1
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Huang X, Su Z, Xie XJ. The Enigmas of Tissue Closure: Inspiration from Drosophila. Curr Issues Mol Biol 2024; 46:8710-8725. [PMID: 39194731 DOI: 10.3390/cimb46080514] [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: 05/31/2024] [Revised: 07/26/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Hollow structures are essential for development and physiological activity. The construction and maintenance of hollow structures never cease throughout the lives of multicellular animals. Epithelial tissue closure is the main strategy used by living organisms to build hollow structures. The high diversity of hollow structures and the simplicity of their development in Drosophila make it an excellent model for the study of hollow structure morphogenesis. In this review, we summarize the tissue closure processes in Drosophila that give rise to or maintain hollow structures and highlight the molecular mechanisms and distinct cell biology involved in these processes.
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Affiliation(s)
- Xiaoying Huang
- Department of Histology and Embryology, Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Zhongjing Su
- Department of Histology and Embryology, Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Xiao-Jun Xie
- Department of Histology and Embryology, Shantou University Medical College, Shantou 515041, China
- Cancer Research Center, Shantou University Medical College, Shantou 515041, China
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2
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Kumar N, Mim MS, Dowling A, Zartman JJ. Reverse engineering morphogenesis through Bayesian optimization of physics-based models. NPJ Syst Biol Appl 2024; 10:49. [PMID: 38714708 PMCID: PMC11076624 DOI: 10.1038/s41540-024-00375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 04/17/2024] [Indexed: 05/10/2024] Open
Abstract
Morphogenetic programs coordinate cell signaling and mechanical interactions to shape organs. In systems and synthetic biology, a key challenge is determining optimal cellular interactions for predicting organ shape, size, and function. Physics-based models defining the subcellular force distribution facilitate this, but it is challenging to calibrate parameters in these models from data. To solve this inverse problem, we created a Bayesian optimization framework to determine the optimal cellular force distribution such that the predicted organ shapes match the experimentally observed organ shapes. This integrative framework employs Gaussian Process Regression, a non-parametric kernel-based probabilistic machine learning modeling paradigm, to learn the mapping functions relating to the morphogenetic programs that maintain the final organ shape. We calibrated and tested the method on Drosophila wing imaginal discs to study mechanisms that regulate epithelial processes ranging from development to cancer. The parameter estimation framework successfully infers the underlying changes in core parameters needed to match simulation data with imaging data of wing discs perturbed with collagenase. The computational pipeline identifies distinct parameter sets mimicking wild-type shapes. It enables a global sensitivity analysis to support the regulation of actomyosin contractility and basal ECM stiffness to generate and maintain the curved shape of the wing imaginal disc. The optimization framework, combined with experimental imaging, identified that Piezo, a mechanosensitive ion channel, impacts fold formation by regulating the apical-basal balance of actomyosin contractility and elasticity of ECM. This workflow is extensible toward reverse-engineering morphogenesis across organ systems and for real-time control of complex multicellular systems.
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Affiliation(s)
- Nilay Kumar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Mayesha Sahir Mim
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
- Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Alexander Dowling
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jeremiah J Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN, 46556, USA.
