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Mukherjee S, Rigaud S, Seok SC, Fu G, Prochenka A, Dworkin M, Gascoigne NRJ, Vieland VJ, Sauer K, Das J. In silico modeling of Itk activation kinetics in thymocytes suggests competing positive and negative IP4 mediated feedbacks increase robustness. PLoS One 2013; 8:e73937. [PMID: 24066087 PMCID: PMC3774804 DOI: 10.1371/journal.pone.0073937] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/25/2013] [Indexed: 12/29/2022] Open
Abstract
The inositol-phosphate messenger inositol(1,3,4,5)tetrakisphosphate (IP4) is essential for thymocyte positive selection by regulating plasma-membrane association of the protein tyrosine kinase Itk downstream of the T cell receptor (TCR). IP4 can act as a soluble analog of the phosphoinositide 3-kinase (PI3K) membrane lipid product phosphatidylinositol(3,4,5)trisphosphate (PIP3). PIP3 recruits signaling proteins such as Itk to cellular membranes by binding to PH and other domains. In thymocytes, low-dose IP4 binding to the Itk PH domain surprisingly promoted and high-dose IP4 inhibited PIP3 binding of Itk PH domains. However, the mechanisms that underlie the regulation of membrane recruitment of Itk by IP4 and PIP3 remain unclear. The distinct Itk PH domain ability to oligomerize is consistent with a cooperative-allosteric mode of IP4 action. However, other possibilities cannot be ruled out due to difficulties in quantitatively measuring the interactions between Itk, IP4 and PIP3, and in generating non-oligomerizing Itk PH domain mutants. This has hindered a full mechanistic understanding of how IP4 controls Itk function. By combining experimentally measured kinetics of PLCγ1 phosphorylation by Itk with in silico modeling of multiple Itk signaling circuits and a maximum entropy (MaxEnt) based computational approach, we show that those in silico models which are most robust against variations of protein and lipid expression levels and kinetic rates at the single cell level share a cooperative-allosteric mode of Itk regulation by IP4 involving oligomeric Itk PH domains at the plasma membrane. This identifies MaxEnt as an excellent tool for quantifying robustness for complex TCR signaling circuits and provides testable predictions to further elucidate a controversial mechanism of PIP3 signaling.
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Affiliation(s)
- Sayak Mukherjee
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Stephanie Rigaud
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sang-Cheol Seok
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Guo Fu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Agnieszka Prochenka
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Michael Dworkin
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Mathematics, The Ohio State University, Columbus, Ohio, United States of America
| | - Nicholas R. J. Gascoigne
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Veronica J. Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Statistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Karsten Sauer
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (KS); (JD)
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Physics, The Ohio State University, Columbus, Ohio, United States of America
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (KS); (JD)
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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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Li C, Han J, Yao Q, Zou C, Xu Y, Zhang C, Shang D, Zhou L, Zou C, Sun Z, Li J, Zhang Y, Yang H, Gao X, Li X. Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways. Nucleic Acids Res 2013; 41:e101. [PMID: 23482392 PMCID: PMC3643575 DOI: 10.1093/nar/gkt161] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Various 'omics' technologies, including microarrays and gas chromatography mass spectrometry, can be used to identify hundreds of interesting genes, proteins and metabolites, such as differential genes, proteins and metabolites associated with diseases. Identifying metabolic pathways has become an invaluable aid to understanding the genes and metabolites associated with studying conditions. However, the classical methods used to identify pathways fail to accurately consider joint power of interesting gene/metabolite and the key regions impacted by them within metabolic pathways. In this study, we propose a powerful analytical method referred to as Subpathway-GM for the identification of metabolic subpathways. This provides a more accurate level of pathway analysis by integrating information from genes and metabolites, and their positions and cascade regions within the given pathway. We analyzed two colorectal cancer and one metastatic prostate cancer data sets and demonstrated that Subpathway-GM was able to identify disease-relevant subpathways whose corresponding entire pathways might be ignored using classical entire pathway identification methods. Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways.
