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Huang L, Chen X, Yang X, Zhang Y, Liang Y, Qiu X. Elucidating epigenetic mechanisms governing odontogenic differentiation in dental pulp stem cells: an in-depth exploration. Front Cell Dev Biol 2024; 12:1394582. [PMID: 38863943 PMCID: PMC11165363 DOI: 10.3389/fcell.2024.1394582] [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: 03/01/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Epigenetics refers to the mechanisms such as DNA methylation and histone modification that influence gene expression without altering the DNA sequence. These epigenetic modifications can regulate gene transcription, splicing, and stability, thereby impacting cell differentiation, development, and disease occurrence. The formation of dentin is intrinsically linked to the odontogenic differentiation of dental pulp stem cells (DPSCs), which are recognized as the optimal cell source for dentin-pulp regeneration due to their varied odontogenic potential, strong proliferative and angiogenic characteristics, and ready accessibility Numerous studies have demonstrated the critical role of epigenetic regulation in DPSCs differentiation into specific cell types. This review thus provides a comprehensive review of the mechanisms by which epigenetic regulation controls the odontogenesis fate of DPSCs.
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Affiliation(s)
| | | | | | | | | | - Xiaoling Qiu
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
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Daneshian Y, Lewallen EA, Badreldin AA, Dietz AB, Stein GS, Cool SM, Ryoo HM, Cho YD, van Wijnen AJ. Fundamentals and Translational Applications of Stem Cells and Biomaterials in Dental, Oral and Craniofacial Regenerative Medicine. Crit Rev Eukaryot Gene Expr 2024; 34:37-60. [PMID: 38912962 DOI: 10.1615/critreveukaryotgeneexpr.2024053036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Regenerative dental medicine continuously expands to improve treatments for prevalent clinical problems in dental and oral medicine. Stem cell based translational opportunities include regenerative therapies for tooth restoration, root canal therapy, and inflammatory processes (e.g., periodontitis). The potential of regenerative approaches relies on the biological properties of dental stem cells. These and other multipotent somatic mesenchymal stem cell (MSC) types can in principle be applied as either autologous or allogeneic sources in dental procedures. Dental stem cells have distinct developmental origins and biological markers that determine their translational utility. Dental regenerative medicine is supported by mechanistic knowledge of the molecular pathways that regulate dental stem cell growth and differentiation. Cell fate determination and lineage progression of dental stem cells is regulated by multiple cell signaling pathways (e.g., WNTs, BMPs) and epigenetic mechanisms, including DNA modifications, histone modifications, and non-coding RNAs (e.g., miRNAs and lncRNAs). This review also considers a broad range of novel approaches in which stem cells are applied in combination with biopolymers, ceramics, and composite materials, as well as small molecules (agonistic or anti-agonistic ligands) and natural compounds. Materials that mimic the microenvironment of the stem cell niche are also presented. Promising concepts in bone and dental tissue engineering continue to drive innovation in dental and non-dental restorative procedures.
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Affiliation(s)
- Yasaman Daneshian
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT, United States of America
| | - Eric A Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, USA
| | - Amr A Badreldin
- Laboratory of Molecular Signaling, Division of Oral and Systemic Health Sciences, School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Allan B Dietz
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Gary S Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405; University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Simon M Cool
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland, Australia
| | - Hyun-Mo Ryoo
- School of Dentistry, Seoul National University, 28 Yeonkun-dong, Chongro-gu Seoul, 110-749, Republic of Korea
| | - Young Dan Cho
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, 101 Daehak‑no, Jongno‑gu, Seoul 03080, Republic of Korea
| | - Andre J van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
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Eggermann T, Monk D, de Nanclares GP, Kagami M, Giabicani E, Riccio A, Tümer Z, Kalish JM, Tauber M, Duis J, Weksberg R, Maher ER, Begemann M, Elbracht M. Imprinting disorders. Nat Rev Dis Primers 2023; 9:33. [PMID: 37386011 DOI: 10.1038/s41572-023-00443-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Imprinting disorders (ImpDis) are congenital conditions that are characterized by disturbances of genomic imprinting. The most common individual ImpDis are Prader-Willi syndrome, Angelman syndrome and Beckwith-Wiedemann syndrome. Individual ImpDis have similar clinical features, such as growth disturbances and developmental delay, but the disorders are heterogeneous and the key clinical manifestations are often non-specific, rendering diagnosis difficult. Four types of genomic and imprinting defect (ImpDef) affecting differentially methylated regions (DMRs) can cause ImpDis. These defects affect the monoallelic and parent-of-origin-specific expression of imprinted genes. The regulation within DMRs as well as their functional consequences are mainly unknown, but functional cross-talk between imprinted genes and functional pathways has been identified, giving insight into the pathophysiology of ImpDefs. Treatment of ImpDis is symptomatic. Targeted therapies are lacking owing to the rarity of these disorders; however, personalized treatments are in development. Understanding the underlying mechanisms of ImpDis, and improving diagnosis and treatment of these disorders, requires a multidisciplinary approach with input from patient representatives.
