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Mohl DA, Lagies S, Zodel K, Zumkeller M, Peighambari A, Ganner A, Plattner DA, Neumann-Haefelin E, Adlesic M, Frew IJ, Kammerer B. Integrated Metabolomic and Transcriptomic Analysis of Modified Nucleosides for Biomarker Discovery in Clear Cell Renal Cell Carcinoma. Cells 2023; 12:cells12081102. [PMID: 37190010 DOI: 10.3390/cells12081102] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers. The biallelic inactivation of the von Hippel-Lindau tumor suppressor gene (VHL) is the truncal driver mutation of most cases of ccRCC. Cancer cells are metabolically reprogrammed and excrete modified nucleosides in larger amounts due to their increased RNA turnover. Modified nucleosides occur in RNAs and cannot be recycled by salvage pathways. Their potential as biomarkers has been demonstrated for breast or pancreatic cancer. To assess their suitability as biomarkers in ccRCC, we used an established murine ccRCC model, harboring Vhl, Trp53 and Rb1 (VPR) knockouts. Cell culture media of this ccRCC model and primary murine proximal tubular epithelial cells (PECs) were investigated by HPLC coupled to triple-quadrupole mass spectrometry using multiple-reaction monitoring. VPR cell lines were significantly distinguishable from PEC cell lines and excreted higher amounts of modified nucleosides such as pseudouridine, 5-methylcytidine or 2'-O-methylcytidine. The method's reliability was confirmed in serum-starved VPR cells. RNA-sequencing revealed the upregulation of specific enzymes responsible for the formation of those modified nucleosides in the ccRCC model. These enzymes included Nsun2, Nsun5, Pus1, Pus7, Naf1 and Fbl. In this study, we identified potential biomarkers for ccRCC for validation in clinical trials.
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Affiliation(s)
- Daniel A Mohl
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Simon Lagies
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | - Kyra Zodel
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Matthias Zumkeller
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Asin Peighambari
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Athina Ganner
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Dietmar A Plattner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Elke Neumann-Haefelin
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Mojca Adlesic
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Ian J Frew
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Signalling Research Centre BIOSS, University of Freiburg, 79104 Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Faculty of Medicine and Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Bernd Kammerer
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centre BIOSS, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
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Lagies S, Pan D, Mohl DA, Plattner DA, Gentle IE, Kammerer B. Mitochondrial Metabolomics of Sym1-Depleted Yeast Cells Revealed Them to Be Lysine Auxotroph. Cells 2023; 12:692. [PMID: 36899826 PMCID: PMC10000845 DOI: 10.3390/cells12050692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Metabolomics has expanded from cellular to subcellular level to elucidate subcellular compartmentalization. By applying isolated mitochondria to metabolome analysis, the hallmark of mitochondrial metabolites has been unraveled, showing compartment-specific distribution and regulation of metabolites. This method was employed in this work to study a mitochondrial inner membrane protein Sym1, whose human ortholog MPV17 is related to mitochondria DNA depletion syndrome. Gas chromatography-mass spectrometry-based metabolic profiling was combined with targeted liquid chromatography-mass spectrometry analysis to cover more metabolites. Furthermore, we applied a workflow employing ultra-high performance liquid chromatography-quadrupole time of flight mass spectrometry with a powerful chemometrics platform, focusing on only significantly changed metabolites. This workflow highly reduced the complexity of acquired data without losing metabolites of interest. Consequently, forty-one novel metabolites were identified in addition to the combined method, of which two metabolites, 4-guanidinobutanal and 4-guanidinobutanoate, were identified for the first time in Saccharomyces cerevisiae. With compartment-specific metabolomics, we identified sym1Δ cells as lysine auxotroph. The highly reduced carbamoyl-aspartate and orotic acid indicate a potential role of the mitochondrial inner membrane protein Sym1 in pyrimidine metabolism.
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Affiliation(s)
- Simon Lagies
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Daqiang Pan
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Pharmaceutical Science, University of Freiburg, 79104 Freiburg, Germany
| | - Daniel A. Mohl
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Dietmar A. Plattner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Ian E. Gentle
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Kammerer
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
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Li J, Wang F, Liu Y, Wang H, Ni B. N 6-methyladenosine (m 6A) in pancreatic cancer: Regulatory mechanisms and future direction. Int J Biol Sci 2021; 17:2323-2335. [PMID: 34239358 PMCID: PMC8241726 DOI: 10.7150/ijbs.60115] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A), the most abundant RNA modification in eukaryotes, plays a pivotal role in regulating many cellular and biological processes. Aberrant m6A modification has recently been involved in carcinogenesis in various cancers, including pancreatic cancer. Pancreatic cancer is one of the deadliest cancers. It is a heterogeneous malignant disease characterized by a plethora of diverse genetic and epigenetic events. Increasing evidence suggests that dysregulation of m6A regulatory factors, such as methyltransferases, demethylases, and m6A-binding proteins, profoundly affects the development and progression of pancreatic cancer. In addition, m6A regulators and m6A target transcripts may be promising early diagnostic and prognostic cancer biomarkers, as well as therapeutic targets. In this review, we highlight the biological functions and mechanisms of m6A in pancreatic cancer and discuss the potential of m6A modification in clinical applications.
