1
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Maurya D, Rai G, Mandal D, Mondal BC. Transient caspase-mediated activation of caspase-activated DNase causes DNA damage required for phagocytic macrophage differentiation. Cell Rep 2024; 43:114251. [PMID: 38761374 DOI: 10.1016/j.celrep.2024.114251] [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: 12/05/2023] [Revised: 04/04/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
Phagocytic macrophages are crucial for innate immunity and tissue homeostasis. Most tissue-resident macrophages develop from embryonic precursors that populate every organ before birth to lifelong self-renew. However, the mechanisms for versatile macrophage differentiation remain unknown. Here, we use in vivo genetic and cell biological analysis of the Drosophila larval hematopoietic organ, the lymph gland that produces macrophages. We show that the developmentally regulated transient activation of caspase-activated DNase (CAD)-mediated DNA strand breaks in intermediate progenitors is essential for macrophage differentiation. Insulin receptor-mediated PI3K/Akt signaling regulates the apoptosis signal-regulating kinase 1 (Ask1)/c-Jun kinase (JNK) axis to control sublethal levels of caspase activation, causing DNA strand breaks during macrophage development. Furthermore, caspase activity is also required for embryonic-origin macrophage development and efficient phagocytosis. Our study provides insights into developmental signaling and CAD-mediated DNA strand breaks associated with multifunctional and heterogeneous macrophage differentiation.
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Affiliation(s)
- Deepak Maurya
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Gayatri Rai
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Debleena Mandal
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Bama Charan Mondal
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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2
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Sulekh S, Ikegawa Y, Naito S, Oji A, Hiratani I, Yoo SK. A feedback loop that drives cell death and proliferation and its defect in intestinal stem cells. Life Sci Alliance 2024; 7:e202302238. [PMID: 38296349 PMCID: PMC10830383 DOI: 10.26508/lsa.202302238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 02/05/2024] Open
Abstract
Cell death and proliferation are at a glance dichotomic events, but occasionally coupled. Caspases, traditionally known to execute apoptosis, play non-apoptotic roles, but their exact mechanism remains elusive. Here, using Drosophila intestinal stem cells (ISCs), we discovered that activation of caspases induces massive cell proliferation rather than cell death. We elucidate that a positive feedback circuit exists between caspases and JNK, which can simultaneously drive cell proliferation and cell death. In ISCs, signalling from JNK to caspases is defective, which skews the balance towards proliferation. Mechanistically, two-tiered regulation of the DIAP1 inhibitor rpr, through its transcription and its protein localization, exists. This work provides a conceptual framework that explains how caspases perform apoptotic and non-apoptotic functions in vivo and how ISCs accomplish their resistance to cell death.
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Affiliation(s)
- Shivakshi Sulekh
- https://ror.org/023rffy11 Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Division of Developmental Biology and Regenerative Medicine, Kobe University, Kobe, Japan
| | - Yuko Ikegawa
- https://ror.org/023rffy11 Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Saki Naito
- https://ror.org/023rffy11 Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Asami Oji
- https://ror.org/023rffy11 Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, Japan
| | - Ichiro Hiratani
- Division of Developmental Biology and Regenerative Medicine, Kobe University, Kobe, Japan
- https://ror.org/023rffy11 Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, Japan
| | - Sa Kan Yoo
- https://ror.org/023rffy11 Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Division of Developmental Biology and Regenerative Medicine, Kobe University, Kobe, Japan
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, Japan
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3
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Cumming T, Levayer R. Toward a predictive understanding of epithelial cell death. Semin Cell Dev Biol 2024; 156:44-57. [PMID: 37400292 DOI: 10.1016/j.semcdb.2023.06.008] [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: 03/30/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
Epithelial cell death is highly prevalent during development and tissue homeostasis. While we have a rather good understanding of the molecular regulators of programmed cell death, especially for apoptosis, we still fail to predict when, where, how many and which specific cells will die in a tissue. This likely relies on the much more complex picture of apoptosis regulation in a tissular and epithelial context, which entails cell autonomous but also non-cell autonomous factors, diverse feedback and multiple layers of regulation of the commitment to apoptosis. In this review, we illustrate this complexity of epithelial apoptosis regulation by describing these different layers of control, all demonstrating that local cell death probability is a complex emerging feature. We first focus on non-cell autonomous factors that can locally modulate the rate of cell death, including cell competition, mechanical input and geometry as well as systemic effects. We then describe the multiple feedback mechanisms generated by cell death itself. We also outline the multiple layers of regulation of epithelial cell death, including the coordination of extrusion and regulation occurring downstream of effector caspases. Eventually, we propose a roadmap to reach a more predictive understanding of cell death regulation in an epithelial context.
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Affiliation(s)
- Tom Cumming
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr. Roux, 75015 Paris, France; Sorbonne Université, Collège Doctoral, F75005 Paris, France
| | - Romain Levayer
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr. Roux, 75015 Paris, France.
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4
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Bhushan V, Nita-Lazar A. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. J Proteome Res 2024. [PMID: 38451675 DOI: 10.1021/acs.jproteome.3c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.
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Affiliation(s)
- Vanya Bhushan
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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5
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Matamoro-Vidal A, Cumming T, Davidović A, Levillayer F, Levayer R. Patterned apoptosis has an instructive role for local growth and tissue shape regulation in a fast-growing epithelium. Curr Biol 2024; 34:376-388.e7. [PMID: 38215743 PMCID: PMC10808510 DOI: 10.1016/j.cub.2023.12.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/13/2023] [Accepted: 12/11/2023] [Indexed: 01/14/2024]
Abstract
What regulates organ size and shape remains one fundamental mystery of modern biology. Research in this area has primarily focused on deciphering the regulation in time and space of growth and cell division, while the contribution of cell death has been overall neglected. This includes studies of the Drosophila wing, one of the best-characterized systems for the study of growth and patterning, undergoing massive growth during larval stage and important morphogenetic remodeling during pupal stage. So far, it has been assumed that cell death was relatively neglectable in this tissue both during larval stage and pupal stage, and as a result, the pattern of growth was usually attributed to the distribution of cell division. Here, using systematic mapping and registration combined with quantitative assessment of clone size and disappearance as well as live imaging, we outline a persistent pattern of cell death and clone elimination emerging in the larval wing disc and persisting during pupal wing morphogenesis. Local variation of cell death is associated with local variation of clone size, pointing to an impact of cell death on local growth that is not fully compensated by proliferation. Using morphometric analyses of adult wing shape and genetic perturbations, we provide evidence that patterned death locally and globally affects adult wing shape and size. This study describes a roadmap for precise assessment of the contribution of cell death to tissue shape and outlines an important instructive role of cell death in modulating quantitatively local growth and morphogenesis of a fast-growing tissue.
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Affiliation(s)
- Alexis Matamoro-Vidal
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, Université Paris Cité, Cell Death and Epithelial Homeostasis Unit, 75015 Paris, France
| | - Tom Cumming
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, Université Paris Cité, Cell Death and Epithelial Homeostasis Unit, 75015 Paris, France; PPU program Institut Pasteur, Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Anđela Davidović
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Florence Levillayer
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, Université Paris Cité, Cell Death and Epithelial Homeostasis Unit, 75015 Paris, France
| | - Romain Levayer
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, Université Paris Cité, Cell Death and Epithelial Homeostasis Unit, 75015 Paris, France.
