Molecular Medicine Reports Molecular Medicine Reports 1791-2997 1791-3004 D.A. Spandidos 10.3892/mmr.2017.8250 mmr-17-02-2827 Articles Proteomic analysis of synovial fluid in osteoarthritis using SWATH-mass spectrometry LiaoWeixiong 1 LiZhongli 2 LiTanshi 1 ZhangQiang 2 ZhangHeng 1 WangXinzheng 3 Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, P.R. China National Center of Biomedical Analysis, Beijing 100850, P.R. China Correspondence to: Professor Zhongli Li, Department of Orthopedics, Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853, P.R. China, E-mail: lizhongli301@163.com 022018 11122017 17 2 2827 2836 27102016 16062017 Copyright: © Liao et al. 2018 This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

The lack of early diagnostic maneuvers and effective pharmacotherapy for osteoarthritis (OA) is predominantly attributed to current limited understanding of its pathogenesis. In the present study, the alteration of synovial fluid (SF) proteome in OA were analyzed using SWATH-mass spectrometry (SWATH-MS) to further elucidate the pathogenesis of OA. SF samples were collected from 10 OA and 10 rheumatoid arthritis (RA) patients undergoing arthroplasty and 10 patients undergoing arthroscopy for traumatic arthritis (meniscus injury without cartilage lesion). According to the Kellgren-Lawrence (KL) radiographic grading criteria, all the OA and RA patients were classified as KL grade 4. SWATH-MS was applied to identify differentially expressed proteins specifically regulated in OA. Differentially expressed proteins identified by SWATH-MS were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Proteins of interest were quantified by enzyme-linked immunosorbent assay (ELISA) following identification. With the use of SWATH-MS, 131 proteins were identified to be differentially expressed in OA, of which 93 corresponded to upregulation and 38 to downregulation. Complement C1r was the most significantly upregulated protein in OA. Twenty-eight out of the 131 proteins were specifically regulated in OA, of which 17 were upregulated and 11 were downregulated. Dickkopf-related protein 2 (DKK2) was one of the proteins specifically upregulated in OA. Furthermore, KEGG pathway annotation indicated that differentially expressed proteins in OA were enriched in complement and coagulation cascades. ELISA indicated that OA severity was positively correlated with the levels of complement C1r (r=0.549; P<0.001) and DKK2 (r=0.79; P<0.001) in the SF. The results indicate that complement and coagulation cascades are involved in the pathogenesis of OA. Differentially expressed proteins, including complement C1r and DKK2 may be used as potential biomarkers or drug targets, which may facilitate with intervention of OA.

 proteomics synovial fluid osteoarthritis SWATH-mass spectrometry complement C1r dickkopf-related protein 2 Introduction

Osteoarthritis (OA) is a degenerative joint disorder characterized by articular cartilage degradation, osteophyte formation, synovium hyperplasia, subchondral bone cysts and sclerosis. It is one of the leading causes of pain and dysfunction in the joints among the aging population (1). Despite the high prevalence of OA, its pathogenesis remains unclear. At present, the diagnosis of OA primarily depends on clinical symptoms and radiographic findings. However, the majority of individuals are clinically asymptomatic at the early stages of OA, and pathological degradation of the articular cartilage already exists before the symptoms arise. Furthermore, radiographs may appear normal at this stage due to lack of sensitivity in visualizing minimal cartilage lesions. Thus, the diagnostic methods currently in use have limitations in detecting preclinical OA and provide an inaccurate assessment of disease progression. Although multiple translational techniques detect early OA processes, it remains unknown as to whether they truly represent the initial events. Therefore, the clinical diagnosis of early OA is one of the greatest challenges in this field (2). Currently, there is no definitely effective medication for the treatment of early OA. Traditional medications, such as glucosamine and hyaluronic acid, once thought of as effective, have no longer been recommended by the latest American Academy of Orthopaedic Surgeons guideline due to evidence of a lack of efficacy (3). The medications currently used for the treatment of OA are predominantly aimed at relieving pain, but do not prevent disease progression. These limitations give rise to the interest in proteomic studies to identify candidate biomarkers and drug targets, which may facilitate early diagnosis and intervention of OA. Additionally, proteomic studies provide greater insight into OA pathogenesis and original insights into the molecular mechanisms involved in disease progression.

