1
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Chu YD, Chen MC, Yeh CT, Lai MW. Hijacking host extracellular vesicle machinery by hepatotropic viruses: current understandings and future prospects. J Biomed Sci 2024; 31:97. [PMID: 39369194 PMCID: PMC11453063 DOI: 10.1186/s12929-024-01063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/25/2024] [Indexed: 10/07/2024] Open
Abstract
Recent advances in studies exploring the roles of extracellular vesicles (EVs) in viral transmission and replication have illuminated hepatotropic viruses, such as hepatitis A (HAV), hepatitis B (HBV), hepatitis C (HCV), hepatitis D (HDV), and hepatitis E (HEV). While previous investigations have uncovered these viruses' ability to exploit cellular EV pathways for replication and transmission, most have focused on the impacts of exosomal pathways. With an improved understanding of EVs, four main subtypes, including exosomes, microvesicles, large oncosomes, and apoptotic bodies, have been categorized based on size and biogenic pathways. However, there remains a noticeable gap in comprehensive reviews summarizing recent findings and outlining future perspectives for EV studies related to hepatotropic viruses. This review aims to consolidate insights into EV pathways utilized by hepatotropic viruses, offering guidance for the future research direction in this field. By comprehending the diverse range of hepatotropic virus-associated EVs and their role in cellular communication during productive viral infections, this review may offer valuable insights for targeting therapeutics and devising strategies to combat virulent hepatotropic virus infections and the associated incidence of liver cancer.
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Affiliation(s)
- Yu-De Chu
- Liver Research Center, Chang Gung Memorial Hospital, 5F., No. 15, Wenhua 1st Rd., Guishan Dist., Taoyuan City, 333, Taiwan
| | - Mi-Chi Chen
- Liver Research Center, Chang Gung Memorial Hospital, 5F., No. 15, Wenhua 1st Rd., Guishan Dist., Taoyuan City, 333, Taiwan
- Department of Pediatric, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, 5F., No. 15, Wenhua 1st Rd., Guishan Dist., Taoyuan City, 333, Taiwan.
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
| | - Ming-Wei Lai
- Liver Research Center, Chang Gung Memorial Hospital, 5F., No. 15, Wenhua 1st Rd., Guishan Dist., Taoyuan City, 333, Taiwan.
- Department of Pediatric, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
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2
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Ikezu T, Yang Y, Verderio C, Krämer-Albers EM. Extracellular Vesicle-Mediated Neuron-Glia Communications in the Central Nervous System. J Neurosci 2024; 44:e1170242024. [PMID: 39358029 PMCID: PMC11450539 DOI: 10.1523/jneurosci.1170-24.2024] [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: 06/19/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 10/04/2024] Open
Abstract
Communication between neurons and glia significantly influences the development maturation, plasticity, and disease progressions of the nervous system. As a new signaling modality, extracellular vesicles display a diverse role for robust functional regulation of neurons through their protein and nucleic acid cargoes. This review highlights recent breakthroughs in the research of signaling mechanisms between glia and neurons mediated by extracellular vesicles that are important for neural development, axonal maintenance, synaptic functions, and disease progression in the mammalian nervous system. We will discuss the biological roles of extracellular vesicles released from neurons, astroglia, microglia, and oligodendroglia in the nervous system and their implications in neurodegenerative disorders.
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Affiliation(s)
- Tsuneya Ikezu
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224
| | - Yongjie Yang
- Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts 02111
| | - Claudia Verderio
- Department of Biomedical Sciences, CNR Institute of Neuroscience, Università Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Eva-Maria Krämer-Albers
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, 55128 Mainz, Rhineland Palatinate, Germany
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3
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Li Y, Zhang H, Yang F, Zhu D, Chen S, Wang Z, Wei Z, Yang Z, Jia J, Zhang Y, Wang D, Ma M, Kang X. Mechanisms and therapeutic potential of disulphidptosis in cancer. Cell Prolif 2024:e13752. [PMID: 39354653 DOI: 10.1111/cpr.13752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/30/2024] [Accepted: 09/14/2024] [Indexed: 10/04/2024] Open
Abstract
SLC7A11 plays a pivotal role in tumour development by facilitating cystine import to enhance glutathione synthesis and counteract oxidative stress. Disulphidptosis, an emerging form of cell death observed in cells with high expression of SLC7A11 under glucose deprivation, is regulated through reduction-oxidation reactions and disulphide bond formation. This process leads to contraction and collapse of the F-actin cytoskeleton from the plasma membrane, ultimately resulting in cellular demise. Compared to other forms of cell death, disulphidptosis exhibits distinctive characteristics and regulatory mechanisms. This mechanism provides novel insights and innovative strategies for cancer treatment while also inspiring potential therapeutic approaches for other diseases. Our review focuses on elucidating the molecular mechanism underlying disulphidptosis and its connection with the actin cytoskeleton, identifying alternative metabolic forms of cell death, as well as offering insights into disulphidptosis-based cancer therapy. A comprehensive understanding of disulphidptosis will contribute to our knowledge about fundamental cellular homeostasis and facilitate the development of groundbreaking therapies for disease treatment.
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Affiliation(s)
- Yanhu Li
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Haijun Zhang
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
- The Second People's Hospital of Gansu Province, Lanzhou, PR China
| | - Fengguang Yang
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Daxue Zhu
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Shijie Chen
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Zhaoheng Wang
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Ziyan Wei
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Zhili Yang
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Jingwen Jia
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Yizhi Zhang
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Dongxin Wang
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Mingdong Ma
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
| | - Xuewen Kang
- Lanzhou University Second Hospital, Lanzhou, PR China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, PR China
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4
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Merret PE, Sparfel L, Lavau C, Lagadic-Gossmann D, Martin-Chouly C. Extracellular vesicles as a potential source of biomarkers for endocrine disruptors in MASLD: A short review on the case of DEHP. Biochimie 2024:S0300-9084(24)00219-0. [PMID: 39307409 DOI: 10.1016/j.biochi.2024.09.009] [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: 02/14/2024] [Revised: 08/28/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024]
Abstract
Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) is a chronic disease with increasing prevalence and for which non-invasive biomarkers are needed. Environmental endocrine disruptors (EDs) are known to be involved in the onset and progression of MASLD and assays to monitor their impact on the liver are being developed. Extracellular vesicles (EVs) mediate cell communication and their content reflects the pathophysiological state of the cells from which they are released. They can thus serve as biomarkers of the pathological state of the liver and of exposure to EDs. In this review, we present the relationships between DEHP (Di(2-ethylhexyl) phthalate) and MASLD and highlight the potential of EVs as biomarkers of DEHP exposure and the resulting progression of MASLD.
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Affiliation(s)
- Pierre-Etienne Merret
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France
| | - Lydie Sparfel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France
| | - Catherine Lavau
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France
| | - Dominique Lagadic-Gossmann
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France.
| | - Corinne Martin-Chouly
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France.
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5
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Tsering T, Nadeau A, Wu T, Dickinson K, Burnier JV. Extracellular vesicle-associated DNA: ten years since its discovery in human blood. Cell Death Dis 2024; 15:668. [PMID: 39266560 PMCID: PMC11393322 DOI: 10.1038/s41419-024-07003-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 07/29/2024] [Accepted: 08/14/2024] [Indexed: 09/14/2024]
Abstract
Extracellular vesicles (EVs) have emerged as key players in intercellular communication, facilitating the transfer of crucial cargo between cells. Liquid biopsy, particularly through the isolation of EVs, has unveiled a rich source of potential biomarkers for health and disease, encompassing proteins and nucleic acids. A milestone in this exploration occurred a decade ago with the identification of extracellular vesicle-associated DNA (EV-DNA) in the bloodstream of a patient diagnosed with pancreatic cancer. Subsequent years have witnessed substantial advancements, deepening our insights into the molecular intricacies of EV-DNA emission, detection, and analysis. Understanding the complexities surrounding the release of EV-DNA and addressing the challenges inherent in EV-DNA research are pivotal steps toward enhancing liquid biopsy-based strategies. These strategies, crucial for the detection and monitoring of various pathological conditions, particularly cancer, rely on a comprehensive understanding of why and how EV-DNA is released. In our review, we aim to provide a thorough summary of a decade's worth of research on EV-DNA. We will delve into diverse mechanisms of EV-DNA emission, its potential as a biomarker, its functional capabilities, discordant findings in the field, and the hurdles hindering its clinical application. Looking ahead to the next decade, we envision that advancements in EV isolation and detection techniques, coupled with improved standardization and data sharing, will catalyze the development of novel strategies exploiting EV-DNA as both a source of biomarkers and therapeutic targets.
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Affiliation(s)
- Thupten Tsering
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pathology, McGill University, Montreal, QC, Canada
| | - Amélie Nadeau
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pathology, McGill University, Montreal, QC, Canada
| | - Tad Wu
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pathology, McGill University, Montreal, QC, Canada
| | - Kyle Dickinson
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Julia V Burnier
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Department of Pathology, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
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6
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Nanavati BN, Noordstra I, Lwin AKO, Brooks JW, Rae J, Parton RG, Verma S, Duszyc K, Green KJ, Yap AS. The desmosome-intermediate filament system facilitates mechanotransduction at adherens junctions for epithelial homeostasis. Curr Biol 2024; 34:4081-4090.e5. [PMID: 39153481 PMCID: PMC11387132 DOI: 10.1016/j.cub.2024.07.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 12/04/2023] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Epithelial homeostasis can be critically influenced by how cells respond to mechanical forces, both local changes in force balance between cells and altered tissue-level forces.1 Coupling of specialized cell-cell adhesions to their cytoskeletons provides epithelia with diverse strategies to respond to mechanical stresses.2,3,4 Desmosomes confer tissue resilience when their associated intermediate filaments (IFs)2,3 stiffen in response to strain,5,6,7,8,9,10,11 while mechanotransduction associated with the E-cadherin apparatus12,13 at adherens junctions (AJs) actively modulates actomyosin by RhoA signaling. Although desmosomes and AJs make complementary contributions to mechanical homeostasis in epithelia,6,8 there is increasing evidence to suggest that these cytoskeletal-adhesion systems can interact functionally and biochemically.8,14,15,16,17,18,19,20 We now report that the desmosome-IF system integrated by desmoplakin (DP) facilitates active tension sensing at AJs for epithelial homeostasis. DP function is necessary for mechanosensitive RhoA signaling at AJs to be activated when tension was applied to epithelial monolayers. This effect required DP to anchor IFs to desmosomes and recruit the dystonin (DST) cytolinker to apical junctions. DP RNAi reduced the mechanical load that was applied to the cadherin complex by increased monolayer tension. Consistent with reduced mechanical signal strength, DP RNAi compromised assembly of the Myosin VI-E-cadherin mechanosensor that activates RhoA. The integrated DP-IF system therefore supports AJ mechanotransduction by enhancing the mechanical load of tissue tension that is transmitted to E-cadherin. This crosstalk was necessary for efficient elimination of apoptotic epithelial cells by apical extrusion, demonstrating its contribution to epithelial homeostasis.
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Affiliation(s)
- Bageshri Naimish Nanavati
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Ivar Noordstra
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Angela K O Lwin
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - John W Brooks
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - James Rae
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Robert G Parton
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Suzie Verma
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kinga Duszyc
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kathleen J Green
- Departments of Pathology and Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL 06011, USA
| | - Alpha S Yap
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.
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7
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Zhou H, Hu S, Yan W. Extracellular vesicles as modifiers of epigenomic profiles. Trends Genet 2024; 40:797-809. [PMID: 38845265 DOI: 10.1016/j.tig.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 09/12/2024]
Abstract
Extracellular vesicles (EVs), emerging as novel mediators between intercellular communication, encapsulate distinct bioactive cargoes to modulate multiple biological events, such as epigenetic remodeling. In essence, EVs and epigenomic profiles are tightly linked and reciprocally regulated. Epigenetic factors, including histone and DNA modifications, noncoding RNAs, and protein post-translational modifications (PTMs) dynamically regulate EV biogenesis to contribute to EV heterogeneity. Alternatively, EVs actively modify DNA, RNA, and histone profiles in recipient cells by delivering RNA and protein cargoes for downstream epigenetic enzyme regulation. Moreover, EVs display great potential as diagnostic markers and drug-delivery vehicles for therapeutic applications. The combination of parental cell epigenomic modification with single EV characterization would be a promising strategy for EV engineering to enhance the epidrug loading efficacy and accuracy.
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Affiliation(s)
- Haifeng Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Sheng Hu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wei Yan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China..
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8
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Putthanbut N, Lee JY, Borlongan CV. Extracellular vesicle therapy in neurological disorders. J Biomed Sci 2024; 31:85. [PMID: 39183263 PMCID: PMC11346291 DOI: 10.1186/s12929-024-01075-w] [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: 06/17/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024] Open
Abstract
Extracellular vesicles (EVs) are vital for cell-to-cell communication, transferring proteins, lipids, and nucleic acids in various physiological and pathological processes. They play crucial roles in immune modulation and tissue regeneration but are also involved in pathogenic conditions like inflammation and degenerative disorders. EVs have heterogeneous populations and cargo, with numerous subpopulations currently under investigations. EV therapy shows promise in stimulating tissue repair and serving as a drug delivery vehicle, offering advantages over cell therapy, such as ease of engineering and minimal risk of tumorigenesis. However, challenges remain, including inconsistent nomenclature, complex characterization, and underdeveloped large-scale production protocols. This review highlights the recent advances and significance of EVs heterogeneity, emphasizing the need for a better understanding of their roles in disease pathologies to develop tailored EV therapies for clinical applications in neurological disorders.
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Affiliation(s)
- Napasiri Putthanbut
- Department of Neurosurgery, Center of Aging and Brain Repair, University of South Florida, Tampa, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Salaya, Thailand
| | - Jea Young Lee
- Department of Neurosurgery, Center of Aging and Brain Repair, University of South Florida, Tampa, USA
| | - Cesario V Borlongan
- Department of Neurosurgery, Center of Aging and Brain Repair, University of South Florida, Tampa, USA.