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Affiliation(s)
- Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany.
| | - David Monk
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Guiomar Perez de Nanclares
- Rare Diseases Research Group, Molecular (Epi)Genetics Laboratory, Bioaraba Research Health Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Spain
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Eloïse Giabicani
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, APHP, Hôpital Armand Trousseau, Endocrinologie Moléculaire et Pathologies d'Empreinte, Paris, France
| | - Andrea Riccio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università della Campania Luigi Vanvitelli, Caserta, Italy
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer M Kalish
- Division of Human Genetics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Departments of Pediatrics and Genetics at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maithé Tauber
- Centre de Référence Maladies Rares PRADORT (syndrome de PRADer-Willi et autres Obésités Rares avec Troubles du comportement alimentaire), Hôpital des Enfants, CHU Toulouse, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse, France
| | - Jessica Duis
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Department of Paediatrics and Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
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Victor AK, Hedgecock T, Donaldson M, Johnson D, Rand CM, Weese-Mayer DE, Reiter LT. Analysis and comparisons of gene expression changes in patient- derived neurons from ROHHAD, CCHS, and PWS. Front Pediatr 2023; 11:1090084. [PMID: 37234859 PMCID: PMC10206321 DOI: 10.3389/fped.2023.1090084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Background Rapid-onset obesity with hypothalamic dysfunction, hypoventilation, and autonomic dysregulation (ROHHAD) syndrome is an ultra-rare neurocristopathy with no known genetic or environmental etiology. Rapid-onset obesity over a 3-12 month period with onset between ages 1.5-7 years of age is followed by an unfolding constellation of symptoms including severe hypoventilation that can lead to cardiorespiratory arrest in previously healthy children if not identified early and intervention provided. Congenital Central Hypoventilation syndrome (CCHS) and Prader-Willi syndrome (PWS) have overlapping clinical features with ROHHAD and known genetic etiologies. Here we compare patient neurons from three pediatric syndromes (ROHHAD, CCHS, and PWS) and neurotypical control subjects to identify molecular overlap that may explain the clinical similarities. Methods Dental pulp stem cells (DPSC) from neurotypical control, ROHHAD, and CCHS subjects were differentiated into neuronal cultures for RNA sequencing (RNAseq). Differential expression analysis identified transcripts variably regulated in ROHHAD and CCHS vs. neurotypical control neurons. In addition, we used previously published PWS transcript data to compare both groups to PWS patient-derived DPSC neurons. Enrichment analysis was performed on RNAseq data and downstream protein expression analysis was performed using immunoblotting. Results We identified three transcripts differentially regulated in all three syndromes vs. neurotypical control subjects. Gene ontology analysis on the ROHHAD dataset revealed enrichments in several molecular pathways that may contribute to disease pathology. Importantly, we found 58 transcripts differentially expressed in both ROHHAD and CCHS patient neurons vs. control neurons. Finally, we validated transcript level changes in expression of ADORA2A, a gene encoding for an adenosine receptor, at the protein level in CCHS neurons and found variable, although significant, changes in ROHHAD neurons. Conclusions The molecular overlap between CCHS and ROHHAD neurons suggests that the clinical phenotypes in these syndromes likely arise from or affect similar transcriptional pathways. Further, gene ontology analysis identified enrichments in ATPase transmembrane transporters, acetylglucosaminyltransferases, and phagocytic vesicle membrane proteins that may contribute to the ROHHAD phenotype. Finally, our data imply that the rapid-onset obesity seen in both ROHHAD and PWS likely arise from different molecular mechanisms. The data presented here describes important preliminary findings that warrant further validation.
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Affiliation(s)
- A. Kaitlyn Victor
- IPBS Program, Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Tayler Hedgecock
- IPBS Program, Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Martin Donaldson
- Department of Pediatric Dentistry and Community Oral Health, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Daniel Johnson
- Molecular Bioinformatics Core, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Casey M. Rand
- Department of Pediatrics, Division of Autonomic Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago and Stanley Manne Children’s Research Institute, Chicago, IL, United States
| | - Debra E. Weese-Mayer
- Department of Pediatrics, Division of Autonomic Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago and Stanley Manne Children’s Research Institute, Chicago, IL, United States
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lawrence T. Reiter
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States
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Giabicani E, Pham A, Sélénou C, Sobrier ML, Andrique C, Lesieur J, Linglart A, Poliard A, Chaussain C, Netchine I. Dental pulp stem cells as a promising model to study imprinting diseases. Int J Oral Sci 2022; 14:19. [PMID: 35368018 PMCID: PMC8976849 DOI: 10.1038/s41368-022-00169-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Parental imprinting is an epigenetic process leading to monoallelic expression of certain genes depending on their parental origin. Imprinting diseases are characterized by growth and metabolic issues starting from birth to adulthood. They are mainly due to methylation defects in imprinting control region that drive the abnormal expression of imprinted genes. We currently lack relevant animal or cellular models to unravel the pathophysiology of growth failure in these diseases. We aimed to characterize the methylation of imprinting regions in dental pulp stem cells and during their differentiation in osteogenic cells (involved in growth regulation) to assess the interest of this cells in modeling imprinting diseases. We collected dental pulp stem cells from five controls and four patients (three with Silver-Russell syndrome and one with Beckwith-Wiedemann syndrome). Methylation analysis of imprinting control regions involved in these syndromes showed a normal profile in controls and the imprinting defect in patients. These results were maintained in dental pulp stem cells cultured under osteogenic conditions. Furthermore, we confirmed the same pattern in six other loci involved in imprinting diseases in humans. We also confirmed monoallelic expression of H19 (an imprinted gene) in controls and its biallelic expression in one patient. Extensive imprinting control regions methylation analysis shows the strong potential of dental pulp stem cells in modeling imprinting diseases, in which imprinting regions are preserved in culture and during osteogenic differentiation. This will allow to perform in vitro functional and therapeutic tests in cells derived from dental pulp stem cells and generate other cell-types.
