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Sridharan D, Dougherty JA, Ahmed U, Sanghvi SK, Alvi SB, Park KH, Islam H, Knoblaugh SE, Singh H, Kirby ED, Khan M. Bioorthogonal non-canonical amino acid tagging to track transplanted human induced pluripotent stem cell-specific proteome. Stem Cell Res Ther 2024; 15:186. [PMID: 38926849 PMCID: PMC11210150 DOI: 10.1186/s13287-024-03792-3] [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: 01/19/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Human induced pluripotent stem cells (hiPSCs) and their differentiated cell types have a great potential for tissue repair and regeneration. While the primary focus of using hiPSCs has historically been to regenerate damaged tissue, emerging studies have shown a more potent effect of hiPSC-derived paracrine factors on tissue regeneration. However, the precise contents of the transplanted hiPSC-derived cell secretome are ambiguous. This is mainly due to the lack of tools to distinguish cell-specific secretome from host-derived proteins in a complex tissue microenvironment in vivo. METHODS In this study, we present the generation and characterization of a novel hiPSC line, L274G-hiPSC, expressing the murine mutant methionyl-tRNA synthetase, L274GMmMetRS, which can be used for tracking the cell specific proteome via biorthogonal non-canonical amino acid tagging (BONCAT). We assessed the trilineage differentiation potential of the L274G-hiPSCs in vitro and in vivo. Furthermore, we assessed the cell-specific proteome labelling in the L274G-hiPSC derived cardiomyocytes (L274G-hiPSC-CMs) in vitro following co-culture with wild type human umbilical vein derived endothelial cells and in vivo post transplantation in murine hearts. RESULTS We demonstrated that the L274G-hiPSCs exhibit typical hiPSC characteristics and that we can efficiently track the cell-specific proteome in their differentiated progenies belonging to the three germ lineages, including L274G-hiPSC-CMs. Finally, we demonstrated cell-specific BONCAT in transplanted L274G-hiPSC-CMs. CONCLUSION The novel L274G-hiPSC line can be used to study the cell-specific proteome of hiPSCs in vitro and in vivo, to delineate mechanisms underlying hiPSC-based cell therapies for a variety of regenerative medicine applications.
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Affiliation(s)
- Divya Sridharan
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Julie A Dougherty
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Uzair Ahmed
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Shridhar K Sanghvi
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
- Department of Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, USA
| | - Syed Baseeruddin Alvi
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Ki Ho Park
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Helena Islam
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Sue E Knoblaugh
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Harpreet Singh
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
| | - Elizabeth D Kirby
- Department of Psychology, The Ohio State University, Columbus, OH, USA
- Chronic Brain Injury Program, The Ohio State University, Columbus, OH, USA
| | - Mahmood Khan
- Division of Basic and Translational Sciences, Department of Emergency Medicine, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
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2
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Bareja A, Lee DE, Ho T, Waitt G, McKay LH, Hannou SA, Orenduff MC, McGreevy KM, Binder A, Ryan CP, Soderblom EJ, Belsky DW, Ferrucci L, Das JK, Banskota N, Kraus VB, Huebner JL, Kraus WE, Huffman KM, Baht GS, Horvath S, Parmer RJ, Miles LA, White JP. Liver-derived plasminogen mediates muscle stem cell expansion during caloric restriction through the plasminogen receptor Plg-R KT. Cell Rep 2024; 43:113881. [PMID: 38442019 PMCID: PMC11075744 DOI: 10.1016/j.celrep.2024.113881] [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: 10/04/2022] [Revised: 08/08/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
An intriguing effect of short-term caloric restriction (CR) is the expansion of certain stem cell populations, including muscle stem cells (satellite cells), which facilitate an accelerated regenerative program after injury. Here, we utilized the MetRSL274G (MetRS) transgenic mouse to identify liver-secreted plasminogen as a candidate for regulating satellite cell expansion during short-term CR. Knockdown of circulating plasminogen prevents satellite cell expansion during short-term CR. Furthermore, loss of the plasminogen receptor KT (Plg-RKT) is also sufficient to prevent CR-related satellite cell expansion, consistent with direct signaling of plasminogen through the plasminogen receptor Plg-RKT/ERK kinase to promote proliferation of satellite cells. Importantly, we are able to replicate many of these findings in human participants from the CALERIE trial. Our results demonstrate that CR enhances liver protein secretion of plasminogen, which signals directly to the muscle satellite cell through Plg-RKT to promote proliferation and subsequent muscle resilience during CR.
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Affiliation(s)
- Akshay Bareja
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - David E Lee
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Tricia Ho
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Greg Waitt
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Lauren H McKay
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of Chapel Hill, Chapel Hill, NC, USA
| | - Sarah A Hannou
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Melissa C Orenduff
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - Kristen M McGreevy
- Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Alexandra Binder
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA; Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Calen P Ryan
- Columbia University Mailman School of Public Health, New York, NY, USA
| | - Erik J Soderblom
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Daniel W Belsky
- Columbia University Mailman School of Public Health, New York, NY, USA
| | - Luigi Ferrucci
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jayanta Kumar Das
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nirad Banskota
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Virginia B Kraus
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Janet L Huebner
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA
| | - William E Kraus
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Kim M Huffman
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA
| | - Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA; Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC 27701, USA
| | - Steve Horvath
- Computational Biology and Genomics Core, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA; Altos Labs, San Diego, CA, USA
| | - Robert J Parmer
- Department of Medicine, Veterans Administration San Diego Healthcare System, San Diego, CA, USA; Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lindsey A Miles
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - James P White
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27701, USA; Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC 27701, USA.
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3
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Thompson SD, Barrett KL, Rugel CL, Redmond R, Rudofski A, Kurian J, Curtin JL, Dayanidhi S, Lavasani M. Sex-specific preservation of neuromuscular function and metabolism following systemic transplantation of multipotent adult stem cells in a murine model of progeria. GeroScience 2024; 46:1285-1302. [PMID: 37535205 PMCID: PMC10828301 DOI: 10.1007/s11357-023-00892-5] [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: 06/13/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Onset and rates of sarcopenia, a disease characterized by a loss of muscle mass and function with age, vary greatly between sexes. Currently, no clinical interventions successfully arrest age-related muscle impairments since the decline is frequently multifactorial. Previously, we found that systemic transplantation of our unique adult multipotent muscle-derived stem/progenitor cells (MDSPCs) isolated from young mice-but not old-extends the health-span in DNA damage mouse models of progeria, a disease of accelerated aging. Additionally, induced neovascularization in the muscles and brain-where no transplanted cells were detected-strongly suggests a systemic therapeutic mechanism, possibly activated through circulating secreted factors. Herein, we used ZMPSTE24-deficient mice, a lamin A defect progeria model, to investigate the ability of young MDSPCs to preserve neuromuscular tissue structure and function. We show that progeroid ZMPST24-deficient mice faithfully exhibit sarcopenia and age-related metabolic dysfunction. However, systemic transplantation of young MDSPCs into ZMPSTE24-deficient progeroid mice sustained healthy function and histopathology of muscular tissues throughout their 6-month life span in a sex-specific manner. Indeed, female-but not male-mice systemically transplanted with young MDSPCs demonstrated significant preservation of muscle endurance, muscle fiber size, mitochondrial respirometry, and neuromuscular junction morphometrics. These novel findings strongly suggest that young MDSPCs modulate the systemic environment of aged animals by secreted rejuvenating factors to maintain a healthy homeostasis in a sex-specific manner and that the female muscle microenvironment remains responsive to exogenous regenerative cues in older age. This work highlights the age- and sex-related differences in neuromuscular tissue degeneration and the future prospect of preserving health in older adults with systemic regenerative treatments.
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Affiliation(s)
- Seth D Thompson
- Shirley Ryan AbilityLab, 355 E. Erie St, Chicago, IL, 60611, USA.
- Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, 60611, USA.
