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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: 0.5] [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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2
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Tang J, Lian SB, Bai Y, Lv MM, Wen Y, Song QG. Comprehensive analysis of plasma miRNA and related ceRNA network in non-syndromic cleft lip and/or palate. Int J Pediatr Otorhinolaryngol 2022; 162:111306. [PMID: 36087427 DOI: 10.1016/j.ijporl.2022.111306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND Non-syndromic cleft lip and/or palate (NSCL/P) is a common maxillofacial birth defect, and the etiology of which is complex and still unclear. Accumulating studies indicate that long non-coding RNAs(lncRNAs) and microRNAs(miRNAs) play important roles in NSCL/P. However, the potential regulatory associations remain largely unknown. In this study, we screened differentially expressed miRNAs and constructed competing endogenous RNA (ceRNA) networks to lay a foundation for further research on the regulatory mechanism of ncRNAs in NSCL/P. METHODS NSCL/P plasma RNA was analyzed by miRNA sequencing. The bioinformatics database, GEO and STRING database, GO and KEGG enrichment analysis and Cytoscape software were used to analyze and screen lncRNAs and mRNAs potentially related to differential miRNAs. The expression levels of lncRNA, miRNA and mRNA in ceRNA network were detected by RT-qPCR. RESULTS In NSCL/P plasma samples, there were 47 differentially expressed miRNAs in CPO group and 36 differentially expressed miRNAs in CL/P group. GO and KEGG enrichment analysis showed that cell cycle, cell response to DNA damage stimulation, and the TGF-βsignaling pathway were relevant to the formation of NSCL/P. The RT-qPCR results showed that the expression levels of lncRNA NEAT1, hsa-miR-130 b-3p, hsa-miR-212-3p, hsa-miR-200 b-3p and SMAD2 were different in NSCL/P. CONCLUSIONS We found that differentially expressed miR-212-3p, miR-200 b-3p and miR-130 b-3p may be involved in the pathogenesis of cleft palate by regulating related target genes.
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Affiliation(s)
- Jing Tang
- Hospital of Stomatology, Zunyi Medical University, 563000, Zunyi City, Guizhou Province, China.
| | - Shu-Bo Lian
- Hospital of Stomatology, Zunyi Medical University, 563000, Zunyi City, Guizhou Province, China.
| | - Yu Bai
- Hospital of Stomatology, Zunyi Medical University, 563000, Zunyi City, Guizhou Province, China.
| | - Ming-Min Lv
- Hospital of Stomatology, Zunyi Medical University, 563000, Zunyi City, Guizhou Province, China.
| | - Yu Wen
- Hospital of Stomatology, Zunyi Medical University, 563000, Zunyi City, Guizhou Province, China.
| | - Qing-Gao Song
- Hospital of Stomatology, Zunyi Medical University, 563000, Zunyi City, Guizhou Province, China.
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Nicoletti ADS, Visacri MB, da Ronda CRDSC, Vasconcelos PEDNS, Quintanilha JCF, de Souza RN, Ventura DDS, Eguti A, Silva LFDS, Perroud Junior MW, Catharino RR, Reis LO, Dos Santos LA, Durán N, Fávaro WJ, Lancellotti M, da Costa JL, Moriel P, Pincinato EDC. Differentially expressed plasmatic microRNAs in Brazilian patients with Coronavirus disease 2019 (COVID-19): preliminary results. Mol Biol Rep 2022; 49:6931-6943. [PMID: 35301654 PMCID: PMC8929466 DOI: 10.1007/s11033-022-07338-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/03/2022] [Indexed: 01/08/2023]
Abstract
Background Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is known that host microRNAs (miRNAs) can be modulated to favor viral infection or to protect the host. Herein, we report preliminary results of a study aiming at identifying differentially expressed plasmatic miRNAs in Brazilian patients with COVID-19. Methods and results miRNAs were extracted from the plasma of eight patients with COVID-19 (four patients with mild COVID-19 and four patients with severe/critical COVID-19) and four healthy controls. Patients and controls were matched for sex and age. miRNA expression levels were detected using high-throughput sequencing. Differential miRNA expression and enrichment analyses were further evaluated. A total of 18 miRNAs were differentially expressed between patients with COVID-19 and controls. miR-4433b-5p, miR-6780b-3p, miR-6883-3p, miR-320b, miR-7111-3p, miR-4755-3p, miR-320c, and miR-6511a-3p were the most important miRNAs significantly involved in the PI3K/AKT, Wnt/β-catenin, and STAT3 signaling pathways. Moreover, 42 miRNAs were differentially expressed between severe/critical and mild patients with COVID-19. miR-451a, miR-101-3p, miR-185-5p, miR-30d-5p, miR-25-3p, miR-342-3p, miR-30e-5p, miR-150-5p, miR-15b-5p, and miR-29c-3p were the most important miRNAs significantly involved in the Wnt/β-catenin, NF-κβ, and STAT3 signaling pathways. Conclusions If validated by quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) in a larger number of participants, the miRNAs identified in this study might be used as possible biomarkers for the diagnosis and severity of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07338-9.