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Argaez-Sosa AA, Rodas-Junco BA, Carrillo-Cocom LM, Rojas-Herrera RA, Coral-Sosa A, Aguilar-Ayala FJ, Aguilar-Pérez D, Nic-Can GI. Higher Expression of DNA (de)methylation-Related Genes Reduces Adipogenicity in Dental Pulp Stem Cells. Front Cell Dev Biol 2022; 10:791667. [PMID: 35281092 PMCID: PMC8907981 DOI: 10.3389/fcell.2022.791667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Obesity is a significant health concern that has reached alarming proportions worldwide. The overconsumption of high-energy foods may cause metabolic dysfunction and promote the generation of new adipocytes by contributing to several obesity-related diseases. Such concerns demand a deeper understanding of the origin of adipocytes if we want to develop new therapeutic approaches. Recent findings indicate that adipocyte development is facilitated by tight epigenetic reprogramming, which is required to activate the gene program to change the fate of mesenchymal stem cells (MSCs) into mature adipocytes. Like adipose tissue, different tissues are also potential sources of adipocyte-generating MSCs, so it is interesting to explore whether the epigenetic mechanisms of adipogenic differentiation vary from one depot to another. To investigate how DNA methylation (an epigenetic mark that plays an essential role in controlling transcription and cellular differentiation) contributes to adipogenic potential, dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PLSCs) were analyzed during adipogenic differentiation in vitro. Here, we show that the capacity to differentiate from DPSCs or PLSCs to adipocytes may be associated with the expression pattern of DNA methylation-related genes acquired during the induction of the adipogenic program. Our study provides insights into the details of DNA methylation during the adipogenic determination of dental stem cells, which can be a starting point to identify the factors that affect the differentiation of these cells and provide new strategies to regulate differentiation and adipocyte expansion.
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Affiliation(s)
- Adaylu A. Argaez-Sosa
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Beatriz A. Rodas-Junco
- Laboratorio Translacional de Células Troncales, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Mexico
- CONACYT-Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Leydi M. Carrillo-Cocom
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Rafael A. Rojas-Herrera
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Abel Coral-Sosa
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Fernando J. Aguilar-Ayala
- Laboratorio Translacional de Células Troncales, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - David Aguilar-Pérez
- Laboratorio Translacional de Células Troncales, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Geovanny I. Nic-Can
- Laboratorio Translacional de Células Troncales, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Mexico
- CONACYT-Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
- *Correspondence: Geovanny I. Nic-Can, ,
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BMPR2 promoter methylation and its expression in valvular heart disease complicated with pulmonary artery hypertension. Aging (Albany NY) 2021; 13:24580-24604. [PMID: 34793329 PMCID: PMC8660616 DOI: 10.18632/aging.203690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/28/2021] [Indexed: 11/25/2022]
Abstract
Valvular heart disease (VHD) is a common heart disease that affects blood flow. It usually requires heart surgery. Valvular heart disease complicated with pulmonary artery hypertension (VHD-PAH) may be lethal due to heart failure that results from increased heart burden. It is important for these patients to seek early treatment in order to minimize the heart damage. However, there is no reliable diagnosis method in VHD. In this study, we found DNA methylation was increased at the promoter of BMPR2 gene in the VHD patients compared with the healthy controls. This finding was confirmed by an independent cohort study of VHD patients and healthy controls. In addition, BMPR2 mRNA levels were reduced in the plasma of the VHD patients. There is strong correlation between BMPR2 promoter DNA methylation and the severity of VHD. Indeed, we found that both BMPR2 promoter DNA methylation and BMPR2 mRNA levels in the plasma are good biomarkers of VHD by themselves, with the respective AUC value of 0.879 and 0.725, respectively. When they were used in combination, the diagnostic value was even better, with the AUC value of 0.93. Consistent with the results in the VHD patients, we observed decreased BMPR2 and increased fibrosis in the lung of a PAH model mouse. BMPR2 was also decreased in the hearts of the PAH mice, whereas BMP4 was increased. Furthermore, BMPR2 was reduced in the heart valve tissue samples of human VHD patients after valve replacement with moderate/severe PAH compared with those with mild PAH. There was also increased apoptosis in the hearts of the PAH mice. BMPR2 promoter DNA methylation and its expression appear to be good biomarkers for VHD. Our results also suggest that DNA methylation may cause PAH through deregulation of BMP signaling and increased apoptosis.
