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Liu Z, Mo F, Dong X, Chen G, Gao J, Zhang J. Loxl3 Affects Palatal Shelf Elevation by Regulating Cell Proliferation and Collagen Deposition. Int J Mol Sci 2025; 26:4815. [PMID: 40429955 PMCID: PMC12111807 DOI: 10.3390/ijms26104815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 05/09/2025] [Accepted: 05/15/2025] [Indexed: 05/29/2025] Open
Abstract
Cleft palate is one of the most common congenital abnormalities and one of the main symptoms of Stickler syndrome. Secondary palate development is a complex multi-step process that involves raising the palatal frame from a vertical to a horizontal position. Lysyl oxidase-like 3 (LOXL3), a member of the lysyl oxidase family responsible for the crosslinking in collagen, is also one of the mutated genes detected in Stickler syndrome. Loss of Loxl3 causes delayed palatal shelf elevation, which in turn resulted in cleft palate. However, the precise mechanisms of palatal shelf delayed elevation remain unclear. In this study, we deeply investigated the mechanism of Loxl3 induced delayed elevation in palatal shelves. We found that Loxl3 deficiency caused reduced cell proliferation in both medial and posterior palatal mesenchyme through BrdU labeling and Western blot analysis (p < 0.05, p < 0.01), decreased migration of palatal mesenchymal cells through cell scratch assay (p < 0.05), and decreased expression of genes associated with proliferation through Western blot analysis (p < 0.05, p < 0.01) at E14. We found that the specific deletion of Loxl3 in the palatal mesenchyme resulted in delayed elevation but normal fusion of palatal shelves, also reduced cell proliferation and collagen fibers deposition in medial palatal mesenchyme through BrdU labeling and histological analysis (p < 0.05, p < 0.01). Thus, our data suggest that Loxl3 regulates cell proliferation and collagen fibers deposition in the palatal mesenchyme, thus controlling palatal shelf elevation.
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Affiliation(s)
| | | | | | | | - Jiangang Gao
- School of Life Science, Shandong University, Qingdao 266237, China; (Z.L.); (F.M.); (X.D.); (G.C.)
| | - Jian Zhang
- School of Life Science, Shandong University, Qingdao 266237, China; (Z.L.); (F.M.); (X.D.); (G.C.)
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Horita H, Tsukiboshi Y, Ogata K, Ogata A, Kurita H, Yamashita S, Yamashita H, Inagaki N, Horiguchi H, Yoshioka H. Sasa veitchii Extract Mitigates Mycophenolate Mofetil-Induced Human Palatal Cell Proliferation Inhibition by Downregulating microRNA-4680-3p. PLANTS (BASEL, SWITZERLAND) 2025; 14:1150. [PMID: 40219219 PMCID: PMC11991523 DOI: 10.3390/plants14071150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 03/29/2025] [Accepted: 04/05/2025] [Indexed: 04/14/2025]
Abstract
Cleft palate is a common birth defect worldwide and is caused by both genetic and environmental factors. Intrauterine drug exposure is one of the environmental factors that can induce cleft palate. Mycophenolate mofetil (MPM) is an immunosuppressant drug with teratogenic effects, including cleft palate. However, the research on MPM-induced cleft palate remains limited. Sasa veitchii extract (SE), a medical plant extract, is commercially available in Asia and has been reported to show effectiveness against oral diseases. The purpose of the present study is to evaluate whether SE protects against MPM-induced immunosuppression in human embryonic palatal mesenchymal (HEPM) cells. Cell viability and G1 phase-related cell cycle markers were assessed by co-treatment with MPM and SE. Furthermore, we quantified cleft palate-associated miRNA levels and the expression of its downstream genes. MPM treatment reduced cell viability in a concentration-dependent manner. Co-treatment with SE alleviated MPM-induced inhibition of HEPM cell proliferation. Additionally, SE reduced MPM-induced miR-4680-3p upregulation and the downregulation of its downstream genes (ERBB2 and JADE1). These results suggest that SE alleviated MPM-induced cell proliferation inhibition through modulating miR-4680-3p expression.
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Affiliation(s)
- Hanane Horita
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani 509-0293, Gifu, Japan
| | - Yosuke Tsukiboshi
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani 509-0293, Gifu, Japan
| | - Kenichi Ogata
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Fukuoka, Japan
| | - Aya Ogata
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani 509-0293, Gifu, Japan
| | - Hisaka Kurita
- Laboratory of Medical Therapeutics and Molecular Therapeutics, Gifu Pharmaceutical University, 1-25-4 Daigakunishi, Gifu 501-1196, Gifu, Japan
| | - Shuji Yamashita
- Laboratory of Community Pharmaceutical Practice and Science, Gifu Pharmaceutical University, 1-25-4 Daigakunishi, Gifu 501-1196, Gifu, Japan
| | - Hirotaka Yamashita
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani 509-0293, Gifu, Japan
- Department of Pharmacology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara 903-0215, Okinawa, Japan
| | - Naoki Inagaki
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani 509-0293, Gifu, Japan
| | - Hyogo Horiguchi
- Department of Hygiene, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0374, Kanagawa, Japan
| | - Hiroki Yoshioka
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani 509-0293, Gifu, Japan
- Department of Hygiene, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0374, Kanagawa, Japan
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3
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Yoshioka H, Horita H, Tsukiboshi Y, Kurita H, Ogata A, Ogata K. Cleft Palate Induced by Mycophenolate Mofetil Is Associated with miR-4680-3p and let-7c-5p in Human Palate Cells. Noncoding RNA 2025; 11:12. [PMID: 39997612 PMCID: PMC11858478 DOI: 10.3390/ncrna11010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 01/13/2025] [Accepted: 02/04/2025] [Indexed: 02/26/2025] Open
Abstract
Background/Objectives: Cleft palate is a birth defect associated with environmental and genetic factors. Disturbance of microRNAs (miRNAs) and exposure to medicinal agents during pregnancy can cause cleft palate. Although an association between medicine-induced cleft palate and miRNAs has been suggested, it remains to be fully elucidated. This study aimed to clarify the molecular mechanism underlying mycophenolate mofetil (MPM)-induced inhibition of cell proliferation and miRNA expression in human embryonic palatal mesenchymal (HEPM) cells. Methods: Cell viability, apoptosis, and cell cycle-related markers were evaluated 48 h after MPM treatment. In addition, miRNA levels and expression of their downstream genes were measured, and a rescue experiment was performed using miR-4680-3p and/or let-7c-5p inhibitors. Results: MPM dose-dependently reduced HEPM cell viability. Additionally, MPM treatment suppressed cyclin-D1, cyclin E1, cyclin-dependent kinase (CDK)-2, and CDK6 expression in HEPM cells. Furthermore, MPM upregulated miR-4680-3p and let-7c-5p expression and downregulated the downstream genes of each miRNA. Moreover, miR-4680-3p and/or let-7c-5p inhibitors alleviated MPM-induced inhibition of cell proliferation. Conclusions: These results suggest that MPM-induced cleft palate is associated with miR-4680-3p and let-7c-5p expression in HEPM cells.
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Affiliation(s)
- Hiroki Yoshioka
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani, Gifu 509-0293, Japan
- Department of Hygiene, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Hanane Horita
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani, Gifu 509-0293, Japan
| | - Yosuke Tsukiboshi
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani, Gifu 509-0293, Japan
| | - Hisaka Kurita
- Laboratory of Medical Therapeutics and Molecular Therapeutics, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, Gifu 501-1196, Japan
| | - Aya Ogata
- Faculty of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani, Gifu 509-0293, Japan
| | - Kenichi Ogata
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Im H, Song Y, Kim JK, Park DK, Kim DS, Kim H, Shin JO. Molecular Regulation of Palatogenesis and Clefting: An Integrative Analysis of Genetic, Epigenetic Networks, and Environmental Interactions. Int J Mol Sci 2025; 26:1382. [PMID: 39941150 PMCID: PMC11818578 DOI: 10.3390/ijms26031382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2025] [Revised: 02/03/2025] [Accepted: 02/04/2025] [Indexed: 02/16/2025] Open
Abstract
Palatogenesis is a complex developmental process requiring temporospatially coordinated cellular and molecular events. The following review focuses on genetic, epigenetic, and environmental aspects directing palatal formation and their implication in orofacial clefting genesis. Essential for palatal shelf development and elevation (TGF-β, BMP, FGF, and WNT), the subsequent processes of fusion (SHH) and proliferation, migration, differentiation, and apoptosis of neural crest-derived cells are controlled through signaling pathways. Interruptions to these processes may result in the birth defect cleft lip and/or palate (CL/P), which happens in approximately 1 in every 700 live births worldwide. Recent progress has emphasized epigenetic regulations via the class of non-coding RNAs with microRNAs based on critically important biological processes, such as proliferation, apoptosis, and epithelial-mesenchymal transition. These environmental risks (maternal smoking, alcohol, retinoic acid, and folate deficiency) interact with genetic and epigenetic factors during palatogenesis, while teratogens like dexamethasone and TCDD inhibit palatal fusion. In orofacial cleft, genetic, epigenetic, and environmental impact on the complex epidemiology. This is an extensive review, offering current perspectives on gene-environment interactions, as well as non-coding RNAs, in palatogenesis and emphasizing open questions regarding these interactions in palatal development.