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6
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Nishida H, Albero AB, Onoue K, Ikegawa Y, Sulekh S, Sakizli U, Minami Y, Yonemura S, Wang YC, Yoo SK. Necrosensor: a genetically encoded fluorescent sensor for visualizing necrosis in Drosophila. Biol Open 2024; 13:bio060104. [PMID: 38156558 PMCID: PMC10836653 DOI: 10.1242/bio.060104] [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: 08/04/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Historically, necrosis has been considered a passive process, which is induced by extreme stress or damage. However, recent findings of necroptosis, a programmed form of necrosis, shed a new light on necrosis. It has been challenging to detect necrosis reliably in vivo, partly due to the lack of genetically encoded sensors to detect necrosis. This is in stark contrast with the availability of many genetically encoded biosensors for apoptosis. Here we developed Necrosensor, a genetically encoded fluorescent sensor that detects necrosis in Drosophila, by utilizing HMGB1, which is released from the nucleus as a damage-associated molecular pattern (DAMP). We demonstrate that Necrosensor is able to detect necrosis induced by various stresses in multiple tissues in both live and fixed conditions. Necrosensor also detects physiological necrosis that occurs during spermatogenesis in the testis. Using Necrosensor, we discovered previously unidentified, physiological necrosis of hemocyte progenitors in the hematopoietic lymph gland of developing larvae. This work provides a new transgenic system that enables in vivo detection of necrosis in real time without any intervention.
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Affiliation(s)
- Hiroshi Nishida
- Division of Cell Physiology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, 650-0047, Japan
| | | | - Kenta Onoue
- Laboratory for Ultrastructural Research, RIKEN BDR, Kobe, 650-0047, Japan
| | - Yuko Ikegawa
- Laboratory of Molecular Cell Biology and Development, Kyoto University, Kobe, 650-0047, Japan
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, 650-0047, Japan
| | - Shivakshi Sulekh
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, 650-0047, Japan
- Division of Developmental Biology and Regenerative Medicine, Graduate School of Medicine, Kobe University, Kobe, 650-0047, Japan
| | - Ugurcan Sakizli
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, 650-0047, Japan
- Division of Developmental Biology and Regenerative Medicine, Graduate School of Medicine, Kobe University, Kobe, 650-0047, Japan
| | - Yasuhiro Minami
- Division of Cell Physiology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan
| | - Shigenobu Yonemura
- Laboratory for Ultrastructural Research, RIKEN BDR, Kobe, 650-0047, Japan
- Department of Cell Biology, Tokushima University Graduate School of Medicine, Tokushima, 770-8503, Japan
| | - Yu-Chiun Wang
- Laboratory for Epithelial Morphogenesis, RIKEN BDR, Kobe, 650-0047, Japan
| | - Sa Kan Yoo
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, 650-0047, Japan
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, 650-0047, Japan
- Division of Developmental Biology and Regenerative Medicine, Graduate School of Medicine, Kobe University, Kobe, 650-0047, Japan
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7
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Li Y, Zhang Y, Dinesh-Kumar SP. TurboID-Based Proximity Labeling: A Method to Decipher Protein-Protein Interactions in Plants. Methods Mol Biol 2024; 2724:257-272. [PMID: 37987912 DOI: 10.1007/978-1-0716-3485-1_19] [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] [Indexed: 11/22/2023]
Abstract
Proteins form complex networks through interaction to drive biological processes. Thus, dissecting protein-protein interactions (PPIs) is essential for interpreting cellular processes. To overcome the drawbacks of traditional approaches for analyzing PPIs, enzyme-catalyzed proximity labeling (PL) techniques based on peroxidases or biotin ligases have been developed and successfully utilized in mammalian systems. However, the use of toxic H2O2 in peroxidase-based PL, the requirement of long incubation time (16-24 h), and higher incubation temperature (37 °C) with biotin in BioID-based PL significantly restricted their applications in plants. TurboID-based PL, a recently developed approach, circumvents the limitations of these methods by providing rapid PL of proteins under room temperature. We recently optimized the use of TurboID-based PL in plants and demonstrated that it performs better than BioID in labeling endogenous proteins. Here, we describe a step-by-step protocol for TurboID-based PL in studying PPIs in planta, including Agrobacterium-based transient expression of proteins, biotin treatment, protein extraction, removal of free biotin, quantification, and enrichment of the biotinylated proteins by affinity purification. We describe the PL using plant viral immune receptor N, which belongs to the nucleotide-binding leucine-rich repeat (NLR) class of immune receptors, as a model. The method described could be easily adapted to study PPI networks of other proteins in Nicotiana benthamiana and provides valuable information for future application of TurboID-based PL in other plant species.
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Affiliation(s)
- Yuanyuan Li
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA.
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8
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Guo J, Guo S, Lu S, Gong J, Wang L, Ding L, Chen Q, Liu W. The development of proximity labeling technology and its applications in mammals, plants, and microorganisms. Cell Commun Signal 2023; 21:269. [PMID: 37777761 PMCID: PMC10544124 DOI: 10.1186/s12964-023-01310-1] [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: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.
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Affiliation(s)
- Jieyu Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Siao Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Jun Gong
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Liqiong Ding
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Qingjie Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
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9
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Shinoda N, Horikoshi M, Taira Y, Muramoto M, Hirayama S, Murata S, Miura M. Caspase cleaves Drosophila BubR1 to modulate spindle assembly checkpoint function and lifespan of the organism. FEBS J 2023; 290:4200-4223. [PMID: 37151120 DOI: 10.1111/febs.16811] [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: 08/01/2022] [Revised: 03/23/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Caspases cleave over 1500 substrates in the human proteome in both lethal and non-lethal scenarios. However, reports of the physiological consequences of substrate cleavage are limited. Additionally, the manner in which caspase cleaves only a subset of substrates in the non-lethal scenario remains to be elucidated. BubR1, a spindle assembly checkpoint component, is a caspase substrate in humans, the physiological function of which remains unclear. Here, we found that caspases, especially Drice, cleave Drosophila BubR1 between the N-terminal KEN box motif and C-terminal kinase domain. By using proximity labelling, we found that Drice, but not Dcp-1, is in proximity to BubR1, suggesting that protein proximity facilitates substrate preference. The cleaved fragments displayed altered subcellular localization and protein-protein interactions. Flies that harboured cleavage-resistant BubR1 showed longer duration of BubR1 localization to the kinetochore upon colchicine treatment. Furthermore, these flies showed extended lifespan. Thus, we propose that the caspase-mediated cleavage of BubR1 limits spindle assembly checkpoint and organismal lifespan. Our results highlight the importance of the individual analysis of substrates in vivo to determine the biological significance of caspase-dependent non-lethal cellular processes.