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Victor AK, Donaldson M, Johnson D, Miller W, Reiter LT. Molecular Changes in Prader-Willi Syndrome Neurons Reveals Clues About Increased Autism Susceptibility. Front Mol Neurosci 2021; 14:747855. [PMID: 34776864 PMCID: PMC8586424 DOI: 10.3389/fnmol.2021.747855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Prader-Willi syndrome (PWS) is a neurodevelopmental disorder characterized by hormonal dysregulation, obesity, intellectual disability, and behavioral problems. Most PWS cases are caused by paternal interstitial deletions of 15q11.2-q13.1, while a smaller number of cases are caused by chromosome 15 maternal uniparental disomy (PW-UPD). Children with PW-UPD are at higher risk for developing autism spectrum disorder (ASD) than the neurotypical population. In this study, we used expression analysis of PW-UPD neurons to try to identify the molecular cause for increased autism risk. Methods: Dental pulp stem cells (DPSC) from neurotypical control and PWS subjects were differentiated to neurons for mRNA sequencing. Significantly differentially expressed transcripts among all groups were identified. Downstream protein analysis including immunocytochemistry and immunoblots were performed to confirm the transcript level data and pathway enrichment findings. Results: We identified 9 transcripts outside of the PWS critical region (15q11.2-q13.1) that may contribute to core PWS phenotypes. Moreover, we discovered a global reduction in mitochondrial transcripts in the PW-UPD + ASD group. We also found decreased mitochondrial abundance along with mitochondrial aggregates in the cell body and neural projections of +ASD neurons. Conclusion: The 9 transcripts we identified common to all PWS subtypes may reveal PWS specific defects during neurodevelopment. Importantly, we found a global reduction in mitochondrial transcripts in PW-UPD + ASD neurons versus control and other PWS subtypes. We then confirmed mitochondrial defects in neurons from individuals with PWS at the cellular level. Quantification of this phenotype supports our hypothesis that the increased incidence of ASD in PW-UPD subjects may arise from mitochondrial defects in developing neurons.
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Affiliation(s)
- A Kaitlyn Victor
- IPBS Program, Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Martin Donaldson
- Department of Pediatric Dentistry and Community Oral Health, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Daniel Johnson
- Molecular Bioinformatics Core, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Winston Miller
- Molecular Bioinformatics Core, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lawrence T Reiter
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States
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Key Markers and Epigenetic Modifications of Dental-Derived Mesenchymal Stromal Cells. Stem Cells Int 2021; 2021:5521715. [PMID: 34046069 PMCID: PMC8128613 DOI: 10.1155/2021/5521715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/08/2021] [Accepted: 04/17/2021] [Indexed: 12/13/2022] Open
Abstract
As a novel research hotspot in tissue regeneration, dental-derived mesenchymal stromal cells (MSCs) are famous for their accessibility, multipotent differentiation ability, and high proliferation. However, cellular heterogeneity is a major obstacle to the clinical application of dental-derived MSCs. Here, we reviewed the heterogeneity of dental-derived MSCs firstly and then discussed the key markers and epigenetic modifications related to the proliferation, differentiation, immunomodulation, and aging of dental-derived MSCs. These messages help to control the composition and function of dental-derived MSCs and thus accelerate the translation of cell therapy into clinical practice.
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10
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Arimura Y, Shindo Y, Yamanaka R, Mochizuki M, Hotta K, Nakahara T, Ito E, Yoshioka T, Oka K. Peripheral-neuron-like properties of differentiated human dental pulp stem cells (hDPSCs). PLoS One 2021; 16:e0251356. [PMID: 33956879 PMCID: PMC8101759 DOI: 10.1371/journal.pone.0251356] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
Elucidating the mechanisms underlying human pain sensation requires the establishment of an in vitro model of pain reception comprising human cells expressing pain-sensing receptors and function properly as neurons. Human dental pulp stem cells (hDPSCs) are mesenchymal stem cells and a promising candidate for producing human neuronal cells, however, the functional properties of differentiated hDPSCs have not yet been fully characterized. In this study, we demonstrated neuronal differentiation of hDPSCs via both their expression of neuronal marker proteins and their neuronal function examined using Ca2+ imaging. Moreover, to confirm the ability of nociception, Ca2+ responses in differentiated hDPSCs were compared to those of rat dorsal root ganglion (DRG) neurons. Those cells showed similar responses to glutamate, ATP and agonists of transient receptor potential (TRP) channels. Since TRP channels are implicated in nociception, differentiated hDPSCs provide a useful in vitro model of human peripheral neuron response to stimuli interpreted as pain.
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Affiliation(s)
- Yuki Arimura
- Faculty of Science and Technology, Department of Bioscience and Informatics, Keio University, Kanagawa, Japan
| | - Yutaka Shindo
- Faculty of Science and Technology, Department of Bioscience and Informatics, Keio University, Kanagawa, Japan
| | - Ryu Yamanaka
- Faculty of Science and Technology, Department of Bioscience and Informatics, Keio University, Kanagawa, Japan
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Yamaguchi, Japan
| | - Mai Mochizuki
- Faculty of Science and Technology, Department of Bioscience and Informatics, Keio University, Kanagawa, Japan
- Department of Life Science Dentistry, The Nippon Dental University, Tokyo, Japan
- Department of Developmental and Regenerative Dentistry, School of Life Dentistry at Tokyo, The Nippon Dental University, Tokyo, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Kohji Hotta
- Faculty of Science and Technology, Department of Bioscience and Informatics, Keio University, Kanagawa, Japan
| | - Taka Nakahara
- Department of Developmental and Regenerative Dentistry, School of Life Dentistry at Tokyo, The Nippon Dental University, Tokyo, Japan
| | - Etsuro Ito
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Department of Biology, Waseda University, Tokyo, Japan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tohru Yoshioka
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kotaro Oka
- Faculty of Science and Technology, Department of Bioscience and Informatics, Keio University, Kanagawa, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail:
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11
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Laufer BI, Gomez JA, Jianu JM, LaSalle JM. Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature. Epigenetics Chromatin 2021; 14:13. [PMID: 33750431 PMCID: PMC7942011 DOI: 10.1186/s13072-021-00387-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated). Results DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development. Conclusions Taken together, these results support a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00387-7.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA. .,Genome Center, University of California, Davis, CA, 95616, USA. .,MIND Institute, University of California, Davis, CA, 95616, USA.