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Affiliation(s)
| | | | - Carla Regina da Silva Correa da Ronda
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil
| | | | | | | | | | - Adriana Eguti
- Hospital Estadual Sumaré Dr. Leandro Francheschini, Sumaré, SP, Brazil
| | | | - Mauricio Wesley Perroud Junior
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil.,Hospital Estadual Sumaré Dr. Leandro Francheschini, Sumaré, SP, Brazil
| | - Rodrigo Ramos Catharino
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil.,Innovare Biomarkers Laboratory, University of Campinas, Campinas, SP, Brazil
| | | | | | - Nelson Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Campinas, SP, Brazil
| | - Wagner José Fávaro
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Campinas, SP, Brazil
| | - Marcelo Lancellotti
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil
| | - José Luiz da Costa
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil
| | - Patricia Moriel
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil.
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4
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Seelan RS, Pisano MM, Greene RM. MicroRNAs as Biomarkers for Birth Defects. Microrna 2022; 11:2-11. [PMID: 35168515 DOI: 10.2174/2211536611666220215123423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 11/22/2022]
Abstract
It is estimated that 2-4% of live births will have a birth defect (BD). The availability of biomarkers for the prenatal detection of BDs will facilitate early risk assessment, prompt medical intervention and ameliorating disease severity. miRNA expression levels are often found to be altered in many diseases. There is, thus, a growing interest in determining whether miRNAs, particularly extracellular miRNAs, can predict, diagnose, or monitor BDs. These miRNAs, typically encapsulated in exosomes, are released by cells (including those of the fetus and placenta) into the extracellular milieu, such as blood, urine, saliva and cerebrospinal fluid, thereby enabling interaction with target cells. Exosomal miRNAs are stable, protected from degradation, and retain functionality. The observation that placental and fetal miRNAs can be detected in maternal serum, provides a strong rationale for adopting miRNAs as noninvasive prenatal biomarkers for BDs. In this mini-review, we examine the current state of research involving the use of miRNAs as prognostic and diagnostic biomarkers for BD.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - M Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
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5
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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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6
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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: 0.7] [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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Shi XM, Bai YC, Gao YR, Bu N, Song HY, Huang LH, Zhao YH, Wang SH. Comprehensive Analysis of Differentially Expressed lncRNAs miRNAs and mRNA and Their ceRNA Network of Patients With Rare-Earth Pneumoconiosis. Front Genet 2021; 12:700398. [PMID: 34349786 PMCID: PMC8326912 DOI: 10.3389/fgene.2021.700398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
Rare-earth pneumoconiosis (REP) is the main occupational disease of rare earth exposed workers and there is no specific treatment. In this study, we performed high-throughput sequencing on the plasma of nine REP to describe and analyze the expression profiles of long non-coding RNA (lncRNA), micro RNA (miRNA) and mRNA and investigate their regulatory networks. Our results identified a total of 125 lncRNAs, 5 miRNAs, and 82 mRNAs were differentially expressed in the plasma of patients with REP. Furthermore, Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to analyze the differentially expressed non-coding RNAs (ncRNA). We found the differential expression of ncRNA are mainly related to the response of cells to stimulation, Hedgehog signaling pathway and so on. We also constructed lncRNA-miRNA-mRNA networks to further explore their underlying mechanism and possible relationships in REP. We found that in the competitive endogenous RNA (ceRNA) networks, lncRNA acts as a sponge of miRNA to regulate the target gene. The expression results were verified by qRT-PCR and the protein interaction networks of differentially expressed genes were constructed via the STRING database. OncoLnc online platform was used to do the lung cancer survival analysis among the top five mRNA analyzed by Protein-protein interaction (PPI) network analysis. We found miR-16-2-3p may used as biomarker for REP, because it is closely related to the occurrence and prognosis of REP through inflammatory reaction and in lung squamous cell carcinoma, its expression levels were positively correlated with the overall survival rate of patients.
