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Jiang H, Zhang X, Wu Y, Zhang B, Wei J, Li J, Huang Y, Chen L, He X. Bioinformatics identification and validation of biomarkers and infiltrating immune cells in endometriosis. Front Immunol 2022; 13:944683. [PMID: 36524127 PMCID: PMC9745028 DOI: 10.3389/fimmu.2022.944683] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022] Open
Abstract
Background Endometriosis (EM) is a common gynecological disorder that often leads to irregular menstruation and infertility. The pathogenesis of EM remains unclear and delays in diagnosis are common. Thus, it is urgent to explore potential biomarkers and underlying molecular mechanisms for EM diagnosis and therapies. Methods Three EM-related datasets (GSE11691, GSE25628, and GSE86534) were downloaded from the Gene Expression Omnibus (GEO) which were integrated into a combined dataset after removing batch effect. Differentially expressed immune cell-related genes were obtained by CIBERSORT, WGCNA, and the identification of differentially expressed genes. Random forest model (RF), support vector machine model (SVM), and generalized linear model (GLM) were then constructed and the biomarkers for EM were determined. A nomogram evaluating the risk of disease was constructed and the validity was assessed by the calibration curve, DCA curve, and clinical impact curve. Single-gene Gene Set Enrichment Analysis (GSEA)was performed to explore the molecular mechanisms of biomarkers. The ceRNA regulatory network of biomarkers was created by Cytoscape and potential target drugs were obtained in the DGIdb database (Drug-Gene Interaction database).The expression levels of biomarkers from clinical samples was quantified by RT-qPCR. Results The ratio of eight immune cells was significantly different between the eutopic and ectopic endometrium samples. A total of eight differentially expressed immune cell-related genes were investigated. The SVM model was a relatively suitable model for the prediction of EM and five genes (CXCL12, PDGFRL, AGTR1, PTGER3, and S1PR1) were selected from the model as biomarkers. The calibration curve, DCA curve, and clinical impact curve indicated that the nomogram based on the five biomarkers had a robust ability to predict disease. Single gene GSEA result suggested that all five biomarkers were involved in labyrinthine layer morphogenesis and transmembrane transport-related biological processes in EM. A ceRNA regulatory network containing 184 nodes and 251 edges was constructed. Seven drugs targeting CXCL12, 49 drugs targeting AGTR1, 16 drugs targeting PTGER3, and 21 drugs targeting S1PR1 were extracted as potential drugs for EM therapy. Finally, the expression of PDGFRL and S1PR1 in clinical samples was validated by RT-qPCR, which was consistent with the result of public database. Conclusions In summary, we identified five biomarkers (CXCL12, PDGFRL, AGTR1, PTGER3, and S1PR1) and constructed diagnostic model, furthermore predicted the potential therapeutic drugs for EM. Collectively, these findings provide new insights into EM diagnosis and treatment.
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Affiliation(s)
- Hong Jiang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Xia Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Yalan Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Baozhu Zhang
- Department of Obstetrics and Gynecology, Fu’an Hospital, Fuan, Fujian, China
| | - Juanbing Wei
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Jianhua Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Yuxiu Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Lihong Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Xinqin He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China,*Correspondence: Xinqin He,
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Castro I, Carvajal P, Jara D, Aguilera S, Heathcote B, Barrera MJ, Aliaga-Tobar V, Maracaja-Coutinho V, Urzúa U, Quest AFG, González S, Molina C, Hermoso M, González MJ. Small RNA Expression Profiling Reveals hsa-miR-181d-5p Downregulation Associated With TNF-α Overexpression in Sjögren’s Syndrome Patients. Front Immunol 2022; 13:870094. [PMID: 35432384 PMCID: PMC9010469 DOI: 10.3389/fimmu.2022.870094] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/14/2022] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (sRNA), that alter gene expression by binding to target messenger RNAs (mRNAs) and repressing translation. Dysregulated miRNA expression has been implicated in the pathogenesis of autoimmune diseases such as Sjögren’s syndrome (SS). The aim of this study was to characterize the global profile of sRNAs in labial salivary glands (LSG) from SS-patients and to validate potential miRNA candidates implicated in glandular inflammation. LSG from 21 SS-patients and 9 sicca controls were analyzed. A global next generation sequencing (NGS)-based sRNA profiling approach was employed to identify direct targets whereby