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Affiliation(s)
- Hyuna Im
- Department of Anatomy, College of Medicine, Soonchunhyang University, Cheonan 33151, Republic of Korea (D.-K.P.); (D.-S.K.)
| | - Yujeong Song
- Department of Anatomy, College of Medicine, Soonchunhyang University, Cheonan 33151, Republic of Korea (D.-K.P.); (D.-S.K.)
| | - Jae Kyeom Kim
- Department of Food and Biotechnology, Korea University, Sejong 339770, Republic of Korea
- Department of Health Behavior and Nutrition Sciences, University of Delaware, Newark, DE 19711, USA
| | - Dae-Kyoon Park
- Department of Anatomy, College of Medicine, Soonchunhyang University, Cheonan 33151, Republic of Korea (D.-K.P.); (D.-S.K.)
| | - Duk-Soo Kim
- Department of Anatomy, College of Medicine, Soonchunhyang University, Cheonan 33151, Republic of Korea (D.-K.P.); (D.-S.K.)
| | - Hankyu Kim
- Department of Anatomy, College of Medicine, Soonchunhyang University, Cheonan 33151, Republic of Korea (D.-K.P.); (D.-S.K.)
| | - Jeong-Oh Shin
- Department of Anatomy, College of Medicine, Soonchunhyang University, Cheonan 33151, Republic of Korea (D.-K.P.); (D.-S.K.)
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Dong X, Chen Q, Du H, Qiu L. 2,3,7,8-Tetrachlorodibenzo-p-Dioxin Suppresses Mesenchymal Cell Proliferation and Migration Through miR-214-3p in Cleft Palate. Cleft Palate Craniofac J 2024:10556656241286314. [PMID: 39314083 DOI: 10.1177/10556656241286314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024] Open
Abstract
OBJECTIVE The aetiology of CL/P is complicated, with both genetic and environmental factors. This study aimed to investigate the association between TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) exposure and changes in the expression of miR-214-3p in the context of cleft palate. DESIGN In this study, we established a fetal mouse cleft palate model using TCDD and differentially expressed miRNAs were analysed by microarray analysis and verified by qRT-PCR. Finally, we demonstrated the effects of TCDD and microRNAs on the proliferation and migration of mesenchymal cells by using CCK8, EDU, Transwell, and wound-healing assays. RESULTS Our findings revealed significant upregulation of miRNAs such as miR-214-3p, miR-296-5p, and miR-33-5p in the TCDD intervention group, while miRNAs like miR-92a-3p, miR-126a-3p, and miR-411-5p were significantly downregulated. Notably, qRT-PCR testing confirmed a significant difference in miR-214-3P expression. Further investigations involved the overexpression of miR-214-3p, reducing cell proliferation and migration in primary mouse embryonic palatal mesenchymal (MEPM) cells. CONCLUSIONS These results are consistent with the finding that TCDD suppresses palatal mesenchymal cell proliferation and migration through miR-214-3p. In conclusion, miR-214-3p probably plays a role in TCDD-induced cleft palates in mice.
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Affiliation(s)
- Xiaobo Dong
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing 404000, P.R. China
| | - Qiang Chen
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing 404000, P.R. China
- Department of Paediatrics Surgery, Chongqing University Three Gorges Hospital, Chongqing 404000 P.R. China
| | - Haojuan Du
- Chongqing Key Laboratory of Pediatrics, Chongqing 404000, P.R. China
| | - Lin Qiu
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing 404000, P.R. China
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Borah K, Das HS, Seth S, Mallick K, Rahaman Z, Mallik S. A review on advancements in feature selection and feature extraction for high-dimensional NGS data analysis. Funct Integr Genomics 2024; 24:139. [PMID: 39158621 DOI: 10.1007/s10142-024-01415-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/20/2024]
Abstract
Recent advancements in biomedical technologies and the proliferation of high-dimensional Next Generation Sequencing (NGS) datasets have led to significant growth in the bulk and density of data. The NGS high-dimensional data, characterized by a large number of genomics, transcriptomics, proteomics, and metagenomics features relative to the number of biological samples, presents significant challenges for reducing feature dimensionality. The high dimensionality of NGS data poses significant challenges for data analysis, including increased computational burden, potential overfitting, and difficulty in interpreting results. Feature selection and feature extraction are two pivotal techniques employed to address these challenges by reducing the dimensionality of the data, thereby enhancing model performance, interpretability, and computational efficiency. Feature selection and feature extraction can be categorized into statistical and machine learning methods. The present study conducts a comprehensive and comparative review of various statistical, machine learning, and deep learning-based feature selection and extraction techniques specifically tailored for NGS and microarray data interpretation of humankind. A thorough literature search was performed to gather information on these techniques, focusing on array-based and NGS data analysis. Various techniques, including deep learning architectures, machine learning algorithms, and statistical methods, have been explored for microarray, bulk RNA-Seq, and single-cell, single-cell RNA-Seq (scRNA-Seq) technology-based datasets surveyed here. The study provides an overview of these techniques, highlighting their applications, advantages, and limitations in the context of high-dimensional NGS data. This review provides better insights for readers to apply feature selection and feature extraction techniques to enhance the performance of predictive models, uncover underlying biological patterns, and gain deeper insights into massive and complex NGS and microarray data.
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Affiliation(s)
- Kasmika Borah
- Department of Computer Science and Information Technology, Cotton University, Panbazar, Guwahati, 781001, Assam, India
| | - Himanish Shekhar Das
- Department of Computer Science and Information Technology, Cotton University, Panbazar, Guwahati, 781001, Assam, India.
| | - Soumita Seth
- Department of Computer Science and Engineering, Future Institute of Engineering and Management, Narendrapur, Kolkata, 700150, West Bengal, India
| | - Koushik Mallick
- Department of Computer Science and Engineering, RCC Institute of Information Technology, Canal S Rd, Beleghata, Kolkata, 700015, West Bengal, India
| | | | - Saurav Mallik
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, 02115, USA.
- Department of Pharmacology & Toxicology, University of Arizona, Tucson, AZ, 85721, USA.
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Peng H, Xu J, Liu K, Liu F, Zhang A, Zhang X. EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors. Brief Funct Genomics 2024; 23:373-383. [PMID: 37642217 DOI: 10.1093/bfgp/elad040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Reconstructing functional gene regulatory networks (GRNs) is a primary prerequisite for understanding pathogenic mechanisms and curing diseases in animals, and it also provides an important foundation for cultivating vegetable and fruit varieties that are resistant to diseases and corrosion in plants. Many computational methods have been developed to infer GRNs, but most of the regulatory relationships between genes obtained by these methods are biased. Eliminating indirect effects in GRNs remains a significant challenge for researchers. In this work, we propose a novel approach for inferring functional GRNs, named EIEPCF (eliminating indirect effects produced by confounding factors), which eliminates indirect effects caused by confounding factors. This method eliminates the influence of confounding factors on regulatory factors and target genes by measuring the similarity between their residuals. The validation results of the EIEPCF method on simulation studies, the gold-standard networks provided by the DREAM3 Challenge and the real gene networks of Escherichia coli demonstrate that it achieves significantly higher accuracy compared to other popular computational methods for inferring GRNs. As a case study, we utilized the EIEPCF method to reconstruct the cold-resistant specific GRN from gene expression data of cold-resistant in Arabidopsis thaliana. The source code and data are available at https://github.com/zhanglab-wbgcas/EIEPCF.