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12
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Masuda K, Han X, Kato H, Sato H, Zhang Y, Sun X, Hirofuji Y, Yamaza H, Yamada A, Fukumoto S. Dental Pulp-Derived Mesenchymal Stem Cells for Modeling Genetic Disorders. Int J Mol Sci 2021; 22:ijms22052269. [PMID: 33668763 PMCID: PMC7956585 DOI: 10.3390/ijms22052269] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/20/2022] Open
Abstract
A subpopulation of mesenchymal stem cells, developmentally derived from multipotent neural crest cells that form multiple facial tissues, resides within the dental pulp of human teeth. These stem cells show high proliferative capacity in vitro and are multipotent, including adipogenic, myogenic, osteogenic, chondrogenic, and neurogenic potential. Teeth containing viable cells are harvested via minimally invasive procedures, based on various clinical diagnoses, but then usually discarded as medical waste, indicating the relatively low ethical considerations to reuse these cells for medical applications. Previous studies have demonstrated that stem cells derived from healthy subjects are an excellent source for cell-based medicine, tissue regeneration, and bioengineering. Furthermore, stem cells donated by patients affected by genetic disorders can serve as in vitro models of disease-specific genetic variants, indicating additional applications of these stem cells with high plasticity. This review discusses the benefits, limitations, and perspectives of patient-derived dental pulp stem cells as alternatives that may complement other excellent, yet incomplete stem cell models, such as induced pluripotent stem cells, together with our recent data.
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Affiliation(s)
- Keiji Masuda
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan; (X.H.); (H.S.); (Y.Z.); (X.S.); (Y.H.); (H.Y.)
- Correspondence: (K.M.); (S.F.); Tel.: +81-92-642-6402 (K.M. & S.F.)
| | - Xu Han
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan; (X.H.); (H.S.); (Y.Z.); (X.S.); (Y.H.); (H.Y.)
| | - Hiroki Kato
- Department of Molecular Cell Biology and Oral Anatomy, Graduate School of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan;
| | - Hiroshi Sato
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan; (X.H.); (H.S.); (Y.Z.); (X.S.); (Y.H.); (H.Y.)
| | - Yu Zhang
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan; (X.H.); (H.S.); (Y.Z.); (X.S.); (Y.H.); (H.Y.)
| | - Xiao Sun
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan; (X.H.); (H.S.); (Y.Z.); (X.S.); (Y.H.); (H.Y.)
| | - Yuta Hirofuji
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan; (X.H.); (H.S.); (Y.Z.); (X.S.); (Y.H.); (H.Y.)
| | - Haruyoshi Yamaza
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan; (X.H.); (H.S.); (Y.Z.); (X.S.); (Y.H.); (H.Y.)
| | - Aya Yamada
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Graduate School of Dentistry, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8577, Japan;
| | - Satoshi Fukumoto
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Maidashi 3-1-1, Higashi-Ku, Fukuoka 812-8582, Japan; (X.H.); (H.S.); (Y.Z.); (X.S.); (Y.H.); (H.Y.)
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Graduate School of Dentistry, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8577, Japan;
- Correspondence: (K.M.); (S.F.); Tel.: +81-92-642-6402 (K.M. & S.F.)
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13
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Epigenetic Regulation of Dental Pulp Stem Cell Fate. Stem Cells Int 2020; 2020:8876265. [PMID: 33149742 PMCID: PMC7603635 DOI: 10.1155/2020/8876265] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/21/2020] [Accepted: 09/24/2020] [Indexed: 02/05/2023] Open
Abstract
Epigenetic regulation, mainly involving DNA methylation, histone modification, and noncoding RNAs, affects gene expression without modifying the primary DNA sequence and modulates cell fate. Mesenchymal stem cells derived from dental pulp, also called dental pulp stem cells (DPSCs), exhibit multipotent differentiation capacity and can promote various biological processes, including odontogenesis, osteogenesis, angiogenesis, myogenesis, and chondrogenesis. Over the past decades, increased attention has been attracted by the use of DPSCs in the field of regenerative medicine. According to a series of studies, epigenetic regulation is essential for DPSCs to differentiate into specialized cells. In this review, we summarize the mechanisms involved in the epigenetic regulation of the fate of DPSCs.