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Affiliation(s)
- Natsuki Shinoda
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Misuzu Horikoshi
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Yusuke Taira
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Masaya Muramoto
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Shoshiro Hirayama
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Japan
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10
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Nabhan AB. Pathophysiology, Clinical Implications and Management of Orofacial Neuropathic Pain- with special attention to Trigeminal neuralgia: A Narrative Review. BIOMEDICAL AND PHARMACOLOGY JOURNAL 2023; 16:835-846. [DOI: 10.13005/bpj/2666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Background: It is a widely held belief that if the trigeminal nerve is damaged, the victim would experience agonising and unrelenting external pain. A lesion to the trigeminal nerve may have a wide-reaching effect, such as on one side of the face in particular, or it might have a more localised effect, such as on some or all of your gums. The risk of damage increases the likelihood that it will be difficult to speak and swallow. This nerve provides sensation to a part of your face that may be constantly aching or tingling for some people. However, the trigeminal nerve injury-related persistent orofacial pain might be brought on by a wide variety of unknown triggers. Aim: In this study investigate the clinical manifestations of chronic orofacial pain brought on by a damage to the trigeminal nerve, as well as the diagnostic and therapeutic approaches available to treat this condition. Methodology Through the use of search phrases such as "Trigeminal nerve injury," "Trigeminal ganglion," "Trigeminal spinal subnucleus caudalis," "Craniofacial pain," "Oral prognosis," and "treatment," the computerised databases for the last twenty years have been investigated. There are now two hundred objects in total that have been accumulated. There have been around fifty of them that are pertinent to the discussion that is going on in this work. Majority of the patients fair enough with the pharmacology treatment/drugs like the carbamazepine & oxcarbazepine which forms the first line treatment options followed by lamotrigine & baclofen encompassing the second line of drugs along with adjuvant drug support of topiramate, levetiracetam, gabapentin, pregabalin. As the field of science has explored &advanced for the latest treatment options include microvascular decompression, gamma knife radiosurgery, percutaneous rhizotomies variable based on the evidences & guidelines 54 Conclusion: New diagnostic criteria and treatment alternatives have become available for people who suffer from trigeminal neuropathy and orofacial neuropathic pain as a result of recent developments in fundamental animal research that have led to their development. Despite the results, more research needs to investigate a greater variety of distinct non-neuronal cell feature approaches.
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Affiliation(s)
- Abdullah Bin Nabhan
- Oral Medicine and Orofacial Pain, College of Dentistry, Prince Sattam Bin Abdulaziz University, Al Kharj, Riyadh, Saudi Arabia
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11
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Galasso A, Xu DC, Hill C, Iakovleva D, Stefana MI, Baena‐Lopez LA. Non-apoptotic caspase activation ensures the homeostasis of ovarian somatic stem cells. EMBO Rep 2023; 24:e51716. [PMID: 37039000 PMCID: PMC10240206 DOI: 10.15252/embr.202051716] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/22/2023] [Accepted: 03/14/2023] [Indexed: 04/12/2023] Open
Abstract
Current evidence has associated caspase activation with the regulation of basic cellular functions without causing apoptosis. Malfunction of non-apoptotic caspase activities may contribute to specific neurological disorders, metabolic diseases, autoimmune conditions and cancers. However, our understanding of non-apoptotic caspase functions remains limited. Here, we show that non-apoptotic caspase activation prevents the intracellular accumulation of the Patched receptor in autophagosomes and the subsequent Patched-dependent induction of autophagy in Drosophila follicular stem cells. These events ultimately sustain Hedgehog signalling and the physiological properties of ovarian somatic stem cells and their progeny under moderate thermal stress. Importantly, our key findings are partially conserved in ovarian somatic cells of human origin. These observations attribute to caspases a pro-survival role under certain cellular conditions.
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Affiliation(s)
- Alessia Galasso
- Faculty of Medicine CentreImperial College London, South Kensington CampusLondonUK
| | - Derek Cui Xu
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Claire Hill
- School of Medicine, Dentistry and Biomedical SciencesQueen's University Belfast MedicineBelfastUK
| | - Daria Iakovleva
- Center for Regenerative MedicineUniversity of EdinburghEdinburghUK
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12
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Nakano S, Kashio S, Nishimura K, Takeishi A, Kosakamoto H, Obata F, Kuranaga E, Chihara T, Yamauchi Y, Isobe T, Miura M. Damage sensing mediated by serine proteases Hayan and Persephone for Toll pathway activation in apoptosis-deficient flies. PLoS Genet 2023; 19:e1010761. [PMID: 37319131 DOI: 10.1371/journal.pgen.1010761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The mechanisms by which the innate immune system senses damage have been extensively explored in multicellular organisms. In Drosophila, various types of tissue damage, including epidermal injury, tumor formation, cell competition, and apoptosis deficiency, induce sterile activation of the Toll pathway, a process that requires the use of extracellular serine protease (SP) cascades. Upon infection, the SP Spätzle (Spz)-processing enzyme (SPE) cleaves and activates the Toll ligand Spz downstream of two paralogous SPs, Hayan and Persephone (Psh). However, upon tissue damage, it is not fully understood which SPs establish Spz activation cascades nor what damage-associated molecules can activate SPs. In this study, using newly generated uncleavable spz mutant flies, we revealed that Spz cleavage is required for the sterile activation of the Toll pathway, which is induced by apoptosis-deficient damage of wing epidermal cells in adult Drosophila. Proteomic analysis of hemolymph, followed by experiments with Drosophila Schneider 2 (S2) cells, revealed that among hemolymph SPs, both SPE and Melanization Protease 1 (MP1) have high capacities to cleave Spz. Additionally, in S2 cells, MP1 acts downstream of Hayan and Psh in a similar manner to SPE. Using genetic analysis, we found that the upstream SPs Hayan and Psh contributes to the sterile activation of the Toll pathway. While SPE/MP1 double mutants show more impairment of Toll activation upon infection than SPE single mutants, Toll activation is not eliminated in these apoptosis-deficient flies. This suggests that Hayan and Psh sense necrotic damage, inducing Spz cleavage by SPs other than SPE and MP1. Furthermore, hydrogen peroxide, a representative damage-associated molecule, activates the Psh-Spz cascade in S2 cells overexpressing Psh. Considering that reactive oxygen species (ROS) were detected in apoptosis-deficient wings, our findings highlight the importance of ROS as signaling molecules that induce the activation of SPs such as Psh in response to damage.
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Affiliation(s)
- Shotaro Nakano
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Soshiro Kashio
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kei Nishimura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Asuka Takeishi
- Neural Circuit of Multisensory Integration RIKEN Hakubi Research Team, RIKEN Center for Brain Science, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Hina Kosakamoto
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Fumiaki Obata
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Erina Kuranaga
- Laboratory of Histogenetic Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Takahiro Chihara
- Program of Biomedical Science and Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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13
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Ascoët S, Touchard A, Téné N, Lefranc B, Leprince J, Paquet F, Jouvensal L, Barassé V, Treilhou M, Billet A, Bonnafé E. The mechanism underlying toxicity of a venom peptide against insects reveals how ants are master at disrupting membranes. iScience 2023; 26:106157. [PMID: 36879819 PMCID: PMC9985030 DOI: 10.1016/j.isci.2023.106157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Hymenopterans represent one of the most abundant groups of venomous organisms but remain little explored due to the difficult access to their venom. The development of proteo-transcriptomic allowed us to explore diversity of their toxins offering interesting perspectives to identify new biological active peptides. This study focuses on U9 function, a linear, amphiphilic and polycationic peptide isolated from ant Tetramorium bicarinatum venom. It shares physicochemical properties with M-Tb1a, exhibiting cytotoxic effects through membrane permeabilization. In the present study, we conducted a comparative functional investigation of U9 and M-Tb1a and explored the mechanisms underlying their cytotoxicity against insect cells. After showing that both peptides induced the formation of pores in cell membrane, we demonstrated that U9 induced mitochondrial damage and, at high concentrations, localized into cells and induced caspase activation. This functional investigation highlighted an original mechanism of U9 questioning on potential valorization and endogen activity in T. bicarinatum venom.
