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Duran P, Yang BA, Plaster E, Eiken M, Loebel C, Aguilar CA. Tracking of Nascent Matrix Deposition during Muscle Stem Cell Activation across Lifespan Using Engineered Hydrogels. Adv Biol (Weinh) 2024; 8:e2400091. [PMID: 38616175 DOI: 10.1002/adbi.202400091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/22/2024] [Indexed: 04/16/2024]
Abstract
Adult stem cells occupy a niche that contributes to their function, but how stem cells rebuild their microenvironment after injury remains an open-ended question. Herein, biomaterial-based systems and metabolic labeling are utilized to evaluate how skeletal muscle stem cells deposit extracellular matrix. Muscle stem cells and committed myoblasts are observed to generate less nascent matrix than muscle resident fibro-adipogenic progenitors. When cultured on substrates that matched the stiffness of physiological uninjured and injured muscles, muscle stem cells increased nascent matrix deposition with activation kinetics. Reducing the ability to deposit nascent matrix by an inhibitor of vesicle trafficking (Exo-1) attenuated muscle stem cell function and mimicked impairments observed from muscle stem cells isolated from old muscles. Old muscle stem cells are observed to deposit less nascent matrix than young muscle stem cells, which is rescued with therapeutic supplementation of insulin-like growth factors. These results highlight the role of nascent matrix production with muscle stem cell activation.
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Affiliation(s)
- Pamela Duran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Benjamin A Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eleanor Plaster
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madeline Eiken
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Materials Science & Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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Jacobson KR, Saleh AM, Lipp SN, Tian C, Watson AR, Luetkemeyer CM, Ocken AR, Spencer SL, Kinzer-Ursem TL, Calve S. Extracellular matrix protein composition dynamically changes during murine forelimb development. iScience 2024; 27:108838. [PMID: 38303699 PMCID: PMC10831947 DOI: 10.1016/j.isci.2024.108838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/02/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
The extracellular matrix (ECM) is an integral part of multicellular organisms, connecting different cell layers and tissue types. During morphogenesis and growth, tissues undergo substantial reorganization. While it is intuitive that the ECM remodels in concert, little is known regarding how matrix composition and organization change during development. Here, we quantified ECM protein dynamics in the murine forelimb during appendicular musculoskeletal morphogenesis (embryonic days 11.5-14.5) using tissue fractionation, bioorthogonal non-canonical amino acid tagging, and mass spectrometry. Our analyses indicated that ECM protein (matrisome) composition in the embryonic forelimb changed as a function of development and growth, was distinct from other developing organs (brain), and was altered in a model of disease (osteogenesis imperfecta murine). Additionally, the tissue distribution for select matrisome was assessed via immunohistochemistry in the wild-type embryonic and postnatal musculoskeletal system. This resource will guide future research investigating the role of the matrisome during complex tissue development.
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Affiliation(s)
- Kathryn R. Jacobson
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah N. Lipp
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- The Indiana University Medical Scientist/Engineer Training Program, Indiana University, Indianapolis, IN 46202, USA
| | - Chengzhe Tian
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Research Center for Molecular Medicine (CEMM) of the Austrian Academy of Sciences, Vienna, Austria
| | - Audrey R. Watson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Callan M. Luetkemeyer
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Alexander R. Ocken
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sabrina L. Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Tamara L. Kinzer-Ursem
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah Calve
- Purdue University Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
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Duran P, Yang BA, Plaster E, Eiken M, Loebel C, Aguilar CA. Quantification of local matrix deposition during muscle stem cell activation using engineered hydrogels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576326. [PMID: 38328131 PMCID: PMC10849481 DOI: 10.1101/2024.01.20.576326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Adult stem cells occupy a niche that contributes to their function, but how stem cells remodel their microenvironment remains an open-ended question. Herein, biomaterials-based systems and metabolic labeling were utilized to evaluate how skeletal muscle stem cells deposit extracellular matrix. Muscle stem cells and committed myoblasts were observed to generate less nascent matrix than muscle resident fibro-adipogenic progenitors. When cultured on substrates that matched the stiffness of physiological uninjured and injured muscles, the increased nascent matrix deposition was associated with stem cell activation. Reducing the ability to deposit nascent matrix in muscle stem cells attenuated function and mimicked impairments observed from muscle stem cells isolated from old aged muscles, which could be rescued with therapeutic supplementation of insulin-like growth factors. These results highlight how nascent matrix production is critical for maintaining healthy stem cell function.
