-specific T cells. Additionally, endogenous Tim-3+ T cells were also significantly better at cytokine production and had increased cytotoxicity. Tim-3 expression correlated with better cell survival in homeostatic conditions after the virus had been cleared. Bulk RNA sequencing and TCR sequencing revealed that Tim-3-expressing effector CD8+ T cells had a distinct pattern of effector gene upregulation, with increased expansion of a subset of TCR clones. Mechanistically, Tim-3 signals enhances phosphorylation of Foxo1, inhibiting its entry into the nucleus, conferring enhanced effector function. Thus, Tim-3 signaling contributes positively to an effective CD8+ T cell response during acute infection. These findings may lead to a better understanding of CD8+ T cell function in different settings, including in tumors.
2025-07-01 | GSE300893 | GEO
Project description:To find out genes regulated by geranylgeraniol (GGOH) treatment in peritoneal macrophage, we compared gene expression of cells treated with 200ng ml LPS and 250 micromolar compactin versus 200ng ml LPS, 250 micromolar compactin and 100micromolar GGOH. To find out upregulated or downregulated genes regulated by GGOH treatment in peritoneal macrophage (LPS+CPN treated cell).
2013-11-12 | E-GEOD-48646 | biostudies-arrayexpress