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Ustriyana P, Schulte F, Gombedza F, Gil-Bona A, Paruchuri S, Bidlack FB, Hardt M, Landis WJ, Sahai N. Spatial survey of non-collagenous proteins in mineralizing and non-mineralizing vertebrate tissues ex vivo. Bone Rep 2021; 14:100754. [PMID: 33665237 PMCID: PMC7900015 DOI: 10.1016/j.bonr.2021.100754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 11/24/2022] Open
Abstract
Bone biomineralization is a complex process in which type I collagen and associated non-collagenous proteins (NCPs), including glycoproteins and proteoglycans, interact closely with inorganic calcium and phosphate ions to control the precipitation of nanosized, non-stoichiometric hydroxyapatite (HAP, idealized stoichiometry Ca10(PO4)6(OH)2) within the organic matrix of a tissue. The ability of certain vertebrate tissues to mineralize is critically related to several aspects of their function. The goal of this study was to identify specific NCPs in mineralizing and non-mineralizing tissues of two animal models, rat and turkey, and to determine whether some NCPs are unique to each type of tissue. The tissues investigated were rat femur (mineralizing) and tail tendon (non-mineralizing) and turkey leg tendon (having both mineralizing and non-mineralizing regions in the same individual specimen). An experimental approach ex vivo was designed for this investigation by combining sequential protein extraction with comprehensive protein mapping using proteomics and Western blotting. The extraction method enabled separation of various NCPs based on their association with either the extracellular organic collagenous matrix phases or the inorganic mineral phases of the tissues. The proteomics work generated a complete picture of NCPs in different tissues and animal species. Subsequently, Western blotting provided validation for some of the proteomics findings. The survey then yielded generalized results relevant to various protein families, rather than only individual NCPs. This study focused primarily on the NCPs belonging to the small leucine-rich proteoglycan (SLRP) family and the small integrin-binding ligand N-linked glycoproteins (SIBLINGs). SLRPs were found to be associated only with the collagenous matrix, a result suggesting that they are mainly involved in structural matrix organization and not in mineralization. SIBLINGs as well as matrix Gla (γ-carboxyglutamate) protein were strictly localized within the inorganic mineral phase of mineralizing tissues, a finding suggesting that their roles are limited to mineralization. The results from this study indicated that osteocalcin was closely involved in mineralization but did not preclude possible additional roles as a hormone. This report provides for the first time a spatial survey and comparison of NCPs from mineralizing and non-mineralizing tissues ex vivo and defines the proteome of turkey leg tendons as a model for vertebrate mineralization.
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Key Words
- B, rat bone
- BSP, bone sialoprotein
- DCN, decorin
- E, EDTA extract
- ECM, extracellular matrix
- G, guanidine-HCl-only extract (for non-mineralizing tissues)
- G1, first guanidine-HCl extract
- G2, second guanidine-HCl extract
- Gla, gamma-carboxylated glutamic acid
- MGP, matrix Gla protein
- MT, turkey mineralizing tendon
- Mineralization
- NCP, non-collagenous protein
- NMT, turkey never-mineralizing tendon
- NT, turkey not-yet-mineralized tendon
- Non-collagenous protein
- OCN, osteocalcin
- OPN, osteopontin
- Proteomics
- SIBLING, small integrin-binding ligand N-linked glycoprotein
- SLRP, small leucine-rich proteoglycan
- T, rat tail tendon
- TLT, turkey leg tendon (gastrocnemius)
- TNAP, tissue-nonspecific alkaline phosphatase
- Type I collagen
- Vertebrate
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Affiliation(s)
- Putu Ustriyana
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH 44325, USA
| | - Fabian Schulte
- The Forsyth Institute, Cambridge, MA 02142, USA
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Farai Gombedza
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | - Ana Gil-Bona
- The Forsyth Institute, Cambridge, MA 02142, USA
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Sailaja Paruchuri
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | - Felicitas B. Bidlack
- The Forsyth Institute, Cambridge, MA 02142, USA
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Markus Hardt
- The Forsyth Institute, Cambridge, MA 02142, USA
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - William J. Landis
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH 44325, USA
| | - Nita Sahai
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, OH 44325, USA
- Department of Geosciences, The University of Akron, Akron, OH 44325, USA
- Integrated Bioscience Program, The University of Akron, Akron, OH 44325, USA