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Affiliation(s)
| | | | | | | | | | | | - Yu-hang Zhao
- School of Public Health, Baotou Medical College, Baotou, China
| | - Su-hua Wang
- School of Public Health, Baotou Medical College, Baotou, China
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8
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Jia S, Zhang Q, Wang Y, Wang Y, Liu D, He Y, Wei X, Gu H, Ma W, Luo W, Yuan Z. PIWI-interacting RNA sequencing profiles in maternal plasma-derived exosomes reveal novel non-invasive prenatal biomarkers for the early diagnosis of nonsyndromic cleft lip and palate. EBioMedicine 2021; 65:103253. [PMID: 33639402 PMCID: PMC7921467 DOI: 10.1016/j.ebiom.2021.103253] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/10/2021] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
Background Congenital malformations are common birth defects with high neonatal morbidity and mortality. It is essential to find simpler and more efficient biomarkers for early prenatal diagnosis. Therefore, we investigated PIWI-interacting RNAs (piRNAs) as potential prenatal biomarkers in plasma-derived exosomes from pregnant women carrying foetuses with congenital malformations. Methods Small RNA sequencing was used to screen piRNA biomarkers in plasma-derived exosomes of five pregnant women carrying foetuses with nonsyndromic cleft lip and palate (nsCLP) and five women carrying normal foetuses. Differentially expressed piRNAs were verified in 270 pregnant women, including 111 paired women carrying foetuses with congenital malformations and normal foetuses (at 24 gestational weeks), 10 paired women carrying foetuses with nsCLP and normal foetuses (at 15–19 gestational weeks), and 28 women at different stages of normal pregnancy. piRNA biomarkers were also verified in placentas, umbilical cords, fetal medial calf muscles, and lip tissues of nsCLP and normal foetuses. Findings We identified a biomarker panel of three pregnancy-associated exosomal piRNAs (hsa-piR-009228, hsa-piR-016659, and hsa-piR-020496) could distinguish nsCLP foetuses from normal foetuses. These three piRNAs had better diagnostic accuracy for nsCLP at the early gestational stage, at which time typical malformations were not detected upon prenatal ultrasound screening, and had diagnostic value for neural tube defects (NTDs) and congenital heart defects (CHDs). Interpretation Our work revealed the potential clinical applications of piRNAs for predicting nsCLP, NTDs, and CHDs. Funding National Key Research and Development Program, National Natural Science Foundation of China, and LiaoNing Revitalization Talents Program .
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Affiliation(s)
- Shanshan Jia
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Qiang Zhang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China; Department of Pulmonary and Critical Care Medicine, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Yu Wang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China; Department of Ultrasound, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Yanfu Wang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Dan Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Yiwen He
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Xiaowei Wei
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Wei Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Wenting Luo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, PR China.
