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Garcia JPT, Tayo LL. Theoretical Studies of DNA Microarray Present Potential Molecular and Cellular Interconnectivity of Signaling Pathways in Immune System Dysregulation. Genes (Basel) 2024; 15:393. [PMID: 38674328 PMCID: PMC11049615 DOI: 10.3390/genes15040393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 04/28/2024] Open
Abstract
Autoimmunity is defined as the inability to regulate immunological activities in the body, especially in response to external triggers, leading to the attack of the tissues and organs of the host. Outcomes include the onset of autoimmune diseases whose effects are primarily due to dysregulated immune responses. In past years, there have been cases that show an increased susceptibility to other autoimmune disorders in patients who are already experiencing the same type of disease. Research in this field has started analyzing the potential molecular and cellular causes of this interconnectedness, bearing in mind the possibility of advancing drugs and therapies for the treatment of autoimmunity. With that, this study aimed to determine the correlation of four autoimmune diseases, which are type 1 diabetes (T1D), psoriasis (PSR), systemic sclerosis (SSc), and systemic lupus erythematosus (SLE), by identifying highly preserved co-expressed genes among datasets using WGCNA. Functional annotation was then employed to characterize these sets of genes based on their systemic relationship as a whole to elucidate the biological processes, cellular components, and molecular functions of the pathways they are involved in. Lastly, drug repurposing analysis was performed to screen candidate drugs for repositioning that could regulate the abnormal expression of genes among the diseases. A total of thirteen modules were obtained from the analysis, the majority of which were associated with transcriptional, post-transcriptional, and post-translational modification processes. Also, the evaluation based on KEGG suggested the possible role of TH17 differentiation in the simultaneous onset of the four diseases. Furthermore, clomiphene was the top drug candidate for regulating overexpressed hub genes; meanwhile, prilocaine was the top drug for regulating under-expressed hub genes. This study was geared towards utilizing transcriptomics approaches for the assessment of microarray data, which is different from the use of traditional genomic analyses. Such a research design for investigating correlations among autoimmune diseases may be the first of its kind.
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Affiliation(s)
- Jon Patrick T. Garcia
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
- School of Graduate Studies, Mapúa University, Manila 1002, Philippines
| | - Lemmuel L. Tayo
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
- Department of Biology, School of Medicine and Health Sciences, Mapúa University, Makati 1200, Philippines
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2
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Zhang X, Liu Y, Yang R, Guo Y, Yan M, Xiao Y, Dong Y, Zhang R, Qin Y, Bu Y, Zhang Y, Gao H. Phosphorylation of RasGRP1 by Shc3 prevents RasGRP1 degradation and contributes to Ras/c-Jun activation in hepatocellular carcinoma. Mol Cell Biochem 2023:10.1007/s11010-023-04839-4. [PMID: 37646951 DOI: 10.1007/s11010-023-04839-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023]
Abstract
Ras guanine nucleotide-releasing protein 1 (RasGRP1), a Ras activator, is upregulated in hepatocellular carcinoma (HCC) and other kinds of cancer and is associated with the poor prognosis of patients. However, little is known about the underlying regulatory mechanisms of RasGRP1 in the context of cancer. Here, we report that RasGRP1 physically interacted with the adaptor protein Src homolog and collagen homolog 3 (Shc3). Moreover, RasGRP1 C-terminus domain (aa 607-797) bound to the central collagen-homology 1 (CH1) domain of Shc3. Subsequently, Shc3 enhanced the RasGRP1 tyrosine phosphorylation rate and stability by inhibiting its ubiquitination. Notably, the phosphorylation-mimicking mutants of RasGRP1, RasGRP1 Y704A, and Y748A, rescued the phosphorylation and ubiquitination levels of RasGRP1 in HCC cells. Further investigation showed that the RasGRP1 and Shc3 interaction induced activation of Ras and c-Jun, resulting in cell proliferation in vitro. Moreover, the regulation of Shc3/RasGRP1/Ras/c-Jun signal transduction was confirmed in vivo using the subcutaneous xenograft mouse model. Thus, we propose that continuous Shc3 overexpression may be a possible mechanism for maintaining RasGRP1 stability and that persistent activation of Ras/c-Jun signaling through the interaction of RasGRP1 and Shc3 is a key event increasing cell proliferation. Our findings suggest that the interaction of RasGRP1 and Shc3 plays an important role in HCC tumorigenesis and suggests the potential clinical usage of novel biomarkers and therapeutic targets in HCC.
