1
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Pourabbas R, Farajzadeh S, Babaloo A, Pazhohan A, Sadighi M, Hajebrahimi S, Pourabbas S, Tenenbaum HC. The association between oral inflammatory load and semen and sperm functional analysis: A cross-sectional study. J Dent Res Dent Clin Dent Prospects 2023; 17:188-195. [PMID: 38023802 PMCID: PMC10676540 DOI: 10.34172/joddd.2023.37106] [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: 02/26/2023] [Accepted: 08/15/2023] [Indexed: 12/01/2023] Open
Abstract
Background Studies have suggested a correlation between periodontitis and reduced male fertility. Inflammation has been described as the link between these ailments. Oral inflammatory load (OIL) can be measured through oral polymorphonuclear neutrophil (oPMN) count, which is associated with periodontal diseases. This cross-sectional study assessed the possible correlation between OIL and the functional parameters of sperm cells. Methods In 229 volunteers, oral rinse and semen samples were assessed for oPMN, semen polymorphonuclears (sPMNs), sperm concentration, total sperm count, motility, morphology, and sperm DNA fragmentation index (SDFi). A multiple linear regression model was conducted to evaluate the relationships between oPMN and semen parameters. Results The effect of elevated oPMN counts on total motility rate, progressive rate, and percentage of sperm cells with normal morphology was significant (P<0.001), with an inverse relationship, i.e., with every unit increase in oPMN count, the mentioned parameters would decline by 0.573, 0.367, and 0.407 units, respectively. oPMN counts also correlated positively with sPMN counts and SDFi (P<0.001), i.e., with every unit increase in the oPMN measures, sPMN counts would increase by 0.126 million/mL, with an 0.733% increase in SDFi. However, there was no significant association between oPMN counts and sperm concentration. Conclusion OIL, as represented by oPMN counts, might affect male fertility as there is a positive correlation between the levels of these inflammatory cells and decreased sperm motility, abnormal morphological changes, increased sPMN counts, and increased SDFi.
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Affiliation(s)
- Reza Pourabbas
- Department of Periodontology, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
- Dental and Periodontal Research Center, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Samin Farajzadeh
- Department of Periodontology, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amirreza Babaloo
- Department of Periodontology, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Azar Pazhohan
- Omid Infertility Treatment Center, Valiasr Hospital, Tabriz, Iran
| | - Mehrnoosh Sadighi
- Department of Periodontology, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sakineh Hajebrahimi
- Research Center for Evidence-based Medicine, Urology Department, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sajjad Pourabbas
- School of Kinesiology and Health Sciences, York University, Toronto, Canada
| | - Howard C Tenenbaum
- Faculty of Dentistry, University of Toronto, Toronto, Canada
- Faculty of Medicine, University of Toronto, Toronto, Canada
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2
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Bernabei I, So A, Busso N, Nasi S. Cartilage calcification in osteoarthritis: mechanisms and clinical relevance. Nat Rev Rheumatol 2023; 19:10-27. [PMID: 36509917 DOI: 10.1038/s41584-022-00875-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 12/14/2022]
Abstract
Pathological calcification of cartilage is a hallmark of osteoarthritis (OA). Calcification can be observed both at the cartilage surface and in its deeper layers. The formation of calcium-containing crystals, typically basic calcium phosphate (BCP) and calcium pyrophosphate dihydrate (CPP) crystals, is an active, highly regulated and complex biological process that is initiated by chondrocytes and modified by genetic factors, dysregulated mitophagy or apoptosis, inflammation and the activation of specific cellular-signalling pathways. The links between OA and BCP deposition are stronger than those observed between OA and CPP deposition. Here, we review the molecular processes involved in cartilage calcification in OA and summarize the effects of calcium crystals on chondrocytes, synovial fibroblasts, macrophages and bone cells. Finally, we highlight therapeutic pathways leading to decreased joint calcification and potential new drugs that could treat not only OA but also other diseases associated with pathological calcification.