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Affiliation(s)
- Huixiang Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 China
- University of Chinese Academy of Sciences, Beijing 100049 China
| | - Jing Xu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 China
- University of Chinese Academy of Sciences, Beijing 100049 China
| | - Kangchen Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 China
- University of Chinese Academy of Sciences, Beijing 100049 China
| | - Fang Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 China
| | - Aidi Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 China
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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Tsukiboshi Y, Mikami Y, Horita H, Ogata A, Noguchi A, Yokota S, Ogata K, Yoshioka H. Protective effect of Sasa veitchii extract against all-trans-retinoic acid-induced inhibition of proliferation of cultured human palate cells. NAGOYA JOURNAL OF MEDICAL SCIENCE 2024; 86:223-236. [PMID: 38962411 PMCID: PMC11219230 DOI: 10.18999/nagjms.86.2.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/01/2023] [Indexed: 07/05/2024]
Abstract
Cleft palate is the most common facial birth defect worldwide. It is caused by environmental factors or genetic mutations. Environmental factors such as pharmaceutical exposure in women are known to induce cleft palate. The aim of the present study was to investigate the protective effect of Sasa veitchii extract against medicine-induced inhibition of proliferation of human embryonic palatal mesenchymal cells. We demonstrated that all-trans-retinoic acid inhibited human embryonic palatal mesenchymal cell proliferation in a dose-dependent manner, whereas dexamethasone treatment had no effect on cell proliferation. Cotreatment with Sasa veitchii extract repressed all-trans-retinoic acid-induced toxicity in human embryonic palatal mesenchymal cells. We found that cotreatment with Sasa veitchii extract protected all-trans-retinoic acid-induced cyclin D1 downregulation in human embryonic palatal mesenchymal cells. Furthermore, Sasa veitchii extract suppressed all-trans-retinoic acid-induced miR-4680-3p expression. Additionally, the expression levels of the genes that function downstream of the target genes ( ERBB2 and JADE1 ) of miR-4680-3p in signaling pathways were enhanced by cotreatment with Sasa veitchii extract and all-trans-retinoic acid compared to all-trans-retinoic acid treatment. These results suggest that Sasa veitchii extract suppresses all-trans-retinoic acid-induced inhibition of cell proliferation via modulation of miR-4680-3p expression.
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Affiliation(s)
- Yosuke Tsukiboshi
- Department of Pharmacy, Gifu University of Medical Science, Kani, Japan
| | - Yurie Mikami
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Hanane Horita
- Department of Pharmacy, Gifu University of Medical Science, Kani, Japan
| | - Aya Ogata
- Department of Pharmacy, Gifu University of Medical Science, Kani, Japan
| | - Azumi Noguchi
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Satoshi Yokota
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences, Kawasaki, Japan
| | - Kenichi Ogata
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Hiroki Yoshioka
- Department of Pharmacy, Gifu University of Medical Science, Kani, Japan
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9
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Tsukiboshi Y, Noguchi A, Horita H, Mikami Y, Yokota S, Ogata K, Yoshioka H. Let-7c-5p associate with inhibition of phenobarbital-induced cell proliferation in human palate cells. Biochem Biophys Res Commun 2024; 696:149516. [PMID: 38241808 DOI: 10.1016/j.bbrc.2024.149516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
Cleft palate (CP) is one of the most common congenital diseases, and is accompanied by a complicated etiology. Medical exposure in women is among one of the reasons leading to CP. Recently, it has been reported that microRNA (miRNA) plays a crucial role in palate formation and the disruption of miRNA that influence the development of CP. Although association with pharmaceuticals and miRNAs were suggested, it has remained largely unknow. The aim of the current investigation is to elucidate upon the miRNA associated with the inhibition of phenobarbital (PB)-induced cell proliferation in human embryonic palatal mesenchymal (HEPM) cells. We showed that PB inhibited HEPM cell viability in a dose-dependent manner. We demonstrated that PB treatment suppressed cyclin-D1 expression in HEPM cells. Furthermore, PB upregulated let-7c-5p expression and downregulated the expression of two downstream genes (BACH1 and PAX3). Finally, we demonstrated that the let-7c-5p inhibitor alleviated PB-induced inhibition of cell proliferation and altered BACH1 and PAX3 expression levels. These results suggest that PB suppresses cell viability by modulating let-7c-5p expression.
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Affiliation(s)
- Yosuke Tsukiboshi
- Department of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani, Gifu, 509-0293, Japan
| | - Azumi Noguchi
- Department Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8588, Japan
| | - Hanane Horita
- Department of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani, Gifu, 509-0293, Japan
| | - Yurie Mikami
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Satoshi Yokota
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences, 3-25-26 Tono-machi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kenichi Ogata
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Hiroki Yoshioka
- Department of Pharmacy, Gifu University of Medical Science, 4-3-3 Nijigaoka, Kani, Gifu, 509-0293, Japan.
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10
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Cordoba-Caballero J, Perkins JR, García-Criado F, Gallego D, Navarro-Sánchez A, Moreno-Estellés M, Garcés C, Bonet F, Romá-Mateo C, Toro R, Perez B, Sanz P, Kohl M, Rojano E, Seoane P, Ranea JAG. Exploring miRNA-target gene pair detection in disease with coRmiT. Brief Bioinform 2024; 25:bbae060. [PMID: 38436559 PMCID: PMC10939301 DOI: 10.1093/bib/bbae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 03/05/2024] Open
Abstract
A wide range of approaches can be used to detect micro RNA (miRNA)-target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.
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Affiliation(s)
- Jose Cordoba-Caballero
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
| | - James R Perkins
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
| | - Federico García-Criado
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
| | - Diana Gallego
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
- Instituto de Investigación Sanitaria IdiPaZ, Madrid, Spain
| | - Alicia Navarro-Sánchez
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
| | - Mireia Moreno-Estellés
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Jaime Roig 11, 46010, Valencia, Spain
| | - Concepción Garcés
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
| | - Fernando Bonet
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Carlos Romá-Mateo
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
- Incliva Biomedical Research Institute, 46010, València, Spain
| | - Rocio Toro
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Belén Perez
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
- Instituto de Investigación Sanitaria IdiPaZ, Madrid, Spain
| | - Pascual Sanz
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Jaime Roig 11, 46010, Valencia, Spain
| | - Matthias Kohl
- Faculty of Medical and Life Sciences, Furtwangen University, Germany
| | - Elena Rojano
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
| | - Juan A G Ranea
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Instituto Nacional de Bioinformática (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII), C/ Sinesio Delgado, 4, Madrid, 28029, Spain
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11
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Tsukiboshi Y, Horita H, Mikami Y, Noguchi A, Yokota S, Ogata K, Yoshioka H. Involvement of microRNA-4680-3p against phenytoin-induced cell proliferation inhibition in human palate cells. J Toxicol Sci 2024; 49:1-8. [PMID: 38191190 DOI: 10.2131/jts.49.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Cleft palate (CP) is one of the most common birth defects and is caused by a combination of genetic and/or environmental factors. Environmental factors such as pharmaceutical exposure in pregnant women are known to induce CP. Recently, microRNA (miRNA) was found to be affected by environmental factors. The aim of the present study was to investigate the involvement of miRNA against phenytoin (PHE)-induced inhibition of proliferation in human embryonic palatal mesenchymal (HEPM) cells. We demonstrated that PHE inhibited HEPM cell proliferation in a dose-dependent manner. We found that treatment with PHE downregulated cyclin-D1 and cyclin-E expressions in HEPM cells. Furthermore, PHE increased miR-4680-3p expression and decreased two downstream genes (ERBB2 and JADE1). Importantly, an miR-4680-3p-specific inhibitor restored HEPM cell proliferation and altered expression of ERBB2 and JADE1 in cells treated with PHE. These results suggest that PHE suppresses cell proliferation via modulation of miR-4680-3p expression.
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Affiliation(s)
| | - Hanane Horita
- Department of Pharmacy, Gifu University of Medical Science
| | - Yurie Mikami
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University
| | - Azumi Noguchi
- Department Cell Biology, Nagasaki University Graduate School of Biomedical Sciences
| | - Satoshi Yokota
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences
| | - Kenichi Ogata
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University
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12
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Zhao X, Peng X, Wang Z, Zheng X, Wang X, Wang Y, Chen J, Yuan D, Liu Y, Du J. MicroRNAs in Small Extracellular Vesicles from Amniotic Fluid and Maternal Plasma Associated with Fetal Palate Development in Mice. Int J Mol Sci 2023; 24:17173. [PMID: 38139002 PMCID: PMC10743272 DOI: 10.3390/ijms242417173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Cleft palate (CP) is a common congenital birth defect. Cellular and morphological processes change dynamically during palatogenesis, and any disturbance in this process could result in CP. However, the molecular mechanisms steering this fundamental phase remain unclear. One study suggesting a role for miRNAs in palate development via maternal small extracellular vesicles (SEVs) drew our attention to their potential involvement in palatogenesis. In this study, we used an in vitro model to determine how SEVs derived from amniotic fluid (ASVs) and maternal plasma (MSVs) influence the biological behaviors of mouse embryonic palatal mesenchyme (MEPM) cells and medial edge epithelial (MEE) cells; we also compared time-dependent differential expression (DE) miRNAs in ASVs and MSVs with the DE mRNAs in palate tissue from E13.5 to E15.5 to study the dynamic co-regulation of miRNAs and mRNAs during palatogenesis in vivo. Our results demonstrate that some pivotal biological activities, such as MEPM proliferation, migration, osteogenesis, and MEE apoptosis, might be directed, in part, by stage-specific MSVs and ASVs. We further identified interconnected networks and key miRNAs such as miR-744-5p, miR-323-5p, and miR-3102-5p, offering a roadmap for mechanistic investigations and the identification of early CP biomarkers.