Advances in proteomic technologies have facilitated extensive proteomic characterization of various body fluids, including serum (4) and urine (5) in OA. However, evaluating the synovial fluid (SF) proteome is more likely to yield a higher concentration of potential biomarkers than serum and urine, as SF is in direct contact with articular cartilage, synovium, ligament, meniscus and joint capsule. Alterations in metabolism of any of these tissues during disease progression are reflected as alterations in the proteomic profile of SF, which is also less influenced by systematic conditions. Therefore, it is considered more appropriate to detect the proteomic profile in SF than in other body fluids. There are also certain studies designed to investigate the expression of certain proteins in SF from OA patients (6). These studies focused on evaluating the expression of certain proteins, but failed to screen novel proteins that are differentially expressed in SF. With the use of quantitative proteomic technologies, a series of novel proteins differentially expressed in SF from OA patients have been identified in previous studies (7,8). However, the majority of these investigations were performed using low resolution mass spectrometry (MS) and with minimal fractionation of the samples, which limited the depth of coverage. Isobaric tags for relative and absolute quantification is a labeling method with high throughput, easy automation, high resolution and quantification accuracy, which enables quantitative proteomics analysis of four samples simultaneously under the same experimental conditions (9). This technology has also been applied to investigate alterations of the proteomic profile in OA in previous studies (10,11). Although a greater number of novel proteins were identified to be differentially expressed using this method (10,11), whether these proteins are specifically regulated in OA remains unclear due to a lack of effective standard controls or inter-controls.

SWATH-MS is an emerging data-independent acquisition method, whichgenerates a single file containing fragment ion spectra of all ionized species of a sample (12). When combined with a targeted data analysis strategy, SWATH-MS was demonstrated to achieve favorable accuracy, dynamic range, and reproducibility of selected reaction monitoring, which is considered to be the golden standard in quantitative proteomic technology (13). In order to identify differentially expressed proteins specifically regulated in OA and further elucidate the disease pathogenesis, SWATH-MS was performed to compare the SF proteome in OA, rheumatoid arthritis (RA) and traumatic arthritis (meniscus injury without cartilage defect). Subsequently, proteins of interest were quantified by enzyme-linked immunosorbent assay (ELISA). To the best of our knowledge, no comparative analysis with respect to the SF proteome has been conducted in these three types of knee disorders using SWATH-MS.

 Materials and methods <sec> <title>Subjects

The present study was initiated following approval from the Ethical Committee of the Chinese PLA General Hospital and informed consent was obtained from all the subjects. SF samples were acquired from 30 patients who had received surgical treatment for a knee disorder between September 2014 and January 2015 in the Orthopedics Department of the Chinese PLA General Hospital (Beijing, China). A total of 10 knee OA patients (4 men and 6 women; age, 64–72 years; mean age, 67 years) undergoing arthroplasty were defined as the study group, 10 knee RA patients (4 men and 6 women; age, 45–69 years; mean age, 60 years) undergoing arthroplasty served as the inter-control group, and 10 patients (7 men and 3 women; age, 23–47 years; mean age, 29 years) undergoing arthroscopy for traumatic knee arthritis (meniscus injury without cartilage defect) within 7 days after injury served as the standard control group. The diagnosis of knee OA and RA was based upon the criteria of the American College of Rheumatology (14). The severity of knee OA and RA was evaluated by the Kellgren-Lawrence (KL) radiographic grading criteria (Fig. 1), according to which all the knee OA and RA patients recruited were classified as KL grade 4. All the patient data were retrieved from our institutional database through chart review.

 Sample preparation and protein digestion

SF samples (1–2 ml) were aspirated from the affected knee using a sterile puncture needle prior to surgery and 50 µl proteinase inhibitor cocktail (Roche Molecular Diagnostics, Pleasanton, CA, USA) was immediately added to the sample after collection. The mixture was centrifuged at 19,228 × g for 20 min at 4°C (Hettich MIKRO 22R; Hettich Benelux, Tuttlingen, Germany) to remove cells and debris. For the comprehensive shotgun analysis, all the SF samples were depleted of the 14 most abundant proteins with the multiple affinity removal system (MARS Hu-14 spin cartridge; Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer's instruction. After reduction and alkylation with 10 mM tris (2-carboxyethyl) phosphine (Sigma-Aldrich; Merck KGaA, Darmstadt, Germany) and 20 mM iodoacetamide (Sigma-Aldrich; Merck KGaA), the samples were subjected to protein quantification using the Bradford Assay according to the manufacturer's instructions with a commercial Bradford reagent (Bio-Rad Laboratories, Hercules, CA, USA). Subsequently, the samples were diluted with 1 M urea and digested with sequencing-grade trypsin (Promega Corporation, Madison, WI, USA) at a protease/protein ratio of 1:30 overnight at 37°C. Following digestion, the samples were stored at −80°C until use.

 Shotgun proteomic measurement

The processed peptides were measured using a Triple TOF 5600 Plus mass spectrometer (SCIEX, Framingham, MA, USA) operated in data-dependent acquisition (DDA) mode. The mass spectrometer was interfaced with a NanoLC Ultra 2D Plus HPLC system (Eksigent Technologies, Dublin, CA, USA) as previously described (12,13). Peptides were directly injected onto a 20-cm PicoFrit emitter and separated using a 120-min gradient from 2–35% (buffer A: 0.1% Formic acid and 2% acetonitrile; buffer B: 0.1% Formic acid and 90% acetonitrile) at a flow rate of 300 nl/min. MS1 spectra were collected in the range 350–1,250 m/z for 250 msec. The 20 most intense precursors with charge state 2–5, which exceeded 250 counts per sec were selected for fragmentation, and MS2 spectra were collected in the range 100–1,500 m/z for 50 msec. The precursor ions were dynamically excluded from reselection for 20 sec.

