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Gomes FA, Souza Junior DR, Massafera MP, Ronsein GE. Robust assessment of sample preparation protocols for proteomics of cells and tissues. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141030. [PMID: 38944097 DOI: 10.1016/j.bbapap.2024.141030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
In proteomic studies, the reliability and reproducibility of results hinge on well-executed protein extraction and digestion protocols. Here, we systematically compared three established digestion methods for macrophages, namely filter-assisted sample preparation (FASP), in-solution, and in-gel digestion protocols. We also compared lyophilization and manual lysis for liver tissue protein extraction, each of them tested using either sodium deoxycholate (SDC)- or RIPA-based lysis buffer. For the macrophage cell line, FASP using passivated filter units outperformed the other tested methods regarding the number of identified peptides and proteins. However, a careful standardization has shown that all three methods can yield robust results across a wide range of starting material (even starting with 1 μg of proteins). Importantly, inter and intra-day coefficients of variance (CVs) were determined for all sample preparation protocols. Thus, the median inter-day CVs for in-solution, in-gel and FASP protocols were respectively 10, 8 and 9%, very similar to the median CVs obtained for the intra-day analysis (9, 8 and 8%, respectively). Moreover, FASP digestion presented 80% of proteins with a CV lower than 25%, followed closely by in-gel digestion (78%) and in-solution sample preparation (72%) protocols. For tissue proteomics, both manual lysis and lyophilization presented similar proteome coverage and reproducibility, but the efficiency of protein extraction depended on the lysis buffer used, with RIPA buffer showing better results. In conclusion, although each sample preparation method has its own particularity, they are all suited for successful proteomic experiments if a careful standardization of the sample preparation workflow is carried out.
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Affiliation(s)
- Francielle Aguiar Gomes
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | | | - Graziella Eliza Ronsein
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
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2
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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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3
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Halstenbach T, Topitsch A, Schilling O, Iglhaut G, Nelson K, Fretwurst T. Mass spectrometry-based proteomic applications in dental implants research. Proteomics Clin Appl 2024; 18:e2300019. [PMID: 38342588 DOI: 10.1002/prca.202300019] [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: 07/21/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 02/13/2024]
Abstract
Dental implants have been established as successful treatment options for missing teeth with steadily increasing demands. Today, the primary areas of research in dental implantology revolve around osseointegration, soft and hard tissue grafting as well as peri-implantitis diagnostics, prevention, and treatment. This review provides a comprehensive overview of the current literature on the application of MS-based proteomics in dental implant research, highlights how explorative proteomics provided insights into the biology of peri-implant soft and hard tissues and how proteomics facilitated the stratification between healthy and diseased implants, enabling the identification of potential new diagnostic markers. Additionally, this review illuminates technical aspects, and provides recommendations for future study designs based on the current evidence.
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Affiliation(s)
- Tim Halstenbach
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Annika Topitsch
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Gerhard Iglhaut
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Katja Nelson
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral- and Craniomaxillofacial Surgery/Translational Implantology, Division of Regenerative Oral Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
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4
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Schurman CA, Kaya S, Dole N, Luna NMM, Castillo N, Potter R, Rose JP, Bons J, King CD, Burton JB, Schilling B, Melov S, Tang S, Schaible E, Alliston T. Aging impairs the osteocytic regulation of collagen integrity and bone quality. Bone Res 2024; 12:13. [PMID: 38409111 PMCID: PMC10897167 DOI: 10.1038/s41413-023-00303-7] [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: 05/22/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 02/28/2024] Open
Abstract
Poor bone quality is a major factor in skeletal fragility in elderly individuals. The molecular mechanisms that establish and maintain bone quality, independent of bone mass, are unknown but are thought to be primarily determined by osteocytes. We hypothesize that the age-related decline in bone quality results from the suppression of osteocyte perilacunar/canalicular remodeling (PLR), which maintains bone material properties. We examined bones from young and aged mice with osteocyte-intrinsic repression of TGFβ signaling (TβRIIocy-/-) that suppresses PLR. The control aged bone displayed decreased TGFβ signaling and PLR, but aging did not worsen the existing PLR suppression in male TβRIIocy-/- bone. This relationship impacted the behavior of collagen material at the nanoscale and tissue scale in macromechanical tests. The effects of age on bone mass, density, and mineral material behavior were independent of osteocytic TGFβ. We determined that the decline in bone quality with age arises from the loss of osteocyte function and the loss of TGFβ-dependent maintenance of collagen integrity.
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Affiliation(s)
- Charles A Schurman
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Serra Kaya
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Neha Dole
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Nadja M Maldonado Luna
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA
| | - Natalia Castillo
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Ryan Potter
- Washington University in St Louis, Department of Orthopedics, St. Louis, MO, 63130, USA
| | - Jacob P Rose
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Jordan B Burton
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Simon Tang
- Washington University in St Louis, Department of Orthopedics, St. Louis, MO, 63130, USA
| | - Eric Schaible
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA.
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA.
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5
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Li T, Kambanis J, Sorenson TL, Sunde M, Shen Y. From Fundamental Amyloid Protein Self-Assembly to Development of Bioplastics. Biomacromolecules 2024; 25:5-23. [PMID: 38147506 PMCID: PMC10777412 DOI: 10.1021/acs.biomac.3c01129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023]
Abstract
Proteins can self-assemble into a range of nanostructures as a result of molecular interactions. Amyloid nanofibrils, as one of them, were first discovered with regard to the relevance of neurodegenerative diseases but now have been exploited as building blocks to generate multiscale materials with designed functions for versatile applications. This review interconnects the mechanism of amyloid fibrillation, the current approaches to synthesizing amyloid protein-based materials, and the application in bioplastic development. We focus on the fundamental structures of self-assembled amyloid fibrils and how external factors can affect protein aggregation to optimize the process. Protein self-assembly is essentially the autonomous congregation of smaller protein units into larger, organized structures. Since the properties of the self-assembly can be manipulated by changing intrinsic factors and external conditions, protein self-assembly serves as an excellent building block for bioplastic development. Building on these principles, general processing methods and pathways from raw protein sources to mature state materials are proposed, providing a guide for the development of large-scale production. Additionally, this review discusses the diverse properties of protein-based amyloid nanofibrils and how they can be utilized as bioplastics. The economic feasibility of the protein bioplastics is also compared to conventional plastics in large-scale production scenarios, supporting their potential as sustainable bioplastics for future applications.
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Affiliation(s)
- Tianchen Li
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Jordan Kambanis
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Timothy L. Sorenson
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Margaret Sunde
- School
of Medical Sciences and Sydney Nano, The
University of Sydney, Sydney NSW 2006, Australia
| | - Yi Shen
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
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6
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Rose JP, Schurman CA, King CD, Bons J, Patel SK, Burton JB, O’Broin A, Alliston T, Schilling B. Deep coverage and quantification of the bone proteome provides enhanced opportunities for new discoveries in skeletal biology and disease. PLoS One 2023; 18:e0292268. [PMID: 37816044 PMCID: PMC10564166 DOI: 10.1371/journal.pone.0292268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
Dysregulation of cell signaling in chondrocytes and in bone cells, such as osteocytes, osteoblasts, osteoclasts, and an elevated burden of senescent cells in cartilage and bone, are implicated in osteoarthritis (OA). Mass spectrometric analyses provides a crucial molecular tool-kit to understand complex signaling relationships in age-related diseases, such as OA. Here we introduce a novel mass spectrometric workflow to promote proteomic studies of bone. This workflow uses highly specialized steps, including extensive overnight demineralization, pulverization, and incubation for 72 h in 6 M guanidine hydrochloride and EDTA, followed by proteolytic digestion. Analysis on a high-resolution Orbitrap Eclipse and Orbitrap Exploris 480 mass spectrometer using Data-Independent Acquisition (DIA) provides deep coverage of the bone proteome, and preserves post-translational modifications, such as hydroxyproline. A spectral library-free quantification strategy, directDIA, identified and quantified over 2,000 protein groups (with ≥ 2 unique peptides) from calcium-rich bone matrices. Key components identified were proteins of the extracellular matrix (ECM), bone-specific proteins (e.g., secreted protein acidic and cysteine rich, SPARC, and bone sialoprotein 2, IBSP), and signaling proteins (e.g., transforming growth factor beta-2, TGFB2), and lysyl oxidase homolog 2 (LOXL2), an important protein in collagen crosslinking. Post-translational modifications (PTMs) were identified without the need for specific enrichment. This includes collagen hydroxyproline modifications, chemical modifications for collagen self-assembly and network formation. Multiple senescence factors were identified, such as complement component 3 (C3) protein of the complement system and many matrix metalloproteinases, that might be monitored during age-related bone disease progression. Our innovative workflow yields in-depth protein coverage and quantification strategies to discover underlying biological mechanisms of bone aging and to provide tools to monitor therapeutic interventions. These novel tools to monitor the bone proteome open novel horizons to investigate bone-specific diseases, many of which are age-related.
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Affiliation(s)
- Jacob P. Rose
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | | | - Christina D. King
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Sandip K. Patel
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Jordan B. Burton
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Amy O’Broin
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, Unted States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, CA, United States of America
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7
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Egashira K, Ino Y, Nakai Y, Ohira T, Akiyama T, Moriyama K, Yamamoto Y, Kimura M, Ryo A, Saito T, Inaba Y, Hirano H, Kumagai K, Kimura Y. Identification of gravity-responsive proteins in the femur of spaceflight mice using a quantitative proteomic approach. J Proteomics 2023; 288:104976. [PMID: 37482271 DOI: 10.1016/j.jprot.2023.104976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
Although the microgravity (μ-g) environment that astronauts encounter during spaceflight can cause severe acute bone loss, the molecular mechanism of this bone loss remains unclear. To investigate the gravity-response proteins involved in bone metabolism, it is important to comprehensively determine which proteins exhibit differential abundance associated with mechanical stimuli. However, comprehensive proteomic analysis using small bone samples is difficult because protein extraction in mineralized bone tissue is inefficient. Here, we established a high-sensitivity analysis system for mouse bone proteins using data-independent acquisition mass spectrometry. This system successfully detected 40 proteins in the femoral diaphysis showing differential abundance between mice raised in a μ-g environment, where the bone mass was reduced by gravity unloading, and mice raised in an artificial 1-gravity environment on the International Space Station. Additionally, 22 proteins, including noncollagenous bone matrix proteins, showed similar abundance between the two groups in the mandible, where bone mass was unaltered due to mastication stimuli, suggesting that these proteins are responsive to mechanical stimuli. One of these proteins, SPARCL1, is suggested to promote osteoclastogenesis induced by receptor activator of nuclear factor-κB ligand. We expect these findings to lead to new insights into the mechanisms of bone metabolism induced by mechanical stimuli. SIGNIFICANCE: We aimed to investigate the gravity-response proteins involved in bone metabolism. To this end, we established a comprehensive analysis system for mouse bone proteins using data-independent acquisition mass spectrometry, which is particularly useful in comprehensively analyzing the bone proteome using small sample volumes. In addition, a comprehensive proteomic analysis of the femoral diaphysis and mandible, which exhibit different degrees of bone loss in mice raised on the International Space Station, identified proteins that respond to mechanical stimuli. SPARCL1, a mechanical stimulus-responsive protein, was consequently suggested to be involved in osteoclast differentiation associated with bone remodeling. Our findings represent an important step toward elucidating the molecular mechanism of bone metabolism induced by mechanical stimuli.
