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Deichsel S, Gahr BM, Mastel H, Preiss A, Nagel AC. Numerous Serine/Threonine Kinases Affect Blood Cell Homeostasis in Drosophila melanogaster. Cells 2024; 13:576. [PMID: 38607015 PMCID: PMC11011202 DOI: 10.3390/cells13070576] [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: 02/20/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Blood cells in Drosophila serve primarily innate immune responses. Various stressors influence blood cell homeostasis regarding both numbers and the proportion of blood cell types. The principle molecular mechanisms governing hematopoiesis are conserved amongst species and involve major signaling pathways like Notch, Toll, JNK, JAK/Stat or RTK. Albeit signaling pathways generally rely on the activity of protein kinases, their specific contribution to hematopoiesis remains understudied. Here, we assess the role of Serine/Threonine kinases with the potential to phosphorylate the transcription factor Su(H) in crystal cell homeostasis. Su(H) is central to Notch signal transduction, and its inhibition by phosphorylation impedes crystal cell formation. Overall, nearly twenty percent of all Drosophila Serine/Threonine kinases were studied in two assays, global and hemocyte-specific overexpression and downregulation, respectively. Unexpectedly, the majority of kinases influenced crystal cell numbers, albeit only a few were related to hematopoiesis so far. Four kinases appeared essential for crystal cell formation, whereas most kinases restrained crystal cell development. This group comprises all kinase classes, indicative of the complex regulatory network underlying blood cell homeostasis. The rather indiscriminative response we observed opens the possibility that blood cells measure their overall phospho-status as a proxy for stress-signals, and activate an adaptive immune response accordingly.
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Affiliation(s)
- Sebastian Deichsel
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Bernd M. Gahr
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Helena Mastel
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Anette Preiss
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Anja C. Nagel
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
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Xu X, Li Y, Chen T, Hou C, Yang L, Zhu P, Zhang Y, Li T. VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis. Brief Bioinform 2023; 25:bbad480. [PMID: 38156562 PMCID: PMC10782907 DOI: 10.1093/bib/bbad480] [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: 04/11/2023] [Revised: 11/14/2023] [Accepted: 12/03/2023] [Indexed: 12/30/2023] Open
Abstract
Disrupted protein phosphorylation due to genetic variation is a widespread phenomenon that triggers oncogenic transformation of healthy cells. However, few relevant phosphorylation disruption events have been verified due to limited biological experimental methods. Because of the lack of reliable benchmark datasets, current bioinformatics methods primarily use sequence-based traits to study variant impact on phosphorylation (VIP). Here, we increased the number of experimentally supported VIP events from less than 30 to 740 by manually curating and reanalyzing multi-omics data from 916 patients provided by the Clinical Proteomic Tumor Analysis Consortium. To predict VIP events in cancer cells, we developed VIPpred, a machine learning method characterized by multidimensional features that exhibits robust performance across different cancer types. Our method provided a pan-cancer landscape of VIP events, which are enriched in cancer-related pathways and cancer driver genes. We found that variant-induced increases in phosphorylation events tend to inhibit the protein degradation of oncogenes and promote tumor suppressor protein degradation. Our work provides new insights into phosphorylation-related cancer biology as well as novel avenues for precision therapy.
