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Shi C, Jiao P, Chen Z, Ma L, Yao S. Exploring the roles of noncoding RNAs in craniofacial abnormalities: A systematic review. Dev Biol 2024; 505:75-84. [PMID: 37923186 DOI: 10.1016/j.ydbio.2023.10.007] [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: 07/23/2023] [Revised: 10/04/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
Congenital craniofacial abnormalities are congenital anomalies of variable expressivity and severity with a recognizable set of abnormalities, which are derived from five identifiable primordial structures. They can occur unilaterally or bilaterally and include various malformations such as cleft lip with/without palate, craniosynostosis, and craniofacial microsomia. To date, the molecular etiology of craniofacial abnormalities is largely unknown. Noncoding RNAs (ncRNAs), including microRNAs, long ncRNAs, circular RNAs and PIWI-interacting RNAs, function as major regulators of cellular epigenetic hallmarks via regulation of various molecular and cellular processes. Recently, aberrant expression of ncRNAs has been implicated in many diseases, including craniofacial abnormalities. Consequently, this review focuses on the role and mechanism of ncRNAs in regulating craniofacial development in the hope of providing clues to identify potential therapeutic targets.
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Affiliation(s)
- Cheng Shi
- The Affiliated Stomatology Hospital of Suzhou Vocational Health College, Suzhou, 215000, China; Nanjing Municipal Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Pengfei Jiao
- The Affiliated Stomatology Hospital of Suzhou Vocational Health College, Suzhou, 215000, China
| | - Zhiyi Chen
- Suzhou Stomatological Hospital, Suzhou, 215000, China
| | - Lan Ma
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210000, China.
| | - Siyue Yao
- The Affiliated Stomatology Hospital of Suzhou Vocational Health College, Suzhou, 215000, China.
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2
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Seelan RS, Greene RM, Pisano MM. Role of lncRNAs and circRNAs in Orofacial Clefts. Microrna 2023; 12:171-176. [PMID: 38009000 DOI: 10.2174/2211536612666230524153442] [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: 09/16/2022] [Revised: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 11/28/2023]
Abstract
Different modes of gene regulation, such as histone modification, transcription factor binding, DNA methylation, and microRNA (miRNA) expression, are critical for the spatiotemporal expression of genes in developing orofacial tissues. Aberrant regulation in any of these modes may contribute to orofacial defects. Noncoding RNAs (ncRNAs), such as long ncRNAs (lncRNAs) and circular RNAs (circRNAs), have been shown to alter miRNA expression, and are thus emerging as novel contributors to gene regulation. Some of these appear to function as 'miRNA sponges', thereby diminishing the availability of these miRNAs to inhibit the expression of target genes. Such ncRNAs are also termed competitive endogenous RNAs (ceRNAs). Here, we examine emerging data that shed light on how lncRNAs and circRNAs may alter miRNA regulation, thus affecting orofacial development and potentially contributing to orofacial clefting.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, KY 40202, USA
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, KY 40202, USA
| | - M Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, KY 40202, USA
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3
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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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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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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: 1.0] [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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Sun M, Yang J, Jiang D, Bao G. Overexpression of hsa_circ_0094742 inhibits IL-1β-induced decline in CHON-001 cell viability by targeting microRNA-127-5p. Histol Histopathol 2021; 36:207-216. [PMID: 33665792 DOI: 10.14670/hh-18-325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Osteoarthritis (OA) is a public health problem that affects 240 million people globally; however, the current treatment options for OA are not effective. Therefore, there is still an urgent need to identify novel strategies to reduce the incidence and progression of OA. The circular RNA hsa_circ_0094742 was reported to be downregulated in patients with OA. However, the underlying mechanism remains unclear. The levels of hsa_circ_0094742 in CHON-001 were detected by reverse transcription quantitative polymerase chain reaction. Moreover, Cell Counting Kit-8 assay and Ki67 staining were used to determine the cell viability. The protein expression of biomarkers was detected by western blot analysis. In addition, the putative downstream target of hsa_circ_0094742 was predicted using the Circinteractome and TargetScan online databases. The putative targeting relationship was verified by dual luciferase reporter assay and fluorescence in situ hybridization. Next, cell apoptosis was determined by Annexin V/PI staining. hsa_circ_0094742 overexpression (OE) inhibited interleukin (IL)-1β-induced decline in the viability of CHON-001 cells and primary human chondrocytes. Furthermore, IL-1β-induced alterations in aggrecan, matrix metallopeptidase 13, X-linked inhibitor of apoptosis protein (XIAP), Bax and active caspase 3 were reversed by hsa_circ_0094742 OE. Luciferase reporter assay indicated that miR-127-5p was the downstream target of hsa_circ_0094742, and latexin was the target of miR-127-5p. hsa_circ_0094742 OE inhibited IL-1β-induced decline in CHON-001 cell viability by targeting miRNA-127-5p. The findings of the present study revealed the biological rational of the use of hsa_circ_0094742 OE as an anti-IL-1β effector in human chondrocytes. These findings may prompt further research on hsa_circ_0094742 as a potent circRNA target for the treatment of OA.