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14
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Sui B, Wu D, Xiang L, Fu Y, Kou X, Shi S. Dental Pulp Stem Cells: From Discovery to Clinical Application. J Endod 2020; 46:S46-S55. [DOI: 10.1016/j.joen.2020.06.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Lin CY, Tsai MS, Kuo PJ, Chin YT, Weng IT, Wu Y, Huang HM, Hsiung CN, Lin HY, Lee SY. 2,3,5,4'-Tetrahydroxystilbene-2-O-β-d-glucoside promotes the effects of dental pulp stem cells on rebuilding periodontal tissues in experimental periodontal defects. J Periodontol 2020; 92:306-316. [PMID: 32790879 DOI: 10.1002/jper.19-0563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/10/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND This study aimed to investigate the regenerative effects of 2,3,5,4'-tetrahydroxystilbene-2-O-β-d-glucoside (THSG)-treated human dental pulp stem cells (DPSC) on the healing of experimental periodontal defects in rats. METHODS The maxillary first molars of 30 male Sprague-Dawley rats were extracted, and after healing, bilateral periodontal defects were surgically created mesially in second molars. The defects were treated with Matrigel (as control), DPSC, or DPSC + THSG. After 2 weeks, the healed defects were evaluated using microcomputed tomography and through histological and immunohistochemical analyses. RESULTS In the microcomputed tomography analysis, more new bone formation in the DPSC and DPSC + THSG groups was observed compared with the control group. The periodontal bone supporting ratio in site with DPSC + THSG was significantly higher than that in DPSC. Histologically, an enhanced new bone formation and more significant periodontal attachment were observed in the DPSC + THSG group. The expression levels of proliferating cell nuclear antigen (PCNA), vascular endothelial growth factor (VEGF), and osteopontin (OPN) in the DPSC + THSG group were significantly greater than those in other groups. CONCLUSIONS THSG-revolutionized DPSCs significantly shortened the regenerative period of periodontal defects by enhancing the cell recruitment and possibly the angiogenesis in rat models, which illustrate the critical implications for a clinical application and provide a novel tactic for periodontitis treatment.
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Affiliation(s)
- Chi-Yu Lin
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Center for Tooth Bank and Dental Stem Cell Technology, Taipei Medical University, Taipei, Taiwan
| | - Min-Shi Tsai
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Wan-Fang Medical Center, Taipei Medical University, Taipei, Taiwan
| | - Po-Jan Kuo
- Department of Periodontology, School of Dentistry, National Defense Medical Center and Tri-Service General Hospital, Taipei, Taiwan
| | - Yu-Tang Chin
- Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan.,PhD Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - I-Tsen Weng
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Wan-Fang Medical Center, Taipei Medical University, Taipei, Taiwan
| | - Yen Wu
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Wan-Fang Medical Center, Taipei Medical University, Taipei, Taiwan
| | - Haw-Ming Huang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chao-Nan Hsiung
- College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Hung-Yun Lin
- Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan.,PhD Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Yang Lee
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Center for Tooth Bank and Dental Stem Cell Technology, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Wan-Fang Medical Center, Taipei Medical University, Taipei, Taiwan
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16
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Jamali S, Mousavi E, Darvish M, Jabbari G, Nasrabadi N, Ahmadizadeh H. Dental Pulpal Tissue Regeneration, Pulpal Vitality Testing, and Healing of Apical Lesions Following Stem Cell Transplant: A Systematic Review and Meta-Analysis. PESQUISA BRASILEIRA EM ODONTOPEDIATRIA E CLÍNICA INTEGRADA 2020. [DOI: 10.1590/pboci.2020.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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17
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Guerrero-Jiménez M, Nic-Can GI, Castro-Linares N, Aguilar-Ayala FJ, Canul-Chan M, Rojas-Herrera RA, Peñaloza-Cuevas R, Rodas-Junco BA. In vitro histomorphometric comparison of dental pulp tissue in different teeth. PeerJ 2019; 7:e8212. [PMID: 31824782 PMCID: PMC6901003 DOI: 10.7717/peerj.8212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/14/2019] [Indexed: 11/20/2022] Open
Abstract
Background Dental pulp (DP) represents an accessible and valuable source promising of stem cells for clinical application. However, there are some disadvantages associated with the isolation of dental pulp stem cells (DPSCs), which include the size and weight of the pulp tissue needed to yield sufficient cells for culturing in vitro. Therefore, the objective of this study was to compare in vitro histomorphometry of DP from permanent (premolars, third molar), supernumerary and deciduous teeth of patients between 5 and 25 years old with regards to weight, length, width and the cell density in the four regions of the DP in order to obtain quantitative parameters in a tissue that represents a valuable source of stem cells. Methods DPs were obtained from 10 central incisors deciduous, 20 permanent teeth (10 premolars, 10 third molars) and 10 supernumeraries (six mesiodents and four inferior premolar shapes). The pulps were carefully removed, and the entire tissue was weighed. The pulp length and the width were measured with a digital Vernier caliper. The cellular density analysis was performed according to the four regions of the DP (coronal, cervical, medial and apical) in histological slides using photography and the ImageJ® program for quantification. Results The Pearson correlation test revealed that DP weight among different types of teeth is correlated with age in male patients. A significant positive correlation was noted between length and width of the DP with age in both genders. The mean DP weight for supernumerary and third molar teeth was greater than deciduous and premolar teeth. Finally, the histological analysis showed that the coronal and apical portions of DP in supernumerary and premolar teeth have the highest cell density. Conclusions The DP of supernumerary teeth has quantitatively the best morphometric parameters and cell density comparable with the quality of DP obtained from deciduous teeth.