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Affiliation(s)
- Xige Zhao
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
| | - Xia Peng
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
| | - Zhiwei Wang
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
| | - Xiaoyu Zheng
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
| | - Xiaotong Wang
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
| | - Yijia Wang
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
| | - Jing Chen
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
| | - Dong Yuan
- Department of Geriatric Dentistry, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China;
| | - Ying Liu
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
| | - Juan Du
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China; (X.Z.); (X.P.); (Z.W.); (X.Z.); (X.W.); (Y.W.); (J.C.); (Y.L.)
- Department of Geriatric Dentistry, Capital Medical University School of Stomatology, Tiantan Xili No. 4, Beijing 100050, China;
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13
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Gao Z, Tang J, Xia J, Zheng CH, Wei PJ. CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2853-2861. [PMID: 37267145 DOI: 10.1109/tcbb.2023.3282212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Gene regulatory networks (GRNs) participate in many biological processes, and reconstructing them plays an important role in systems biology. Although many advanced methods have been proposed for GRN reconstruction, their predictive performance is far from the ideal standard, so it is urgent to design a more effective method to reconstruct GRN. Moreover, most methods only consider the gene expression data, ignoring the network structure information contained in GRN. In this study, we propose a supervised model named CNNGRN, which infers GRN from bulk time-series expression data via convolutional neural network (CNN) model, with a more informative feature. Bulk time series gene expression data imply the intricate regulatory associations between genes, and the network structure feature of ground-truth GRN contains rich neighbor information. Hence, CNNGRN integrates the above two features as model inputs. In addition, CNN is adopted to extract intricate features of genes and infer the potential associations between regulators and target genes. Moreover, feature importance visualization experiments are implemented to seek the key features. Experimental results show that CNNGRN achieved competitive performance on benchmark datasets compared to the state-of-the-art computational methods. Finally, hub genes identified based on CNNGRN have been confirmed to be involved in biological processes through literature.
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14
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Iwaya C, Suzuki A, Iwata J. MicroRNAs and Gene Regulatory Networks Related to Cleft Lip and Palate. Int J Mol Sci 2023; 24:3552. [PMID: 36834963 PMCID: PMC9958963 DOI: 10.3390/ijms24043552] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cleft lip and palate is one of the most common congenital birth defects and has a complex etiology. Either genetic or environmental factors, or both, are involved at various degrees, and the type and severity of clefts vary. One of the longstanding questions is how environmental factors lead to craniofacial developmental anomalies. Recent studies highlight non-coding RNAs as potential epigenetic regulators in cleft lip and palate. In this review, we will discuss microRNAs, a type of small non-coding RNAs that can simultaneously regulate expression of many downstream target genes, as a causative mechanism of cleft lip and palate in humans and mice.
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Affiliation(s)
- Chihiro Iwaya
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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15
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Chen Q, Xie Y, Dong X, Zhang X, Zhang Y, Yuan X, Ding X, Qiu L. TCDD induces cleft palate through exosomes derived from mesenchymal cells. Toxicol Res (Camb) 2022; 11:901-910. [PMID: 36569487 PMCID: PMC9773059 DOI: 10.1093/toxres/tfac068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/31/2022] [Accepted: 09/10/2022] [Indexed: 12/24/2022] Open
Abstract
TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) is a ubiquitous environmental toxicant and a notable teratogenic agent for cleft palate (CP), a common congenital structural malformation that can result from abnormalities during palatal shelf connection and/or fusion. The development of the palate requires precise coordination between mesenchymal and epithelial cells. Exosomes are vesicles secreted by cells and participate in organ development by transferring various bioactive molecules between cells and regulating cell proliferation, migration, apoptosis, and epithelial-mesenchymal transition (EMT); these vesicles represent a new method of intercellular communication. To explore how TCDD could influence palatal cell behaviors and communication, we treated mesenchymal cells with TCDD, collected the exosomes secreted by the cells, assessed the 2 types of palatal cells, and then observed the effects of TCDD-induced exosomes. We found that the effects of TCDD-induced exosomes were equal to those of TCDD. Thus, TCDD might change the genetic materials of palatal cells and exosomes to cause dysregulated gene expression from parental cells, affect cellular information communicators, and induce abnormal cellular behaviors that could lead to CP.
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Affiliation(s)
- Qiang Chen
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Children Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400000 P.R. China
- Department of Pediatrics Surgery, Chongqing University Three Gorges Hospital, Chongqing 400000 P.R. China
| | - Yue Xie
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Children Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400000 P.R. China
| | - Xiaobo Dong
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Children Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400000 P.R. China
| | - Xiao Zhang
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Children Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400000 P.R. China
| | - Yunxuan Zhang
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Children Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400000 P.R. China
| | - Xingang Yuan
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Children Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400000 P.R. China
| | - Xionghui Ding
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Children Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400000 P.R. China
| | - Lin Qiu
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Children Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400000 P.R. China
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16
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Yan F, Simon L, Suzuki A, Iwaya C, Jia P, Iwata J, Zhao Z. Spatiotemporal MicroRNA-Gene Expression Network Related to Orofacial Clefts. J Dent Res 2022; 101:1398-1407. [PMID: 35774010 PMCID: PMC9516630 DOI: 10.1177/00220345221105816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Craniofacial structures change dynamically in morphology during development through the coordinated regulation of various cellular molecules. However, it remains unclear how these complex mechanisms are regulated in a spatiotemporal manner. Here we applied natural cubic splines to model gene and microRNA (miRNA) expression from embryonic day (E) 10.5 to E14.5 in the proximal and distal regions of the maxillary processes to identify spatiotemporal patterns of gene and miRNA expression, followed by constructing corresponding regulatory networks. Three major groups of differentially expressed genes (DEGs) were identified, including 3,927 temporal, 314 spatial, and 494 spatiotemporal DEGs. Unsupervised clustering further resolved these spatiotemporal DEGs into 8 clusters with distinct expression patterns. Interestingly, we found 2 clusters of differentially expressed miRNAs: 1 had 80 miRNAs monotonically decreasing and the other had 97 increasing across developmental stages. To evaluate the phenotypic relevance of these DEGs during craniofacial development, we integrated data from the CleftGeneDB database and constructed the regulatory networks of genes related to orofacial clefts. Our analysis revealed 2 hub miRNAs, mmu-miR-325-3p and mmu-miR-384-5p, that repressed cleft-related genes Adamts3, Runx2, Fgfr2, Acvr1, and Edn2, while their expression increased over time. On the contrary, 2 hub miRNAs, mmu-miR-218-5p and mmu-miR-338-5p, repressed cleft-related genes Pbx2, Ermp1, Snai1, Tbx2, and Bmi1, while their expression decreased over time. Our experiments indicated that these miRNA mimics significantly inhibited cell proliferation in mouse embryonic palatal mesenchymal (MEPM) cells and O9-1 cells through the regulation of genes associated with cleft palate and validated the role of our regulatory networks in orofacial clefts. To facilitate interactive exploration of these data, we developed a user-friendly web tool to visualize the gene and miRNA expression patterns across developmental stages, as well as the regulatory networks (https://fyan.shinyapps.io/facebase_shiny/). Taken together, our results provide a valuable resource that serves as a reference map for future research in craniofacial development.