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9
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Zhu G, Zhang C, Wang Y, Wang Y, Li D, Yu X, Zhu W, Fu C, Lou S, Fan L, Ma L, Wang L, Pan Y. Variants in miRNA regulome and their association with the risk of nonsyndromic orofacial clefts. Epigenomics 2020; 12:1109-1121. [PMID: 32408759 DOI: 10.2217/epi-2020-0124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: To investigate the associations between single nucleotide polymorphisms (SNPs) in miRNA regulome and nonsyndromic orofacial clefts. Materials & methods: The associations were evaluated by logistic regression model in stage I (504 cases and 455 controls) and stage II (1500 cases and 1386 controls). Functional experiments including luciferase activity assay, cell apoptosis and proliferation, serum miRNA expression, and mouse embryo RNA sequencing were performed. Results: Rs3830766 in the enhancer of hsa-miR-4260 was associated with cleft lip only (CLO) and enhancer activity. Hsa-miR-4260 expression decreased in the serum of CLO. Overexpression of miR-4260 inhibited cell proliferation and promoted cell apoptosis. UBB was the target gene of hsa-miR-4260. Conclusion: Rs3830766 in the hsa-miR-4260 enhancer that can interact with UBB was relevant to CLO.
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Affiliation(s)
- Guirong Zhu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Chi Zhang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yuting Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yuli Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Dandan Li
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Xin Yu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Weihao Zhu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Chengyi Fu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Shu Lou
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Liwen Fan
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Lan Ma
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China
| | - Lin Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yongchu Pan
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
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10
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Effects of Cardiac Sympathetic Neurodegeneration and PPAR γ Activation on Rhesus Macaque Whole Blood miRNA and mRNA Expression Profiles. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9426204. [PMID: 32462037 PMCID: PMC7212295 DOI: 10.1155/2020/9426204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/13/2020] [Accepted: 04/03/2020] [Indexed: 02/02/2023]
Abstract
Degeneration of sympathetic innervation of the heart occurs in numerous diseases, including diabetes, idiopathic REM sleep disorder, and Parkinson's disease (PD). In PD, cardiac sympathetic denervation occurs in 80-90% of patients and can begin before the onset of motor symptoms. Today, there are no disease-modifying therapies for cardiac sympathetic neurodegeneration, and biomarkers are limited to radioimaging techniques. Analysis of expression levels of coding mRNA and noncoding RNAs, such as microRNAs (miRNAs), can uncover pathways involved in disease, leading to the discovery of biomarkers, pathological mechanisms, and potential drug targets. Whole blood in particular is a clinically relevant source of biomarkers, as blood sampling is inexpensive and simple to perform. Our research group has previously developed a nonhuman primate model of cardiac sympathetic denervation by intravenous administration of the catecholaminergic neurotoxin 6-hydroxydopamine (6-OHDA). In this rhesus macaque (Macaca mulatta) model, imaging with positron emission tomography showed that oral administration of the peroxisome proliferator-activated receptor gamma (PPARγ) agonist pioglitazone (n = 5; 5 mg/kg daily) significantly decreased cardiac inflammation and oxidative stress compared to placebo (n = 5). Here, we report our analysis of miRNA and mRNA expression levels over time in the whole blood of these monkeys. Differential expression of three miRNAs was induced by 6-OHDA (mml-miR-16-2-3p, mml-miR-133d-3p, and mml-miR-1262-5p) and two miRNAs by pioglitazone (mml-miR-204-5p and mml-miR-146b-5p) at 12 weeks posttoxin, while expression of mRNAs involved in inflammatory cytokines and receptors was not significantly affected. Overall, this study contributes to the characterization of rhesus coding and noncoding RNA profiles in normal and disease-like conditions, which may facilitate the identification and clinical translation of biomarkers of cardiac neurodegeneration and neuroprotection.
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11
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Mendes SMDA, Espinosa DDSG, Moreira PEDO, Marques D, Fagundes NCF, Ribeiro-Dos-Santos Â. miRNAs as biomarkers of orofacial clefts: A systematic review. J Oral Pathol Med 2019; 49:201-209. [PMID: 31479540 DOI: 10.1111/jop.12950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/05/2019] [Accepted: 08/11/2019] [Indexed: 01/26/2023]
Abstract
Orofacial clefts are facial malformations caused by the improper development of the lips and palate. Many genetic and epigenetic molecules have been involved in the mechanisms of orofacial clefts, one of which are miRNAs. This systematic review aimed to identify miRNAs associated to non-syndromic orofacial clefts in humans. After applying a series of criteria, four studies were selected for analysis. In total, one hundred miRNAs were observed in the literature, of which 57 were reported as upregulated and 43 as downregulated in all orofacial cleft classifications. Moreover, nine miRNAs were differentially expressed only in cleft palate patients, which might suggest distinct regulatory mechanisms for the etiology of cleft lips and palates. We suggest broader population sampling in order to include diverse ethnic groups in the future, as well as analyses toward identifying miRNA target genes and pathways. We highlight the need for experimental validation and of these results to allow further translational approaches and clinical applications.