- Northwestern University Interdepartmental Neuroscience (NUIN) Graduate Program, Northwestern University, Chicago, IL, 60611, USA.
| | - Kelsey L Barrett
- Shirley Ryan AbilityLab, 355 E. Erie St, Chicago, IL, 60611, USA
| | - Chelsea L Rugel
- Shirley Ryan AbilityLab, 355 E. Erie St, Chicago, IL, 60611, USA
- Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, 60611, USA
- Northwestern University Interdepartmental Neuroscience (NUIN) Graduate Program, Northwestern University, Chicago, IL, 60611, USA
| | - Robin Redmond
- Shirley Ryan AbilityLab, 355 E. Erie St, Chicago, IL, 60611, USA
| | - Alexia Rudofski
- Shirley Ryan AbilityLab, 355 E. Erie St, Chicago, IL, 60611, USA
| | - Jacob Kurian
- Department of Biomedical Engineering, Northwestern University, Chicago, IL, 60611, USA
| | - Jodi L Curtin
- Shirley Ryan AbilityLab, 355 E. Erie St, Chicago, IL, 60611, USA
| | - Sudarshan Dayanidhi
- Shirley Ryan AbilityLab, 355 E. Erie St, Chicago, IL, 60611, USA
- Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, 60611, USA
| | - Mitra Lavasani
- Shirley Ryan AbilityLab, 355 E. Erie St, Chicago, IL, 60611, USA.
- Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, 60611, USA.
- Northwestern University Interdepartmental Neuroscience (NUIN) Graduate Program, Northwestern University, Chicago, IL, 60611, USA.
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4
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Wu W, Krijgsveld J. Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication. Mol Cell Proteomics 2024; 23:100692. [PMID: 38081362 PMCID: PMC10793180 DOI: 10.1016/j.mcpro.2023.100692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Abstract
A significant portion of mammalian proteomes is secreted to the extracellular space to fulfill crucial roles in cell-to-cell communication. To best recapitulate the intricate and multi-faceted crosstalk between cells in a live organism, there is an ever-increasing need for methods to study protein secretion in model systems that include multiple cell types. In addition, posttranslational modifications further expand the complexity and versatility of cellular communication. This review aims to summarize recent strategies and model systems that employ cellular coculture, chemical biology tools, protein enrichment, and proteomic methods to characterize the composition and function of cellular secretomes. This is all geared towards gaining better understanding of organismal biology in vivo mediated by secretory signaling.
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Affiliation(s)
- Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore, Singapore.
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty, Heidelberg University, Heidelberg, Germany.
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5
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Burgess JD, Amerna D, Norton ES, Parsons TM, Perkerson RB, Faroqi AH, Wszolek ZK, Guerrero Cazares H, Kanekiyo T, Delenclos M, McLean PJ. A mutant methionyl-tRNA synthetase-based toolkit to assess induced-mesenchymal stromal cell secretome in mixed-culture disease models. Stem Cell Res Ther 2023; 14:289. [PMID: 37798772 PMCID: PMC10557244 DOI: 10.1186/s13287-023-03515-0] [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: 04/20/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Mesenchymal stromal cells (MSCs) have a dynamic secretome that plays a critical role in tissue repair and regeneration. However, studying the MSC secretome in mixed-culture disease models remains challenging. This study aimed to develop a mutant methionyl-tRNA synthetase-based toolkit (MetRSL274G) to selectively profile secreted proteins from MSCs in mixed-culture systems and demonstrate its potential for investigating MSC responses to pathological stimulation. METHODS We used CRISPR/Cas9 homology-directed repair to stably integrate MetRSL274G into cells, enabling the incorporation of the non-canonical amino acid, azidonorleucine (ANL), and facilitating selective protein isolation using click chemistry. MetRSL274G was integrated into both in H4 cells and induced pluripotent stem cells (iPSCs) for a series of proof-of-concept studies. Following iPSC differentiation into induced-MSCs, we validated their identity and co-cultured MetRSL274G-expressing iMSCs with naïve or lipopolysaccharide (LPS)-treated THP-1 cells. We then profiled the iMSC secretome using antibody arrays. RESULTS Our results showed successful integration of MetRSL274G into targeted cells, allowing specific isolation of proteins from mixed-culture environments. We also demonstrated that the secretome of MetRSL274G-expressing iMSCs can be differentiated from that of THP-1 cells in co-culture and is altered when co-cultured with LPS-treated THP-1 cells compared to naïve THP-1 cells. CONCLUSIONS The MetRSL274G-based toolkit we have generated enables selective profiling of the MSC secretome in mixed-culture disease models. This approach has broad applications for examining not only MSC responses to models of pathological conditions, but any other cell type that can be differentiated from iPSCs. This can potentially reveal novel MSC-mediated repair mechanisms and advancing our understanding of tissue regeneration processes.
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Affiliation(s)
- Jeremy D Burgess
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
- Regenerative Sciences Training Program, Center for Regenerative Medicine, Mayo Clinic, Jacksonville, FL, USA
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Danilyn Amerna
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Emily S Norton
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
- Regenerative Sciences Training Program, Center for Regenerative Medicine, Mayo Clinic, Jacksonville, FL, USA
- Department of Neurosurgery, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Tammee M Parsons
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Ralph B Perkerson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Ayman H Faroqi
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Zbigniew K Wszolek
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Hugo Guerrero Cazares
- Department of Neurosurgery, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Marion Delenclos
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Pamela J McLean
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
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6
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Swietlik JJ, Bärthel S, Falcomatà C, Fink D, Sinha A, Cheng J, Ebner S, Landgraf P, Dieterich DC, Daub H, Saur D, Meissner F. Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation. Nat Commun 2023; 14:2642. [PMID: 37156840 PMCID: PMC10167354 DOI: 10.1038/s41467-023-38171-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive azidonorleucine labeling, click chemistry enrichment, and mass spectrometry-based proteomics and secretomics strategy to dissect aberrant signals in pancreatic ductal adenocarcinoma (PDAC). Our in-depth co-culture and in vivo analyses cover more than 10,000 cancer cell-derived proteins and reveal systematic differences between molecular PDAC subtypes. Secreted proteins, such as chemokines and EMT-promoting matrisome proteins, associated with distinct macrophage polarization and tumor stromal composition, differentiate classical and mesenchymal PDAC. Intriguingly, more than 1,600 cancer cell-derived proteins including cytokines and pre-metastatic niche formation-associated factors in mouse serum reflect tumor activity in circulation. Our findings highlight how cell-selective proteomics can accelerate the discovery of diagnostic markers and therapeutic targets in cancer.
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Affiliation(s)
- Jonathan J Swietlik
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Diana Fink
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ankit Sinha
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jingyuan Cheng
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefan Ebner
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniela C Dieterich
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Henrik Daub
- NEOsphere Biotechnologies GmbH, Martinsried, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany.
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7
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Burgess JD, Amerna D, Norton ES, Parsons TM, Perkerson RB, Faroqi AH, Wszolek ZK, Cazares HG, Kanekiyo T, Delenclos M, McLean PJ. A Mutant Methionyl-tRNA Synthetase-Based toolkit to assess induced-Mesenchymal Stromal Cell secretome in mixed-culture disease models. RESEARCH SQUARE 2023:rs.3.rs-2838195. [PMID: 37205579 PMCID: PMC10187403 DOI: 10.21203/rs.3.rs-2838195/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Background Mesenchymal stromal cells (MSCs) have a dynamic secretome that plays a critical role in tissue repair and regeneration. However, studying the MSC secretome in mixed-culture disease models remains challenging. This study aimed to develop a mutant methionyl-tRNA synthetase-based toolkit (MetRS L274G ) to selectively profile secreted proteins from MSCs in mixed-culture systems and demonstrate its potential for investigating MSC responses to pathological stimulation. Methods We used CRISPR/Cas9 homology-directed repair to stably integrate MetRS L274G into cells, enabling the incorporation of the non-canonical amino acid, azidonorleucine (ANL), and facilitating selective protein isolation using click chemistry. MetRS L274G was integrated into both in H4 cells and induced pluripotent stem cells (iPSCs) for a series of proof-of-concept studies. Following iPSC differentiation into induced-MSCs, we validated their identity and co-cultured MetRS L274G -expressing iMSCs with naïve or lipopolysaccharide- (LPS) treated THP-1 cells. We then profiled the iMSC secretome using antibody arrays. Results Our results showed successful integration of MetRS L274G into targeted cells, allowing specific isolation of proteins from mixed-culture environments. We also demonstrated that the secretome of MetRS L274G -expressing iMSCs can be differentiated from that of THP-1 cells in co-culture, and is altered when co-cultured with LPS-treated THP-1 cells compared to naïve THP-1 cells. Conclusions The MetRS L274G -based toolkit we have generated enables selective profiling of the MSC secretome in mixed-culture disease models. This approach has broad applications for examining not only MSC responses to models of pathological conditions, but any other cell type that can be differentiated from iPSCs. This can potentially reveal novel MSC-mediated repair mechanisms and advancing our understanding of tissue regeneration processes.