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Affiliation(s)
- F. Yan
- Center for Precision Health, School of
Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston,
TX, USA
| | - L.M. Simon
- Therapeutic Innovation Center, Baylor College
of Medicine, Houston, TX, USA
| | - A. Suzuki
- Department of Diagnostic and Biomedical
Sciences, School of Dentistry, The University of Texas Health Science Center at Houston,
Houston, TX, USA
- Center for Craniofacial Research, The
University of Texas Health Science Center at Houston, Houston, TX, USA
| | - C. Iwaya
- Department of Diagnostic and Biomedical
Sciences, School of Dentistry, The University of Texas Health Science Center at Houston,
Houston, TX, USA
- Center for Craniofacial Research, The
University of Texas Health Science Center at Houston, Houston, TX, USA
| | - P. Jia
- Center for Precision Health, School of
Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston,
TX, USA
| | - J. Iwata
- Department of Diagnostic and Biomedical
Sciences, School of Dentistry, The University of Texas Health Science Center at Houston,
Houston, TX, USA
- Center for Craniofacial Research, The
University of Texas Health Science Center at Houston, Houston, TX, USA
- MD Anderson Cancer Center UTHealth Graduate
School of Biomedical Sciences, Houston, TX, USA
| | - Z. Zhao
- Center for Precision Health, School of
Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston,
TX, USA
- MD Anderson Cancer Center UTHealth Graduate
School of Biomedical Sciences, Houston, TX, USA
- Human Genetics Center, School of Public
Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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17
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Schuler R, Bugacov A, Hacia J, Ho T, Iwata J, Pearlman L, Samuels B, Williams C, Zhao Z, Kesselman C, Chai Y. FaceBase: A Community-Driven Hub for Data-Intensive Research. J Dent Res 2022; 101:1289-1298. [PMID: 35912790 PMCID: PMC9516628 DOI: 10.1177/00220345221107905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The FaceBase Consortium, funded by the National Institute of Dental and Craniofacial Research of the National Institutes of Health, was established in 2009 with the recognition that dental and craniofacial research are increasingly data-intensive disciplines. Data sharing is critical for the validation and reproducibility of results as well as to enable reuse of data. In service of these goals, data ought to be FAIR: Findable, Accessible, Interoperable, and Reusable. The FaceBase data repository and educational resources exemplify the FAIR principles and support a broad user community including researchers in craniofacial development, molecular genetics, and genomics. FaceBase demonstrates that a model in which researchers "self-curate" their data can be successful and scalable. We present the results of the first 2.5 y of FaceBase's operations as an open community and summarize the data sets published during this period. We then describe a research highlight from work on the identification of regulatory networks and noncoding RNAs involved in cleft lip with/without cleft palate that both used and in turn contributed new findings to publicly available FaceBase resources. Collectively, FaceBase serves as a dynamic and continuously evolving resource to facilitate data-intensive research, enhance data reproducibility, and perform deep phenotyping across multiple species in dental and craniofacial research.
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Affiliation(s)
- R.E. Schuler
- Viterbi School of Engineering,
Information Sciences Institute, University of Southern California, Marina del Rey,
CA, USA
| | - A. Bugacov
- Viterbi School of Engineering,
Information Sciences Institute, University of Southern California, Marina del Rey,
CA, USA
| | - J.G. Hacia
- Keck School of Medicine, Biochemistry
and Molecular Medicine, University of Southern California, Los Angeles, CA,
USA
| | - T.V. Ho
- Ostrow School of Dentistry, Center for
Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA,
USA
| | - J. Iwata
- School of Dentistry, Diagnostic &
Biomedical Sciences, The University of Texas Health Science Center at Houston,
Houston, TX, USA
| | - L. Pearlman
- Viterbi School of Engineering,
Information Sciences Institute, University of Southern California, Marina del Rey,
CA, USA
| | - B.D. Samuels
- Ostrow School of Dentistry, Center for
Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA,
USA
| | - C. Williams
- Viterbi School of Engineering,
Information Sciences Institute, University of Southern California, Marina del Rey,
CA, USA
| | - Z. Zhao
- School of Biomedical Informatics,
Center for Precision Health, The University of Texas Health Science Center at
Houston, Houston, TX, USA
| | - C. Kesselman
- Viterbi School of Engineering,
Information Sciences Institute, University of Southern California, Marina del Rey,
CA, USA
| | - Y. Chai
- Ostrow School of Dentistry, Center for
Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA,
USA
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18
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A Novel Strategy for Identifying NSCLC MicroRNA Biomarkers and Their Mechanism Analysis Based on a Brand-New CeRNA-Hub-FFL Network. Int J Mol Sci 2022; 23:ijms231911303. [PMID: 36232605 PMCID: PMC9569765 DOI: 10.3390/ijms231911303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Finding reliable miRNA markers and revealing their potential mechanisms will play an important role in the diagnosis and treatment of NSCLC. Most existing computational methods for identifying miRNA biomarkers only consider the expression variation of miRNAs or rely heavily on training sets. These deficiencies lead to high false-positive rates. The independent regulatory model is an important complement to traditional models of co-regulation and is more impervious to the dataset. In addition, previous studies of miRNA mechanisms in the development of non-small cell lung cancer (NSCLC) have mostly focused on the post-transcriptional level and did not distinguish between NSCLC subtypes. For the above problems, we improved mainly in two areas: miRNA identification based on both the NOG network and biological functions of miRNA target genes; and the construction of a 4-node directed competitive regulatory network to illustrate the mechanisms. NSCLC was classified as lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) in this work. One miRNA biomarker of LUAD (miR-708-5p) and four of LUSC (miR-183-5p, miR-140-5p, miR-766-5p, and miR-766-3p) were obtained. They were validated using literature and external datasets. The ceRNA-hub-FFL involving transcription factors (TFs), microRNAs (miRNAs), mRNAs, and long non-coding RNAs (lncRNAs) was constructed. There were multiple interactions among these components within the net at the transcriptional, post-transcriptional, and protein levels. New regulations were revealed by the network. Meanwhile, the network revealed the reasons for the previous conflicting conclusions on the roles of CD44, ACTB, and ITGB1 in NSCLC, and demonstrated the necessity of typing studies on NSCLC. The novel miRNA markers screening method and the 4-node directed competitive ceRNA-hub-FFL network constructed in this work can provide new ideas for screening tumor markers and understanding tumor development mechanisms in depth.
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19
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Yan Y, Yuan J, Luo X, Yu X, Lu J, Hou W, He X, Zhang L, Cao J, Wang H. microRNA-140 Regulates PDGFRα and Is Involved in Adipocyte Differentiation. Front Mol Biosci 2022; 9:907148. [PMID: 35832736 PMCID: PMC9271708 DOI: 10.3389/fmolb.2022.907148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/16/2022] [Indexed: 12/23/2022] Open
Abstract
In recent years, the studies of the role of microRNAs in adipogenesis and adipocyte development and the corresponding molecular mechanisms have received great attention. In this work, we investigated the function of miR-140 in the process of adipogenesis and the molecular pathways involved, and we found that adipogenic treatment promoted the miR-140-5p RNA level in preadipocytes. Over-expression of miR-140-5p in preadipocytes accelerated lipogenesis along with adipogenic differentiation by transcriptional modulation of adipogenesis-linked genes. Meanwhile, silencing endogenous miR-140-5p dampened adipogenesis. Platelet-derived growth factor receptor alpha (PDGFRα) was shown to be a miR-140-5p target gene. miR-140-5p over-expression in preadipocyte 3T3-L1 diminished PDGFRα expression, but silencing of miR-140-5p augmented it. In addition, over-expression of PDGFRα suppressed adipogenic differentiation and lipogenesis, while its knockdown enhanced these biological processes of preadipocyte 3T3-L1. Altogether, our current findings reveal that miR-140-5p induces lipogenesis and adipogenic differentiation in 3T3-L1 cells by targeting PDGFRα, therefore regulating adipogenesis. Our research provides molecular targets and a theoretical basis for the treatment of obesity-related metabolic diseases.
