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Lin JJ, Ning T, Jia SC, Li KJ, Huang YC, Liu Q, Lin JH, Zhang XT. Evaluation of genetic response of mesenchymal stem cells to nanosecond pulsed electric fields by whole transcriptome sequencing. World J Stem Cells 2024; 16:305-323. [PMID: 38577234 PMCID: PMC10989289 DOI: 10.4252/wjsc.v16.i3.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Mesenchymal stem cells (MSCs) modulated by various exogenous signals have been applied extensively in regenerative medicine research. Notably, nanosecond pulsed electric fields (nsPEFs), characterized by short duration and high strength, significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways. Consequently, we used transcriptomics to study changes in messenger RNA (mRNA), long noncoding RNA (lncRNA), microRNA (miRNA), and circular RNA expression during nsPEFs application. AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs. METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing. MSCs were pretreated with 5-pulse nsPEFs (100 ns at 10 kV/cm, 1 Hz), followed by total RNA isolation. Each transcript was normalized by fragments per kilobase per million. Fold change and difference significance were applied to screen the differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions, complemented by quantitative polymerase chain reaction verification. RESULTS In total, 263 DEGs were discovered, with 92 upregulated and 171 downregulated. DEGs were predominantly enriched in epithelial cell proliferation, osteoblast differentiation, mesenchymal cell differentiation, nuclear division, and wound healing. Regarding cellular components, DEGs are primarily involved in condensed chromosome, chromosomal region, actin cytoskeleton, and kinetochore. From aspect of molecular functions, DEGs are mainly involved in glycosaminoglycan binding, integrin binding, nuclear steroid receptor activity, cytoskeletal motor activity, and steroid binding. Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation. CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs, 2 miRNAs, and 65 lncRNAs. Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways, which are involved in vesicular transport, calcium ion transport, cytoskeleton, and cell differentiation.
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Affiliation(s)
- Jian-Jing Lin
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Tong Ning
- Institute of Medical Science, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, Shandong Province, China
| | - Shi-Cheng Jia
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Ke-Jia Li
- Department of Biomedical Engineering, Institute of Future Technology, Peking University, Beijing 100871, China
| | - Yong-Can Huang
- Shenzhen Engineering Laboratory of Orthopaedic Regenerative Technologies, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Qiang Liu
- Arthritis Clinical and Research Center, Peking University People's Hospital, Beijing 100044, China
| | - Jian-Hao Lin
- Arthritis Clinical and Research Center, Peking University People's Hospital, Beijing 100044, China
| | - Xin-Tao Zhang
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China.
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Liu H, Wen Z, Liu Z, Yang Y, Wang H, Xia X, Ye J, Liu Y. Unlocking the potential of amorphous calcium carbonate: A star ascending in the realm of biomedical application. Acta Pharm Sin B 2024; 14:602-622. [PMID: 38322345 PMCID: PMC10840486 DOI: 10.1016/j.apsb.2023.08.027] [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: 06/12/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 02/08/2024] Open
Abstract
Calcium-based biomaterials have been intensively studied in the field of drug delivery owing to their excellent biocompatibility and biodegradability. Calcium-based materials can also deliver contrast agents, which can enhance real-time imaging and exert a Ca2+-interfering therapeutic effect. Based on these characteristics, amorphous calcium carbonate (ACC), as a brunch of calcium-based biomaterials, has the potential to become a widely used biomaterial. Highly functional ACC can be either discovered in natural organisms or obtained by chemical synthesis However, the standalone presence of ACC is unstable in vivo. Additives are required to be used as stabilizers or core-shell structures formed by permeable layers or lipids with modified molecules constructed to maintain the stability of ACC until the ACC carrier reaches its destination. ACC has high chemical instability and can produce biocompatible products when exposed to an acidic condition in vivo, such as Ca2+ with an immune-regulating ability and CO2 with an imaging-enhancing ability. Owing to these characteristics, ACC has been studied for self-sacrificing templates of carrier construction, targeted delivery of oncology drugs, immunomodulation, tumor imaging, tissue engineering, and calcium supplementation. Emphasis in this paper has been placed on the origin, structural features, and multiple applications of ACC. Meanwhile, ACC faces many challenges in clinical translation, and long-term basic research is required to overcome these challenges. We hope that this study will contribute to future innovative research on ACC.