 SWATH-MS measurement

SWATH-MS measurements were performed with peptide mixtures generated by digesting SF samples. The unfractionated, total peptide samples were analyzed to minimize confounding factors introduced by sample handling. The same liquid chromatography-MS/MS system used for DDA measurements was used for SWATH analysis (12,13). In SWATH-MS mode, the instrument was specifically tuned to optimize the quadrupole settings for the selection of 25-m/z wide precursor ion selection windows. Using an isolation width of 25 m/z, a set of overlapping windows was constructed, covering the precursor mass range of 400–1,200 m/z. The effective isolation windows were considered as being 400–425, 424–449, 448–473 m/z, and so on. SWATH-MS2 spectra were collected from 100–1,500 m/z. The collision energy was optimized for each window according to the calculation for a charge 2+ion centered upon the window with a spread of 15 eV. An accumulation time of 50 msec was used for all fragment ion scans in high-sensitivity mode, and for each SWATH-MS cycle, a survey scan in high-resolution mode was acquired for 50 msec. SWATH-MS measurements were repeated three times on each sample to access the technical variability. Differentially expressed proteins identified by SWATH-MS were subjected to gene ontology (GO) and KEGG pathway annotation.

 ELISA

Another 90 SF samples were obtained from 36 knee OA patients (17 men and 19 women, aged 57–74 years; mean age, 65 years), 36 knee RA patients (15 men and 21 women, aged 41–70 years; mean age, 58 years) and 18 patients (12 men and 6 women, aged 21–47 years;mean age, 28 years) with traumatic knee arthritis (meniscus injury without cartilage defect) to detect the level of complement C1r and that of Dickkopf-related protein 2 (DKK2). According to the KL radiographic grading criteria, 18 out of the 36 knee OA patients were classified as KL grade 2, and the other 18 as KL grade 4. Similarly, 18 out of the 36 knee RA patients were categorized as KL grade 2, and the other 18 as KL grade 4. The levelsof complement C1r and that of DKK2 in SF were measured by ELISA (MyBioSource; R&D Systems, Inc., Minneapolis, MN, USA) according to the manufacturer's instructions.

 Statistical analysis

Statistical analysis was performed with SPSS software (Version 17.0; SPSS Inc, Chicago, IL, USA). Data were expressed as the mean ± standard deviation. One way analysis of variance followed by a post hoc Tukey test for multiple comparisons was performed to compare the quantitative data from different groups. Pearson's correlation coefficient was used to analyze the correlation between protein level and disease severity. P<0.05 was considered to indicate a statistically significant difference.

 Results <sec> <title>SWATH-MS

To evaluate technical variability, each sample was analyzed in triplicate. As presented in Fig. 2, total ion current chromatograms from triplicates of the same sample exhibited high similarity, whereas those from different samples displayed obvious variation. The results revealed small technical variability and excellent reproducibility of SWATH-MS measurements and great variation in proteomic profiles of SF from the different groups.

Proteins were regarded to be differentially expressed when ion intensity between groups was significantly different (P<0.05) and fold change between groups was >1.5. Based on these criteria, the comparison between OA and traumatic arthritis resulted in the identification of 131 significantly different proteins, of which 93 corresponded to upregulation and 38 to downregulation in OA. Complement C1r was the most significantly upregulated protein in OA (Fig. 3). The comparison between RA and traumatic arthritis led to the identification of 185 significantly different proteins, of which 152 corresponded to upregulation and 33 to downregulation in RA. The comparison between OA and RA gave rise to the identification of 139 significantly different proteins, of which 22 corresponded to upregulation and 117 to downregulation in OA.

Proteins with a fold change >1.5 in OA and a fold change <1.5 in RA were defined as differentially expressed proteins specifically regulated in OA. On the basis of these criteria, 28 proteins were considered to be specifically regulated in OA, of which 17 were upregulated and 11 were downregulated (Table I). DKK2 was one of the proteins specifically upregulated in OA (Fig. 4). Proteins up-/downregulated with a fold change >1.5 in OA and down-/upregulated with a fold change >1.5 in RA were defined as differentially expressed proteins conversely regulated in OA and RA. According to these criteria, 8 proteins were identified to be conversely regulated in OA and RA, of which 3 were upregulated in OA and downregulated in RA, 5 were downregulated in OA and upregulated in RA (Table II).

GO annotation with respect to the 131 differentially expressed proteins in OA demonstrated that the cellular component of these proteins was predominantly derived from the extracellular matrix (ECM), cytoplasmic membrane, cytoplasm, secretory granule and lipoprotein particle. The molecular function of these proteins primarily included binding, transporter, enzyme activator and inhibitor activity. The biological process these proteins participated in predominantly included the acute inflammatory response, complement activation, immune response, response to stimulus, regulation of apoptosis and homeostatic process. KEGG pathway annotation indicated that these proteins were enriched in complement and coagulation cascades (Fig. 5), ECM-receptor interaction and the peroxisome proliferator activated receptor signaling pathway.

