Proteomics approaches for the studies of bone metabolism

Bone is an active tissue, in which bone formation by osteoblast is followed by bone resorption by osteoclasts, in a repeating cycle. Proteomics approaches may allow the detection of changes in cell signal transduction, and the regulatory mechanism of cell differentiation. LC-MS/MS-based quantitative methods can be used with labeling strategies, such as SILAC, iTRAQ, TMT and enzymatic labeling. When used in combination with specific protein enrichment strategies, quantitative proteomics methods can identify various signaling molecules and modulators, and their interacting proteins in bone metabolism, to elucidate biological functions for the newly identified proteins in the cellular context. In this article, we will briefly review recent major advances in the application of proteomics for bone biology, especially from the aspect of cellular signaling. [BMB Reports 2014; 47(3): 141-148]

[1]  Yuan Cheng,et al.  Comparative proteomics of glioma stem cells and differentiated tumor cells identifies S100A9 as a potential therapeutic target , 2013, Journal of cellular biochemistry.

[2]  Kyu-Tae Chang,et al.  Role of gangliosides in the differentiation of human mesenchymal-derived stem cells into osteoblasts and neuronal cells , 2013, BMB reports.

[3]  B. Badran,et al.  Molecular mechanisms of mesenchymal stem cell differentiation towards osteoblasts. , 2013, World journal of stem cells.

[4]  J. Eng,et al.  Protein Kinase PKN1 Represses Wnt/β-Catenin Signaling in Human Melanoma Cells* , 2013, The Journal of Biological Chemistry.

[5]  J. Foekens,et al.  Quantitative proteomic analysis of microdissected breast cancer tissues: comparison of label-free and SILAC-based quantification with shotgun, directed, and targeted MS approaches. , 2013, Journal of proteome research.

[6]  H. Ishikawa,et al.  In vitro analysis of mesenchymal stem cells derived from human teeth and bone marrow , 2013, Odontology.

[7]  Jeroen A. A. Demmers,et al.  Activin A Suppresses Osteoblast Mineralization Capacity by Altering Extracellular Matrix (ECM) Composition and Impairing Matrix Vesicle (MV) Production* , 2013, Molecular & Cellular Proteomics.

[8]  M. Masuda,et al.  Proteomic approaches to the discovery of cancer biomarkers for early detection and personalized medicine. , 2013, Japanese journal of clinical oncology.

[9]  Kyong-Tai Kim,et al.  Comparative secretome analysis of human bone marrow‐derived mesenchymal stem cells during osteogenesis , 2013, Journal of cellular physiology.

[10]  A. Oberg,et al.  Statistical methods for quantitative mass spectrometry proteomic experiments with labeling , 2012, BMC Bioinformatics.

[11]  I. Kratchmarova,et al.  Temporal Profiling and Pulsed SILAC Labeling Identify Novel Secreted Proteins During Ex Vivo Osteoblast Differentiation of Human Stromal Stem Cells* , 2012, Molecular & Cellular Proteomics.

[12]  G. Rho,et al.  In vitro and in vivo osteogenesis of human mesenchymal stem cells derived from skin, bone marrow and dental follicle tissues. , 2012, Differentiation; research in biological diversity.

[13]  R. Moon,et al.  Wnt/β-catenin pathway regulates bone morphogenetic protein (BMP2)-mediated differentiation of dental follicle cells. , 2012, Journal of periodontal research.

[14]  Richard D. Smith,et al.  Advancing the sensitivity of selected reaction monitoring‐based targeted quantitative proteomics , 2012, Proteomics.

[15]  Jin Wang,et al.  Smads, p38 and ERK1/2 are involved in BMP9-induced osteogenic differentiation of C3H10T1/2 mesenchymal stem cells. , 2012, BMB reports.

[16]  O. Lee,et al.  Phosphoproteomic analysis of human mesenchymal stromal cells during osteogenic differentiation. , 2012, Journal of Proteome Research.

[17]  D R Mani,et al.  iTRAQ Labeling is Superior to mTRAQ for Quantitative Global Proteomics and Phosphoproteomics* , 2011, Molecular & Cellular Proteomics.

[18]  J. Chen,et al.  An integrated proteomics analysis of bone tissues in response to mechanical stimulation , 2011, BMC Systems Biology.

[19]  I. Jackson,et al.  Loss of the BMP Antagonist, SMOC-1, Causes Ophthalmo-Acromelic (Waardenburg Anophthalmia) Syndrome in Humans and Mice , 2011, PLoS genetics.

[20]  Ji‐Hyun Lee,et al.  Phospho‐Smad1 modulation by nedd4 e3 ligase in BMP/TGF‐β signaling , 2011, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[21]  M. Dadlez,et al.  Proteomic characterization of biogenesis and functions of matrix vesicles released from mineralizing human osteoblast-like cells. , 2011, Journal of proteomics.