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Affiliation(s)
- Han Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhiyang Wen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zihan Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yanfang Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hongliang Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xuejun Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jun Ye
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuling Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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3
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Matsumura T, Totani H, Gunji Y, Fukuda M, Yokomori R, Deng J, Rethnam M, Yang C, Tan TK, Karasawa T, Kario K, Takahashi M, Osato M, Sanda T, Suda T. A Myb enhancer-guided analysis of basophil and mast cell differentiation. Nat Commun 2022; 13:7064. [PMID: 36400777 PMCID: PMC9674656 DOI: 10.1038/s41467-022-34906-1] [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: 03/03/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
The transcription factor MYB is a crucial regulator of hematopoietic stem and progenitor cells. However, the nature of lineage-specific enhancer usage of the Myb gene is largely unknown. We identify the Myb -68 enhancer, a regulatory element which marks basophils and mast cells. Using the Myb -68 enhancer activity, we show a population of granulocyte-macrophage progenitors with higher potential to differentiate into basophils and mast cells. Single cell RNA-seq demonstrates the differentiation trajectory is continuous from progenitors to mature basophils in vivo, characterizes bone marrow cells with a gene signature of mast cells, and identifies LILRB4 as a surface marker of basophil maturation. Together, our study leads to a better understanding of how MYB expression is regulated in a lineage-associated manner, and also shows how a combination of lineage-related reporter mice and single-cell transcriptomics can overcome the rarity of target cells and enhance our understanding of gene expression programs that control cell differentiation in vivo.
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Affiliation(s)
- Takayoshi Matsumura
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan ,grid.410804.90000000123090000Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Haruhito Totani
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yoshitaka Gunji
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Masahiro Fukuda
- grid.428397.30000 0004 0385 0924Signature Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore ,grid.274841.c0000 0001 0660 6749International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Rui Yokomori
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jianwen Deng
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Malini Rethnam
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chong Yang
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tze King Tan
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tadayoshi Karasawa
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Kazuomi Kario
- grid.410804.90000000123090000Division of Cardiovascular Medicine, Department of Medicine, Jichi Medical University School of Medicine, Tochigi, Japan
| | - Masafumi Takahashi
- grid.410804.90000000123090000Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Motomi Osato
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Takaomi Sanda
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Toshio Suda
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore ,grid.274841.c0000 0001 0660 6749International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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4
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Raimo S, Zura-Miller G, Fezelinia H, Spruce LA, Zakopoulos I, Mohsen AW, Vockley J, Ischiropoulos H. Mitochondrial morphology, bioenergetics and proteomic responses in fatty acid oxidation disorders. Redox Biol 2021; 41:101923. [PMID: 33725513 PMCID: PMC7970426 DOI: 10.1016/j.redox.2021.101923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in nuclear genes encoding for mitochondrial proteins very long-chain acyl-CoA dehydrogenase (VLCAD) and trifunctional protein (TFP) cause rare autosomal recessive disorders. Studies in fibroblasts derived from patients with mutations in VLCAD and TFP exhibit mitochondrial defects. To gain insights on pathological changes that account for the mitochondrial deficits we performed quantitative proteomic, biochemical, and morphometric analyses in fibroblasts derived from subjects with three different VLCAD and three different TFP mutations. Proteomic data that was corroborated by antibody-based detection, indicated reduced levels of VLCAD and TFP protein in cells with VLCAD and TFP mutations respectively, which in part accounted for the diminished fatty acid oxidation capacity. Decreased mitochondrial respiratory capacity in cells with VLCAD and TFP mutations was quantified after glucose removal and cells with TFP mutations had lower levels of glycogen. Despite these energetic deficiencies, the cells with VLCAD and TFP mutations did not exhibit changes in mitochondria morphology, distribution, fusion and fission, quantified by either confocal or transmission electron microscopy and corroborated by proteomic and antibody-based protein analysis. Fibroblasts with VLCAD and to a lesser extend cells with TFP mutations had increased levels of mitochondrial respiratory chain proteins and proteins that facilitate the assembly of respiratory complexes. With the exception of reduced levels of catalase and glutathione S-transferase theta-1 in cells with TFP mutations, the levels of 45 proteins across all major intracellular antioxidant networks were similar between cells with VLCAD and TFP mutations and non-disease controls. Collectively the data indicate that despite the metabolic deficits, cells with VLCAD and TFP mutations maintain their proteomic integrity to preserve cellular and mitochondria architecture, support energy production and protect against oxidative stress.