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Affiliation(s)
- Ilaria Bernabei
- Service of Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alexander So
- Service of Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.
| | - Nathalie Busso
- Service of Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Sonia Nasi
- Service of Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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3
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Song J, Wu J, Poulet B, Liang J, Bai C, Dang X, Wang K, Fan L, Liu R. Proteomics analysis of hip articular cartilage identifies differentially expressed proteins associated with osteonecrosis of the femoral head. Osteoarthritis Cartilage 2021; 29:1081-1092. [PMID: 33892138 DOI: 10.1016/j.joca.2021.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 03/16/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The cartilage degeneration that accompanies subchondral bone necrosis plays an important role in the development of osteonecrosis of femoral head (ONFH). To better understand the molecular basis of cartilage degradation in ONFH, we compared the proteomic profiles of ONFH cartilage with that of fracture control. DESIGN Hip cartilage samples were collected from 16 ONFH patients and 16 matched controls with femoral neck fracture. Proteomics analysis was conducted using tandem mass tag-based quantitation technique. Gene ontology (GO) analysis, KEGG pathway and protein-protein interaction analysis were used to investigate the functions of the altered proteins and biological pathways. Differentially expressed proteins including alpha-2-HS-glycoprotein (AHSG) and Cytokine-like protein 1 (Cytl1) were validated by Western blot (WB) and immunohistochemistry (IHC). RESULTS 303 differentially expressed proteins were identified in ONFH cartilage with 72 up-regulated and 231 down-regulated. Collagen turnover, glycosaminoglycan biosynthesis, metabolic pathways, and complement and coagulation cascades were significantly modified in ONFH cartilage. WB and IHC confirmed the increased expression of AHSG and decreased expression of Cytl1 in ONFH cartilage. CONCLUSIONS Our results reveal the implication of altered protein expression in the development of ONFH, and provide novel clues for pathogenesis studies of cartilage degradation in ONFH.
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Affiliation(s)
- J Song
- Department of Orthopaedics, The Second Affiliated Hospital, Xi'an Jiaotong University, NO.157, Xiwu Road, Xi'an, Shaanxi, 710004, PR China.
| | - J Wu
- Department of Orthopaedics, The Second Affiliated Hospital, Xi'an Jiaotong University, NO.157, Xiwu Road, Xi'an, Shaanxi, 710004, PR China; Department of Orthopaedics, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan Province, 471009, PR China.
| | - B Poulet
- Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, West Derby Road, Liverpool, L7 8TX, UK.
| | - J Liang
- Department of Orthopaedics, The Second Affiliated Hospital, Xi'an Jiaotong University, NO.157, Xiwu Road, Xi'an, Shaanxi, 710004, PR China.
| | - C Bai
- Department of Orthopaedics, The Second Affiliated Hospital, Xi'an Jiaotong University, NO.157, Xiwu Road, Xi'an, Shaanxi, 710004, PR China.
| | - X Dang
- Department of Orthopaedics, The Second Affiliated Hospital, Xi'an Jiaotong University, NO.157, Xiwu Road, Xi'an, Shaanxi, 710004, PR China.
| | - K Wang
- Department of Orthopaedics, The Second Affiliated Hospital, Xi'an Jiaotong University, NO.157, Xiwu Road, Xi'an, Shaanxi, 710004, PR China.
| | - L Fan
- Department of Orthopaedics, The Second Affiliated Hospital, Xi'an Jiaotong University, NO.157, Xiwu Road, Xi'an, Shaanxi, 710004, PR China.
| | - R Liu
- Department of Orthopaedics, The Second Affiliated Hospital, Xi'an Jiaotong University, NO.157, Xiwu Road, Xi'an, Shaanxi, 710004, PR China; Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, West Derby Road, Liverpool, L7 8TX, UK.
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4
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Yan JF, Qin WP, Xiao BC, Wan QQ, Tay FR, Niu LN, Jiao K. Pathological calcification in osteoarthritis: an outcome or a disease initiator? Biol Rev Camb Philos Soc 2020; 95:960-985. [PMID: 32207559 DOI: 10.1111/brv.12595] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022]
Abstract
In the progression of osteoarthritis, pathological calcification in the affected joint is an important feature. The role of these crystallites in the pathogenesis and progression of osteoarthritis is controversial; it remains unclear whether they act as a disease initiator or are present as a result of joint damage. Recent studies reported that the molecular mechanisms regulating physiological calcification of skeletal tissues are similar to those regulating pathological or ectopic calcification of soft tissues. Pathological calcification takes place when the equilibrium is disrupted. Calcium phosphate crystallites are identified in most affected joints and the presence of these crystallites is closely correlated with the extent of joint destruction. These observations suggest that pathological calcification is most likely to be a disease initiator instead of an outcome of osteoarthritis progression. Inhibiting pathological crystallite deposition within joint tissues therefore represents a potential therapeutic target in the management of osteoarthritis.