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Affiliation(s)
- Jian Li
- Department of Pathophysiology, College of High Altitude, Army Medical University (Third Military Medical University), Chongqing 400038, PR China
- Department of General Surgery, Air Force Hospital of Western Theater Command, Chengdu 610021, PR China
| | - Fangjuan Wang
- Department of Cardiology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, PR China
| | - Yongkang Liu
- Department of General Surgery, Air Force Hospital of Western Theater Command, Chengdu 610021, PR China
| | - Huaizhi Wang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 401120, PR China
| | - Bing Ni
- Department of Pathophysiology, College of High Altitude, Army Medical University (Third Military Medical University), Chongqing 400038, PR China
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Wang H, Todd DA, Chiu NHL. Enhanced differentiation of isomeric RNA modifications by reducing the size of ions in ion mobility mass spectrometric measurements. J Anal Sci Technol 2020. [DOI: 10.1186/s40543-020-00243-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractWith the ability to differentiate different molecular sizes, ion mobility spectrometry (IMS) has great potentials in the analysis of isomeric compounds. However, due to the lack of sensitivity and resolution, IMS has not been commonly used. To address the issue on resolution, the goals of this study are to explore a more effective way to perform IMS by reducing the size of ions prior to the IM measurements, and apply the new approach to the differentiation of isomeric RNA modifications. The size reduction of ribonucleoside ions was effectively accomplished by using the collision-induced dissociation process, in which the N-glycosidic bond in ribonucleoside was cleaved and split the ions into two parts—a smaller nucleobase ion and a neutral molecule of ribose sugar. Since the chemical group that corresponds to most of the RNA modifications makes up a relatively small part of the molecular structure of nucleobases, the differentiation of the dissociated nucleobase ions is expected to require a lower ion mobility resolution than the differentiation of bigger isomeric ribonucleoside ions. By using RNA methylation as a model in this study, the proposed method lowered the required resolution by 16% for the differentiation of 1-methyladenosine and N6-methyladenosine. Similar results were also obtained from the differentiation of methylated cytidine isomers. In comparison to the results obtained from using the conventional tandem mass spectrometric method, there was no significant loss of signals when the proposed method was used. The proposed method is expected to be applicable to other types of isomeric compounds. Also, the same approach is applicable on other IMS platforms.
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Walter W, Pfarr N, Meggendorfer M, Jost P, Haferlach T, Weichert W. Next-generation diagnostics for precision oncology: Preanalytical considerations, technical challenges, and available technologies. Semin Cancer Biol 2020; 84:3-15. [PMID: 33171257 DOI: 10.1016/j.semcancer.2020.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 12/13/2022]
Abstract
Molecular diagnostics as the centrepiece of precision oncology has gone through revolutionary developments over the last decade, becoming tremendously broad, deep and precise with still ongoing advancements. In the majority of scenarios, treatment selection for cancer patients without any type of molecular characterization is no longer conceivable. Considering the impact of sample quality on the reliability of molecular analyses and the importance of the results for the fate of an individual patient, it is surprising how sparsely preanalytical and analytical requirements are addressed scientifically. Standardization and rigorous quality assessment continue to play only a marginal role in the field. Within this review, we will systematically discuss influencing preanalytic parameters and technology setups affecting molecular test results. We will shed light on the specifics of different analytes, technical modalities, and analysis pipelines. The review will have a certain focus on broad molecular genetic tumour testing with next generation sequencing but will go beyond that including other molecular diagnostic modalities and will give a glimpse into the future of molecular testing.
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Affiliation(s)
| | - Nicole Pfarr
- Institute of Pathology, Technical University Munich, Germany
| | | | - Philipp Jost
- Medical Department III for Hematology and Oncology, Klinikum rechts der Isar, Technical University Munich, Germany; German Cancer Consostium (DKTK), Partner Site Munich, Germany
| | | | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Germany; German Cancer Consostium (DKTK), Partner Site Munich, Germany.
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Braun LM, Lagies S, Klar RFU, Hussung S, Fritsch RM, Kammerer B, Wittel UA. Metabolic Profiling of Early and Late Recurrent Pancreatic Ductal Adenocarcinoma Using Patient-Derived Organoid Cultures. Cancers (Basel) 2020; 12:cancers12061440. [PMID: 32492856 PMCID: PMC7352957 DOI: 10.3390/cancers12061440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is associated with high mortality and will become the second most common cause of cancer-associated mortality by 2030. The poor prognosis arises from a lack of sensitive biomarkers, limited therapeutic options, and the astonishingly high recurrence rate after surgery of 60-80%. The factors driving this recurrence, however, remain enigmatic. Therefore, we generated patient-derived organoids (PDOs) from early- and late-recurrent PDAC patients. Cellular identity of PDOs was confirmed by qPCR, ddPCR, and IHC analyses. This is the first study investigating the metabolism in PDOs of different, clinically significant PDAC entities by untargeted GC/MS profiling. Partial least square discriminant analysis unveiled global alterations between the two sample groups. We identified nine metabolites to be increased in early recurrent PDOs in comparison to late recurrent PDOs. More than four-times increased were fumarate, malate, glutamate, aspartate, and glutamine. Hence, α-keto acids were elevated in PDO-conditioned medium derived from early recurrent patients. We therefore speculate that an increased anaplerotic metabolism fuels the Krebs-cycle and a corresponding higher accessibility to energy fastens the recurrence in PDAC patients. Therein, a therapeutic intervention could delay PDAC recurrence and prolong survival of affected patients or could serve as biomarker to predict recurrence in the future.