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Affiliation(s)
- Kenji Egashira
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan; R&D Headquarters, LION Corporation, Tokyo 132-0035, Japan
| | - Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Yusuke Nakai
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Takashi Ohira
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan; Department of Physiology and Regenerative Medicine, Kindai University Faculty of Medicine, Osaka 589-8511, Japan
| | - Tomoko Akiyama
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Kayano Moriyama
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Yu Yamamoto
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan; R&D Headquarters, LION Corporation, Tokyo 132-0035, Japan
| | - Mitsuo Kimura
- R&D Headquarters, LION Corporation, Tokyo 132-0035, Japan
| | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Tomoyuki Saito
- Yokohama Brain and Spine Center, Yokohama 235-0012, Japan
| | - Yutaka Inaba
- Department of Orthopaedic Surgery, Yokohama City University, Yokohama 236-0004, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Ken Kumagai
- Department of Orthopaedic Surgery, Yokohama City University, Yokohama 236-0004, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan.
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8
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Feng K, Yu M, Lou X, Wang D, Wang L, Ren W. Multi-omics analysis of bone marrow mesenchymal stem cell differentiation differences in osteoporosis. Genomics 2023; 115:110668. [PMID: 37315871 DOI: 10.1016/j.ygeno.2023.110668] [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: 12/05/2022] [Revised: 05/28/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Osteoporosis is a systemic skeletal disease characterized by low bone mass and degradation of bone tissue microarchitecture, leading to enhanced bone fragility and increased fracture risk. However, the pathogenesis of osteoporosis is unclear. Our results showed that BMSCs dervied from ovariectomized rats had a higher capacity for osteogenesis and lipogenic differentiation compared to the control group. In the meantime, we identified a total of 205 differentially expressed proteins and 2294 differentially expressed genes in BMSCs isolated from ovariectomized rats by proteomics analysis and transcriptome sequencing, respectively. These differentially expressed proteins and genes were mainly involved in ECM-receptor interaction signaling pathway. We speculate that BMSCs derived from ovariectomized rats have a higher potential for bone formation because expression of ECM collagen or genes encoding collagen in the bone ECM in BMSCs isolated from ovariectomized rats are increased compared with that from control group, which provided the prerequisite for the increased bone turnover effect. To conclusion, our results may provid new ideas for further research on the pathogenesis of osteoporosis.
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Affiliation(s)
- Kai Feng
- The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Mengyuan Yu
- The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Xingyue Lou
- College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Duo Wang
- College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Lei Wang
- The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, Henan, China; Institutes of Health Central Plain of Xinxiang Medical University, Xinxiang 453003, Henan, China; College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, Henan, China.
| | - Wenjie Ren
- The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, Henan, China; Institutes of Health Central Plain of Xinxiang Medical University, Xinxiang 453003, Henan, China.
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9
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Johnston E, Buckley M. Age-Related Changes in Post-Translational Modifications of Proteins from Whole Male and Female Skeletal Elements. Molecules 2023; 28:4899. [PMID: 37446562 DOI: 10.3390/molecules28134899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
One of the key questions in forensic cases relates to some form of age inference, whether this is how old a crime scene is, when in time a particular crime was committed, or how old the victim was at the time of the crime. These age-related estimations are currently achieved through morphological methods with varying degrees of accuracy. As a result, biomolecular approaches are considered of great interest, with the relative abundances of several protein markers already recognized for their potential forensic significance; however, one of the greatest advantages of proteomic investigations over genomics ones is the wide range of post-translational modifications (PTMs) that make for a complex but highly dynamic resource of information. Here, we explore the abundance of several PTMs including the glycosylation, deamidation, and oxidation of several key proteins (collagen, fetuin A, biglycan, serum albumin, fibronectin and osteopontin) as being of potential value to the development of an age estimation tool worthy of further evaluation in forensic contexts. We find that glycosylations lowered into adulthood but deamidation and oxidation increased in the same age range.
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Affiliation(s)
- Elizabeth Johnston
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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10
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Zhang J, Lu Y, Zheng S, Ma Z, Wu M, Zhang Y, Cao H. Identification of donkey-hide gelatin and donkey-bone gelatin based on marker peptides. Lebensm Wiss Technol 2023; 182:114881. [DOI: 10.1016/j.lwt.2023.114881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
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11
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Sorvina A, Antoniou M, Esmaeili Z, Kochetkova M. Unusual Suspects: Bone and Cartilage ECM Proteins as Carcinoma Facilitators. Cancers (Basel) 2023; 15:cancers15030791. [PMID: 36765749 PMCID: PMC9913341 DOI: 10.3390/cancers15030791] [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: 12/31/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The extracellular matrix (ECM) is the complex three-dimensional network of fibrous proteins and proteoglycans that constitutes an essential part of every tissue to provide support for normal tissue homeostasis. Tissue specificity of the ECM in its topology and structure supports unique biochemical and mechanical properties of each organ. Cancers, like normal tissues, require the ECM to maintain multiple processes governing tumor development, progression and spread. A large body of experimental and clinical evidence has now accumulated to demonstrate essential roles of numerous ECM components in all cancer types. Latest findings also suggest that multiple tumor types express, and use to their advantage, atypical ECM components that are not found in the cancer tissue of origin. However, the understanding of cancer-specific expression patterns of these ECM proteins and their exact roles in selected tumor types is still sketchy. In this review, we summarize the latest data on the aberrant expression of bone and cartilage ECM proteins in epithelial cancers and their specific functions in the pathogenesis of carcinomas and discuss future directions in exploring the utility of this selective group of ECM components as future drug targets.
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12
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Ferreira MJS, Mancini FE, Humphreys PA, Ogene L, Buckley M, Domingos MAN, Kimber SJ. Pluripotent stem cells for skeletal tissue engineering. Crit Rev Biotechnol 2022; 42:774-793. [PMID: 34488516 DOI: 10.1080/07388551.2021.1968785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here, we review the use of human pluripotent stem cells for skeletal tissue engineering. A number of approaches have been used for generating cartilage and bone from both human embryonic stem cells and induced pluripotent stem cells. These range from protocols relying on intrinsic cell interactions and signals from co-cultured cells to those attempting to recapitulate the series of steps occurring during mammalian skeletal development. The importance of generating authentic tissues rather than just differentiated cells is emphasized and enabling technologies for doing this are reported. We also review the different methods for characterization of skeletal cells and constructs at the tissue and single-cell level, and indicate newer resources not yet fully utilized in this field. There have been many challenges in this research area but the technologies to overcome these are beginning to appear, often adopted from related fields. This makes it more likely that cost-effective and efficacious human pluripotent stem cell-engineered constructs may become available for skeletal repair in the near future.
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Affiliation(s)
- Miguel J S Ferreira
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
| | - Fabrizio E Mancini
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul A Humphreys
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Leona Ogene
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Marco A N Domingos
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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13
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Bolamperti S, Villa I, Rubinacci A. Bone remodeling: an operational process ensuring survival and bone mechanical competence. Bone Res 2022; 10:48. [PMID: 35851054 PMCID: PMC9293977 DOI: 10.1038/s41413-022-00219-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 05/02/2022] [Accepted: 05/15/2022] [Indexed: 12/12/2022] Open
Abstract
Bone remodeling replaces old and damaged bone with new bone through a sequence of cellular events occurring on the same surface without any change in bone shape. It was initially thought that the basic multicellular unit (BMU) responsible for bone remodeling consists of osteoclasts and osteoblasts functioning through a hierarchical sequence of events organized into distinct stages. However, recent discoveries have indicated that all bone cells participate in BMU formation by interacting both simultaneously and at different differentiation stages with their progenitors, other cells, and bone matrix constituents. Therefore, bone remodeling is currently considered a physiological outcome of continuous cellular operational processes optimized to confer a survival advantage. Bone remodeling defines the primary activities that BMUs need to perform to renew successfully bone structural units. Hence, this review summarizes the current understanding of bone remodeling and future research directions with the aim of providing a clinically relevant biological background with which to identify targets for therapeutic strategies in osteoporosis.
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Affiliation(s)
- Simona Bolamperti
- Osteoporosis and Bone and Mineral Metabolism Unit, IRCCS San Raffaele Hospital, Via Olgettina 60, 20132, Milano, Italy
| | - Isabella Villa
- Osteoporosis and Bone and Mineral Metabolism Unit, IRCCS San Raffaele Hospital, Via Olgettina 60, 20132, Milano, Italy
| | - Alessandro Rubinacci
- Osteoporosis and Bone and Mineral Metabolism Unit, IRCCS San Raffaele Hospital, Via Olgettina 60, 20132, Milano, Italy.
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14
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Ntasi G, Palomo IR, Marino G, Piaz FD, Sirano F, Cappellini E, Birolo L, Petrone P. Molecular signatures written in bone proteins of 79 AD victims from Herculaneum and Pompeii. Sci Rep 2022; 12:8401. [PMID: 35624181 PMCID: PMC9142588 DOI: 10.1038/s41598-022-12042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/18/2022] [Indexed: 11/09/2022] Open
Abstract
An extensive proteomic analysis was performed on a set of 12 bones of human victims of the eruption that in AD 79 rapidly buried Pompeii and Herculaneum, allowing the detection of molecular signatures imprinted in the surviving protein components. Bone collagen survived the heat of the eruption, bearing a piece of individual biological history encoded in chemical modifications. Here we show that the human bone proteomes from Pompeii are more degraded than those from the inhabitants of Herculaneum, despite the latter were exposed to temperatures much higher than those experienced in Pompeii. The analysis of the specimens from Pompeii shows lower content of non-collagenous proteins, higher deamidation level and higher extent of collagen modification. In Pompeii, the slow decomposition of victims' soft tissues in the natural dry-wet hydrogeological soil cycles damaged their bone proteome more than what was experienced at Herculaneum by the rapid vanishing of body tissues from intense heat, under the environmental condition of a permanent waterlogged burial context. Results herein presented are the first proteomic analyses of bones exposed to eruptive conditions, but also delivered encouraging results for potential biomarkers that might also impact future development of forensic bone proteomics.