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Affiliation(s)
- Serena Raimo
- Children's Hospital of Philadelphia Research Institute and Division of Neonatology, Departments of Pediatrics and Systems Pharmacology and Translational Therapeutics, the Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriella Zura-Miller
- Children's Hospital of Philadelphia Research Institute and Division of Neonatology, Departments of Pediatrics and Systems Pharmacology and Translational Therapeutics, the Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hossein Fezelinia
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Biomedical Health and Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lynn A Spruce
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Iordanis Zakopoulos
- Children's Hospital of Philadelphia Research Institute and Division of Neonatology, Departments of Pediatrics and Systems Pharmacology and Translational Therapeutics, the Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Al-Walid Mohsen
- Division of Medical Genetics, Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, School of Public Health, Pittsburgh, PA 15261, USA
| | - Jerry Vockley
- Division of Medical Genetics, Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, School of Public Health, Pittsburgh, PA 15261, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute and Division of Neonatology, Departments of Pediatrics and Systems Pharmacology and Translational Therapeutics, the Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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5
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Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs. Animals (Basel) 2020; 10:ani10071114. [PMID: 32610571 PMCID: PMC7401585 DOI: 10.3390/ani10071114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 12/16/2022] Open
Abstract
MeiShan and Large White pigs differ in their female fecundity. However, the mechanisms behind the gene expression and regulation that cause these differences remain unclear. In this study, we profiled circRNAs and identified 5,879 circRNAs from the ovaries of MeiShan and Large White pigs. Eighty-five circRNAs were differentially expressed between the two pig breeds. Of these, 37 were up-regulated and 48 were down-regulated in MeiShan pigs. Gene ontology enrichment analysis suggested that the differentially expressed circRNA were involved in the hormone-mediated signaling pathway. We verified that circSCIN and its parent gene, scinderin (SCIN), were differentially expressed by reverse transcription and quantitative PCR (RT-qPCR). Luciferase assays demonstrated that circSCIN can target and sponge miR-133 and miR-148a/b. The identification of differentially expressed circRNAs (DECs) and their regulatory functions increased our understanding of the differences in reproductive efficiency between MeiShan and Large White pigs.
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6
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Zheng W, Wen H. Investigating dual Ca 2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation. Proteins 2020; 88:1528-1539. [PMID: 32557910 DOI: 10.1002/prot.25971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 05/26/2020] [Accepted: 06/14/2020] [Indexed: 11/09/2022]
Abstract
The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles. A deep understanding of the complex Ca2+ -activation/inhibition mechanism of RyRs requires detailed structural and dynamic information for RyRs in different functional states (eg, with Ca2+ bound to activating or inhibitory sites). Recently, high-resolution structures of the RyR isoform 1 (RyR1) were solved by cryo-electron microscopy, revealing the location of a Ca2+ binding site for activation. Toward elucidating the Ca2+ -modulation mechanism of RyR1, we performed extensive molecular dynamics simulation of the core RyR1 structure in the presence and absence of activating and solvent Ca2+ (total simulation time is >5 μs). In the presence of solvent Ca2+ , Ca2+ binding to the activating site enhanced dynamics of RyR1 with higher inter-subunit flexibility, asymmetric inter-subunit motions, outward domain motions and partial pore dilation, which may prime RyR1 for subsequent channel opening. In contrast, the solvent Ca2+ alone reduced dynamics of RyR1 and led to inward domain motions and pore contraction, which may cause inhibition. Combining our simulation with the map of disease mutation sites in RyR1, we constructed a wiring diagram of key domains coupled via specific hydrogen bonds involving the mutation sites, some of which were modulated by Ca2+ binding. The structural and dynamic information gained from this study will inform future mutational and functional studies of RyR1 activation and inhibition by Ca2+ .
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, New York, USA
| | - Han Wen
- Department of Physics, University at Buffalo, Buffalo, New York, USA
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7
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Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin. J Muscle Res Cell Motil 2019; 41:153-162. [DOI: 10.1007/s10974-019-09571-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 12/14/2019] [Indexed: 12/30/2022]
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8
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Jespersen NE, Leyrat C, Gérard FC, Bourhis JM, Blondel D, Jamin M, Barbar E. The LC8-RavP ensemble Structure Evinces A Role for LC8 in Regulating Lyssavirus Polymerase Functionality. J Mol Biol 2019; 431:4959-4977. [PMID: 31634467 PMCID: PMC7060403 DOI: 10.1016/j.jmb.2019.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/11/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022]
Abstract
The rabies and Ebola viruses recruit the highly conserved host protein LC8 for their own reproductive success. In vivo knockouts of the LC8 recognition motif within the rabies virus phosphoprotein (RavP) result in completely nonlethal viral infections. In this work, we examine the molecular role LC8 plays in viral lethality. We show that RavP and LC8 colocalize in rabies infected cells, and that LC8 interactions are essential for efficient viral polymerase functionality. NMR, SAXS, and molecular modeling demonstrate that LC8 binding to a disordered linker adjacent to an endogenous dimerization domain results in restrictions in RavP domain orientations. The resulting ensemble structure of RavP-LC8 tetrameric complex is similar to that of a related virus phosphoprotein that does not bind LC8, suggesting that with RavP, LC8 binding acts as a switch to induce a more active conformation. The high conservation of the LC8 motif in Lyssavirus phosphoproteins and its presence in other analogous proteins such as the Ebola virus VP35 evinces a broader purpose for LC8 in regulating downstream phosphoprotein functions vital for viral replication.