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Affiliation(s)
- Xiaofeng Xu
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Li
- Department of Computer Science and Technology, Taiyuan University of Technology, Taiyuan, Shanxi 030024, China
| | - Taoyu Chen
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chao Hou
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Liang Yang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Peiyu Zhu
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yi Zhang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tingting Li
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing 100191, China
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Mo D, Liu C, Chen Y, Cheng X, Shen J, Zhao L, Zhang J. The mitochondrial ribosomal protein mRpL4 regulates Notch signaling. EMBO Rep 2023; 24:e55764. [PMID: 37009823 PMCID: PMC10240210 DOI: 10.15252/embr.202255764] [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: 07/10/2022] [Revised: 03/07/2023] [Accepted: 03/18/2023] [Indexed: 04/04/2023] Open
Abstract
Mitochondrial ribosomal proteins (MRPs) assemble as specialized ribosome to synthesize mtDNA-encoded proteins, which are essential for mitochondrial bioenergetic and metabolic processes. MRPs are required for fundamental cellular activities during animal development, but their roles beyond mitochondrial protein translation are poorly understood. Here, we report a conserved role of the mitochondrial ribosomal protein L4 (mRpL4) in Notch signaling. Genetic analyses demonstrate that mRpL4 is required in the Notch signal-receiving cells to permit target gene transcription during Drosophila wing development. We find that mRpL4 physically and genetically interacts with the WD40 repeat protein wap and activates the transcription of Notch signaling targets. We show that human mRpL4 is capable of replacing fly mRpL4 during wing development. Furthermore, knockout of mRpL4 in zebrafish leads to downregulated expression of Notch signaling components. Thus, we have discovered a previously unknown function of mRpL4 during animal development.
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Affiliation(s)
- Dongqing Mo
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Chenglin Liu
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Yao Chen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Xinkai Cheng
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Jie Shen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Long Zhao
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of FisheriesOcean University of ChinaQingdaoChina
- Key Laboratory of Mariculture (OUC)Ministry of EducationQingdaoChina
| | - Junzheng Zhang
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant ProtectionChina Agricultural UniversityBeijingChina
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Fechner J, Ketelhut M, Maier D, Preiss A, Nagel AC. The Binding of CSL Proteins to Either Co-Activators or Co-Repressors Protects from Proteasomal Degradation Induced by MAPK-Dependent Phosphorylation. Int J Mol Sci 2022; 23:ijms232012336. [PMID: 36293193 PMCID: PMC9604145 DOI: 10.3390/ijms232012336] [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: 09/28/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
The primary role of Notch is to specify cellular identities, whereby the cells respond to amazingly small changes in Notch signalling activity. Hence, dosage of Notch components is crucial to regulation. Central to Notch signal transduction are CSL proteins: together with respective cofactors, they mediate the activation or the silencing of Notch target genes. CSL proteins are extremely similar amongst species regarding sequence and structure. We noticed that the fly homologue suppressor of hairless (Su(H)) is stabilised in transcription complexes. Using specific transgenic fly lines and HeLa RBPJKO cells we provide evidence that Su(H) is subjected to proteasomal degradation with a half-life of about two hours if not protected by binding to co-repressor hairless or co-activator Notch. Moreover, Su(H) stability is controlled by MAPK-dependent phosphorylation, matching earlier data for RBPJ in human cells. The homologous murine and human RBPJ proteins, however, are largely resistant to degradation in our system. Mutating presumptive protein contact sites, however, sensitised RBPJ for proteolysis. Overall, our data highlight the similarities in the regulation of CSL protein stability across species and imply that turnover of CSL proteins may be a conserved means of regulating Notch signalling output directly at the level of transcription.
