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Suzuki S, Sasaki K, Fahreza RR, Nemoto E, Yamada S. The histone deacetylase inhibitor MS-275 enhances the matrix mineralization of dental pulp stem cells by inducing fibronectin expression. J Dent Sci 2024; 19:1680-1690. [PMID: 39035291 PMCID: PMC11259625 DOI: 10.1016/j.jds.2023.11.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/24/2023] [Indexed: 07/23/2024] Open
Abstract
Background/purpose The acetylation of histone H3 proteins keeps local chromatin regions open and accessible, thereby facilitating transcriptional events. We recently reported integrative epigenomic and transcriptome analyses of differentiating dental pulp stem cells (DPSCs). A significant increase in the number of super-enhancers, which are local genomic locations marked by condensed open chromatin peaks that facilitate transcriptional events, in differentiating DPSCs were observed. However, it is still unclear whether histone deacetylase (HDACs) inhibitors (HDACis) have beneficial effects on the odontogenic differentiation of DPSCs and on the matrix mineralization-inducing ability of DPSCs. Materials and methods DPSCs were cultured in an odontogenic induction medium for a prolonged period in the presence of HDACis, MS-275 and Trichostatin A (TSA). ATAC-seq and RNA-seq samples were collected from differentiating DPSCs to explore the epigenomic and transcriptomic alterations induced by HDACis and identify key target proteins that mediate HDACis-induced phenotypic changes. Results MS-275 and TSA did not change whole-genome open chromatin accessibility or increase odontogenic differentiation, as assessed by alkaline phosphate activity. However, the matrix mineralization-inducing ability assessed by calcified nodule formation was significantly increased by MS-275 but not by TSA. FN1, which encodes fibronectin, was identified as upregulated by MS-275. The knockdown of fibronectin evidently suppressed MS-275-induced calcified nodule formation. Conclusion MS-275 induced calcified nodule formation by the mechanistic upregulation of FN1, independent of epigenomic alterations. Hence, the application of MS-275 as direct capping materials has therapeutic potential for promoting reparative dentin formation by constructing a fibronectin-organizing physiological extracellular matrix environment that is adequate for matrix mineralization.
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Affiliation(s)
- Shigeki Suzuki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Kento Sasaki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Rahmad Rifqi Fahreza
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Eiji Nemoto
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Satoru Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
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Sasaki K, Suzuki S, Fahreza RR, Nemoto E, Yamada S. Dynamic changes in chromatin accessibility during the differentiation of dental pulp stem cells reveal that induction of odontogenic gene expression is linked with specific enhancer construction. J Dent Sci 2024; 19:1705-1713. [PMID: 39035322 PMCID: PMC11259614 DOI: 10.1016/j.jds.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 07/23/2024] Open
Affiliation(s)
- Kento Sasaki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Shigeki Suzuki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Rahmad Rifqi Fahreza
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Eiji Nemoto
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Satoru Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
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Yamamoto T, Yuan H, Suzuki S, Nemoto E, Saito M, Yamada S. Procyanidin B2 enhances anti-inflammatory responses of periodontal ligament cells by inhibiting the dominant negative pro-inflammatory isoforms of peroxisome proliferator-activated receptor γ. J Dent Sci 2024; 19:1801-1810. [PMID: 39035263 PMCID: PMC11259626 DOI: 10.1016/j.jds.2023.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 09/23/2023] [Indexed: 07/23/2024] Open
Abstract
Background/purpose Periodontal breakdown in periodontitis is exacerbated by pro-inflammatory responses of periodontal stromal cells such as periodontal ligament fibroblasts (PDLFs). Procyanidin B2 (PB2) is a ligand of the peroxisome proliferator-activated receptor (PPARγ). Herein, we investigated the expression of PPARγ isoforms in PDLFs and periodontal tissue, and examined the effects of PB2 on PPARγ isoform-dependent antiinflammatory responses. Materials and methods PPARγ isoforms were examined by PCR. PPARγ isoform-dependent inflammatory functions and anti-inflammatory effects of PB2 in PDLFs were evaluated based on IL-6 expression. Co-immunoprecipitation analysis of fixed chromatin-tethered protein (CoIPfctp) was conducted to investigate the association of each PPARγ isoform with the NF-κB-transcriptional complex. The effects of PB2 on periodontitis progression were evaluated using a ligature-induced murine periodontitis model. Results Three isoforms of PPARγ were expressed in PDLFs and periodontal tissues, consisting of the main full-length isoform (PPARγ) and two dominant negative isoforms that lack the ligand binding domain, namely the ubiquitously-expressed isoform (PPARγ-UBI) and unknown isoform (PPARγ-PDL). PPARγ and PPARγ-UBI were predominantly expressed. CoIP-fctp revealed that PPARγ-UBI was selectively associated with NF-κB p65, a key transcriptional factor of IL-6 expression. PB2 suppressed LPS-induced-IL-6 expression exacerbated by the over-expression of PPARγ-UBI. In the murine periodontitis model, topical application of PB2 significantly mitigated alveolar bone loss. Conclusion These results suggest that the anti-inflammatory effects of PB2 in periodontal tissues/cells are distinct, and these effects arise from the inhibition of PPARγ-UBI; hence, the application of PB2 and modification of the splicing event in three PPARγ isoforms have therapeutic potential for preventing periodontitis.