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3
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Manara V, Radoani M, Belli R, Peroni D, Destefanis F, Angheben L, Tome G, Tebaldi T, Bellosta P. NOC1 is a direct MYC target, and its protein interactome dissects its activity in controlling nucleolar function. Front Cell Dev Biol 2023; 11:1293420. [PMID: 38213308 PMCID: PMC10782387 DOI: 10.3389/fcell.2023.1293420] [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: 09/13/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
The nucleolus is a subnuclear compartment critical in ribosome biogenesis and cellular stress responses. These mechanisms are governed by a complex interplay of proteins, including NOC1, a member of the NOC family of nucleolar proteins responsible for controlling rRNA processing and ribosomal maturation. This study reveals a novel relationship between NOC1 and MYC transcription factor, known for its crucial role in controlling ribosomal biogenesis, cell growth, and proliferation. Here, we demonstrate that NOC1 functions as a direct target of MYC, as it is transcriptionally induced through a functional MYC-binding E-box sequence in the NOC1 promoter region. Furthermore, protein interactome analysis reveals that NOC1-complex includes the nucleolar proteins NOC2 and NOC3 and other nucleolar components such as Nucleostemin1 Ns1 transporters of ribosomal subunits and components involved in rRNA processing and maturation. In response to MYC, NOC1 expression and localization within the nucleolus significantly increase, suggesting a direct functional link between MYC activity and NOC1 function. Notably, NOC1 over-expression leads to the formation of large nuclear granules and enlarged nucleoli, which co-localize with nucleolar fibrillarin and Ns1. Additionally, we demonstrate that NOC1 expression is necessary for Ns1 nucleolar localization, suggesting a role for NOC1 in maintaining nucleolar structure. Finally, the co-expression of NOC1 and MYC enhances nucleolus size and maintains their co-localization, outlining another aspect of the cooperation between NOC1 and MYC in nucleolar dynamics. This study also reveals an enrichment with NOC1 with few proteins involved in RNA processing, modification, and splicing. Moreover, proteins such as Ythdc1, Flacc, and splenito are known to mediate N6-methyladenosine (m6A) methylation of mRNAs in nuclear export, revealing NOC1's potential involvement in coordinating RNA splicing and nuclear mRNA export. In summary, we uncovered novel roles for NOC1 in nucleolar homeostasis and established its direct connection with MYC in the network governing nucleolar structure and function. These findings also highlight NOC1's interaction with proteins relevant to specific RNA functions, suggesting a broader role in addition to its control of nucleolar homeostasis and providing new insight that can be further investigated.
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Affiliation(s)
- Valeria Manara
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Marco Radoani
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Romina Belli
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Daniele Peroni
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Francesca Destefanis
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
- Institute of Evolutionary Biology CSIC Universitat Pompeu Fabra, Barcelona, Spain
| | - Luca Angheben
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Gabriele Tome
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Toma Tebaldi
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Paola Bellosta
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
- Department of Medicine, NYU Langone Medical Center, New York, NY, United States
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4
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Kumar N, Dowling A, Zartman J. Reverse engineering morphogenesis through Bayesian optimization of physics-based models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.553928. [PMID: 37662294 PMCID: PMC10473585 DOI: 10.1101/2023.08.21.553928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Morphogenetic programs direct the cell signaling and nonlinear mechanical interactions between multiple cell types and tissue layers to define organ shape and size. A key challenge for systems and synthetic biology is determining optimal combinations of intra- and inter-cellular interactions to predict an organ's shape, size, and function. Physics-based mechanistic models that define the subcellular force distribution facilitate this, but it is extremely challenging to calibrate parameters in these models from data. To solve this inverse problem, we created a Bayesian optimization framework to determine the optimal cellular force distribution such that the predicted organ shapes match the desired organ shapes observed within the experimental imaging data. This integrative framework employs Gaussian Process Regression (GPR), a non-parametric kernel-based probabilistic machine learning modeling paradigm, to learn the mapping functions relating to the morphogenetic programs that generate and maintain the final organ shape. We calibrated and tested the method on cross-sections of Drosophila wing imaginal discs, a highly informative model organ system, to study mechanisms that regulate epithelial processes that range from development to cancer. As a specific test case, the parameter estimation framework successfully infers the underlying changes in core parameters needed to match simulation data with time series imaging data of wing discs perturbed with collagenase. Unexpectedly, the framework also identifies multiple distinct parameter sets that generate shapes similar to wild-type organ shapes. This platform enables an efficient, global sensitivity analysis to support the necessity of both actomyosin contractility and basal ECM stiffness to generate and maintain the curved shape of the wing imaginal disc. The optimization framework, combined with fixed tissue imaging, identified that Piezo, a mechanosensitive ion channel, impacts fold formation by regulating the apical-basal balance of actomyosin contractility and elasticity of ECM. This framework is extensible toward reverse-engineering the morphogenesis of any organ system and can be utilized in real-time control of complex multicellular systems.