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Affiliation(s)
- Steven Ascoët
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Axel Touchard
- CNRS, UMR Ecologie des Forêts de Guyane, AgroParisTech, CIRAD, INRA, Université de Guyane, Université des Antilles, Campus Agronomique, BP316 97310 Kourou, France
| | - Nathan Téné
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Benjamin Lefranc
- Inserm U1239, NorDiC, Laboratoire de Différenciation et Communication Neuroendocrine, Endocrine et Germinale, Université de Rouen-Normandie, 76000 Rouen, France
- Inserm US51, HeRacLeS, Université de Rouen-Normandie, 76000 Rouen, France
| | - Jérôme Leprince
- Inserm U1239, NorDiC, Laboratoire de Différenciation et Communication Neuroendocrine, Endocrine et Germinale, Université de Rouen-Normandie, 76000 Rouen, France
- Inserm US51, HeRacLeS, Université de Rouen-Normandie, 76000 Rouen, France
| | - Françoise Paquet
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron CS-80054, 45071 Orléans, France
| | - Laurence Jouvensal
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron CS-80054, 45071 Orléans, France
| | - Valentine Barassé
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Michel Treilhou
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Arnaud Billet
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Elsa Bonnafé
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
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14
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Schaack GA, Sullivan OM, Mehle A. Identifying Protein-Protein Interactions by Proximity Biotinylation with AirID and splitAirID. Curr Protoc 2023; 3:e702. [PMID: 36939277 PMCID: PMC10031415 DOI: 10.1002/cpz1.702] [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] [Indexed: 03/21/2023]
Abstract
Proteins frequently function in high-order complexes. Defining protein-protein interactions is essential to acquiring a full understanding of their activity and regulation. Proximity biotinylation has emerged as a highly specific approach to capture transient and stable interactions in living cells or organisms. Proximity biotinylation exploits promiscuous biotinylating enzymes fused to a bait protein, resulting in the biotinylation of adjacent endogenous proteins. Biotinylated interactors are purified under very strict conditions and identified by mass spectrometry to obtain a high-confidence list of candidate binding partners. AirID is a recently described biotin ligase specifically engineered for proximity labeling. This protocol details proximity biotinylation by AirID, using protein complexes that form during a type I interferon response as an example. It covers the construction and validation of AirID fusion proteins and the enrichment and identification of biotinylated interactors. We describe a variation on the protocol using splitAirID. In this case, AirID is split into two inactive fragments and ligase activity is only restored upon dimerization of the bait proteins. This permits selective detection of proteins that interact with homo- or heterodimeric forms of the bait. The protocol considers design strategies, optimization, and the properties of different biotin ligases to identify optimal conditions for each experimental question. We also discuss common pitfalls and how to troubleshoot them. These approaches allow proximity biotinylation to be a powerful tool for defining protein interactomes. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Construction and functional validation of AirID fusion proteins Alternate Protocol: Construction and functional validation of splitAirID fusion proteins Support Protocol: Western blot for biotinylated proteins Basic Protocol 2: Biotinylation, enrichment, and identification of protein interactors.
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Affiliation(s)
| | | | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin – Madison, Madison, WI 53706, USA
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15
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Kietz C, Meinander A. Drosophila caspases as guardians of host-microbe interactions. Cell Death Differ 2023; 30:227-236. [PMID: 35810247 PMCID: PMC9950452 DOI: 10.1038/s41418-022-01038-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
An intact cell death machinery is not only crucial for successful embryonic development and tissue homeostasis, but participates also in the defence against pathogens and contributes to a balanced immune response. Centrally involved in the regulation of both cell death and inflammatory immune responses is the evolutionarily conserved family of cysteine proteases named caspases. The Drosophila melanogaster genome encodes for seven caspases, several of which display dual functions, participating in apoptotic signalling and beyond. Among the Drosophila caspases, the caspase-8 homologue Dredd has a well-characterised role in inflammatory signalling activated by bacterial infections, and functions as a driver of NF-κB-mediated immune responses. Regarding the other Drosophila caspases, studies focusing on tissue-specific immune signalling and host-microbe interactions have recently revealed immunoregulatory functions of the initiator caspase Dronc and the effector caspase Drice. The aim of this review is to give an overview of the signalling cascades involved in the Drosophila humoral innate immune response against pathogens and of their caspase-mediated regulation. Furthermore, the apoptotic role of caspases during antibacterial and antiviral immune activation will be discussed.
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Affiliation(s)
- Christa Kietz
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, BioCity, Turku, Finland
| | - Annika Meinander
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, BioCity, Turku, Finland.
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku, Finland.
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16
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Faria L, Canato S, Jesus TT, Gonçalves M, Guerreiro PS, Lopes CS, Meireles I, Morais-de-Sá E, Paredes J, Janody F. Activation of an actin signaling pathway in pre-malignant mammary epithelial cells by P-cadherin is essential for transformation. Dis Model Mech 2023; 16:dmm049652. [PMID: 36808468 PMCID: PMC9983776 DOI: 10.1242/dmm.049652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 01/19/2023] [Indexed: 02/23/2023] Open
Abstract
Alterations in the expression or function of cell adhesion molecules have been implicated in all steps of tumor progression. Among those, P-cadherin is highly enriched in basal-like breast carcinomas, playing a central role in cancer cell self-renewal, collective cell migration and invasion. To establish a clinically relevant platform for functional exploration of P-cadherin effectors in vivo, we generated a humanized P-cadherin Drosophila model. We report that actin nucleators, Mrtf and Srf, are main P-cadherin effectors in fly. We validated these findings in a human mammary epithelial cell line with conditional activation of the SRC oncogene. We show that, prior to promoting malignant phenotypes, SRC induces a transient increase in P-cadherin expression, which correlates with MRTF-A accumulation, its nuclear translocation and the upregulation of SRF target genes. Moreover, knocking down P-cadherin, or preventing F-actin polymerization, impairs SRF transcriptional activity. Furthermore, blocking MRTF-A nuclear translocation hampers proliferation, self-renewal and invasion. Thus, in addition to sustaining malignant phenotypes, P-cadherin can also play a major role in the early stages of breast carcinogenesis by promoting a transient boost of MRTF-A-SRF signaling through actin regulation.