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Affiliation(s)
- Xinran Zhang
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Yun Liu
- Key Laboratory of Cancer Prevention and Therapy, Department of Pediatric Oncology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, China
| | - Rui Yang
- Department of Critical Care Medicine, Tianjin First Central Hospital, Tianjin Institute of Emergency Medicine, Tianjin, 300192, China
| | - Yuanyuan Guo
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Meiling Yan
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Ying Xiao
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Yunzhuo Dong
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Ruixia Zhang
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Yinpeng Qin
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Yishan Bu
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Yi Zhang
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China
| | - Huier Gao
- Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, 300192, China.
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A Focused Review of Ras Guanine Nucleotide-Releasing Protein 1 in Immune Cells and Cancer. Int J Mol Sci 2023; 24:ijms24021652. [PMID: 36675167 PMCID: PMC9864139 DOI: 10.3390/ijms24021652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Four Ras guanine nucleotide-releasing proteins (RasGRP1 through 4) belong to the family of guanine nucleotide exchange factors (GEFs). RasGRPs catalyze the release of GDP from small GTPases Ras and Rap and facilitate their transition from an inactive GDP-bound to an active GTP-bound state. Thus, they regulate critical cellular responses via many downstream GTPase effectors. Similar to other RasGRPs, the catalytic module of RasGRP1 is composed of the Ras exchange motif (REM) and Cdc25 domain, and the EF hands and C1 domain contribute to its cellular localization and regulation. RasGRP1 can be activated by a diacylglycerol (DAG)-mediated membrane recruitment and protein kinase C (PKC)-mediated phosphorylation. RasGRP1 acts downstream of the T cell receptor (TCR), B cell receptors (BCR), and pre-TCR, and plays an important role in the thymocyte maturation and function of peripheral T cells, B cells, NK cells, mast cells, and neutrophils. The dysregulation of RasGRP1 is known to contribute to numerous disorders that range from autoimmune and inflammatory diseases and schizophrenia to neoplasia. Given its position at the crossroad of cell development, inflammation, and cancer, RASGRP1 has garnered interest from numerous disciplines. In this review, we outline the structure, function, and regulation of RasGRP1 and focus on the existing knowledge of the role of RasGRP1 in leukemia and other cancers.
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Cooke M, Kazanietz MG. Overarching roles of diacylglycerol signaling in cancer development and antitumor immunity. Sci Signal 2022; 15:eabo0264. [PMID: 35412850 DOI: 10.1126/scisignal.abo0264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Diacylglycerol (DAG) is a lipid second messenger that is generated in response to extracellular stimuli and channels intracellular signals that affect mammalian cell proliferation, survival, and motility. DAG exerts a myriad of biological functions through protein kinase C (PKC) and other effectors, such as protein kinase D (PKD) isozymes and small GTPase-regulating proteins (such as RasGRPs). Imbalances in the fine-tuned homeostasis between DAG generation by phospholipase C (PLC) enzymes and termination by DAG kinases (DGKs), as well as dysregulation in the activity or abundance of DAG effectors, have been widely associated with tumor initiation, progression, and metastasis. DAG is also a key orchestrator of T cell function and thus plays a major role in tumor immunosurveillance. In addition, DAG pathways shape the tumor ecosystem by arbitrating the complex, dynamic interaction between cancer cells and the immune landscape, hence representing powerful modifiers of immune checkpoint and adoptive T cell-directed immunotherapy. Exploiting the wide spectrum of DAG signals from an integrated perspective could underscore meaningful advances in targeted cancer therapy.
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Affiliation(s)
- Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Medicine, Einstein Medical Center Philadelphia, Philadelphia, PA 19141, USA
| | - Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Takino JI, Miyazaki S, Nagamine K, Hori T. The Role of RASGRP2 in Vascular Endothelial Cells-A Mini Review. Int J Mol Sci 2021; 22:ijms222011129. [PMID: 34681791 PMCID: PMC8537898 DOI: 10.3390/ijms222011129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
RAS guanyl nucleotide-releasing proteins (RASGRPs) are important proteins that act as guanine nucleotide exchange factors, which activate small GTPases and function as molecular switches for intracellular signals. The RASGRP family is composed of RASGRP1-4 proteins and activates the small GTPases, RAS and RAP. Among them, RASGRP2 has different characteristics from other RASGRPs in that it targets small GTPases and its localizations are different. Many studies related to RASGRP2 have been reported in cells of the blood cell lineage. Furthermore, RASGRP2 has also been reported to be associated with Huntington's disease, tumors, and rheumatoid arthritis. In addition, we also recently reported RASGRP2 expression in vascular endothelial cells, and clarified the involvement of xenopus Rasgrp2 in the vasculogenesis process and multiple signaling pathways of RASGRP2 in human vascular endothelial cells with stable expression of RASGRP2. Therefore, this article outlines the existing knowledge of RASGRP2 and focuses on its expression and role in vascular endothelial cells, and suggests that RASGRP2 functions as a protective factor for maintaining healthy blood vessels.