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Affiliation(s)
- Pamela Duran
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Benjamin A. Yang
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eleanor Plaster
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Madeline Eiken
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Claudia Loebel
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Dept. of Materials Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carlos A. Aguilar
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Israel S, Seyfarth J, Nolte T, Drexler HCA, Fuellen G, Boiani M. Intracellular fraction of zona pellucida protein 3 is required for the oocyte-to-embryo transition in mice. Mol Hum Reprod 2023; 29:gaad038. [PMID: 37930049 PMCID: PMC10640839 DOI: 10.1093/molehr/gaad038] [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: 05/15/2023] [Revised: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
In oocyte biology, the zona pellucida has long been known to operate three extracellular functions downstream of the secretory pathway, namely, encasing the oocytes in ovarian follicles, mediating sperm-oocyte interaction, and preventing premature embryo contact with oviductal epithelium. The present study uncovers a fourth function that is fundamentally distinct from the other three, being critical for embryonic cell survival in mice. Intriguingly, the three proteins of the mouse zona pellucida (ZP1, ZP2, ZP3) were found abundantly present also inside the embryo 4 days after fertilization, as shown by mass spectrometry, immunoblotting, and immunofluorescence. Contrary to current understanding of the roles of ZP proteins, ZP3 was associated more with the cytoskeleton than with secretory vesicles in the subcortical region of metaphase II oocytes and zygotes, and was excluded from regions of cell-cell contact in cleavage-stage embryos. Trim-away-mediated knockdown of ZP3 in fertilized oocytes hampered the first zygotic cleavage, while ZP3 overexpression supported blastocyst formation. Transcriptome analysis of ZP3-knockdown embryos pointed at defects of cytoplasmic translation in the context of embryonic genome activation. This conclusion was supported by reduced protein synthesis in the ZP3-knockdown and by the lack of cleavage arrest when Trim-away was postponed from the one-cell to the late two-cell stage. These data place constraints on the notion that zona proteins only operate in the extracellular space, revealing also a role during the oocyte-to-embryo transition. Ultimately, these data recruit ZP3 into the family of maternal factors that contribute to developmental competence of mouse oocytes.
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Affiliation(s)
- Steffen Israel
- Max Planck Institute for Molecular Biomedicine, Department of Cell & Tissue Dynamics, Muenster, Germany
| | - Julia Seyfarth
- Max Planck Institute for Molecular Biomedicine, Department of Cell & Tissue Dynamics, Muenster, Germany
| | - Thomas Nolte
- Max Planck Institute for Molecular Biomedicine, Department of Cell & Tissue Dynamics, Muenster, Germany
| | - Hannes C A Drexler
- Max Planck Institute for Molecular Biomedicine, Department of Cell & Tissue Dynamics, Muenster, Germany
| | - Georg Fuellen
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research (IBIMA), Rostock, Germany
| | - Michele Boiani
- Max Planck Institute for Molecular Biomedicine, Department of Cell & Tissue Dynamics, Muenster, Germany
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Tavakoli S, Evans A, Oommen OP, Creemers L, Nandi JB, Hilborn J, Varghese OP. Unveiling extracellular matrix assembly: Insights and approaches through bioorthogonal chemistry. Mater Today Bio 2023; 22:100768. [PMID: 37600348 PMCID: PMC10432810 DOI: 10.1016/j.mtbio.2023.100768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023] Open
Abstract
Visualizing cells, tissues, and their components specifically without interference with cellular functions, such as biochemical reactions, and cellular viability remains important for biomedical researchers worldwide. For an improved understanding of disease progression, tissue formation during development, and tissue regeneration, labeling extracellular matrix (ECM) components secreted by cells persists is required. Bioorthogonal chemistry approaches offer solutions to visualizing and labeling ECM constituents without interfering with other chemical or biological events. Although biorthogonal chemistry has been studied extensively for several applications, this review summarizes the recent advancements in using biorthogonal chemistry specifically for metabolic labeling and visualization of ECM proteins and glycosaminoglycans that are secreted by cells and living tissues. Challenges, limitations, and future directions surrounding biorthogonal chemistry involved in the labeling of ECM components are discussed. Finally, potential solutions for improvements to biorthogonal chemical approaches are suggested. This would provide theoretical guidance for labeling and visualization of de novo proteins and polysaccharides present in ECM that are cell-secreted for example during tissue remodeling or in vitro differentiation of stem cells.