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Affiliation(s)
- Georgia Ntasi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Ismael Rodriguez Palomo
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gennaro Marino
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Department of Humanities, University Suor Orsola Benincasa, Naples, Italy
| | - Fabrizio Dal Piaz
- Department of Medicine, Surgery and Dentistry, University of Salerno, Fisciano, Salerno, Italy
| | | | - Enrico Cappellini
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy. .,Task Force Di Ateneo "Metodologie Analitiche per la Salvaguardia dei Beni Culturali", University of Naples Federico II, Naples, Italy.
| | - Pierpaolo Petrone
- Task Force Di Ateneo "Metodologie Analitiche per la Salvaguardia dei Beni Culturali", University of Naples Federico II, Naples, Italy.,Department of Advanced Biomedical Sciences, Departmental Section of Legal Medicine, Anatomy and Histology, University of Naples Federico II, Naples, Italy
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15
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Faraldi M, Mangiavini L, Conte C, Banfi G, Napoli N, Lombardi G. A novel methodological approach to simultaneously extract high-quality total RNA and proteins from cortical and trabecular bone. Open Biol 2022; 12:210387. [PMID: 35506206 PMCID: PMC9065961 DOI: 10.1098/rsob.210387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Molecular differences between cortical and trabecular bone, of relevance to understanding the pathophysiological basis of bone diseases, can be determined only through effective isolation methods for RNA and proteins. Here we present a TRIzol-based method, which combines bone pulverization and homogenization to extract simultaneously total RNA and proteins from human cortical and trabecular bone from the same carrot. RNA integrity and purity were determined as the 260/280 nm and 260/230 nm absorbance ratios and the 28S/18S rRNA ratio. Protein integrity and quality were evaluated by Coomassie blue staining. Reverse transcription quantitative polymerase chain reaction and immunoblotting for bone-specific genes and proteins were performed to verify the suitability of the isolated material in downstream applications. The 260/280 nm and 260/230 nm absorbance ratios were, on average, less than or equal to 1.8. Bands on agarose gel were consistent with intact RNA, with mean 28S/18S ratios of 1.68 ± 0.35 and 1.88 ± 0.10 for cortical and trabecular bone, respectively. Band patterns after Coomassie blue staining confirmed protein integrity. Successful gene and protein expression analysis, with relevant differences between the two compartments, highlighted the suitability of the material in downstream applications. The method presented here is appropriate and effective for the study of human bone.
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Affiliation(s)
- Martina Faraldi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Laura Mangiavini
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy,Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Caterina Conte
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan, Italy
| | - Giuseppe Banfi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy,Vita-Salute San Raffaele University, Milan, Italy
| | - Nicola Napoli
- Unit of Endocrinology and Diabetes, Departmental Faculty of Medicine and Surgery, Campus Bio-Medico University of Rome, Rome, Italy,Division of Bone and Mineral Diseases, Washington University in St Louis, St Louis, MO, USA
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy,Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland
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16
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Rose J, Basisty N, Zee T, Wehrfritz C, Bose N, Desprez PY, Kapahi P, Stoller M, Schilling B. Comprehensive proteomic quantification of bladder stone progression in a cystinuric mouse model using data-independent acquisitions. PLoS One 2022; 17:e0250137. [PMID: 35771811 PMCID: PMC9246204 DOI: 10.1371/journal.pone.0250137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/03/2022] [Indexed: 11/21/2022] Open
Abstract
Cystinuria is one of various disorders that cause biomineralization in the urinary system, including bladder stone formation in humans. It is most prevalent in children and adolescents and more aggressive in males. There is no cure, and only limited disease management techniques help to solubilize the stones. Recurrence, even after treatment, occurs frequently. Other than a buildup of cystine, little is known about factors involved in the formation, expansion, and recurrence of these stones. This study sought to define the growth of bladder stones, guided by micro-computed tomography imaging, and to profile dynamic stone proteome changes in a cystinuria mouse model. After bladder stones developed in vivo, they were harvested and separated into four developmental stages (sand, small, medium and large stone), based on their size. Data-dependent and data-independent acquisitions allowed deep profiling of stone proteomics. The proteomic signatures and pathways illustrated major changes as the stones grew. Stones initiate from a small nidus, grow outward, and show major enrichment in ribosomal proteins and factors related to coagulation and platelet degranulation, suggesting a major dysregulation in specific pathways that can be targeted for new therapeutic options.
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Affiliation(s)
- Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Tiffany Zee
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Cameron Wehrfritz
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Neelanjan Bose
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | | | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Marshall Stoller
- University of California San Francisco, San Francisco, CA, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, CA, United States of America
- * E-mail:
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17
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Bundgaard L, Åhrman E, Malmström J, Auf dem Keller U, Walters M, Jacobsen S. Effective protein extraction combined with data independent acquisition analysis reveals a comprehensive and quantifiable insight into the proteomes of articular cartilage and subchondral bone. Osteoarthritis Cartilage 2022; 30:137-146. [PMID: 34547431 DOI: 10.1016/j.joca.2021.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/31/2021] [Accepted: 09/13/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The objectives of this study was to establish a sensitive and reproducible method to map the cartilage and subchondral bone proteomes in quantitative terms, and mine the proteomes for proteins of particular interest in the pathogenesis of osteoarthritis (OA). The horse was used as a model animal. DESIGN Protein was extracted from articular cartilage and subchondral bone samples from three horses in triplicate by pressure cycling technology or ultrasonication. Digested proteins were analysed by data independent acquisition based mass spectrometry. Data was processed using a pre-established spectral library as reference database (FDR 1%). RESULTS We identified to our knowledge the hitherto most comprehensive quantitative cartilage (1758 proteins) and subchondral bone (1482 proteins) proteomes in all species presented to date. Both extraction methods were sensitive and reproducible and the high consistency of the identified proteomes (>97% overlap) indicated that both methods preserved the diversity among the extracted proteins. Proteome mining revealed a substantial number of quantifiable cartilage and bone matrix proteins and proteins involved in osteogenesis and bone remodeling, including ACAN, BGN, PRELP, FMOD, COMP, ACP5, BMP3, BMP6, BGLAP, TGFB1, IGF1, ALP, MMP3, and collagens. A number of proteins, including COMP and TNN, were identified in different protein isoforms with potential unique biological roles. CONCLUSION We have successfully developed two sensitive and reproducible non-species specific workflows enabling a comprehensive quantitative insight into the proteomes of cartilage and subchondral bone. This facilitates the prospect of investigating the molecular events at the osteochondral unit in the pathogenesis of OA in future projects.
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Affiliation(s)
- L Bundgaard
- Section of Medicine and Surgery, Department of Veterinary Clinical Sciences, University of Copenhagen, 2630 Taastrup, Denmark. Section for Protein Science and Biotherapeutics, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - E Åhrman
- Division of Infection Medicine Proteomics, Department of Clinical Sciences, Lund University, Lund 221 84, Sweden.
| | - J Malmström
- Division of Infection Medicine Proteomics, Department of Clinical Sciences, Lund University, Lund 221 84, Sweden.
| | - U Auf dem Keller
- Section for Protein Science and Biotherapeutics, DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - M Walters
- Section of Medicine and Surgery, Department of Veterinary Clinical Sciences, University of Copenhagen, 2630 Taastrup, Denmark.
| | - S Jacobsen
- Section of Medicine and Surgery, Department of Veterinary Clinical Sciences, University of Copenhagen, 2630 Taastrup, Denmark.
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18
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Abood A, Farber CR. Using "-omics" Data to Inform Genome-wide Association Studies (GWASs) in the Osteoporosis Field. Curr Osteoporos Rep 2021; 19:369-380. [PMID: 34125409 PMCID: PMC8767463 DOI: 10.1007/s11914-021-00684-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2021] [Indexed: 01/12/2023]
Abstract
PURPOSE OF REVIEW Osteoporosis constitutes a major societal health problem. Genome-wide association studies (GWASs) have identified over 1100 loci influencing bone mineral density (BMD); however, few of the causal genes have been identified. Here, we review approaches that use "-omics" data and genetic- and systems genetics-based analytical strategies to facilitate causal gene discovery. RECENT FINDINGS The bone field is beginning to adopt approaches that are commonplace in other disease disciplines. The slower progress has been due in part to the lack of large-scale "omics" data on bone and bone cells. This is however changing, and approaches such as eQTL colocalization, transcriptome-wide association studies (TWASs), network, and integrative approaches are beginning to provide significant insight into the genes responsible for BMD GWAS associations. The use of "-omics" data to inform BMD GWASs has increased in recent years, leading to the identification of novel regulators of BMD in humans. The ultimate goal will be to use this information to develop more effective therapies to treat and ultimately prevent osteoporosis.
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Affiliation(s)
- Abdullah Abood
- Center for Public Health Genomics, University of Virginia, 800717, Charlottesville, VA, 22908, USA
- Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia, 800717, Charlottesville, VA, 22908, USA.
- Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA.
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19
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Proteomic and genomic analysis of acid dentin lysate with focus on TGF-β signaling. Sci Rep 2021; 11:12247. [PMID: 34112817 PMCID: PMC8192760 DOI: 10.1038/s41598-021-89996-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/19/2021] [Indexed: 02/05/2023] Open
Abstract
Particulate autologous tooth roots are increasingly used for alveolar bone augmentation; however, the proteomic profile of acid dentin lysate and the respective cellular response have not been investigated. Here we show that TGF-β1 is among the 226 proteins of acid dentin lysate (ADL) prepared from porcine teeth. RNA sequencing identified 231 strongly regulated genes when gingival fibroblasts were exposed to ADL. Out of these genes, about one third required activation of the TGF-β receptor type I kinase including interleukin 11 (IL11) and NADPH oxidase 4 (NOX4). Reverse transcription-quantitative polymerase chain reaction and immunoassay confirmed the TGF-β-dependent expression of IL11 and NOX4. The activation of canonical TGF-β signaling by ADL was further confirmed by the phosphorylation of Smad3 and translocation of Smad2/3, using Western blot and immunofluorescence staining, respectively. Finally, we showed that TGF-β activity released from dentin by acid lysis adsorbs to titanium and collagen membranes. These findings suggest that dentin particles are a rich source of TGF-β causing a major response of gingival fibroblasts.