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Affiliation(s)
- Jun-ichi Takino
- Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshingai, Kure, Hiroshima 737-0112, Japan; (S.M.); (T.H.)
- Correspondence: ; Tel.: +81-823-73-8584
| | - Shouhei Miyazaki
- Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshingai, Kure, Hiroshima 737-0112, Japan; (S.M.); (T.H.)
| | - Kentaro Nagamine
- Faculty of Health Sciences, Hiroshima International University, 5-1-1 Hirokoshingai, Kure, Hiroshima 737-0112, Japan;
| | - Takamitsu Hori
- Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshingai, Kure, Hiroshima 737-0112, Japan; (S.M.); (T.H.)
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Regulation of the Small GTPase Ras and Its Relevance to Human Disease. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:19-43. [PMID: 33977469 DOI: 10.1007/978-1-0716-1190-6_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ras research has experienced a considerable boost in recent years, not least prompted by the Ras initiative launched by the NCI in 2013 ( https://www.cancer.gov/research/key-initiatives/ras ), accompanied and conditioned by a strongly reinvigorated determination within the Ras community to develop therapeutics attacking directly the Ras oncoproteins. As a member of the small G-protein superfamily, function and transforming activity of Ras all revolve about its GDP/GTP loading status. For one thing, the extent of GTP loading will determine the proportion of active Ras in the cell, with implications for intensity and quality of downstream signaling. But also the rate of nucleotide exchange, i.e., the Ras-GDP/GTP cycling rate, can have a major impact on Ras function, as illustrated perhaps most impressively by newly discovered fast-cycling oncogenic mutants of the Ras-related GTPase Rac1. Thus, while the last years have witnessed memorable new findings and technical developments in the Ras field, leading to an improved insight into many aspects of Ras biology, they have not jolted at the basics, but rather deepened our view of the fundamental regulatory principles of Ras activity control. In this brief review, we revisit the role and mechanisms of Ras nucleotide loading and its implications for cancer in the light of recent findings.
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Oh M, Kim SY, Gil JE, Byun JS, Cha DW, Ku B, Lee W, Kim WK, Oh KJ, Lee EW, Bae KH, Lee SC, Han BS. Nurr1 performs its anti-inflammatory function by regulating RasGRP1 expression in neuro-inflammation. Sci Rep 2020; 10:10755. [PMID: 32612143 PMCID: PMC7329810 DOI: 10.1038/s41598-020-67549-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 06/10/2020] [Indexed: 12/21/2022] Open
Abstract
Nurr1, a transcription factor belonging to the orphan nuclear receptor, has an essential role in the generation and maintenance of dopaminergic neurons and is important in the pathogenesis of Parkinson’ disease (PD). In addition, Nurr1 has a non-neuronal function, and it is especially well known that Nurr1 has an anti-inflammatory function in the Parkinson’s disease model. However, the molecular mechanisms of Nurr1 have not been elucidated. In this study, we describe a novel mechanism of Nurr1 function. To provide new insights into the molecular mechanisms of Nurr1 in the inflammatory response, we performed Chromatin immunoprecipitation sequencing (ChIP-Seq) on LPS-induced inflammation in BV2 cells and finally identified the RasGRP1 gene as a novel target of Nurr1. Here, we show that Nurr1 directly binds to the RasGRP1 intron to regulate its expression. Moreover, we also identified that RasGRP1 regulates the Ras-Raf-MEK-ERK signaling cascade in LPS-induced inflammation signaling. Finally, we conclude that RasGRP1 is a novel regulator of Nurr1’s mediated inflammation signaling.
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Affiliation(s)
- Mihee Oh
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Sun Young Kim
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jung-Eun Gil
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jeong-Su Byun
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Dong-Wook Cha
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, 34113, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | | | - Won-Kon Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, 34113, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, 34113, Republic of Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Kwang-Hee Bae
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, 34113, Republic of Korea
| | - Sang Chul Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea. .,Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, 34113, Republic of Korea.
| | - Baek-Soo Han
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea. .,Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea. .,Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, 34113, Republic of Korea.