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9
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Wu Q, Du J, Bae EJ, Choi Y. Pyroptosis in Skeleton Diseases: A Potential Therapeutic Target Based on Inflammatory Cell Death. Int J Mol Sci 2024; 25:9068. [PMID: 39201755 PMCID: PMC11354934 DOI: 10.3390/ijms25169068] [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: 06/25/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
Skeletal disorders, including fractures, osteoporosis, osteoarthritis, rheumatoid arthritis, and spinal degenerative conditions, along with associated spinal cord injuries, significantly impair daily life and impose a substantial burden. Many of these conditions are notably linked to inflammation, with some classified as inflammatory diseases. Pyroptosis, a newly recognized form of inflammatory cell death, is primarily triggered by inflammasomes and executed by caspases, leading to inflammation and cell death through gasdermin proteins. Emerging research underscores the pivotal role of pyroptosis in skeletal disorders. This review explores the pyroptosis signaling pathways and their involvement in skeletal diseases, the modulation of pyroptosis by other signals in these conditions, and the current evidence supporting the therapeutic potential of targeting pyroptosis in treating skeletal disorders, aiming to offer novel insights for their management.
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Affiliation(s)
- Qian Wu
- Department of Biochemistry and Molecular Biology, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea (J.D.)
| | - Jiacheng Du
- Department of Biochemistry and Molecular Biology, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea (J.D.)
| | - Eun Ju Bae
- School of Pharmacy, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Yunjung Choi
- Division of Rheumatology, Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju 54896, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
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10
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Meng Z, Saei AA, Gharibi H, Zhang X, Lyu H, Lundström SL, Végvári Á, Gaetani M, Zubarev RA. Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates. Anal Chem 2024; 96:13533-13541. [PMID: 39110629 PMCID: PMC11339726 DOI: 10.1021/acs.analchem.4c02051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/21/2024]
Abstract
Here, we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics and demonstrates its utility in studying proteolytic events in programmed cell death. With gel-assisted proteome position integral shift (GAPPIS), we quantified over 7000 proteins in staurosporine-induced apoptotic HeLa cells and identified 84 proteins exhibiting in a statistically significant manner at least two of the following features: (i) a negative MW shift; (ii) an elevated ratio in a pair of a semitryptic and tryptic peptide, (iii) a negative shift in the standard deviation of MW estimated for different peptides, and (iv) a negative shift in skewness of the same data. Of these proteins, 58 molecules were previously unreported caspase 3 substrates. Further analysis identified the preferred cleavage sites consistent with the known caspase cleavages after the DXXD motif. As a powerful tool for high-throughput MW analysis simultaneously with the conventional expression analysis, the GAPPIS assay can prove useful in studying a broad range of biological processes involving proteolytic events.
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Affiliation(s)
- Zhaowei Meng
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Chemical
Proteomics Unit, Science for Life Laboratory
(SciLifeLab), Stockholm 17165, Sweden
- Chemical
Proteomics, Swedish National Infrastructure
for Biological Mass Spectrometry (BioMS), Stockholm 17177, Sweden
| | - Amir Ata Saei
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Hassan Gharibi
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Chemical
Proteomics Unit, Science for Life Laboratory
(SciLifeLab), Stockholm 17165, Sweden
- Chemical
Proteomics, Swedish National Infrastructure
for Biological Mass Spectrometry (BioMS), Stockholm 17177, Sweden
| | - Xuepei Zhang
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Chemical
Proteomics Unit, Science for Life Laboratory
(SciLifeLab), Stockholm 17165, Sweden
- Chemical
Proteomics, Swedish National Infrastructure
for Biological Mass Spectrometry (BioMS), Stockholm 17177, Sweden
| | - Hezheng Lyu
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- HDXperts
AB, Danderyd 18212, Sweden
| | - Susanna L. Lundström
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Chemical
Proteomics Unit, Science for Life Laboratory
(SciLifeLab), Stockholm 17165, Sweden
- Chemical
Proteomics, Swedish National Infrastructure
for Biological Mass Spectrometry (BioMS), Stockholm 17177, Sweden
| | - Ákos Végvári
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Massimiliano Gaetani
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Chemical
Proteomics Unit, Science for Life Laboratory
(SciLifeLab), Stockholm 17165, Sweden
- Chemical
Proteomics, Swedish National Infrastructure
for Biological Mass Spectrometry (BioMS), Stockholm 17177, Sweden
| | - Roman A. Zubarev
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Chemical
Proteomics, Swedish National Infrastructure
for Biological Mass Spectrometry (BioMS), Stockholm 17177, Sweden
- The National
Medical Research Center for Endocrinology, Moscow 115478, Russia
- Department
of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow 119048, Russia
- Department
of Pharmaceutical and Toxicological Chemistry, RUDN University, 6 Miklukho-Maklaya
St., Moscow 117198, Russia
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11
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Fang Y, Gong Z, You M, Peng K. Identification of a novel caspase cleavage motif AEAD. Virol Sin 2024:S1995-820X(24)00115-9. [PMID: 39098717 DOI: 10.1016/j.virs.2024.08.001] [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: 03/14/2023] [Accepted: 06/16/2023] [Indexed: 08/06/2024] Open
Abstract
Infections of many viruses induce caspase activation to regulate multiple cellular pathways, including programmed cell death, immune signaling and etc. Characterizations of caspase cleavage sites and substrates are important for understanding the regulation mechanisms of caspase activation. Here, we identified and analyzed a novel caspase cleavage motif AEAD, and confirmed its caspase dependent cleavage activity in natural substrate, such as nitric oxide-associated protein 1 (NOA1). Fusing the enhanced green fluorescent protein (EGFP) with the mitochondrial marker protein Tom20 through the AEAD motif peptide localized EGFP to the mitochondria. Upon the activation of caspase triggered by Sendai virus (SeV) or herpes simplex virus type 1 (HSV-1) infection, EGFP diffusely localized to the cell due to the caspase-mediated cleavage, thus allowing visual detection of the virus-induced caspase activation. An AEAD peptide-derived inhibitor Z-AEAD-FMK were developed, which significantly inhibited the activities of caspases-1, -3, -6, -7, -8 and -9, exhibiting a broad caspase inhibition effect. The inhibitor further prevented caspases-mediated cleavage of downstream substrates, including BID, PARP1, LMNA, pro-IL-1β, pro-IL-18, GSDMD and GSDME, protecting cells from virus-induced apoptotic and pyroptotic cell death. Together, our findings provide a new perspective for the identification of novel caspase cleavage motifs and the development of new caspase inhibitors and anti-inflammatory drugs.
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Affiliation(s)
- Yujie Fang
- State Key Laboratory of Virology, Center for Antiviral Research, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, 430071, China
| | - Miaomiao You
- State Key Laboratory of Virology, Center for Antiviral Research, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Peng
- State Key Laboratory of Virology, Center for Antiviral Research, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Provincial Key Laboratory of Jiangxia, Wuhan, 430207, China.
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12
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Matter A, Kaufman C, Zürcher N, Lenggenhager D, Grehten P, Bartholdi D, Horka L, Häberle J, Makris G. LEMD2-associated progeroid syndrome: Expanding the phenotype of the nuclear envelopathy caused by a defect in LEMD2 gene. Aging Cell 2024; 23:e14189. [PMID: 38757373 PMCID: PMC11320348 DOI: 10.1111/acel.14189] [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: 01/12/2024] [Revised: 03/27/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Nuclear envelopathies are rare genetic diseases that compromise the integrity of the nuclear envelope. Patients with a defect in LEM domain nuclear envelope protein 2 (LEMD2) leading to LEMD2-associated progeroid syndrome are exceedingly scarce in number, yet they exhibit shared clinical features including skeletal abnormalities and a prematurely-aged appearance. Our study broadens the understanding of LEMD2-associated progeroid syndrome by detailing its phenotypic and molecular characteristics in the first female and fourth reported case, highlighting a distinct impact on metabolic functions. The patient's history revealed growth delay, facial and skeletal abnormalities, and recurrent abdominal pain crises caused by hepatomegaly. Comparisons with the previously documented cases emphasized similarities in skeletal and facial features while showcasing unique variations, notably in cardiac and hepatic manifestations. In vitro experiments conducted on patient-derived peripheral blood and urinary epithelial cells and LEMD2-downregulated HepG2 cells confirmed abnormalities in the structure of the nuclear envelope in all three tissue-types. Overall, our work offers a comprehensive profile of a patient with LEMD2-related syndrome, emphasizing the hepatic involvement in the disease and broadening our understanding of clinical and molecular implications. This study not only contributes specific insights into LEMD2-related conditions but also underscores potential therapeutic paths for disorders affecting nuclear envelope dynamics.
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Affiliation(s)
- Alyssia Matter
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
| | - Christina Kaufman
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
| | - Nadia Zürcher
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
| | - Daniela Lenggenhager
- Department of Pathology and Molecular PathologyUniversity Hospital ZurichZurichSwitzerland
| | - Patrice Grehten
- Department of Diagnostic ImagingUniversity Children's Hospital ZurichZurichSwitzerland
| | - Deborah Bartholdi
- Department of Human Genetics, InselspitalBern University HospitalBernSwitzerland
| | - Laura Horka
- Department of Endocrinology, Diabetology and Clinical NutritionUniversity Hospital ZurichZurichSwitzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
| | - Georgios Makris
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
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13
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Cordova A, Niese B, Sweet P, Kamat P, Phillip JM, Gordon V, Contreras LM. Quantitative morphological analysis of Deinococcus radiodurans elucidates complex dose-dependent nucleoid condensation during recovery from ionizing radiation. Appl Environ Microbiol 2024; 90:e0010824. [PMID: 38864629 PMCID: PMC11323932 DOI: 10.1128/aem.00108-24] [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: 01/20/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024] Open
Abstract
The extremophile Deinococcus radiodurans maintains a highly organized and condensed nucleoid as its default state, possibly contributing to its high tolerance to ionizing radiation (IR). Previous studies of the D. radiodurans nucleoid were limited by reliance on manual image annotation and qualitative metrics. Here, we introduce a high-throughput approach to quantify the geometric properties of cells and nucleoids using confocal microscopy, digital reconstructions of cells, and computational modeling. We utilize this novel approach to investigate the dynamic process of nucleoid condensation in response to IR stress. Our quantitative analysis reveals that at the population level, exposure to IR induced nucleoid compaction and decreased the size of D. radiodurans cells. Morphological analysis and clustering identified six distinct sub-populations across all tested experimental conditions. Results indicate that exposure to IR induced fractional redistributions of cells across sub-populations to exhibit morphologies associated with greater nucleoid condensation and decreased the abundance of sub-populations associated with cell division. Nucleoid-associated proteins (NAPs) may link nucleoid compaction and stress tolerance, but their roles in regulating compaction in D. radiodurans are unknown. Imaging of genomic mutants of known and suspected NAPs that contribute to nucleoid condensation found that deletion of nucleic acid-binding proteins, not previously described as NAPs, can remodel the nucleoid by driving condensation or decondensation in the absence of stress and that IR increased the abundance of these morphological states. Thus, our integrated analysis introduces a new methodology for studying environmental influences on bacterial nucleoids and provides an opportunity to further investigate potential regulators of nucleoid condensation.IMPORTANCEDeinococcus radiodurans, an extremophile known for its stress tolerance, constitutively maintains a highly condensed nucleoid. Qualitative studies have described nucleoid behavior under a variety of conditions. However, a lack of quantitative data regarding nucleoid organization and dynamics has limited our understanding of the regulatory mechanisms controlling nucleoid organization in D. radiodurans. Here, we introduce a quantitative approach that enables high-throughput quantitative measurements of subcellular spatial characteristics in bacterial cells. Applying this to wild-type or single-protein-deficient populations of D. radiodurans subjected to ionizing radiation, we identified significant stress-responsive changes in cell shape, nucleoid organization, and morphology. These findings highlight this methodology's adaptability and capacity for quantitatively analyzing the cellular response to stressors for screening cellular proteins involved in bacterial nucleoid organization.