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Affiliation(s)
- Sissy Maria Dos Anjos Mendes
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | | | - Diego Marques
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
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12
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Gao Y, Zang Q, Song H, Fu S, Sun W, Zhang W, Wang X, Li Y, Jiao X. Comprehensive analysis of differentially expressed profiles of non‑coding RNAs in peripheral blood and ceRNA regulatory networks in non‑syndromic orofacial clefts. Mol Med Rep 2019; 20:513-528. [PMID: 31115538 PMCID: PMC6579990 DOI: 10.3892/mmr.2019.10261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 04/11/2019] [Indexed: 12/29/2022] Open
Abstract
Non-syndromic orofacial clefts (NSOC), which include cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO), are common congenital birth defects in humans. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs or miRs) play important roles in NSOC; however, the potential regulatory associations between them remain largely unknown. In this study, we performed next-generation RNA sequencing (RNA-seq) to identify transcriptome profiles, including mRNAs, lncRNAs and miRNAs, in patients with CL/P and CPO. A total of 36 lncRNAs, 1,341 mRNAs and 60 miRNAs were found to be differentially expressed in the CL/P group compared to the control group, and 57 lncRNAs, 1,255 mRNAs and 162 miRNAs were found to be differentially expressed in the CPO group compared to the control group. Subsequently, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to validate the expression of selected lncRNAs, miRNAs and mRNAs. In addition, bioinformatics methods were employed to explore the potential functions of ncRNAs and to construct lncRNA-miRNA-mRNA regulatory networks. To the best of our knowledge, this is the first study to comprehensively analyze regulated non-coding RNAs (ncRNAs) in CL/P and CPO, providing a novel perspective on the etiology of NSOC and laying the foundation for future research into the potential regulatory mechanisms of ncRNAs and mRNAs in NSOC.
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Affiliation(s)
- Yuwei Gao
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Qiguang Zang
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Hongquan Song
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Wei Zhang
- Department of Oral Maxillofacial Surgery, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xiaotong Wang
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yong Li
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xiaohui Jiao
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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13
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Li A, Qin G, Suzuki A, Gajera M, Iwata J, Jia P, Zhao Z. Network-based identification of critical regulators as putative drivers of human cleft lip. BMC Med Genomics 2019; 12:16. [PMID: 30704473 PMCID: PMC6357351 DOI: 10.1186/s12920-018-0458-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Cleft lip (CL) is one of the most common congenital birth defects with complex etiology. While genome-wide association studies (GWAS) have made significant advances in our understanding of mutations and their related genes with potential involvement in the etiology of CL, it remains unknown how these genes are functionally regulated and interact with each other in lip development. Currently, identifying the disease-causing genes in human CL is urgently needed. So far, the causative CL genes have been largely undiscovered, making it challenging to design experiments to validate the functional influence of the mutations identified from large genomic studies such as CL GWAS. RESULTS Transcription factors (TFs) and microRNAs (miRNAs) are two important regulators in cellular system. In this study, we aimed to investigate the genetic interactions among TFs, miRNAs and the CL genes curated from the previous studies. We constructed miRNA-TF co-regulatory networks, from which the critical regulators as putative drivers in CL were examined. Based on the constructed networks, we identified ten critical hub genes with prior evidence in CL. Furthermore, the analysis of partitioned regulatory modules highlighted a number of biological processes involved in the pathology of CL, including a novel pathway "Signaling pathway regulating pluripotency of stem cells". Our subnetwork analysis pinpointed two candidate miRNAs, hsa-mir-27b and hsa-mir-497, activating the Wnt pathway that was associated with CL. Our results were supported by an independent gene expression dataset in CL. CONCLUSIONS This study represents the first regulatory network analysis of CL genes. Our work presents a global view of the CL regulatory network and a novel approach on investigating critical miRNAs, TFs and genes via combinatory regulatory networks in craniofacial development. The top genes and miRNAs will be important candidates for future experimental validation of their functions in CL.