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8
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Pamplona R, Jové M, Gómez J, Barja G. Whole organism aging: Parabiosis, inflammaging, epigenetics, and peripheral and central aging clocks. The ARS of aging. Exp Gerontol 2023; 174:112137. [PMID: 36871903 DOI: 10.1016/j.exger.2023.112137] [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: 12/31/2022] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
The strong interest shown in the study of the causes of aging in recent decades has uncovered many mechanisms that could contribute to the rate of aging. These include mitochondrial ROS production, DNA modification and repair, lipid peroxidation-induced membrane fatty acid unsaturation, autophagy, telomere shortening rate, apoptosis, proteostasis, senescent cells, and most likely there are many others waiting to be discovered. However, all these well-known mechanisms work only or mainly at the cellular level. Although it is known that organs within a single individual do not age at exactly the same rate, there is a well-defined species longevity. Therefore, loose coordination of aging rate among the different cells and tissues is needed to ensure species lifespan. In this article we focus on less known extracellular, systemic, and whole organism level mechanisms that could loosely coordinate aging of the whole individual to keep it within the margins of its species longevity. We discuss heterochronic parabiosis experiments, systemic factors distributed through the vascular system like DAMPs, mitochondrial DNA and its fragments, TF-like vascular proteins, and inflammaging, as well as epigenetic and proposed aging clocks situated at different levels of organization from individual cells to the brain. These interorgan systems can help to determine species longevity as a further adaptation to the ecosystem.
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Affiliation(s)
- Reinald Pamplona
- Department of Experimental Medicine, University of Lleida (UdL), Lleida Biomedical Research Institute (IRBLleida), E25198 Lleida, Spain
| | - Mariona Jové
- Department of Experimental Medicine, University of Lleida (UdL), Lleida Biomedical Research Institute (IRBLleida), E25198 Lleida, Spain
| | - José Gómez
- Department of Biology and Geology, Physics and Inorganic Chemistry, ESCET, Rey Juan Carlos University, E28933 Móstoles, Madrid, Spain
| | - Gustavo Barja
- Faculty of Biological Sciences, Complutense University of Madrid (UCM), E28040 Madrid, Spain.
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9
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Kehrloesser S, Cast O, Elliott TS, Ernst RJ, Machel AC, Chen JX, Chin JW, Miller ML. Cell-of-origin-specific proteomics of extracellular vesicles. PNAS NEXUS 2023; 2:pgad107. [PMID: 37091541 PMCID: PMC10119638 DOI: 10.1093/pnasnexus/pgad107] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/21/2023] [Indexed: 04/25/2023]
Abstract
The ability to assign cellular origin to low-abundance secreted factors in extracellular vesicles (EVs) would greatly facilitate the analysis of paracrine-mediated signaling. Here, we report a method, named selective isolation of extracellular vesicles (SIEVE), which uses cell type-specific proteome labeling via stochastic orthogonal recoding of translation (SORT) to install bioorthogonal reactive groups into the proteins derived from the cells targeted for labeling. We establish the native purification of intact EVs from a target cell, via a bioorthogonal tetrazine ligation, leading to copurification of the largely unlabeled EV proteome from the same cell. SIEVE enables capture of EV proteins at levels comparable with those obtained by antibody-based methods, which capture all EVs regardless of cellular origin, and at levels 20× higher than direct capture of SORT-labeled proteins. Using proteomic analysis, we analyze nonlabeled cargo proteins of EVs and show that the enhanced sensitivity of SIEVE allows for unbiased and comprehensive analysis of EV proteins from subpopulations of cells as well as for cell-specific EV proteomics in complex coculture systems. SIEVE can be applied with high efficiency in a diverse range of existing model systems for cell-cell communication and has direct applications for cell-of-origin EV analysis and for protein biomarker discovery.
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Affiliation(s)
- Sebastian Kehrloesser
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Oliver Cast
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Russell J Ernst
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Anne C Machel
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Jia-Xuan Chen
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Martin L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Oncology Data Science, Oncology R&D, AstraZeneca, 1 Francis Crick Ave, Cambridge CB2 0AA, UK
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10
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Prabhakar P, Pielot R, Landgraf P, Wissing J, Bayrhammer A, van Ham M, Gundelfinger ED, Jänsch L, Dieterich DC, Müller A. Monitoring regional astrocyte diversity by cell type-specific proteomic labeling in vivo. Glia 2023; 71:682-703. [PMID: 36401581 DOI: 10.1002/glia.24304] [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: 07/05/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
Abstract
Astrocytes exhibit regional heterogeneity in morphology, function and molecular composition to support and modulate neuronal function and signaling in a region-specific manner. To characterize regional heterogeneity of astrocytic proteomes of different brain regions we established an inducible Aldh1l1-methionyl-tRNA-synthetaseL274G (MetRSL274G ) mouse line that allows astrocyte-specific metabolic labeling of newly synthesized proteins by azidonorleucine (ANL) in vivo and subsequent isolation of tagged proteins by click chemistry. We analyzed astrocytic proteins from four different brain regions by mass spectrometry. The induced expression of MetRSL274G is restricted to astrocytes and identified proteins show a high overlap with proteins compiled in "AstroProt," a newly established database for astrocytic proteins. Gene enrichment analysis reveals a high similarity among brain regions with subtle differences in enriched biological processes and in abundances of key astrocytic proteins for hippocampus, cortex and striatum. However, the cerebellar proteome stands out with proteins being highly associated with the calcium signaling pathway or with bipolar disorder. Subregional analysis of single astrocyte TAMRA intensities in hippocampal layers indicates distinct subregional heterogeneity of astrocytes and highlights the applicability of our toolbox to study differences of astrocytic proteomes in vivo.
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Affiliation(s)
- Priyadharshini Prabhakar
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Rainer Pielot
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Josef Wissing
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anne Bayrhammer
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Marco van Ham
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eckart D Gundelfinger
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.,Leibniz Institute for Neurobiology, RG Neuroplasticity, Magdeburg, Germany
| | - Lothar Jänsch
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Daniela C Dieterich
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Anke Müller
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
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11
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Rodriguez SL, Carver CM, Dosch AJ, Huffman DM, Duke Boynton FD, Ayasoufi K, Schafer MJ. An optimized mouse parabiosis protocol for investigation of aging and rejuvenative mechanisms. FRONTIERS IN AGING 2022; 3:993658. [PMID: 36276605 PMCID: PMC9582328 DOI: 10.3389/fragi.2022.993658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/06/2022] [Indexed: 11/07/2022]
Abstract
Surgical parabiosis enables sharing of the circulating milieu between two organisms. This powerful model presents diverse complications based on age, strain, sex, and other experimental parameters. Here, we provide an optimized parabiosis protocol for the surgical union of two mice internally at the elbow and knee joints with continuous external joining of the skin. This protocol incorporates guidance and solutions to complications that can occur, particularly in aging studies, including non-cohesive pairing, variable anesthesia sensitivity, external and internal dehiscence, dehydration, and weight loss. We also offer a straightforward method for validating postoperative blood chimerism and confirming its time course using flow cytometry. Utilization of our optimized protocol can facilitate reproducible parabiosis experimentation to dynamically explore mechanisms of aging and rejuvenation.