 ELISA

As presented in Fig. 6, the mean level of complement C1r in SF from OA was 2,063.1±1,238.1 ng/ml, that from RA was 2,726.4±1,627.8 ng/ml and that from traumatic arthritis was 180.6±102.4 ng/ml. The mean level of complement C1r in SF from RA was significantly higher than those from OA (P=0.033) and traumatic arthritis (P<0.001), and that from OA was also significantly higher than that from traumatic arthritis (P<0.001). According to the KL radiographic grading criteria, the mean level of complement C1r in SF from OA with KL grade 2 was 2,147.8±1,337.2 ng/ml, and that from OA with KL grade 4 was 1,978.4±1,163.1 ng/ml. The mean level of complement C1r in SF from traumatic arthritis was significantly lower than those from OA with KL grade 2 (P<0.001) and KL grade 4 (P<0.001); however, no significant difference was identified between the latter two (P=0.698). The levels of complement C1r in SF from OA were positively correlated with disease severity (r=0.549, P<0.001). Similarly, the mean level of complement C1r in SF from RA with KL grade 2 was 2,920.9±1,743.0 ng/ml, and that from RA with KL grade 4 was 2,531.8±1,528.7 ng/ml. In addition, the mean level of complement C1r in SF from traumatic arthritis was significantly lower than those from RA with KL grade 2 (P<0.001) and KL grade 4 (P<0.001); however, no significant difference was identified between the latter two (P=0.374). The levels of complement C1r in SF from RA were also positively correlated with disease severity (r=0.540, P<0.001).

As shown Fig. 7, the mean level of DKK2 in SF from OA was 186.3±41.0 ng/ml, that from RA was 93.0±34.5 ng/ml and that from traumatic arthritis was 74.2±22.9 ng/ml. The mean level of DKK2 in SF from OA was significantly higher when compared with those from RA (P<0.001) and traumatic arthritis (P<0.001); however, no significant difference was identified between the latter two (P=0.069). According to the KL radiographic grading criteria, the mean level of DKK2 in SF from OA with KL grade 2 was 174.4±42.5 ng/ml, and that from OA with KL grade 4 was 198.2±36.8 ng/ml. The mean level of DKK2 in SF from OA with KL grade 4 was significantly higher than those from OA with KL grade 2 (P=0.045) and traumatic arthritis (P<0.001), and that from OA with KL grade 2 was also significantly higher than that from traumatic arthritis (P<0.001). The levels of DKK2 in SF from OA were positively correlated with disease severity (r=0.796, P<0.001). Similarly, the mean level of DKK2 in SF from RA with KL grade 2 was 89.4±35.4 ng/ml, and that from RA with KL grade 4 was 96.6±34.3 ng/ml. No significant difference was detected between the mean levels of DKK2 in SF from RA with KL grade 2 and traumatic arthritis (P=0.195), between those from RA with KL grade 4 and traumatic arthritis (P=0.057) and between those from RA with KL grade 2 and KL grade 4 (P=0.537). In addition, the levels of DKK2 in SF from RA were positively correlated with disease severity (r=0.287, P=0.035).

 Discussion

OA exerts a great influence on physical and psychological health of the elderly due to its high morbidity and disability rate (1). The lack of early diagnostic maneuvers and effective pharmacotherapy for OA is primarily attributed to the limitations in current understanding of its pathogenesis, which may be further elucidated by investigating the SF proteome. However, for a variety of reasons, previous studies with regard to proteomic analysis of OA were not consistent in demonstrating the pathogenesis and failed to detect effective biomarkers or drug targets to facilitate early diagnosis and intervention of OA. Therefore, this provided the rationale for conducting the present study. In the current study, with the use of SWATH-MS, a total of 131 proteins were identified to be differentially expressed in SF from OA, of which 28 were specifically regulated in OA and eight were conversely regulated in OA and RA. The quantity of differentially expressed proteins identified in the current study is markedly more than in previous studies analyzing SF proteome using other quantitative proteomic technologies (7,8). With the use of two-dimensional polyacrylamide gel electrophoresis, Liu et al (15) identified 10 differential protein spots between the synovial membranes of the bilateral and unilateral knee OA in surgery-induced rabbit models. Similarly, Fernandez-Puente et al (16) developed a multiple reaction monitoring method with which a panel of 14 protein biomarker candidates for OA was identified. Differential proteins identified in the above-mentioned studies, such as lumican (15) and haptoglobin (16) were also identified in the current study. These indicate that, as a novel proteomic technology, SWATH-MS provides a more comprehensive quantification result in delineating the SF proteome and markedly benefits the screening of biomarkers due to its higher resolution and coverage rate.