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5
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Harris RE. Investigating Tissue Regeneration Using the DUAL Control Genetic Ablation System. Methods Mol Biol 2023; 2599:255-270. [PMID: 36427155 DOI: 10.1007/978-1-0716-2847-8_18] [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: 06/14/2023]
Abstract
Genetic ablation is a highly efficient method to study regeneration in vivo by stimulating tissue-specific cell death that subsequently induces regrowth and repair in a developing organism. This approach has been particularly successful in Drosophila, for which various temperature-based genetic ablation tools have been developed to explore the complexities of regeneration in larval imaginal discs. Here, we describe the use of a recently established ablation system called DUAL Control, which can be used to both characterize the damage response and genetically manipulate blastema cells to identify novel regulators of regeneration.
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Affiliation(s)
- R E Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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6
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Crucianelli C, Jaiswal J, Vijayakumar Maya A, Nogay L, Cosolo A, Grass I, Classen AK. Distinct signaling signatures drive compensatory proliferation via S-phase acceleration. PLoS Genet 2022; 18:e1010516. [PMID: 36520882 PMCID: PMC9799308 DOI: 10.1371/journal.pgen.1010516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/29/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
Regeneration relies on cell proliferation to restore damaged tissues. Multiple signaling pathways activated by local or paracrine cues have been identified to promote regenerative proliferation. How different types of tissue damage may activate distinct signaling pathways and how these differences converge on regenerative proliferation is less well defined. To better understand how tissue damage and proliferative signals are integrated during regeneration, we investigate models of compensatory proliferation in Drosophila imaginal discs. We find that compensatory proliferation is associated with a unique cell cycle profile, which is characterized by short G1 and G2 phases and, surprisingly, by acceleration of the S-phase. S-phase acceleration can be induced by two distinct signaling signatures, aligning with inflammatory and non-inflammatory tissue damage. Specifically, non-autonomous activation of JAK/STAT and Myc in response to inflammatory damage, or local activation of Ras/ERK and Hippo/Yki in response to elevated cell death, promote accelerated nucleotide incorporation during S-phase. This previously unappreciated convergence of different damaging insults on the same regenerative cell cycle program reconciles previous conflicting observations on proliferative signaling in different tissue regeneration and tumor models.
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Affiliation(s)
- Carlo Crucianelli
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Janhvi Jaiswal
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Ananthakrishnan Vijayakumar Maya
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics, and Metabolism, Freiburg, Germany
| | - Liyne Nogay
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics, and Metabolism, Freiburg, Germany
| | - Andrea Cosolo
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Isabelle Grass
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Anne-Kathrin Classen
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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7
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Kozlov KN, Golubkova EV, Mamon LA, Samsonova MG, Surkova SY. Drosophila Eye Imaginal Disc as a Model for Processing Epithelial Tissue Images. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922020129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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8
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Sensing microbial infections in the Drosophila melanogaster genetic model organism. Immunogenetics 2022; 74:35-62. [DOI: 10.1007/s00251-021-01239-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/20/2021] [Indexed: 12/17/2022]
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9
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Liu Y, Huang CC, Wang Y, Xu J, Wang G, Bai X. Biological evaluations of decellularized extracellular matrix collagen microparticles prepared based on plant enzymes and aqueous two-phase method. Regen Biomater 2021; 8:rbab002. [PMID: 33738116 PMCID: PMC7955711 DOI: 10.1093/rb/rbab002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 01/25/2023] Open
Abstract
For patients with extensive full-thickness burns who do not have sufficient autologous split-thickness skin for skin grafts, the application of biological skin substitutes may be considered. The aim of this study was to find an optimal new type method for the production of a biovital skin substitute based on acellular dermal matrix (ADM) and preclinical evaluations. In this work, 25 methods of ADM production were assessed. The proposed methods are based on the use of the following enzymes: papain, Carica papaya lipase (CPL), and purification using a polymer/salt aqueous two-phase system. The obtained ADM samples were characterized via scanning electron microscopy (SEM), porosity measurement and water vapor transmission test. Results showed that the collagen bundles of ADM microparticles were intact and orderly. Through differential scanning calorimetry (DSC), thermo gravimetric analysis (TGA) and biocompatibility tests, the results indicated that the proportion of papain and CPL was the same and 5 h processing time are the optimum conditions for ADM preparation and the material showed good biocompatibility. Our results suggested that the potential of developing this kind of decellularization process to manufacture ADM scaffolds for clinical application.