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Affiliation(s)
- Sonia L. Rodriguez
- Department of Physiology and Biomedical Engineering Research, Mayo Clinic, Rochester, MN, United States
| | - Chase M. Carver
- Department of Physiology and Biomedical Engineering Research, Mayo Clinic, Rochester, MN, United States
| | - Andrew J. Dosch
- Department of Physiology and Biomedical Engineering Research, Mayo Clinic, Rochester, MN, United States
| | - Derek M. Huffman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | | | | | - Marissa J. Schafer
- Department of Physiology and Biomedical Engineering Research, Mayo Clinic, Rochester, MN, United States,Department of Neurology, Mayo Clinic, Rochester, MN, United States,Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, United States,*Correspondence: Marissa J. Schafer,
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12
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Brewer KD, Shi SM, Wyss-Coray T. Unraveling protein dynamics to understand the brain - the next molecular frontier. Mol Neurodegener 2022; 17:45. [PMID: 35717317 PMCID: PMC9206758 DOI: 10.1186/s13024-022-00546-8] [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: 02/13/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
The technological revolution to measure global gene expression at the single-cell level is currently transforming our knowledge of the brain and neurological diseases, leading from a basic understanding of genetic regulators and risk factors to one of more complex gene interactions and biological pathways. Looking ahead, our next challenge will be the reliable measurement and understanding of proteins. We describe in this review how to apply new, powerful methods of protein labeling, tracking, and detection. Recent developments of these methods now enable researchers to uncover protein mechanisms in vivo that may previously have only been hypothesized. These methods are also useful for discovering new biology because how proteins regulate systemic interactions is not well understood in most cases, such as how they travel through the bloodstream to distal targets or cross the blood–brain barrier. Genetic sequencing of DNA and RNA have enabled many great discoveries in the past 20 years, and now, the protein methods described here are creating a more complete picture of how cells to whole organisms function. It is likely that these developments will generate another transformation in biomedical research and our understanding of the brain and will ultimately allow for patient-specific medicine on a protein level.
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Affiliation(s)
- Kyle D Brewer
- ChEM-H, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Sophia M Shi
- ChEM-H, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- ChEM-H, Stanford University, Stanford, CA, USA. .,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA. .,Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
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13
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Shin S, Lee S, Choi S, Park N, Kwon Y, Jeong J, Ju S, Chang Y, Park K, Ha C, Lee C. Characterization of the Secretome of a Specific Cell Expressing Mutant Methionyl-tRNA Synthetase in Co-Culture Using Click Chemistry. Int J Mol Sci 2022; 23:ijms23126527. [PMID: 35742968 PMCID: PMC9223471 DOI: 10.3390/ijms23126527] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Co-culture system, in which two or more distinct cell types are cultured together, is advantageous in that it can mimic the environment of the in vivo niche of the cells. In this study, we presented a strategy to analyze the secretome of a specific cell type under the co-culture condition in serum-supplemented media. For the cell-specific secretome analysis, we expressed the mouse mutant methionyl-tRNA synthetase for the incorporation of the non-canonical amino acid, azidonorleucine into the newly synthesized proteins in cells of which the secretome is targeted. The azidonorleucine-tagged secretome could be enriched, based on click chemistry, and distinguished from any other contaminating proteins, either from the cell culture media or the other cells co-cultured with the cells of interest. In order to have more reliable true-positive identifications of cell-specific secretory bodies, we established criteria to exclude any identified human peptide matched to bovine proteins. As a result, we identified a maximum of 719 secreted proteins in the secretome analysis under this co-culture condition. Last, we applied this platform to profile the secretome of mesenchymal stem cells and predicted its therapeutic potential on osteoarthritis based on secretome analysis.
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Affiliation(s)
- Sungho Shin
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
- KHU-KIST Department of Converging Science and Technology, Graduate School, Kyung Hee University, Seoul 02447, Korea;
| | - Seonjeong Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Sunyoung Choi
- Department of Orthopedic Surgery, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.C.); (C.H.)
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Narae Park
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
- KHU-KIST Department of Converging Science and Technology, Graduate School, Kyung Hee University, Seoul 02447, Korea;
| | - Yumi Kwon
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
| | - Jaehoon Jeong
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Korea;
| | - Shinyeong Ju
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
| | - Yunsil Chang
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
- Department of Pediatrics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea
| | - Kangsik Park
- KHU-KIST Department of Converging Science and Technology, Graduate School, Kyung Hee University, Seoul 02447, Korea;
- Department of Physiology, School of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Chulwon Ha
- Department of Orthopedic Surgery, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.C.); (C.H.)
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Cheolju Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (S.L.); (N.P.); (Y.K.); (S.J.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
- Correspondence:
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14
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Perazza LR, Brown-Borg HM, Thompson LV. Physiological Systems in Promoting Frailty. Compr Physiol 2022; 12:3575-3620. [PMID: 35578945 DOI: 10.1002/cphy.c210034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Frailty is a complex syndrome affecting a growing sector of the global population as medical developments have advanced human mortality rates across the world. Our current understanding of frailty is derived from studies conducted in the laboratory as well as the clinic, which have generated largely phenotypic information. Far fewer studies have uncovered biological underpinnings driving the onset and progression of frailty, but the stage is set to advance the field with preclinical and clinical assessment tools, multiomics approaches together with physiological and biochemical methodologies. In this article, we provide comprehensive coverage of topics regarding frailty assessment, preclinical models, interventions, and challenges as well as clinical frameworks and prevalence. We also identify central biological mechanisms that may be at play including mitochondrial dysfunction, epigenetic alterations, and oxidative stress that in turn, affect metabolism, stress responses, and endocrine and neuromuscular systems. We review the role of metabolic syndrome, insulin resistance and visceral obesity, focusing on glucose homeostasis, adenosine monophosphate-activated protein kinase (AMPK), mammalian target of rapamycin (mTOR), and nicotinamide adenine dinucleotide (NAD+ ) as critical players influencing the age-related loss of health. We further focus on how immunometabolic dysfunction associates with oxidative stress in promoting sarcopenia, a key contributor to slowness, weakness, and fatigue. We explore the biological mechanisms involved in stem cell exhaustion that affect regeneration and may contribute to the frailty-associated decline in resilience and adaptation to stress. Together, an overview of the interplay of aging biology with genetic, lifestyle, and environmental factors that contribute to frailty, as well as potential therapeutic targets to lower risk and slow the progression of ongoing disease is covered. © 2022 American Physiological Society. Compr Physiol 12:1-46, 2022.
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Affiliation(s)
- Laís R Perazza
- Department of Physical Therapy and Athletic Training, Boston University, Boston, Massachusetts, USA
| | - Holly M Brown-Borg
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - LaDora V Thompson
- Department of Physical Therapy and Athletic Training, Boston University, Boston, Massachusetts, USA
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15
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Liu C, Wong N, Watanabe E, Hou W, Biral L, DeCastro J, Mehdipour M, Aran K, Conboy M, Conboy I. Mechanisms and minimization of false discovery of metabolic bio-orthogonal non-canonical amino acid proteomics. Rejuvenation Res 2022; 25:95-109. [PMID: 35323026 PMCID: PMC9063144 DOI: 10.1089/rej.2022.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabolic proteomics has been widely used to characterize dynamic protein networks in many areas of biomedicine, including in the arena of tissue aging and rejuvenation. Bio-orthogonal non-canonical amino acid tagging (BONCAT) is based on mutant methionine-tRNA synthases (MetRS) that incorporates metabolic tags, e.g., azido-nor leucine, ANL, into newly synthesized proteins. BONCAT revolutionizes metabolic proteomics, because mutant MetRS transgene allows one to identify cell type specific proteomes in mixed biological environments. This is not possible with other methods, such as stable isotope labeling with amino acids in cell culture (SILAC), isobaric tags for relative and absolute quantitation (iTRAQ) and tandem mass tags (TMT). At the same time, an inherent weakness of BONCAT is that after click chemistry-based enrichment, all identified proteins are assumed to have been metabolically tagged, but there is no confirmation in Mass Spectrometry data that only tagged proteins are detected. As we show here, such assumption is incorrect and accurate negative controls uncover a surprisingly high degree of false positives in BONCAT proteomics. We show not only how to reveal the false discovery and thus improve the accuracy of the analyses and conclusions but also approaches for avoiding it through minimizing non-specific detection of biotin, biotin-independent direct detection of metabolic tags, and improvement of signal to noise ratio through machine learning algorithms.