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8
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Czikora A, Kedei N, Kalish H, Blumberg PM. Importance of the REM (Ras exchange) domain for membrane interactions by RasGRP3. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2350-2360. [PMID: 28912101 DOI: 10.1016/j.bbamem.2017.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 11/18/2022]
Abstract
RasGRP comprises a family of guanine nucleotide exchange factors, regulating the dissociation of GDP from Ras GTPases to enhance the formation of the active GTP-bound form. RasGRP1 possesses REM (Ras exchange), GEF (catalytic), EF-hand, C1, SuPT (suppressor of PT), and PT (plasma membrane-targeting) domains, among which the C1 domain drives membrane localization in response to diacylglycerol or phorbol ester and the PT domain recognizes phosphoinositides. The homologous family member RasGRP3 shows less plasma membrane localization. The objective of this study was to explore the role of the different domains of RasGRP3 in membrane translocation in response to phorbol esters. The full-length RasGRP3 shows limited translocation to the plasma membrane in response to PMA, even when the basic hydrophobic cluster in the PT domain, reported to be critical for RasGRP1 translocation to endogenous activators, is mutated to resemble that of RasGRP1. Moreover, exchange of the C-termini (SuPT-PT domain) of the two proteins had little effect on their plasma membrane translocation. On the other hand, while the C1 domain of RasGRP3 alone showed partial plasma membrane translocation, truncated RasGRP3 constructs, which contain the PT domain and are missing the REM, showed stronger translocation, indicating that the REM of RasGRP3 was a suppressor of its membrane interaction. The REM of RasGRP1 failed to show comparable suppression of RasGRP3 translocation. The marked differences between RasGRP3 and RasGRP1 in membrane interaction necessarily will contribute to their different behavior in cells and are relevant to the design of selective ligands as potential therapeutic agents.
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Affiliation(s)
- Agnes Czikora
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, United States
| | - Noemi Kedei
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, United States
| | - Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science (BEPS), National Institute of Biomedical Imaging and Bioengineering (NIBIB) National Institutes of Health, United States
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, United States.
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Daley SR, Coakley KM, Hu DY, Randall KL, Jenne CN, Limnander A, Myers DR, Polakos NK, Enders A, Roots C, Balakishnan B, Miosge LA, Sjollema G, Bertram EM, Field MA, Shao Y, Andrews TD, Whittle B, Barnes SW, Walker JR, Cyster JG, Goodnow CC, Roose JP. Rasgrp1 mutation increases naive T-cell CD44 expression and drives mTOR-dependent accumulation of Helios⁺ T cells and autoantibodies. eLife 2013; 2:e01020. [PMID: 24336796 PMCID: PMC3858598 DOI: 10.7554/elife.01020] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Missense variants are a major source of human genetic variation. Here we analyze a new mouse missense variant, Rasgrp1Anaef, with an ENU-mutated EF hand in the Rasgrp1 Ras guanine nucleotide exchange factor. Rasgrp1Anaef mice exhibit anti-nuclear autoantibodies and gradually accumulate a CD44hi Helios+ PD-1+ CD4+ T cell population that is dependent on B cells. Despite reduced Rasgrp1-Ras-ERK activation in vitro, thymocyte selection in Rasgrp1Anaef is mostly normal in vivo, although CD44 is overexpressed on naïve thymocytes and T cells in a T-cell-autonomous manner. We identify CD44 expression as a sensitive reporter of tonic mTOR-S6 kinase signaling through a novel mouse strain, chino, with a reduction-of-function mutation in Mtor. Elevated tonic mTOR-S6 signaling occurs in Rasgrp1Anaef naïve CD4+ T cells. CD44 expression, CD4+ T cell subset ratios and serum autoantibodies all returned to normal in Rasgrp1AnaefMtorchino double-mutant mice, demonstrating that increased mTOR activity is essential for the Rasgrp1Anaef T cell dysregulation. DOI:http://dx.doi.org/10.7554/eLife.01020.001 Our DNA contains more than three billion nucleotides. Each of these nucleotides can be an A, C, G or T, and groups of three neighboring nucleotides within our DNA are used to represent the 20 amino acids that are used to make proteins. This means that changing just one nucleotide can cause one amino acid to be replaced by a different amino acid in the protein encoded by that stretch of DNA: AAA and AAG code for the amino acid lysine, for example, but AAC and AAT code for asparagine. Known as missense gene variants, these changes can also increase or decrease the expression of the gene. Every person has thousands of missense gene variants, including about 12,000 inherited from their parents. Sometimes these variants have no consequence, but they can be harmful if replacing the correct amino acid with a different amino acid prevents the protein from performing an important task. In particular, missense gene variants in genes that encode immune system proteins are likely to play a role in diseases of the immune system. For example, variants near a gene called Rasgrp1 have been linked to two autoimmune diseases – type 1 diabetes and Graves’ disease—in which the immune system mistakenly attacks the body’s own cells and tissues. Now Daley et al. have shed new light on