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Affiliation(s)
- Antonio Cordova
- Interdisciplinary Life
Sciences Graduate Program, Department of Molecular Biosciences, The
University of Texas at Austin,
Austin, Texas, USA
- Interdisciplinary Life
Sciences Graduate Program, The University of Texas at
Austin, Austin,
Texas, USA
| | - Brandon Niese
- Department of Physics,
Center for Nonlinear Dynamics, The University of Texas at
Austin, Austin,
Texas, USA
| | - Philip Sweet
- Interdisciplinary Life
Sciences Graduate Program, Department of Molecular Biosciences, The
University of Texas at Austin,
Austin, Texas, USA
| | - Pratik Kamat
- Department of Chemical
and Biomolecular Engineering, Whiting School of Engineering, Johns
Hopkins University,
Baltimore, Maryland,
USA
| | - Jude M. Phillip
- Department of Chemical
and Biomolecular Engineering, Whiting School of Engineering, Johns
Hopkins University,
Baltimore, Maryland,
USA
- Department of
Biomedical Engineering, Institute for Nanobiotechnology, Whiting School
of Engineering, Johns Hopkins
University, Baltimore,
Maryland, USA
| | - Vernita Gordon
- Interdisciplinary Life
Sciences Graduate Program, The University of Texas at
Austin, Austin,
Texas, USA
- Department of Physics,
Center for Nonlinear Dynamics, The University of Texas at
Austin, Austin,
Texas, USA
- LaMontagne Center for
Infectious Disease, The University of Texas at
Austin, Austin,
Texas, USA
| | - Lydia M. Contreras
- Interdisciplinary Life
Sciences Graduate Program, The University of Texas at
Austin, Austin,
Texas, USA
- McKetta Department of
Chemical Engineering, The University of Texas at
Austin, Austin,
Texas, USA
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14
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Sanz-Villafruela J, Bermejo-Casadesús C, Martínez-Alonso M, Moro A, Lima JC, Massaguer A, Espino G. Towards efficient Ir(III) anticancer photodynamic therapy agents by extending π-conjugation on N^N ligands. Dalton Trans 2024; 53:11393-11409. [PMID: 38899369 DOI: 10.1039/d4dt00390j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
In this work we disclose a new family of biscyclometallated Ir(III) complexes of the general formula [Ir(C^N)2(N^N)]Cl (IrL1-IrL5), where HC^N is 1-phenyl-β-carboline and N^N ligands (L1-L5) are different diimine ligands that differ from each other in the number of aromatic rings fused to the bipyridine scaffold. The photophysical properties of IrL1-IrL5 were thoroughly studied, and theoretical calculations were performed for a deeper comprehension of the respective variations along the series. All complexes exhibited high photostability under blue light irradiation. An increase in the number of aromatic rings led to a reduction in the HOMO-LUMO band gap causing a red-shift in the absorbance bands. Although all the complexes generated singlet oxygen (1O2) in aerated aqueous solutions through a photocatalytic process, IrL5 was by far the most efficient photosensitizer. Consequently, IrL5 was highly active in the photocatalytic oxidation of NADH. The formation of aggregates in DMSO at a high concentration (25 mM) was confirmed using different techniques, but was proved to be negligible in the concentration range of biological experiments. Moreover, ICP-MS studies proved that the cellular uptake of IrL2 and IrL3 is much better relative to that of IrL1, IrL4 and IrL5. The antiproliferative activity of IrL1-IrL5 was investigated in the dark and under blue light irradiation against different cancer cell lines. Complexes IrL1-IrL4 were found to be cytotoxic under dark conditions, while IrL5 turned out to be weakly cytotoxic. Despite the low cellular uptake of IrL5, this derivative exhibited a high increase of cytotoxicity upon blue light irradiation resulting in photocytotoxicity indexes (PI) up to 38. IrL1-IrL4 showed lower photocytotoxicity indexes ranging from 1.3 to 17.0. Haemolytic experiments corroborated the compatibility of our complexes with red blood cells. Confocal microscopy studies proved their accumulation in mitochondria, leading to mitochondrial membrane depolarization, and ruled out their localization in lysosomes. Overall, the mitochondria-targeted activity of IrL5, which inhibits considerably the viability of cancer cells upon blue light irradiation, allows us to outline this PS as a new alternative to traditional chemotherapeutic agents.
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Affiliation(s)
- Juan Sanz-Villafruela
- Universidad de Burgos, Departamento de Química, Facultad de Ciencias, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain.
| | - Cristina Bermejo-Casadesús
- Universitat de Girona, Departament de Biologia, Facultat de Ciències, Maria Aurelia Capmany 40, 17003 Girona, Spain.
| | - Marta Martínez-Alonso
- Universidad de Burgos, Departamento de Química, Facultad de Ciencias, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain.
| | - Artur Moro
- Universidade NOVA de Lisboa, LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, 2829-516 Caparica, Portugal
| | - João C Lima
- Universidade NOVA de Lisboa, LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, 2829-516 Caparica, Portugal
| | - Anna Massaguer
- Universitat de Girona, Departament de Biologia, Facultat de Ciències, Maria Aurelia Capmany 40, 17003 Girona, Spain.
| | - Gustavo Espino
- Universidad de Burgos, Departamento de Química, Facultad de Ciencias, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain.
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15
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Wardhani K, Levina A, Grau GER, Lay PA. Fluorescent, phosphorescent, magnetic resonance contrast and radioactive tracer labelling of extracellular vesicles. Chem Soc Rev 2024; 53:6779-6829. [PMID: 38828885 DOI: 10.1039/d2cs00238h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
This review focusses on the significance of fluorescent, phosphorescent labelling and tracking of extracellular vesicles (EVs) for unravelling their biology, pathophysiology, and potential diagnostic and therapeutic uses. Various labeling strategies, such as lipid membrane, surface protein, luminal, nucleic acid, radionuclide, quantum dot labels, and metal complex-based stains, are evaluated for visualizing and characterizing EVs. Direct labelling with fluorescent lipophilic dyes is simple but generally lacks specificity, while surface protein labelling offers selectivity but may affect EV-cell interactions. Luminal and nucleic acid labelling strategies have their own advantages and challenges. Each labelling approach has strengths and weaknesses, which require a suitable probe and technique based on research goals, but new tetranuclear polypyridylruthenium(II) complexes as phosphorescent probes have strong phosphorescence, selective staining, and stability. Future research should prioritize the design of novel fluorescent probes and labelling platforms that can significantly enhance the efficiency, accuracy, and specificity of EV labeling, while preserving their composition and functionality. It is crucial to reduce false positive signals and explore the potential of multimodal imaging techniques to gain comprehensive insights into EVs.
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Affiliation(s)
- Kartika Wardhani
- School of Chemistry, The University of Sydney, Sydney, New South Wales, 2006, Australia.
- Biochemistry and Biotechnology (B-TEK) Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Aviva Levina
- School of Chemistry, The University of Sydney, Sydney, New South Wales, 2006, Australia.
| | - Georges E R Grau
- Sydney Nano, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Sydney Cancer Network, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Marie Bashir Institute, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Vascular Immunology Unit, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Peter A Lay
- School of Chemistry, The University of Sydney, Sydney, New South Wales, 2006, Australia.
- Sydney Nano, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Sydney Cancer Network, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Marie Bashir Institute, The University of Sydney, Sydney, New South Wales, 2006, Australia
- Sydney Analytical, The University of Sydney, Sydney, New South Wales, 2006, Australia
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16
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Zhang F, Liu W, Mao Y, Yang Y, Ling C, Liu Y, Yao F, Zhen Y, Wang X, Zou M. Migrasome, a migration-dependent organelle. Front Cell Dev Biol 2024; 12:1417242. [PMID: 38903534 PMCID: PMC11187097 DOI: 10.3389/fcell.2024.1417242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Migrasomes are organelles produced by migrating cells that form on retraction fibers and are released during cell migration. Migrasomes are involved in physiological and pathological processes such as intercellular communication, cell homeostasis maintenance, signal transduction, disease occurrence and development, and cancer metastasis. In addition, methods and techniques for studying migrasomes are constantly evolving. Here, we review the discovery, formation process, regulation, and known functions of migrasomes, summarize the commonly used specific markers of migrasomes, and the methods for observing migrasomes. Meanwhile, this review also discusses the potential applications of migrasomes in physiological processes, disease diagnosis, treatment, and prognosis, and looks forward to their wider application in biomedicine. In addition, the study of migrasomes will also reveal a new perspective on the mechanism of intercellular communication and promote the further development of life science.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mincheng Zou
- Department of Orthopaedics, Children’s Hospital of Soochow University, Suzhou, China
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17
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Yamada Y, Zheng Z, Jad AK, Yamashita M. Lethal and sublethal effects of programmed cell death pathways on hematopoietic stem cells. Exp Hematol 2024; 134:104214. [PMID: 38582294 DOI: 10.1016/j.exphem.2024.104214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Programmed cell death is an evolutionally conserved cellular process in multicellular organisms that eliminates unnecessary or rogue cells during development, infection, and carcinogenesis. Hematopoietic stem cells (HSCs) are a rare, self-renewing, and multipotent cell population necessary for the establishment and regeneration of the hematopoietic system. Counterintuitively, key components necessary for programmed cell death induction are abundantly expressed in long-lived HSCs, which often survive myeloablative stress by engaging a prosurvival response that counteracts cell death-inducing stimuli. Although HSCs are well known for their apoptosis resistance, recent studies have revealed their unique vulnerability to certain types of programmed necrosis, such as necroptosis and ferroptosis. Moreover, emerging evidence has shown that programmed cell death pathways can be sublethally activated to cause nonlethal consequences such as innate immune response, organelle dysfunction, and mutagenesis. In this review, we summarized recent findings on how divergent cell death programs are molecularly regulated in HSCs. We then discussed potential side effects caused by sublethal activation of programmed cell death pathways on the functionality of surviving HSCs.
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Affiliation(s)
- Yuta Yamada
- Division of Stem Cell and Molecular Medicine, Centre for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Zhiqian Zheng
- Division of Stem Cell and Molecular Medicine, Centre for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Division of Experimental Hematology, Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alaa K Jad
- Division of Stem Cell and Molecular Medicine, Centre for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masayuki Yamashita
- Division of Stem Cell and Molecular Medicine, Centre for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Division of Experimental Hematology, Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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18
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Mardilovich K, Naylor G, Julian L, Phinichkusolchit N, Keeshan K, Blyth K, Olson MF. Caspase-resistant ROCK1 expression prolongs survival of Eµ-Myc B cell lymphoma mice. Dis Model Mech 2024; 17:dmm050631. [PMID: 38616733 PMCID: PMC11139034 DOI: 10.1242/dmm.050631] [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: 11/24/2023] [Accepted: 04/02/2024] [Indexed: 04/16/2024] Open
Abstract
Apoptosis is characterized by membrane blebbing and apoptotic body formation. Caspase cleavage of ROCK1 generates an active fragment that promotes actin-myosin-mediated contraction and membrane blebbing during apoptosis. Expression of caspase-resistant non-cleavable ROCK1 (Rock1 NC) prolonged survival of mice that rapidly develop B cell lymphomas due to Eµ-Myc transgene expression. Eµ-Myc; Rock1 NC mice had significantly fewer bone marrow cells relative to those in Eµ-Myc mice expressing wild-type ROCK1 (Rock1 WT), which was associated with altered cell cycle profiles. Circulating macrophage numbers were lower in Eµ-Myc; Rock1 NC mice, but there were higher levels of bone marrow macrophages, consistent with spontaneous cell death in Eµ-Myc; Rock1 NC mouse bone marrows being more inflammatory. Rock1 WT recipient mice transplanted with pre-neoplastic Eµ-Myc; Rock1 NC bone marrow cells survived longer than mice transplanted with Eµ-Myc; Rock1 WT cells, indicating that the survival benefit was intrinsic to the Eµ-Myc; Rock1 NC bone marrow cells. The results suggest that the apoptotic death of Eµ-Myc; Rock1 NC cells generates a proliferation-suppressive microenvironment in bone marrows that reduces cell numbers and prolongs B cell lymphoma mouse survival.
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Affiliation(s)
- Katerina Mardilovich
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Gregory Naylor
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G16 1QH, UK
| | - Linda Julian
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G16 1QH, UK
| | - Narisa Phinichkusolchit
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G16 1QH, UK
| | - Karen Keeshan
- Wolfson Wohl Cancer Research Centre, Paul O'Gorman Leukemia Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G16 1QH, UK
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G16 1QH, UK
| | - Michael F. Olson
- Toronto Metropolitan University, Department of Chemistry and Biology, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
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19
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Cappe B, Vandenabeele P, Riquet FB. A guide to the expanding field of extracellular vesicles and their release in regulated cell death programs. FEBS J 2024; 291:2068-2090. [PMID: 37872002 DOI: 10.1111/febs.16981] [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: 05/26/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
Homeostasis disruption is visible at the molecular and cellular levels and may often lead to cell death. This vital process allows us to maintain the more extensive system's integrity by keeping the different features (genetic, metabolic, physiologic, and individual) intact. Interestingly, while cells can die in different manners, dying cells still communicate with their environment. This communication was, for a long time, perceived as only driven by the release of soluble factors. However, it has now been reconsidered with the increasing interest in extracellular vesicles (EVs), which are discovered to be released during different regulated cell death programs, with the observation of specific effects. EVs are game changers in the paradigm of cell-cell communication with tremendous implications in fundamental research with regard to noncell autonomous functions, as well as in biomarkers research, all of which are geared toward diagnostic and therapeutic purposes. This review is composed of two main parts. The first is a comprehensive presentation of the state of the art of the EV field at large. In the second part, we focus on EVs discovered to be released during different regulated cell death programs, also known as cell death EVs (cdEVs), and EV-associated specific effects on recipient cells in the context of cell death and inflammation/inflammatory responses.
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Affiliation(s)
- Benjamin Cappe
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research (IRC), Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research (IRC), Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research (IRC), Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
- University of Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, France
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20
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Pan Y, Deng H, Yang C, Lin L, Cai Q, He J. A new gene signature associated with disulfidptosis that forecasts myasthenia gravis and suggests infiltration of immune microenvironment in thymoma patients. Heliyon 2024; 10:e29650. [PMID: 38660242 PMCID: PMC11040115 DOI: 10.1016/j.heliyon.2024.e29650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction The mechanism of thymoma-associated myasthenia gravis (TAMG) is currently unknown, although patients with TAMG experience more severe myasthenic symptoms and have worse prognoses compared to regular thymoma patients. The objective of this research is to create a transcriptome map of TAMG using genes linked to disulfidptosis, detect possible biomarkers, and examine the disparities in the tumor immune microenvironment (TIME) among different thymoma patients. The findings will offer valuable knowledge for personalized treatment alternatives. Methods Thymoma samples' RNA-seq data, along with their corresponding clinical data, were acquired from the TCGA database using methods. Next, genes and disulfidptosis-related lncRNAs(DRLs) were chosen through correlation analysis. Then, a prediction model of TAMG was established by LASSO regression. Subsequent to that, an analysis of the mutation data, the tumor mutational burden (TMB), and the assessment of immune and stromal elements within the tumor microenvironment were conducted. Results A total of 87 patients diagnosed with thymoma were included in the study, with 29 of them having TAMG. We discovered a group of 325 lncRNAs in this sample that showed significant associations with genes related to disulfidptosis, with 25 of them displaying significantly altered expression. Moreover, utilizing LASSO regression, we constructed a predictive model incorporating 11 DRLs. The analysis revealed an area under the curve (AUC) of 0.934 (CI 0.879-0.989), a cut-off value of 0.797, along with a sensitivity of 82.8 % and specificity of 93.1 %. Furthermore, we examined the TIME in both the high-risk and low-risk groups, and observed noteworthy disparities in B cells, T cells, and APC among the two groups (p < 0.05). Conclusion This research offers the initial examination of genes associated with disulfidptosis and TAMG through genomic and transcriptomic analysis. Furthermore, a strong risk forecasting model was created and the significance of TIME in TAMG was also clarified. The discoveries offer significant understanding into the molecular processes of TAMG and present possible indicators for categorizing risk.