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Merl-Pham J, Basak T, Knüppel L, Ramanujam D, Athanason M, Behr J, Engelhardt S, Eickelberg O, Hauck SM, Vanacore R, Staab-Weijnitz CA. Quantitative proteomic profiling of extracellular matrix and site-specific collagen post-translational modifications in an in vitro model of lung fibrosis. Matrix Biol Plus 2019; 1:100005. [PMID: 33543004 DOI: 10.1016/j.mbplus.2019.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Lung fibrosis is characterized by excessive deposition of extracellular matrix (ECM), in particular collagens, by fibroblasts in the interstitium. Transforming growth factor-β1 (TGF-β1) alters the expression of many extracellular matrix (ECM) components produced by fibroblasts, but such changes in ECM composition as well as modulation of collagen post-translational modification (PTM) levels have not been comprehensively investigated. Here, we performed mass spectrometry (MS)-based proteomics analyses to assess changes in the ECM deposited by cultured lung fibroblasts from idiopathic pulmonary fibrosis (IPF) patients upon stimulation with transforming growth factor β1 (TGF-β1). In addition to the ECM changes commonly associated with lung fibrosis, MS-based label-free quantification revealed profound effects on enzymes involved in ECM crosslinking and turnover as well as multiple positive and negative feedback mechanisms of TGF-β1 signaling. Notably, the ECM changes observed in this in vitro model correlated significantly with ECM changes observed in patient samples. Because collagens are subject to multiple PTMs with major implications in disease, we implemented a new bioinformatic platform to analyze MS data that allows for the comprehensive mapping and site-specific quantitation of collagen PTMs in crude ECM preparations. These analyses yielded a comprehensive map of prolyl and lysyl hydroxylations as well as lysyl glycosylations for 15 collagen chains. In addition, site-specific PTM analysis revealed novel sites of prolyl-3-hydroxylation and lysyl glycosylation in type I collagen. Interestingly, the results show, for the first time, that TGF-β1 can modulate prolyl-3-hydroxylation and glycosylation in a site-specific manner. Taken together, this proof of concept study not only reveals unanticipated TGF-β1 mediated regulation of collagen PTMs and other ECM components but also lays the foundation for dissecting their key roles in health and disease. The proteomic data has been deposited to the ProteomeXchange Consortium via the MassIVE partner repository with the data set identifier MSV000082958. Quantitative proteomics of TGF-β-induced changes in ECM composition and collagen PTM in pulmonary fibroblasts TGF-β promotes crosslinking and turnover as well as complex feedback mechanisms that alter fibroblast ECM homeostasis. A novel bioinformatic workflow for MS data analysis enabled global mapping and quantitation of known and novel collagen PTMs Quantitative assessment of prolyl-3-hydroxylation site occupancy and lysine-O-glycosylation microheterogeneity TGF-β1 modulates collagen PTMs in a site-specific manner that may favor collagen accumulation in lung fibrosis
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Key Words
- 3-HyP, 3-hydroxyproline
- 4-HyP, 4-hydroxyproline
- AGC, automatic gain control
- ANXA11, annexin A11
- BGN, biglycan
- COL1A1, collagen-I alpha 1 chain
- Collagen
- Collagen post-translational modifications
- DCN, decorin
- ECM, extracellular matrix
- Extracellular matrix
- FN1, fibronectin 1
- G-HyK, galactosylhydroxylysine
- GG-HyK, glucosylgalactosylhydroxylysine
- HyK, hydroxylysine
- HyP, hydroxyproline
- ILD, interstitial lung disease
- IPF, idiopathic pulmonary fibrosis
- LH, lysyl hydroxylase
- LOX(L), lysyl oxidase(-like)
- LTBP2, latent-transforming growth factor β -binding protein 2
- Lysyl glycosylation
- Lysyl hydroxylation
- P3H, prolyl-3-hydroxylase
- P4H, prolyl-4-hydroxylase
- PAI1, plasminogen activator inhibitor 1
- PCA, principal component analysis
- PLOD (LH), procollagen-lysine,2-oxoglutarate 5-dioxygenases (lysyl hydroxylases)
- PTM, post-translational modification
- Prolyl hydroxylation
- Pulmonary fibrosis
- SEMA7A, semaphorin 7a
- TGF-β, transforming growth factor β
- TGM2, transglutaminase 1
- Transforming growth factor-β
- VCAN, versican
- Xaa, Xaa position in the Gly-Xaa-Yaa repeat in triple-helical collagen
- Yaa, Yaa position in the Gly-Xaa-Yaa repeat in triple-helical collagen
- α-SMA, α-smooth muscle actin