differentially expressed miRNAs were predicted using bioinformatics tools. miRNA levels were validated by TaqMan and target mRNA levels were determined by quantitative real-time PCR. We also performed in vitro assays using recombinant TNF-α. NGS shows that ~30% of sRNAs were miRNAs. In comparison with samples from sicca controls, four miRNAs were found differentially expressed in LSG from SS-patients with low focus score (LFS) and 18 from SS-patients with high focus score (HFS). The miRNA with the most significant changes identified by NGS was hsa-miR-181d-5p and downregulation was confirmed by TaqMan analysis. Levels of TNF-α mRNA, a direct target of hsa-miR-181d-5p, were significantly increased and negatively correlated with hsa-miR-181d-5p presence. Moreover, positive correlations between TNF-α transcript levels, focus score, ESSDAI, and autoantibody levels were also detected. Furthermore, TNF-α stimulation decreased hsa-miR-181d-5p levels in vitro. Downregulation of hsa-miR-181d-5p in LSG from SS-patients could contribute to the glandular pro-inflammatory environment by deregulation of its direct target TNF-α. Further dissection of the pathophysiological mechanisms underlying the hsa-miR-181d-5p-mediated action in inflammatory conditions could be useful to evaluate the benefits of increasing hsa-miR-181d-5p levels for restoration of salivary gland epithelial cell architecture and function.
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Affiliation(s)
- Isabel Castro
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Patricia Carvajal
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Daniela Jara
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sergio Aguilera
- Departamento de Reumatología, Clínica Instituto de Diagnóstico Sociedad Anónima (Indisa), Santiago, Chile
| | - Benjamín Heathcote
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Víctor Aliaga-Tobar
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O’Higgins, Rancagua, Chile
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Ulises Urzúa
- Departamento de Oncología Básico-Clínico, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Andrew F. G. Quest
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Centro de Estudios en Ejercicio, Metabolismo y Cáncer (CEMC), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sergio González
- Escuela de Odontología, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | - Claudio Molina
- Facultad de Odontología, Universidad San Sebastián, Santiago, Chile
| | - Marcela Hermoso
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - María-Julieta González
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- *Correspondence: María-Julieta González, ;
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Prasad SR, Pai A, Shyamala K, Yaji A. Expression of Salivary miRNA 21 in Oral Submucous Fibrosis (OSMF): An Observational Study. Microrna 2021; 9:295-302. [PMID: 31985389 PMCID: PMC8226152 DOI: 10.2174/2211536609666200127143749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/19/2019] [Accepted: 12/09/2019] [Indexed: 11/26/2022]
Abstract
Objective: To observe the expression patterns of salivary mRNA 21 in different stages and grades of OSMF and also in habitual areca nut chewers without OSMF. Subjects and Methods The study consisted of a total of 185 samples, where 61 patients had chewing habits (chewing gutkha and other forms of areca nut) and had OSMF (Group 1). 61 patients had chewing habits but did not have OSMF (Group 2), and 63 were normal healthy patients (control group) without any chewing habits (Group 3). Unstimulated saliva samples were collected from patients following the standard operating procedures. miRNA 21 was isolated and purified from saliva samples using the miRNeasy Mini Kit, Qiagen. The primers for miRNA relative quantification analysis were designed using the Primer Express software of Applied Biosystems. Quantification of all the samples was carried out using SYBR chemistry in an Applied Biosystems Real-Time PCR. Results There was no statistically significant difference between the demographic characteristics of patients. There was a statistically significant difference between the expressions of miRNA 21 amongst the three groups noted in Kruskal Wallis test. (<0.001*) A post hoc test was perfomed to confirm the statistical difference between patients within all three groups. There was no statistically significant difference noted between the OSMF group and patients with chewing habits group (G1 vs. G2 p: 0.10), but there was a significant difference when compared with normal patients. (G1 vs. G3 p: <0.001*) and (G2 vs. G3 <0.001*) Conclusion This study concludes that miRNA 21 is overexpressed in OSMF and chewing habit patients. But the expression levels were not significantly associated with the severity of the disease process. A long term and large scale studies are required to assess its application as a diagnostic profibrotic marker in OSMF.
