Comprehensive Profiling of Cartilage Extracellular Matrix Formation and Maturation Using Sequential Extraction and Label-free Quantitative Proteomics

Articular cartilage is indispensable for joint function but has limited capacity for self-repair. Engineering of neocartilage in vitro is therefore a major target for autologous cartilage repair in arthritis. Previous analysis of neocartilage has targeted cellular organization and specific molecular components. However, the complexity of extracellular matrix (ECM) development in neocartilage has not been investigated by proteomics. To redress this, we developed a mouse neocartilage culture system that produces a cartilaginous ECM. Differential analysis of the tissue proteome of 3-week neocartilage and 3-day postnatal mouse cartilage using solubility-based protein fractionation targeted components involved in neocartilage development, including ECM maturation. Initially, SDS-PAGE analysis of sequential extracts revealed the transition in protein solubility from a high proportion of readily soluble (NaCl-extracted) proteins in juvenile cartilage to a high proportion of poorly soluble (guanidine hydrochloride-extracted) proteins in neocartilage. Label-free quantitative mass spectrometry (LTQ-Orbitrap) and statistical analysis were then used to filter three significant protein groups: proteins enriched according to extraction condition, proteins differentially abundant between juvenile cartilage and neocartilage, and proteins with differential solubility properties between the two tissue types. Classification of proteins differentially abundant between NaCl and guanidine hydrochloride extracts (n = 403) using bioinformatics revealed effective partitioning of readily soluble components from subunits of larger protein complexes. Proteins significantly enriched in neocartilage (n = 78) included proteins previously not reported or with unknown function in cartilage (integrin-binding protein DEL1; coiled-coil domain-containing protein 80; emilin-1 and pigment epithelium derived factor). Proteins with differential extractability between juvenile cartilage and neocartilage included ECM components (nidogen-2, perlecan, collagen VI, matrilin-3, tenascin and thrombospondin-1), and the relationship between protein extractability and ECM ultrastructural organization was supported by electron microscopy. Additionally, one guanidine extract-specific neocartilage protein, protease nexin-1, was confirmed by immunohistochemistry as a novel component of developing articular cartilage in vivo. The extraction profile and matrix-associated immunostaining implicates protease nexin-1 in cartilage development in vitro and in vivo.The cartilage of the mammalian skeletal system has two distinct roles. The epiphyseal cartilage of the growth plate drives endochondral bone growth, and the hyaline cartilage at the weight-bearing surfaces of bones facilitates joint articulation. In both environments, chondrocyte-regulated production, assembly, and turnover of the extracellular matrix (ECM)¹ are essential for the tissue to withstand compressive forces and respond to mechanical loading. The major structural constituents of cartilage ECM are the heterotypic collagen II/IX/XI fibrils and proteoglycan-glycosaminoglycan networks of aggrecan and hyaluronan. Loss of joint function in osteoarthritis (OA) is strongly associated with net loss of aggrecan and collagen breakdown caused by an imbalance of ECM homeostasis (1). In addition, many inherited human chondrodysplasias involve disruption of cartilage matrix assembly or cell-matrix interactions, resulting in abnormal skeletal development and in some cases early onset cartilage degeneration (2, 3).The alterations in chondrocyte metabolism that occur during OA are complex and remain poorly understood (4). An early response to loss or fragmentation of ECM components is attempted tissue repair through secretion of anabolic factors, cell proliferation, and matrix remodeling (5). However, the resulting product is a fibrocartilage that does not recapitulate the composition or precise architecture of the original hyaline articular cartilage. This limited capacity of cartilage for regeneration has driven research into cartilage tissue engineering (6). Production of authentic hyaline cartilage in vitro remains challenging due to the dedifferentiation of primary chondrocytes upon removal from their three-dimensional matrix environment (7). However, improved “neocartilage” culture systems have been developed through evaluation of suitable chondroprogenitor or chondrocyte subpopulations and optimization of exogenous support matrices and growth factors (8, 9). The therapeutic target of neocartilage culture is autologous tissue repair. However, there is fundamental value in using neocartilage systems to elucidate mechanisms of protein integration into the ECM and the role of specific protein interactions during cartilage maturation.Cartilage profiling by 2-DE and mass spectrometry-based proteomics is generating important new insight into mechanisms of cartilage degeneration in vitro and in vivo (10). For example, anabolic factors with potential roles in cartilage repair, including connective tissue growth factor and inhibin βA (activin), were identified in the secretome of human OA cartilage explants (11). Comparison of cartilage protein extracts from normal donors and OA patients revealed significantly increased levels of the serine protease Htra1 in patient cartilage (12) and that Htra1-mediated proteolysis of aggrecan may significantly contribute to OA pathology (13). Targeted analysis of the chondrocyte mitochondrial proteome highlighted OA-related changes in energy production and protection against reactive oxygen species (14). Obtaining sufficient chondrocytes from human donors for proteomics unfortunately requires expansion of the cell population with potential loss of the chondrocyte phenotype during prolonged culture. Other drawbacks encountered with human samples include the clinical heterogeneity of OA, lack of matched controls, and inherent genetic variation of human subjects (15). Alternatively, animal models that recapitulate hallmarks of progressive cartilage degeneration, such as aggrecan loss and articular surface fibrillation, are emerging as a powerful resource, particularly in mice lacking specific proteases or protease target sites (16, 17). The development of techniques for analysis of murine cartilage using proteomics has paved the way for differential analysis of normal and pathological or genetically targeted cartilage (18, 19).Label-free methods for relative peptide quantitation, such as ion intensity measurement and spectral counting, are emerging as reliable and cost-effective alternatives to chemical modification or isotopic peptide labeling (20). Combining orthogonal protein and/or peptide fractionation with high resolution HPLC-MS can achieve proteome-wide coverage (21). Because extensive sample fractionation can introduce redundancy and variation, improved sequence/proteome coverage must be balanced against the cost of additional sample handling and lengthy LC-MS runs (22).Here we describe a novel platform for analysis of mouse cartilage using solubility-based protein fractionation (19) combined with label-free quantitative tandem MS (LTQ-Orbitrap). Sequential extraction of 3-day postnatal (P3) mouse epiphyseal cartilage and 3-week neocartilage cultures revealed a marked transition from a high proportion of readily soluble components in P3 extracts to a greater proportion of poorly soluble proteins in neocartilage. Principal component analysis and hierarchical clustering were used to globally assess the inter-relationships between P3 cartilage and neocartilage NaCl and guanidine hydrochloride (GdnHCl) extracts. At a p value cutoff of 0.05, 403 proteins were classified as extract-specific, whereas 125 proteins were classified as tissue sample-specific. Many of the proteins significantly enriched in neocartilage were annotated by the terms cell adhesion, extracellular matrix, and cytoskeletal remodeling. Further statistical analysis identified a third important protein category in which protein solubility was altered between the P3 and neocartilage. Identification of proteins involved in neocartilage maturation has generated novel insight into the fundamental process of cartilage matrix development with potential for further analysis of engineered cartilaginous tissues with biomedical applications.