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Affiliation(s)
- Yue Pan
- Department of Thoracic Surgery and Oncology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, No.151, Yanjiang Road, 510120, Guangzhou, China
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China
| | - Hongsheng Deng
- Department of Thoracic Surgery and Oncology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, No.151, Yanjiang Road, 510120, Guangzhou, China
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China
| | - Chao Yang
- Department of Thoracic Surgery and Oncology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, No.151, Yanjiang Road, 510120, Guangzhou, China
| | - Lixuan Lin
- Department of Thoracic Surgery and Oncology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, No.151, Yanjiang Road, 510120, Guangzhou, China
| | - Qi Cai
- Department of Thoracic Surgery and Oncology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, No.151, Yanjiang Road, 510120, Guangzhou, China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, No.151, Yanjiang Road, 510120, Guangzhou, China
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21
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Dowdy T, Vilamu HM, Lita A, Li A, Yamasaki T, Zhang L, Chari R, Song H, Zhang M, Zhang W, Briceno N, Davis D, Gilbert MR, Larion M. Targeting the sphingolipid rheostat in IDH1 mut glioma alters cholesterol homeostasis and triggers apoptosis via membrane degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591321. [PMID: 38903071 PMCID: PMC11188108 DOI: 10.1101/2024.04.26.591321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The cross-regulation of metabolism and trafficking is not well understood for the vital sphingolipids and cholesterol constituents of cellular compartments. While reports are starting to surface on how sphingolipids like sphingomyelin (SM) dysregulate cholesterol levels in different cellular compartments (Jiang et al., 2022), limited research is available on the mechanisms driving the relationship between sphingolipids and cholesterol homeostasis, or its biological implications. Previously, we have identified sphingolipid metabolism as a unique vulnerability for IDH1 mut gliomas via a rational drug design. Herein, we show how modulating sphingolipid levels affects cholesterol homeostasis in brain tumors. However, we unexpectedly discovered for the first time that C17 sphingosine and NDMS addition to cancer cells alters cholesterol homeostasis by impacting its cellular synthesis, uptake, and efflux leading to a net decrease in cholesterol levels and inducing apoptosis. Our results reflect a reverse correlation between the levels of sphingosines, NDMS, and unesterified, free cholesterol in the cells. We show that increasing sphingosine and NDMS (a sphingosine analog) levels alter not only the trafficking of cholesterol between membranes but also the efflux and synthesis of cholesterol. We also demonstrate that despite the effort to remove free cholesterol by ABCA1-mediated efflux or by suppressing machinery for the influx (LDLR) and biosynthetic pathway (HMGCR), apoptosis is inevitable for IDH1 mut glioma cells. This is the first study that shows how altering sphingosine levels directly affects cholesterol homeostasis in cancer cells and can be used to manipulate this relationship to induce apoptosis in IDH1 mut gliomas.
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22
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Egorova KS, Kibardin AV, Posvyatenko AV, Ananikov VP. Mechanisms of Biological Effects of Ionic Liquids: From Single Cells to Multicellular Organisms. Chem Rev 2024; 124:4679-4733. [PMID: 38621413 DOI: 10.1021/acs.chemrev.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
The review presents a detailed discussion of the evolving field studying interactions between ionic liquids (ILs) and biological systems. Originating from molten salt electrolytes to present multiapplication substances, ILs have found usage across various fields due to their exceptional physicochemical properties, including excellent tunability. However, their interactions with biological systems and potential influence on living organisms remain largely unexplored. This review examines the cytotoxic effects of ILs on cell cultures, biomolecules, and vertebrate and invertebrate organisms. Our understanding of IL toxicity, while growing in recent years, is yet nascent. The established findings include correlations between harmful effects of ILs and their ability to disturb cellular membranes, their potential to trigger oxidative stress in cells, and their ability to cause cell death via apoptosis. Future research directions proposed in the review include studying the distribution of various ILs within cellular compartments and organelles, investigating metabolic transformations of ILs in cells and organisms, detailed analysis of IL effects on proteins involved in oxidative stress and apoptosis, correlation studies between IL doses, exposure times and resulting adverse effects, and examination of effects of subtoxic concentrations of ILs on various biological objects. This review aims to serve as a critical analysis of the current body of knowledge on IL-related toxicity mechanisms. Furthermore, it can guide researchers toward the design of less toxic ILs and the informed use of ILs in drug development and medicine.
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Affiliation(s)
- Ksenia S Egorova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey V Kibardin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Health of Russian Federation, Moscow 117198, Russia
| | - Alexandra V Posvyatenko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Health of Russian Federation, Moscow 117198, Russia
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
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23
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Le T, Ferling I, Qiu L, Nabaile C, Assunção L, Roskelley CD, Grinstein S, Freeman SA. Redistribution of the glycocalyx exposes phagocytic determinants on apoptotic cells. Dev Cell 2024; 59:853-868.e7. [PMID: 38359833 DOI: 10.1016/j.devcel.2024.01.020] [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: 04/12/2023] [Revised: 11/08/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Phagocytes remove dead and dying cells by engaging "eat-me" ligands such as phosphatidylserine (PtdSer) on the surface of apoptotic targets. However, PtdSer is obscured by the bulky exofacial glycocalyx, which also exposes ligands that activate "don't-eat-me" receptors such as Siglecs. Clearly, unshielding the juxtamembrane "eat-me" ligands is required for the successful engulfment of apoptotic cells, but the mechanisms underlying this process have not been described. Using human and murine cells, we find that apoptosis-induced retraction and weakening of the cytoskeleton that anchors transmembrane proteins cause an inhomogeneous redistribution of the glycocalyx: actin-depleted blebs emerge, lacking the glycocalyx, while the rest of the apoptotic cell body retains sufficient actin to tether the glycocalyx in place. Thus, apoptotic blebs can be engaged by phagocytes and are targeted for engulfment. Therefore, in cells with an elaborate glycocalyx, such as mucinous cancer cells, this "don't-come-close-to-me" barrier must be removed to enable clearance by phagocytosis.
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Affiliation(s)
- Trieu Le
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Iuliia Ferling
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lanhui Qiu
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Clement Nabaile
- Department of Learning and Research in Biology, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
| | - Leonardo Assunção
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Calvin D Roskelley
- Department of Cellular and Physiological Sciences, the Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sergio Grinstein
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Spencer A Freeman
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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24
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Saha P, Hegde M, Chakraborty K, Singha A, Mukerjee N, Ghosh D, Kunnumakkara AB, Khan MS, Ahmad MI, Ghosh A, Kumer A, Sil SK. Targeted inhibition of colorectal cancer proliferation: The dual-modulatory role of 2,4-DTBP on anti-apoptotic Bcl-2 and Survivin proteins. J Cell Mol Med 2024; 28:e18150. [PMID: 38494866 PMCID: PMC10945088 DOI: 10.1111/jcmm.18150] [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: 09/20/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 03/19/2024] Open
Abstract
The anti-apoptotic proteins, Bcl-2 and Survivin, are consistently overexpressed in numerous human malignancies, notably in colorectal cancer. 2,4-Di-tert-butylphenol (2,4-DTBP) is a naturally occurring phenolic compound known for its diverse biological activities, including anti-cancer properties. The mechanism behind 2,4-DTBP-induced inhibition of cell proliferation and apoptosis in human colorectal cancer cells, specifically regarding Bcl-2 and Survivin, remains to be elucidated. In this study, we employed both in silico and in vitro methodologies to underpin this interaction at the molecular level. Molecular docking demonstrated a substantial binding affinity of 2,4-DTBP towards Bcl-2 (ΔG = -9.8 kcal/mol) and Survivin (ΔG = -5.6 kcal/mol), suggesting a potential inhibitory effect. Further, molecular dynamic simulations complemented by MM-GBSA calculations confirmed the significant binding of 2,4-DTBP with Bcl-2 (dGbind = -54.85 ± 6.79 kcal/mol) and Survivin (dGbind = -32.36 ± 1.29 kcal/mol). In vitro assays using HCT116 colorectal cancer cells revealed that 2,4-DTBP inhibited proliferation and promoted apoptosis in both a dose- and time-dependent manner. Fluorescence imaging and scanning electron microscopy illustrated the classical features associated with apoptosis upon 2,4-DTBP exposure. Cell cycle analysis through flow cytometry highlighted a G1 phase arrest and apoptosis assay demonstrated increased apoptotic cell population. Notably, western blotting results indicated a decreased expression of Bcl-2 and Survivin post-treatment. Considering the cytoprotective roles of Bcl-2 and Survivin through the inhibition of mitochondrial dysfunction, our findings of disrupted mitochondrial bioenergetics, characterized by reduced ATP production and oxygen consumption, further accentuate the functional impairment of these proteins. Overall, the integration of in silico and in vitro data suggests that 2,4-DTBP holds promise as a therapeutic agent targeting Bcl-2 and Survivin in colorectal cancer.
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Affiliation(s)
- Partha Saha
- Molecular Genetics and Cell Physiology Laboratory, Department of Human PhysiologyTripura UniversitySuryamaninagarTripuraIndia
| | - Mangala Hegde
- Cancer Biology Laboratory and DBT‐AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) GuwahatiGuwahatiAssamIndia
| | - Kanak Chakraborty
- Molecular Genetics and Cell Physiology Laboratory, Department of Human PhysiologyTripura UniversitySuryamaninagarTripuraIndia
| | - Achinta Singha
- Molecular Genetics and Cell Physiology Laboratory, Department of Human PhysiologyTripura UniversitySuryamaninagarTripuraIndia
| | - Nobendu Mukerjee
- Center for Global Health ResearchSaveetha Medical College and Hospital, Saveetha Institute of Medical and Technical SciencesChennaiTamil NaduIndia
- Department of Health SciencesNovel Global Community Educational FoundationHebershamNew South WalesAustralia
| | - Deepshikha Ghosh
- Cell Biology and Physiology DivisionCSIR‐Indian Institute of Chemical BiologyKolkataWest BengalIndia
| | - Ajaikumar B. Kunnumakkara
- Cancer Biology Laboratory and DBT‐AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) GuwahatiGuwahatiAssamIndia
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Md Irshad Ahmad
- Department of Structural Biology, School of MedicineUTHEALTH Science CenterSan AntonioTexasUSA
| | - Arabinda Ghosh
- Department of Computational Biology and BiotechnologyMahapurusha Srimanta Sankaradeva ViswavidalayaGuwahatiAssamIndia
| | - Ajoy Kumer
- Department of Chemistry, College of Arts and SciencesIUBAT‐International University of Business Agriculture and TechnologyDhakaBangladesh
| | - Samir Kumar Sil
- Molecular Genetics and Cell Physiology Laboratory, Department of Human PhysiologyTripura UniversitySuryamaninagarTripuraIndia
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25
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Pulfer A, Pizzagalli DU, Gagliardi PA, Hinderling L, Lopez P, Zayats R, Carrillo-Barberà P, Antonello P, Palomino-Segura M, Grädel B, Nicolai M, Giusti A, Thelen M, Gambardella LM, Murooka TT, Pertz O, Krause R, Gonzalez SF. Transformer-based spatial-temporal detection of apoptotic cell death in live-cell imaging. eLife 2024; 12:RP90502. [PMID: 38497754 PMCID: PMC10948145 DOI: 10.7554/elife.90502] [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: 03/19/2024] Open
Abstract
Intravital microscopy has revolutionized live-cell imaging by allowing the study of spatial-temporal cell dynamics in living animals. However, the complexity of the data generated by this technology has limited the development of effective computational tools to identify and quantify cell processes. Amongst them, apoptosis is a crucial form of regulated cell death involved in tissue homeostasis and host defense. Live-cell imaging enabled the study of apoptosis at the cellular level, enhancing our understanding of its spatial-temporal regulation. However, at present, no computational method can deliver robust detection of apoptosis in microscopy timelapses. To overcome this limitation, we developed ADeS, a deep learning-based apoptosis detection system that employs the principle of activity recognition. We trained ADeS on extensive datasets containing more than 10,000 apoptotic instances collected both in vitro and in vivo, achieving a classification accuracy above 98% and outperforming state-of-the-art solutions. ADeS is the first method capable of detecting the location and duration of multiple apoptotic events in full microscopy timelapses, surpassing human performance in the same task. We demonstrated the effectiveness and robustness of ADeS across various imaging modalities, cell types, and staining techniques. Finally, we employed ADeS to quantify cell survival in vitro and tissue damage in mice, demonstrating its potential application in toxicity assays, treatment evaluation, and inflammatory dynamics. Our findings suggest that ADeS is a valuable tool for the accurate detection and quantification of apoptosis in live-cell imaging and, in particular, intravital microscopy data, providing insights into the complex spatial-temporal regulation of this process.