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Affiliation(s)
- Chao Liu
- University of California Berkeley, 1438, Stanley Hall B104, Berkeley, Berkeley, California, United States, 94720;
| | - Nathan Wong
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Etsuko Watanabe
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - William Hou
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Leonardo Biral
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Jonalyn DeCastro
- Keck Graduate Institute, 48927, Claremont, California, United States;
| | - Melod Mehdipour
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Kiana Aran
- Keck Graduate Institute, 48927, Claremont, California, United States;
| | - Michael Conboy
- University of California Berkeley, 1438, Berkeley, California, United States;
| | - Irina Conboy
- UC Berkeley, 1438, Bioengineering and QB3, 174, Stanley Hall, Berkeley, California, United States, 94720;
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16
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Metabolic labeling of secreted matrix to investigate cell-material interactions in tissue engineering and mechanobiology. Nat Protoc 2022; 17:618-648. [PMID: 35140408 PMCID: PMC8985381 DOI: 10.1038/s41596-021-00652-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/25/2021] [Indexed: 12/19/2022]
Abstract
Re-creating features of the native extracellular matrix (ECM) with engineered biomaterials has become a valuable tool to probe the influence of ECM properties on cellular functions (e.g., differentiation) and toward the engineering of tissues. However, characterization of newly secreted (nascent) matrix and turnover, which are important in the context of cells interacting with these biomaterials, has been limited by a lack of tools. We developed a protocol to visualize and quantify the spatiotemporal evolution of newly synthesized and deposited matrix by cells that are either cultured atop (2D) or embedded within (3D) biomaterial systems (e.g., hydrogels, fibrous matrices). This technique relies on the incorporation of a noncanonical amino acid (azidohomoalanine) into proteins as they are synthesized. Deposited nascent ECM components are then visualized with fluorescent cyclooctynes via copper-free cycloaddition for spatiotemporal analysis or modified with cleavable biotin probes for identification. Here we describe the preparation of hyaluronic acid hydrogels through ultraviolet or visible light induced cross-linking for 2D and 3D cell culture, as well as the fluorescent labeling of nascent ECM deposited by cells during culture. We also provide protocols for secondary immunofluorescence of specific ECM components and ImageJ-based ECM quantification methods. Hyaluronic acid polymer synthesis takes 2 weeks to complete, and hydrogel formation for 2D or 3D cell culture is performed in 2-3 h. Lastly, we detail the identification of nascent proteins, including enrichment, preparation and analysis with mass spectrometry, which can be completed in 10 d.
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17
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Li R, Liang Y, Lin B. Accumulation of systematic TPM1 mediates inflammation and neuronal remodeling by phosphorylating PKA and regulating the FABP5/NF-κB signaling pathway in the retina of aged mice. Aging Cell 2022; 21:e13566. [PMID: 35148456 PMCID: PMC8920455 DOI: 10.1111/acel.13566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/05/2022] [Accepted: 01/25/2022] [Indexed: 12/23/2022] Open
Abstract
The molecular mechanisms underlying functional decline during normal brain aging are poorly understood. Here, we identified the actin‐associated protein tropomyosin 1 (TPM1) as a new systemic pro‐aging factor associated with function deficits in normal aging retinas. Heterochronic parabiosis and blood plasma treatment confirmed that systemic factors regulated age‐related inflammatory responses and the ectopic dendritic sprouting of rod bipolar (RBC) and horizontal (HC) cells in the aging retina. Proteomic analysis revealed that TPM1 was a potential systemic molecule underlying structural and functional deficits in the aging retina. Recombinant TPM1 protein administration accelerated the activation of glial cells, the dendritic sprouting of RBCs and HCs and functional decline in the retina of young mice, whereas anti‐TPM1 neutralizing antibody treatment ameliorated age‐related structural and function changes in the retina of aged mice. Old mouse plasma (OMP) induced glial cell activation and the dendritic outgrowth of RBCs and HCs in young mice, and yet TMP1‐depleted OMP failed to reproduce the similar effect in young mice. These results confirmed that TPM1 was a systemic pro‐aging factor. Moreover, we demonstrated that systematic TPM1 was an immune‐related molecule, which elicited endogenous TPM1 expression and inflammation by phosphorylating PKA and regulating FABP5/NF‐κB signaling pathway in normal aging retinas. Interestingly, we observed TPM1 upregulation and the ectopic dendritic sprouting of RBCs and HCs in young mouse models of Alzheimer's disease, indicating a potential role of TPM1 in age‐related neurodegenerative diseases. Our data indicate that TPM1 could be targeted for combating the aging process.
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Affiliation(s)
- Rong Li
- School of Optometry The Hong Kong Polytechnic University Kowloon Hong Kong
| | - Yuxiang Liang
- The State Key Laboratory of Brain and Cognitive Sciences The University of Hong Kong Pok Fu Lam Hong Kong
| | - Bin Lin
- School of Optometry The Hong Kong Polytechnic University Kowloon Hong Kong
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18
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Erickson PW, Fulcher JM, Spaltenstein P, Kay MS. Traceless Click-Assisted Native Chemical Ligation Enabled by Protecting Dibenzocyclooctyne from Acid-Mediated Rearrangement with Copper(I). Bioconjug Chem 2021; 32:2233-2244. [PMID: 34619957 DOI: 10.1021/acs.bioconjchem.1c00403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The scope of proteins accessible to total chemical synthesis via native chemical ligation (NCL) is often limited by slow ligation kinetics. Here we describe Click-Assisted NCL (CAN), in which peptides are incorporated with traceless "helping hand" lysine linkers that enable addition of dibenzocyclooctyne (DBCO) and azide handles. The resulting strain-promoted alkyne-azide cycloaddition (SPAAC) increases their effective concentration to greatly accelerate ligations. We demonstrate that copper(I) protects DBCO from acid-mediated rearrangement during acidic peptide cleavage, enabling direct production of DBCO synthetic peptides. Excitingly, triazole-linked model peptides ligated rapidly and accumulated little side product due to the fast reaction time. Using the E. coli ribosomal subunit L32 as a model protein, we further demonstrate that SPAAC, ligation, desulfurization, and linker cleavage steps can be performed in one pot. CAN is a useful method for overcoming challenging ligations involving sterically hindered junctions. Additionally, CAN is anticipated to be an important stepping stone toward a multisegment, one-pot, templated ligation system.
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Affiliation(s)
- Patrick W Erickson
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States.,Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - James M Fulcher
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States.,Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Paul Spaltenstein
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States
| | - Michael S Kay
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States
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19
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Azizian NG, Sullivan DK, Nie L, Pardo S, Molleur D, Chen J, Weintraub ST, Li Y. Selective Labeling and Identification of the Tumor Cell Proteome of Pancreatic Cancer In Vivo. J Proteome Res 2020; 20:858-866. [PMID: 33289385 DOI: 10.1021/acs.jproteome.0c00666] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest cancers. Dissecting the tumor cell proteome from that of the non-tumor cells in the PDAC tumor bulk is critical for tumorigenesis studies, biomarker discovery, and development of therapeutics. However, investigating the tumor cell proteome has proven evasive due to the tumor's extremely complex cellular composition. To circumvent this technical barrier, we have combined bioorthogonal noncanonical amino acid tagging (BONCAT) and data-independent acquisition mass spectrometry (DIA-MS) in an orthotopic PDAC model to specifically identify the tumor cell proteome in vivo. Utilizing the tumor cell-specific expression of a mutant tRNA synthetase transgene, this approach provides tumor cells with the exclusive ability to incorporate an azide-bearing methionine analogue into newly synthesized proteins. The azide-tagged tumor cell proteome is subsequently enriched and purified via a bioorthogonal reaction and then identified and quantified using DIA-MS. Applying this workflow to the orthotopic PDAC model, we have identified thousands of proteins expressed by the tumor cells. Furthermore, by comparing the tumor cell and tumor bulk proteomes, we showed that the approach can distinctly differentiate proteins produced by tumor cells from those of non-tumor cells within the tumor microenvironment. Our study, for the first time, reveals the tumor cell proteome of PDAC under physiological conditions, providing broad applications for tumorigenesis, therapeutics, and biomarker studies in various human cancers.