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Affiliation(s)
- Yi Yan
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Jiahui Yuan
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Xiaomao Luo
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Xiuju Yu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Jiayin Lu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Wei Hou
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyan He
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Liping Zhang
- Department of Medicine, Nephrology Division, Baylor College of Medicine, Houston, GA, United States
| | - Jing Cao
- Department of Animal Husbandry and Veterinary Medicine, Beijing Vocational College of Agriculture, Beijing, China
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- *Correspondence: Haidong Wang,
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20
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Yoshioka H, Suzuki A, Iwaya C, Iwata J. Suppression of microRNA 124-3p and microRNA 340-5p ameliorates retinoic acid-induced cleft palate in mice. Development 2022; 149:275062. [PMID: 35420127 PMCID: PMC9148563 DOI: 10.1242/dev.200476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/25/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex, with genetic and epigenetic, as well as environmental, contributing factors. Recent studies suggest that fetal development is affected by maternal conditions through microRNAs (miRNAs), a group of short noncoding RNAs. Here, we show that miR-129-5p and miR-340-5p suppress cell proliferation in both primary mouse embryonic palatal mesenchymal cells and O9-1 cells, a neural crest cell line, through the regulation of Sox5 and Trp53 by miR-129-5p, and the regulation of Chd7, Fign and Tgfbr1 by miR-340-5p. Notably, miR-340-5p, but not miR-129-5p, was upregulated following all-trans retinoic acid (atRA; tretinoin) administration, and a miR-340-5p inhibitor rescued the cleft palate (CP) phenotype in 47% of atRA-induced CP mice. We have previously reported that a miR-124-3p inhibitor can also partially rescue the CP phenotype in atRA-induced CP mouse model. In this study, we found that a cocktail of miR-124-3p and miR-340-5p inhibitors rescued atRA-induced CP with almost complete penetrance. Taken together, our results suggest that normalization of pathological miRNA expression can be a preventive intervention for CP.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Chihiro Iwaya
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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21
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Suzuki A, Yoshioka H, Liu T, Gull A, Singh N, Le T, Zhao Z, Iwata J. Crucial Roles of microRNA-16-5p and microRNA-27b-3p in Ameloblast Differentiation Through Regulation of Genes Associated With Amelogenesis Imperfecta. Front Genet 2022; 13:788259. [PMID: 35401675 PMCID: PMC8990915 DOI: 10.3389/fgene.2022.788259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Amelogenesis imperfecta is a congenital disorder within a heterogeneous group of conditions characterized by enamel hypoplasia. Patients suffer from early tooth loss, social embarrassment, eating difficulties, and pain due to an abnormally thin, soft, fragile, and discolored enamel with poor aesthetics and functionality. The etiology of amelogenesis imperfecta is complicated by genetic interactions. To identify mouse amelogenesis imperfecta-related genes (mAIGenes) and their respective phenotypes, we conducted a systematic literature review and database search and found and curated 70 mAIGenes across all of the databases. Our pathway enrichment analysis indicated that these genes were enriched in tooth development-associated pathways, forming four distinct groups. To explore how these genes are regulated and affect the phenotype, we predicted microRNA (miRNA)-gene interaction pairs using our bioinformatics pipeline. Our miRNA regulatory network analysis pinpointed that miR-16-5p, miR-27b-3p, and miR-23a/b-3p were hub miRNAs. The function of these hub miRNAs was evaluated through ameloblast differentiation assays with/without the candidate miRNA mimics using cultured mouse ameloblast cells. Our results revealed that overexpression of miR-16-5p and miR-27b-3p, but not miR-23a/b-3p, significantly inhibited ameloblast differentiation through regulation of mAIGenes. Thus, our study shows that miR-16-5p and miR-27b-3p are candidate pathogenic miRNAs for amelogenesis imperfecta.
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Affiliation(s)
- Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Hiroki Yoshioka
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Teng Liu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Aania Gull
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Naina Singh
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Thanh Le
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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22
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Nishimura Y, Kurosawa K. Analysis of Gene-Environment Interactions Related to Developmental Disorders. Front Pharmacol 2022; 13:863664. [PMID: 35370658 PMCID: PMC8969575 DOI: 10.3389/fphar.2022.863664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022] Open
Abstract
Various genetic and environmental factors are associated with developmental disorders (DDs). It has been suggested that interaction between genetic and environmental factors (G × E) is involved in the etiology of DDs. There are two major approaches to analyze the interaction: genome-wide and candidate gene-based approaches. In this mini-review, we demonstrate how these approaches can be applied to reveal the G × E related to DDs focusing on zebrafish and mouse models. We also discuss novel approaches to analyze the G × E associated with DDs.
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Affiliation(s)
- Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children’s Medical Center, Yokohama, Japan
- Department of Clinical Dysmorphology, Mie University Graduate School of Medicine, Tsu, Japan
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23
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Yan H, Jin M, Li Y, Gao Y, Ding Q, Wang X, Zeng W, Chen Y. miR-1 Regulates Differentiation and Proliferation of Goat Hair Follicle Stem Cells by Targeting IGF1R and LEF1 Genes. DNA Cell Biol 2022; 41:190-201. [PMID: 35007429 DOI: 10.1089/dna.2021.0288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hair follicle stem cells (HFSCs) play a significant role in hair development. miR-1 has been reported as an important regulatory factor that affects hair follicle growth and development, but its regulatory mechanism on HFSC development remains unknown. In this study, the molecular mechanism of miR-1 in regulating HFSC proliferation and differentiation was investigated. High-throughput RNA-seq and integrated analysis were performed to identify differentially transcribed mRNAs and microRNAs (miRNAs) in HFSCs co-cultured with dermal papilla cells (named dHFSCs) and control HFSCs. We then determined the molecular function of miR-1 in HFSCs. Compared with HFSCs, 13 differentially transcribed miRNAs were identified in dHFSCs. The in vitro results indicated that the overtranscription of miR-1 inhibited HFSC proliferation, but enhanced HFSC differentiation by targeting IGF1R and LEF1 genes. This study provides new insights into the molecular mechanisms of HFSC development. Approval ID (2014ZX08008-002).
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Affiliation(s)
- Hailong Yan
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong, China
- Shanxi key Laboratory of Inflammatory Neurodegenerative Disease, Institute of Brain Science, Shanxi Datong University, Datong, China
| | - Miaohan Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ye Gao
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong, China
- Shanxi key Laboratory of Inflammatory Neurodegenerative Disease, Institute of Brain Science, Shanxi Datong University, Datong, China
| | - Qiang Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenxian Zeng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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24
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Seelan RS, Pisano MM, Greene RM. MicroRNAs as epigenetic regulators of orofacial development. Differentiation 2022; 124:1-16. [DOI: 10.1016/j.diff.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 11/03/2022]
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25
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Wei Y, Tian Y, Yu X, Miao Z, Xu Y, Pan Y. Advances in research regarding the roles of non-coding RNAs in non-syndromic cleft lip with or without cleft palate: A systematic review. Arch Oral Biol 2021; 134:105319. [PMID: 34864430 DOI: 10.1016/j.archoralbio.2021.105319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To investigate by means of a literature review, what non-coding RNAs engage in non-syndromic cleft lip with or without cleft palate (NSCL/P) and how they lead to the occurrence of this malformation. DESIGN A literature search of online databases (Medline via PubMed, Web of Science, Scopus, and Embase) was performed using appropriate keywords (e.g. non-coding RNA, miRNA, lncRNA, NSCL/P, non-syndromic cleft lip only, and non-syndromic orofacial cleft). The risk of bias in the included studies was then assessed, and a comprehensive review of reported non-coding RNAs associated with NSCL/P was performed. RESULTS The initial search retrieved 133 studies reporting non-coding RNAs associated with NSCL/P; after excluding 18 replicates and 77 ineligible studies, 35 remained. Of these, 16 studies fulfilled all the criteria and were included in the systematic review. These studies established the roles of non-coding RNAs in the development of craniofacial structures. The differential expression of these non-coding RNAs could lead to orofacial clefts, indicating their significance in NSCL/P and their profound research value. CONCLUSION There is evidence that non-coding RNAs are involved in the formation of NSCL/P. Specifically, they play significant roles in the regulation of genes and signalling pathways related to NSCL/P.
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Affiliation(s)
- Yuanyuan Wei
- Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China; Jiangsu Province Key Laboratory of Oral Diseases, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, China
| | - Yu Tian
- Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China; Jiangsu Province Key Laboratory of Oral Diseases, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, China
| | - Xin Yu
- Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China; Jiangsu Province Key Laboratory of Oral Diseases, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, China
| | - Ziyue Miao
- Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China; Jiangsu Province Key Laboratory of Oral Diseases, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, China
| | - Yan Xu
- Department of Orthodontics, Shanghai Stomatological Hospital, Fudan University, Shanghai, China; Shanghai key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, China.
| | - Yongchu Pan
- Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China; Jiangsu Province Key Laboratory of Oral Diseases, China; Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, China.