[22]  T. Komori Signaling networks in RUNX2‐dependent bone development , 2011, Journal of cellular biochemistry.

[23]  X. Wang,et al.  Wnt/beta-catenin signaling activates microRNA-181 expression in hepatocellular carcinoma , 2011, Cell & Bioscience.

[24]  Y. Bae,et al.  Secretome analysis of human BMSCs and identification of SMOC1 as an important ECM protein in osteoblast differentiation. , 2010, Journal of proteome research.

[25]  J. Yates,et al.  Role of PI3K on the regulation of BMP2-induced beta-Catenin activation in human bone marrow stem cells. , 2010, Bone.

[26]  J. Yates,et al.  'Two-stage double-technique hybrid (TSDTH)' identification strategy for the analysis of BMP2-induced transdifferentiation of premyoblast C2C12 cells to osteoblast. , 2009, Journal of proteome research.

[27]  D. Magne,et al.  TNF-alpha and IL-1beta inhibit RUNX2 and collagen expression but increase alkaline phosphatase activity and mineralization in human mesenchymal stem cells. , 2009, Life sciences.

[28]  J. Shaughnessy,et al.  The role of Dickkopf-1 in bone development, homeostasis, and disease. , 2009, Blood.

[29]  M. Kassem,et al.  Osteoblastic cells: differentiation and trans-differentiation. , 2008, Archives of biochemistry and biophysics.

[30]  Je-Yong Choi,et al.  The Correlation of Salvia miltiorrhiza Extract–Induced Regulation of Osteoclastogenesis with the Amount of Components Tanshinone I, Tanshinone IIA, Cryptotanshinone, and Dihydrotanshinone , 2008 .

[31]  John R Yates,et al.  Cancer proteomics by quantitative shotgun proteomics , 2007, Molecular oncology.

[32]  M. Ringuette,et al.  Is SPARC an Evolutionarily Conserved Collagen Chaperone? , 2007, Journal of dental research.

[33]  J. Caetano-Lopes,et al.  Osteoblasts and bone formation. , 2007, Acta reumatologica portuguesa.

[34]  K. Nagashima,et al.  Analysis of the extracellular matrix vesicle proteome in mineralizing osteoblasts , 2007, Journal of cellular physiology.

[35]  M. Lamghari,et al.  Leptin effect on RANKL and OPG expression in MC3T3‐E1 osteoblasts , 2006, Journal of cellular biochemistry.

[36]  Xu Cao,et al.  BMP Signaling and Skeletogenesis , 2006, Annals of the New York Academy of Sciences.

[37]  K. Cadigan,et al.  Wnt signaling: complexity at the surface , 2006, Journal of Cell Science.

[38]  Scott Vandenberg,et al.  Comparing the protein expression profiles of human mesenchymal stem cells and human osteoblasts using gene ontologies. , 2005, Stem cells and development.

[39]  Xizhi Guo,et al.  Wnt/beta-catenin signaling in mesenchymal progenitors controls osteoblast and chondrocyte differentiation during vertebrate skeletogenesis. , 2005, Developmental cell.

[40]  S. Krane Identifying genes that regulate bone remodeling as potential therapeutic targets , 2005, The Journal of experimental medicine.

[41]  Di Chen,et al.  Bone Morphogenetic Proteins , 2004, Growth factors.

[42]  Henrik Birkedal,et al.  Influence of the degradation of the organic matrix on the microscopic fracture behavior of trabecular bone. , 2004, Bone.

[43]  David John Adams,et al.  Regulation of Neuronal Voltage-gated Sodium Channels by the Ubiquitin-Protein Ligases Nedd4 and Nedd4-2* , 2004, Journal of Biological Chemistry.

[44]  Ju-Hyun Kim,et al.  RANKL regulates endothelial cell survival through the phosphatidylinositol 3′‐kinase/Akt signal transduction pathway , 2003, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[45]  J. Lemonnier,et al.  Activation of p38 Mitogen‐Activated Protein Kinase and c‐Jun‐NH2‐Terminal Kinase by BMP‐2 and Their Implication in the Stimulation of Osteoblastic Cell Differentiation , 2003, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[46]  David L. Lacey,et al.  Osteoclast differentiation and activation , 2003, Nature.

[47]  Kenji Wakabayashi,et al.  Proteome analysis of secreted proteins during osteoclast differentiation using two different methods: Two‐dimensional electrophoresis and isotope‐coded affinity tags analysis with two‐dimensional chromatography , 2003, Proteomics.