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Affiliation(s)
- Jian-Fei Yan
- Department of Oral Mucosal Diseases, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 145 changle xi road, Xi'an, Shaanxi, 710032, China
| | - Wen-Pin Qin
- Department of Oral Mucosal Diseases, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 145 changle xi road, Xi'an, Shaanxi, 710032, China
| | - Bo-Cheng Xiao
- Department of Oral Mucosal Diseases, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 145 changle xi road, Xi'an, Shaanxi, 710032, China
| | - Qian-Qian Wan
- Department of Oral Mucosal Diseases, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 145 changle xi road, Xi'an, Shaanxi, 710032, China
| | - Franklin R Tay
- Department of Oral Mucosal Diseases, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 145 changle xi road, Xi'an, Shaanxi, 710032, China.,Department of Endodontics, College of Graduate Studies, Augusta University, 1430, John Wesley Gilbert Drive, Augusta, GA, 30912, U.S.A
| | - Li-Na Niu
- Department of Oral Mucosal Diseases, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 145 changle xi road, Xi'an, Shaanxi, 710032, China
| | - Kai Jiao
- Department of Oral Mucosal Diseases, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, 145 changle xi road, Xi'an, Shaanxi, 710032, China
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Pappa E, Papadopoulos S, Korou LM, Perrea DN, Pneumaticos S, Nikolaou VS. The role of intra-articular administration of Fetuin-A in post-traumatic knee osteoarthritis: an experimental study in a rat model. J Exp Orthop 2019; 6:25. [PMID: 31209645 PMCID: PMC6579801 DOI: 10.1186/s40634-019-0194-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/04/2019] [Indexed: 01/12/2023] Open
Abstract
Background The purpose of this study is to investigate the possible attenuating role of the intra-articular administration of Fetuin-A in post-traumatic secondary osteoarthritis in rats, and also its effect on the systematic levels of interleukins (ILs)-2,4,7, bone morphogenetic proteins (BMPs) 2, 4, 7, C-Reactive Protein (CRP) and Fetuin-A. Methods Thirty male Sprague Dawley rats were separated in two groups where post-traumatic osteoarthritis was induced surgically by Anterior Cruciate Ligament Transection and the transection of the Medial Collateral Ligament of the right knee. In the Control Group, only the surgical intervention took place. In Fetuin Group, along with the induction of osteoarthritis, a single dose of bovine fetuin was administrated intra-articularly, intra-operatively. Both groups were examined for 8 weeks. The levels of interleukins, bone morphogenetic proteins, Fetuin-A and C-Reactive Protein were evaluated by ELISA of peripheral blood in three time periods: preoperatively, 5 and 8 weeks post-operatively. Osteoarthritic lesions of the knee were classified according to the Osteoarthritis Research Society International Grading System and the Modified Mankin Score, by histologic examination. Results IL-2 levels were significantly decreased in the Fetuin Group. No statistical difference was signed on the levels of IL-7, BMP-2,4,7 and Fetuin-A between the two groups. CRP levels were significantly increased in the Fetuin Group in 5 weeks of the experiment. Fetuin Group signed better scores according to the OARSI classification system and Modified Mankin Score, without any statistical significance. Conclusions Intra-articular administration of Fetuin-A restrictively affected the progression of post-traumatic arthritis in rats, as only the levels of IL-2 were decreased as well as limited osteoarthritic lesions were observed on the Fetuin Group.
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Affiliation(s)
- Eleni Pappa
- "KAT" General Hospital of Athens, Nikis 2, 14561, Kifisia, Greece.