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Affiliation(s)
- Shima Tavakoli
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Austin Evans
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Oommen P. Oommen
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Laura Creemers
- Department of Orthopedics, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Jharna Barman Nandi
- Department of Chemistry, Sarojini Naidu College for Women, 30 Jessore Road, Kolkata, 700028, India
| | - Jöns Hilborn
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Oommen P. Varghese
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
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Saleh AM, VanDyk TG, Jacobson KR, Khan SA, Calve S, Kinzer-Ursem TL. An Integrative Biology Approach to Quantify the Biodistribution of Azidohomoalanine In Vivo. Cell Mol Bioeng 2023; 16:99-115. [PMID: 37096070 PMCID: PMC10121978 DOI: 10.1007/s12195-023-00760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/22/2023] [Indexed: 04/26/2023] Open
Abstract
Background Identification and quantitation of newly synthesized proteins (NSPs) are critical to understanding protein dynamics in development and disease. Probing the nascent proteome can be achieved using non-canonical amino acids (ncAAs) to selectively label the NSPs utilizing endogenous translation machinery, which can then be quantitated with mass spectrometry. We have previously demonstrated that labeling the in vivo murine proteome is feasible via injection of azidohomoalanine (Aha), an ncAA and methionine (Met) analog, without the need for Met depletion. Aha labeling can address biological questions wherein temporal protein dynamics are significant. However, accessing this temporal resolution requires a more complete understanding of Aha distribution kinetics in tissues. Results To address these gaps, we created a deterministic, compartmental model of the kinetic transport and incorporation of Aha in mice. Model results demonstrate the ability to predict Aha distribution and protein labeling in a variety of tissues and dosing paradigms. To establish the suitability of the method for in vivo studies, we investigated the impact of Aha administration on normal physiology by analyzing plasma and liver metabolomes following various Aha dosing regimens. We show that Aha administration induces minimal metabolic alterations in mice. Conclusions Our results demonstrate that we can reproducibly predict protein labeling and that the administration of this analog does not significantly alter in vivo physiology over the course of our experimental study. We expect this model to be a useful tool to guide future experiments utilizing this technique to study proteomic responses to stimuli. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-023-00760-4.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Tyler G. VanDyk
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Kathryn R. Jacobson
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
| | - Shaheryar A. Khan
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
- Paul M. Rady Department of Mechanical Engineering, University of Colorado – Boulder, 1111 Engineering Center, 427 UCB, Boulder, CO 80309 USA
| | - Tamara L. Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr, West Lafayette, IN 47906 USA
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907 USA
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Lipp SN, Jacobson KR, Colling HA, Tuttle TG, Miles DT, McCreery KP, Calve S. Mechanical loading is required for initiation of extracellular matrix deposition at the developing murine myotendinous junction. Matrix Biol 2023; 116:28-48. [PMID: 36709857 PMCID: PMC10218368 DOI: 10.1016/j.matbio.2023.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023]
Abstract
The myotendinous junction (MTJ) contributes to the generation of motion by connecting muscle to tendon. At the adult MTJ, a specialized extracellular matrix (ECM) is thought to contribute to the mechanical integrity of the muscle-tendon interface, but the factors that influence MTJ formation during mammalian development are unclear. Here, we combined 3D imaging and proteomics with murine models in which muscle contractility and patterning are disrupted to resolve morphological and compositional changes in the ECM during MTJ development. We found that MTJ-specific ECM deposition can be initiated via static loading due to growth; however, it required cyclic loading to develop a mature morphology. Furthermore, the MTJ can mature without the tendon terminating into cartilage. Based on these results, we describe a model wherein MTJ development depends on mechanical loading but not insertion into an enthesis.
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Affiliation(s)
- Sarah N Lipp
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN 47907, United States; The Indiana University Medical Scientist/Engineer Training Program, Indianapolis, IN 46202, United States
| | - Kathryn R Jacobson
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907, United States
| | - Haley A Colling
- Department of Integrative Physiology, University of Colorado Boulder, 354 UCB, Boulder CO, 80309, United States
| | - Tyler G Tuttle
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, 1111 Engineering Dr, Boulder, CO 80309, United States
| | - Dalton T Miles
- Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, CO 80309, United States
| | - Kaitlin P McCreery
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, 1111 Engineering Dr, Boulder, CO 80309, United States
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN 47907, United States; Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, IN 47907, United States; Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, 1111 Engineering Dr, Boulder, CO 80309, United States.