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Affiliation(s)
- Lídia Faria
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Rua Júlio Amaral de Carvalho, n 45, 4200-135 Porto, Portugal
- Master Programme in Oncology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Sara Canato
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Rua Júlio Amaral de Carvalho, n 45, 4200-135 Porto, Portugal
- Physiology and Cancer Program, Champalimaud Foundation, Avenida de Brasília, 1400-038 Lisboa, Portugal
| | - Tito T. Jesus
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Rua Júlio Amaral de Carvalho, n 45, 4200-135 Porto, Portugal
| | - Margarida Gonçalves
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Patrícia S. Guerreiro
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Rua Júlio Amaral de Carvalho, n 45, 4200-135 Porto, Portugal
- Vector B2B - Drug Developing - Associação Para Investigação em Biotecnologia, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028 Lisboa, Portugal
| | - Carla S. Lopes
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Isabel Meireles
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Rua Júlio Amaral de Carvalho, n 45, 4200-135 Porto, Portugal
| | - Eurico Morais-de-Sá
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Joana Paredes
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Rua Júlio Amaral de Carvalho, n 45, 4200-135 Porto, Portugal
- FMUP, Medical Faculty of University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Florence Janody
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Ipatimup), Rua Júlio Amaral de Carvalho, n 45, 4200-135 Porto, Portugal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal
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17
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Chen MY, Duan X, Wang Q, Ran MJ, Ai H, Zheng Y, Wang YF. Cytochrome c1-like is required for mitochondrial morphogenesis and individualization during spermatogenesis in Drosophila melanogaster. J Exp Biol 2023; 226:286665. [PMID: 36645102 DOI: 10.1242/jeb.245277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023]
Abstract
The Drosophila testis is an excellent system for studying the process from germ stem cells to motile sperm, including the proliferation of male germ cells, meiosis of primary spermatocytes, mitochondrial morphogenesis, and spermatid individualization. We previously demonstrated that ocnus (ocn) plays an essential role in male germ cell development. Among those genes and proteins whose expression levels were changed as a result of ocn knockdown, cytochrome c1-like (cyt-c1L) was downregulated significantly. Here, we show that cyt-c1L is highly expressed in the testis of D. melanogaster. Knockdown or mutation of cyt-c1L in early germ cells of flies resulted in male sterility. Immunofluorescence staining showed that cyt-c1L knockdown testes had no defects in early spermatogenesis; however, in late stages, in contrast to many individualization complexes (ICs) composed of F-actin cones that appeared at different positions in control testes, no actin cones or ICs were observed in cyt-c1L knockdown testes. Furthermore, no mature sperm were found in the seminal vesicle of cyt-c1L knockdown testes whereas the control seminal vesicle was full of mature sperm with needle-like nuclei. cyt-c1L knockdown also caused abnormal mitochondrial morphogenesis during spermatid elongation. Excessive apoptotic signals accumulated in the base of cyt-c1L knockdown fly testes. These results suggest that cyt-c1L may play an important role in spermatogenesis by affecting the mitochondrial morphogenesis and individualization of sperm in D. melanogaster.
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Affiliation(s)
- Meng-Yan Chen
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Xin Duan
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Qian Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Mao-Jiu Ran
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Hui Ai
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Ya Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Yu-Feng Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
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18
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Wang X, Xu P, Liu Y, Wang Z, Lenahan C, Fang Y, Lu J, Zheng J, Wang K, Wang W, Zhou J, Chen S, Zhang J. New Insights of Early Brain Injury after Subarachnoid Hemorrhage: A Focus on the Caspase Family. Curr Neuropharmacol 2023; 21:392-408. [PMID: 35450528 PMCID: PMC10190145 DOI: 10.2174/1570159x20666220420115925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/10/2022] [Accepted: 04/14/2022] [Indexed: 11/22/2022] Open
Abstract
Spontaneous subarachnoid hemorrhage (SAH), primarily caused by ruptured intracranial aneurysms, remains a prominent clinical challenge with a high rate of mortality and morbidity worldwide. Accumulating clinical trials aiming at the prevention of cerebral vasospasm (CVS) have failed to improve the clinical outcome of patients with SAH. Therefore, a growing number of studies have shifted focus to the pathophysiological changes that occur during the periods of early brain injury (EBI). New pharmacological agents aiming to alleviate EBI have become a promising direction to improve outcomes after SAH. Caspases belong to a family of cysteine proteases with diverse functions involved in maintaining metabolism, autophagy, tissue differentiation, regeneration, and neural development. Increasing evidence shows that caspases play a critical role in brain pathology after SAH. Therefore, caspase regulation could be a potential target for SAH treatment. Herein, we provide an overview pertaining to the current knowledge on the role of caspases in EBI after SAH, and we discuss the promising therapeutic value of caspase-related agents after SAH.
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Affiliation(s)
- Xiaoyu Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Penglei Xu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yibo Liu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zefeng Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Cameron Lenahan
- Center for Neuroscience Research, Loma Linda University School of Medicine, Loma Linda, CA, USA
- Burrell College of Osteopathic Medicine, Las Cruces, New Mexico
| | - Yuanjian Fang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianan Lu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingwei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kaikai Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingyi Zhou
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sheng Chen
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Neurosurgery, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine (Huzhou Central Hospital), Huzhou, China
| | - Jianming Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Brain Research Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Collaborative Innovation Center for Brain Science, Zhejiang University, Hangzhou, Zhejiang, China
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19
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Liu D, Tsarouhas V, Samakovlis C. WASH activation controls endosomal recycling and EGFR and Hippo signaling during tumor-suppressive cell competition. Nat Commun 2022; 13:6243. [PMID: 36271083 PMCID: PMC9587002 DOI: 10.1038/s41467-022-34067-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Cell competition is a conserved homeostatic mechanism whereby epithelial cells eliminate neighbors with lower fitness. Cell communication at the interface of wild-type "winner" cells and polarity-deficient (scrib-/-) "losers" is established through Sas-mediated Ptp10D activation in polarity-deficient cells. This tumor-suppressive cell competition restrains EGFR and Hippo signaling and enables Eiger-JNK mediated apoptosis in scrib-/- clones. Here, we show that the activation state of the endosomal actin regulator WASH is a central node linking EGFR and Hippo signaling activation. The tyrosine kinase Btk29A and its substrate WASH are required downstream of Ptp10D for "loser" cell elimination. Constitutively active, phosphomimetic WASH is sufficient to induce both EGFR and Yki activation leading to overgrowth. On the mechanistic level we show that Ptp10D is recycled by the WASH/retromer complex, while EGFR is recycled by the WASH/retriever complex. Constitutive WASH activation selectively interferes with retromer function leading to Ptp10D mistargeting while promoting EGFR recycling and signaling activation. Phospho-WASH also activates aberrant Arp2/3 actin polymerization, leading to cytoskeletal imbalance, Yki activation and reduced apoptosis. Selective manipulation of WASH phosphorylation on sorting endosomes may restrict epithelial tumorous growth.
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Affiliation(s)
- Dan Liu
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Vasilios Tsarouhas
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Christos Samakovlis
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden ,grid.8664.c0000 0001 2165 8627Cardiopulmonary Institute, Justus Liebig University of Giessen, Giessen, Germany
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20
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Deciphering Spatial Protein-Protein Interactions in Brain Using Proximity Labeling. Mol Cell Proteomics 2022; 21:100422. [PMID: 36198386 PMCID: PMC9650050 DOI: 10.1016/j.mcpro.2022.100422] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 01/18/2023] Open
Abstract
Cellular biomolecular complexes including protein-protein, protein-RNA, and protein-DNA interactions regulate and execute most biological functions. In particular in brain, protein-protein interactions (PPIs) mediate or regulate virtually all nerve cell functions, such as neurotransmission, cell-cell communication, neurogenesis, synaptogenesis, and synaptic plasticity. Perturbations of PPIs in specific subsets of neurons and glia are thought to underly a majority of neurobiological disorders. Therefore, understanding biological functions at a cellular level requires a reasonably complete catalog of all physical interactions between proteins. An enzyme-catalyzed method to biotinylate proximal interacting proteins within 10 to 300 nm of each other is being increasingly used to characterize the spatiotemporal features of complex PPIs in brain. Thus, proximity labeling has emerged recently as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and PPIs in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte-neuron junctions. In this review, we summarize recent advances in proximity labeling methods and their application to neurobiology.