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Affiliation(s)
- Nancy G Azizian
- Center for Immunotherapy Research, Houston Methodist Research Institute, Houston, Texas 77030, United States.,Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Delaney K Sullivan
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Litong Nie
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Sammy Pardo
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Dana Molleur
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Junjie Chen
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Yulin Li
- Center for Immunotherapy Research, Houston Methodist Research Institute, Houston, Texas 77030, United States.,Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
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20
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Leopold JA. Endocrine Delivery of MicroRNA-210: A Trusted Traveler That Mediates Pulmonary Hypertension. Circ Res 2020; 127:693-695. [PMID: 32790524 DOI: 10.1161/circresaha.120.317625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jane A Leopold
- From the Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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21
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Mehdipour M, Skinner C, Wong N, Lieb M, Liu C, Etienne J, Kato C, Kiprov D, Conboy MJ, Conboy IM. Rejuvenation of three germ layers tissues by exchanging old blood plasma with saline-albumin. Aging (Albany NY) 2020; 12:8790-8819. [PMID: 32474458 PMCID: PMC7288913 DOI: 10.18632/aging.103418] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 12/15/2022]
Abstract
Heterochronic blood sharing rejuvenates old tissues, and most of the studies on how this works focus on young plasma, its fractions, and a few youthful systemic candidates. However, it was not formally established that young blood is necessary for this multi-tissue rejuvenation. Here, using our recently developed small animal blood exchange process, we replaced half of the plasma in mice with saline containing 5% albumin (terming it a "neutral" age blood exchange, NBE) thus diluting the plasma factors and replenishing the albumin that would be diminished if only saline was used. Our data demonstrate that a single NBE suffices to meet or exceed the rejuvenative effects of enhancing muscle repair, reducing liver adiposity and fibrosis, and increasing hippocampal neurogenesis in old mice, all the key outcomes seen after blood heterochronicity. Comparative proteomic analysis on serum from NBE, and from a similar human clinical procedure of therapeutic plasma exchange (TPE), revealed a molecular re-setting of the systemic signaling milieu, interestingly, elevating the levels of some proteins, which broadly coordinate tissue maintenance and repair and promote immune responses. Moreover, a single TPE yielded functional blood rejuvenation, abrogating the typical old serum inhibition of progenitor cell proliferation. Ectopically added albumin does not seem to be the sole determinant of such rejuvenation, and levels of albumin do not decrease with age nor are increased by NBE/TPE. A model of action (supported by a large body of published data) is that significant dilution of autoregulatory proteins that crosstalk to multiple signaling pathways (with their own feedback loops) would, through changes in gene expression, have long-lasting molecular and functional effects that are consistent with our observations. This work improves our understanding of the systemic paradigms of multi-tissue rejuvenation and suggest a novel and immediate use of the FDA approved TPE for improving the health and resilience of older people.
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Affiliation(s)
- Melod Mehdipour
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
| | - Colin Skinner
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
| | - Nathan Wong
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
| | - Michael Lieb
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
| | - Chao Liu
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
| | - Jessy Etienne
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
| | - Cameron Kato
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
| | - Dobri Kiprov
- California Pacific Medical Center, Apheresis Care Group, San-Francisco, CA 94115, USA
| | - Michael J. Conboy
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
| | - Irina M. Conboy
- Department of Bioengineering and QB3, UC Berkeley, Berkeley, CA 94720, USA
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22
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Iavarone F, Guardiola O, Scagliola A, Andolfi G, Esposito F, Serrano A, Perdiguero E, Brunelli S, Muñoz-Cánoves P, Minchiotti G. Cripto shapes macrophage plasticity and restricts EndMT in injured and diseased skeletal muscle. EMBO Rep 2020; 21:e49075. [PMID: 32107853 PMCID: PMC7132341 DOI: 10.15252/embr.201949075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 12/24/2022] Open
Abstract
Macrophages are characterized by a high plasticity in response to changes in tissue microenvironment, which allows them to acquire different phenotypes and to exert essential functions in complex processes, such as tissue regeneration. Here, we report that the membrane protein Cripto plays a key role in shaping macrophage plasticity in skeletal muscle during regeneration and disease. Conditional deletion of Cripto in the myeloid lineage (CriptoMy‐LOF) perturbs MP plasticity in acutely injured muscle and in mouse models of Duchenne muscular dystrophy (mdx). Specifically, CriptoMy‐LOF macrophages infiltrate the muscle, but fail to properly expand as anti‐inflammatory CD206+ macrophages, which is due, at least in part, to aberrant activation of TGFβ/Smad signaling. This reduction in macrophage plasticity disturbs vascular remodeling by increasing Endothelial‐to‐Mesenchymal Transition (EndMT), reduces muscle regenerative potential, and leads to an exacerbation of the dystrophic phenotype. Thus, in muscle‐infiltrating macrophages, Cripto is required to promote the expansion of the CD206+ anti‐inflammatory macrophage type and to restrict the EndMT process, providing a direct functional link between this macrophage population and endothelial cells.
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Affiliation(s)
- Francescopaolo Iavarone
- Stem Cell Fate Laboratory, CNR, Institute of Genetics and Biophysics "A. Buzzati-Traverso", Naples, Italy
| | - Ombretta Guardiola
- Stem Cell Fate Laboratory, CNR, Institute of Genetics and Biophysics "A. Buzzati-Traverso", Naples, Italy
| | | | - Gennaro Andolfi
- Stem Cell Fate Laboratory, CNR, Institute of Genetics and Biophysics "A. Buzzati-Traverso", Naples, Italy
| | - Federica Esposito
- Stem Cell Fate Laboratory, CNR, Institute of Genetics and Biophysics "A. Buzzati-Traverso", Naples, Italy
| | - Antonio Serrano
- Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Eusebio Perdiguero
- Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Silvia Brunelli
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Pura Muñoz-Cánoves
- Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, CNR, Institute of Genetics and Biophysics "A. Buzzati-Traverso", Naples, Italy
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23
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Denninger JK, Chen X, Turkoglu AM, Sarchet P, Volk AR, Rieskamp JD, Yan P, Kirby ED. Defining the adult hippocampal neural stem cell secretome: In vivo versus in vitro transcriptomic differences and their correlation to secreted protein levels. Brain Res 2020; 1735:146717. [PMID: 32035887 DOI: 10.1016/j.brainres.2020.146717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 01/08/2023]
Abstract
Adult hippocampal neural stem and progenitor cells (NSPCs) secrete a variety of proteins that affect tissue function. Though several individual NSPC-derived proteins have been shown to impact key cellular processes, a broad characterization is lacking. Secretome profiling of low abundance stem cell populations is typically achieved via proteomic characterization of in vitro, isolated cells. Here, we identified hundreds of secreted proteins in conditioned media from in vitro adult mouse hippocampal NSPCs using an antibody array and mass spectrometry. Comparison of protein abundance between antibody array and mass spectrometry plus quantification of several key secreted proteins by ELISA revealed notable disconnect between methods in what proteins were identified as being high versus low abundance, suggesting that data from antibody arrays in particular should be approached with caution. We next assessed the NSPC secretome on a transcriptional level with single cell and bulk RNA sequencing (RNAseq) of cultured NSPCs. Comparison of RNAseq transcript levels of highly secreted proteins revealed that quantification of gene expression did not necessarily predict relative protein abundance. Interestingly, comparing our in vitro NSPC gene expression data with similar data from freshly isolated, in vivo hippocampal NSPCs revealed strong correlations in global gene expression between in vitro and in vivo NSPCs. Understanding the components and functions of the NSPC secretome is essential to understanding how these cells may modulate the hippocampal neurogenic niche. Cumulatively, our data emphasize the importance of using proteomics in conjunction with transcriptomics and highlights the need for better methods of unbiased secretome profiling.