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Affiliation(s)
- Alain Pulfer
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
- Department of Information Technology and Electrical Engineering, ETH ZurichZürichSwitzerland
| | - Diego Ulisse Pizzagalli
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
- Euler Institute, USILuganoSwitzerland
| | | | | | | | | | - Pau Carrillo-Barberà
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universitat de ValènciaValenciaSpain
| | - Paola Antonello
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
- Institute of Cell Biology, University of BernBernSwitzerland
| | | | - Benjamin Grädel
- Institute of Cell Biology, University of BernBernSwitzerland
| | | | - Alessandro Giusti
- Dalle Molle Institute for Artificial Intelligence, IDSIALuganoSwitzerland
| | - Marcus Thelen
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
| | | | | | - Olivier Pertz
- Institute of Cell Biology, University of BernBernSwitzerland
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26
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Sun G. Death and survival from executioner caspase activation. Semin Cell Dev Biol 2024; 156:66-73. [PMID: 37468421 DOI: 10.1016/j.semcdb.2023.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Executioner caspases are evolutionarily conserved regulators of cell death under apoptotic stress. Activated executioner caspases drive apoptotic cell death through cleavage of diverse protein substrates or pyroptotic cell death in the presence of gasdermin E. On the other hand, activation of executioner caspases can also trigger pro-survival and pro-proliferation signals. In recent years, a growing body of studies have demonstrated that cells can survive from executioner caspase activation in response to stress and that the survivors undergo molecular and phenotypic alterations. This review focuses on death and survival from executioner caspase activation, summarizing the role of executioner caspases in apoptotic and pyroptotic cell death and discussing the potential mechanism and consequences of survival from stress-induced executioner caspase activation.
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Affiliation(s)
- Gongping Sun
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
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27
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Liu CJ, Smith JT, Wang Y, Ouellette JN, Rogers JD, Oliner JD, Szulczewski M, Wait E, Brown W, Wax A, Eliceiri KW, Rafter J. Assessing cell viability with dynamic optical coherence microscopy. BIOMEDICAL OPTICS EXPRESS 2024; 15:1408-1417. [PMID: 38495713 PMCID: PMC10942685 DOI: 10.1364/boe.509835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 03/19/2024]
Abstract
Assessing cell viability is important in many fields of research. Current optical methods to assess cell viability typically involve fluorescent dyes, which are often less reliable and have poor permeability in primary tissues. Dynamic optical coherence microscopy (dOCM) is an emerging tool that provides label-free contrast reflecting changes in cellular metabolism. In this work, we compare the live contrast obtained from dOCM to viability dyes, and for the first time to our knowledge, demonstrate that dOCM can distinguish live cells from dead cells in murine syngeneic tumors. We further demonstrate a strong correlation between dOCM live contrast and optical redox ratio by metabolic imaging in primary mouse liver tissue. The dOCM technique opens a new avenue to apply label-free imaging to assess the effects of immuno-oncology agents, targeted therapies, chemotherapy, and cell therapies using live tumor tissues.
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Affiliation(s)
- Chao J. Liu
- Elephas Biosciences
Corporation, 1 Erdman Place, Madison, WI 53717, USA
| | - Jason T. Smith
- Elephas Biosciences
Corporation, 1 Erdman Place, Madison, WI 53717, USA
| | - Yuanbo Wang
- Elephas Biosciences
Corporation, 1 Erdman Place, Madison, WI 53717, USA
| | | | - Jeremy D. Rogers
- Department of Ophthalmology and Visual
Sciences, University of Wisconsin Madison,
2828 Marshall Ct, Madison, WI 53705, USA
| | | | | | - Eric Wait
- Elephas Biosciences
Corporation, 1 Erdman Place, Madison, WI 53717, USA
| | - William Brown
- Lumedica Inc.,
404 Hunt Street, Suite 510, Durham, NC 27701, USA
| | - Adam Wax
- Lumedica Inc.,
404 Hunt Street, Suite 510, Durham, NC 27701, USA
| | - Kevin W. Eliceiri
- Center for Quantitative Cell
Imaging, 1675 Observatory Drive, Madison, WI 53706,
USA
| | - John Rafter
- Elephas Biosciences
Corporation, 1 Erdman Place, Madison, WI 53717, USA
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28
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Mishra P, Sivakumar A, Johnson A, Pernaci C, Warden AS, El-Hachem LR, Hansen E, Badell-Grau RA, Khare V, Ramirez G, Gillette S, Solis AB, Guo P, Coufal N, Cherqui S. Gene editing improves endoplasmic reticulum-mitochondrial contacts and unfolded protein response in Friedreich's ataxia iPSC-derived neurons. Front Pharmacol 2024; 15:1323491. [PMID: 38420191 PMCID: PMC10899513 DOI: 10.3389/fphar.2024.1323491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024] Open
Abstract
Friedreich ataxia (FRDA) is a multisystemic, autosomal recessive disorder caused by homozygous GAA expansion mutation in the first intron of frataxin (FXN) gene. FXN is a mitochondrial protein critical for iron-sulfur cluster biosynthesis and deficiency impairs mitochondrial electron transport chain functions and iron homeostasis within the organelle. Currently, there is no effective treatment for FRDA. We have previously demonstrated that single infusion of wild-type hematopoietic stem and progenitor cells (HSPCs) resulted in prevention of neurologic and cardiac complications of FRDA in YG8R mice, and rescue was mediated by FXN transfer from tissue engrafted, HSPC-derived microglia/macrophages to diseased neurons/myocytes. For a future clinical translation, we developed an autologous stem cell transplantation approach using CRISPR/Cas9 for the excision of the GAA repeats in FRDA patients' CD34+ HSPCs; this strategy leading to increased FXN expression and improved mitochondrial functions. The aim of the current study is to validate the efficiency and safety of our gene editing approach in a disease-relevant model. We generated a cohort of FRDA patient-derived iPSCs and isogenic lines that were gene edited with our CRISPR/Cas9 approach. iPSC derived FRDA neurons displayed characteristic apoptotic and mitochondrial phenotype of the disease, such as non-homogenous microtubule staining in neurites, increased caspase-3 expression, mitochondrial superoxide levels, mitochondrial fragmentation, and partial degradation of the cristae compared to healthy controls. These defects were fully prevented in the gene edited neurons. RNASeq analysis of FRDA and gene edited neurons demonstrated striking improvement in gene clusters associated with endoplasmic reticulum (ER) stress in the isogenic lines. Gene edited neurons demonstrated improved ER-calcium release, normalization of ER stress response gene, XBP-1, and significantly increased ER-mitochondrial contacts that are critical for functional homeostasis of both organelles, as compared to FRDA neurons. Ultrastructural analysis for these contact sites displayed severe ER structural damage in FRDA neurons, that was undetected in gene edited neurons. Taken together, these results represent a novel finding for disease pathogenesis showing dramatic ER structural damage in FRDA, validate the efficacy profile of our FXN gene editing approach in a disease relevant model, and support our approach as an effective strategy for therapeutic intervention for Friedreich's ataxia.
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Affiliation(s)
- Priyanka Mishra
- Department of Pediatrics, Division of Genetics, University of California, San Diego, San Diego, CA, United States
| | - Anusha Sivakumar
- Department of Pediatrics, Division of Genetics, University of California, San Diego, San Diego, CA, United States
| | - Avalon Johnson
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Carla Pernaci
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Anna S. Warden
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Lilas Rony El-Hachem
- Department of Pediatrics, Division of Genetics, University of California, San Diego, San Diego, CA, United States
| | - Emily Hansen
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Rafael A. Badell-Grau
- Department of Pediatrics, Division of Genetics, University of California, San Diego, San Diego, CA, United States
| | - Veenita Khare
- Department of Pediatrics, Division of Genetics, University of California, San Diego, San Diego, CA, United States
| | - Gabriela Ramirez
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Sydney Gillette
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Angelyn B. Solis
- Department of Pediatrics, Division of Genetics, University of California, San Diego, San Diego, CA, United States
| | - Peng Guo
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
| | - Nicole Coufal
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Stephanie Cherqui
- Department of Pediatrics, Division of Genetics, University of California, San Diego, San Diego, CA, United States
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29
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Qin K, Yu M, Fan J, Wang H, Zhao P, Zhao G, Zeng W, Chen C, Wang Y, Wang A, Schwartz Z, Hong J, Song L, Wagstaff W, Haydon RC, Luu HH, Ho SH, Strelzow J, Reid RR, He TC, Shi LL. Canonical and noncanonical Wnt signaling: Multilayered mediators, signaling mechanisms and major signaling crosstalk. Genes Dis 2024; 11:103-134. [PMID: 37588235 PMCID: PMC10425814 DOI: 10.1016/j.gendis.2023.01.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/01/2022] [Accepted: 01/29/2023] [Indexed: 08/18/2023] Open
Abstract
Wnt signaling plays a major role in regulating cell proliferation and differentiation. The Wnt ligands are a family of 19 secreted glycoproteins that mediate their signaling effects via binding to Frizzled receptors and LRP5/6 coreceptors and transducing the signal either through β-catenin in the canonical pathway or through a series of other proteins in the noncanonical pathway. Many of the individual components of both canonical and noncanonical Wnt signaling have additional functions throughout the body, establishing the complex interplay between Wnt signaling and other signaling pathways. This crosstalk between Wnt signaling and other pathways gives Wnt signaling a vital role in many cellular and organ processes. Dysregulation of this system has been implicated in many diseases affecting a wide array of organ systems, including cancer and embryological defects, and can even cause embryonic lethality. The complexity of this system and its interacting proteins have made Wnt signaling a target for many therapeutic treatments. However, both stimulatory and inhibitory treatments come with potential risks that need to be addressed. This review synthesized much of the current knowledge on the Wnt signaling pathway, beginning with the history of Wnt signaling. It thoroughly described the different variants of Wnt signaling, including canonical, noncanonical Wnt/PCP, and the noncanonical Wnt/Ca2+ pathway. Further description involved each of its components and their involvement in other cellular processes. Finally, this review explained the various other pathways and processes that crosstalk with Wnt signaling.
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Affiliation(s)
- Kevin Qin
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Michael Yu
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jiaming Fan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and Department of Clinical Biochemistry, The School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Hongwei Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Piao Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Orthopaedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Guozhi Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Orthopaedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Wei Zeng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Interventional Neurology, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong 523475, China
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Yonghui Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Clinical Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Annie Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Zander Schwartz
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- School of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Jeffrey Hong
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Lily Song
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Sherwin H. Ho
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jason Strelzow
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Lewis L. Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
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Costigan A, Hollville E, Martin SJ. Discriminating Between Apoptosis, Necrosis, Necroptosis, and Ferroptosis by Microscopy and Flow Cytometry. Curr Protoc 2023; 3:e951. [PMID: 38112058 DOI: 10.1002/cpz1.951] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Apoptosis is a mode of programmed cell death that plays important roles in tissue sculpting during development, in the maintenance of tissue homeostasis in the adult, and in the eradication of injured or infected cells during pathological processes. Numerous physiological as well as pathological stimuli trigger apoptosis, such as engagement of plasma-membrane-associated Fas, TRAIL, or TNF receptors, growth factor deprivation, hypoxia, radiation, and exposure to diverse cytotoxic drugs. Apoptosis is coordinated by members of the caspase family of cysteine proteases, which, upon activation, trigger a series of dramatic morphological and biochemical changes including retraction from the substratum, cell shrinkage, extensive and protracted plasma membrane blebbing, chromatin condensation, DNA hydrolysis, nuclear fragmentation, and proteolytic cleavage of numerous caspase substrates. These dramatic structural and biochemical alterations result not only in the controlled dismantling of the cell, but also in the rapid recognition and removal of apoptotic cells by phagocytes through the cell surface display of phagocytotic triggers such as phosphatidylserine. Necrosis, which is typically nonprogrammed or imposed upon the cell by overwhelming membrane or organelle damage, is characterized by high-amplitude cell swelling, followed by rapid plasma membrane rupture and release of cellular contents into the extracellular space. Necrosis is often provoked by infectious agents or severe departure from physiological conditions due to toxins, temperature extremes, or physical injury. However, forms of programmed necrosis (necroptosis, pyroptosis, ferroptosis) can also occur in specific circumstances. Nonprogrammed and programmed necrosis can be distinguished from apoptosis by morphological features, based on the rapid uptake of vital dyes, and through the application of specific inhibitors of key molecules associated with the latter modes of cell death. This unit describes protocols for the measurement of apoptosis and necrosis and for distinguishing apoptosis from programmed as well as conventional necrosis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Analysis of cell morphology by phase-contrast microscopy Alternative Protocol 1: Assessment of morphological changes using eosin-methylene blue staining Alternative Protocol 2: Analysis of nuclear morphology by fluorescence microscopy Support Protocol: Preparation of cytospins Basic Protocol 2: Measurement of plasma membrane composition with annexin V and propidium iodide Basic Protocol 3: Measurement of DNA fragmentation by flow cytometry Alternative Protocol 3: Analysis of DNA fragmentation by the TUNEL assay Basic Protocol 4: Measurement of caspase activation by flow cytometry Basic Protocol 5: Discriminating between apoptosis, necrosis, necroptosis, and ferroptosis.
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Affiliation(s)
- Aoife Costigan
- Molecular Cell Biology Laboratory, Department of Genetics, Trinity College, Dublin, Ireland
| | - Emilie Hollville
- Institute of Medical Sciences, University of Aberdeen Foresterhill, Aberdeen, Scotland, United Kingdom
| | - Seamus J Martin
- Molecular Cell Biology Laboratory, Department of Genetics, Trinity College, Dublin, Ireland
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Duszyc K, von Pein JB, Ramnath D, Currin-Ross D, Verma S, Lim F, Sweet MJ, Schroder K, Yap AS. Apical extrusion prevents apoptosis from activating an acute inflammatory program in epithelia. Dev Cell 2023; 58:2235-2248.e6. [PMID: 37647898 DOI: 10.1016/j.devcel.2023.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Apoptosis is traditionally considered to be an immunologically silent form of cell death. Multiple mechanisms exist to ensure that apoptosis does not stimulate the immune system to cause inflammation or autoimmunity. Against this expectation, we now report that epithelia are programmed to provoke, rather than suppress, inflammation in response to apoptosis. We found that an acute inflammatory response led by neutrophils occurs in zebrafish and cell culture when apoptotic epithelial cells cannot be expelled from the monolayer by apical extrusion. This reflects an intrinsic circuit where ATP released from apoptotic cells stimulates epithelial cells in the immediate vicinity to produce interleukin-8 (IL-8). Apical extrusion therefore prevents inappropriate epithelial inflammation by physically eliminating apoptotic cells before they can activate this pro-inflammatory circuit. This carries the implication that epithelia may be predisposed to inflammation, elicited by sporadic or induced apoptosis, if apical extrusion is compromised.