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Affiliation(s)
- YaWen Liu
- Engineering Research Center of Utilization of Tropical Polysaccharide Resources, College of Food Science and Technology, Hainan University, Haikou, Hainan 570000, China
| | - Ching-Cheng Huang
- Engineering Research Center of Utilization of Tropical Polysaccharide Resources, College of Food Science and Technology, Hainan University, Haikou, Hainan 570000, China
| | - YuanYuan Wang
- Engineering Research Center of Utilization of Tropical Polysaccharide Resources, College of Food Science and Technology, Hainan University, Haikou, Hainan 570000, China
| | - Jun Xu
- Engineering Research Center of Utilization of Tropical Polysaccharide Resources, College of Food Science and Technology, Hainan University, Haikou, Hainan 570000, China
| | - GuoDing Wang
- Engineering Research Center of Utilization of Tropical Polysaccharide Resources, College of Food Science and Technology, Hainan University, Haikou, Hainan 570000, China
| | - XinPeng Bai
- Engineering Research Center of Utilization of Tropical Polysaccharide Resources, College of Food Science and Technology, Hainan University, Haikou, Hainan 570000, China
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10
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Houtz P, Bonfini A, Bing X, Buchon N. Recruitment of Adult Precursor Cells Underlies Limited Repair of the Infected Larval Midgut in Drosophila. Cell Host Microbe 2019; 26:412-425.e5. [PMID: 31492656 DOI: 10.1016/j.chom.2019.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 06/11/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022]
Abstract
Surviving infection requires immune and repair mechanisms. Developing organisms face the additional challenge of integrating these mechanisms with tightly controlled developmental processes. The larval Drosophila midgut lacks dedicated intestinal stem cells. We show that, upon infection, larvae perform limited repair using adult midgut precursors (AMPs). AMPs differentiate in response to damage to generate new enterocytes, transiently depleting their pool. Developmental delay allows for AMP reconstitution, ensuring the completion of metamorphosis. Notch signaling is required for the differentiation of AMPs into the encasing, niche-like peripheral cells (PCs), but not to differentiate PCs into enterocytes. Dpp (TGF-β) signaling is sufficient, but not necessary, to induce PC differentiation into enterocytes. Infection-induced JAK-STAT pathway is both required and sufficient for differentiation of AMPs and PCs into new enterocytes. Altogether, this work highlights the constraints imposed by development on an organism's response to infection and demonstrates the transient use of adult precursors for tissue repair.
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Affiliation(s)
- Philip Houtz
- Cornell Institute of Host-Microbe Interactions and Disease, Department of Entomology, Cornell University, 129 Garden Ave., Ithaca, NY 14853, USA
| | - Alessandro Bonfini
- Cornell Institute of Host-Microbe Interactions and Disease, Department of Entomology, Cornell University, 129 Garden Ave., Ithaca, NY 14853, USA
| | - Xiaoli Bing
- Cornell Institute of Host-Microbe Interactions and Disease, Department of Entomology, Cornell University, 129 Garden Ave., Ithaca, NY 14853, USA
| | - Nicolas Buchon
- Cornell Institute of Host-Microbe Interactions and Disease, Department of Entomology, Cornell University, 129 Garden Ave., Ithaca, NY 14853, USA.