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Affiliation(s)
- Lukas M. Braun
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; (L.M.B.); (S.L.)
- Department of General and Visceral Surgery, University of Freiburg, Medical Center Faculty of Medicine, 79106 Freiburg, Germany
- Institute of Biology II, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Simon Lagies
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; (L.M.B.); (S.L.)
- Institute of Biology II, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Rhena F. U. Klar
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), University of Freiburg Medical Center, 79104 Freiburg, Germany; (R.F.U.K.); (S.H.); (R.M.F.)
- SFB/Collaborative Research Center 850 (CRC 850)—Control of Cell Motility in Morphogenesis, Cancer Invasion and Metastasis, University of Freiburg, 79104 Freiburg, Germany
| | - Saskia Hussung
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), University of Freiburg Medical Center, 79104 Freiburg, Germany; (R.F.U.K.); (S.H.); (R.M.F.)
- German Cancer Consortium, 79104 Freiburg, Germany
| | - Ralph M. Fritsch
- Department of Medicine I (Hematology, Oncology and Stem Cell Transplantation), University of Freiburg Medical Center, 79104 Freiburg, Germany; (R.F.U.K.); (S.H.); (R.M.F.)
- SFB/Collaborative Research Center 850 (CRC 850)—Control of Cell Motility in Morphogenesis, Cancer Invasion and Metastasis, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium, 79104 Freiburg, Germany
- Comprehensive Cancer Center Freiburg, 79104 Freiburg, Germany
- Department of Medical Oncology and Hematology, University Hospital of Zurich, 8091 Zurich, Switzerland
| | - Bernd Kammerer
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; (L.M.B.); (S.L.)
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Correspondence: (B.K.); (U.A.W.)
| | - Uwe A. Wittel
- Department of General and Visceral Surgery, University of Freiburg, Medical Center Faculty of Medicine, 79106 Freiburg, Germany
- Correspondence: (B.K.); (U.A.W.)
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Braun LM, Lagies S, Guenzle J, Fichtner-Feigl S, Wittel UA, Kammerer B. Metabolic Adaptation during nab-Paclitaxel Resistance in Pancreatic Cancer Cell Lines. Cells 2020; 9:cells9051251. [PMID: 32438599 PMCID: PMC7290296 DOI: 10.3390/cells9051251] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/05/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) correlates with high mortality and is about to become one of the major reasons for cancer-related mortality in the next decades. One reason for that high mortality is the limited availability of effective chemotherapy as well as the intrinsic or acquired resistance against it. Here, we report the impact of nab-paclitaxel on the cellular metabolome of PDAC cell lines. After establishment of nab-paclitaxel resistant cell lines, comparison of parental and resistant PDAC cell lines by metabolomics and biochemical assessments revealed altered metabolism, enhanced viability and reduced apoptosis. The results unveiled that acute nab-paclitaxel treatment affected primary metabolism to a minor extent. However, acquisition of resistance led to altered metabolites in both cell lines tested. Specifically, aspartic acid and carbamoyl-aspartic acid were differentially abundant, which might indicate an increased de novo pyrimidine synthesis. This pathway has already shown a similar behavior in other cancerous entities and thus might serve in the future as vulnerable target fighting resistance acquisition occurring in common malignancies.
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Affiliation(s)
- Lukas M. Braun
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; (L.M.B.); (S.L.)
- Department of General- and Visceral Surgery, University of Freiburg Medical Center Faculty of Medicine, 79106 Freiburg, Germany; (J.G.); (S.F.-F.)
| | - Simon Lagies
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; (L.M.B.); (S.L.)
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Institute of Biology II, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Jessica Guenzle
- Department of General- and Visceral Surgery, University of Freiburg Medical Center Faculty of Medicine, 79106 Freiburg, Germany; (J.G.); (S.F.-F.)
| | - Stefan Fichtner-Feigl
- Department of General- and Visceral Surgery, University of Freiburg Medical Center Faculty of Medicine, 79106 Freiburg, Germany; (J.G.); (S.F.-F.)
| | - Uwe A. Wittel
- Department of General- and Visceral Surgery, University of Freiburg Medical Center Faculty of Medicine, 79106 Freiburg, Germany; (J.G.); (S.F.-F.)
- Correspondence: (U.A.W.); (B.K.); Tel.: +49-761-270-25090 (U.A.W.); +49-761-203-97137 (B.K.)
| | - Bernd Kammerer
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; (L.M.B.); (S.L.)
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Correspondence: (U.A.W.); (B.K.); Tel.: +49-761-270-25090 (U.A.W.); +49-761-203-97137 (B.K.)
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