the mechanism by which a missense gene variant in Rasgrp1 can cause autoimmune diseases. Mice with this mutation show signs of autoimmune disease, but their T cells—white blood cells that have a central role in the immune system – develop normally despite this mutation. Instead, Daley et al. found that a specific type of T cell, called T helper cells, accumulated in large numbers in the mutant mice and stimulated cells of a third type—immune cells called B cells—to produce autoantibodies. The production of autoantibodies is a common feature of autoimmune diseases. Daley et al. traced the origins of the T helper cells to excessive activity on a signaling pathway that involves a protein called mTOR, and went on to show that treatment with the drug rapamycin counteracted the accumulation of the T helper cells and reduced the level of autoimmune activity. In addition to exemplifying how changing just one amino acid change can have a profound effect, the work of Daley et al. is an attractive model for exploring how missense gene variants in people can contribute to autoimmune diseases. DOI:http://dx.doi.org/10.7554/eLife.01020.002
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Affiliation(s)
- Stephen R Daley
- Department of Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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10
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Ksionda O, Limnander A, Roose JP. RasGRP Ras guanine nucleotide exchange factors in cancer. FRONTIERS IN BIOLOGY 2013; 8:508-532. [PMID: 24744772 PMCID: PMC3987922 DOI: 10.1007/s11515-013-1276-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RasGRP proteins are activators of Ras and other related small GTPases by the virtue of functioning as guanine nucleotide exchange factors (GEFs). In vertebrates, four RasGRP family members have been described. RasGRP-1 through -4 share many structural domains but there are also subtle differences between each of the different family members. Whereas SOS RasGEFs are ubiquitously expressed, RasGRP proteins are expressed in distinct patterns, such as in different cells of the hematopoietic system and in the brain. Most studies have concentrated on the role of RasGRP proteins in the development and function of immune cell types because of the predominant RasGRP expression profiles in these cells and the immune phenotypes of mice deficient for Rasgrp genes. However, more recent studies demonstrate that RasGRPs also play an important role in tumorigenesis. Examples are skin- and hematological-cancers but also solid malignancies such as melanoma or prostate cancer. These novel studies bring up many new and unanswered questions related to the molecular mechanism of RasGRP-driven oncogenesis, such as new receptor systems that RasGRP appears to respond to as well as regulatory mechanism for RasGRP expression that appear to be perturbed in these cancers. Here we will review some of the known aspects of RasGRP biology in lymphocytes and will discuss the exciting new notion that RasGRP Ras exchange factors play a role in oncogenesis downstream of various growth factor receptors.
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Affiliation(s)
- Olga Ksionda
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andre Limnander
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeroen P. Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
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11
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Jun JE, Rubio I, Roose JP. Regulation of ras exchange factors and cellular localization of ras activation by lipid messengers in T cells. Front Immunol 2013; 4:239. [PMID: 24027568 PMCID: PMC3762125 DOI: 10.3389/fimmu.2013.00239] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 08/02/2013] [Indexed: 11/17/2022] Open
Abstract
The Ras-MAPK signaling pathway is highly conserved throughout evolution and is activated downstream of a wide range of receptor stimuli. Ras guanine nucleotide exchange factors (RasGEFs) catalyze GTP loading of Ras and play a pivotal role in regulating receptor-ligand induced Ras activity. In T cells, three families of functionally important RasGEFs are expressed: RasGRF, RasGRP, and Son of Sevenless (SOS)-family GEFs. Early on it was recognized that Ras activation is critical for T cell development and that the RasGEFs play an important role herein. More recent work has revealed that nuances in Ras activation appear to significantly impact T cell development and selection. These nuances include distinct biochemical patterns of analog versus digital Ras activation, differences in cellular localization of Ras activation, and intricate interplays between the RasGEFs during distinct T cell developmental stages as revealed by various new mouse models. In many instances, the exact nature of these nuances in Ras activation or how these may result from fine-tuning of the RasGEFs is not understood. One large group of biomolecules critically involved in the control of RasGEFs functions are lipid second messengers. Multiple, yet distinct lipid products are generated following T cell receptor (TCR) stimulation and bind to different domains in the RasGRP and SOS RasGEFs to facilitate the activation of the membrane-anchored Ras GTPases. In this review we highlight how different lipid-based elements are generated by various enzymes downstream of the TCR and other receptors and how these dynamic and interrelated lipid products may fine-tune Ras activation by RasGEFs in developing T cells.