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20
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Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
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21
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Bayer J, Vaghela R, Drechsler S, Osuchowski MF, Erben RG, Andrukhova O. The bone is the major source of high circulating intact fibroblast growth factor-23 in acute murine polymicrobial sepsis induced by cecum ligation puncture. PLoS One 2021; 16:e0251317. [PMID: 33989306 PMCID: PMC8121358 DOI: 10.1371/journal.pone.0251317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
Fibroblast growth factor-23 (FGF23), a bone-produced hormone, plays a critical role in mineral homeostasis. Human diseases associated with excessive intact circulating FGF23 (iFGF23) result in hypophosphatemia and low vitamin D hormone in patients with normal kidney function. In addition, there is accumulating evidence linking FGF23 with inflammation. Based on these studies and the frequent observation of hypophosphatemia among septic patients, we sought to elucidate further the relationship between FGF23 and mineral homeostasis in a clinically relevant murine polymicrobial sepsis model. Medium-severity sepsis was induced by cecum ligation puncture (CLP) in adult CD-1 mice of both sexes. Healthy CD-1 mice (without CLP) were used as controls. Forty-eight hours post-CLP, spontaneous urine was collected, and serum, organs and bones were sampled at necropsy. Serum iFGF23 increased ~20-fold in CLP compared to control mice. FGF23 protein concentration was increased in the bones, but not in spleen or liver of CLP mice. Despite the ~20-fold iFGF23 increase, we did not observe any significant changes in mineral homeostasis or parathyroid hormone levels in the blood of CLP animals. Urinary excretion of phosphate, calcium, and sodium remained unchanged in male CLP mice, whereas female CLP mice exhibited lower urinary calcium excretion, relative to healthy controls. In line with renal FGF23 resistance, expression of phosphate-, calcium- and sodium-transporting proteins did not show consistent changes in the kidneys of male and female CLP mice. Renal expression of the co-receptor αKlotho was downregulated in female, but not in male CLP mice. In conclusion, our data demonstrate that the dramatic, sex-independent rise in serum iFGF23 post-CLP was mainly caused by an upregulation of FGF23 secretion in the bone. Surprisingly, the upsurge in circulating iFGF23 did not alter humoral mineral homeostasis in the acutely septic mice. Hence, the biological function of elevated FGF23 in sepsis remains unclear and warrants further studies.
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Affiliation(s)
- Jessica Bayer
- Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ravikumar Vaghela
- Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Susanne Drechsler
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in the AUVA Research Center, Vienna, Austria
| | - Marcin F. Osuchowski
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in the AUVA Research Center, Vienna, Austria
| | - Reinhold G. Erben
- Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
- * E-mail:
| | - Olena Andrukhova
- Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
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22
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Ross DS, Yeh TH, King S, Mathers J, Rybchyn MS, Neist E, Cameron M, Tacey A, Girgis CM, Levinger I, Mason RS, Brennan-Speranza TC. Distinct Effects of a High Fat Diet on Bone in Skeletally Mature and Developing Male C57BL/6J Mice. Nutrients 2021; 13:nu13051666. [PMID: 34068953 PMCID: PMC8157111 DOI: 10.3390/nu13051666] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 01/01/2023] Open
Abstract
Increased risks of skeletal fractures are common in patients with impaired glucose handling and type 2 diabetes mellitus (T2DM). The pathogenesis of skeletal fragility in these patients remains ill-defined as patients present with normal to high bone mineral density. With increasing cases of glucose intolerance and T2DM it is imperative that we develop an accurate rodent model for further investigation. We hypothesized that a high fat diet (60%) administered to developing male C57BL/6J mice that had not reached skeletal maturity would over represent bone microarchitectural implications, and that skeletally mature mice would better represent adult-onset glucose intolerance and the pre-diabetes phenotype. Two groups of developing (8 week) and mature (12 week) male C57BL/6J mice were placed onto either a normal chow (NC) or high fat diet (HFD) for 10 weeks. Oral glucose tolerance tests were performed throughout the study period. Long bones were excised and analysed for ex vivo biomechanical testing, micro-computed tomography, 2D histomorphometry and gene/protein expression analyses. The HFD increased fasting blood glucose and significantly reduced glucose tolerance in both age groups by week 7 of the diets. The HFD reduced biomechanical strength, both cortical and trabecular indices in the developing mice, but only affected cortical outcomes in the mature mice. Similar results were reflected in the 2D histomorphometry. Tibial gene expression revealed decreased bone formation in the HFD mice of both age groups, i.e., decreased osteocalcin expression and increased sclerostin RNA expression. In the mature mice only, while the HFD led to a non-significant reduction in runt-related transcription factor 2 (Runx2) RNA expression, this decrease became significant at the protein level in the femora. Our mature HFD mouse model more accurately represents late-onset impaired glucose tolerance/pre-T2DM cases in humans and can be used to uncover potential insights into reduced bone formation as a mechanism of skeletal fragility in these patients.
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Affiliation(s)
- Dean S. Ross
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
| | - Tzu-Hsuan Yeh
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
| | - Shalinie King
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
- Faculty of Medicine and Health, School of Dentistry, University of Sydney, Sydney 2006, Australia
| | - Julia Mathers
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
| | - Mark S. Rybchyn
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
| | - Elysia Neist
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
| | - Melissa Cameron
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
| | - Alexander Tacey
- Institute for Health and Sport (IHES), Victoria University, Melbourne 3011, Australia; (A.T.); (I.L.)
- Australian Institute for Musculoskeletal Science (AIMSS), University of Melbourne and Western Health, St Albans 3021, Australia
| | - Christian M. Girgis
- Department of Diabetes and Endocrinology, Westmead Hospital, Sydney 2145, Australia;
- Department of Endocrinology, Royal North Shore Hospital, Sydney 2065, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia
| | - Itamar Levinger
- Institute for Health and Sport (IHES), Victoria University, Melbourne 3011, Australia; (A.T.); (I.L.)
- Australian Institute for Musculoskeletal Science (AIMSS), University of Melbourne and Western Health, St Albans 3021, Australia
| | - Rebecca S. Mason
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
| | - Tara C. Brennan-Speranza
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Sydney 2006, Australia; (D.S.R.); (T.-H.Y.); (S.K.); (J.M.); (M.S.R.); (E.N.); (M.C.); (R.S.M.)
- Faculty of Medicine and Health, School of Public Health, University of Sydney, Sydney 2006, Australia
- Correspondence: ; Tel.: +61-2-9351-4099
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Alcorta-Sevillano N, Macías I, Infante A, Rodríguez CI. Deciphering the Relevance of Bone ECM Signaling. Cells 2020; 9:E2630. [PMID: 33297501 PMCID: PMC7762413 DOI: 10.3390/cells9122630] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Bone mineral density, a bone matrix parameter frequently used to predict fracture risk, is not the only one to affect bone fragility. Other factors, including the extracellular matrix (ECM) composition and microarchitecture, are of paramount relevance in this process. The bone ECM is a noncellular three-dimensional structure secreted by cells into the extracellular space, which comprises inorganic and organic compounds. The main inorganic components of the ECM are calcium-deficient apatite and trace elements, while the organic ECM consists of collagen type I and noncollagenous proteins. Bone ECM dynamically interacts with osteoblasts and osteoclasts to regulate the formation of new bone during regeneration. Thus, the composition and structure of inorganic and organic bone matrix may directly affect bone quality. Moreover, proteins that compose ECM, beyond their structural role have other crucial biological functions, thanks to their ability to bind multiple interacting partners like other ECM proteins, growth factors, signal receptors and adhesion molecules. Thus, ECM proteins provide a complex network of biochemical and physiological signals. Herein, we summarize different ECM factors that are essential to bone strength besides, discussing how these parameters are altered in pathological conditions related with bone fragility.
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Affiliation(s)
| | | | - Arantza Infante
- Stem Cells and Cell Therapy Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Plaza de Cruces S/N, Barakaldo, 48903 Bizkaia, Spain; (N.A.-S.); (I.M.)
| | - Clara I. Rodríguez
- Stem Cells and Cell Therapy Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Plaza de Cruces S/N, Barakaldo, 48903 Bizkaia, Spain; (N.A.-S.); (I.M.)
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24
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Lanigan LT, Mackie M, Feine S, Hublin JJ, Schmitz RW, Wilcke A, Collins MJ, Cappellini E, Olsen JV, Taurozzi AJ, Welker F. Multi-protease analysis of Pleistocene bone proteomes. J Proteomics 2020; 228:103889. [DOI: 10.1016/j.jprot.2020.103889] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/08/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
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25
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Emami A, Talaei-Khozani T, Vojdani Z, Zarei Fard N. Comparative assessment of the efficiency of various decellularization agents for bone tissue engineering. J Biomed Mater Res B Appl Biomater 2020; 109:19-32. [PMID: 32627321 DOI: 10.1002/jbm.b.34677] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/16/2020] [Accepted: 06/16/2020] [Indexed: 12/23/2022]
Abstract
Bone regeneration can be possible through grafts or engineered bone replacement when bone defects are larger than the critical size. Decellularized bone extracellular matrix (ECM) is an alternative that is able to accelerate tissue regeneration, while decellularization protocols influence engineered bone quality. The objective of this study was to compare the quality of decellularized bone produced through different methods. Four decellularization methods were employed using (a) sodium lauryl ether sulfate (SLES), (b) sodium dodecyl sulfate (SDS) 0.5%, (c) SDS 1% and (d) trypsin/EDTA. All samples were then washed in triton X-100. DNA quantification, hematoxylin and eosin, and Hoechst staining showed that although DNA was depleted in all scaffolds, treatment with SLES led to a significantly lower DNA content. Glycosaminoglycan quantification, Raman confocal microscopy, alcian blue and PAS staining exhibited higher carbohydrate retention in the scaffolds treated with SLES and SDS 0.5%. Raman spectra, scanning electron microscopy and trichrom Masson staining showed more collagen content in SLES and SDS-treated scaffolds compared to trypsin/EDTA-treated scaffolds. Therefore, although trypsin/EDTA could efficiently decellularize the scaffolds, it washed out the ECM contents. Also, both MTT and attachment tests showed a significantly higher cell viability in SLES-treated scaffolds. Raman spectra revealed that while the first washing procedure did not remove SLES traces in the scaffolds, excessive washing reduced ECM contents. In conclusion, SLES and, to a lesser degree, SDS 0.5% protocols could efficiently preserve ultrastructure and ECM constituents of decellularized bone tissue and can thus be suggested as nontoxic and safe protocols for bone regeneration.
