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Yadalam PK, Sharma S, Natarajan PM, Ardila CM. Gradient boosting-based classification of interactome hub genes in periimplantitis with periodontitis - an integrated bioinformatic approach. FRONTIERS IN ORAL HEALTH 2024; 5:1462845. [PMID: 39659491 PMCID: PMC11628506 DOI: 10.3389/froh.2024.1462845] [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: 07/10/2024] [Accepted: 11/12/2024] [Indexed: 12/12/2024] Open
Abstract
Introduction Peri-implantitis, a destructive inflammatory condition affecting the tissues surrounding dental implants, shares pathological similarities with periodontitis, a chronic inflammatory disease that impacts the supporting structures of natural teeth. This study utilizes a network-based approach to classify interactome hub genes associated with peri-implantitis and periodontitis, aiming to improve understanding of disease mechanisms and identify potential therapeutic targets. Methods We employed gradient boosting and Weighted Gene Co-expression Network Analysis (WGCNA) to predict and classify these interactome hub genes. Gene expression data related to these diseases were sourced from the NCBI GEO dataset GSE223924, and differential gene expression analysis was conducted using the NCBI GEO R tool. Through WGCNA, we constructed a co-expression network to identify key hub genes, while gradient boosting was used to predict these hub genes. Results Our analysis revealed a co-expression network comprising 216 genes, including prominent hub genes such as IL17RC, CCN2, BMP7, TPM1, and TIMP1, which are implicated in periodontal disease. The gradient boosting model achieved an 88.2% accuracy in classifying interactome hub genes in samples related to peri-implantitis and periodontitis. Discussion These identified genes play roles in inflammation, osteoclast genesis, angiogenesis, and immune response regulation. This study highlights essential hub genes and molecular pathways associated with peri-implantitis and periodontitis, suggesting potential therapeutic targets for developing innovative treatment strategies.
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Affiliation(s)
- Pradeep Kumar Yadalam
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Sarvagya Sharma
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Prabhu Manickam Natarajan
- Department of Clinical Sciences, Center of Medical and Bio-allied Health Sciences and Research, College of Dentistry, Ajman University, Ajman, United Arab Emirates
| | - Carlos M. Ardila
- Department of Basic Sciences, Biomedical Stomatology Research Group, School of Dentistry, University of Antioquia, Medellín, Colombia
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Isshiki T, Naiel S, Vierhout M, Otsubo K, Ali P, Tsubouchi K, Yazdanshenas P, Kumaran V, Dvorkin-Gheva A, Kolb MRJ, Ask K. Therapeutic strategies to target connective tissue growth factor in fibrotic lung diseases. Pharmacol Ther 2024; 253:108578. [PMID: 38103794 DOI: 10.1016/j.pharmthera.2023.108578] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
The treatment of interstitial lung diseases, including idiopathic pulmonary fibrosis (IPF), remains challenging as current available antifibrotic agents are not effective in halting disease progression. Connective tissue growth factor (CTGF), also known as cellular communication factor 2 (CCN2), is a member of the CCN family of proteins that regulates cell signaling through cell surface receptors such as integrins, the activity of cytokines/growth factors, and the turnover of extracellular matrix (ECM) proteins. Accumulating evidence indicates that CTGF plays a crucial role in promoting lung fibrosis through multiple processes, including inducing transdifferentiation of fibroblasts to myofibroblasts, epithelial-mesenchymal transition (EMT), and cooperating with other fibrotic mediators such as TGF-β. Increased expression of CTGF has been observed in fibrotic lungs and inhibiting CTGF signaling has been shown to suppress lung fibrosis in several animal models. Thus, the CTGF signaling pathway is emerging as a potential therapeutic target in IPF and other pulmonary fibrotic conditions. This review provides a comprehensive overview of the current evidence on the pathogenic role of CTGF in pulmonary fibrosis and discusses the current therapeutic agents targeting CTGF using a systematic review approach.
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Affiliation(s)
- Takuma Isshiki
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 48L, Canada; Department of Respiratory Medicine, Toho University School of Medicine, 6-11-1 Omori Nisi, Ota-ku, Tokyo 143-8541, Japan
| | - Safaa Naiel
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 48L, Canada
| | - Megan Vierhout
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 48L, Canada
| | - Kohei Otsubo
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Pareesa Ali
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 48L, Canada
| | - Kazuya Tsubouchi
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Parichehr Yazdanshenas
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 48L, Canada
| | - Vaishnavi Kumaran
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 48L, Canada
| | - Anna Dvorkin-Gheva
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 48L, Canada
| | - Martin R J Kolb
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada
| | - Kjetil Ask
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, 5o Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada; Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 48L, Canada.