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26
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Chen M, Xie Y, Luo Y, Xie Y, Wu N, Peng S, Chen Q. Exosomes-a potential indicator and mediator of cleft lip and palate: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1485. [PMID: 34734037 PMCID: PMC8506753 DOI: 10.21037/atm-21-4198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/07/2021] [Indexed: 11/28/2022]
Abstract
Objective This article summarizes the recent literature on noncoding ribonucleic acids (ncRNAs) in relation to cleft lip with or without palate and exosomes and their usage in craniofacial diseases. Background Cleft lip with or without cleft palate (CL/P) is a common congenital malformation with genetic and environmental risk factors that affects numerous children and families. Surgical procedures can correct deformations; however, residual sequelae remain after surgery. Studies exploring the pathogenesis of CL/P are crucial for its early diagnosis and treatment and can inform treatment strategy decisions, etiology searches, and treatment during pregnancy. Recently, research has shown that most disease-related genes are ncRNAs, which are important transcripts in the human transcriptome. ncRNAs include microRNAs, long noncoding RNAs, and circular RNAs. These ncRNAs play essential roles in various pathophysiological processes, including cell proliferation, migration, apoptosis, and epithelial-mesenchymal transition. Previous studies on protein-coding genes have identified a number of genes related to CL/P; however, the pathogenesis of CL/P has not yet been thoroughly explained. Exosomes are vehicles that transfer various bioactive molecules between cells and represent a new method of intercellular communication. Research has shown that exosomes are related to some craniofacial diseases. Methods We searched the PubMed database for recently published English-language articles using the following keywords: “cleft lip with or without palate,” “noncoding RNA,” “exosomes,” and “craniofacial diseases”. We then reviewed the retrieved articles. Conclusions As exosomes serve as cellular communicators and the palate consists of epithelial and mesenchymal cells, communication between the two cell types may affect its formation. Thus, exosomes could represent a new indicator and mediator of CL/P.
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Affiliation(s)
- Meng Chen
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yue Xie
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yarui Luo
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China.,Department of Outpatient, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yimin Xie
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Na Wu
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Shulei Peng
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China.,Department of Sleep Medicine Centre, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Qiang Chen
- Department of Paediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
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27
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Yoshioka H, Li A, Suzuki A, Ramakrishnan SS, Zhao Z, Iwata J. Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice. Hum Mol Genet 2021; 30:1881-1893. [PMID: 34104955 PMCID: PMC8444451 DOI: 10.1093/hmg/ddab151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/17/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
The etiology of cleft lip with/without cleft palate (CL/P), one of the most frequent craniofacial birth defects worldwide, is complicated by contributions of both genetic and environmental factors. Understanding the etiology of these conditions is essential for developing preventive strategies. This study thus aims to identify regulatory networks of microRNAs (miRNAs), transcriptional factors (TFs) and non-TF genes associated with cleft lip (CL) that are conserved in humans and mice. Notably, we found that miR-27b, miR-133b, miR-205, miR-376b and miR-376c were involved in the regulation of CL-associated gene expression in both humans and mice. Among the candidate miRNAs, the overexpression of miR-27b, miR-133b and miR-205, but not miR-376b and miR-376c, significantly inhibited cell proliferation through suppression of CL-associated genes (miR-27b suppressed PAX9 and RARA; miR-133b suppressed FGFR1, PAX7, and SUMO1; and miR-205 suppressed PAX9 and RARA) in cultured human and mouse lip mesenchymal cells. Taken together, our results suggest that elevated expression of miR-27b, miR-133b and miR-205 may play a crucial role in CL through the suppression of genes associated with CL.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Sai Shankar Ramakrishnan
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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28
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Fu C, Lou S, Zhu G, Fan L, Yu X, Zhu W, Ma L, Wang L, Pan Y. Identification of New miRNA-mRNA Networks in the Development of Non-syndromic Cleft Lip With or Without Cleft Palate. Front Cell Dev Biol 2021; 9:631057. [PMID: 33732700 PMCID: PMC7957012 DOI: 10.3389/fcell.2021.631057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/18/2021] [Indexed: 12/18/2022] Open
Abstract
Objective: To identify new microRNA (miRNA)-mRNA networks in non-syndromic cleft lip with or without cleft palate (NSCL/P). Materials and Methods: Overlapping differentially expressed miRNAs (DEMs) were selected from cleft palate patients (GSE47939) and murine embryonic orofacial tissues (GSE20880). Next, the target genes of DEMs were predicted by Targetscan, miRDB, and FUNRICH, and further filtered through differentially expressed genes (DEGs) from NSCL/P patients and controls (GSE42589), MGI, MalaCards, and DECIPHER databases. The results were then confirmed by in vitro experiments. NSCL/P lip tissues were obtained to explore the expression of miRNAs and their target genes. Results: Let-7c-5p and miR-193a-3p were identified as DEMs, and their overexpression inhibited cell proliferation and promoted cell apoptosis. PIGA and TGFB2 were confirmed as targets of let-7c-5p and miR-193a-3p, respectively, and were involved in craniofacial development in mice. Negative correlation between miRNA and mRNA expression was detected in the NSCL/P lip tissues. They were also associated with the occurrence of NSCL/P based on the MGI, MalaCards, and DECIPHER databases. Conclusions: Let-7c-5p-PIGA and miR-193a-3p-TGFB2 networks may be involved in the development of NSCL/P.
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Affiliation(s)
- Chengyi Fu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Liwen Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Xin Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Weihao Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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29
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Yoshioka H, Ramakrishnan SS, Shim J, Suzuki A, Iwata J. Excessive All-Trans Retinoic Acid Inhibits Cell Proliferation Through Upregulated MicroRNA-4680-3p in Cultured Human Palate Cells. Front Cell Dev Biol 2021; 9:618876. [PMID: 33585479 PMCID: PMC7876327 DOI: 10.3389/fcell.2021.618876] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 01/05/2021] [Indexed: 01/19/2023] Open
Abstract
Cleft palate is the second most common congenital birth defect, and both environmental and genetic factors are involved in the etiology of the disease. However, it remains largely unknown how environmental factors affect palate development. Our previous studies show that several microRNAs (miRs) suppress the expression of genes involved in cleft palate. Here we show that miR-4680-3p plays a crucial role in cleft palate pathogenesis. We found that all-trans retinoic acid (atRA) specifically induces miR-4680-3p in cultured human embryonic palatal mesenchymal (HEPM) cells. Overexpression of miR-4680-3p inhibited cell proliferation in a dose-dependent manner through the suppression of expression of ERBB2 and JADE1, which are known cleft palate-related genes. Importantly, a miR-4680-3p-specific inhibitor normalized cell proliferation and altered expression of ERBB2 and JADE1 in cells treated with atRA. Taken together, our results suggest that upregulation of miR-4680-3p induced by atRA may cause cleft palate through suppression of ERBB2 and JADE1. Thus, miRs may be potential targets for the prevention and diagnosis of cleft palate.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Sai Shankar Ramakrishnan
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Junbo Shim
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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30
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Yoshioka H, Mikami Y, Ramakrishnan SS, Suzuki A, Iwata J. MicroRNA-124-3p Plays a Crucial Role in Cleft Palate Induced by Retinoic Acid. Front Cell Dev Biol 2021; 9:621045. [PMID: 34178974 PMCID: PMC8219963 DOI: 10.3389/fcell.2021.621045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/05/2021] [Indexed: 01/13/2023] Open
Abstract
Cleft lip with/without cleft palate (CL/P) is one of the most common congenital birth defects, showing the complexity of both genetic and environmental contributions [e.g., maternal exposure to alcohol, cigarette, and retinoic acid (RA)] in humans. Recent studies suggest that epigenetic factors, including microRNAs (miRs), are altered by various environmental factors. In this study, to investigate whether and how miRs are involved in cleft palate (CP) induced by excessive intake of all-trans RA (atRA), we evaluated top 10 candidate miRs, which were selected through our bioinformatic analyses, in mouse embryonic palatal mesenchymal (MEPM) cells as well as in mouse embryos treated with atRA. Among them, overexpression of miR-27a-3p, miR-27b-3p, and miR-124-3p resulted in the significant reduction of cell proliferation in MEPM cells through the downregulation of CP-associated genes. Notably, we found that excessive atRA upregulated the expression of miR-124-3p, but not of miR-27a-3p and miR-27b-3p, in both in vivo and in vitro. Importantly, treatment with a specific inhibitor for miR-124-3p restored decreased cell proliferation through the normalization of target gene expression in atRA-treated MEPM cells and atRA-exposed mouse embryos, resulting in the rescue of CP in mice. Taken together, our results indicate that atRA causes CP through the induction of miR-124-3p in mice.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Yurie Mikami
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Sai Shankar Ramakrishnan
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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31
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Yan F, Jia P, Yoshioka H, Suzuki A, Iwata J, Zhao Z. A developmental stage-specific network approach for studying dynamic co-regulation of transcription factors and microRNAs during craniofacial development. Development 2020; 147:226075. [PMID: 33234712 DOI: 10.1242/dev.192948] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/10/2020] [Indexed: 12/21/2022]
Abstract
Craniofacial development is regulated through dynamic and complex mechanisms that involve various signaling cascades and gene regulations. Disruption of such regulations can result in craniofacial birth defects. Here, we propose the first developmental stage-specific network approach by integrating two crucial regulators, transcription factors (TFs) and microRNAs (miRNAs), to study their co-regulation during craniofacial development. Specifically, we used TFs, miRNAs and non-TF genes to form feed-forward loops (FFLs) using genomic data covering mouse embryonic days E10.5 to E14.5. We identified key novel regulators (TFs Foxm1, Hif1a, Zbtb16, Myog, Myod1 and Tcf7, and miRNAs miR-340-5p and miR-129-5p) and target genes (Col1a1, Sgms2 and Slc8a3) expression of which changed in a developmental stage-dependent manner. We found that the Wnt-FoxO-Hippo pathway (from E10.5 to E11.5), tissue remodeling (from E12.5 to E13.5) and miR-129-5p-mediated Col1a1 regulation (from E10.5 to E14.5) might play crucial roles in craniofacial development. Enrichment analyses further suggested their functions. Our experiments validated the regulatory roles of miR-340-5p and Foxm1 in the Wnt-FoxO-Hippo subnetwork, as well as the role of miR-129-5p in the miR-129-5p-Col1a1 subnetwork. Thus, our study helps understand the comprehensive regulatory mechanisms for craniofacial development.