| | - Savvas Papadopoulos
- Department of Pathology, "Hygeia" General Hospital of Athens, Athens, Greece
| | - Laskarina-Maria Korou
- Laboratory of Experimental Surgery and Research "N.S. Christeas", Athens Medical School, Athens, Greece
| | - Despina N Perrea
- Laboratory of Experimental Surgery and Research "N.S. Christeas", Athens Medical School, Athens, Greece
| | - Spiridon Pneumaticos
- 3rd Department of Orthopaedics, KAT Hospital, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | - Vasileios S Nikolaou
- 2nd Department of Orthopaedics, Agia Olga Hospital, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
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6
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Favero M, Belluzzi E, Frallonardo P, Peruzzo L, Tauro L, Oliviero F, Ramonda R, Punzi L. Synovial fluid fetuin-A levels in patients affected by osteoarthritis with or without evidence of calcium crystals. Rheumatology (Oxford) 2019; 58:729-730. [PMID: 30649542 DOI: 10.1093/rheumatology/key435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2018] [Indexed: 09/01/2023] Open
Affiliation(s)
- Marta Favero
- Rheumatology Unit, Department of Medicine - DIMED, University Hospital of Padova, Italy
| | - Elisa Belluzzi
- Rheumatology Unit, Department of Medicine - DIMED, University Hospital of Padova, Italy
| | - Paola Frallonardo
- Rheumatology Unit, Department of Medicine - DIMED, University Hospital of Padova, Italy
| | - Luca Peruzzo
- Institute for Geosciences and Earth Resources IGG-CNR, Italy
| | - Leonardo Tauro
- Department of Geosciences, University of Padova, Padova, Italy
| | - Francesca Oliviero
- Rheumatology Unit, Department of Medicine - DIMED, University Hospital of Padova, Italy
| | - Roberta Ramonda
- Rheumatology Unit, Department of Medicine - DIMED, University Hospital of Padova, Italy
| | - Leonardo Punzi
- Rheumatology Unit, Department of Medicine - DIMED, University Hospital of Padova, Italy
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7
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Kiapour AM, Sieker JT, Proffen BL, Lam TT, Fleming BC, Murray MM. Synovial fluid proteome changes in ACL injury-induced posttraumatic osteoarthritis: Proteomics analysis of porcine knee synovial fluid. PLoS One 2019; 14:e0212662. [PMID: 30822327 PMCID: PMC6396923 DOI: 10.1371/journal.pone.0212662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 02/07/2019] [Indexed: 01/26/2023] Open
Abstract
Surgical transection of the anterior cruciate ligament (ACL) in the porcine model leads to posttraumatic osteoarthritis if left untreated. However, a recently developed surgical treatment, bridge-enhanced ACL repair, prevents further cartilage damage. Since the synovial fluid bathes all the intrinsic structures of knee, we reasoned that a comparative analysis of synovial fluid protein contents could help to better understand the observed chondroprotective effects of the bridge-enhanced ACL repair. We hypothesized that post-surgical changes in the synovial fluid proteome would be different in the untreated and repaired knees, and those changes would correlate with the degree of cartilage damage. Thirty adolescent Yucatan mini-pigs underwent unilateral ACL transection and were randomly assigned to either no further treatment (ACLT, n = 14) or bridge-enhanced ACL repair (BEAR, n = 16). We used an isotopically labeled high resolution LC MS/MS-based proteomics approach to analyze the protein profile of synovial fluid at 6 and 12 months after ACL transection in untreated and repaired porcine knees. A linear mixed effect model was used to compare the normalized protein abundance levels between the groups at each time point. Bivariate linear regression analyses were used to assess the correlations between the macroscopic cartilage damage (total lesion area) and normalized abundance levels of each of the identified secreted proteins. There were no significant differences in cartilage lesion area or quantitative abundance levels of the secreted proteins between the ACLT and BEAR groups at 6 months. However, by 12 months, greater cartilage damage was seen in the ACLT group compared to the BEAR group (p = 0.005). This damage was accompanied by differences in the abundance levels of secreted proteins, with higher levels of Vitamin K-dependent protein C (p = 0.001), and lower levels of Apolipoprotein A4 (p = 0.021) and Cartilage intermediate layer protein 1 (p = 0.049) in the ACLT group compared to the BEAR group. There were also group differences in the secreted proteins that significantly changed in abundance between 6 and 12 months in ACLT and BEAR knees. Increased concentration of Ig lambda-1 chain C regions and decreased concentration of Hemopexin, Clusterin, Coagulation factor 12 and Cartilage intermediate layer protein 1 were associated with greater cartilage lesion area. In general, ACLT knees had higher concentrations of pro-inflammatory proteins and lower concentrations of anti-inflammatory proteins than BEAR group. In addition, the ACLT group had a lower and declining synovial concentrations of CILP, in contrast to a consistently high abundance of CILP in repaired knees. These differences suggest that the knees treated with bridge-enhanced ACL repair may be maintaining an environment that is more protective of the extracellular matrix, a function which is not seen in the ACLT knees.