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Affiliation(s)
- Tadahiro Yamamoto
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Hang Yuan
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Shigeki Suzuki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Eiji Nemoto
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Masahiro Saito
- Department of Restorative Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Satoru Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
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Yoshida K, Suzuki S, Yuan H, Sato A, Hirata-Tsuchiya S, Saito M, Yamada S, Shiba H. Public RNA-seq data-based identification and functional analyses reveal that MXRA5 retains proliferative and migratory abilities of dental pulp stem cells. Sci Rep 2023; 13:15574. [PMID: 37730838 PMCID: PMC10511426 DOI: 10.1038/s41598-023-42684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/13/2023] [Indexed: 09/22/2023] Open
Abstract
Dental pulp stem cells (DPSC) usually remain quiescent in the dental pulp tissue; however, once the dental pulp tissue is injured, DPSCs potently proliferate and migrate into the injury microenvironment and contribute to immuno-modulation and tissue repair. However, the key molecules that physiologically support the potent proliferation and migration of DPSCs have not been revealed. In this study, we searched publicly available transcriptome raw data sets, which contain comparable (i.e., equivalently cultured) DPSC and mesenchymal stem cell data. Three data sets were extracted from the Gene Expression Omnibus database and then processed and analyzed. MXRA5 was identified as the predominant DPSC-enriched gene associated with the extracellular matrix. MXRA5 is detected in human dental pulp tissues. Loss of MXRA5 drastically decreases the proliferation and migration of DSPCs, concomitantly with reduced expression of the genes associated with the cell cycle and microtubules. In addition to the known full-length isoform of MXRA5, a novel splice variant of MXRA5 was cloned in DPSCs. Recombinant MXRA5 coded by the novel splice variant potently induced the haptotaxis migration of DPSCs, which was inhibited by microtubule inhibitors. Collectively, MXRA5 is a key extracellular matrix protein in dental pulp tissue for maintaining the proliferation and migration of DPSCs.
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Affiliation(s)
- Kazuma Yoshida
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Shigeki Suzuki
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan.
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, 980-8575, Japan.
| | - Hang Yuan
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, 980-8575, Japan
| | - Akiko Sato
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, 980-8575, Japan
| | - Shizu Hirata-Tsuchiya
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Masahiro Saito
- Department of Restorative Dentistry, Tohoku University Graduate School of Dentistry, Sendai, 980-8575, Japan
| | - Satoru Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, 980-8575, Japan
| | - Hideki Shiba
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
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Suzuki S, Yamada S. Epigenetics in susceptibility, progression, and diagnosis of periodontitis. JAPANESE DENTAL SCIENCE REVIEW 2022; 58:183-192. [PMID: 35754944 PMCID: PMC9218144 DOI: 10.1016/j.jdsr.2022.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/14/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022] Open
Abstract
Periodontitis is characterized by irreversible destruction of periodontal tissue. At present, the accepted etiology of periodontitis is based on a three-factor theory including pathogenic bacteria, host factors, and acquired factors. Periodontitis development usually takes a decade or longer and is therefore called chronic periodontitis (CP). To search for genetic factors associated with CP, several genome-wide association study (GWAS) analyses were conducted; however, polymorphisms associated with CP have not been identified. Epigenetics, on the other hand, involves acquired transcriptional regulatory mechanisms due to reversibly altered chromatin accessibility. Epigenetic status is a condition specific to each tissue and cell, mostly determined by the responses of host cells to stimulations by local factors, like bacterial inflammation, and systemic factors such as nutrition status, metabolic diseases, and health conditions. Significantly, epigenetic status has been linked with the onset and progression of several acquired diseases. Thus, epigenetic factors in periodontal tissues are attractive targets for periodontitis diagnosis and treatments. In this review, we introduce accumulating evidence to reveal the epigenetic background effects related to periodontitis caused by genetic factors, systemic diseases, and local environmental factors, such as smoking, and clarify the underlying mechanisms by which epigenetic alteration influences the susceptibility of periodontitis.