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Affiliation(s)
- Jesse E Jun
- Department of Anatomy, University of California San Francisco , San Francisco, CA , USA
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12
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Iwig JS, Vercoulen Y, Das R, Barros T, Limnander A, Che Y, Pelton JG, Wemmer DE, Roose JP, Kuriyan J. Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1. eLife 2013; 2:e00813. [PMID: 23908768 PMCID: PMC3728621 DOI: 10.7554/elife.00813] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/18/2013] [Indexed: 11/13/2022] Open
Abstract
RasGRP1 and SOS are Ras-specific nucleotide exchange factors that have distinct roles in lymphocyte development. RasGRP1 is important in some cancers and autoimmune diseases but, in contrast to SOS, its regulatory mechanisms are poorly understood. Activating signals lead to the membrane recruitment of RasGRP1 and Ras engagement, but it is unclear how interactions between RasGRP1 and Ras are suppressed in the absence of such signals. We present a crystal structure of a fragment of RasGRP1 in which the Ras-binding site is blocked by an interdomain linker and the membrane-interaction surface of RasGRP1 is hidden within a dimerization interface that may be stabilized by the C-terminal oligomerization domain. NMR data demonstrate that calcium binding to the regulatory module generates substantial conformational changes that are incompatible with the inactive assembly. These features allow RasGRP1 to be maintained in an inactive state that is poised for activation by calcium and membrane-localization signals. DOI:http://dx.doi.org/10.7554/eLife.00813.001 Individual cells within the human body must grow, divide or specialize to perform the tasks required of them. The fates of these cells are often directed by proteins in the Ras family, which detect signals from elsewhere in the body and orchestrate responses within each cell. The activities of these proteins must be tightly controlled, because cancers and developmental diseases can result if Ras proteins are not properly regulated. Binding to the small molecule GTP activates Ras and causes conformational changes that allow it to interact with other proteins in various signaling pathways in the cell. GTP is loaded into Ras by proteins called nucleotide exchange factors, which can replace ‘used’ nucleotides with ‘fresh’ ones to activate Ras. These nucleotide exchange factors are also tightly regulated. For example, the genes for many exchange factors are only switched on after particular signals are received, which can restrict their presence to defined times and locations (e.g., cells or tissues). Also, when activating signals are absent, nucleotide exchange factors commonly reside in the cytoplasm, whereas the Ras proteins remain bound to lipid membranes inside the cell. RasGRP1 is a nucleotide exchange factor that controls the development of immune cells, and leukemia and lupus can result if it is not regulated correctly. However, many questions about RasGRP1 remain unanswered, including how it is able to remain inactive, and how it is activated by various different signals. Iwig et al. have now revealed the mechanisms through which RasGRP1 suppresses Ras signaling in immune cells by solving the structures of two fragments of RasGRP1 and then using a combination of structural, biochemical and cell-based methods to explore how it is activated. These analyses revealed that inactive RasGRP1 adopts a conformation in which one of its regulatory elements blocks access to the Ras binding site. Surprisingly, RasGRP1 can form dimers; this hides the portions of the protein that associate with the membrane and thereby keeps RasGRP1 away from Ras. Iwig et al. also found that two signals, calcium ions and a lipid called diacylglycerol, overcome these inhibitory mechanisms by changing the conformation of RasGRP1 and recruiting it to the membrane. These studies provide a framework for understanding how disease-associated mutations in RasGRP1 bypass the regulatory mechanisms that insure proper immune cell development, and will be critical for developing therapeutic agents that inhibit RasGRP1 activity. DOI:http://dx.doi.org/10.7554/eLife.00813.002
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Affiliation(s)
- Jeffrey S Iwig
- Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , United States ; California Institute for Quantitative Biosciences , University of California, Berkeley , Berkeley , United States
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Regulation of RasGRP1 function in T cell development and activation by its unique tail domain. PLoS One 2012; 7:e38796. [PMID: 22719950 PMCID: PMC3373593 DOI: 10.1371/journal.pone.0038796] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/07/2012] [Indexed: 12/30/2022] Open
Abstract
The Ras-guanyl nucleotide exchange factor RasGRP1 plays a critical role in T cell receptor-mediated Erk activation. Previous studies have emphasized the importance of RasGRP1 in the positive selection of thymocytes, activation of T cells, and control of autoimmunity. RasGRP1 consists of a number of well-characterized domains, which it shares with its other family members; however, RasGRP1 also contains an ∼200 residue-long tail domain, the function of which is unknown. To elucidate the physiological role of this domain, we generated knock-in mice expressing RasGRP1 without the tail domain. Further analysis of these knock-in mice showed that thymocytes lacking the tail domain of RasGRP1 underwent aberrant thymic selection and, following TCR stimulation, were unable to activate Erk. Furthermore, the deletion of the tail domain led to enhanced CD4+ T cell expansion in aged mice, as well as the production of autoantibodies. Mechanistically, the tail-deleted form of RasGRP1 was not able to traffic to the cell membrane following stimulation, indicating a potential reason for its inability to activate Erk. While the DAG-binding C1 domain of RasGRP1 has long been recognized as an important factor mediating Erk activation, we have revealed the physiological relevance of the tail domain in RasGRP1 function and control of Erk signaling.