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Affiliation(s)
- Kinga Duszyc
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia.
| | - Jessica B von Pein
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
| | - Divya Ramnath
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
| | - Denni Currin-Ross
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
| | - Suzie Verma
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
| | - Fayth Lim
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
| | - Matthew J Sweet
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
| | - Kate Schroder
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
| | - Alpha S Yap
- Division of Cell and Developmental Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia.
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Wu Y, Chen X, Zhu L, Wang D, Li X, Song J, Wang D, Yu X, Li Y, Tang BZ. Endoplasmic Reticulum-Targeted Aggregation-Induced Emission Luminogen for Synergetic Tumor Ablation with Glibenclamide. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37903083 DOI: 10.1021/acsami.3c10940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Photodynamic therapy based on fluorescence illumination of subcellular organelles and in situ bursts of reactive oxygen species (ROS) has been recognized as a promising strategy for cancer theranostics. However, the short life of ROS and unclarified anticancer mechanism seriously restrict the application. Herein, we rationally designed and facilely synthesized a 2,6-dimethylpyridine-based triphenylamine (TPA) derivative TPA-DMPy with aggregation-induced emission (AIE) features and production of type-I ROS. Except for its selective binding to the endoplasmic reticulum (ER), TPA-DMPy, in synergy with glibenclamide, a medicinal agent used against diabetes, induced significant apoptosis of cancer cells in vitro and in vivo. Additionally, TPA-DMPy greatly incited the release of calcium from ER upon light irradiation to further aggravate the depolarization of ER membrane potential caused by glibenclamide, thus inducing fatal ER stress and crosstalk between ER and mitochondria. Our study extends the biological design and application of AIE luminogens and provides new insights into discovering novel anticancer targets and agents.
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Affiliation(s)
- Yifan Wu
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiaohui Chen
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong 523808, China
| | - Liwei Zhu
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Deliang Wang
- Department of Materials Chemistry, Huzhou University, Huzhou, Zhejiang 313000, China
| | - Xue Li
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Jiayi Song
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Dong Wang
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiyong Yu
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Ying Li
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Ben Zhong Tang
- Shenzhen Institute of Aggregate Science and Engineering, School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
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Kim J, Hong SP, Lee S, Lee W, Lee D, Kim R, Park YJ, Moon S, Park K, Cha B, Kim JI. Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids. Hum Genomics 2023; 17:96. [PMID: 37898819 PMCID: PMC10613368 DOI: 10.1186/s40246-023-00533-0] [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: 05/10/2023] [Accepted: 09/11/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Fragmentomics, the investigation of fragmentation patterns of cell-free DNA (cfDNA), has emerged as a promising strategy for the early detection of multiple cancers in the field of liquid biopsy. However, the clinical application of this approach has been hindered by a limited understanding of cfDNA biology. Furthermore, the prevalence of hematopoietic cell-derived cfDNA in plasma complicates the in vivo investigation of tissue-specific cfDNA other than that of hematopoietic origin. While conventional two-dimensional cell lines have contributed to research on cfDNA biology, their limited representation of in vivo tissue contexts underscores the need for more robust models. In this study, we propose three-dimensional organoids as a novel in vitro model for studying cfDNA biology, focusing on multifaceted fragmentomic analyses. RESULTS We established nine patient-derived organoid lines from normal lung airway, normal gastric, and gastric cancer tissues. We then extracted cfDNA from the culture medium of these organoids in both proliferative and apoptotic states. Using whole-genome sequencing data from cfDNA, we analyzed various fragmentomic features, including fragment size, footprints, end motifs, and repeat types at the end. The distribution of cfDNA fragment sizes in organoids, especially in apoptosis samples, was similar to that found in plasma, implying occupancy by mononucleosomes. The footprints determined by sequencing depth exhibited distinct patterns depending on fragment sizes, reflecting occupancy by a variety of DNA-binding proteins. Notably, we discovered that short fragments (< 118 bp) were exclusively enriched in the proliferative state and exhibited distinct fragmentomic profiles, characterized by 3 bp palindromic end motifs and specific repeats. CONCLUSIONS In conclusion, our results highlight the utility of in vitro organoid models as a valuable tool for studying cfDNA biology and its associated fragmentation patterns. This, in turn, will pave the way for further enhancements in noninvasive cancer detection methodologies based on fragmentomics.
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Affiliation(s)
- Jaeryuk Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung-Pyo Hong
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seyoon Lee
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Woochan Lee
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dakyung Lee
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Rokhyun Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Jun Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sungji Moon
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyunghyuk Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bukyoung Cha
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea.
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
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Gonzalez-Martinez N, Gibson MI. Post-thaw application of ROCK-inhibitors increases cryopreserved T-cell yield. RSC Med Chem 2023; 14:2058-2067. [PMID: 37859712 PMCID: PMC10583820 DOI: 10.1039/d3md00378g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/18/2023] [Indexed: 10/21/2023] Open
Abstract
Emerging cell-based therapies such as CAR-T (Chimeric Antigen Receptor T) cells require cryopreservation to store and deliver intact and viable cells. Conventional cryopreservation formulations use DMSO to mitigate cold-induced damage, but do not address all the biochemical damage mechanisms induced by cold stress, such as programmed cell death (apoptosis). Rho-associated protein kinases (ROCK) are a key component of apoptosis, and their activation contributes to apoptotic blebbing. Here we demonstrate that the ROCK inhibitor fasudil hydrochloride, when supplemented into the thawing medium of T-cells increases the overall yield of healthy cells. Cell yield was highest using 5 or 10% DMSO cryopreservation solutions, with lower DMSO concentrations (2.5%) leading to significant physical damage to the cells. After optimisation, the post-thaw yield of T-cells increased by approximately 20% using this inhibitor, a significant increase in the context of a therapy. Flow cytometry analysis did not show a significant reduction in the relative percentage of cell populations undergoing apoptosis, but there was a small reduction in the 8 hours following thawing. Fasudil also led to a reduction in reactive oxygen species. Addition of fasudil into the cryopreservation solution, followed by dilution (rather than washing) upon thaw also gave a 20% increase in cell yield, demonstrating how this could be deployed in a cell-therapy context, without needing to change clinical thawing routines. Overall, this shows that modulation of post-thaw biochemical pathways which lead to apoptosis (or other degradative pathways) can be effectively targeted as a strategy to increase T-cell yield and function post-thaw.
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Affiliation(s)
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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35
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Gregory CD. Hijacking homeostasis: Regulation of the tumor microenvironment by apoptosis. Immunol Rev 2023; 319:100-127. [PMID: 37553811 PMCID: PMC10952466 DOI: 10.1111/imr.13259] [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: 04/25/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023]
Abstract
Cancers are genetically driven, rogue tissues which generate dysfunctional, obdurate organs by hijacking normal, homeostatic programs. Apoptosis is an evolutionarily conserved regulated cell death program and a profoundly important homeostatic mechanism that is common (alongside tumor cell proliferation) in actively growing cancers, as well as in tumors responding to cytotoxic anti-cancer therapies. Although well known for its cell-autonomous tumor-suppressive qualities, apoptosis harbors pro-oncogenic properties which are deployed through non-cell-autonomous mechanisms and which generally remain poorly defined. Here, the roles of apoptosis in tumor biology are reviewed, with particular focus on the secreted and fragmentation products of apoptotic tumor cells and their effects on tumor-associated macrophages, key supportive cells in the aberrant homeostasis of the tumor microenvironment. Historical aspects of cell loss in tumor growth kinetics are considered and the impact (and potential impact) on tumor growth of apoptotic-cell clearance (efferocytosis) as well as released soluble and extracellular vesicle-associated factors are discussed from the perspectives of inflammation, tissue repair, and regeneration programs. An "apoptosis-centric" view is proposed in which dying tumor cells provide an important platform for intricate intercellular communication networks in growing cancers. The perspective has implications for future research and for improving cancer diagnosis and therapy.
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Affiliation(s)
- Christopher D. Gregory
- Centre for Inflammation ResearchInstitute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarterEdinburghUK
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36
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Barbaste A, Schott S, Benassayag C, Suzanne M. Dissecting morphogenetic apoptosis through a genetic screen in Drosophila. Life Sci Alliance 2023; 6:e202301967. [PMID: 37495395 PMCID: PMC10372408 DOI: 10.26508/lsa.202301967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
Apoptosis is an essential cellular process both in normal development and pathological contexts. Screens performed to date have focused on the cell autonomous aspect of the process, deciphering the apoptotic cascade leading to cell destruction through the activation of caspases. However, the nonautonomous aspect of the apoptotic pathway, including signals regulating the apoptotic pattern or those sent by the apoptotic cell to its surroundings, is still poorly understood. Here, we describe an unbiased RNAi-based genetic screen whose goal is to identify elements of the "morphogenetic apoptosis pathway" in an integrated model system, the Drosophila leg. We screened about 1,400 candidates, using adult joint morphology, morphogenetic fold formation, and apoptotic pattern as readouts for the identification of potential apoptosis-related genes. We identified 41 genes potentially involved in specific aspects of morphogenetic apoptosis: (1) regulation of the apoptotic process; (2) formation, extrusion, and elimination of apoptotic bodies; and (3) contribution to morphogenesis downstream of apoptosis.
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Affiliation(s)
- Audrey Barbaste
- Laboratoire de Biologie Cellulaire et Moléculaire des Mécanismes du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sonia Schott
- Laboratoire de Biologie Cellulaire et Moléculaire des Mécanismes du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Corinne Benassayag
- Laboratoire de Biologie Cellulaire et Moléculaire des Mécanismes du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Magali Suzanne
- Laboratoire de Biologie Cellulaire et Moléculaire des Mécanismes du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
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Lee SA, Liu F, Yuwono C, Phan M, Chong S, Biazik J, Tay ACY, Janitz M, Riordan SM, Lan R, Wehrhahn MC, Zhang L. Emerging Aeromonas enteric infections: their association with inflammatory bowel disease and novel pathogenic mechanisms. Microbiol Spectr 2023; 11:e0108823. [PMID: 37732778 PMCID: PMC10581128 DOI: 10.1128/spectrum.01088-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
Aeromonas species are emerging human enteric pathogens. This study examines the isolation of Aeromonas and other enteric bacterial pathogens from patients with and without inflammatory bowel disease (IBD). This study also investigates the intestinal epithelial pathogenic mechanisms of Aeromonas veronii. The isolation rates of seven enteric bacterial pathogens from 2,279 patients with IBD and 373,276 non-IBD patients were compared. An A. veronii strain (AS1) isolated from intestinal biopsies of a patient with IBD was used for pathogenic mechanism investigation, and Escherichia coli K12 was used as a bacterial control. HT-29 cells were used as a model of human intestinal epithelium. A significantly higher isolation of Aeromonas species was found in patients with IBD as compared to non-IBD patients (P = 0.0001, odds ratio = 2.11). A. veronii upregulated 177 inflammatory genes and downregulated 52 protein-coding genes affecting chromatin assembly, multiple small nuclear RNAs, multiple nucleolar RNAs, and 55 cytoplasmic tRNAs in HT-29 cells. These downregulation effects were unique to A. veronii and not observed in HT-29 cells infected with E. coli K12. A. veronii induced intestinal epithelial apoptosis involving the intrinsic pathway. A. veronii caused epithelial microvilli shortening and damage and epithelial production of IL-8. In conclusion, this study for the first time reports the association between IBD and Aeromonas enteric infection detected by bacterial cultivation. This study also reports that A. veronii damages intestinal epithelial cells via multiple mechanisms, of which the downregulating cytoplasmic tRNA, small nuclear RNA, and small nucleolar RNA are novel bacterial pathogenic mechanisms. IMPORTANCE This study for the first time reports the association between inflammatory bowel disease (IBD) and Aeromonas enteric infection detected by bacterial pathogen cultivation, highlighting the need of clinical and public health attention. The finding that patients with IBD are more susceptible to Aeromonas enteric infection suggests that detection of Aeromonas enteric infection should be routinely performed for the diagnosis and treatment of IBD. This study also reports novel bacterial pathogenic mechanisms employed by Aeromonas veronii. Through comparative transcriptomic analysis and other techniques, this study revealed the pathogenic mechanisms by which A. veronii causes damage to intestinal epithelial cells. Among the various pathogenic mechanisms identified, the downregulating tRNA, small nuclear and nucleolar RNAs in human intestinal epithelial cells are novel bacterial pathogenic mechanisms.