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Key Words
- 5mC, 5-methylcytocine
- AP, aggressive periodontitis
- ATAC-seq, assay for transposase-accessible chromatin sequencing
- CP, chronic periodontitis
- DNA methylation
- ECM, extracellular matrix
- Epigenetics
- Epigenome
- GWAS, genome-wide association study
- H3K27ac, acetylation of histone H3 lysine 27
- H3K27me3, trimethylation of histone H3 lysine 27
- H3K4me3, trimethylation of histone H3 lysine 4
- H3K9ac, histone H3 lysine 9
- HATs, histone acetyltransferases
- HDACs, histone deacetylases
- Histone modifications
- LPS, lipopolysaccharide
- PDL, periodontal ligament
- Periodontal ligament
- Periodontitis
- ceRNA, competing endogenous RNA
- lncRNAs, long ncRNAs
- m6A, N6-methyladenosine
- ncRNAs, non-coding RNAs
- sEV, small extracellular vesicles
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Affiliation(s)
- Shigeki Suzuki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Satoru Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
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Suzuki S, Yuan H, Hirata-Tsuchiya S, Yoshida K, Sato A, Nemoto E, Shiba H, Yamada S. DMP-1 promoter-associated antisense strand non-coding RNA, panRNA-DMP-1, physically associates with EGFR to repress EGF-induced squamous cell carcinoma migration. Mol Cell Biochem 2021; 476:1673-1690. [PMID: 33420898 DOI: 10.1007/s11010-020-04046-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/26/2020] [Indexed: 02/06/2023]
Abstract
Accumulating evidence suggests that specific non-coding RNAs exist in many types of malignant tissues, and are involved in cancer invasion and metastasis. However, little is known about the precise roles of non-coding RNAs in squamous cell carcinoma (SQCC) invasion and migration. Recently, the dentin matrix protein-1 (DMP-1) gene locus was identified as a transcriptionally active site in squamous cell carcinoma (SQCC) tissue and cells. However, it is unclear whether RNA associated with cell migration exist at the DMP-1 gene locus in SQCC cells. We identified a novel promoter-associated non-coding RNA in the antisense strand of DMP-1 gene locus, promoter-associated non-coding RNA (panRNA)-DMP-1, by the RACE method in SQCC cells and tissues, and characterized the functions of panRNA-DMP-1 in EGF-driven SQCC cell migration. The inhibition of endogenous panRNA-DMP-1 expression by specific siRNAs and exogenous over-expression of panRNA-DMP-1 resulted in increased and suppressed cellular migration toward EGF in SQCC cells, respectively, and nuclear expression of panRNA-DMP-1 was induced by EGF stimulation. Mechanistically, suppression of panRNA-DMP-1 expression increased EGFR nuclear localization upon EGF treatment and nuclear panRNA-DMP-1 physically interacted with EGFR, which was confirmed by RNA immunoprecipitation assay using a bacteriophage-delivered PP7 RNA labeling system. Furthermore, co-immunoprecipitation assay revealed that suppression of panRNA-DMP-1 stabilized EGFR interaction with STAT3, a known co-transcription factors of EGFR, to induce migratory properties in many cancer cells. Based on these findings, panRNA-DMP-1 is an EGFR-associating RNA that inhibits the EGF-induced migratory properties of SQCC possibly by regulating EGFR nuclear localization and EGFR binding to STAT3.
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Affiliation(s)
- Shigeki Suzuki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan.
| | - Hang Yuan
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Shizu Hirata-Tsuchiya
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Kazuma Yoshida
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Akiko Sato
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Eiji Nemoto
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Hideki Shiba
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Satoru Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
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Zhang S, Wan H, Wang P, Liu M, Li G, Zhang C, Sun Y. Extracellular matrix protein DMP1 suppresses osteogenic differentiation of Mesenchymal Stem Cells. Biochem Biophys Res Commun 2018; 501:968-973. [PMID: 29775615 DOI: 10.1016/j.bbrc.2018.05.092] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 05/14/2018] [Indexed: 01/11/2023]
Abstract
Mesenchymal Stem Cells (MSCs) are self-renewing and multipotent stem cells which was investigated for diverse clinical applications. However, complex mechanism of MSCs fate determination is still not fully disclosed. Extracellular matrix (ECM) proteins contribute to maintain MSCs stemness by providing extracellular microenvironment. Increasing evidences show that ECM proteins could also regulate the fate of MSCs directly. Dentin matrix protein 1 (DMP1) is an ECM protein enrich in bone tissue and terminal cells, which well-known in promoting osteoblasts and osteocytes maturation, and facilitate mineralization. Recently, our experiment indicated that DMP1 was also expressed in MSCs of long bone. In present study, it is found that DMP1 expressed in Prx1 positive MSCs. And, DMP1 is down-regulated in early osteoblasts and up-regulated again in mature osteoblasts. DMP1 conditional knockout mice model under Prx1cre was generated to explore whether DMP1 regulates MSCs osteogenic differentiation. Specific ablation of DMP1 in Prx1 positive MSCs increased bone mass in vivo and promoted osteoblasts activity in vitro. This study provides a new understanding of DMP1's function in regulation of osteogenesis: not only an enhancer of bone formation, but also a negative regulator of MSCs differentiation in bone.
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Affiliation(s)
- Shufan Zhang
- Department of Oral Implantology, School of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Huixuan Wan
- Department of Oral Implantology, School of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Peng Wang
- Department of Oral Implantology, School of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Mengmeng Liu
- Department of Oral Implantology, School of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Gongchen Li
- Department of Oral Implantology, School of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Chunxue Zhang
- Tongji University School of Medicine, Stem Cell Translational Research Center, Tongji Hospital, Shanghai, 200065, China
| | - Yao Sun
- Department of Oral Implantology, School of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China.
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