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Affiliation(s)
- Fangfang Yan
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hiroki Yoshioka
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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32
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Garland MA, Sun B, Zhang S, Reynolds K, Ji Y, Zhou CJ. Role of epigenetics and miRNAs in orofacial clefts. Birth Defects Res 2020; 112:1635-1659. [PMID: 32926553 DOI: 10.1002/bdr2.1802] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/17/2020] [Accepted: 08/23/2020] [Indexed: 12/13/2022]
Abstract
Orofacial clefts (OFCs) have multiple etiologies and likely result from an interplay between genetic and environmental factors. Within the last decade, studies have implicated specific epigenetic modifications and noncoding RNAs as additional facets of OFC etiology. Altered gene expression through DNA methylation and histone modification offer novel insights into how specific genes contribute to distinct OFC subtypes. Epigenetics research has also provided further evidence that cleft lip only (CLO) is a cleft subtype with distinct etiology. Polymorphisms or misexpression of genes encoding microRNAs, as well as their targets, contribute to OFC risk. The ability to experimentally manipulate epigenetic changes and noncoding RNAs in animal models, such as zebrafish, Xenopus, mice, and rats, has offered novel insights into the mechanisms of various OFC subtypes. Although much remains to be understood, recent advancements in our understanding of OFC etiology may advise future strategies of research and preventive care.
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Affiliation(s)
- Michael A Garland
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA
| | - Bo Sun
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA
| | - Shuwen Zhang
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA
| | - Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, California, USA
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33
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Li A, Mallik S, Luo H, Jia P, Lee DF, Zhao Z. H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:180-191. [PMID: 32585626 PMCID: PMC7321791 DOI: 10.1016/j.omtn.2020.05.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/17/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs (lncRNAs) have recently been found to be important in gene regulation. lncRNA H19 has been reported to play an oncogenic role in many human cancers. Its specific regulatory role is still elusive. In this study, we developed a novel analytic approach by integrating the synergistic regulation among lncRNAs (e.g., H19), transcription factors (TFs), target genes, and microRNAs (miRNAs) and then applied it to the pan-cancer expression datasets from The Cancer Genome Atlas (TCGA). Using linear regression models, we identified 88 H19-TF-gene co-regulatory triplets, in which 93% of the TF-gene pairs were related to cancer, indicating that our approach was effective to identify disease-related lncRNA-TF-gene co-regulation mechanisms. lncRNAs can function as miRNA sponges. Our further experiments found that H19 might regulate SP1-TGFBR2 through let-7b and miR-200b, ETS1-TGFBR2 through miR-29a and miR-200b, and STAT3-KLF11 through miR-17 in breast cancer cell lines. Our work suggests that miRNA-mediated lncRNA-TF-gene co-regulation is complicated yet important in cancer.
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Affiliation(s)
- Aimin Li
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi 710048, China; Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Haidan Luo
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dung-Fang Lee
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.
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34
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Luo Z, Dou J, Xie F, Lu J, Han Q, Zhou X, Kong J, Chen D, Liu A. miR-203a-3p promotes loureirin A-induced hair follicle stem cells differentiation by targeting Smad1. Anat Rec (Hoboken) 2020; 304:531-540. [PMID: 32589363 DOI: 10.1002/ar.24480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/22/2023]
Abstract
MicroRNAs (miRNAs) participate in the repair of skin trauma. Our previous study indicated that loureirin A promoted hair follicle stem cells (HFSCs) to repair skin epidermis. However, the mechanism of miRNA-mediated regulation of loureirin A-induced HFSC differentiation remained to be explored. In the present study, HFSCs from rat vibrissa were identified by immunofluorescence in vitro. Microarray and quantitative real time polymerase chain reaction analyses demonstrated that miR-203a-3p was upregulated in differentiated HFSCs induced by loureirin A. The expression of cytoskeletal keratin (CK) 5 and involucrin was promoted by miR-203a-3p mimics while repressed by a miR-203a-3p inhibitor. Smad1 was identified as a key target of miR-203a-3p using target prediction tools. Luciferase reporter gene test confirmed a special target association between miR-203a-3p and Smad1. Short interfering Smad1 was transfected into HFSCs, and the expression levels of CK5 and involucrin were upregulated. Thus, it can be inferred that miR-203a-3p negatively regulated the expression of Smad1 and promoted the differentiation of loureirin A-induced HFSCs. Bone morphogenetic protein (BMP) signal inhibition and Wnt activation coregulate skin injury repair. BMP/Smad1 signaling is involved in maintaining the characteristics of HFSCs and inhibiting their differentiation. Our results showed that miR-203a-3p reduces Smad1 to release BMP inhibition. Taken together, miR-203a-3p/Smad1 is a potential therapeutic molecular target in skin wound healing, and may play an active role in wound repair and regenerative medicine.
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Affiliation(s)
- Ziwei Luo
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
| | - Jianping Dou
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
| | - Fangfang Xie
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
| | - Jianghua Lu
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
| | - Qianting Han
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
| | - Xianxi Zhou
- Center for Experimental Teaching, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
| | - Jiechen Kong
- Center for Experimental Teaching, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
| | - Dongfeng Chen
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
| | - Aijun Liu
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China
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35
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Qin G, Mallik S, Mitra R, Li A, Jia P, Eischen CM, Zhao Z. MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Sci Rep 2020; 10:852. [PMID: 31965022 PMCID: PMC6972857 DOI: 10.1038/s41598-020-57834-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/24/2019] [Indexed: 12/11/2022] Open
Abstract
Recent studies have revealed that feed-forward loops (FFLs) as regulatory motifs have synergistic roles in cellular systems and their disruption may cause diseases including cancer. FFLs may include two regulators such as transcription factors (TFs) and microRNAs (miRNAs). In this study, we extensively investigated TF and miRNA regulation pairs, their FFLs, and TF-miRNA mediated regulatory networks in two major types of testicular germ cell tumors (TGCT): seminoma (SE) and non-seminoma (NSE). Specifically, we identified differentially expressed mRNA genes and miRNAs in 103 tumors using the transcriptomic data from The Cancer Genome Atlas. Next, we determined significantly correlated TF-gene/miRNA and miRNA-gene/TF pairs with regulation direction. Subsequently, we determined 288 and 664 dysregulated TF-miRNA-gene FFLs in SE and NSE, respectively. By constructing dysregulated FFL networks, we found that many hub nodes (12 out of 30 for SE and 8 out of 32 for NSE) in the top ranked FFLs could predict subtype-classification (Random Forest classifier, average accuracy ≥90%). These hub molecules were validated by an independent dataset. Our network analysis pinpointed several SE-specific dysregulated miRNAs (miR-200c-3p, miR-25-3p, and miR-302a-3p) and genes (EPHA2, JUN, KLF4, PLXDC2, RND3, SPI1, and TIMP3) and NSE-specific dysregulated miRNAs (miR-367-3p, miR-519d-3p, and miR-96-5p) and genes (NR2F1 and NR2F2). This study is the first systematic investigation of TF and miRNA regulation and their co-regulation in two major TGCT subtypes.
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Affiliation(s)
- Guimin Qin
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ramkrishna Mitra
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Christine M Eischen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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