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Affiliation(s)
- Asrin Emami
- Department of Anatomical Sciences, School of Medicine, Laboratory for Stem Cell Research, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Tahereh Talaei-Khozani
- Department of Anatomical Sciences, School of Medicine, Laboratory for Stem Cell Research, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Vojdani
- Department of Anatomical Sciences, School of Medicine, Laboratory for Stem Cell Research, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nehleh Zarei Fard
- Department of Anatomical Sciences, School of Medicine, Laboratory for Stem Cell Research, Shiraz University of Medical Sciences, Shiraz, Iran
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26
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Busso CS, Guidry JJ, Gonzalez JJ, Zorba V, Son LS, Winsauer PJ, Walvekar RR. A comprehensive analysis of sialolith proteins and the clinical implications. Clin Proteomics 2020; 17:12. [PMID: 32265614 PMCID: PMC7110646 DOI: 10.1186/s12014-020-09275-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/06/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Sialolithiasis or salivary gland stones are associated with high clinical morbidity. The advances in the treatment of sialolithiasis has been limited, however, by our understanding of their composition. More specifically, there is little information regarding the formation and composition of the protein matrix, the role of mineralogical deposition, or the contributions of cell epithelium and secretions from the salivary glands. A better understanding of these stone characteristics could pave the way for future non-invasive treatment strategies. METHODS Twenty-nine high-quality ductal stone samples were analyzed. The preparation included successive washings to avoid contamination from saliva and blood. The sialoliths were macerated in liquid nitrogen and the maceration was subjected to a sequential, four-step, protein extraction. The four fractions were pooled together, and a standardized aliquot was subjected to tandem liquid chromatography mass spectrometry (LCMS). The data output was subjected to a basic descriptive statistical analysis for parametric confirmation and a subsequent G.O.-KEGG data base functional analysis and classification for biological interpretation. RESULTS The LC-MS output detected 6934 proteins, 824 of which were unique for individual stones. An example of our sialolith protein data is available via ProteomeXchange with the identifier PXD012422. More important, the sialoliths averaged 53% homology with bone-forming proteins that served as a standard comparison, which favorably compared with 62% homology identified among all sialolith sample proteins. The non-homologous protein fraction had a highly variable protein identity. The G.O.-KEGG functional analysis indicated that extracellular exosomes are a primary cellular component in sialolithiasis. Light and electron microscopy also confirmed the presence of exosomal-like features and the presence of intracellular microcrystals. CONCLUSION Sialolith formation presents similarities with the hyperoxaluria that forms kidney stones, which suggests the possibility of a common origin. Further verification of a common origin could fundamentally change the way in which lithiasis is studied and treated.
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Affiliation(s)
- Carlos S. Busso
- Department of Otolaryngology and Bio-communication, Louisiana State University Medical School Health Sciences Center, 533 Bolivar St. Suite 566, New Orleans, LA 70112 USA
| | - Jessie J. Guidry
- Department of Biochemistry and Molecular Biology, and The LSUHSC Proteomics Facility Core, Louisiana State University Medical School Health Sciences Center, 533 Bolivar St. Suite 331, New Orleans, LA 70112 USA
| | - Jhanis J. Gonzalez
- Laser Technologies Group Energy Storage & Distributed Resources Division, Lawrence Berkeley National Laboratory 70R0108B, University of California Berkeley, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Applied Spectra, Inc, 950 Riverside Parkway, West Sacramento, CA 95605 USA
| | - Vassilia Zorba
- Laser Technologies Group Energy Storage & Distributed Resources Division, Lawrence Berkeley National Laboratory 70R0108B, University of California Berkeley, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Leslie S. Son
- Department of Academic Affairs, Our Lady of the Lake Regional Medical Center, 7777 Hennessy Blvd, Baton Rouge, LA 70808 USA
| | - Peter J. Winsauer
- Department of Pharmacology and Experimental Therapeutics, LSU Health Sciences Center, 1901 Perdido Street, New Orleans, LA 70112 USA
| | - Rohan R. Walvekar
- Department of Otolaryngology Head Neck Surgery, Louisiana State University Medical School Health Sciences Center, 533 Bolivar St. Suite 566, New Orleans, LA 70112 USA
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27
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Calciolari E, Donos N. Proteomic and Transcriptomic Approaches for Studying Bone Regeneration in Health and Systemically Compromised Conditions. Proteomics Clin Appl 2020; 14:e1900084. [PMID: 32131137 DOI: 10.1002/prca.201900084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/05/2020] [Indexed: 01/04/2023]
Abstract
Bone regeneration is a complex biological process, where the molecular mechanisms are only partially understood. In an ageing population, where the prevalence of chronic diseases with an impact on bone metabolism is increasing, it becomes crucial to identify new strategies that would improve regenerative outcomes also in medically compromised patients. In this context, omics are demonstrating a great potential, as they offer new insights on the molecular mechanisms regulating physiologic/pathologic bone healing and, at the same time, allow the identification of new diagnostic and therapeutic targets. This review provides an overview on the current evidence on the use of transcriptomic and proteomic approaches in bone regeneration research, particularly in relation to type 1 diabetes and osteoporosis, and discusses future scenarios and potential benefits and limitations on the integration of multi-omics. It is suggested that future research will leverage the synergy of omics with statistical modeling and bioinformatics to prompt the understanding of the biology underpinning bone formation in health and medically compromised conditions. With an eye toward personalized medicine, new strategies combining the mining of large datasets and bioinformatic data with a detailed characterization of relevant phenotypes will need to be pursued to further the understanding of disease mechanisms.
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Affiliation(s)
- Elena Calciolari
- Centre for Oral Immunobiology and Regenerative Medicine & Centre for Oral Clinical Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London, E1 2AD, UK.,Department of Medicine and Surgery, School of Dental Medicine, University of Parma, via Gramsci 14, Parma, 43126, Italy
| | - Nikolaos Donos
- Centre for Oral Immunobiology and Regenerative Medicine & Centre for Oral Clinical Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London, E1 2AD, UK
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28
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Rybchyn MS, Islam KS, Brennan-Speranza TC, Cheng Z, Brennan SC, Chang W, Mason RS, Conigrave AD. Homer1 mediates CaSR-dependent activation of mTOR complex 2 and initiates a novel pathway for AKT-dependent β-catenin stabilization in osteoblasts. J Biol Chem 2019; 294:16337-16350. [PMID: 31527082 PMCID: PMC6827303 DOI: 10.1074/jbc.ra118.006587] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 08/19/2019] [Indexed: 11/06/2022] Open
Abstract
The calcium-sensing receptor (CaSR) is critical for skeletal development, but its mechanism of action in osteoblasts is not well-characterized. In the central nervous system (CNS), Homer scaffolding proteins form signaling complexes with two CaSR-related members of the G protein-coupled receptor (GPCR) family C, metabotropic glutamate receptor 1 (mGluR1) and mGluR5. Here, we show that CaSR and Homer1 are co-expressed in mineralized mouse bone and also co-localize in primary human osteoblasts. Co-immunoprecipitation experiments confirmed that Homer1 associates with CaSR in primary human osteoblasts. The CaSR-Homer1 protein complex, whose formation was increased in response to extracellular Ca2+, was bound to mechanistic target of rapamycin (mTOR) complex 2 (mTORC2), a protein kinase that phosphorylates and activates AKT Ser/Thr kinase (AKT) at Ser473 siRNA-based gene-silencing assays with primary osteoblasts revealed that both CaSR and Homer1 are required for extracellular Ca2+-stimulated AKT phosphorylation and thereby inhibit apoptosis and promote AKT-dependent β-catenin stabilization and cellular differentiation. To confirm the role of the CaSR-Homer1 complex in AKT initiation, we show that in HEK-293 cells, co-transfection with both Homer1c and CaSR, but neither with Homer1c nor CaSR alone, establishes sensitivity of AKT-Ser473 phosphorylation to increases in extracellular Ca2+ concentrations. These findings indicate that Homer1 mediates CaSR-dependent AKT activation via mTORC2 and thereby stabilizes β-catenin in osteoblasts.
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Affiliation(s)
- Mark S Rybchyn
- Discipline of Physiology, School of Medical Sciences and Bosch Institute, University of Sydney, New South Wales 2006, Australia
| | - Kazi S Islam
- School of Life and Environmental Science, Charles Perkins Centre (D17) and Bosch Institute, University of Sydney, New South Wales 2006, Australia
| | - Tara C Brennan-Speranza
- Discipline of Physiology, School of Medical Sciences and Bosch Institute, University of Sydney, New South Wales 2006, Australia
| | - Zhiqiang Cheng
- School of Medicine, University of California, San Francisco, California 94121
| | - Sarah C Brennan
- School of Life and Environmental Science, Charles Perkins Centre (D17) and Bosch Institute, University of Sydney, New South Wales 2006, Australia
| | - Wenhan Chang
- School of Medicine, University of California, San Francisco, California 94121
| | - Rebecca S Mason
- Discipline of Physiology, School of Medical Sciences and Bosch Institute, University of Sydney, New South Wales 2006, Australia
| | - Arthur David Conigrave
- School of Life and Environmental Science, Charles Perkins Centre (D17) and Bosch Institute, University of Sydney, New South Wales 2006, Australia
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29
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Díaz-Martín RD, Ambrosio JR, Flores RM, Gonzáles-Pozos S, Valencia-Caballero L. Cytoskeletal and extracellular matrix proteins resist the burning of bones. Forensic Sci Int 2019; 305:110027. [PMID: 31704515 DOI: 10.1016/j.forsciint.2019.110027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/07/2019] [Accepted: 10/27/2019] [Indexed: 02/07/2023]
Abstract
Due the proteins from bone remains are highly resistant to pass of time and environmental conditions, they could tell us about the events that probably happened in the past. In the forensic and physical anthropology context, burnt bone remains are one of the most common pieces of recovered evidence and, generally, they are associated with funerary practices, criminal scenes or massive catastrophic events. In the present study, bone pieces of pigs were calcined at different calcination temperatures, and proteins were searched using biochemical, immunochemical and ultrastructure visualization under these experimentally conditions. For this purpose, it was successfully developed a non-demineralizing protein extraction method from burnt bone remains and the use of specific antibodies permitted the identification of different extracellular matrix and intracellular proteins. While collagen proteins type I and IV were identified and detected under middle and high calcination temperatures (300°C and 600°C); cytoskeletal proteins as actin, tubulin and, the microtubule associated protein Tau, were found under calcination process, even up high calcination temperatures. Under ultrastructural analysis, fibrous materials with a classical disposition of collagens were observed even at high calcination temperatures of the burnt bone remains. The protein identification and characterization in burnt bones as performed in present studies, is clearly demonstrating that using specific strategies for protein characterizations it is possible to found protein biomarkers in burnt bone remains and this strategy could be useful for forensic and anthropological purposes.
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Affiliation(s)
- Rubén Darío Díaz-Martín
- Departamento de Innovación en Material Biológico Humano (DIMBIH), Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México; Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Javier R Ambrosio
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Ricardo Mondragón Flores
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), México
| | | | - Lorena Valencia-Caballero
- Departamento de Innovación en Material Biológico Humano (DIMBIH), Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México.