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21
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Disruption of the lipolysis pathway results in stem cell death through a sterile immunity-like pathway in adult Drosophila. Cell Rep 2022; 39:110958. [PMID: 35732115 PMCID: PMC9377423 DOI: 10.1016/j.celrep.2022.110958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/26/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
We previously showed that the Arf1-mediated lipolysis pathway sustains stem cells and cancer stem cells (CSCs); its ablation resulted in necrosis of stem cells and CSCs, which further triggers a systemic antitumor immune response. Here we show that knocking down Arf1 in intestinal stem cells (ISCs) causes metabolic stress, which promotes the expression and translocation of ISC-produced damage-associated molecular patterns (DAMPs; Pretaporter [Prtp] and calreticulin [Calr]). DAMPs regulate macroglobulin complement-related (Mcr) expression and secretion. The secreted Mcr influences the expression and localization of enterocyte (EC)-produced Draper (Drpr) and LRP1 receptors (pattern recognition receptors [PRRs]) to activate autophagy in ECs for ATP production. The secreted ATP possibly feeds back to kill ISCs by activating inflammasome-like pyroptosis. We identify an evolutionarily conserved pathway that sustains stem cells and CSCs, and its ablation results in an immunogenic cascade that promotes death of stem cells and CSCs as well as antitumor immunity. Aggarwal et al. show that disruption of Arf1-mediated lipolysis results in stem cell death through a sterile immunity-like pathway in adult Drosophila. They identify an evolutionarily conserved pathway that specifically sustains stem cells and cancer stem cells (CSCs), and its ablation results in an immunogenic cascade that promotes death of stem cells and CSCs as well as antitumor immunity.
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22
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Dehkordi MH, Munn RGK, Fearnhead HO. Non-Canonical Roles of Apoptotic Caspases in the Nervous System. Front Cell Dev Biol 2022; 10:840023. [PMID: 35281082 PMCID: PMC8904960 DOI: 10.3389/fcell.2022.840023] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Caspases are a family of cysteine proteases that predominantly cleave their substrates after aspartic acid residues. Much of what we know of caspases emerged from investigation a highly conserved form of programmed cell death called apoptosis. This form of cell death is regulated by several caspases, including caspase-2, caspase-3, caspase-7, caspase-8 and caspase-9. However, these “killer” apoptotic caspases have emerged as versatile enzymes that play key roles in a wide range of non-apoptotic processes. Much of what we understand about these non-apoptotic roles is built on work investigating how “killer” caspases control a range of neuronal cell behaviors. This review will attempt to provide an up to date synopsis of these roles.
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Affiliation(s)
- Mahshid H. Dehkordi
- Pharmacology and Therapeutics, National University of Ireland Galway, Galway, Ireland
| | | | - Howard O. Fearnhead
- Pharmacology and Therapeutics, National University of Ireland Galway, Galway, Ireland
- *Correspondence: Howard O. Fearnhead,
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23
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Agwunobi DO, Zhang M, Zhang X, Wang T, Yu Z, Liu J. Transcriptome profile of Haemaphysalis longicornis (Acari: Ixodidae) exposed to Cymbopogon citratus essential oil and citronellal suggest a cytotoxic mode of action involving mitochondrial Ca 2+ overload and depolarization. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 179:104971. [PMID: 34802521 DOI: 10.1016/j.pestbp.2021.104971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Haemaphysalis longicornis is an ixodid tick species of medical and veterinary importance. Investigation into the acaricidal activities of botanicals have increased recently but information about their molecular mechanism of action is scarce. Here, RNA-seq analysis of the ticks exposed to Cymbopogon citratus essential oil and citronellal was performed and the responsive genes were identified. More than 6.39 G clean reads with Q20 ≥ 94.88% were obtained for each H. longicornis sample, with an average GC content of 50.94%. Using the Trinity method, 166,710 unigenes with a mean length of 869 bp and a maximum contig length of 29,156 bp were obtained. The upregulation of genes was concentration-dependent in most of the treated groups. Many genes responsive to C. citratus oil and citronellal were stress-related and they include genes associated with adrenergic signaling/calcium channels, cGMP-PKG signaling, apoptosis, focal adhesion, ECM-receptor interaction, ubiquitin-mediated proteolysis, mTOR signaling pathway, and longevity regulating pathway. The upregulation of genes (CACNAID, ADCY9, TPM1, and MYH6) associated with calcium channels suggests a neurotoxic mode of action, whereas, the upregulation of apoptosis-associated genes (CYC, DRONC, CASP7, CASP9, BCL2L1, bcl-xL, etc.) suggests a cytotoxic mode of action. The metabolism of C. citratus essential oil generates oxidative stress which increases the intra-mitochondrial free Ca2+ and triggers the formation of reactive oxygen species (ROS) that culminates to mitochondrial depolarization, ATP depletion, and either necrotic or apoptotic death. The neurotoxic and cytotoxic effects exhibited by the monoterpenes in H. longicornis is vital and could be exploited for the advancement of acaricide development and eco-friendly tick control.
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Affiliation(s)
- Desmond O Agwunobi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Meng Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiaojing Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Tongxuan Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
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24
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Zhang B, Zhang Y, Liu JL. Highly effective proximate labeling in Drosophila. G3-GENES GENOMES GENETICS 2021; 11:6173991. [PMID: 33724396 PMCID: PMC8104946 DOI: 10.1093/g3journal/jkab077] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022]
Abstract
The protein-protein interaction (PPI) is a basic strategy for life to operate. The analysis of PPIs in multicellular organisms is very important but extremely challenging because PPIs are particularly dynamic and variable among different development stages, tissues, cells, and even organelles. Therefore, understanding PPI needs a good resolution of time and space. More importantly, understanding in vivo PPI needs to be realized in situ. Proximity-based biotinylation combined with mass spectrometry (MS) has emerged as a powerful approach to study PPI networks and protein subcellular compartmentation. TurboID, the newly engineered promiscuous ligase, has been reported to label proximate proteins effectively in various species. In Drosophila, we systematically apply TurboID-mediated biotinylation in a wide range of developmental stages and tissues, and demonstrate the feasibility of TurboID-mediated labeling system in desired cell types. For a proof-of-principle, we use the TurboID-mediated biotinylation coupled with MS to distinguish CTP synthase with or without the ability to form filamentous cytoophidia, retrieving two distinct sets of proximate proteomes. Therefore, this makes it possible to map PPIs in vivo and in situ at a defined spatiotemporal resolution, and demonstrates a referable resource for cytoophidium proteome in Drosophila.