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14
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Abstract
Ras guanyl nucleotide releasing proteins (RasGRPs) are guanyl nucleotide exchange factors that activate Ras and related GTPases such as Rap. Like Sos proteins, RasGRPs have a catalytic region composed of a Ras exchange motif (REM) and a CDC25 domain. RasGRPs also possess a pair of atypical EF hands that may bind calcium in vivo and a C1 domain resembling the diacylglycerol (DAG)-binding domain of protein kinase C. DAG directly activates RasGRPs by a membrane recruitment mechanism as well as indirectly by PKC-mediated phosphorylation. RasGRPs are prominently expressed in blood cells. RasGRP1 acts downstream of TCR, while RasGRP1 and RasGRP3 both act downstream of BCR. Together, they regulate Ras in adaptive immune cells. RasGRP2, through Rap, plays a role in controlling platelet adhesion, while RasGRP4 controls Ras activation in mast cells. RasGRP malfunction likely contributes to autoimmunity and may contribute to blood malignancies. RasGRPs might prove to be viable drug targets. The intracellular site of RasGRP action and the relationship between RasGRPs and other Ras regulatory mechanisms are subjects of lively debate.
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Affiliation(s)
- James C Stone
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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15
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Limnander A, Weiss A. Ca-dependent Ras/Erk signaling mediates negative selection of autoreactive B cells. Small GTPases 2011; 2:282-288. [PMID: 22292132 DOI: 10.4161/sgtp.2.5.17794] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 08/08/2011] [Accepted: 08/18/2011] [Indexed: 12/17/2022] Open
Abstract
Signaling via the Ras/Erk pathway has long been recognized to be critical in lymphocyte development and function, yet the mechanisms that control the distinct functional outputs of this pathway in different cellular contexts remain poorly understood. Our recent results have demonstrated unexpected involvement of Ras/Erk signaling in the sensitization of B cells to apoptosis in order to eliminate autoreactive cells. Increases in cytosolic Ca(2+) are necessary and sufficient to induce activation of this Ras/Erk pathway, and the biochemical events involved in its activation are different from the ones involved in diacylglycerol (DAG)-mediated Ras/Erk activation. Developmental regulation of upstream mediators of these distinct pathways contributes to their predominant activation at different stages of B cell development. These findings have revealed a mechanism by which antigen stimulation can activate distinct Ras/Erk pathways at different developmental stages to mediate appropriate functional outputs that control the selection, development and activation of B cells. Despite these recent findings, however, much remains to be learned about the molecular mechanisms that confer functional specificity to common Ras/Erk signaling modules.
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Affiliation(s)
- Andre Limnander
- Department of Medicine; Howard Hughes Medical Institute; Rosalind Russell Medical Research Center for Arthritis; University of California at San Francisco; San Francisco, CA USA
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16
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Chen L, Fu Y, Ren M, Xiao B, Rubin CS. A RasGRP, C. elegans RGEF-1b, couples external stimuli to behavior by activating LET-60 (Ras) in sensory neurons. Neuron 2011; 70:51-65. [PMID: 21482356 PMCID: PMC3081643 DOI: 10.1016/j.neuron.2011.02.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2011] [Indexed: 11/17/2022]
Abstract
RasGRPs, which load GTP onto Ras and Rap1, are expressed in vertebrate and invertebrate neurons. The functions, regulation, and mechanisms of action of neuronal RasGRPs are unknown. Here, we show how C. elegans RGEF-1b, a prototypical neuronal RasGRP, regulates a critical behavior. Chemotaxis to volatile odorants was disrupted in RGEF-1b-deficient (rgef-1⁻/⁻) animals and wild-type animals expressing dominant-negative RGEF-1b in AWC sensory neurons. AWC-specific expression of RGEF-1b-GFP restored chemotaxis in rgef-1⁻/⁻ mutants. Signals disseminated by RGEF-1b in AWC neurons activated a LET-60 (Ras)-MPK-1 (ERK) signaling cascade. Other RGEF-1b and LET-60 effectors were dispensable for chemotaxis. A bifunctional C1 domain controlled intracellular targeting and catalytic activity of RGEF-1b and was essential for sensory signaling in vivo. Chemotaxis was unaffected when Ca²+-binding EF hands and a conserved phosphorylation site of RGEF-1b were inactivated. Diacylglycerol-activated RGEF-1b links external stimuli (odorants) to behavior (chemotaxis) by activating the LET-60-MPK-1 pathway in specific neurons.