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30
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Bell PA, Solis N, Kizhakkedathu JN, Matthew I, Overall CM. Proteomic and N-Terminomic TAILS Analyses of Human Alveolar Bone Proteins: Improved Protein Extraction Methodology and LysargiNase Digestion Strategies Increase Proteome Coverage and Missing Protein Identification. J Proteome Res 2019; 18:4167-4179. [DOI: 10.1021/acs.jproteome.9b00445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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31
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Nielson CM, Jacobs JM, Orwoll ES. Proteomic studies of bone and skeletal health outcomes. Bone 2019; 126:18-26. [PMID: 30954730 PMCID: PMC7302501 DOI: 10.1016/j.bone.2019.03.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022]
Abstract
Proteins are an essential part of essentially all biological processes, and there is enormous variation in protein forms and concentrations that is not reflected in DNA or RNA. Recently there have been rapid advances in the ability to measure protein sequence, modification and concentration, particularly with methods based in mass spectrometry. Global measures of proteins in tissues or in the circulation provide a broad assessment of the proteome that can be extremely useful for discovery, and targeted proteomic measures can yield specific and sensitive assessments of specific peptides and proteins. While most proteomic measures are directed at the detection of consensus peptide sequences, mass spectrometry based proteomic methods also allow a detailed examination of the peptide sequence differences that result from genetic variants and that may have important effects on protein function. In evaluating proteomic data, a number of analytical considerations are important, including an understanding of missing data, the challenge of multiple testing and replication, and the use of rapidly evolving methods in systems biology. While proteomics has not yet had a major impact in skeletal research, interesting recent research has used these approaches in the study of bone cell biology and the discovery of biomarkers of skeletal disorders. Proteomics can be expected to have an increasing influence in the study of bone biology and pathophysiology.
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Affiliation(s)
| | - Jon M Jacobs
- Pacific Northwest National Laboratory, Richland, WA, USA
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32
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Gatenholm B, Gobom J, Skillbäck T, Blennow K, Zetterberg H, Brittberg M. Peptidomic analysis of cartilage and subchondral bone in OA patients. Eur J Clin Invest 2019; 49:e13082. [PMID: 30725487 DOI: 10.1111/eci.13082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/09/2018] [Accepted: 12/10/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND The objective of this study was to develop a method for directly analysing osteochondral samples straight out of the operating room without cell culturing, thereby enabling identification of potential peptide biomarkers to better understand the mechanisms involved in the development of osteoarthritis and pain. MATERIAL AND METHODS Osteochondral plugs from wounded and macroscopically nonwounded zones of the femur condyle were collected from six patients with manifest osteoarthritis (OA) undergoing total knee arthroplasty (TKA). The samples were demineralized and supernatant was collected and isotopically marked with Tandem Mass Tag (TMT) labelling and analysed using liquid chromatography coupled with tandem mass spectrometry LC-MS/MS. RESULTS Using peptidomics, 6292 endogenous peptides were identified. Five hundred sixty-six peptides (8 identified endogenous peptides) differed significantly (P-value 0.10) from wounded zones compared to nonwounded zones. CONCLUSION This pilot study shows promising results for enabling peptidomic analysis of cartilage and bone straight out of the operating room. With further refinement, peptidomics can potentially become a diagnostic tool for OA, and improve the knowledge of disease progression and genesis of pain.
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Affiliation(s)
- Birgitta Gatenholm
- Department of Orthopaedics, Institute of Clinical Sciences, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska University Hospital, Mölndal, Sweden
| | - Johan Gobom
- Institute of Neuroscience and Physiology, Department of Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Tobias Skillbäck
- Institute of Neuroscience and Physiology, Department of Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Mats Brittberg
- Department of Orthopaedics, Institute of Clinical Sciences, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Hallands Sjukhus, Kungsbacka, Sweden
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33
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Li W, Wang X, Chang L, Wang F. MiR-377 inhibits wear particle-induced osteolysis via targeting RANKL. Cell Biol Int 2019; 43:658-668. [PMID: 30958621 DOI: 10.1002/cbin.11143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/20/2019] [Accepted: 03/23/2019] [Indexed: 12/28/2022]
Abstract
Periprosthetic osteolysis caused by wear particles is the main factor that affects the long-term efficacy of artificial joint replacement, and macrophages play a vital role in the pathogenesis of periprosthetic osteolysis, while the potential mechanism underlying this is still unclear. To investigate the underlying role of miR-377 in wear particle-induced osteolysis (PIO), blood samples from patients undergoing arthroplasty were collected for analyzing the correlation between miR-377 expression and the clinicopathological parameters of PIO. Peripheral blood macrophages were obtained to compare the miR-377 and receptor activator of NF-κB ligand (RANKL) expressions. Bone marrow macrophages (BMMs) following titanium (Ti) particle treatment and/or miR-377 mimic transfection were used. The expressions of RANKL, pro-inflammatory cytokines interleukin 6 (IL-6) and tumor necrosis factor-α (TNF-α) and the osteoclast-related molecules tartrate-resistant acid phosphatase (TRAP) and cathepsin K (CTSK) were determined using real-time polymerase chain reaction or western blotting or enzyme-linked immunosorbent assay or TRAP staining, when appropriate. The interaction between miR-377 and RANKL was assessed by luciferase reporter assay. The in vivo role of miR-377 in PIO was evaluated using a mouse calvarial osteolysis model. There were significant differences in downregulated miR-377 expression between the different numbers of particles in the joint prostheses. The Ti particle treatment increased pro-inflammatory cytokine levels, downregulated RANKL and increased osteoclast activity in BMMs, while miR-377 overexpression led to the opposite effect. Taken together, miR-377 downregulated the target gene RANKL, resulting in PIO inhibition. MiR-377 relieved PIO by negatively regulating RANKL.
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Affiliation(s)
- Wei Li
- Department of Rehabilitation Medicine, The Third Hospital of Hebei Medical University, Shijiazhuang, 050050, China
| | - Xiaomeng Wang
- Department of Joint Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, 050050, China
| | - Li Chang
- Department of Rehabilitation Medicine, The Third Hospital of Hebei Medical University, Shijiazhuang, 050050, China
| | - Fei Wang
- Department of Joint Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, 050050, China
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Horn IR, Kenens Y, Palmblad NM, van der Plas-Duivesteijn SJ, Langeveld BW, Meijer HJM, Dalebout H, Marissen RJ, Fischer A, Vincent Florens FB, Niemann J, Rijsdijk KF, Schulp AS, Laros JFJ, Gravendeel B. Palaeoproteomics of bird bones for taxonomic classification. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ivo R Horn
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
| | - Yvo Kenens
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
| | - N Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Bram W Langeveld
- Natural History Museum Rotterdam, Museumpark, Rotterdam, The Netherlands
| | - Hanneke J M Meijer
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
- University Museum, Department of Natural History, University of Bergen, Bergen, Norway
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob J Marissen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anja Fischer
- University of Amsterdam, Faculty of Humanities, Amsterdam, The Netherlands
| | - F B Vincent Florens
- Tropical Island Biodiversity, Ecology and Conservation Pole of Research, University of Mauritius, Réduit, Mauritius
| | - Jonas Niemann
- Natural History Museum of Denmark, Copenhagen, Denmark
| | - Kenneth F Rijsdijk
- BIOMAC group, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Faculty of Natural Sciences, Science Park, Amsterdam, The Netherlands
| | - Anne S Schulp
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
| | | | - Barbara Gravendeel
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg, BE Leiden, The Netherlands
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35
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Cunniffe GM, Díaz-Payno PJ, Sheehy EJ, Critchley SE, Almeida HV, Pitacco P, Carroll SF, Mahon OR, Dunne A, Levingstone TJ, Moran CJ, Brady RT, O'Brien FJ, Brama PA, Kelly DJ. Tissue-specific extracellular matrix scaffolds for the regeneration of spatially complex musculoskeletal tissues. Biomaterials 2019; 188:63-73. [DOI: 10.1016/j.biomaterials.2018.09.044] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/18/2018] [Accepted: 09/28/2018] [Indexed: 01/09/2023]
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36
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Homayounfar N, Khan MM, Ji Y, Khoury ZH, Oates TW, Goodlett DR, Chellaiah M, Masri R. The effect of embryonic origin on the osteoinductive potential of bone allografts. J Prosthet Dent 2018; 121:651-658. [PMID: 30598313 DOI: 10.1016/j.prosdent.2018.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 11/15/2022]
Abstract
STATEMENT OF PROBLEM Allografts with osteoinduction potential are widely used to augment bone in surgical and prosthetic rehabilitations. However, osteoinduction potential varies among commercially available allografts. Donor bones are derived from different embryonic origins, either the neural crest or mesoderm. Whether the origin of the bones affects the osteoinductivity of allograftsis is unclear. PURPOSE The purpose of this ex vivo study was to investigate the osteoinduction potential of allografts derived from bones with distinct embryonic origins. MATERIAL AND METHODS Allografts were obtained from human frontal and parietal bones at 2 different ages (fetal and adult). The specimens were divided into 4 groups: adult frontal (n=5), adult parietal (n=5), fetal frontal (n=10), and fetal parietal (n=10). Two investigations were conducted to assess the osteoinductive potential of these allografts. First, the osteogenesis of human osteoblasts exposed to these allografts were evaluated by analyzing the expression of runt-related transcription factor 2 (RUNX2), collagen type 1 alpha 2 chain (COL1A2), and bone gamma-carboxyglutamate protein (BGLAP) genes using quantitative real-time polymerase chain reaction (qRT-PCR). Second, the protein content of the adult frontal and parietal bone matrices was analyzed using liquid chromatography tandem mass spectrometry (LC-MS/MS). One-way ANOVA and the t test were used for statistical analyses of the gene and protein expression of the groups (α=.05). RESULTS No difference was found in the gene expression of the cells exposed to frontal or parietal bones. However, all 3 genes were significantly overexpressed in cells treated with fetal bones compared with adult bones. No difference was found in protein expression between adult frontal and adult parietal bones. CONCLUSIONS No difference was found in the osteoinductive capacity of frontal and parietal bones used as allografts. However, the osteoinductivity of fetal bones can be higher than that of adult bones. Further microanalyses are needed to determine the protein content of fetal bones.
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Affiliation(s)
- Negar Homayounfar
- Assistant Professor, Department of Advanced Oral Sciences and Therapeutics, University of Maryland School of Dentistry, Baltimore, Md.
| | - Mohd M Khan
- Graduate student, University of Maryland School of Medicine, Baltimore, Md
| | - Yadong Ji
- Research Scientist, Department of Advanced Oral Sciences and Therapeutics, University of Maryland School of Dentistry, Baltimore, Md
| | - Zaid H Khoury
- Graduate student, Department of Oncology and Diagnostic Sciences, University of Maryland School of Dentistry, Baltimore, Md
| | - Thomas W Oates
- Professor, Department of Advanced Oral Sciences and Therapeutics, University of Maryland School of Dentistry, Baltimore, Md
| | - David R Goodlett
- Professor, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Md
| | - Meenakshi Chellaiah
- Professor, Department of Oncology and Diagnostic Sciences, University of Maryland School of Dentistry, Baltimore, Md
| | - Radi Masri
- Associate Professor, Department of Advanced Oral Sciences and Therapeutics, University of Maryland School of Dentistry, Baltimore, Md
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Strauss FJ, Stähli A, Beer L, Mitulović G, Gilmozzi V, Haspel N, Schwab G, Gruber R. Acid bone lysate activates TGFβ signalling in human oral fibroblasts. Sci Rep 2018; 8:16065. [PMID: 30375456 PMCID: PMC6207660 DOI: 10.1038/s41598-018-34418-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
Demineralized bone matrix is a widely used allograft from which not only the inorganic mineral but also embedded growth factors are removed by hydrochloric acid (HCl). The cellular response to the growth factors released during the preparation of demineralized bone matrix, however, has not been studied. Here we investigated the in vitro impact of acid bone lysate (ABL) prepared from porcine cortical bone chips on oral fibroblasts. Proteomic analysis of ABL revealed a large spectrum of bone-derived proteins including TGF-β1. Whole genome microarrays and RT-PCR together with the pharmacologic blocking of TGF-β receptor type I kinase with SB431542 showed that ABL activates the TGF-β target genes interleukin 11, proteoglycan 4, and NADPH oxidase 4. Interleukin 11 expression was confirmed at the protein level by ELISA. Immunofluorescence and Western blot showed the nuclear localization of Smad2/3 and increased phosphorylation of Smad3 with ABL, respectively. This effect was independent of whether ABL was prepared from mandible, calvaria or tibia. These results demonstrate that TGF-β is a major growth factor that is removed upon the preparation of demineralized bone matrix.