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11
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Zhu C, Liu J, He B, Qu X, Peng D. The role of human immortal skin keratinocytes‐acellular dermal matrix scaffold in skin repair and regeneration. J Cell Biochem 2019; 120:12182-12191. [PMID: 30937961 DOI: 10.1002/jcb.28588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 01/17/2019] [Accepted: 01/24/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Chongtao Zhu
- Laser Medical Center, The First People's Hospital of Yunnan Province The Affiliated Hospital of Kunming University of Science and Technology Kunming Yunnan China
| | - Jiankun Liu
- Department of Gastroenterology 920th Hospital of PLA Joint Logistics Support Force Kunming Yunnan China
| | - Bin He
- Department of Burn Leshan Jiading Hospital Leshan Sichuan China
| | - Xiaowen Qu
- Laser Medical Center, The First People's Hospital of Yunnan Province The Affiliated Hospital of Kunming University of Science and Technology Kunming Yunnan China
| | - Daizhi Peng
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital Third Military Medical University Chongqing China
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12
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Two Sides of the Same Coin - Compensatory Proliferation in Regeneration and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1167:65-85. [PMID: 31520349 DOI: 10.1007/978-3-030-23629-8_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Apoptosis has long been regarded as a tumor suppressor mechanism and evasion from apoptosis is considered to be one hallmark of cancer. However, this principle is not always consistent with clinical data which often illustrate a correlation between apoptosis and poor prognosis. Work in the last 15 years has provided an explanation for this apparent paradox. Apoptotic cells communicate with their environment and can produce signals which promote compensatory proliferation of surviving cells. This behavior of apoptotic cells is important for tissue regeneration in several model organisms, ranging from hydra to mammals. However, it may also play an important feature for tumorigenesis and tumor relapse. Several distinct forms of apoptosis-induced compensatory proliferation (AiP) have been identified, many of which involve reactive oxygen species (ROS) and immune cells. One type of AiP, "undead" AiP, in which apoptotic cells are kept in an immortalized state and continuously divide, may have particular relevance for tumorigenesis. Furthermore, given that chemo- and radiotherapy often aim to kill tumor cells, an improved understanding of the effects of apoptotic cells on the tumor and the tumor environment is of critical importance for the well-being of the patient. In this review, we summarize the current knowledge of AiP and focus our attention on recent findings obtained in Drosophila and other model organisms, and relate them to tumorigenesis.
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13
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Abdullah C, Duronio RJ. The many fates of tissue regeneration. PLoS Genet 2018; 14:e1007728. [PMID: 30462634 PMCID: PMC6248895 DOI: 10.1371/journal.pgen.1007728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Christopher Abdullah
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- SPIRE Postdoctoral Fellowship Program, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Robert J. Duronio
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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14
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Diwanji N, Bergmann A. An unexpected friend - ROS in apoptosis-induced compensatory proliferation: Implications for regeneration and cancer. Semin Cell Dev Biol 2018; 80:74-82. [PMID: 28688927 PMCID: PMC5756134 DOI: 10.1016/j.semcdb.2017.07.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/23/2017] [Accepted: 07/04/2017] [Indexed: 12/21/2022]
Abstract
Apoptosis-induced compensatory proliferation (AiP) is a form of compensatory proliferation that is triggered by apoptotic cell death to maintain tissue homeostasis. As such, AiP is essential for many tissue repair processes including regeneration. The apoptotic effectors, termed caspases, not only execute apoptosis, but are also directly involved in the generation of the signals required for AiP. Reactive oxygen species (ROS) play an important role for regenerative processes. Recently, it was shown in Drosophila that apoptotic caspases can mediate the generation of ROS for promoting AiP. This review summarizes and discusses these findings in the context of regenerative processes and cancer.
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Affiliation(s)
- Neha Diwanji
- University of Massachusetts Medical School, Department of Molecular, Cell and Cancer Biology, 364 Plantation Street - LRB419, Worcester, MA, 01605, USA.
| | - Andreas Bergmann
- University of Massachusetts Medical School, Department of Molecular, Cell and Cancer Biology, 364 Plantation Street - LRB419, Worcester, MA, 01605, USA.
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15
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Shiroor DA, Bohr TE, Adler CE. Chemical Amputation and Regeneration of the Pharynx in the Planarian Schmidtea mediterranea. J Vis Exp 2018. [PMID: 29630058 DOI: 10.3791/57168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Planarians are flatworms that are extremely efficient at regeneration. They owe this ability to a large number of stem cells that can rapidly respond to any type of injury. Common injury models in these animals remove large amounts of tissue, which damages multiple organs. To overcome this broad tissue damage, we describe here a method to selectively remove a single organ, the pharynx, in the planarian Schmidtea mediterranea. We achieve this by soaking animals in a solution containing the cytochrome oxidase inhibitor sodium azide. Brief exposure to sodium azide causes extrusion of the pharynx from the animal, which we call "chemical amputation." Chemical amputation removes the entire pharynx, and generates a small wound where the pharynx attaches to the intestine. After extensive rinsing, all amputated animals regenerate a fully functional pharynx in approximately one week. Stem cells in the rest of the body drive regeneration of the new pharynx. Here, we provide a detailed protocol for chemical amputation, and describe both histological and behavioral methods to assess successful amputation and regeneration.