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Nikoloudaki G. Functions of Matricellular Proteins in Dental Tissues and Their Emerging Roles in Orofacial Tissue Development, Maintenance, and Disease. Int J Mol Sci 2021; 22:ijms22126626. [PMID: 34205668 PMCID: PMC8235165 DOI: 10.3390/ijms22126626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/04/2023] Open
Abstract
Matricellular proteins (MCPs) are defined as extracellular matrix (ECM) associated proteins that are important regulators and integrators of microenvironmental signals, contributing to the dynamic nature of ECM signalling. There is a growing understanding of the role of matricellular proteins in cellular processes governing tissue development as well as in disease pathogenesis. In this review, the expression and functions of different MP family members (periostin, CCNs, TSPs, SIBLINGs and others) are presented, specifically in relation to craniofacial development and the maintenance of orofacial tissues, including bone, gingiva, oral mucosa, palate and the dental pulp. As will be discussed, each MP family member has been shown to have non-redundant roles in development, tissue homeostasis, wound healing, pathology and tumorigenesis of orofacial and dental tissues.
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Affiliation(s)
- Georgia Nikoloudaki
- Schulich Dentistry Department, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada; ; Tel.: +1-519-661-2111 (ext. 81102)
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
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Yasenchuk Y, Marchenko E, Baigonakova G, Gunther S, Kokorev O, Gunter V, Chekalkin T, Topolnitskiy E, Obrosov A, Kang JH. Study on tensile, bending, fatigue, and in vivo behavior of porous SHS-TiNi alloy used as a bone substitute. Biomed Mater 2021; 16:021001. [PMID: 32629431 DOI: 10.1088/1748-605x/aba327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intermetallic porous SHS-TiNi alloys exhibit tangled and specific stress-strain characteristics. This article aims to evaluate the findings emanating from experiments using standard and proprietary instruments. Fatigue testing under repeated complex loading was used to measure the total number of load cycles before failure of the SHS-TiNi samples occurred. Of the tested samples, seventy percent passed through 106 cycles without failure due to the reversible martensite transformation in the TiNi phase, one of the prevailing constituents of a multiphase matrix. The fractured surfaces were analyzed using scanning electron microscopy and confocal laser scanning instruments. Microscopy studies showed that the entire surface of the sample is concealed by miscellaneous strata that result from the SHS processand effectively protect the porous alloy in a corrosive environment. Numerous non-metallic inclusions, which are also attributed to the SHS reaction, do not have a significant impact on the deformation behavior and fatigue performance. In this context, the successful in vivo functioning of porous grafts assessed in a canine rib-plasty model allows the bone substitute to be congruentially deformed in the body without rejection or degradation; it thus has a long operational life, often greater than 17 ×106 (22 × 60 × 24 × 540) cycles. It acknowledges the potential benefits of SHS-TiNi as a superior osteoplastic material and its high resistance to corrosion fatigue.
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Affiliation(s)
- Yuri Yasenchuk
- Research Institute of Medical Materials, Tomsk State University, 634045 Tomsk, Russia
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The in vitro effects of CCN2 on odontoblast-like cells. Arch Oral Biol 2018; 94:54-61. [PMID: 30168419 DOI: 10.1016/j.archoralbio.2018.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/30/2018] [Accepted: 06/18/2018] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To investigate the in vitro effects of CCN2 on odontoblast-like cells proliferation and differentiation. DESIGN MDPC-23 cells were cultured in DMEM supplemented with 5% FBS. CCN2 was either added to culture media or coated onto culture polystyrene, addition or coating of dH2O was served as control. In the addition group, CCN2 (100 ng/mL) was added into culture media. In the coating group, CCN2 at the concentration of 1000 ng/mL was employed. Cell proliferation was performed using CCK-8 assay. Cell differentiation and mineralization were analyzed by ALPase activity assay, real time RT-PCR and alizarin red staining. One-way ANOVA with post-hoc tukey HSD test was used for statistical analysis. RESULTS MDPC-23 cells exhibited robust proliferative activity upon exposure to either soluble or immobilized CCN2. ALP activity of cells cultured on CCN2-modified surface was continuously strengthened from day six (0.831 ± 0.024 units/μg protein versus 0.563 ± 0.006 units/μg protein of control) till day eight (1.035 ± 0.139 units/μg protein versus 0.704 ± 0.061 units/μg protein of control). Gene expression of BSP, OCN and OPN were promoted by soluble CCN2 after 48 h exposure. Moreover, gene expression of BSP, OCN, OPN, ALP, COL1 A1, Runx-2, DSPP and DMP-1 was significantly enhanced by immobilized CCN2. Finally, mineralization of MDPC-23 cells was accelerated by both soluble and immobilized CCN2 to different extent. CONCLUSIONS The findings indicate that CCN2 promoted proliferation, odontogenic gene expression and mineralization of MDPC-23 cells. It is proposed that CCN2 may be a promising adjunctive formula for dentin regeneration.