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Affiliation(s)
- Chunquan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
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Abstract
Natural killer (NK) cells have important functions in cancer immunosurveillance, BM allograft rejection, fighting infections, tissue homeostasis, and reproduction. NK cell-based therapies are promising treatments for blood cancers. Overcoming their currently limited efficacy requires a better understanding of the molecular mechanisms controlling NK cell development and dampening their effector functions. NK cells recognize the loss of self-antigens or up-regulation of stress-induced ligands on pathogen-infected or tumor cells through invariant NK cell receptors (NKRs), and then kill such stressed cells. Two second-messenger pathways downstream of NKRs are required for NK cell maturation and effector responses: PIP(3) generation by PI3K and generation of diacylglycerol and IP(3) by phospholipase-Cγ (PLCγ). In the present study, we identify a novel role for the phosphorylated IP(3) metabolite inositol (1,3,4,5)tetrakisphosphate (IP(4)) in NK cells. IP(4) promotes NK cell terminal differentiation and acquisition of a mature NKR repertoire. However, in mature NK cells, IP(4) limits NKR-induced IFNγ secretion, granule exocytosis, and target-cell killing, in part by inhibiting the PIP(3) effector-kinase Akt. This identifies IP(4) as an important novel regulator of NK cell development and function and expands our understanding of the therapeutically important mechanisms dampening NK cell responses. Our results further suggest that PI3K regulation by soluble IP(4) is a broadly important signaling paradigm.
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Li C, Shang D, Wang Y, Li J, Han J, Wang S, Yao Q, Wang Y, Zhang Y, Zhang C, Xu Y, Jiang W, Li X. Characterizing the network of drugs and their affected metabolic subpathways. PLoS One 2012; 7:e47326. [PMID: 23112813 PMCID: PMC3480395 DOI: 10.1371/journal.pone.0047326] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 09/14/2012] [Indexed: 12/21/2022] Open
Abstract
A fundamental issue in biology and medicine is illustration of the overall drug impact which is always the consequence of changes in local regions of metabolic pathways (subpathways). To gain insights into the global relationship between drugs and their affected metabolic subpathways, we constructed a drug-metabolic subpathway network (DRSN). This network included 3925 significant drug-metabolic subpathway associations representing drug dual effects. Through analyses based on network biology, we found that if drugs were linked to the same subpathways in the DRSN, they tended to share the same indications and side effects. Furthermore, if drugs shared more subpathways, they tended to share more side effects. We then calculated the association score by integrating drug-affected subpathways and disease-related subpathways to quantify the extent of the associations between each drug class and disease class. The results showed some close drug-disease associations such as sex hormone drugs and cancer suggesting drug dual effects. Surprisingly, most drugs displayed close associations with their side effects rather than their indications. To further investigate the mechanism of drug dual effects, we classified all the subpathways in the DRSN into therapeutic and non-therapeutic subpathways representing drug therapeutic effects and side effects. Compared to drug side effects, the therapeutic effects tended to work through tissue-specific genes and these genes tend to be expressed in the adrenal gland, liver and kidney; while drug side effects always occurred in the liver, bone marrow and trachea. Taken together, the DRSN could provide great insights into understanding the global relationship between drugs and metabolic subpathways.