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Affiliation(s)
- Jiyeon K Denninger
- Department of Psychology, College of Arts and Sciences, The Ohio State University, United States
| | - Xi Chen
- Comprehensive Cancer Center, The Ohio State University, United States
| | - Altan M Turkoglu
- College of Arts and Sciences, The Ohio State University, United States
| | - Patricia Sarchet
- Comprehensive Cancer Center, The Ohio State University, United States
| | - Abby R Volk
- College of Arts and Sciences, The Ohio State University, United States
| | - Joshua D Rieskamp
- Neuroscience Graduate Program, The Ohio State University, United States
| | - Pearlly Yan
- Comprehensive Cancer Center, The Ohio State University, United States; Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, United States
| | - Elizabeth D Kirby
- Department of Psychology, College of Arts and Sciences, The Ohio State University, United States; Department of Neuroscience, The Ohio State University, United States; Chronic Brain Injury Initiative, The Ohio State University, United States.
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24
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The Effects of Parabiosis on Aging and Age-Related Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1260:107-122. [PMID: 32304032 DOI: 10.1007/978-3-030-42667-5_5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Parabiosis refers to the union of two living organisms by surgical operation, leading to the development of a shared circulatory system. It enables researchers to ask whether or not transmissible factors in the blood of one parabiont have physiological effects on its partner. In other words, parabiosis allows researchers to explore whether circulating factors in the bloodstream can alter tissue function. Heterochronic parabiosis, the pairing together of a young and aged organism, provides a unique experimental design to assess the effects of systemic milieu on the age-related processes. In the last 15 years, this experimental approach to study the aging processes at the whole organism level underwent a renaissance, with several studies demonstrating the rejuvenating effects of youthful systemic milieu on aging processes in the nervous system, skeletal muscle, heart, liver and other organs. The crucial question still mainly unanswered is the nature of circulating molecules that mediate "pro-youthful" effects of young and "pro-aging" effects of old system milieu.
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25
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Mehdipour M, Etienne J, Chen CC, Gathwala R, Rehman M, Kato C, Liu C, Liu Y, Zuo Y, Conboy MJ, Conboy IM. Rejuvenation of brain, liver and muscle by simultaneous pharmacological modulation of two signaling determinants, that change in opposite directions with age. Aging (Albany NY) 2019; 11:5628-5645. [PMID: 31422380 PMCID: PMC6710051 DOI: 10.18632/aging.102148] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022]
Abstract
We hypothesize that altered intensities of a few morphogenic pathways account for most/all the phenotypes of aging. Investigating this has revealed a novel approach to rejuvenate multiple mammalian tissues by defined pharmacology. Specifically, we pursued the simultaneous youthful in vivo calibration of two determinants: TGF-beta which activates ALK5/pSmad 2,3 and goes up with age, and oxytocin (OT) which activates MAPK and diminishes with age. The dose of Alk5 inhibitor (Alk5i) was reduced by 10-fold and the duration of treatment was shortened (to minimize overt skewing of cell-signaling pathways), yet the positive outcomes were broadened, as compared with our previous studies. Alk5i plus OT quickly and robustly enhanced neurogenesis, reduced neuro-inflammation, improved cognitive performance, and rejuvenated livers and muscle in old mice. Interestingly, the combination also diminished the numbers of cells that express the CDK inhibitor and marker of senescence p16 in vivo. Summarily, simultaneously re-normalizing two pathways that change with age in opposite ways (up vs. down) synergistically reverses multiple symptoms of aging.
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Affiliation(s)
- Melod Mehdipour
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jessy Etienne
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chia-Chien Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ranveer Gathwala
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maryam Rehman
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cameron Kato
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chao Liu
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yutong Liu
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yi Zuo
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael J Conboy
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Irina M Conboy
- Department of Bioengineering and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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26
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Abstract
Age is the primary risk factor for the vast majority of disorders, including neurodegenerative diseases impacting brain function. Whether the consequences of aging at the biological level can be reversed, or age-related changes prevented, to change the trajectory of such disorders is thus of extreme interest and value. Studies using young plasma, the acellular component of blood, have demonstrated that aging is malleable, with the ability to restore functions in old animals. Fascinatingly, this functional improvement is even observed in the brain, despite the blood-brain barrier, indicating that peripheral sources can effectively impact central sites leading to clinically relevant changes such as enhancement of cognitive function. A plasma-based approach is also attractive as aging is inherently complex, with an array of mechanisms dysregulated in diverse cells and organs throughout the body leading to disturbed function. Plasma, containing a natural mixture of components, has the ability to act multimodally, modulating diverse mechanisms that can converge to change the trajectory of age-related diseases. Here we review the evidence that plasma modulates aging processes in the brain and consider the therapeutic applications that derive from these observations. Plasma and plasma-derived therapeutics are an attractive translation of this concept, requiring critical consideration of benefits, risks, and ethics. Ultimately, knowledge derived from this science will drive a comprehensive molecular understanding to deliver optimized therapeutics. The potential of highly differentiated, multimodal therapeutics for treatment of age-related brain disorders provides an exciting new clinical approach to address the complex etiology of aging.
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Affiliation(s)
- Viktoria Kheifets
- Alkahest Inc., 125 Shoreway Road, Suite D, San Carlos, CA, 94070, USA
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27
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Saleh AM, Wilding KM, Calve S, Bundy BC, Kinzer-Ursem TL. Non-canonical amino acid labeling in proteomics and biotechnology. J Biol Eng 2019; 13:43. [PMID: 31139251 PMCID: PMC6529998 DOI: 10.1186/s13036-019-0166-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/11/2019] [Indexed: 02/03/2023] Open
Abstract
Metabolic labeling of proteins with non-canonical amino acids (ncAAs) provides unique bioorthogonal chemical groups during de novo synthesis by taking advantage of both endogenous and heterologous protein synthesis machineries. Labeled proteins can then be selectively conjugated to fluorophores, affinity reagents, peptides, polymers, nanoparticles or surfaces for a wide variety of downstream applications in proteomics and biotechnology. In this review, we focus on techniques in which proteins are residue- and site-specifically labeled with ncAAs containing bioorthogonal handles. These ncAA-labeled proteins are: readily enriched from cells and tissues for identification via mass spectrometry-based proteomic analysis; selectively purified for downstream biotechnology applications; or labeled with fluorophores for in situ analysis. To facilitate the wider use of these techniques, we provide decision trees to help guide the design of future experiments. It is expected that the use of ncAA labeling will continue to expand into new application areas where spatial and temporal analysis of proteome dynamics and engineering new chemistries and new function into proteins are desired.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Kristen M. Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
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28
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Abstract
Stem cells can reside in a state of reversible growth arrest, or quiescence, for prolonged periods of time. Although quiescence has long been viewed as a dormant, low-activity state, increasing evidence suggests that quiescence represents states of poised potential and active restraint, as stem cells "idle" in anticipation of activation, proliferation, and differentiation. Improved understanding of quiescent stem cell dynamics is leading to novel approaches to enhance maintenance and repair of aged or diseased tissues. In this Review, we discuss recent advances in our understanding of stem cell quiescence and techniques enabling more refined analyses of quiescence in vivo.
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Affiliation(s)
- Cindy T J van Velthoven
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Center for Tissue Regeneration, Repair and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
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29
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Cell-type-specific metabolic labeling, detection and identification of nascent proteomes in vivo. Nat Protoc 2019; 14:556-575. [DOI: 10.1038/s41596-018-0106-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Ashapkin VV, Kutueva LI, Vanyushin BF. Epigenetic Clock: Just a Convenient Marker or an Active Driver of Aging? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1178:175-206. [PMID: 31493228 DOI: 10.1007/978-3-030-25650-0_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A global DNA hypomethylation and local changes in the methylation levels of specific DNA loci occur during aging in mammals. Global hypomethylation mainly affects highly methylated repeat sequences, such as transposable elements; it is an essentially stochastic process usually referred to as "epigenetic drift." Specific changes in DNA methylation affect various genome sequences and could be either hypomethylation or hypermethylation, but the prevailing tendencies are hypermethylation of promoter sequences associated with CpG islands and hypomethylation of CpG poor genes. Methylation levels of multiple CpG sites display a strong correlation to age common between individuals of the same species. Collectively, methylation of such CpG sites could be used as "epigenetic clocks" to predict biological age. Furthermore, the discrepancy between epigenetic and chronological ages could be predictive of all-cause mortality and multiple age-associated diseases. Random changes in DNA methylation (epigenetic drift) could also affect the aging phenotype, causing accidental changes in gene expression and increasing the transcriptional noise between cells of the same tissue. Both effects could become detrimental to tissue functioning and cause a gradual decline in organ function during aging. Strong evidence shows that epigenetic systems contribute to lifespan control in various organisms. Similar to other cell systems, the epigenome is prone to gradual degradation due to the genome damage, stressful agents and other aging factors. However, unlike mutations and many other hallmarks of aging, age-related epigenetic changes could be fully or partially reversed to a "young" state.