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Gagliani EK, Gutzwiller LM, Kuang Y, Odaka Y, Hoffmeister P, Hauff S, Turkiewicz A, Harding-Theobald E, Dolph PJ, Borggrefe T, Oswald F, Gebelein B, Kovall RA. A Drosophila Su(H) model of Adams-Oliver Syndrome reveals cofactor titration as a mechanism underlying developmental defects. PLoS Genet 2022; 18:e1010335. [PMID: 35951645 PMCID: PMC9398005 DOI: 10.1371/journal.pgen.1010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 08/23/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Notch signaling is a conserved pathway that converts extracellular receptor-ligand interactions into changes in gene expression via a single transcription factor (CBF1/RBPJ in mammals; Su(H) in Drosophila). In humans, RBPJ variants have been linked to Adams-Oliver syndrome (AOS), a rare autosomal dominant disorder characterized by scalp, cranium, and limb defects. Here, we found that a previously described Drosophila Su(H) allele encodes a missense mutation that alters an analogous residue found in an AOS-associated RBPJ variant. Importantly, genetic studies support a model that heterozygous Drosophila with the AOS-like Su(H) allele behave in an opposing manner to heterozygous flies with a Su(H) null allele, due to a dominant activity of sequestering either the Notch co-activator or the antagonistic Hairless co-repressor. Consistent with this model, AOS-like Su(H) and Rbpj variants have decreased DNA binding activity compared to wild type proteins, but these variants do not significantly alter protein binding to the Notch co-activator or the fly and mammalian co-repressors, respectively. Taken together, these data suggest a cofactor sequestration mechanism underlies AOS phenotypes associated with RBPJ variants, whereby the AOS-associated RBPJ allele encodes a protein with compromised DNA binding activity that retains cofactor binding, resulting in Notch target gene dysregulation. Adams-Oliver Syndrome (AOS) is a rare disease defined by missing skin/skull tissue, limb malformations, and cardiovascular abnormalities. Human genetic studies have revealed that ~40% of AOS patients inherit dominant mutations within specific genes in the Notch signaling pathway. Notch signaling is a highly conserved cell-to-cell communication pathway found in all metazoans and plays crucial roles during embryogenesis and tissue homeostasis in organisms from Drosophila (fruit-flies) to mammals. The Notch receptor converts cell-to-cell interactions into a Notch signal that enters the nucleus and activates target genes by binding to a highly conserved transcription factor. Here, we took advantage of the unexpected finding that a previously described dominant allele in the Drosophila Notch pathway transcription factor contains a missense variant in an analogous residue found in a family with AOS. Using this novel animal model of AOS along with biochemical DNA binding, protein-protein interaction, and transcriptional reporter assays, we found that this transcription factor variant selectively compromises DNA binding but not binding to the Notch signal nor binding to other proteins in the Notch pathway. Taken together with prior human genetic studies, these data suggest AOS phenotypes associated with variants in the Notch pathway transcription factor are caused by a dominant mechanism that sequesters the Notch signal, leading to Notch target gene dysregulation.
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Affiliation(s)
- Ellen K. Gagliani
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Lisa M. Gutzwiller
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Yi Kuang
- Graduate program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Yoshinobu Odaka
- Biology Department, University of Cincinnati Blue Ash College, Cincinnati, Ohio, United States of America
| | - Phillipp Hoffmeister
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine, Ulm, Germany
| | - Stefanie Hauff
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine, Ulm, Germany
| | | | - Emily Harding-Theobald
- Department of Biology, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Patrick J. Dolph
- Department of Biology, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine, Ulm, Germany
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: (BG); (RAK)
| | - Rhett A. Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: (BG); (RAK)
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Logeay R, Géminard C, Lassus P, Rodríguez-Vázquez M, Kantar D, Heron-Milhavet L, Fischer B, Bray SJ, Colinge J, Djiane A. Mechanisms underlying the cooperation between loss of epithelial polarity and Notch signaling during neoplastic growth in Drosophila. Development 2022; 149:274230. [PMID: 35005772 DOI: 10.1242/dev.200110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/17/2021] [Indexed: 12/16/2022]
Abstract
Aggressive neoplastic growth can be initiated by a limited number of genetic alterations, such as the well-established cooperation between loss of cell architecture and hyperactive signaling pathways. However, our understanding of how these different alterations interact and influence each other remains very incomplete. Using Drosophila paradigms of imaginal wing disc epithelial growth, we have monitored the changes in Notch pathway activity according to the polarity status of cells (scrib mutant). We show that the scrib mutation impacts the direct transcriptional output of the Notch pathway, without altering the global distribution of Su(H), the Notch-dedicated transcription factor. The Notch-dependent neoplasms require, however, the action of a group of transcription factors, similar to those previously identified for Ras/scrib neoplasm (namely AP-1, Stat92E, Ftz-F1 and basic leucine zipper factors), further suggesting the importance of this transcription factor network during neoplastic growth. Finally, our work highlights some Notch/scrib specificities, in particular the role of the PAR domain-containing basic leucine zipper transcription factor and Notch direct target Pdp1 for neoplastic growth.