[48]  A. Economides,et al.  0163-769X/03/$20.00/0 Endocrine Reviews 24(2):218–235 Printed in U.S.A. Copyright © 2003 by The Endocrine Society doi: 10.1210/er.2002-0023 Bone Morphogenetic Proteins, Their Antagonists, and the Skeleton , 2022 .

[49]  Blagoy Blagoev,et al.  A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling , 2003, Nature Biotechnology.

[50]  Matthias Mann,et al.  Mass spectrometric-based approaches in quantitative proteomics. , 2003, Methods.

[51]  K. Wakabayashi,et al.  PDGF BB purified from osteoclasts acts as osteoblastogenesis inhibitory factor (OBIF). , 2002, Journal of biomolecular techniques : JBT.

[52]  N. Takahashi,et al.  Regulatory mechanisms of osteoblast and osteoclast differentiation. , 2002, Oral diseases.

[53]  G. Sukhikh,et al.  Mesenchymal Stem Cells , 2002, Bulletin of Experimental Biology and Medicine.

[54]  K. Wakabayashi,et al.  Platelet‐Derived Growth Factor BB Secreted From Osteoclasts Acts as an Osteoblastogenesis Inhibitory Factor , 2002, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[55]  E. Rofstad,et al.  Transvascular and interstitial transport of a 19 kDa linear molecule in human melanoma xenografts measured by contrast‐enhanced magnetic resonance imaging , 2001, Journal of magnetic resonance imaging : JMRI.

[56]  H. Nah,et al.  The Roles of Annexins and Types II and X Collagen in Matrix Vesicle-mediated Mineralization of Growth Plate Cartilage* , 2000, The Journal of Biological Chemistry.

[57]  S. Teitelbaum,et al.  Bone resorption by osteoclasts. , 2000, Science.

[58]  G. Karsenty,et al.  The osteoblast: a sophisticated fibroblast under central surveillance. , 2000, Science.

[59]  T. Martin,et al.  Modulation of osteoclast differentiation and function by the new members of the tumor necrosis factor receptor and ligand families. , 1999, Endocrine reviews.

[60]  N. Udagawa,et al.  A new member of tumor necrosis factor ligand family, ODF/OPGL/TRANCE/RANKL, regulates osteoclast differentiation and function. , 1999, Biochemical and biophysical research communications.

[61]  J. Baum,et al.  Folding of peptide models of collagen and misfolding in disease. , 1999, Current opinion in structural biology.

[62]  D. Lacey,et al.  Osteoprotegerin Ligand Is a Cytokine that Regulates Osteoclast Differentiation and Activation , 1998, Cell.

[63]  K Yano,et al.  Osteoclast differentiation factor is a ligand for osteoprotegerin/osteoclastogenesis-inhibitory factor and is identical to TRANCE/RANKL. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[64]  R. Dubose,et al.  A homologue of the TNF receptor and its ligand enhance T-cell growth and dendritic-cell function , 1997, Nature.

[65]  G. Karsenty,et al.  Osf2/Cbfa1: A Transcriptional Activator of Osteoblast Differentiation , 1997, Cell.

[66]  L. N. Wu,et al.  Association between proteoglycans and matrix vesicles in the extracellular matrix of growth plate cartilage. , 1991, The Journal of biological chemistry.

[67]  Friedenstein Aj,et al.  Origin of bone marrow stromal mechanocytes in radiochimeras and heterotopic transplants. , 1978 .

[68]  G. Rho,et al.  Multilineage potential and proteomic profiling of human dental stem cells derived from a single donor. , 2014, Experimental cell research.

[69]  H. Deng,et al.  Wnt/β-catenin signaling activates bone morphogenetic protein 2 expression in osteoblasts. , 2013, Bone.

[70]  R. Hájek,et al.  Proteomic Analysis in Multiple Myeloma Research , 2011, Molecular biotechnology.

[71]  M. Dadlez,et al.  Proteome analysis of matrix vesicles isolated from femurs of chicken embryo , 2008, Proteomics.

[72]  B. Riggs,et al.  The expression of osteoprotegerin and RANK ligand and the support of osteoclast formation by stromal-osteoblast lineage cells is developmentally regulated. , 2000, Endocrinology.

[73]  J. Massagué TGF-beta signal transduction. , 1998, Annual review of biochemistry.

[74]  T. Yokozawa,et al.  Confirmation that magnesium lithospermate B has a hydroxyl radical-scavenging action. , 1995, Experimental and toxicologic pathology : official journal of the Gesellschaft fur Toxikologische Pathologie.

[75]  A. Friedenstein,et al.  Origin of bone marrow stromal mechanocytes in radiochimeras and heterotopic transplants. , 1978, Experimental hematology.