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Affiliation(s)
- Ata M. Kiapour
- Department of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States of America
- * E-mail:
| | - Jakob T. Sieker
- Department of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Benedikt L. Proffen
- Department of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - TuKiet T. Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States of America
- MS & Proteomics Resource, W.M. Keck Biotechnology Resource Laboratory, Yale University, New Haven, CT, United States of America
| | - Braden C. Fleming
- Department of Orthopaedics, Warren Alpert Medical School of Brown University & Rhode Island Hospital, Providence, RI, United States of America
| | - Martha M. Murray
- Department of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States of America
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8
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Pappa E, Perrea DS, Pneumaticos S, Nikolaou VS. Role of fetuin A in the diagnosis and treatment of joint arthritis. World J Orthop 2017; 8:461-464. [PMID: 28660137 PMCID: PMC5478488 DOI: 10.5312/wjo.v8.i6.461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/23/2017] [Accepted: 05/05/2017] [Indexed: 02/06/2023] Open
Abstract
Osteoarthritis is a slowly progressive disease which includes the intervention of several cytokines, macrophage metalleinoproteinases reaction, leading to the degradation of the local cartilage but also having an impact on the serum acute phase proteins (APPs). Subsequently, biomarkers seem to be essential to estimate its progression and the need for any surgical intervention such as total arthroplasty, but also can be used as therapeutic agents. Recently, among APPs, fetuin A drew attention regarding its possible anti-inflammatory role in animal models but also as a therapeutic agent in the inflammatory joint disease in clinical trials. In contrast with other APPs such as C-reactive protein, fetuin A appears to be lower in the serum of patients with degenerative joint disease in comparison with the healthy ones, and also acts as an antagonist of the anti-proliferative potential of transforming growth factor-β (TGF-β) cytokines. Because of its lower serum levels in arthritis, an unregulated binding of TGF-β and bone morphogenetic proteins takes place leading to further arthritic lesions. The purpose of the present review is to assess the current evidence regarding the multipotent role of the alpha-2-HS-glycoprotein or as also known Fetuin-a in animal models but also as a biomarker of the degenerative joint arthritis in clinical trials.
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9
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Swan AL, Stekel DJ, Hodgman C, Allaway D, Alqahtani MH, Mobasheri A, Bacardit J. A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data. BMC Genomics 2015; 16 Suppl 1:S2. [PMID: 25923811 PMCID: PMC4315157 DOI: 10.1186/1471-2164-16-s1-s2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Investigations into novel biomarkers using omics techniques generate large amounts of data. Due to their size and numbers of attributes, these data are suitable for analysis with machine learning methods. A key component of typical machine learning pipelines for omics data is feature selection, which is used to reduce the raw high-dimensional data into a tractable number of features. Feature selection needs to balance the objective of using as few features as possible, while maintaining high predictive power. This balance is crucial when the goal of data analysis is the identification of highly accurate but small panels of biomarkers with potential clinical utility. In this paper we propose a heuristic for the selection of very small feature subsets, via an iterative feature elimination process that is guided by rule-based machine learning, called RGIFE (Rule-guided Iterative Feature Elimination). We use this heuristic to identify putative biomarkers of osteoarthritis (OA), articular cartilage degradation and synovial inflammation, using both proteomic and transcriptomic datasets. RESULTS AND DISCUSSION Our RGIFE heuristic increased the classification accuracies achieved for all datasets when no feature selection is used, and performed well in a comparison with other feature selection methods. Using this method the datasets were reduced to a smaller number of genes or proteins, including those known to be relevant to OA, cartilage degradation and joint inflammation. The results have shown the RGIFE feature reduction method to be suitable for analysing both proteomic and transcriptomics data. Methods that generate large 'omics' datasets are increasingly being used in the area of rheumatology. CONCLUSIONS Feature reduction methods are advantageous for the analysis of omics data in the field of rheumatology, as the applications of such techniques are likely to result in improvements in diagnosis, treatment and drug discovery.
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Affiliation(s)
- Anna L Swan
- School of Biosciences, Faculty of Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
| | - Dov J Stekel
- School of Biosciences, Faculty of Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
| | - Charlie Hodgman
- School of Biosciences, Faculty of Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
- The D-BOARD European Consortium for Biomarker Discovery, The Universities of Surrey, Nottingham and Newcastle, United Kingdom
| | - David Allaway
- WALTHAM® Centre for Pet Nutrition, Waltham-on-the-Wolds, Melton Mowbray, Leicestershire, LE14 4RT, United Kingdom
| | - Mohammed H Alqahtani
- Center of Excellence in Genomic Medicine Research (CEGMR), King AbdulAziz University, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Ali Mobasheri
- The D-BOARD European Consortium for Biomarker Discovery, The Universities of Surrey, Nottingham and Newcastle, United Kingdom
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Duke of Kent Building, Guildford, Surrey, GU2 7XH, United Kingdom
- Center of Excellence in Genomic Medicine Research (CEGMR), King AbdulAziz University, Jeddah, 21589, Kingdom of Saudi Arabia
- Arthritis Research UK Centre for Sport, Exercise, and Osteoarthritis, Arthritis Research UK Pain Centre, Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Faculty of Medicine and Health Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Jaume Bacardit
- The D-BOARD European Consortium for Biomarker Discovery, The Universities of Surrey, Nottingham and Newcastle, United Kingdom
- The Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Claremont Tower, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
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