The hypothesis that the complement system may participate in OA pathogenesis is substantiated by the identification of complement C1r and enrichment of differentially expressed proteins in complement and coagulation cascades. The results are consistent with those reported by Wang et al (17), which indicates abnormally high expression levels and activation of complement components in SF and synovial membranes from OA. Complement activation in turn results in the formation of membrane attack complex (MAC) on chondrocytes, which either kills the cells or causes them to produce matrix-degrading enzymes, inflammatory mediators and other complement effectors, all of which promote joint pathology. A previous study indicates that MAC mediates collagenase expression and cartilage destruction primarily via extracellular signal-regulated kinase-dependent c-Fos induction (18). In addition, complement activation and MAC assembly also stimulate the cell cycle by inducing expression of c-Jun, JunD, and c-Fos mRNAs (19), which appears to have a potential correlation with the pathology of hyperosteogeny and synovial hyperplasia in OA. These findings provide a rationale for targeting the complement system as a disease-modifying therapeutic strategy for OA.

DKK2 is one of the proteins that is specifically upregulated in OA, the alteration of which has been confirmed by subsequent ELISA in the present study. As a Wnt signaling antagonist, the overexpression of DKK2 contributes to the abnormal phenotype and poor mineralization of OA osteoblasts by altering the Wnt signaling pathway, which is crucial for osteogenesis and regulates terminal osteoblast differentiation (20). The upregulation of DKK2 in OA osteoblasts may be associated with the hypoxic condition and ischemic episode caused by modification of subchondral bone vascularization (21). Besides DKK2, there are many other proteins specifically regulated in OA. These proteins and their possible underlying mechanism in OA pathogenesis are as follows: i) Adiponectin is a protein hormone secreted predominantly by differentiated adipocytes, it increases intercellular adhesion molecule-1 (ICAM-1) expression levels in OA synovial fibroblasts via the liver kinase B1/calmodulin-dependent protein kinase II, AMP-activated protein kinase, c-Jun, and activator protein 1 signaling pathway. Adiponectin-induced ICAM-1 expression promotes the adhesion of monocytes to OA synovial fibroblasts, which may be involved in the pathogenesis of OA (22). Furthermore, adiponectin enhances production of nitric oxide, interleukin (IL)-6, matrix metalloproteinase (MMP)-1 and MMP-3 in OA chondrocytes in a mitogen-activated protein kinase-dependent manner (23). ii) The mechanisms by which β2-microglobulin induces joint destruction is to induce the release of MMP-1 without concomitant release of tissue inhibitor of metalloproteinase-1 (TIMP-1) from OA synovial fibroblasts, leading to an increase in the MMP-1/TIMP-1 ratio, which is indicative of uncontrolled collagenolysis. The release of MMP-1 induced by β2-microglobulin may be inhibited by doxycycline (24). iii) Thioredoxin, known as a cellular reducing catalyst induced by oxidative stress, is involved in the redox regulation of transcription factors, such as nuclear factor (NF)-κB. It appears to accelerate the nuclear translocation of NF-κB, a major transcriptional regulator for production of IL-6 and IL-8 on stimulation with tumor necrosis factor-a (25). iv) As for annexin A2, a discoidin domain receptor 2 (DDR-2) binding protein in the DDR-2/MMP signaling pathway, its phosphorylation by phosphorylated-DDR-2 leads to MMP-13 secretion (26).

Glutathione S-transferase (GST) is one of the proteins conversely regulated in OA and RA identified in the present study. The differential expression of GST in OA coincides with the results documented by Ostalowska et al (27), which indicate aberrant changes in the activities of antioxidant enzymes, including superoxide dismutase and GST in SF from OA. GST is critically important for cellular defense against oxidative stress-induced apoptosis in OA chondrocytes, possibly by elimination of 4-hydroxynonenal, one of the most abundant and reactive aldehydes of lipid peroxidation products (28). Hyaluronan and proteoglycan link protein is another protein conversely regulated in OA and RA. It has been reported that LP stabilizes the proteoglycan aggregates towards dissociation, and helps to protect them from degradation under conditions where tissue catabolism is promoted (29).

There were certain limitations of the current study. Due to ethical restrictions, patients undergoing arthroscopy for traumatic knee arthritis were selected, rather than healthy individuals, and served as the standard control group. However, as SF samples were acquired within 7 days after injury and patients in this group all exhibited intact articular cartilage under arthroscopy, it is reasonable for us to consider that these samples are most similar to those from healthy individuals in the proteomic profile. Furthermore, to investigate proteins specifically regulated in OA, the design of the inter-control group requires more diversification. In addition to RA, other arthropathies due to systemic lupus erythematosus, ankylosing spondylitis, gout, psoriasis or haemochromatosis should be included as inter-control groups.

In conclusion, the findings of the present study provide an improved understanding of the pathogenesis of OA, and may facilitate the early diagnosis and treatment of OA following the identification of various potential biomarkers and drug targets.

 Acknowledgements

The authors would like to thank Dr Yang Liu for assistance in acquisition of SF samples, and Dr Can Huang for assistance with collection of patient data.