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Affiliation(s)
- Seul A. Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Christopher Yuwono
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Monique Phan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sarah Chong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Joanna Biazik
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Alfred Chin Yen Tay
- Helicobacter Research Laboratory, School of Pathology and Laboratory Medicine, Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Stephen M. Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael C. Wehrhahn
- Douglass Hanly Moir Pathology, a Sonic Healthcare Australia Pathology Practice, Macquarie Park, New South Wales, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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38
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Lin W, Fang J, Wei S, He G, Liu J, Li X, Peng X, Li D, Yang S, Li X, Yang L, Li H. Extracellular vesicle-cell adhesion molecules in tumours: biofunctions and clinical applications. Cell Commun Signal 2023; 21:246. [PMID: 37735659 PMCID: PMC10512615 DOI: 10.1186/s12964-023-01236-8] [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: 04/09/2023] [Accepted: 07/18/2023] [Indexed: 09/23/2023] Open
Abstract
Cell adhesion molecule (CAM) is an umbrella term for several families of molecules, including the cadherin family, integrin family, selectin family, immunoglobulin superfamily, and some currently unclassified adhesion molecules. Extracellular vesicles (EVs) are important information mediators in cell-to-cell communication. Recent evidence has confirmed that CAMs transported by EVs interact with recipient cells to influence EV distribution in vivo and regulate multiple cellular processes. This review focuses on the loading of CAMs onto EVs, the roles of CAMs in regulating EV distribution, and the known and possible mechanisms of these actions. Moreover, herein, we summarize the impacts of CAMs transported by EVs to the tumour microenvironment (TME) on the malignant behaviour of tumour cells (proliferation, metastasis, immune escape, and so on). In addition, from the standpoint of clinical applications, the significance and challenges of using of EV-CAMs in the diagnosis and therapy of tumours are discussed. Finally, considering recent advances in the understanding of EV-CAMs, we outline significant challenges in this field that require urgent attention to advance research and promote the clinical applications of EV-CAMs. Video Abstract.
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Affiliation(s)
- Weikai Lin
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Jianjun Fang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Shibo Wei
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Guangpeng He
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Jiaxing Liu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Xian Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Dai Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Shuo Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China
| | - Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China.
| | - Hangyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Shenyang Clinical Medical Research Center for Diagnosis, Treatment and Health Management of Early Digestive Cancer, Shenyang, 110032, China.
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van de Wakker SI, Meijers FM, Sluijter JPG, Vader P. Extracellular Vesicle Heterogeneity and Its Impact for Regenerative Medicine Applications. Pharmacol Rev 2023; 75:1043-1061. [PMID: 37280097 DOI: 10.1124/pharmrev.123.000841] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/20/2023] [Accepted: 05/01/2023] [Indexed: 06/08/2023] Open
Abstract
Extracellular vesicles (EVs) are cell-derived membrane-enclosed particles that are involved in physiologic and pathologic processes. EVs are increasingly being studied for therapeutic applications in the field of regenerative medicine. Therapeutic application of stem cell-derived EVs has shown great potential to stimulate tissue repair. However, the exact mechanisms through which they induce this effect have not been fully clarified. This may to a large extent be attributed to a lack of knowledge on EV heterogeneity. Recent studies suggest that EVs represent a heterogeneous population of vesicles with distinct functions. The heterogeneity of EVs can be attributed to differences in their biogenesis, and as such, they can be classified into distinct populations that can then be further subcategorized into various subpopulations. A better understanding of EV heterogeneity is crucial for elucidating their mechanisms of action in tissue regeneration. This review provides an overview of the latest insights on EV heterogeneity related to tissue repair, including the different characteristics that contribute to such heterogeneity and the functional differences among EV subtypes. It also sheds light on the challenges that hinder clinical translation of EVs. Additionally, innovative EV isolation techniques for studying EV heterogeneity are discussed. Improved knowledge of active EV subtypes would promote the development of tailored EV therapies and aid researchers in the translation of EV-based therapeutics to the clinic. SIGNIFICANCE STATEMENT: Within this review we discuss the differences in regenerative properties of extracellular vesicle (EV) subpopulations and implications of EV heterogeneity for development of EV-based therapeutics. We aim to provide new insights into which aspects are leading to heterogeneity in EV preparations and stress the importance of EV heterogeneity studies for clinical applications.
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Affiliation(s)
- Simonides Immanuel van de Wakker
- Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (S.I.V.D.W., F.M.M., J.P.G.S., P.V.) and CDL Research, University Medical Center Utrecht, The Netherlands (P.V.)
| | - Fleur Michelle Meijers
- Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (S.I.V.D.W., F.M.M., J.P.G.S., P.V.) and CDL Research, University Medical Center Utrecht, The Netherlands (P.V.)
| | - Joost Petrus Gerardus Sluijter
- Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (S.I.V.D.W., F.M.M., J.P.G.S., P.V.) and CDL Research, University Medical Center Utrecht, The Netherlands (P.V.)
| | - Pieter Vader
- Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (S.I.V.D.W., F.M.M., J.P.G.S., P.V.) and CDL Research, University Medical Center Utrecht, The Netherlands (P.V.)
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40
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Kinoshita N, Gessho M, Torii T, Ashida Y, Akamatsu M, Guo AK, Lee S, Katsuno T, Nakajima W, Budirahardja Y, Miyoshi D, Todokoro T, Ishida H, Nishikata T, Kawauchi K. The iron chelator deferriferrichrysin induces paraptosis via extracellular signal-related kinase activation in cancer cells. Genes Cells 2023; 28:653-662. [PMID: 37264202 DOI: 10.1111/gtc.13053] [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: 03/17/2023] [Revised: 05/08/2023] [Accepted: 05/22/2023] [Indexed: 06/03/2023]
Abstract
Cancer cells generally exhibit increased iron uptake, which contributes to their abnormal growth and metastatic ability. Iron chelators have thus recently attracted attention as potential anticancer agents. Here, we show that deferriferrichrysin (Dfcy), a natural product from Aspergillus oryzae acts as an iron chelator to induce paraptosis (a programmed cell death pathway characterized by ER dilation) in MCF-7 human breast cancer cells and H1299 human lung cancer cells. We first examined the anticancer efficacy of Dfcy in cancer cells and found that Dfcy induced ER dilation and reduced the number of viable cells. Extracellular signal-related kinase (ERK) was activated by Dfcy treatment, and the MEK inhibitor U0126, a small molecule commonly used to inhibit ERK activity, prevented the increase in ER dilation in Dfcy-treated cells. Concomitantly, the decrease in the number of viable cells upon treatment with Dfcy was attenuated by U0126. Taken together, these results demonstrate that the iron chelator Dfcy exhibits anticancer effects via induction of ERK-dependent paraptosis.
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Affiliation(s)
- Natsuki Kinoshita
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Masaya Gessho
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Takeru Torii
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Yukako Ashida
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Minori Akamatsu
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Alvin Kunyao Guo
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Sunmin Lee
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Tatsuya Katsuno
- Center of Anatomical, Pathological and Forensic Medical Researches, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Wataru Nakajima
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Yemima Budirahardja
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Daisuke Miyoshi
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | | | - Hiroki Ishida
- Research Institute, Gekkeikan Sake Co., Ltd, Kyoto, Japan
| | - Takahito Nishikata
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Keiko Kawauchi
- Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
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41
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Sanchez EE, Tello-Lafoz M, Guo AJ, de Jesus M, Elbanna YA, Winer BY, Budhu S, Chan E, Rosiek E, Kondo T, DuSold J, Taylor N, Altan-Bonnet G, Olson MF, Huse M. Apoptotic contraction drives target cell release by cytotoxic T cells. Nat Immunol 2023; 24:1434-1442. [PMID: 37500886 PMCID: PMC11138163 DOI: 10.1038/s41590-023-01572-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/22/2023] [Indexed: 07/29/2023]
Abstract
Cytotoxic T lymphocytes (CTLs) fight intracellular pathogens and cancer by identifying and destroying infected or transformed target cells1. To kill, CTLs form a specialized cytotoxic immune synapse (IS) with a target of interest and then release toxic perforin and granzymes into the interface to elicit programmed cell death2-5. The IS then dissolves, enabling CTLs to search for additional prey and professional phagocytes to clear the corpse6. While the mechanisms governing IS assembly have been studied extensively, far less is known about target cell release. Here, we applied time-lapse imaging to explore the basis for IS dissolution and found that it occurred concomitantly with the cytoskeletal contraction of apoptotic targets. Genetic and pharmacological perturbation of this contraction response indicated that it was both necessary and sufficient for CTL dissociation. We also found that mechanical amplification of apoptotic contractility promoted faster CTL detachment and serial killing. Collectively, these results establish a biophysical basis for IS dissolution and highlight the importance of mechanosensory feedback in the regulation of cell-cell interactions.
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Affiliation(s)
- Elisa E Sanchez
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Tello-Lafoz
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aixuan J Guo
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miguel de Jesus
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yassmin A Elbanna
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Y Winer
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sadna Budhu
- Department of Pharmacology, Weill-Cornell Medical College, New York, NY, USA
| | - Eric Chan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Rosiek
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taisuke Kondo
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Justyn DuSold
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Naomi Taylor
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Michael F Olson
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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42
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Powis G, Meuillet EJ, Indarte M, Booher G, Kirkpatrick L. Pleckstrin Homology [PH] domain, structure, mechanism, and contribution to human disease. Biomed Pharmacother 2023; 165:115024. [PMID: 37399719 DOI: 10.1016/j.biopha.2023.115024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
The pleckstrin homology [PH] domain is a structural fold found in more than 250 proteins making it the 11th most common domain in the human proteome. 25% of family members have more than one PH domain and some PH domains are split by one, or several other, protein domains although still folding to give functioning PH domains. We review mechanisms of PH domain activity, the role PH domain mutation plays in human disease including cancer, hyperproliferation, neurodegeneration, inflammation, and infection, and discuss pharmacotherapeutic approaches to regulate PH domain activity for the treatment of human disease. Almost half PH domain family members bind phosphatidylinositols [PIs] that attach the host protein to cell membranes where they interact with other membrane proteins to give signaling complexes or cytoskeleton scaffold platforms. A PH domain in its native state may fold over other protein domains thereby preventing substrate access to a catalytic site or binding with other proteins. The resulting autoinhibition can be released by PI binding to the PH domain, or by protein phosphorylation thus providing fine tuning of the cellular control of PH domain protein activity. For many years the PH domain was thought to be undruggable until high-resolution structures of human PH domains allowed structure-based design of novel inhibitors that selectively bind the PH domain. Allosteric inhibitors of the Akt1 PH domain have already been tested in cancer patients and for proteus syndrome, with several other PH domain inhibitors in preclinical development for treatment of other human diseases.
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Affiliation(s)
- Garth Powis
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA.
| | | | - Martin Indarte
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Garrett Booher
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Lynn Kirkpatrick
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
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43
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Gregory CD, Rimmer MP. Extracellular vesicles arising from apoptosis: forms, functions, and applications. J Pathol 2023; 260:592-608. [PMID: 37294158 PMCID: PMC10952477 DOI: 10.1002/path.6138] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 06/10/2023]
Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed subcellular bodies produced by most, if not all cells. Research over the last two decades has recognised the importance of EVs in intercellular communication and horizontal transfer of biological material. EVs range in diameter from tens of nanometres up to several micrometres and are able to transfer a spectrum of biologically active cargoes - from whole organelles, through macromolecules including nucleic acids and proteins, to metabolites and small molecules - from their cells of origin to recipient cells, which may consequently become physiologically or pathologically altered. Based on their modes of biogenesis, the most renowned EV classes are (1) microvesicles, (2) exosomes (both produced by healthy cells), and (3) EVs from cells undergoing regulated death by apoptosis (ApoEVs). Microvesicles bud directly from the plasma membrane, while exosomes are derived from endosomal compartments. Current knowledge of the formation and functional properties of ApoEVs lags behind that of microvesicles and exosomes, but burgeoning evidence indicates that ApoEVs carry manifold cargoes, including mitochondria, ribosomes, DNA, RNAs, and proteins, and perform diverse functions in health and disease. Here we review this evidence, which demonstrates substantial diversity in the luminal and surface membrane cargoes of ApoEVs, permitted by their very broad size range (from around 50 nm to >5 μm; the larger often termed apoptotic bodies), strongly suggests their origins through both microvesicle- and exosome-like biogenesis pathways, and indicates routes through which they interact with recipient cells. We discuss the capacity of ApoEVs to recycle cargoes and modulate inflammatory, immunological, and cell fate programmes in normal physiology and in pathological scenarios such as cancer and atherosclerosis. Finally, we provide a perspective on clinical applications of ApoEVs in diagnostics and therapeutics. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Christopher D Gregory
- Centre for Inflammation ResearchInstitute for Regeneration and Repair, University of EdinburghEdinburghUK
| | - Michael P Rimmer
- Centre for Reproductive HealthInstitute for Regeneration and Repair, University of EdinburghEdinburghUK
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44
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Patel U, Susman D, Allan AL. Influence of Extracellular Vesicles on Lung Stromal Cells during Breast Cancer Metastasis. Int J Mol Sci 2023; 24:11801. [PMID: 37511559 PMCID: PMC10380344 DOI: 10.3390/ijms241411801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer is a prominent cause of cancer diagnosis and death in women globally, with over 90% of deaths being attributed to complications that arise from metastasis. One of the common locations for breast cancer metastasis is the lung, which is associated with significant morbidity and mortality. Curative treatments for metastatic breast cancer patients are not available and the molecular mechanisms that underlie lung metastasis are not fully understood. In order to better treat these patients, identifying events that occur both prior to and during metastatic spread to the lung is essential. Several studies have demonstrated that breast cancer-derived extracellular vesicles secreted from the primary breast tumor play a key role in establishing the lung pre-metastatic niche to support colonization of metastatic tumor cells. In this review, we summarize recent work supporting the influence of extracellular vesicles on stromal components of the lung to construct the pre-metastatic niche and support metastasis. Furthermore, we discuss the potential clinical applications of utilizing extracellular vesicles for diagnosis and treatment. Together, this review highlights the dynamic nature of extracellular vesicles, their roles in breast cancer metastasis to the lung, and their value as potential biomarkers and therapeutics for cancer prevention.