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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, 710048, Shaanxi, China.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA
| | - Guimin Qin
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.,School of Software, Xidian University, Xi'an, 710071, Shaanxi, China
| | - 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
| | - Mona Gajera
- 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
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA. .,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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14
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Han T, Wu N, Wang Y, Shen W, Zou J. miR‑16‑2‑3p inhibits cell proliferation and migration and induces apoptosis by targeting PDPK1 in maxillary primordium mesenchymal cells. Int J Mol Med 2019; 43:1441-1451. [PMID: 30664182 PMCID: PMC6365086 DOI: 10.3892/ijmm.2019.4070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/16/2019] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) post-transcriptionally regulate gene expression by targeting the 3′ untranslated region (UTR) of target genes, and serve diverse roles in cell proliferation, differentiation and apoptosis. However, the association between miR-16-2-3p and 3-phosphoinositide-dependent protein kinase-1 (PDPK1) in nonsyndromic cleft lip (NSCL) remains unclear. In the present study, a luciferase activity assay indicated that miR-16-2-3p negatively regulated PDPK1 in maxillary primordium mesenchymal cells (MPMCs). In addition, it was confirmed that the expression levels of miR-16-2-3p was markedly increased in cleft lip tissues compared with those in adjacent normal lip tissues. A negative correlation between miR-16-2-3p and PDPK1 in cleft lip tissues was observed. Furthermore, miR-16-2-3p inhibited cell proliferation and migration, and induced apoptosis of MPMCs via repressing PDPK1. Finally, miR-16-2-3p exerted its suppressive role in MPMCs by inhibiting the PDPK1/protein kinase B signaling pathway. These results indicate that miR-16-2-3p may inhibit cell proliferation and migration, and promote apoptosis in MPMCs through repression of PDPK1 and may be a potential target for future clinical prevention and treatment of NSCL.
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Affiliation(s)
- Tao Han
- Department of Burns and Plastic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Ni Wu
- Department of Burns and Plastic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Youjing Wang
- Department of Burns and Plastic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Weimin Shen
- Department of Burns and Plastic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Jijun Zou
- Department of Burns and Plastic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
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15
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Schoen C, Glennon JC, Abghari S, Bloemen M, Aschrafi A, Carels CEL, Von den Hoff JW. Differential microRNA expression in cultured palatal fibroblasts from infants with cleft palate and controls. Eur J Orthod 2018; 40:90-96. [PMID: 28486694 DOI: 10.1093/ejo/cjx034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background The role of microRNAs (miRNAs) in animal models of palatogenesis has been shown, but only limited research has been carried out in humans. To date, no miRNA expression study on tissues or cells from cleft palate patients has been published. We compared miRNA expression in palatal fibroblasts from cleft palate patients and age-matched controls. Material and Methods Cultured palatal fibroblasts from 10 non-syndromic cleft lip and palate patients (nsCLP; mean age: 18 ± 2 months), 5 non-syndromic cleft palate only patients (nsCPO; mean age: 17 ± 2 months), and 10 controls (mean age: 24 ± 5 months) were analysed with next-generation small RNA sequencing. All subjects are from Western European descent. Sequence reads were bioinformatically processed and the differentially expressed miRNAs were technically validated using quantitative reverse-transcription polymerase chain reaction (RT-qPCR). Results Using RNA sequencing, three miRNAs (hsa-miR-93-5p, hsa-miR-18a-5p, and hsa-miR-92a-3p) were up-regulated and six (hsa-miR-29c-5p, hsa-miR-549a, hsa-miR-3182, hsa-miR-181a-5p, hsa-miR-451a, and hsa-miR-92b-5p) were down-regulated in nsCPO fibroblasts. One miRNA (hsa-miR-505-3p) was down-regulated in nsCLP fibroblasts. Of these, hsa-miR-505-3p, hsa-miR-92a, hsa-miR-181a, and hsa-miR-451a were also differentially expressed using RT-PCR with a higher fold change than in RNAseq. Limitations The small sample size may limit the value of the data. In addition, interpretation of the data is complicated by the fact that biopsy samples are taken after birth, while the origin of the cleft lies in the embryonic period. This, together with possible effects of the culture medium, implies that only cell-autonomous genetic and epigenetic differences might be detected. Conclusions For the first time, we have shown that several miRNAs appear to be dysregulated in palatal fibroblasts from patients with nsCLP and nsCPO. Furthermore, large-scale genomic and expression studies are needed to validate these findings.