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Hu M, Ling Z, Ren X. Extracellular matrix dynamics: tracking in biological systems and their implications. J Biol Eng 2022; 16:13. [PMID: 35637526 PMCID: PMC9153193 DOI: 10.1186/s13036-022-00292-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/11/2022] [Indexed: 12/23/2022] Open
Abstract
The extracellular matrix (ECM) constitutes the main acellular microenvironment of cells in almost all tissues and organs. The ECM not only provides mechanical support, but also mediates numerous biochemical interactions to guide cell survival, proliferation, differentiation, and migration. Thus, better understanding the everchanging temporal and spatial shifts in ECM composition and structure – the ECM dynamics – will provide fundamental insight regarding extracellular regulation of tissue homeostasis and how tissue states transition from one to another during diverse pathophysiological processes. This review outlines the mechanisms mediating ECM-cell interactions and highlights how changes in the ECM modulate tissue development and disease progression, using the lung as the primary model organ. We then discuss existing methodologies for revealing ECM compositional dynamics, with a particular focus on tracking newly synthesized ECM proteins. Finally, we discuss the ramifications ECM dynamics have on tissue engineering and how to implement spatial and temporal specific extracellular microenvironments into bioengineered tissues. Overall, this review communicates the current capabilities for studying native ECM dynamics and delineates new research directions in discovering and implementing ECM dynamics to push the frontier forward.
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Affiliation(s)
- Michael Hu
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Zihan Ling
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.
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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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10
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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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11
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Lipp SN, Jacobson KR, Hains DS, Schwarderer AL, Calve S. 3D Mapping Reveals a Complex and Transient Interstitial Matrix During Murine Kidney Development. J Am Soc Nephrol 2021; 32:1649-1665. [PMID: 33875569 PMCID: PMC8425666 DOI: 10.1681/asn.2020081204] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/20/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The extracellular matrix (ECM) is a network of proteins and glycosaminoglycans that provides structural and biochemical cues to cells. In the kidney, the ECM is critical for nephrogenesis; however, the dynamics of ECM composition and how it relates to 3D structure during development is unknown. METHODS Using embryonic day 14.5 (E14.5), E18.5, postnatal day 3 (P3), and adult kidneys, we fractionated proteins based on differential solubilities, performed liquid chromatography-tandem mass spectrometry, and identified changes in ECM protein content (matrisome). Decellularized kidneys were stained for ECM proteins and imaged in 3D using confocal microscopy. RESULTS We observed an increase in interstitial ECM that connects the stromal mesenchyme to the basement membrane (TNXB, COL6A1, COL6A2, COL6A3) between the embryo and adult, and a transient elevation of interstitial matrix proteins (COL5A2, COL12A1, COL26A1, ELN, EMID1, FBN1, LTBP4, THSD4) at perinatal time points. Basement membrane proteins critical for metanephric induction (FRAS1, FREM2) were highest in abundance in the embryo, whereas proteins necessary for integrity of the glomerular basement membrane (COL4A3, COL4A4, COL4A5, LAMB2) were more abundant in the adult. 3D visualization revealed a complex interstitial matrix that dramatically changed over development, including the perinatal formation of fibrillar structures that appear to support the medullary rays. CONCLUSION By correlating 3D ECM spatiotemporal organization with global protein abundance, we revealed novel changes in the interstitial matrix during kidney development. This new information regarding the ECM in developing kidneys offers the potential to inform the design of regenerative scaffolds that can guide nephrogenesis in vitro.