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Affiliation(s)
- Marytere Guerrero-Jiménez
- Laboratorio Traslacional de Células Troncales de la Cavidad Bucal, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Geovanny I Nic-Can
- Laboratorio Traslacional de Células Troncales de la Cavidad Bucal, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Yucatán, México.,CONACYT-Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Nelly Castro-Linares
- Laboratorio Traslacional de Células Troncales de la Cavidad Bucal, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Fernando Javier Aguilar-Ayala
- Laboratorio Traslacional de Células Troncales de la Cavidad Bucal, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Michel Canul-Chan
- Facultad de Ciencias Químicas, Universidad Veracruzana, Orizaba, Veracruz, México
| | - Rafael A Rojas-Herrera
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Ricardo Peñaloza-Cuevas
- Laboratorio Traslacional de Células Troncales de la Cavidad Bucal, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Beatriz A Rodas-Junco
- Laboratorio Traslacional de Células Troncales de la Cavidad Bucal, Facultad de Odontología, Universidad Autónoma de Yucatán, Mérida, Yucatán, México.,CONACYT-Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
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18
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Atkinson SP. A Preview of Selected Articles. Stem Cells Transl Med 2019. [PMCID: PMC6646695 DOI: 10.1002/sctm.19-0198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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19
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Lim WJ, Kim KH, Kim JY, Jeong S, Kim N. Identification of DNA-Methylated CpG Islands Associated With Gene Silencing in the Adult Body Tissues of the Ogye Chicken Using RNA-Seq and Reduced Representation Bisulfite Sequencing. Front Genet 2019; 10:346. [PMID: 31040866 PMCID: PMC6476954 DOI: 10.3389/fgene.2019.00346] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic mark that plays an essential role in regulating gene expression. CpG islands are DNA methylations regions in promoters known to regulate gene expression through transcriptional silencing of the corresponding gene. DNA methylation at CpG islands is crucial for gene expression and tissue-specific processes. At the current time, a limited number of studies have reported on gene expression associated with DNA methylation in diverse adult tissues at the genome-wide level. Expression levels are rarely affected by DNA methylation in normal adult tissues; however, statistical differences in gene expression level correlated with DNA methylation have recently been revealed. In this study, we examined 20 pairs of DNA methylomes and transcriptomes from RNA-seq and reduced representation bisulfite sequencing (RRBS) data using adult Ogye chicken tissues. A total of 3,133 CpG islands were identified from 20 tissue data in a single chicken sample which could affect downstream genes. Analyzing these CpG island and gene pairs, 121 significant units were statistically correlated. Among them, six genes (CLDN3, DECR2, EVA1B, NME4, NTSR1, and XPNPEP2) were highly significantly changed by altered DNA methylation. Finally, our data demonstrated how DNA methylation correlated to gene expression in normal adult tissues. Our source codes can be found at https://github.com/wjlim/correlation-between-rna-seq-and-RRBS.
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Affiliation(s)
- Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, South Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, South Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, South Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, South Korea
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20
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Abstract
Adult stem cells are excellent cell resource for cell therapy and regenerative medicine. Dental pulp stem cells (DPSCs) have been discovered and well known in various application. Here, we reviewed the history of dental pulp stem cell study and the detail experimental method including isolation, culture, cryopreservation, and the differentiation strategy to different cell lineage. Moreover, we discussed the future potential application of the combination of tissue engineering and of DPSC differentiation. This review will help the new learner to quickly get into the DPSC filed.
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Affiliation(s)
- Xianrui Yang
- Department of Orthodontics, State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Li Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, 430062 Hubei China
| | - Li Xiao
- Department of Stomatology, Sichuan Academy of Medical Science & Sichuan Provincial People’s Hospital, Chengdu, 610072 China
| | - Donghui Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, 430062 Hubei China
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21
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Victor AK, Reiter LT. Dental pulp stem cells for the study of neurogenetic disorders. Hum Mol Genet 2018; 26:R166-R171. [PMID: 28582499 DOI: 10.1093/hmg/ddx208] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/08/2023] Open
Abstract
Dental pulp stem cells (DPSC) are a relatively new alternative stem cell source for the study of neurogenetic disorders. DPSC can be obtained non-invasively and collected from long-distances remaining viable during transportation. These highly proliferative cells express stem cell markers and retain the ability to differentiate down multiple cell lineages including chondrocytes, adipocytes, osteoblasts, and multiple neuronal cell types. The neural crest origin of DPSC makes them a useful source of primary cells for modeling neurological disorders at the molecular level. In this brief review, we will discuss recent developments in DPSC research that highlight the molecular etiology of DPSC derived neurons and how they may contribute to our understanding of neurogenetic disorders.