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Affiliation(s)
- Franz Josef Strauss
- Department of Oral Biology, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria
- Department of Conservative Dentistry, School of Dentistry, University of Chile, Sergio Livingstone 943, Santiago, Chile
| | - Alexandra Stähli
- Department of Oral Biology, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria
- Department of Periodontology, School of Dental Medicine, University of Bern, Freiburgstrasse 7, 3010, Bern, Switzerland
| | - Lucian Beer
- Department of Biomedical Imaging and Image-guided Therapy, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Christian Doppler Laboratory for Cardiac and Thoracic Diagnosis and Regeneration, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Goran Mitulović
- Clinical Department of Laboratory Medicine Proteomics Core Facility, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Valentina Gilmozzi
- Department of Oral Biology, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria
| | - Nina Haspel
- Department of Oral Biology, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria
| | - Gerhild Schwab
- Department of Oral Biology, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria
| | - Reinhard Gruber
- Department of Oral Biology, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria.
- Department of Periodontology, School of Dental Medicine, University of Bern, Freiburgstrasse 7, 3010, Bern, Switzerland.
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38
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Calciolari E, Donos N. The use of omics profiling to improve outcomes of bone regeneration and osseointegration. How far are we from personalized medicine in dentistry? J Proteomics 2018; 188:85-96. [DOI: 10.1016/j.jprot.2018.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/25/2018] [Accepted: 01/30/2018] [Indexed: 12/12/2022]
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Prieto-Bonete G, Pérez-Cárceles MD, Maurandi-López A, Pérez-Martínez C, Luna A. Association between protein profile and postmortem interval in human bone remains. J Proteomics 2018; 192:54-63. [PMID: 30145274 DOI: 10.1016/j.jprot.2018.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/08/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022]
Abstract
Proteomic techniques in bones forensic samples are increasingly, being applied. The main aim of forensic sciences is the estimation of postmortem interval. Most current techniques are useful for the first post-mortem stages. However, in the case of osseous remains, these techniques may be difficult to use due to the high level of decomposition of the sample. Our objective was to attempt to know whether there is a protein profile in human bone remains that would enable a late postmortem. interval ranging from 5 to 20 years postmortem to be estimated. A total of 40 femur bones from 40 different cadavers (data range 5-20 years) were use. Of the 275 total proteins, we excluded the circulating ones (n = 227), leaving a total of 48 proteins (29 structural and 19 functional) were found. A multiple correspondence analysis was applied on the 48 proteins. Finally selecting 32 proteins that allowed us to discriminate between the. two groups of postmortem interval. Analysis of the protein profile present in bone permits an approximation of the date of death within the studied interval, and could be used to complement other tests for estimating the postmortem interval.
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Affiliation(s)
| | | | - Antonio Maurandi-López
- Department of Didactics of Mathematical and Social Sciences, University of Murcia, Spain
| | | | - Aurelio Luna
- Department of Legal and Forensic Medicine, University of Murcia, Spain
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40
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Mason KE, Anex D, Grey T, Hart B, Parker G. Protein-based forensic identification using genetically variant peptides in human bone. Forensic Sci Int 2018; 288:89-96. [DOI: 10.1016/j.forsciint.2018.04.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 01/17/2023]
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41
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Comparative proteomic analysis of fluoride treated rat bone provides new insights into the molecular mechanisms of fluoride toxicity. Toxicol Lett 2018; 291:39-50. [DOI: 10.1016/j.toxlet.2018.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 11/23/2022]
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42
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Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ. A guide to ancient protein studies. Nat Ecol Evol 2018; 2:791-799. [PMID: 29581591 DOI: 10.1038/s41559-018-0510-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Beatrice Demarchi
- Department of Life Science and Systems Biology, University of Turin, Turin, Italy.,BioArCh, Department of Archaeology, University of York, York, UK
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, University of Oklahoma, Norman, OK, USA.,Institute for Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - Matthew J Collins
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,BioArCh, Department of Archaeology, University of York, York, UK
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Comparison of secretome from osteoblasts derived from sclerotic versus non-sclerotic subchondral bone in OA: A pilot study. PLoS One 2018; 13:e0194591. [PMID: 29547667 PMCID: PMC5856400 DOI: 10.1371/journal.pone.0194591] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/06/2018] [Indexed: 01/24/2023] Open
Abstract
Objective Osteoarthritis (OA) is characterized by cartilage degradation but also by other joint tissues modifications like subchondral bone sclerosis. In this study, we used a proteomic approach to compare secretome of osteoblast isolated from sclerotic (SC) or non sclerotic (NSC) area of OA subchondral bone. Design Secretome was analyzed using differential quantitative and relative label free analysis on nanoUPLC G2 HDMS system. mRNA of the more differentially secreted proteins were quantified by RT-PCR in cell culture from 5 other patients. Finally, osteomodulin and fibulin-3 sequences were quantified by western blot and immunoassays in serum and culture supernatants. Results 175 proteins were identified in NSC osteoblast secretome. Data are available via ProteomeXchange with identifier PXD008494. Compared to NSC osteoblast secretome, 12 proteins were significantly less secreted (Osteomodulin, IGFBP5, VCAM-1, IGF2, 78 kDa glucose-regulated protein, versican, calumenin, IGFBP2, thrombospondin-4, periostin, reticulocalbin 1 and osteonectin), and 13 proteins were significantly more secreted by SC osteoblasts (CHI3L1, fibulin-3, SERPINE2, IGFBP6, SH3BGRL3, SERPINE1, reticulocalbin3, alpha-2-HS-glycoprotein, TIMP-2, IGFBP3, TIMP-1, SERPINF1, CSF-1). Similar changes in osteomodulin, IGF2, SERPINE1, fibulin-3 and CHI3L1 mRNA levels were observed. ELISAs assays confirm the decrease by half of osteomodulin protein in SC osteoblasts supernatant compared to NSC and in OA patients serum compared to healthy subjects. Fibulin-3 epitopes Fib3-1, Fib3-2 and Fib3-3 were also increased in SC osteoblasts supernatant compared to NSC. Conclusions We highlighted some proteins differentially secreted by the osteoblasts coming from OA subchondral bone sclerosis. These changes contribute to explain some features observed in OA subchondral bone, like the increase of bone remodeling or abnormalities in bone matrix mineralization. Among identified proteins, osteomodulin was found decreased and fibulin-3 increased in serum of OA patients. These findings suggest that osteomodulin and fibulin-3 fragments could be biomarkers to monitor early changes in subchondral bone metabolism in OA.
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Guo L, Cai T, Chen K, Wang R, Wang J, Cui C, Yuan J, Zhang K, Liu Z, Deng Y, Xiao G, Wu C. Kindlin-2 regulates mesenchymal stem cell differentiation through control of YAP1/TAZ. J Cell Biol 2018; 217:1431-1451. [PMID: 29496737 PMCID: PMC5881491 DOI: 10.1083/jcb.201612177] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 10/22/2017] [Accepted: 12/27/2017] [Indexed: 12/22/2022] Open
Abstract
Mesenchymal stem cell (MSC) fate decision is strongly influenced by cell microenvironment. Guo et al. identify kindlin-2 as a key determinant of MSC lineage commitment and delineate a novel signaling pathway consisting of kindlin-2, RhoA, MLCK, AIP4, and YAP1/TAZ that senses mechanical cues of the cell microenvironment and controls MSC differentiation. Precise control of mesenchymal stem cell (MSC) differentiation is critical for tissue development and regeneration. We show here that kindlin-2 is a key determinant of MSC fate decision. Depletion of kindlin-2 in MSCs is sufficient to induce adipogenesis and inhibit osteogenesis in vitro and in vivo. Mechanistically, kindlin-2 regulates MSC differentiation through controlling YAP1/TAZ at both the transcript and protein levels. Kindlin-2 physically associates with myosin light-chain kinase in response to mechanical cues of cell microenvironment and intracellular signaling events and promotes myosin light-chain phosphorylation. Loss of kindlin-2 inhibits RhoA activation and reduces myosin light-chain phosphorylation, stress fiber formation, and focal adhesion assembly, resulting in increased Ser127 phosphorylation, nuclear exclusion, and ubiquitin ligase atrophin-1 interacting protein 4–mediated degradation of YAP1/TAZ. Our findings reveal a novel kindlin-2 signaling axis that senses the mechanical cues of cell microenvironment and controls MSC fate decision, and they suggest a new strategy to regulate MSC differentiation, tissue repair, and regeneration.
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Affiliation(s)
- Ling Guo
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Ting Cai
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Keng Chen
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Rong Wang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jiaxin Wang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Chunhong Cui
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jifan Yuan
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Kuo Zhang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhongzhen Liu
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Yi Deng
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Guozhi Xiao
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Department of Biochemistry, Rush University Medical Center, Chicago, IL
| | - Chuanyue Wu
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, and Department of Biology, Southern University of Science and Technology, Shenzhen, China .,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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45
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Kershaw JL, Botting CH, Brownlow A, Hall AJ. Not just fat: investigating the proteome of cetacean blubber tissue. CONSERVATION PHYSIOLOGY 2018; 6:coy003. [PMID: 29479430 PMCID: PMC5814904 DOI: 10.1093/conphys/coy003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/14/2017] [Accepted: 01/24/2018] [Indexed: 06/01/2023]
Abstract
Mammalian adipose tissue is increasingly being recognized as an endocrine organ involved in the regulation of a number of metabolic processes and pathways. It responds to signals from different hormone systems and the central nervous system, and expresses a variety of protein factors with important paracrine and endocrine functions. This study presents a first step towards the systematic analysis of the protein content of cetacean adipose tissue, the blubber, in order to investigate the kinds of proteins present and their relative abundance. Full depth blubber subsamples were collected from dead-stranded harbour porpoises (Phocoena phocoena) (n = 21). Three total protein extraction methods were trialled, and the highest total protein yields with the lowest extraction variability were achieved using a RIPA cell lysis and extraction buffer based protocol. Extracted proteins were separated using 1D Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE), and identified using nanoflow Liquid Chromatography Electrospray Ionization in tandem with Mass Spectrometry (nLC-ESI-MS/MS). A range of proteins were identified (n = 295) and classed into eight functional groups, the most abundant of which were involved in cell function and metabolism (45%), immune response and inflammation (15%) and lipid metabolism (11%). These proteins likely originate both from the various cell types within the blubber tissue itself, and from the circulation. They therefore have the potential to capture information on the cellular and physiological stresses experienced by individuals at the time of sampling. The importance of this proteomic approach is two-fold: Firstly, it could help to assign novel functions to marine mammal blubber in keeping with current understanding of the multi-functional role of adipose tissue in other mammals. Secondly, it could lead to the development of a suite of biomarkers to better monitor the physiological state and health of live individuals though remote blubber biopsy sampling.