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Affiliation(s)
- Shesha R Prasad
- Department of Oral Medicine and Radiology, The Oxford Dental College and Hospital, Bommanhalli, Hosur Road, Bangalore-560068, India
| | - Anuradha Pai
- Department of Oral Medicine and Radiology, The Oxford Dental College and Hospital, Bommanhalli, Hosur Road, Bangalore-560068, India
| | - K Shyamala
- Department of Oral and Maxillofacial Pathology, Raja Rajeswari Dental College & Hospital, Kumbalgodu, Bangalore - 560074, India
| | - Anisha Yaji
- Oral Medicine and Radiologist, Dental Department, Sri Krishna Sevashrama Hospital, Jaynagar, Bangalore - 560041, India
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One-Carbon Metabolism Links Nutrition Intake to Embryonic Development via Epigenetic Mechanisms. Stem Cells Int 2019; 2019:3894101. [PMID: 30956668 PMCID: PMC6431457 DOI: 10.1155/2019/3894101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/06/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023] Open
Abstract
Beyond energy production, nutrient metabolism plays a crucial role in stem cell lineage determination. Changes in metabolism based on nutrient availability and dietary habits impact stem cell identity. Evidence suggests a strong link between metabolism and epigenetic mechanisms occurring during embryonic development and later life of offspring. Metabolism regulates epigenetic mechanisms such as modifications of DNA, histones, and microRNAs. In turn, these epigenetic mechanisms regulate metabolic pathways to modify the metabolome. One-carbon metabolism (OCM) is a crucial metabolic process involving transfer of the methyl groups leading to regulation of multiple cellular activities. OCM cycles and its related micronutrients are ubiquitously present in stem cells and feed into the epigenetic mechanisms. In this review, we briefly introduce the OCM process and involved micronutrients and discuss OCM-associated epigenetic modifications, including DNA methylation, histone modification, and microRNAs. We further consider the underlying OCM-mediated link between nutrition and epigenetic modifications in embryonic development.
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Abstract
Owing to the development of new technologies, the epigenome, a second dimensional method for genome analysis has emerged. Epigenetic mechanisms, including DNA methylation, histone modifications and noncoding RNAs, regulate gene expression without changing the genetic sequence. These epigenetic mechanisms normally modulate gene expression, trans-generational effects and inherited expression states in various biological processes. Abnormal epigenetic patterns typically cause pathological conditions, including cancers, age-related diseases, and specific cartilage and bone diseases. Facing the rapidly developing epigenetic field, we reviewed epigenetic mechanisms and their involvement with the skeletal system and their role in skeletal development, homeostasis and degeneration. Finally, we discuss the prospects for the future of epigenetics.
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Tang J, Yu Y, Yang W. Long noncoding RNA and its contribution to autism spectrum disorders. CNS Neurosci Ther 2017; 23:645-656. [PMID: 28635106 PMCID: PMC6492731 DOI: 10.1111/cns.12710] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 12/13/2022] Open
Abstract
Recent studies have indicated that long noncoding RNAs (lncRNAs) play important roles in multiple processes, such as epigenetic regulation, gene expression regulation, development, nutrition-related and other diseases, toxic response, and response to drugs. Although the functional roles and mechanisms of several lncRNAs have been discovered, a better understanding of the vast majority of lncRNAs remains elusive. To understand the functional roles and mechanisms of lncRNAs is critical because these transcripts represent the majority of the transcriptional output of the mammalian genome. Recent studies have also suggested that lncRNAs are more abundant in the human brain and are involved in neurodevelopment and neurodevelopmental disorders, including autism spectrum disorders (ASDs). In this study, we review several known functions of lncRNAs and the potential contribution of lncRNAs to ASDs and to other genetic syndromes that have a similar clinical presentation to ASDs, such as fragile X syndrome and Rett syndrome.