 Abbreviations DDA

data-dependent acquisition

 DDR-2

discoidin domain receptor 2

 DKK2

Dickkopf-related protein 2

 ECM

extracellular matrix

 ELISA

enzyme-linked immunosorbent assay

 GO

gene ontology

 GST

glutathione S-transferase

 ICAM-1

intercellular adhesion molecule-1

 KEGG

Kyoto Encyclopedia of Genes and Genomes

 LP

link protein

 MAC

membrane attack complex

 OA

osteoarthritis

 RA

rheumatoid arthritis

 SF

synovial fluid

 SWATH-MS

SWATH-mass spectrometry

 TIMP-1

tissue inhibitor of metalloproteinase-1

 References NeogiTThe epidemiology and impact of pain in osteoarthritisOsteoarthritis Cartilage2111451153201310.1016/j.joca.2013.03.018239731243753584 ArnscheidtCMederARolauffsBEarly diagnosis of osteoarthritis: Clinical reality and promising experimental techniquesZ Orthop Unfall154254268201626894867 JevsevarDSTreatment of osteoarthritis of the knee: Evidence-based guideline, 2nd editionJ Am Acad Orthop Surg21571576201310.5435/JAAOS-21-09-57123996988 JiaoQWeiLChenCLiPWangXLiYGuoLZhangCWeiXCartilage oligomeric matrix protein and hyaluronic acid are sensitive serum biomarkers for early cartilage lesions in the knee jointBiomarkers21146151201610.3109/1354750X.2015.111854726634947 NemirovskiyOLiWWSzekely-KlepserGDesign and validation of an immunoaffinity LC-MS/MS assay for the quantification of a collagen type II neoepitope peptide in human urine: Application as a biomarker of osteoarthritisMethods Mol Biol641253270201010.1007/978-1-60761-711-2_1520407952 DuanYHaoDLiMWuZLiDYangXQiuGIncreased synovial fluid visfatin is positively linked to cartilage degradation biomarkers in osteoarthritisRheumatol Int32985990201210.1007/s00296-010-1731-821246369 YamagiwaHSarkarGCharlesworthMCMcCormickDJBolanderMETwo-dimensional gel electrophoresis of synovial fluid: Method for detecting candidate protein markers for osteoarthritisJ Orthop Sci8482490200310.1007/s00776-003-0657-312898298 GobezieRKhoAKrastinsBSarracinoDAThornhillTSChaseMMillettPJLeeDMHigh abundance synovial fluid proteome: Distinct profiles in health and osteoarthritisArthritis Res Ther9R36200710.1186/ar2172174075611906814 WuWWWangGBaekSJShenRFComparative study of three proteomic quantitative methods, DIGE, cICAT and iTRAQ, using 2D gel- or LC-MALDI TOF/TOFJ Proteome Res5651658200610.1021/pr050405o16512681 BalakrishnanLBhattacharjeeMAhmadSNirujogiRSRenuseSSubbannayyaYMarimuthuASrikanthSMRajuRDhillonMDifferential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patientsClin Proteomics111201410.1186/1559-0275-11-1243935433918105 LouridoLCalamiaVMateosJFernández-PuentePFernández-TajesJBlancoFJRuiz-RomeroCQuantitative proteomic profiling of human articular cartilage degradation in osteoarthritisJ Proteome Res1360966106201410.1021/pr501024p25383958 GilletLCNavarroPTateSRöstHSelevsekNReiterLBonnerRAebersoldRTargeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysisMol Cell Proteomics11O111.016717201210.1074/mcp.O111.016717222617253433915 CollinsBCGilletLCRosenbergerGRöstHLVichalkovskiAGstaigerMAebersoldRQuantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 systemNat Methods1012461253201310.1038/nmeth.270324162925 AletahaDNeogiTSilmanAJFunovitsJFelsonDTBinghamCOIIIBirnbaumNSBurmesterGRBykerkVPCohenMD2010 Rheumatoid arthritis classification criteria: An american college of rheumatology/european league against rheumatism collaborative initiativeArthritis Rheum6225692581201010.1002/art.2758420872595 LiuWHeJLinRLiangJLuoQDifferential proteomics of the synovial membrane between bilateral and unilateral knee osteoarthritis in surgery–induced rabbit modelsMol Med Rep1422432249201610.3892/mmr.2016.551127430254 Fernandez-PuentePCalamiaVGonzález-RodríguezLLouridoLCamacho-EncinaMOreiroNRuiz-RomeroCBlancoFJMultiplexed mass spectrometry monitoring of biomarker candidates for osteoarthritisJ Proteomics152216225201710.1016/j.jprot.2016.11.01227865793 WangQRozelleALLepusCMScanzelloCRSongJJLarsenDMCrishJFBebekGRitterSYLindstromTMIdentification of a central role for complement in osteoarthritisNat Med1716741679201110.1038/nm.2543220573463257059 LitherlandGJEliasMSHuiWMacdonaldCDCatterallJBBarterMJFarrenMJJeffersonMRowanADProtein kinase C isoforms zeta and iota mediate collagenase expression and cartilage destruction via STAT3- and ERK-dependent c-fos inductionJ Biol Chem2852241422425201010.1074/jbc.M110.120121204630082903406 RusHGNiculescuFShinMLSublytic complement attack induces cell cycle in oligodendrocytesJ Immunol1564892490019968648139 ChanTFCouchourelDAbedEDelalandreADuvalNLajeunesseDElevated Dickkopf-2 levels contribute to the abnormal phenotype of human osteoarthritic osteoblastsJ Bone Miner Res2613991410201110.1002/jbmr.35821312269 BouvardBAbedEYéléhé-OkoumaMBianchiAMainardDNetterPJouzeauJYLajeunesseDReboulPHypoxia and vitamin D differently contribute to leptin and dickkopf-related protein 2 production in human osteoarthritic subchondral bone osteoblastsArthritis Res Ther16459201410.1186/s13075-014-0459-3253127214302570 ChenHTTsouHKChenJCShihJMChenYJTangCHAdiponectin enhances intercellular adhesion molecule-1 expression and promotes monocyte adhesion in human synovial fibroblastsPLoS One9e92741201410.1371/journal.pone.0092741246675773965461 KoskinenAJuslinSNieminenRMoilanenTVuolteenahoKMoilanenEAdiponectin associates with markers of cartilage degradation in osteoarthritis and induces production of proinflammatory and catabolic factors through mitogen-activated protein kinase pathwaysArthritis Res Ther13R184201110.1186/ar3512220779993334633 MoeSMSinghGKBaileyAMbeta2-microglobulin induces MMP-1 but not TIMP-1 expression in human synovial fibroblastsKidney Int5720232034200010.1046/j.1523-1755.2000.00052.x10792621 YoshidaSKatohTTetsukaTUnoKMatsuiNOkamotoTInvolvement of thioredoxin in rheumatoid arthritis: Its costimulatory roles in the TNF-alpha-induced production of IL-6 and IL-8 from cultured synovial fibroblastsJ Immunol163351358199910384135 ZhaoWZhangCShiMZhangJLiMXueXZhangZShuZZhuJMuNThe discoidin domain receptor 2/annexin A2/matrix metalloproteinase 13 loop promotes joint destruction in arthritis through promoting migration and invasion of fibroblast-like synoviocytesArthritis Rheumatol6623552367201410.1002/art.3869624819400 OstalowskaABirknerEWiechaMKasperczykSKasperczykAKapolkaDZon-GiebelALipid peroxidation and antioxidant enzymes in synovial fluid of patients with primary and secondary osteoarthritis of the knee jointOsteoarthritis Cartilage14139145200610.1016/j.joca.2005.08.00916289733 VaillancourtFFahmiHShiQLavignePRangerPFernandesJCBenderdourM4-Hydroxynonenal induces apoptosis in human osteoarthritic chondrocytes: The protective role of glutathione-S-transferaseArthritis Res Ther10R107200810.1186/ar2503187824422592788 RodriguezERoughleyPLink protein can retard the degradation of hyaluronan in proteoglycan aggregatesOsteoarthritis Cartilage14823829200610.1016/j.joca.2006.02.00816584896