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Affiliation(s)
- Rémi Logeay
- IRCM, Inserm, University of Montpellier, ICM, Montpellier, France
| | - Charles Géminard
- IRCM, Inserm, University of Montpellier, ICM, Montpellier, France
| | - Patrice Lassus
- IRCM, Inserm, University of Montpellier, ICM, CNRS, Montpellier, France
| | | | - Diala Kantar
- IRCM, Inserm, University of Montpellier, ICM, Montpellier, France
| | | | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Sarah J Bray
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Jacques Colinge
- IRCM, Inserm, University of Montpellier, ICM, Montpellier, France
| | - Alexandre Djiane
- IRCM, Inserm, University of Montpellier, ICM, Montpellier, France
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Pan L, Hoffmeister P, Turkiewicz A, Huynh NND, Große-Berkenbusch A, Knippschild U, Gebhardt JCM, Baumann B, Borggrefe T, Oswald F. Transcription Factor RBPJL Is Able to Repress Notch Target Gene Expression but Is Non-Responsive to Notch Activation. Cancers (Basel) 2021; 13:cancers13195027. [PMID: 34638511 PMCID: PMC8508133 DOI: 10.3390/cancers13195027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/01/2022] Open
Abstract
Simple Summary The transcription factor RBPJ is an integral part of the Notch signaling cascade. RBPJ can function as a coactivator when Notch signaling is activated but acts as a repressor in the absence of a Notch stimulus. Here, we characterized the function of RBPJL, a pancreas-specific paralog of RBPJ. Upon depletion of RBPJ using CRISPR/Cas9, we observed specific upregulation of Notch target gene expression. Reconstitution with RBPJL can compensate for the lack of RBPJ function in the repression of Notch target genes but is not able to mediate the Notch-dependent activation of gene expression. On the molecular level, we identified a limited capacity of RBPJL to interact with activated Notch1–4. Abstract The Notch signaling pathway is an evolutionary conserved signal transduction cascade present in almost all tissues and is required for embryonic and postnatal development, as well as for stem cell maintenance, but it is also implicated in tumorigenesis including pancreatic cancer and leukemia. The transcription factor RBPJ forms a coactivator complex in the presence of a Notch signal, whereas it represses Notch target genes in the absence of a Notch stimulus. In the pancreas, a specific paralog of RBPJ, called RBPJL, is expressed and found as part of the heterotrimeric PTF1-complex. However, the function of RBPJL in Notch signaling remains elusive. Using molecular modeling, biochemical and functional assays, as well as single-molecule time-lapse imaging, we show that RBPJL and RBPJ, despite limited sequence homology, possess a high degree of structural similarity. RBPJL is specifically expressed in the exocrine pancreas, whereas it is mostly undetectable in pancreatic tumour cell lines. Importantly, RBPJL is not able to interact with Notch−1 to −4 and it does not support Notch-mediated transactivation. However, RBPJL can bind to canonical RBPJ DNA elements and shows migration dynamics comparable to that of RBPJ in the nuclei of living cells. Importantly, RBPJL is able to interact with SHARP/SPEN, the central corepressor of the Notch pathway. In line with this, RBPJL is able to fully reconstitute transcriptional repression at Notch target genes in cells lacking RBPJ. Together, RBPJL can act as an antagonist of RBPJ, which renders cells unresponsive to the activation of Notch.
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Affiliation(s)
- Leiling Pan
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (L.P.); (P.H.)
| | - Philipp Hoffmeister
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (L.P.); (P.H.)
| | - Aleksandra Turkiewicz
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany;
| | - N. N. Duyen Huynh
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.D.H.); (A.G.-B.); (J.C.M.G.)
| | - Andreas Große-Berkenbusch
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.D.H.); (A.G.-B.); (J.C.M.G.)
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - J. Christof M. Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.D.H.); (A.G.-B.); (J.C.M.G.)
| | - Bernd Baumann
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany;
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany;
- Correspondence: (T.B.); (F.O.); Tel.: +49-731-500-44544 (F.O.)
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (L.P.); (P.H.)
- Correspondence: (T.B.); (F.O.); Tel.: +49-731-500-44544 (F.O.)
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