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Affiliation(s)
| | - Lawrence T Reiter
- Department of Neurology.,Department of Pediatrics.,Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
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22
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Ciernia AV, Careaga M, Ashwood P, LaSalle J. Microglia from offspring of dams with allergic asthma exhibit epigenomic alterations in genes dysregulated in autism. Glia 2018; 66:505-521. [PMID: 29134693 PMCID: PMC5767155 DOI: 10.1002/glia.23261] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/18/2017] [Accepted: 10/25/2017] [Indexed: 12/24/2022]
Abstract
Dysregulation in immune responses during pregnancy increases the risk of a having a child with an autism spectrum disorder (ASD). Asthma is one of the most common chronic diseases among pregnant women, and symptoms often worsen during pregnancy. We recently developed a mouse model of maternal allergic asthma (MAA) that induces changes in sociability, repetitive, and perseverative behaviors in the offspring. Since epigenetic changes help a static genome adapt to the maternal environment, activation of the immune system may epigenetically alter fetal microglia, the brain's resident immune cells. We therefore tested the hypothesis that epigenomic alterations to microglia may be involved in behavioral abnormalities observed in MAA offspring. We used the genome-wide approaches of whole genome bisulfite sequencing to examine DNA methylation and RNA sequencing to examine gene expression in microglia from juvenile MAA offspring. Differentially methylated regions were enriched for immune signaling pathways and important microglial developmental transcription factor binding motifs. Differential expression analysis identified genes involved in controlling microglial sensitivity to the environment and shaping neuronal connections in the developing brain. Differentially expressed genes significantly overlapped genes with altered expression in human ASD cortex, supporting a role for microglia in the pathogenesis of ASD.
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Affiliation(s)
- Annie Vogel Ciernia
- Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616
| | - Milo Careaga
- MIND Institute, 2825 50 Street, Sacramento, CA 95817, University of California, Davis
| | - Paul Ashwood
- MIND Institute, 2825 50 Street, Sacramento, CA 95817, University of California, Davis
| | - Janine LaSalle
- Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616
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23
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Urraca N, Hope K, Victor AK, Belgard TG, Memon R, Goorha S, Valdez C, Tran QT, Sanchez S, Ramirez J, Donaldson M, Bridges D, Reiter LT. Significant transcriptional changes in 15q duplication but not Angelman syndrome deletion stem cell-derived neurons. Mol Autism 2018; 9:6. [PMID: 29423132 PMCID: PMC5787244 DOI: 10.1186/s13229-018-0191-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/15/2018] [Indexed: 01/09/2023] Open
Abstract
Background The inability to analyze gene expression in living neurons from Angelman (AS) and Duplication 15q (Dup15q) syndrome subjects has limited our understanding of these disorders at the molecular level. Method Here, we use dental pulp stem cells (DPSC) from AS deletion, 15q Duplication, and neurotypical control subjects for whole transcriptome analysis. We identified 20 genes unique to AS neurons, 120 genes unique to 15q duplication, and 3 shared transcripts that were differentially expressed in DPSC neurons vs controls. Results Copy number correlated with gene expression for most genes across the 15q11.2-q13.1 critical region. Two thirds of the genes differentially expressed in 15q duplication neurons were downregulated compared to controls including several transcription factors, while in AS differential expression was restricted primarily to the 15q region. Here, we show significant downregulation of the transcription factors FOXO1 and HAND2 in neurons from 15q duplication, but not AS deletion subjects suggesting that disruptions in transcriptional regulation may be a driving factor in the autism phenotype in Dup15q syndrome. Downstream analysis revealed downregulation of the ASD associated genes EHPB2 and RORA, both genes with FOXO1 binding sites. Genes upregulated in either Dup15q cortex or idiopathic ASD cortex both overlapped significantly with the most upregulated genes in Dup15q DPSC-derived neurons. Conclusions Finding a significant increase in both HERC2 and UBE3A in Dup15q neurons and significant decrease in these two genes in AS deletion neurons may explain differences between AS deletion class and UBE3A specific classes of AS mutation where HERC2 is expressed at normal levels. Also, we identified an enrichment for FOXO1-regulated transcripts in Dup15q neurons including ASD-associated genes EHPB2 and RORA indicating a possible connection between this syndromic form of ASD and idiopathic cases.
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Affiliation(s)
- Nora Urraca
- Department of Neurology, The University of Tennessee Health Science Center, 855 Monroe Ave., Link 415, Memphis, TN 38163 USA
| | - Kevin Hope
- Department of Neurology, The University of Tennessee Health Science Center, 855 Monroe Ave., Link 415, Memphis, TN 38163 USA
- IPBS Program, The University of Tennessee Health Science Center, Memphis, TN 38163 USA
| | - A. Kaitlyn Victor
- Department of Neurology, The University of Tennessee Health Science Center, 855 Monroe Ave., Link 415, Memphis, TN 38163 USA
- IPBS Program, The University of Tennessee Health Science Center, Memphis, TN 38163 USA
| | - T. Grant Belgard
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Rawaha Memon
- Department of Pediatric Dentistry, The University of Tennessee Health Science Center, Memphis, TN 38163 USA
| | - Sarita Goorha
- Department of Neurology, The University of Tennessee Health Science Center, 855 Monroe Ave., Link 415, Memphis, TN 38163 USA
| | - Colleen Valdez
- Department of Neurology, The University of Tennessee Health Science Center, 855 Monroe Ave., Link 415, Memphis, TN 38163 USA
| | - Quynh T. Tran
- Department of Preventive Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163 USA
| | - Silvia Sanchez
- Instituto Nacional de Pediatria, 04530 Mexico City, Mexico
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, University of Basque Country, Bilbao, Spain
| | - Martin Donaldson
- Department of Pediatric Dentistry, The University of Tennessee Health Science Center, Memphis, TN 38163 USA
| | - Dave Bridges
- Department of Nutritional Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109 USA
| | - Lawrence T. Reiter
- Department of Neurology, The University of Tennessee Health Science Center, 855 Monroe Ave., Link 415, Memphis, TN 38163 USA
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN 38163 USA
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