The Kellgren-Lawrence radiographic grading criteria. (A) Grade 1, doubtful narrowing of joint space and possible osteophytic lipping. (B) Grade 2, definite osteophytes and possible narrowing of joint space. (C) Grade 3, moderate multiple osteophytes, definite narrowing of joints space, some sclerosis and possible deformity of bone contour. (D) Grade 4, large osteophytes, marked narrowing of joint space, severe sclerosis and definite deformity of bone contour.

TIC chromatogram from traumatic arthritis, RA and OA using liquid chromatography-MS/MS analysis. The chromatogram demonstrated an effective chromatographic separation for the SF proteome. The peaks existed all the time rather than only fora period of time. The shapes of all chromatographic peaks were sharp and symmetrical. In addition, this chromatogram indicated small technical variability and excellent reproducibility of SWATH-MS and great variation in the SF proteome from the different groups. TIC, total ion current; RA, rheumatoid arthritis; OA, osteoarthritis; MS, mass spectrometry; SF, synovial fluid.

Quantification results of complement C1r using SWATH-MS.XICs demonstrated the relative abundance of peptides from complement C1r in SF from (A) traumatic arthritis, (B) RA and (C) OA. Spectrum of peptides from complement C1r in SF from (D) traumatic arthritis, (E) RA and (F) OA. Relative quantification results were derived from comparing the summed XIC peak areas of the fragment ion peak groups, as indicated by the arrow. XIC, extracted ion chromatograms; MS, mass spectrometry; SF, synovial fluid; RA, rheumatoid arthritis; OA, osteoarthritis.

Quantification results of DKK2 using SWATH-MS.XICs indicated relative abundance of peptides from DKK2 in SF from (A) traumatic arthritis, (B) RA and (C) OA. Spectrum of peptides from DKK2 in SF from (D) traumatic arthritis, (E) RA and (F) OA. Relative quantification results derived from comparing the summed XIC peak areas of the fragment ion peak groups, as indicated by the arrow. DKK2, Dickkopf-related protein 2; SF, synovial fluid; MS, mass spectrometry; RA, rheumatoid arthritis; OA, osteoarthritis.