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Affiliation(s)
- Lu Chen
- Department of Molecular Pharmacology, Atran Laboratories, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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The human Rgr oncogene is overexpressed in T-cell malignancies and induces transformation by acting as a GEF for Ras and Ral. Oncogene 2011; 30:3661-71. [PMID: 21441953 PMCID: PMC3126870 DOI: 10.1038/onc.2011.93] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Ras superfamily of GTPases is involved in the modification of many cellular processes including cellular motility, proliferation and differentiation. Our laboratory has previously identified the RalGDS-related (Rgr) oncogene in a DMBA (7,12-dimethylbenz[α]anthracene)-induced rabbit squamous cell carcinoma and its human orthologue, hRgr. In this study, we analyzed the expression levels of the human hRgr transcript in a panel of human hematopoietic malignancies and found that a truncated form (diseased-truncated (Dtr-hrgr)) was significantly overexpressed in many T-cell-derived neoplasms. Although the Rgr proto-oncogene belongs to the RalGDS family of guanine nucleotide exchange factors (GEFs), we show that upon the introduction of hRgr into fibroblast cell lines, it is able to elicit the activation of both Ral and Ras GTPases. Moreover, in vitro guanine nucleotide exchange assays confirm that hRgr promotes Ral and Ras activation through GDP dissociation, which is a critical characteristic of GEF proteins. hRgr has guanine nucleotide exchange activity for both small GTPases and this activity was reduced when a point mutation within the catalytic domain (CDC25) of the protein, (cd) Dtr-hRgr, was utilized. These observations prompted the analysis of the biological effects of hRgr and (cd) hRgr expression in cultured cells. Here, we show that hRgr increases proliferation in low serum, increases invasion, reduces anchorage dependence and promotes the progression into the S phase of the cell cycle; properties that are abolished or severely reduced in the presence of the catalytic dead mutant. We conclude that the ability of hRgr to activate both Ral and Ras is responsible for its transformation-inducing phenotype and it could be an important contributor in the development of some T-cell malignancies.
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Zahedi B, Goo HJ, Beaulieu N, Tazmini G, Kay RJ, Cornell RB. Phosphoinositide 3-kinase regulates plasma membrane targeting of the Ras-specific exchange factor RasGRP1. J Biol Chem 2011; 286:12712-23. [PMID: 21285350 DOI: 10.1074/jbc.m110.189605] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Receptor-induced targeting of exchange factors to specific cellular membranes is the predominant mechanism for initiating and compartmentalizing signal transduction by Ras GTPases. The exchange factor RasGRP1 has a C1 domain that binds the lipid diacylglycerol and thus can potentially mediate membrane localization in response to receptors that are coupled to diacylglycerol-generating phospholipase Cs. However, the C1 domain is insufficient for targeting RasGRP1 to the plasma membrane. We found that a basic/hydrophobic cluster of amino acids within the plasma membrane-targeting domain of RasGRP1 is instead responsible for plasma membrane targeting. This basic/hydrophobic cluster binds directly to phospholipid vesicles containing phosphoinositides via electrostatic interactions with polyanionic phosphoinositide headgroups and insertion of a tryptophan into the lipid bilayer. B cell antigen receptor ligation and other stimuli induce plasma membrane targeting of RasGRP1 by activating the phosphoinositide 3-kinase signaling pathway, which generates phosphoinositides within the plasma membrane. Direct detection of phosphoinositides by the basic/hydrophobic cluster of RasGRP1 provides a novel mechanism for coupling and co-compartmentalizing phosphoinositide 3-kinase and Ras signaling and, in coordination with diacylglycerol detection by the C1 domain, gives RasGRP1 the potential to serve as an integrator of converging signals from the phosphoinositide 3-kinase and phospholipase C pathways.
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Affiliation(s)
- Bari Zahedi
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3
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