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Affiliation(s)
- Sarah N. Lipp
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
- Medical Scientist/Engineer Training Program, Indiana University, Indianapolis, Indiana
| | - Kathryn R. Jacobson
- Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana
| | - David S. Hains
- Department of Pediatrics, School of Medicine, Indiana University, Riley Children’s Hospital, Indianapolis, Indiana
| | - Andrew L. Schwarderer
- Department of Pediatrics, School of Medicine, Indiana University, Riley Children’s Hospital, Indianapolis, Indiana
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
- Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado
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12
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Narayanan N, Calve S. Extracellular matrix at the muscle - tendon interface: functional roles, techniques to explore and implications for regenerative medicine. Connect Tissue Res 2021; 62:53-71. [PMID: 32856502 PMCID: PMC7718290 DOI: 10.1080/03008207.2020.1814263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The muscle-tendon interface is an anatomically specialized region that is involved in the efficient transmission of force from muscle to tendon. Due to constant exposure to loading, the interface is susceptible to injury. Current treatment methods do not meet the socioeconomic demands of reduced recovery time without compromising the risk of reinjury, requiring the need for developing alternative strategies. The extracellular matrix (ECM) present in muscle, tendon, and at the interface of these tissues consists of unique molecules that play significant roles in homeostasis and repair. Better, understanding the function of the ECM during development, injury, and aging has the potential to unearth critical missing information that is essential for accelerating the repair at the muscle-tendon interface. Recently, advanced techniques have emerged to explore the ECM for identifying specific roles in musculoskeletal biology. Simultaneously, there is a tremendous increase in the scope for regenerative medicine strategies to address the current clinical deficiencies. Advancements in ECM research can be coupled with the latest regenerative medicine techniques to develop next generation therapies that harness ECM for treating defects at the muscle-tendon interface. The current work provides a comprehensive review on the role of muscle and tendon ECM to provide insights about the role of ECM in the muscle-tendon interface and discusses the latest research techniques to explore the ECM to gathered information for developing regenerative medicine strategies.
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Affiliation(s)
- Naagarajan Narayanan
- Paul M. Rady Department of Mechanical Engineering, University of Colorado – Boulder, 1111 Engineering Drive, Boulder, Colorado 80309 – 0427
| | - Sarah Calve
- Paul M. Rady Department of Mechanical Engineering, University of Colorado – Boulder, 1111 Engineering Drive, Boulder, Colorado 80309 – 0427
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13
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Galindo Casas M, Stargardt P, Mairhofer J, Wiltschi B. Decoupling Protein Production from Cell Growth Enhances the Site-Specific Incorporation of Noncanonical Amino Acids in E. coli. ACS Synth Biol 2020; 9:3052-3066. [PMID: 33150786 DOI: 10.1021/acssynbio.0c00298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The site-specific incorporation of noncanonical amino acids (ncAAs) into proteins by amber stop codon suppression has become a routine method in academic laboratories. This approach requires an amber suppressor tRNACUA to read the amber codon and an aminoacyl-tRNA synthetase to charge the tRNACUA with the ncAA. However, a major drawback is the low yield of the mutant protein in comparison to the wild type. This effect primarily results from the competition of release factor 1 with the charged suppressor tRNACUA for the amber codon at the A-site of the ribosome. A number of laboratories have attempted to improve the incorporation efficiency of ncAAs with moderate results. We aimed at increasing the efficiency to produce high yields of ncAA-functionalized proteins in a scalable setting for industrial application. To do this, we inserted an ncAA into the enhanced green fluorescent protein and an antibody mimetic molecule using an industrial E. coli strain, which produces recombinant proteins independent of cell growth. The controlled decoupling of recombinant protein production from cell growth considerably increased the incorporation of the ncAA, producing substantially higher protein yields versus the reference E. coli strain BL21(DE3). The target proteins were expressed at high levels, and the ncAA was efficiently incorporated with excellent fidelity while the protein function was preserved.
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Affiliation(s)
- Meritxell Galindo Casas
- acib − Austrian Center of Industrial Biotechnology, 8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | | | | | - Birgit Wiltschi
- acib − Austrian Center of Industrial Biotechnology, 8010 Graz, Austria
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14
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Chung CZ, Amikura K, Söll D. Using Genetic Code Expansion for Protein Biochemical Studies. Front Bioeng Biotechnol 2020; 8:598577. [PMID: 33195171 PMCID: PMC7604363 DOI: 10.3389/fbioe.2020.598577] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/29/2020] [Indexed: 01/31/2023] Open
Abstract
Protein identification has gone beyond simply using protein/peptide tags and labeling canonical amino acids. Genetic code expansion has allowed residue- or site-specific incorporation of non-canonical amino acids into proteins. By taking advantage of the unique properties of non-canonical amino acids, we can identify spatiotemporal-specific protein states within living cells. Insertion of more than one non-canonical amino acid allows for selective labeling that can aid in the identification of weak or transient protein-protein interactions. This review will discuss recent studies applying genetic code expansion for protein labeling and identifying protein-protein interactions and offer considerations for future work in expanding genetic code expansion methods.