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Affiliation(s)
- Nathan E Jespersen
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Cedric Leyrat
- Institut de Génomique Fonctionnelle, CNRS UMR-5203 INSERM U1191, University of Montpellier, Montpellier, France
| | - Francine C Gérard
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Jean-Marie Bourhis
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Danielle Blondel
- Institut de Biologie Intégrative de La Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Marc Jamin
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Elisar Barbar
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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9
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Brosey CA, Tainer JA. Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Curr Opin Struct Biol 2019; 58:197-213. [PMID: 31204190 PMCID: PMC6778498 DOI: 10.1016/j.sbi.2019.04.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 11/27/2022]
Abstract
Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape and dynamics that unveil biological function. Here, we discuss evolving SAXS theory, methods, and applications that extend the field of small-angle scattering beyond simple shape characterization. SAXS, coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved (TR-SAXS) methods, is now providing high-resolution insight into macromolecular flexibility and ensembles, delineating biophysical landscapes, and facilitating high-throughput library screening to assess macromolecular properties and to create opportunities for drug discovery. Looking forward, we consider SAXS in the integrative era of hybrid structural biology methods, its potential for illuminating cellular supramolecular and mesoscale structures, and its capacity to complement high-throughput bioinformatics sequencing data. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Chris A Brosey
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - John A Tainer
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Abstract
Gelsolin (GSN), one of the most abundant actin-binding proteins, is involved in cell motility, shape and metabolism. As a member of the GSN superfamily, GSN is a highly structured protein in eukaryotic cells that can be regulated by calcium concentration, intracellular pH, temperature and phosphatidylinositol-4,5-bisphosphate. GSN plays an important role in cellular mechanisms as well as in different cellular interactions. Because of its participation in immunologic processes and its interaction with different cells of the immune system, GSN is a potential candidate for various therapeutic applications. In this review, we summarise the structure of GSN as well as its regulating and functional roles, focusing on distinct diseases such as Alzheimer's disease, rheumatoid arthritis and cancer. A short overview of GSN as a therapeutic target in today's medicine is also provided.
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11
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Qi C, Lin J, Fu LH, Huang P. Calcium-based biomaterials for diagnosis, treatment, and theranostics. Chem Soc Rev 2018; 47:357-403. [DOI: 10.1039/c6cs00746e] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Calcium-based biomaterials with good biosafety and bio-absorbability are promising for biomedical applications such as diagnosis, treatment, and theranostics.
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Affiliation(s)
- Chao Qi
- Guangdong Key Laboratory for Biomedical
- Measurements and Ultrasound Imaging
- Laboratory of Evolutionary Theranostics
- School of Biomedical Engineering
- Health Science Center
| | - Jing Lin
- Guangdong Key Laboratory for Biomedical
- Measurements and Ultrasound Imaging
- Laboratory of Evolutionary Theranostics
- School of Biomedical Engineering
- Health Science Center
| | - Lian-Hua Fu
- Guangdong Key Laboratory for Biomedical
- Measurements and Ultrasound Imaging
- Laboratory of Evolutionary Theranostics
- School of Biomedical Engineering
- Health Science Center
| | - Peng Huang
- Guangdong Key Laboratory for Biomedical
- Measurements and Ultrasound Imaging
- Laboratory of Evolutionary Theranostics
- School of Biomedical Engineering
- Health Science Center
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12
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Molecular basis of a novel renal amyloidosis due to N184K gelsolin variant. Sci Rep 2016; 6:33463. [PMID: 27633054 PMCID: PMC5025852 DOI: 10.1038/srep33463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/16/2016] [Indexed: 12/23/2022] Open
Abstract
Mutations in gelsolin are responsible for a systemic amyloidosis first described in 1969. Until recently, the disease was associated with two substitutions of the same residue, leading to the loss of the calcium binding site. Novel interest arose in 2014 when the N184K variant of the protein was identified as the etiological agent of a novel kidney-localized amyloidosis. Here we provide a first rationale for N184K pathogenicity. We show that the mutation induces a destabilization of gelsolin second domain, without compromising its calcium binding capacity. X-ray data combined with molecular dynamics simulations demonstrates that the primary source of the destabilization is a loss of connectivity in proximity of the metal. Such rearrangement of the H-bond network does not have a major impact on the overall fold of the domain, nevertheless, it increases the flexibility of a stretch of the protein, which is consequently processed by furin protease. Overall our data suggest that the N184K variant is subjected to the same aberrant proteolytic events responsible for the formation of amyloidogenic fragments in the previously characterized mutants. At the same time our data suggest that a broader number of mutations, unrelated to the metal binding site, can lead to a pathogenic phenotype.
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