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Affiliation(s)
- Christian Schoen
- Departments of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeffrey C Glennon
- Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Shaghayegh Abghari
- Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjon Bloemen
- Departments of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institute of Health, Bethesda, USA
| | - Carine E L Carels
- Departments of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Oral Health Sciences, KU Leuven, University Hospitals, Belgium.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johannes W Von den Hoff
- Departments of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
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16
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Wu N, Yan J, Han T, Zou J, Shen W. Integrated assessment of differentially expressed plasma microRNAs in subtypes of nonsyndromic orofacial clefts. Medicine (Baltimore) 2018; 97:e11224. [PMID: 29924053 PMCID: PMC6023672 DOI: 10.1097/md.0000000000011224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Orofacial clefts include cleft lip only (CLO), cleft palate only (CPO), and cleft lip with palate (CLP). Previously, we reported the expression profile of plasma microRNAs in CLO, CPO, and CLP, respectively. However, the interaction of each subtype remains poorly investigated. METHODS In this study, we integrated the expression profiles of plasma miRNAs in these 3 subtypes, and assessed the distinct and overlapping dysregulated miRNAs using Venn diagrams. Their respective target genes reported in the literature were further analyzed using pathway analysis. RESULTS AND CONCLUSION The results showed that distinct or overlapping signaling pathways were involved in CLO, CPO, and CLP. The common key gene targets reflected functional relationships to the Wnt, Notch, TGF-beta, and Hedgehog signaling pathways. Further studies should examine the mechanism of the potential target genes, which may provide new avenues for future clinical prevention and therapy.
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17
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Li J, Zou J, Li Q, Chen L, Gao Y, Yan H, Zhou B, Li J. Assessment of differentially expressed plasma microRNAs in nonsyndromic cleft palate and nonsyndromic cleft lip with cleft palate. Oncotarget 2018; 7:86266-86279. [PMID: 27863433 PMCID: PMC5349912 DOI: 10.18632/oncotarget.13379] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/05/2016] [Indexed: 01/08/2023] Open
Abstract
Plasma microRNAs (miRNAs) have recently emerged as a new class of regulatory molecules that influence many biological functions. However, the expression profile of plasma microRNAs in nonsyndromic cleft palate (NSCP) or nonsyndromic cleft lip with cleft palate (NSCLP) remains poorly investigated. In this study, we used Agilent human miRNA microarray chips to monitor miRNA levels in three NSCP plasma samples (mixed as the CP group), three NSCLP plasma samples (mixed as the CLP group) and three normal plasma samples (mixed as the Control group). Six selected plasma miRNAs were validated in samples from an additional 16 CP, 33 CLP and 8 healthy children using qRT-PCR. Using Venn diagrams, distinct and overlapping dysregulated miRNAs were identified. Their respective target genes were further assessed using gene ontology and pathway analysis. The results show that distinct or overlapping biological processes and signalling pathways were involved in CP and CLP. Our study showed that the common key gene targets reflected functional relationships to the Notch, Wnt, phosphatidylinositol and Hedgehog signalling pathways. Further studies should examine the mechanism of the potential target genes, which may provide new avenues for future clinical prevention and therapy.