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Affiliation(s)
- Jie Tang
- The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Preventive MedicineSchool of Public HealthGuangzhou Medical UniversityXinzaoPanyu DistrictGuangzhouChina
| | - Yizhen Yu
- Department of Child and Women Health CareSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Wei Yang
- Department of Nutrition and Food HygieneHubei Key Laboratory of Food Nutrition and SafetyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Nutrition and Food HygieneMOE Key Lab of Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Park SJ, Saito-Adachi M, Komiyama Y, Nakai K. Advances, practice, and clinical perspectives in high-throughput sequencing. Oral Dis 2016; 22:353-64. [DOI: 10.1111/odi.12403] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023]
Affiliation(s)
- S-J Park
- Human Genome Center; The Institute of Medical Science; The University of Tokyo; Tokyo Japan
| | - M Saito-Adachi
- Division of Cancer Genomics; National Cancer Center Research Institute; Tokyo Japan
| | - Y Komiyama
- Human Genome Center; The Institute of Medical Science; The University of Tokyo; Tokyo Japan
| | - K Nakai
- Human Genome Center; The Institute of Medical Science; The University of Tokyo; Tokyo Japan
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Wong DTW. Salivary extracellular noncoding RNA: emerging biomarkers for molecular diagnostics. Clin Ther 2015; 37:540-51. [PMID: 25795433 DOI: 10.1016/j.clinthera.2015.02.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 01/05/2023]
Abstract
Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, nourished by body's vasculature. Although many circulatory molecules (DNA, RNA, and proteins) can also be present in saliva, saliva harbors unique molecular constituents that can be discriminatory for oral and systemic disease screening and detection. Many studies have reported that salivary constituents can discriminate oral diseases (oral cancer and Sjögren's syndrome) and also systemic diseases (lung cancer, breast cancer, pancreatic cancer, and ovarian cancer). Noncoding RNAs (ncRNAs) are emerging new regulators of diverse biological functions, playing important roles in oncogenesis and tumor progression. Indeed, the short size of these molecules makes them stable in different body fluids such as urine, blood, and saliva, being not as susceptible as mRNAs to degradation by RNases. Here, the current status and clinical implications of the ncRNAs present in human saliva are reviewed for translational applications and basic biological research. The development of noninvasive salivary test (based on ncRNAs profiles) for disease detection could have effective applications into the clinical context with a translational significance as emerging molecular biomarkers for non-invasively disease detection, not only by reducing the cost to the health care system but also by benefitting patients.
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Affiliation(s)
- David T W Wong
- Division of Oral Biology, School of Dentistry; Jonnson Comprehensive Cancer Center, Department of Head and Neck Surgery, David Geffen School of Medicine; School of Engineering, University of California Los Angeles, Los Angeles, California.
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Seo JY, Park YJ, Yi YA, Hwang JY, Lee IB, Cho BH, Son HH, Seo DG. Epigenetics: general characteristics and implications for oral health. Restor Dent Endod 2014; 40:14-22. [PMID: 25671208 PMCID: PMC4320272 DOI: 10.5395/rde.2015.40.1.14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 09/11/2014] [Indexed: 01/08/2023] Open
Abstract
Genetic information such as DNA sequences has been limited to fully explain mechanisms of gene regulation and disease process. Epigenetic mechanisms, which include DNA methylation, histone modification and non-coding RNAs, can regulate gene expression and affect progression of disease. Although studies focused on epigenetics are being actively investigated in the field of medicine and biology, epigenetics in dental research is at the early stages. However, studies on epigenetics in dentistry deserve attention because epigenetic mechanisms play important roles in gene expression during tooth development and may affect oral diseases. In addition, understanding of epigenetic alteration is important for developing new therapeutic methods. This review article aims to outline the general features of epigenetic mechanisms and describe its future implications in the field of dentistry.
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Affiliation(s)
- Ji-Yun Seo
- Department of Conservative Dentistry, Seoul National University School of Dentistry and Dental Research Institute, Seoul, Korea
| | - Yoon-Jung Park
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul, Korea
| | - Young-Ah Yi
- Department of Dentistry, Inje University Seoul Paik Hospital, Seoul, Korea
| | - Ji-Yun Hwang
- Nutrition Education Major, Graduate School of Education, Sangmyung University, Seoul, Korea
| | - In-Bog Lee
- Department of Conservative Dentistry, Seoul National University School of Dentistry and Dental Research Institute, Seoul, Korea
| | - Byeong-Hoon Cho
- Department of Conservative Dentistry, Seoul National University School of Dentistry and Dental Research Institute, Seoul, Korea
| | - Ho-Hyun Son
- Department of Conservative Dentistry, Seoul National University School of Dentistry and Dental Research Institute, Seoul, Korea
| | - Deog-Gyu Seo
- Department of Conservative Dentistry, Seoul National University School of Dentistry and Dental Research Institute, Seoul, Korea
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