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Ritelli M, Chiarelli N, Zoppi N, Dordoni C, Quinzani S, Traversa M, Venturini M, Calzavara-Pinton P, Colombi M. Insights in the etiopathology of galactosyltransferase II (GalT-II) deficiency from transcriptome-wide expression profiling of skin fibroblasts of two sisters with compound heterozygosity for two novel B3GALT6 mutations. Mol Genet Metab Rep 2014. [PMID: 28649518 PMCID: PMC5471164 DOI: 10.1016/j.ymgmr.2014.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mutations in B3GALT6, encoding the galactosyltransferase II (GalT-II) involved in the synthesis of the glycosaminoglycan (GAG) linkage region of proteoglycans (PGs), have recently been associated with a spectrum of connective tissue disorders, including spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMDJL1) and Ehlers–Danlos-like syndrome. Here, we report on two sisters compound heterozygous for two novel B3GALT6 mutations that presented with severe short stature and progressive kyphoscoliosis, joint hypermobility and laxity, hyperextensible skin, platyspondyly, short ilia, and elbow malalignment. Microarray-based transcriptome analysis revealed the differential expression of several genes encoding extracellular matrix (ECM) structural components, including COMP, SPP1, COL5A1, and COL15A1, enzymes involved in GAG synthesis and in ECM remodeling, such as CSGALNACT1, CHPF, LOXL3, and STEAP4, signaling transduction molecules of the TGFβ/BMP pathway, i.e., GDF6, GDF15, and BMPER, and transcription factors of the HOX and LIM families implicated in skeletal and limb development. Immunofluorescence analyses confirmed the down-regulated expression of some of these genes, in particular of the cartilage oligomeric matrix protein and osteopontin, encoded by COMP and SPP1, respectively, and showed the predominant reduction and disassembly of the heparan sulfate specific GAGs, as well as of the PG perlecan and type III and V collagens. The key role of GalT-II in GAG synthesis and the crucial biological functions of PGs are consistent with the perturbation of many physiological functions that are critical for the correct architecture and homeostasis of various connective tissues, including skin, bone, cartilage, tendons, and ligaments, and generates the wide phenotypic spectrum of GalT-II-deficient patients. Clinical features/molecular characterization of two patients with spondyloepimetaphyseal dysplasia with joint laxity type 1 Identification of two novel B3GALT6 mutations First report of transcriptome-wide gene expression profiling on GalT-II-deficient fibroblasts Immunofluorescence studies of several ECM structural components in GalT-II-deficient cells Enlargement of the knowledge on the GalT-II deficiency’s molecular pathogenesis
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Key Words
- ATCS, adducted-thumb club foot syndrome
- Abs, antibodies
- B3GALT6
- BMP, bone morphogenetic proteins
- C4ST, chondroitin 4-sulfotransferase
- C6ST, chondroitin 6-sulfotransferase
- COLLI, type I collagen
- COLLIII, type III collagen
- COLLV, type V collagen
- COLLs, collagens
- COMP, cartilage oligomeric matrix protein
- CS, chondroitin sulfate
- CSGALNACT1, chondroitin sulfate N-acetylgalactosaminyltransferase 1
- CTDs, connective tissue disorders
- Cartilage oligomeric matrix protein
- ChPF, chondroitin polymerizing factor
- ChSy, chondroitin synthase
- D4ST, dermatan 4 sulfotransferase 1
- DCN, decorin
- DEGs, differentially expressed genes
- DS, dermatan sulfate
- ECM, extracellular matrix
- EDS, Ehlers–Danlos syndrome
- Ehlers–Danlos syndrome
- FN, fibronectin
- GAGs, glycosaminoglycans
- GO, gene ontology
- Gal, galactose
- GalNAc, N-acetylgalactosamine
- GalNAc4S-6ST, GalNAc 4-sulfate 6-O-sulfotransferase
- GalNAcT, β1,4-N-acetylgalactosaminyltransferase
- GalNAcT-16, N-acetylgalactosaminyltransferase 16
- GalT-I/II, galactosyltransferase I and II
- GalT-II deficiency
- GlcA, glucuronic acid
- GlcAT, glucuronosyltransferase
- GlcNAc, N-acetylglucosamine
- GlcNAcT, α1,4-N-acetylglucosaminyltransferase
- HA, hyaluronic acid
- HAS2, hyaluronan synthase 2
- HOX, homeobox gene family
- HPO, human phenotype ontology
- HS, heparan sulfate
- Hep, heparin
- IF, immunofluorescence microscopy studies
- IdoA, iduronic acid
- OPN, osteopontin
- Osteopontin
- PGs, proteoglycans
- PTC, premature termination codon of translation
- SEMDJL1, spondyloepimetaphyseal dysplasia with joint laxity type 1
- Spondyloepimetaphyseal dysplasia with joint laxity type 1
- TNs, tenascins
- Xyl, xylose
- XylT, xylosyltransferase
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Marco Ritelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Nicola Chiarelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Nicoletta Zoppi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Chiara Dordoni
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Stefano Quinzani
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Michele Traversa
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Marina Venturini
- Division of Dermatology, Department of Clinical and Experimental Sciences, Spedali Civili University Hospital, Brescia, Italy
| | - Piergiacomo Calzavara-Pinton
- Division of Dermatology, Department of Clinical and Experimental Sciences, Spedali Civili University Hospital, Brescia, Italy
| | - Marina Colombi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
- Corresponding author at: Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
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