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Affiliation(s)
- Joanna L Kershaw
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews KY16 8LB, UK
| | - Catherine H Botting
- Biomedical Sciences Research Complex, School of Chemistry, Biomolecular Sciences Building Annexe, North Haugh, University of St Andrews, St Andrews KY16 9ST, UK
| | - Andrew Brownlow
- Scottish Marine Animals Strandings Scheme, SAC Consulting Veterinary Services, Inverness IV2 5NA, UK
| | - Ailsa J Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews KY16 8LB, UK
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46
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Wadsworth C, Buckley M. Characterization of Proteomes Extracted through Collagen-based Stable Isotope and Radiocarbon Dating Methods. J Proteome Res 2017; 17:429-439. [DOI: 10.1021/acs.jproteome.7b00624] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Caroline Wadsworth
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Pérez-Martínez C, Pérez-Cárceles MD, Legaz I, Prieto-Bonete G, Luna A. Quantification of nitrogenous bases, DNA and Collagen type I for the estimation of the postmortem interval in bone remains. Forensic Sci Int 2017; 281:106-112. [PMID: 29125988 DOI: 10.1016/j.forsciint.2017.10.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 10/02/2017] [Accepted: 10/29/2017] [Indexed: 11/28/2022]
Abstract
Estimating the postmortem interval (PMI) is an important goal in forensic medicine and continues to be one of the most difficult tasks of the forensic investigator. Few accurate methods exist to determine the time since death of skeletonized human remains due to the great number of intrinsic and external factors that may alter the normal course of postmortem change. The purpose of this research was to assess the usefulness of various biochemical parameters, such as nitrogenous bases (adenine, guanine, purines, cytosine, thymine, pyrimidines, hypoxanthine and xanthine), DNA and Collagen Type I peptides to estimate PMI. These parameters were analysed in cortical bone for the establishment of data in a total of 80 long bones of 80 corpses (50 males, 30 females) with a mean age of 68.31 years (S.D.=18.021, range=20-97). The bones were removed from the cement niches of a cemetery in Murcia (south-eastern Spain), where they had lain for between 5 and 47 years (mean time 23.83 years, S.D.=10.85). Our results show a significant decrease in adenine (p=0.0004), guanine (p=0.0001), purines (p=0.0001), cytosine (p=0.0001), thymine (p=0.0226), pyrimidines (p=0.0002) and the number of peptides of Collagen type I (p=0.0053) in those with a PMI≥20 years. In a curvilinear regression analysis the results show that 30.6% of the variable PMI could be explained by guanine concentration, in bones with a PMI<20 years, while in cases of a PMI≥20 years, the variable that best explained membership of this group was adenine (38.0%). In the discriminant analysis applied to the all the variables as a function of PMI when two groups were established, 86.7% of the cases were correctly classified. These results show that the quantification of Collagen type I proteins and nitrogenous bases could be used as a complementary tool, together with other analyses, in the estimation of PMI.
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Affiliation(s)
| | | | - Isabel Legaz
- Department of Legal and Forensic Medicine, University of Murcia, Spain
| | | | - Aurelio Luna
- Department of Legal and Forensic Medicine, University of Murcia, Spain
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48
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Thomas B, McIntosh D, Fildes T, Smith L, Hargrave F, Islam M, Thompson T, Layfield R, Scott D, Shaw B, Burrell CL, Gonzalez S, Taylor S. Second-harmonic generation imaging of collagen in ancient bone. Bone Rep 2017; 7:137-144. [PMID: 29124084 PMCID: PMC5671394 DOI: 10.1016/j.bonr.2017.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/27/2017] [Accepted: 10/24/2017] [Indexed: 12/01/2022] Open
Abstract
Second-harmonic generation imaging (SHG) captures triple helical collagen molecules near tissue surfaces. Biomedical research routinely utilizes various imaging software packages to quantify SHG signals for collagen content and distribution estimates in modern tissue samples including bone. For the first time using SHG, samples of modern, medieval, and ice age bones were imaged to test the applicability of SHG to ancient bone from a variety of ages, settings, and taxa. Four independent techniques including Raman spectroscopy, FTIR spectroscopy, radiocarbon dating protocols, and mass spectrometry-based protein sequencing, confirm the presence of protein, consistent with the hypothesis that SHG imaging detects ancient bone collagen. These results suggest that future studies have the potential to use SHG imaging to provide new insights into the composition of ancient bone, to characterize ancient bone disorders, to investigate collagen preservation within and between various taxa, and to monitor collagen decay regimes in different depositional environments. Second-Harmonic Generation (SHG) confocal laser scanning microscopy is used to investigate collagen remnants in ancient bone. Four independent techniques confirm the presence of collagen remnants in ancient bone samples with SHG-detected collagen. SHG imaging can visualise collagen remnants in ancient bone of various taxa, ages, and settings.
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Affiliation(s)
- B Thomas
- Mass Spectrometry Research Group, University of Liverpool, Brownlow Hill, Liverpool L69 3GJ, UK
| | - D McIntosh
- Mass Spectrometry Research Group, University of Liverpool, Brownlow Hill, Liverpool L69 3GJ, UK
| | - T Fildes
- Mass Spectrometry Research Group, University of Liverpool, Brownlow Hill, Liverpool L69 3GJ, UK.,Norton Priory Museum, Runcorn WA7 1SX, UK
| | - L Smith
- Norton Priory Museum, Runcorn WA7 1SX, UK
| | - F Hargrave
- Norton Priory Museum, Runcorn WA7 1SX, UK
| | - M Islam
- School of Science and Engineering, Teesside University, Borough Road, Middlesbrough TS1 3BA, UK
| | - T Thompson
- School of Science and Engineering, Teesside University, Borough Road, Middlesbrough TS1 3BA, UK
| | - R Layfield
- School of Life Sciences, University of Nottingham Medical School, Nottingham NG9 6HZ, UK
| | - D Scott
- School of Life Sciences, University of Nottingham Medical School, Nottingham NG9 6HZ, UK
| | - B Shaw
- School of Life Sciences, University of Nottingham Medical School, Nottingham NG9 6HZ, UK
| | - C L Burrell
- Liverpool John Moores University, Liverpool, UK
| | - S Gonzalez
- Liverpool John Moores University, Liverpool, UK
| | - S Taylor
- Mass Spectrometry Research Group, University of Liverpool, Brownlow Hill, Liverpool L69 3GJ, UK
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Ashraf Kharaz Y, Zamboulis D, Sanders K, Comerford E, Clegg P, Peffers M. Comparison between chaotropic and detergent-based sample preparation workflow in tendon for mass spectrometry analysis. Proteomics 2017; 17:1700018. [PMID: 28547889 PMCID: PMC5575552 DOI: 10.1002/pmic.201700018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/16/2017] [Accepted: 05/19/2017] [Indexed: 01/12/2023]
Abstract
Exploring the tendon proteome is a challenging but important task for understanding the mechanisms of physiological/pathological processes during ageing and disease and for the development of new treatments. Several extraction methods have been utilised for tendon mass spectrometry, however different extraction methods have not been simultaneously compared. In the present study we compared protein extraction in tendon with two chaotropic agents, guanidine hydrochloride (GnHCl) and urea, a detergent, RapiGest™, and their combinations for shotgun mass spectrometry. An initial proteomic analysis was performed following urea, GnHCl, and RapiGest™ extraction of equine superficial digital flexor tendon (SDFT) tissue. Subsequently, another proteomic analysis was performed following extraction with GnHCl, Rapigest™, and their combinations. Between the two chaotropic agents, GnHCl extracted more proteins, whilst a greater number of proteins were solely identified after Rapigest™ extraction. Protein extraction with a combination of GnHCl followed by RapiGest™ on the insoluble pellet demonstrated, after label-free quantification, increased abundance of identified collagen proteins and low sample to sample variability. In contrast, GnHCl extraction on its own showed increased abundance of identified proteoglycans and cellular proteins. Therefore, the selection of protein extraction method for tendon tissue for mass spectrometry analysis should reflect the focus of the study.
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Affiliation(s)
- Yalda Ashraf Kharaz
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Danae Zamboulis
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Karen Sanders
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Eithne Comerford
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | - Peter Clegg
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
- The MRC‐Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA)LiverpoolUK
| | - Mandy Peffers
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
- The MRC‐Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA)LiverpoolUK
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Procopio N, Chamberlain AT, Buckley M. Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones. J Proteome Res 2017; 16:2016-2029. [PMID: 28436665 DOI: 10.1021/acs.jproteome.6b01070] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteomic methods are acquiring greater importance in archaeology and palaeontology due to the longevity of proteins in skeletal remains. There are also developing interests in forensic applications, offering the potential to shed light on post-mortem intervals and age at death estimation. However, our understanding of intra- and interskeletal proteome variations is currently severely limited. Here, we evaluated the proteomes obtained from five distinct subsamples of different skeletal elements from buried pig carcasses to ascertain the extent of variation within and between individuals. We found that reproducibility of data depends on the skeletal element used for sampling and that intrabone differences exceed those observed between the same skeletal element sampled from different individuals. Interestingly, the abundance of several serum proteins appeared to correlate with biological age with relative concentrations of alpha-1 antitrypsin and chromogranin-A increasing and those of fetuin-A decreasing. We also observed a surprising level of divergence in data from different LC-MS/MS runs on aliquots of similar samples analyzed months apart, adding constraints to the comparison of results of such methods across different studies.
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Affiliation(s)
- Noemi Procopio
- School of Earth and Environmental Sciences, The University of Manchester, Manchester Institute of Biotechnology , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Andrew T Chamberlain
- School of Earth and Environmental Sciences, The University of Manchester , Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Michael Buckley
- School of Earth and Environmental Sciences, The University of Manchester, Manchester Institute of Biotechnology , 131 Princess Street, Manchester, M1 7DN, United Kingdom
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