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Affiliation(s)
- Bo Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanbing Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
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25
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DNase II mediates a parthanatos-like developmental cell death pathway in Drosophila primordial germ cells. Nat Commun 2021; 12:2285. [PMID: 33863891 PMCID: PMC8052343 DOI: 10.1038/s41467-021-22622-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 03/23/2021] [Indexed: 02/02/2023] Open
Abstract
During Drosophila embryonic development, cell death eliminates 30% of the primordial germ cells (PGCs). Inhibiting apoptosis does not prevent PGC death, suggesting a divergence from the conventional apoptotic program. Here, we demonstrate that PGCs normally activate an intrinsic alternative cell death (ACD) pathway mediated by DNase II release from lysosomes, leading to nuclear translocation and subsequent DNA double-strand breaks (DSBs). DSBs activate the DNA damage-sensing enzyme, Poly(ADP-ribose) (PAR) polymerase-1 (PARP-1) and the ATR/Chk1 branch of the DNA damage response. PARP-1 and DNase II engage in a positive feedback amplification loop mediated by the release of PAR polymers from the nucleus and the nuclear accumulation of DNase II in an AIF- and CypA-dependent manner, ultimately resulting in PGC death. Given the anatomical and molecular similarities with an ACD pathway called parthanatos, these findings reveal a parthanatos-like cell death pathway active during Drosophila development.
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26
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Ji Z, Chuen J, Kiparaki M, Baker N. Cell competition removes segmental aneuploid cells from Drosophila imaginal disc-derived tissues based on ribosomal protein gene dose. eLife 2021; 10:61172. [PMID: 33847264 PMCID: PMC8043752 DOI: 10.7554/elife.61172] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/08/2021] [Indexed: 12/22/2022] Open
Abstract
Aneuploidy causes birth defects and miscarriages, occurs in nearly all cancers and is a hallmark of aging. Individual aneuploid cells can be eliminated from developing tissues by unknown mechanisms. Cells with ribosomal protein (Rp) gene mutations are also eliminated, by cell competition with normal cells. Because Rp genes are spread across the genome, their copy number is a potential marker for aneuploidy. We found that elimination of imaginal disc cells with irradiation-induced genome damage often required cell competition genes. Segmentally aneuploid cells derived from targeted chromosome excisions were eliminated by the RpS12-Xrp1 cell competition pathway if they differed from neighboring cells in Rp gene dose, whereas cells with normal doses of the Rp and eIF2γ genes survived and differentiated adult tissues. Thus, cell competition, triggered by differences in Rp gene dose between cells, is a significant mechanism for the elimination of aneuploid somatic cells, likely to contribute to preventing cancer. Aneuploid cells emerge when cellular division goes awry and a cell ends up with the wrong number of chromosomes, the tiny genetic structures carrying the instructions that control life’s processes. Aneuploidy can lead to fatal conditions during development, and to cancer in an adult organism. A safety mechanism may exist that helps the body to detect and remove these cells. Yet, exactly this happens is still poorly understood: in particular, it is unclear how cells manage to ‘count’ their chromosomes. One way they could do so is through the ribosomes, the molecular ‘factories’ that create the building blocks required for life. In a cell, every chromosome carries genes that code for the proteins (known as Rps) forming ribosomes. Aneuploidy will alter the number of Rp genes, and in turn the amount and type of Rps the cell produces, so that ribosomes and the genes for Rps could act as a ‘readout’ of aneuploidy. Ji et al set out to test this theory in fruit flies. The first experiment used a genetic manipulation technique called site-specific recombination to remove parts of chromosomes from cells in the developing eye and wing. Cells which retained all their Rp genes survived, while those that were missing some usually died – but only when the surrounding cells were normal. In this situation, healthy cells eliminated their damaged neighbours through a process known as cell competition. A second experiment, using radiation as an alternative method of damaging chromosomes, also gave similar results. The work by Ji et al. reveals how the body can detect and eliminate aneuploid cells, potentially before they can cause harm. If the same mechanism applies in humans, boosting cell competition may, one day, helps to combat diseases like cancer.
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Affiliation(s)
- Zhejun Ji
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Jacky Chuen
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Marianthi Kiparaki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Nicholas Baker
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
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27
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Proximity Biotin Labeling Reveals Kaposi's Sarcoma-Associated Herpesvirus Interferon Regulatory Factor Networks. J Virol 2021; 95:JVI.02049-20. [PMID: 33597212 PMCID: PMC8104114 DOI: 10.1128/jvi.02049-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/10/2021] [Indexed: 01/04/2023] Open
Abstract
Viral protein interaction with a host protein shows at least two sides: (i) taking host protein functions for its own benefit and (ii) disruption of existing host protein complex formation to inhibit undesirable host responses. Due to the use of affinity precipitation approaches, the majority of studies have focused on how the virus takes advantage of the newly formed protein interactions for its own replication. Studies on “hit-and-run” effects by viral proteins are difficult when using traditional affinity precipitation-based techniques under dynamic conditions, because only proteins interacting at a specific instance in time can be precipitated by affinity purification. Recent advances in proximity labeling (PL) have enabled identification of both static and dynamic protein-protein interactions. In this study, we applied a PL method by generating recombinant Kaposi’s sarcoma-associated herpesvirus (KSHV). KSHV, a gammaherpesvirus, uniquely encodes four interferon regulatory factors (IRF-1 to -4) that suppress host interferon responses, and we examined KSHV IRF-1 and IRF-4 neighbor proteins to identify cellular proteins involved in innate immune regulation. PL identified 213 and 70 proteins as neighboring proteins of viral IRF-1 (vIRF-1) and vIRF-4 during viral reactivation, and 47 proteins were shared between the two vIRFs; the list also includes three viral proteins, ORF17, thymidine kinase, and vIRF-4. Functional annotation of respective interacting proteins showed highly overlapping biological roles such as mRNA processing and transcriptional regulation by TP53. Innate immune regulation by these commonly interacting 44 cellular proteins was examined with small interfering RNAs (siRNAs), and the splicing factor 3B family proteins were found to be associated with interferon transcription and to act as suppressors of KSHV reactivation. We propose that recombinant mini-TurboID-KSHV is a powerful tool to probe key cellular proteins that play a role in KSHV replication and that selective splicing factors have a function in the regulation of innate immune responses. IMPORTANCE Viral protein interaction with a host protein shows at least two sides: (i) taking host protein functions for its own benefit and (ii) disruption of existing host protein complex formation to inhibit undesirable host responses. Due to the use of affinity precipitation approaches, the majority of studies have focused on how the virus takes advantage of the newly formed protein interactions for its own replication. Proximity labeling (PL), however, can also highlight transient and negative effects—those interactions which lead to dissociation from the existing protein complex. Here, we highlight the power of PL in combination with recombinant KSHV to study viral host interactions.
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28
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Qin W, Cho KF, Cavanagh PE, Ting AY. Deciphering molecular interactions by proximity labeling. Nat Methods 2021; 18:133-143. [PMID: 33432242 PMCID: PMC10548357 DOI: 10.1038/s41592-020-01010-5] [Citation(s) in RCA: 219] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Many biological processes are executed and regulated through the molecular interactions of proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the endogenous interaction partners of specific protein 'baits', via genetic fusion to promiscuous enzymes that catalyze the generation of diffusible reactive species in living cells. Tagged molecules that interact with baits can then be enriched and identified by mass spectrometry or nucleic acid sequencing. Here we review the development of PL technologies and highlight studies that have applied PL to the discovery and analysis of molecular interactions. In particular, we focus on the use of PL for mapping protein-protein, protein-RNA and protein-DNA interactions in living cells and organisms.