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Cellular and molecular actions of CCN2/CTGF and its role under physiological and pathological conditions. Clin Sci (Lond) 2014; 128:181-96. [DOI: 10.1042/cs20140264] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CCN family protein 2 (CCN2), also widely known as connective tissue growth factor (CTGF), is one of the founding members of the CCN family of matricellular proteins. Extensive investigation on CCN2 over decades has revealed the novel molecular action and functional properties of this unique signalling modulator. By its interaction with multiple molecular counterparts, CCN2 yields highly diverse and context-dependent biological outcomes in a variety of microenvironments. Nowadays, CCN2 is recognized to conduct the harmonized development of relevant tissues, such as cartilage and bone, in the skeletal system, by manipulating extracellular signalling molecules involved therein by acting as a hub through a web. However, on the other hand, CCN2 occasionally plays profound roles in major human biological disorders, including fibrosis and malignancies in major organs and tissues, by modulating the actions of key molecules involved in these clinical entities. In this review, the physiological and pathological roles of this unique protein are comprehensively summarized from a molecular network-based viewpoint of CCN2 functionalities.
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Matsushita Y, Sakamoto K, Tamamura Y, Shibata Y, Minamizato T, Kihara T, Ito M, Katsube KI, Hiraoka S, Koseki H, Harada K, Yamaguchi A. CCN3 protein participates in bone regeneration as an inhibitory factor. J Biol Chem 2013; 288:19973-85. [PMID: 23653360 DOI: 10.1074/jbc.m113.454652] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
CCN3, a member of the CCN protein family, inhibits osteoblast differentiation in vitro. However, the role of CCN3 in bone regeneration has not been well elucidated. In this study, we investigated the role of CCN3 in bone regeneration. We identified the Ccn3 gene by microarray analysis as a highly expressed gene at the early phase of bone regeneration in a mouse bone regeneration model. We confirmed the up-regulation of Ccn3 at the early phase of bone regeneration by RT-PCR, Western blot, and immunofluorescence analyses. Ccn3 transgenic mice, in which Ccn3 expression was driven by 2.3-kb Col1a1 promoter, showed osteopenia compared with wild-type mice, but Ccn3 knock-out mice showed no skeletal changes compared with wild-type mice. We analyzed the bone regeneration process in Ccn3 transgenic mice and Ccn3 knock-out mice by microcomputed tomography and histological analyses. Bone regeneration in Ccn3 knock-out mice was accelerated compared with that in wild-type mice. The mRNA expression levels of osteoblast-related genes (Runx2, Sp7, Col1a1, Alpl, and Bglap) in Ccn3 knock-out mice were up-regulated earlier than those in wild-type mice, as demonstrated by RT-PCR. Bone regeneration in Ccn3 transgenic mice showed no significant changes compared with that in wild-type mice. Phosphorylation of Smad1/5 was highly up-regulated at bone regeneration sites in Ccn3 KO mice compared with wild-type mice. These results indicate that CCN3 is up-regulated in the early phase of bone regeneration and acts as a negative regulator for bone regeneration. This study may contribute to the development of new strategies for bone regeneration therapy.
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Affiliation(s)
- Yuki Matsushita
- Section of Oral Pathology, International Research Center for Molecular Science in Tooth and Bone Diseases, Tokyo Medical and Dental University, Tokyo 113-8549, Japan
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Anti-fibrotic effect of CCN3 accompanied by altered gene expression profile of the CCN family. J Cell Commun Signal 2012; 7:11-8. [PMID: 23065484 DOI: 10.1007/s12079-012-0180-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 09/27/2012] [Indexed: 12/24/2022] Open
Abstract
CCN family proteins 2 and 3 (CCN2 and CCN3) belong to the CCN family of proteins, all having a high level of structural similarity. It is widely known that CCN2 is a profibrotic molecule that mediates the development of fibrotic disorders in many different tissues and organs. In contrast, CCN3 has been recently suggested to act as an anti-fibrotic factor in several tissues. This CCN3 action was shown earlier to be exerted by the repression of the CCN2 gene expression in kidney tissue, whereas different findings were obtained for liver cells. Thus, the molecular action of CCN3 yielding its anti-fibrotic effect is still controversial. Here, using a general model of fibrosis, we evaluated the effect of CCN3 overexpression on the gene expression of all of the CCN family members, as well as on that of fibrotic marker genes. As a result, repression of CCN2 gene expression was modest, while type I collagen and α-smooth muscle actin gene expression was prominently repressed. Interestingly, not only CCN2, but also CCN4 gene expression showed a decrease upon CCN3 overexpression. These findings indicate that fibrotic gene induction is under the control of a complex molecular network conducted by CCN family members functioning together.
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