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Affiliation(s)
- Vasily V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Lyudmila I Kutueva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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31
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Zhang MW, Zhao P, Yung WH, Sheng Y, Ke Y, Qian ZM. Tissue iron is negatively correlated with TERC or TERT mRNA expression: A heterochronic parabiosis study in mice. Aging (Albany NY) 2018; 10:3834-3850. [PMID: 30555055 PMCID: PMC6326661 DOI: 10.18632/aging.101676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/18/2018] [Indexed: 12/21/2022]
Abstract
To test the hypothesis that iron accumulation in tissues with age is a key harmful factor for the development of aging, we established heterochronic parabiosis-pairings and investigated changes in serum iron, the expression of major iron transport proteins and iron contents, as well as telomerase reverse transcriptase (TERT), telomerase RNA component (TERC), and telomere length in the liver, kidney and heart of Y-O(O) (old pairing with young), Y-O(Y) (young pairing with old), O-O (pairings between two old) and Y-Y (pairings between two young) mice. We demonstrated that the reduced serum iron, increased iron and reduced expression of TERT and TERC in the tissues of aged mice are reversible by exposure to a younger mouse’s circulation. All of these measurements in young mice are reversible by exposure to an older mouse’s circulation. Correlation analysis showed that tissue iron is negatively correlated with TERT and TERC expression in the liver, kidney and heart of parabiotic mice. These findings provide new evidence for the key role of iron in aging and also imply the existence of rejuvenating factors in young serum with an anti-ageing role that act by reversing the impaired activity of iron metabolism in old mice.
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Affiliation(s)
- Meng-Wan Zhang
- National Clinical Research Center for Aging and Medicine, Huashan Hostital, Laboratory of Neuropharmacology, School of Pharmacy, Fudan University, Shanghai 201203, PRC
| | - Peng Zhao
- National Clinical Research Center for Aging and Medicine, Huashan Hostital, Laboratory of Neuropharmacology, School of Pharmacy, Fudan University, Shanghai 201203, PRC
| | - Wing-Ho Yung
- School of Biomedical Sciences and Gerald Choa Neuroscience Centre, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Yuan Sheng
- National Clinical Research Center for Aging and Medicine, Huashan Hostital, Laboratory of Neuropharmacology, School of Pharmacy, Fudan University, Shanghai 201203, PRC
| | - Ya Ke
- School of Biomedical Sciences and Gerald Choa Neuroscience Centre, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Zhong-Ming Qian
- National Clinical Research Center for Aging and Medicine, Huashan Hostital, Laboratory of Neuropharmacology, School of Pharmacy, Fudan University, Shanghai 201203, PRC.,Laboratory of Neuropharmacology, Institute of Translational & Precision Medicine, Nantong University, Nantong 226019, PRC
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32
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Sadlowski C, Balderston S, Sandhu M, Hajian R, Liu C, Tran TP, Conboy MJ, Paredes J, Murthy N, Conboy IM, Aran K. Graphene-based biosensor for on-chip detection of bio-orthogonally labeled proteins to identify the circulating biomarkers of aging during heterochronic parabiosis. LAB ON A CHIP 2018; 18:3230-3238. [PMID: 30239548 PMCID: PMC6200589 DOI: 10.1039/c8lc00446c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Studies of heterochronic parabiosis, where two animals of different ages are joined surgically, provided proof-of-principle results that systemic proteins have broad age-specific effects on tissue health and repair. In an effort to identify these systemic proteins, we previously developed a method to selectively label the proteome of only one animal joined in parabiosis utilizing bio-orthogonal non-canonical amino acid tagging (BONCAT), which can metabolically label proteins during their de novo synthesis by incorporating a methionine substitute, azido-nor-leucine (ANL), in cells expressing a mutant methionyl-tRNA synthetase (MetRSL274G). Once labeled, we can selectively identify the proteins produced by the MetRSL274G transgenic mouse in the setting of heterochronic parabiosis. This approach enabled the detection of several rejuvenating protein candidates from the young parabiont, which were transferred to the old mammalian tissue through their shared circulation. Although BONCAT is a very powerful technology, the challenges associated with its complexity including large starting material requirements and cost of ANL-labeled protein detection, such as modified antibody arrays and mass spectrometry, limit its application. Herein, we propose a lab-on-a-chip technology, termed Click-A+Chip for facile and rapid digital detection of ANL-labeled proteomes present in minute amount of sample, to replace conventional assays. Click-A+Chip is a graphene-based field effect biosensor (gFEB) which utilizes novel on-chip click-chemistry to specifically bind to ANL-labeled biomolecules. In this study, Click-A+Chip is utilized for the capture of ANL-labeled proteins transferred from young to old parabiotic mouse partners. Moreover, we were able to identify the young-derived ANL-labeled Lif-1 and leptin in parabiotic systemic milieu, confirming previous data as well as providing novel findings on the relative levels of these factors in young versus old parabionts. Summarily, our results demonstrate that Click-A+Chip can be used for rapid detection and identification of ANL-labeled proteins, significantly reducing the sample size, complexity, cost and time associated with BONCAT analysis.
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Affiliation(s)
| | - Sarah Balderston
- Keck Graduate Institute, Claremont Colleges, Claremont
CA
- Scripps College, Claremont Colleges, Claremont CA
| | - Mandeep Sandhu
- Keck Graduate Institute, Claremont Colleges, Claremont
CA
- Scripps College, Claremont Colleges, Claremont CA
| | - Reza Hajian
- Keck Graduate Institute, Claremont Colleges, Claremont
CA
| | - Chao Liu
- University of California, Berkeley, Berkeley CA
| | | | | | | | | | | | - Kiana Aran
- University of California, Berkeley, Berkeley CA
- Keck Graduate Institute, Claremont Colleges, Claremont
CA
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Yang AC, du Bois H, Olsson N, Gate D, Lehallier B, Berdnik D, Brewer KD, Bertozzi CR, Elias JE, Wyss-Coray T. Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics. J Am Chem Soc 2018; 140:7046-7051. [PMID: 29775058 DOI: 10.1021/jacs.8b03074] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bioorthogonal tools enable cell-type-specific proteomics, a prerequisite to understanding biological processes in multicellular organisms. Here we report two engineered aminoacyl-tRNA synthetases for mammalian bioorthogonal labeling: a tyrosyl ( ScTyrY43G) and a phenylalanyl ( MmPheT413G) tRNA synthetase that incorporate azide-bearing noncanonical amino acids specifically into the nascent proteomes of host cells. Azide-labeled proteins are chemoselectively tagged via azide-alkyne cycloadditions with fluorophores for imaging or affinity resins for mass spectrometric characterization. Both mutant synthetases label human, hamster, and mouse cell line proteins and selectively activate their azido-bearing amino acids over 10-fold above the canonical. ScTyrY43G and MmPheT413G label overlapping but distinct proteomes in human cell lines, with broader proteome coverage upon their coexpression. In mice, ScTyrY43G and MmPheT413G label the melanoma tumor proteome and plasma secretome. This work furnishes new tools for mammalian residue-specific bioorthogonal chemistry, and enables more robust and comprehensive cell-type-specific proteomics in live mammals.
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Affiliation(s)
| | | | | | | | | | - Daniela Berdnik
- Center for Tissue Regeneration, Repair and Restoration , V.A. Palo Alto Healthcare System , Palo Alto , California 94304 , United States
| | | | | | | | - Tony Wyss-Coray
- Center for Tissue Regeneration, Repair and Restoration , V.A. Palo Alto Healthcare System , Palo Alto , California 94304 , United States
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