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Affiliation(s)
- Wei Qin
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kelvin F Cho
- Department of Genetics, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Peter E Cavanagh
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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29
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Arthurton L, Nahotko DA, Alonso J, Wendler F, Baena‐Lopez LA. Non-apoptotic caspase activation preserves Drosophila intestinal progenitor cells in quiescence. EMBO Rep 2020; 21:e48892. [PMID: 33135280 PMCID: PMC7726796 DOI: 10.15252/embr.201948892] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/21/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Caspase malfunction in stem cells often precedes the appearance and progression of multiple types of cancer, including human colorectal cancer. However, the caspase-dependent regulation of intestinal stem cell properties remains poorly understood. Here, we demonstrate that Dronc, the Drosophila ortholog of caspase-9/2 in mammals, limits the number of intestinal progenitor cells and their entry into the enterocyte differentiation programme. Strikingly, these unexpected roles for Dronc are non-apoptotic and have been uncovered under experimental conditions without epithelial replenishment. Supporting the non-apoptotic nature of these functions, we show that they require the enzymatic activity of Dronc, but are largely independent of the apoptotic pathway. Alternatively, our genetic and functional data suggest that they are linked to the caspase-mediated regulation of Notch signalling. Our findings provide novel insights into the non-apoptotic, caspase-dependent modulation of stem cell properties that could improve our understanding of the origin of intestinal malignancies.
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Affiliation(s)
- Lewis Arthurton
- Sir William Dunn School of PathologyUniversity of OxfordOxfordshireUK
| | | | - Jana Alonso
- Laboratorio de Agrobiología Juan José Bravo Rodríguez (Cabildo Insular de La Palma)Unidad Técnica del IPNA‐CSICSanta Cruz de La PalmaSpain
| | - Franz Wendler
- Sir William Dunn School of PathologyUniversity of OxfordOxfordshireUK
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30
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Sun G, Ding XA, Argaw Y, Guo X, Montell DJ. Akt1 and dCIZ1 promote cell survival from apoptotic caspase activation during regeneration and oncogenic overgrowth. Nat Commun 2020; 11:5726. [PMID: 33184261 PMCID: PMC7664998 DOI: 10.1038/s41467-020-19068-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2020] [Indexed: 01/07/2023] Open
Abstract
Apoptosis is an ancient and evolutionarily conserved cell suicide program. During apoptosis, executioner caspase enzyme activation has been considered a point of no return. However, emerging evidence suggests that some cells can survive caspase activation following exposure to apoptosis-inducing stresses, raising questions as to the physiological significance and underlying molecular mechanisms of this unexpected phenomenon. Here, we show that, following severe tissue injury, Drosophila wing disc cells that survive executioner caspase activation contribute to tissue regeneration. Through RNAi screening, we identify akt1 and a previously uncharacterized Drosophila gene CG8108, which is homologous to the human gene CIZ1, as essential for survival from the executioner caspase activation. We also show that cells expressing activated oncogenes experience apoptotic caspase activation, and that Akt1 and dCIZ1 are required for their survival and overgrowth. Thus, survival following executioner caspase activation is a normal tissue repair mechanism usurped to promote oncogene-driven overgrowth.
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Affiliation(s)
- Gongping Sun
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA.
| | - Xun Austin Ding
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Yewubdar Argaw
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Xiaoran Guo
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Denise J Montell
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA.
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31
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Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
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Ford DJ, Zraly CB, Perez JH, Dingwall AK. The Drosophila MLR COMPASS-like complex regulates bantam miRNA expression differentially in the context of cell fate. Dev Biol 2020; 468:41-53. [PMID: 32946789 DOI: 10.1016/j.ydbio.2020.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
The conserved MLR COMPASS-like complexes are histone modifiers that are recruited by a variety of transcription factors to enhancer regions where they act as necessary epigenetic tools for enhancer establishment and function. A critical in vivo target of the Drosophila MLR complex is the bantam miRNA that regulates cell survival and functions in feedback regulation of cellular signaling pathways during development. We determine that loss of Drosophila MLR complex function in developing wing and eye imaginal discs results in growth and patterning defects that are sensitive to bantam levels. Consistent with an essential regulatory role in modulating bantam transcription, the MLR complex binds to tissue-specific bantam enhancers and contributes to fine-tuning expression levels during larval tissue development. In wing imaginal discs, the MLR complex attenuates bantam enhancer activity by negatively regulating expression; whereas, in differentiating eye discs, the complex exerts either positive or negative regulatory activity on bantam transcription depending on cell fate. Furthermore, while the MLR complex is not required to control bantam levels in undifferentiated eye cells anterior to the morphogenetic furrow, it serves to prepare critical enhancer control of bantam transcription for later regulation upon differentiation. Our investigation into the transcriptional regulation of a single target in a developmental context has provided novel insights as to how the MLR complex contributes to the precise timing of gene expression, and how the complex functions to help orchestrate the regulatory output of conserved signaling pathways during animal development.
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Affiliation(s)
- David J Ford
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - John Hertenstein Perez
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA; Department of Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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33
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Bosch JA, Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells: An update. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e392. [PMID: 32909689 DOI: 10.1002/wdev.392] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we provide an updated description and comparison of proximity labeling methods, as well as their applications and improvements. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. This article is categorized under: Technologies > Analysis of Proteins.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chiao-Lin Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
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Tyra LK, Nandi N, Tracy C, Krämer H. Yorkie Growth-Promoting Activity Is Limited by Atg1-Mediated Phosphorylation. Dev Cell 2020; 52:605-616.e7. [PMID: 32032548 DOI: 10.1016/j.devcel.2020.01.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/26/2019] [Accepted: 01/09/2020] [Indexed: 01/31/2023]
Abstract
The expression of multiple growth-promoting genes is coordinated by the transcriptional co-activator Yorkie with its major regulatory input provided by the Hippo-Warts kinase cascade. Here, we identify Atg1/ULK1-mediated phosphorylation of Yorkie as an additional inhibitory input independent of the Hippo-Warts pathway. Two serine residues in Yorkie, S74 and S97, are Atg1/ULK1 consensus target sites and are phosphorylated by ULK1 in vitro, thereby preventing its binding to Scalloped. In vivo, gain of function of Atg1, or its activator Acinus, caused elevated Yorkie phosphorylation and inhibited Yorkie's growth-promoting activity. Loss of function of Atg1 or Acinus raised expression of Yorkie target genes and increased tissue size. Unlike Atg1's role in autophagy, Atg1-mediated phosphorylation of Yorkie does not require Atg13. Atg1 is activated by starvation and other cellular stressors and therefore can impose temporary stress-induced constraints on the growth-promoting gene networks under the control of Hippo-Yorkie signaling.
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Affiliation(s)
- Lauren K Tyra
- Peter O'Donnell Jr. Brain Institute, Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Nilay Nandi
- Peter O'Donnell Jr. Brain Institute, Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Charles Tracy
- Peter O'Donnell Jr. Brain Institute, Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Helmut Krämer
- Peter O'Donnell Jr. Brain Institute, Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA.
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