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Affiliation(s)
- Chunquan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Yan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Jing Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Shuyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Qianlan Yao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Yingying Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People’s Republic of China
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Shears SB, Ganapathi SB, Gokhale NA, Schenk TMH, Wang H, Weaver JD, Zaremba A, Zhou Y. Defining signal transduction by inositol phosphates. Subcell Biochem 2012; 59:389-412. [PMID: 22374098 PMCID: PMC3925325 DOI: 10.1007/978-94-007-3015-1_13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ins(1,4,5)P(3) is a classical intracellular messenger: stimulus-dependent changes in its levels elicits biological effects through its release of intracellular Ca(2+) stores. The Ins(1,4,5)P(3) response is "switched off" by its metabolism to a range of additional inositol phosphates. These metabolites have themselves come to be collectively described as a signaling "family". The validity of that latter definition is critically examined in this review. That is, we assess the strength of the hypothesis that Ins(1,4,5)P(3) metabolites are themselves "classical" signals. Put another way, what is the evidence that the biological function of a particular inositol phosphate depends upon stimulus dependent changes in its levels? In this assessment, examples of an inositol phosphate acting as a cofactor (i.e. its function is not stimulus-dependent) do not satisfy our signaling criteria. We conclude that Ins(3,4,5,6)P(4) is, to date, the only Ins(1,4,5)P(3) metabolite that has been validated to act as a second messenger.
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Key Words
- adenosine deaminase
- akt
- β-cells
- calcium
- camp
- camkii
- chloride channel
- clc3
- compartmentalization
- dna repair
- endosomes
- erk
- frizzled receptor
- gap1ip4bp
- mrna export
- ins(1,4,5)p3
- ins(1,4,5)p4 receptor
- ins(1,3,4)p3
- ins(1,3,4,5)p4
- ins(1,3,4,5)p4 receptor
- ins(1,4,5,6)p4
- ins(3,4,5,6)p4
- ins(1,3,4,5,6)p5
- insp6
- insulin
- ipmk
- ipk2
- ip5k
- itp
- itpk1
- itpkb
- lymphocytes
- ku
- neutrophils
- protein phosphatase
- ptdins(4,5)p2
- ptdins(3,4,5)p3
- ph domain
- pten
- rasa3
- transcription
- wnt ligand
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Section, Laboratory of Signal Transduction, NIEHS, NIH, DHHS, Research Triangle Park, 27709, NC, USA, USA,
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Genini S, Badaoui B, Sclep G, Bishop SC, Waddington D, Pinard van der Laan MH, Klopp C, Cabau C, Seyfert HM, Petzl W, Jensen K, Glass EJ, de Greeff A, Smith HE, Smits MA, Olsaker I, Boman GM, Pisoni G, Moroni P, Castiglioni B, Cremonesi P, Del Corvo M, Foulon E, Foucras G, Rupp R, Giuffra E. Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources. BMC Genomics 2011; 12:225. [PMID: 21569310 PMCID: PMC3118214 DOI: 10.1186/1471-2164-12-225] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 05/11/2011] [Indexed: 12/30/2022] Open
Abstract
Background Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on single studies. Using the program Pointillist, we performed meta-analysis of transcription-profiling data from six independent studies of infections with mammary gland pathogens, including samples from cattle challenged in vivo with S. aureus, E. coli, and S. uberis, samples from goats challenged in vivo with S. aureus, as well as cattle macrophages and ovine dendritic cells infected in vitro with S. aureus. We combined different time points from those studies, testing different responses to mastitis infection: overall (common signature), early stage, late stage, and cattle-specific. Results Ingenuity Pathway Analysis of affected genes showed that the four meta-analysis combinations share biological functions and pathways (e.g. protein ubiquitination and polyamine regulation) which are intrinsic to the general disease response. In the overall response, pathways related to immune response and inflammation, as well as biological functions related to lipid metabolism were altered. This latter observation is consistent with the milk fat content depression commonly observed during mastitis infection. Complementarities between early and late stage responses were found, with a prominence of metabolic and stress signals in the early stage and of the immune response related to the lipid metabolism in the late stage; both mechanisms apparently modulated by few genes, including XBP1 and SREBF1. The cattle-specific response was characterized by alteration of the immune response and by modification of lipid metabolism. Comparison of E. coli and S. aureus infections in cattle in vivo revealed that affected genes showing opposite regulation had the same altered biological functions and provided evidence that E. coli caused a stronger host response. Conclusions This meta-analysis approach reinforces previous findings but also reveals several novel themes, including the involvement of genes, biological functions, and pathways that were not identified in individual studies. As such, it provides an interesting proof of principle for future studies combining information from diverse heterogeneous sources.