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Affiliation(s)
- Divya A Shiroor
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University
| | - Tisha E Bohr
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University
| | - Carolyn E Adler
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University;
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16
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Mi B, Liu G, Zhou W, Lv H, Zha K, Liu Y, Wu Q, Liu J. Bioinformatics analysis of fibroblasts exposed to TGF‑β at the early proliferation phase of wound repair. Mol Med Rep 2017; 16:8146-8154. [PMID: 28983581 PMCID: PMC5779900 DOI: 10.3892/mmr.2017.7619] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022] Open
Abstract
The aim of the current study was to identify gene signatures during the early proliferation stage of wound repair and the effect of TGF-β on fibroblasts and reveal their potential mechanisms. The gene expression profiles of GSE79621 and GSE27165 were obtained from GEO database. Differentially expressed genes (DEGs) were identified using Morpheus and co-expressed DEGs were selected using Venn Diagram. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Protein-protein interaction (PPI) networks of the DEGs were constructed using Cytoscape software. PPI interaction network was divided into subnetworks using the MCODE algorithm and the function of the top one module was analyzed using DAVID. The results revealed that upregulated DEGs were significantly enriched in biological process, including the Arp2/3 complex-mediated actin nucleation, positive regulation of hyaluronan cable assembly, purine nucleobase biosynthetic process, de novo inosine monophosphate biosynthetic process, positive regulation of epithelial cell proliferation, whereas the downregulated DEGs were enriched in the regulation of blood pressure, negative regulation of cell proliferation, ossification, negative regulation of gene expression and type I interferon signaling pathway. KEGG pathway analysis showed that the upregulated DEGs were enriched in shigellosis, pathogenic Escherichia coli infection, the mitogen-activated protein kinase signaling pathway, Ras signaling pathway and bacterial invasion of epithelial cells. The downregulated DEGs were enriched in systemic lupus erythematosus, lysosome, arachidonic acid metabolism, thyroid cancer and allograft rejection. The top 10 hub genes were identified from the PPI network. The top module analysis revealed that the included genes were involved in ion channel, neuroactive ligand-receptor interaction pathway, purine metabolism and intestinal immune network for IgA production pathway. The functional analysis revealed that TGF-β may promote fibroblast migration and proliferation and defend against microorganisms at the early proliferation stage of wound repair. Furthermore, these results may provide references for chronic wound repair.
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Affiliation(s)
- Bobin Mi
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Guohui Liu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Wu Zhou
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Huijuan Lv
- Department of Rheumatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710000, P.R. China
| | - Kun Zha
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yi Liu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Qipeng Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jing Liu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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Killers creating new life: caspases drive apoptosis-induced proliferation in tissue repair and disease. Cell Death Differ 2017; 24:1390-1400. [PMID: 28362431 PMCID: PMC5520457 DOI: 10.1038/cdd.2017.47] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/26/2017] [Accepted: 02/28/2017] [Indexed: 02/06/2023] Open
Abstract
Apoptosis is a carefully orchestrated and tightly controlled form of cell death, conserved across metazoans. As the executioners of apoptotic cell death, cysteine-dependent aspartate-directed proteases (caspases) are critical drivers of this cellular disassembly. Early studies of genetically programmed cell death demonstrated that the selective activation of caspases induces apoptosis and the precise elimination of excess cells, thereby sculpting structures and refining tissues. However, over the past decade there has been a fundamental shift in our understanding of the roles of caspases during cell death-a shift precipitated by the revelation that apoptotic cells actively engage with their surrounding environment throughout the death process, and caspases can trigger a myriad of signals, some of which drive concurrent cell proliferation regenerating damaged structures and building up lost tissues. This caspase-driven compensatory proliferation is referred to as apoptosis-induced proliferation (AiP). Diverse mechanisms of AiP have been found across species, ranging from planaria to mammals. In this review, we summarize the current knowledge of AiP and we highlight recent advances in the field including the involvement of reactive oxygen species and macrophage-like immune cells in one form of AiP, novel regulatory mechanisms affecting caspases during AiP, and emerging clinical data demonstrating the critical importance of AiP in cancer.
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