Pathway enrichment of differentially expressed proteins in complement and coagulation cascades. Proteins in red boxes corresponded to upregulation in OA and those in green boxes indicated downregulation in OA. OA, osteoarthritis.

Enzyme-linked immunosorbent assay results of complement C1r. (A and B) Box plot presentation of complement C1r concentrations in synovial fluidfrom traumatic arthritis, RA and OA patients. (C and D) Scatter plot presentation of the associationbetween complement C1r concentrations and disease severity. The plot indicated that complement C1r concentrations were positively correlated with OA (r=0.549, P<0.001) and RA severity (r=0.540, P<0.001). RA, rheumatoid arthritis; OA, osteoarthritis; KL, Kellgren-Lawrence grade.

Enzyme-linked immunosorbent assay results of DKK2. (A and B) Box plot presentation of DKK2 concentrations in synovial fluidfrom traumatic arthritis, RA and OA patients. (C and D) Scatter plot presentation of the association between DKK2 concentrations and disease severity. The plot indicated that DKK2 concentrations were positively correlated with OA (r=0.796, P<0.001) and RA severity (r=0.287, P=0.035). DKK2, Dickkopf-related protein 2; RA, rheumatoid arthritis; OA, osteoarthritis; KL, Kellgren-Lawrence grade.

Differentially expressed proteins specifically regulated in osteoarthritis identified by SWATH-mass spectrometry.

Protein ID Accession Protein name t-value P-value Fold change
  1 E7ES66 Glycocalicin −9.835 0.0006 5.251
  2 P02748 Complement component C9 41.185   2.08E-06 3.898
  3 Q15848 Adiponectin   7.933 0.00137 3.575
  4 P01833 Polymeric immunoglobulin receptor −3.682 0.02117 3.056
  5 P10643 Complement component C7 12.308 0.00025 2.900
  6 F8W1Q3 Biotinidase −54.461   6.81E-07 2.676
  7 O95497 Pantetheinase −17.427   6.36E-05 2.391
  8 F6SYF8 Dickkopf-related protein 2 −19.531   4.05E-05 2.178
  9 P01024 Complement C3 20.642   3.25E-05 1.981
10 P04208 Ig λ chain V–I region WAH −3.730 0.0203 1.918
11 P01019 Angiotensinogen −43.998   1.60E-06 1.846
12 Q5VY30 Plasma retinol-binding protein (1–182) −5.867 0.00421 1.830
13 F5H6I0 β2-microglobulin 30.320   7.05E-06 1.781
14 P02768 Serum albumin −51.884   8.26E-07 1.723
15 P02760 Protein AMBP −11.934 0.00028 1.709
16 P10599 Thioredoxin   3.941 0.01694 1.647
17 P07355-2 Annexin A2 26.293   1.24E-05 1.622
18 P01857 Ig γ-1 chain C region   6.790 0.00246 0.546
19 P04207 Ig κ chain V–III region CLL   8.997 0.00084 0.534
20 P01861 Ig γ-4 chain C region   8.329 0.00114 0.505
21 P02647 Apolipoprotein A-I 66.441   3.07E-07 0.484
22 P58546 Myotrophin   4.805 0.00862 0.456
23 C9JIZ6 Saposin-D   7.474 0.00171 0.340
24 E9PGN7 Plasma protease C1 inhibitor 14.422 0.00013 0.327
25 P60174 Triosephosphate isomerase 15.263 0.00011 0.322
26 Q9H299 SH3 domain-binding glutamic acid-rich-like protein 3 8.893 0.00088 0.268
27 B7Z6Z4 Myosin light polypeptide 6 24.641   1.61E-05 0.151
28 Q14624-2 Isoform 2 of Inter-α-trypsin inhibitor heavy chain H4 75.790   1.82E-07 0.076

Differentially expressed proteins conversely regulated in OA and RA identified by SWATH-MS.

Protein ID Accession Protein name P-value (OA) Fold change (OA) P-value (RA) Fold change (RA)
1 P09211 Glutathione S-transferase 0.01097 2.051   2.87E-06 0.527
2 P13611-2 Isoform V1 of Versican core protein   5.08E-05 1.985   2.34E-05 0.380
3 P10915 Hyaluronan and proteoglycan link protein   1.28E-05 1.636   4.36E-06 0.212
4 P37837 Transaldolase 0.00826 0.577 0.00022 5.286
5 P07737 Profilin-1 0.03004 0.572   3.57E-05 4.777
6 P63104 14-3-3 protein zeta/delta   1.82E-07 0.501   1.28E-05 2.567
7 P06727 Apolipoprotein A-IV   1.73E-06 0.463   1.24E-06 1.536
8 P01880 Ig delta chain C region 0.02884 0.261   3.47E-05 2.521

OA, osteoarthritis; RA, rheumatoid arthritis.