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Affiliation(s)
- Sem Genini
- Parco Tecnologico Padano - CERSA, Via Einstein, 26900 Lodi, Italy.
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Kuo HC, Lin YJ, Juo SHH, Hsu YW, Chen WC, Yang KD, Liang CD, Yang S, Chao MC, Yu HR, Wang S, Lin LY, Chang WC. Lack of association between ORAI1/CRACM1 gene polymorphisms and Kawasaki disease in the Taiwanese children. J Clin Immunol 2011; 31:650-5. [PMID: 21487896 DOI: 10.1007/s10875-011-9524-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Accepted: 03/28/2011] [Indexed: 02/01/2023]
Abstract
OBJECTIVE Kawasaki disease (KD) is characterized by systemic vasculitis of an unknown cause. A previous study has indicated that a polymorphism of the inositol 1,4,5-trisphosphate 3-kinase C (ITPKC) gene is involved in the susceptibility to KD. ORAI (also known as CRACM1) is one of the components of store-operated calcium channels involved in regulating immune and inflammatory reactions. This study was conducted to investigate if polymorphisms in ORAI1/CRACM1, a gene downstream from ITPKC, are associated with KD susceptibility and clinical outcomes. MATERIALS AND METHODS A total of 1,056 subjects (341 KD patients and 715 controls) were investigated to identify five tagging single nucleotide polymorphisms (tSNPs) in ORAI1/CRACM1 (rs12313273, rs6486795, rs7135617, rs12320939, and rs712853) by using the TaqMan Allelic Discrimination assay. RESULTS No significant associations between genotype and allele frequency of the five ORAI1/CRACM1 tSNPs were observed in the KD patients and controls. In KD patients, no significant associations between ORAI1/CRACM1 polymorphisms and coronary artery lesion (CAL) formation or intravenous immunoglobulin (IVIG) treatment response were observed. The results from haplotype analysis were insignificant. CONCLUSIONS This study showed for the first time that ORAI1/CRACM1 polymorphisms are not associated with KD susceptibility, CAL formation, or IVIG treatment response in the Taiwanese population.
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Affiliation(s)
- Ho-Chang Kuo
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Kaohsiung, Taiwan
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Abstract
Second messenger molecules relay, amplify, and diversify cell surface receptor signals. Two important examples are phosphorylated D-myo-inositol derivatives, such as phosphoinositide lipids within cellular membranes, and soluble inositol phosphates. Here, we review how phosphoinositide metabolism generates multiple second messengers with important roles in T-cell development and function. They include soluble inositol(1,4,5)trisphosphate, long known for its Ca(2+)-mobilizing function, and phosphatidylinositol(3,4,5)trisphosphate, whose generation by phosphoinositide 3-kinase and turnover by the phosphatases PTEN and SHIP control a key "hub" of TCR signaling. More recent studies unveiled important second messenger functions for diacylglycerol, phosphatidic acid, and soluble inositol(1,3,4,5)tetrakisphosphate (IP(4)) in immune cells. Inositol(1,3,4,5)tetrakisphosphate acts as a soluble phosphatidylinositol(3,4,5)trisphosphate analog to control protein membrane recruitment. We propose that phosphoinositide lipids and soluble inositol phosphates (IPs) can act as complementary partners whose interplay could have broadly important roles in cellular signaling.
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Affiliation(s)
- Yina H Huang
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Mackay F, Figgett WA, Saulep D, Lepage M, Hibbs ML. B-cell stage and context-dependent requirements for survival signals from BAFF and the B-cell receptor. Immunol Rev 2010; 237:205-25. [DOI: 10.1111/j.1600-065x.2010.00944.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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