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Affiliation(s)
- Mingqi Sun
- Department of Orthopaedic Trauma, the Second Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia, China
| | - Junli Yang
- Physical Examination Center, the Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia, China
| | - Dianming Jiang
- Department of Orthopedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Guoyu Bao
- Department of Orthopaedic Trauma, the Second Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia, China.
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Iwata J. Gene-Environment Interplay and MicroRNAs in Cleft Lip and Cleft Palate. ORAL SCIENCE INTERNATIONAL 2021; 18:3-13. [PMID: 36855534 PMCID: PMC9969970 DOI: 10.1002/osi2.1072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cleft lip (CL) with/without cleft palate (CP) (hereafter CL/P) is the second most common congenital birth defect, affecting 7.94 to 9.92 children per 10,000 live births worldwide, followed by Down syndrome. An increasing number of genes have been identified as affecting susceptibility and/or as causative genes for CL/P in mouse genetic and chemically-induced CL and CP studies, as well as in human genome-wide association studies and linkage analysis. While marked progress has been made in the identification of genetic and environmental risk factors for CL/P, the interplays between these factors are not yet fully understood. This review aims to summarize our current knowledge of CL and CP from genetically engineered mouse models and environmental factors that have been studied in mice. Understanding the regulatory mechanism(s) of craniofacial development may not only advance our understanding of craniofacial developmental biology, but could also provide approaches for the prevention of birth defects and for tissue engineering in craniofacial tissue regeneration.
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Affiliation(s)
- Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, Texas, 77054 USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, Texas, 77054 USA.,Pediatric Research Center, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, 77030 USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, 77030 USA
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Li W, Ma N, Yuwen T, Yu B, Zhou Y, Yao Y, Li Q, Chen X, Wan J, Zhang Y, Zhang W. Comprehensive analysis of circRNA expression profiles and circRNA-associated competing endogenous RNA networks in the development of mouse thymus. J Cell Mol Med 2020; 24:6340-6349. [PMID: 32307889 PMCID: PMC7294154 DOI: 10.1111/jcmm.15276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/19/2020] [Accepted: 03/28/2020] [Indexed: 12/13/2022] Open
Abstract
The thymus plays an irreplaceable role as a primary lymphoid organ. However, the complicate processes of its development and involution are incompletely understood. Accumulating evidence indicates that non-coding RNAs play key roles in the regulation of biological development. At present, the studies of the circRNA profiles and of circRNA-associated competing endogenous RNAs (ceRNAs) in the thymus are still scarce. Here, deep-RNA sequencing was used to study the biological mechanisms underlying the development process (from 2-week-old to 6-week-old) and the recession process (from 6-week-old to 3-month-old) of the mouse thymus. It was found that 196 circRNAs, 233 miRNAs and 3807 mRNAs were significantly dysregulated. The circRNA-associated ceRNA networks were constructed in the mouse thymus, which were mainly involved in early embryonic development and the proliferation and division of T cells. Taken together, these results elucidated the regulatory roles of ceRNAs in the development and involution processes of the mouse thymus.
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Affiliation(s)
- Wenting Li
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Nana Ma
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Ting Yuwen
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Bo Yu
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yao Zhou
- Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China
| | - Yufei Yao
- Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China
| | - Qi Li
- Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China
| | - Xiaofan Chen
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.,Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yu Zhang
- Hainan Provincial Key Laboratory for human reproductive medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China.,Department of Reproductive Medicine, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Hainan, China
| | - Wei Zhang
- Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, China
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Ha J, Park C, Park C, Park S. IMIPMF: Inferring miRNA-disease interactions using probabilistic matrix factorization. J Biomed Inform 2020; 102:103358. [DOI: 10.1016/j.jbi.2019.103358] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/11/2019] [Accepted: 12/12/2019] [Indexed: 12/09/2022]
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