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Affiliation(s)
- Christina Z. Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
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15
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Jacobson KR, Lipp S, Acuna A, Leng Y, Bu Y, Calve S. Comparative Analysis of the Extracellular Matrix Proteome across the Myotendinous Junction. J Proteome Res 2020; 19:3955-3967. [PMID: 32830507 DOI: 10.1021/acs.jproteome.0c00248] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The myotendinous junction is a highly interdigitated interface designed to transfer muscle-generated force to tendon. Understanding how this interface is formed and organized, as well as identifying tendon- and muscle-specific extracellular matrix (ECM), is critical for designing effective regenerative therapies to restore functionality to damaged muscle-tendon units. However, a comparative analysis of the ECM proteome across this interface has not been conducted. The goal of this study was to resolve the distribution of ECM proteins that are uniformly expressed as well as those specific to each of the muscle, tendon, and junction tissues. The soleus muscles from 5-month-old wild-type C57BL/6 mice were harvested and dissected into the central muscle (M) away from tendon, the junction between muscle and tendon (J) and the tendon (T). Tissues were processed by either homogenizing in guanidine hydrochloride or fractionating to isolate the ECM from more soluble intracellular components and then analyzed using liquid chromatography-tandem mass spectrometry. Overall, we found that both tissue processing methods generated similar ECM profiles. Many ECM were found across the muscle-tendon unit, including type I collagen and associated fibril-regulating proteins. The ECM identified exclusively in M were primarily related to the basal lamina, whereas those specific to T and J tissue included thrombospondins and other matricellular ECM. Type XXII collagen (COL22A1) was restricted to J, and we identified COL5A3 as a potential marker of the muscle-tendon interface. Immunohistochemical analysis of key proteins confirmed the restriction of some basal lamina proteins to M, tenascin-C to T, and COL22A1 to J. COL5A3, PRELP, and POSTN were visualized in the tissue surrounding the junction, suggesting that these proteins play a role in stabilizing the interface. This comparative map provides a guide for tissue-specific ECM that can facilitate the spatial visualization of M, J, and T tissues and inform musculoskeletal regenerative therapies.
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Affiliation(s)
- Kathryn R Jacobson
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, Indiana 47907, United States
| | - Sarah Lipp
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Andrea Acuna
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Yue Leng
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Ye Bu
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Sarah Calve
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, Indiana 47907, United States.,Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States.,Paul M. Rady Department of Mechanical Engineering, University of Colorado-Boulder, 1111 Engineering Center, 427 UCB, Boulder, Colorado 80309, United States
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16
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Ocken AR, Ku MM, Kinzer-Ursem TL, Calve S. Perlecan Knockdown Significantly Alters Extracellular Matrix Composition and Organization During Cartilage Development. Mol Cell Proteomics 2020; 19:1220-1235. [PMID: 32381549 PMCID: PMC7338092 DOI: 10.1074/mcp.ra120.001998] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/05/2020] [Indexed: 02/05/2023] Open
Abstract
Perlecan is a critical proteoglycan found in the extracellular matrix (ECM) of cartilage. In healthy cartilage, perlecan regulates cartilage biomechanics and we previously demonstrated perlecan deficiency leads to reduced cellular and ECM stiffness in vivo This change in mechanics may lead to the early onset osteoarthritis seen in disorders resulting from perlecan knockdown such as Schwartz-Jampel syndrome (SJS). To identify how perlecan knockdown affects the material properties of developing cartilage, we used imaging and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to study the ECM in a murine model of SJS, Hspg2C1532Y-Neo Perlecan knockdown led to defective pericellular matrix formation, whereas the abundance of bulk ECM proteins, including many collagens, increased. Post-translational modifications and ultrastructure of collagens were not significantly different; however, LC-MS/MS analysis showed more protein was secreted by Hspg2C1532Y-Neo cartilage in vitro, suggesting that the incorporation of newly synthesized ECM was impaired. In addition, glycosaminoglycan deposition was atypical, which may explain the previously observed decrease in mechanics. Overall, these findings provide insight into the influence of perlecan on functional cartilage assembly and the progression of osteoarthritis in SJS.
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Affiliation(s)
- Alexander R Ocken
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Madeline M Ku
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | | | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana.
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