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Affiliation(s)
- Urvi Patel
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 5W9, Canada
| | - David Susman
- Department of Anatomy & Cell Biology, Western University, London, ON N6A 5W9, Canada
| | - Alison L Allan
- Departments of Anatomy & Cell Biology and Oncology, Western University, London, ON N6A 5W9, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Lawson Health Research Institute, London, ON N6A 5W9, Canada
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45
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Yu L, Zhu G, Zhang Z, Yu Y, Zeng L, Xu Z, Weng J, Xia J, Li J, Pathak JL. Apoptotic bodies: bioactive treasure left behind by the dying cells with robust diagnostic and therapeutic application potentials. J Nanobiotechnology 2023; 21:218. [PMID: 37434199 DOI: 10.1186/s12951-023-01969-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023] Open
Abstract
Apoptosis, a form of programmed cell death, is essential for growth and tissue homeostasis. Apoptotic bodies (ApoBDs) are a form of extracellular vesicles (EVs) released by dying cells in the last stage of apoptosis and were previously regarded as debris of dead cells. Recent studies unraveled that ApoBDs are not cell debris but the bioactive treasure left behind by the dying cells with an important role in intercellular communications related to human health and various diseases. Defective clearance of ApoBDs and infected-cells-derived ApoBDs are possible etiology of some diseases. Therefore, it is necessary to explore the function and mechanism of the action of ApoBDs in different physiological and pathological conditions. Recent advances in ApoBDs have elucidated the immunomodulatory, virus removal, vascular protection, tissue regenerative, and disease diagnostic potential of ApoBDs. Moreover, ApoBDs can be used as drug carriers enhancing drug stability, cellular uptake, and targeted therapy efficacy. These reports from the literature indicate that ApoBDs hold promising potential for diagnosis, prognosis, and treatment of various diseases, including cancer, systemic inflammatory diseases, cardiovascular diseases, and tissue regeneration. This review summarizes the recent advances in ApoBDs-related research and discusses the role of ApoBDs in health and diseases as well as the challenges and prospects of ApoBDs-based diagnostic and therapeutic applications.
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Affiliation(s)
- Lina Yu
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China.
| | - Guanxiong Zhu
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China
| | - Zeyu Zhang
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China
| | - Yang Yu
- Department of Sports and Health, Guangzhou Sport University, Guangzhou, China
| | - Liting Zeng
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China
| | - Zidan Xu
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China
| | - Jinlong Weng
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China
| | - Junyi Xia
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China
| | - Jiang Li
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China.
| | - Janak L Pathak
- Department of Preventive Dentistry, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.
- School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China.
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46
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You W, Zhou T, Knoops K, Berendschot TTJM, van Zandvoort MAMJ, Germeraad WTV, Benedikter B, Webers CAB, Reutelingsperger CPM, Gorgels TGMF. Stressed neuronal cells can recover from profound membrane blebbing, nuclear condensation and mitochondrial fragmentation, but not from cytochrome c release. Sci Rep 2023; 13:11045. [PMID: 37422517 PMCID: PMC10329692 DOI: 10.1038/s41598-023-38210-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023] Open
Abstract
Loss of neurons in chronic neurodegenerative diseases may occur over a period of many years. Once initiated, neuronal cell death is accompanied by distinct phenotypic changes including cell shrinkage, neurite retraction, mitochondrial fragmentation, nuclear condensation, membrane blebbing and phosphatidylserine (PS) exposure at the plasma membrane. It is still poorly understood which events mark the point of no return for dying neurons. Here we analyzed the neuronal cell line SH-SY5Y expressing cytochrome C (Cyto.C)-GFP. Cells were exposed temporarily to ethanol (EtOH) and tracked longitudinally in time by light and fluorescent microscopy. Exposure to EtOH induced elevation of intracellular Ca2+ and reactive oxygen species, cell shrinkage, neurite retraction, mitochondrial fragmentation, nuclear condensation, membrane blebbing, PS exposure and Cyto.C release into the cytosol. Removing EtOH at predetermined time points revealed that all phenomena except Cyto.C release occurred in a phase of neuronal cell death in which full recovery to a neurite-bearing cell was still possible. Our findings underscore a strategy of treating chronic neurodegenerative diseases by removing stressors from neurons and harnessing intracellular targets that delay or prevent trespassing the point of no return.
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Affiliation(s)
- Wenting You
- University Eye Clinic Maastricht UMC+, Maastricht University Medical Center+, 6229 HX, Maastricht, The Netherlands
- Department of Biochemistry, CARIM School for Cardiovascular Disease, Maastricht University, 6229 ER, Maastricht, The Netherlands
- Department of Mental Health and Neuroscience, Maastricht University, 6229 ER, Maastricht, The Netherlands
| | - Tao Zhou
- University Eye Clinic Maastricht UMC+, Maastricht University Medical Center+, 6229 HX, Maastricht, The Netherlands
| | - Kèvin Knoops
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER, Maastricht, The Netherlands
| | - Tos T J M Berendschot
- University Eye Clinic Maastricht UMC+, Maastricht University Medical Center+, 6229 HX, Maastricht, The Netherlands
| | - Marc A M J van Zandvoort
- Department of Molecular Cell Biology, CARIM School for Cardiovascular Disease, Maastricht University, 6229 ER, Maastricht, The Netherlands
- Institute of Molecular Cardiovascular Research, Universitätsklinikum Aachen, 52074, Aachen, Germany
| | - Wilfred T V Germeraad
- Division of Hematology, Department of Internal Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Birke Benedikter
- University Eye Clinic Maastricht UMC+, Maastricht University Medical Center+, 6229 HX, Maastricht, The Netherlands
| | - Carroll A B Webers
- University Eye Clinic Maastricht UMC+, Maastricht University Medical Center+, 6229 HX, Maastricht, The Netherlands
| | - Chris P M Reutelingsperger
- Department of Biochemistry, CARIM School for Cardiovascular Disease, Maastricht University, 6229 ER, Maastricht, The Netherlands.
| | - Theo G M F Gorgels
- University Eye Clinic Maastricht UMC+, Maastricht University Medical Center+, 6229 HX, Maastricht, The Netherlands.
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47
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Fortuni B, Ricci M, Vitale R, Inose T, Zhang Q, Hutchison JA, Hirai K, Fujita Y, Toyouchi S, Krzyzowska S, Van Zundert I, Rocha S, Uji-I H. SERS Endoscopy for Monitoring Intracellular Drug Dynamics. ACS Sens 2023; 8:2340-2347. [PMID: 37219991 DOI: 10.1021/acssensors.3c00394] [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] [Indexed: 05/25/2023]
Abstract
Understanding the dynamics and distribution of medicinal drugs in living cells is essential for the design and discovery of treatments. The tools available for revealing this information are, however, extremely limited. Here, we report the application of surface-enhanced Raman scattering (SERS) endoscopy, using plasmonic nanowires as SERS probes, to monitor the intracellular fate and dynamics of a common chemo-drug, doxorubicin, in A549 cancer cells. The unique spatio-temporal resolution of this technique reveals unprecedented information on the mode of action of doxorubicin: its localization in the nucleus, its complexation with medium components, and its intercalation with DNA as a function of time. Notably, we were able to discriminate these factors for the direct administration of doxorubicin or the use of a doxorubicin delivery system. The results reported here show that SERS endoscopy may have an important future role in medicinal chemistry for studying the dynamics and mechanism of action of drugs in cells.
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Affiliation(s)
- Beatrice Fortuni
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Monica Ricci
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Raffaele Vitale
- U. Lille, CNRS, LASIRE, Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Cité Scientifique, F-59000 Lille, France
| | - Tomoko Inose
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Qiang Zhang
- Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
| | - James Andell Hutchison
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kenji Hirai
- Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
| | - Yasuhiko Fujita
- Toray Research Center, Inc., Sonoyama 3-3-7, Otsu, Shiga 520-8567, Japan
| | - Shuichi Toyouchi
- Research Institute for Light-Induced Acceleration System (RILACS), Osaka Metropolitan University, 1-2 Gakuencho, Nakaku, Sakai, Osaka 599-8570, Japan
| | - Sandra Krzyzowska
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Indra Van Zundert
- Synthetic Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Susana Rocha
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Hiroshi Uji-I
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
- Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
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48
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Kira A, Tatsutomi I, Saito K, Murata M, Hattori I, Kajita H, Muraki N, Oda Y, Satoh S, Tsukamoto Y, Kimura S, Onoue K, Yonemura S, Arakawa S, Kato H, Hirashima T, Kawane K. Apoptotic extracellular vesicle formation via local phosphatidylserine exposure drives efficient cell extrusion. Dev Cell 2023:S1534-5807(23)00241-1. [PMID: 37315563 DOI: 10.1016/j.devcel.2023.05.008] [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: 02/12/2022] [Revised: 01/29/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
Cell extrusion is a universal mode of cell removal from tissues, and it plays an important role in regulating cell numbers and eliminating unwanted cells. However, the underlying mechanisms of cell delamination from the cell layer are unclear. Here, we report a conserved execution mechanism of apoptotic cell extrusion. We found extracellular vesicle (EV) formation in extruding mammalian and Drosophila cells at a site opposite to the extrusion direction. Lipid-scramblase-mediated local exposure of phosphatidylserine is responsible for EV formation and is crucial for executing cell extrusion. Inhibition of this process disrupts prompt cell delamination and tissue homeostasis. Although the EV has hallmarks of an apoptotic body, its formation is governed by the mechanism of microvesicle formation. Experimental and mathematical modeling analysis illustrated that EV formation promotes neighboring cells' invasion. This study showed that membrane dynamics play a crucial role in cell exit by connecting the actions of the extruding cell and neighboring cells.
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Affiliation(s)
- Akihito Kira
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Ichiko Tatsutomi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Keisuke Saito
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Machiko Murata
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Izumi Hattori
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Haruna Kajita
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Naoko Muraki
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Yukako Oda
- Department of Cell Growth and Differentiation, Center for iPS Cell Research & Application, Kyoto University, Kyoto 606-8507, Japan
| | - Saya Satoh
- Institute of Cardiovascular Immunology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Yuta Tsukamoto
- Institute of Cardiovascular Immunology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Seisuke Kimura
- Department of Industrial Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan; Center for Plant Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Kenta Onoue
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan
| | - Shigenobu Yonemura
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan; Department of Cell Biology, Tokushima University Graduate School of Medicine, Tokushima 770-8503, Japan
| | - Satoko Arakawa
- Research Core, Institute of Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Tsuyoshi Hirashima
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan.
| | - Kohki Kawane
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.
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49
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Dohnalkova E, Bayer RL, Guo Q, Bamidele AO, Kim Lee HS, Valenzuela-Pérez L, Krishnan A, Pavelko KD, Guisot NES, Bunyard P, Kim YB, Ibrahim SH, Gores GJ, Hirsova P. Rho-associated protein kinase 1 inhibition in hepatocytes attenuates nonalcoholic steatohepatitis. Hepatol Commun 2023; 7:02009842-202306010-00031. [PMID: 37267252 DOI: 10.1097/hc9.0000000000000171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND NASH is the progressive form of NAFLD characterized by lipotoxicity, hepatocyte injury, tissue inflammation, and fibrosis. Previously, Rho-associated protein kinase (ROCK) 1 has been implicated in lipotoxic signaling in hepatocytes in vitro and high-fat diet-induced lipogenesis in vivo. However, whether ROCK1 plays a role in liver inflammation and fibrosis during NASH is unclear. Here, we hypothesized that pathogenic activation of ROCK1 promotes murine NASH pathogenesis. METHODS AND RESULTS Patients with NASH had increased hepatic ROCK1 expression compared with patients with fatty liver. Similarly, hepatic ROCK1 levels and activity were increased in mice with NASH induced by a western-like diet that is high in fat, fructose, and cholesterol (FFC). Hepatocyte-specific ROCK1 knockout mice on the FFC diet displayed a decrease in liver steatosis, hepatic cell death, liver inflammation, and fibrosis compared with littermate FFC-fed controls. Mechanistically, these effects were associated with a significant attenuation of myeloid cell recruitment. Interestingly, myeloid cell-specific ROCK1 deletion did not affect NASH development in FFC-fed mice. To explore the therapeutic opportunities, mice with established NASH received ROCKi, a novel small molecule kinase inhibitor of ROCK1/2, which preferentially accumulates in liver tissue. ROCK inhibitor treatment ameliorated insulin resistance and decreased liver injury, inflammation, and fibrosis. CONCLUSIONS Genetic or pharmacologic inhibition of ROCK1 activity attenuates murine NASH, suggesting that ROCK1 may be a therapeutic target for treating human NASH.
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Affiliation(s)
- Ester Dohnalkova
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biological and Medical Sciences, Charles University, Hradec Kralove, Czech Republic
| | - Rachel L Bayer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Qianqian Guo
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Adebowale O Bamidele
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Hyun Se Kim Lee
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Anuradha Krishnan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kevin D Pavelko
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Young-Bum Kim
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Samar H Ibrahim
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Pediatric Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Gregory J Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Petra Hirsova
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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50
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Park JW, Tyl MD, Cristea IM. Orchestration of Mitochondrial Function and Remodeling by Post-Translational Modifications Provide Insight into Mechanisms of Viral Infection. Biomolecules 2023; 13:biom13050869. [PMID: 37238738 DOI: 10.3390/biom13050869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The regulation of mitochondria structure and function is at the core of numerous viral infections. Acting in support of the host or of virus replication, mitochondria regulation facilitates control of energy metabolism, apoptosis, and immune signaling. Accumulating studies have pointed to post-translational modification (PTM) of mitochondrial proteins as a critical component of such regulatory mechanisms. Mitochondrial PTMs have been implicated in the pathology of several diseases and emerging evidence is starting to highlight essential roles in the context of viral infections. Here, we provide an overview of the growing arsenal of PTMs decorating mitochondrial proteins and their possible contribution to the infection-induced modulation of bioenergetics, apoptosis, and immune responses. We further consider links between PTM changes and mitochondrial structure remodeling, as well as the enzymatic and non-enzymatic mechanisms underlying mitochondrial PTM regulation. Finally, we highlight some of the methods, including mass spectrometry-based analyses, available for the identification, prioritization, and mechanistic interrogation of PTMs.
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Affiliation(s)
- Ji Woo Park
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Matthew D Tyl
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
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