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Affiliation(s)
- Jingyun Li
- State Key Laboratory of Reproductive Medicine, Department of Plastic and Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Jijun Zou
- Department of Burns and Plastic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Qian Li
- State Key Laboratory of Reproductive Medicine, Department of Plastic and Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Ling Chen
- State Key Laboratory of Reproductive Medicine, Department of Plastic and Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Yanli Gao
- State Key Laboratory of Reproductive Medicine, Department of Plastic and Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Hui Yan
- State Key Laboratory of Reproductive Medicine, Department of Plastic and Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Bei Zhou
- State Key Laboratory of Reproductive Medicine, Department of Plastic and Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Jun Li
- State Key Laboratory of Reproductive Medicine, Department of Plastic and Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
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18
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Huang QL, Zhou FJ, Wu CB, Xu C, Qian WY, Fan DP, Cai XS. Circulating Biomarkers for Predicting Infliximab Response in Rheumatoid Arthritis: A Systematic Bioinformatics Analysis. Med Sci Monit 2017; 23:1849-1855. [PMID: 28413214 PMCID: PMC5404751 DOI: 10.12659/msm.900897] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background Infliximab shows good efficacy in treating refractory rheumatoid arthritis (RA). However, many patients responded poorly and related studies were inconsistent in predictive biomarkers. This study aimed to identify circulating biomarkers for predicting infliximab response in RA. Material/Methods Public databases of Gene Expression Omnibus (GEO) and ArrayExpress were searched for related microarray datasets, focused on the response to infliximab in RA. All peripheral blood samples were collected before infliximab treatment and gene expression profiles were measured using microarray. Differential genes associated with infliximab efficacy were analyzed. The genes recognized by half of the datasets were regarded as candidate biomarkers and validated by prospective datasets. Results Eight microarray datasets were identified with 374 blood samples of RA patients, among which 191 (51.1%) were diagnosed as non-responders in the subsequent infliximab treatment. Five genes (FKBP1A, FGF12, ANO1, LRRC31, and AKR1D1) were associated with the efficacy and recognized by half of the datasets. The 5-gene model showed a good predictive power in random- and prospective-designed studies, with AUC (area under receiver operating characteristic [ROC] curve)=0.963 and 1.000, and it was also applicable at the early phase of treatment (at week 2) for predicting the response at week 14 (AUC=1.000). In the placebo group, the model failed to predict the response (AUC=0.697), indicating the model’s specificity in infliximab treatment. Conclusions The model of FKBP1A, FGF12, ANO1, LRRC31, and AKR1D1 in peripheral blood is useful for efficiently predicting the response to infliximab treatment in rheumatoid arthritis.
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Affiliation(s)
- Qiu-Lan Huang
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Fu-Jiang Zhou
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Cheng-Bin Wu
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Chao Xu
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Wen-Ying Qian
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - De-Ping Fan
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Xu-Shan Cai
- Department of Clinical Laboratory Medicine, Maternal and Child Healthcare Hospital of Jiading, Shanghai, China (mainland)
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19
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Schoen C, Aschrafi A, Thonissen M, Poelmans G, Von den Hoff JW, Carels CEL. MicroRNAs in Palatogenesis and Cleft Palate. Front Physiol 2017; 8:165. [PMID: 28420997 PMCID: PMC5378724 DOI: 10.3389/fphys.2017.00165] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/06/2017] [Indexed: 01/01/2023] Open
Abstract
Palatogenesis requires a precise spatiotemporal regulation of gene expression, which is controlled by an intricate network of transcription factors and their corresponding DNA motifs. Even minor perturbations of this network may cause cleft palate, the most common congenital craniofacial defect in humans. MicroRNAs (miRNAs), a class of small regulatory non-coding RNAs, have elicited strong interest as key regulators of embryological development, and as etiological factors in disease. MiRNAs function as post-transcriptional repressors of gene expression and are therefore able to fine-tune gene regulatory networks. Several miRNAs are already identified to be involved in congenital diseases. Recent evidence from research in zebrafish and mice indicates that miRNAs are key factors in both normal palatogenesis and cleft palate formation. Here, we provide an overview of recently identified molecular mechanisms underlying palatogenesis involving specific miRNAs, and discuss how dysregulation of these miRNAs may result in cleft palate.
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Affiliation(s)
- Christian Schoen
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of HealthBethesda, MD, USA
| | - Michelle Thonissen
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical CenterNijmegen, Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegen, Netherlands.,Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences, Radboud UniversityNijmegen, Netherlands
| | - Johannes W Von den Hoff
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Carine E L Carels
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical CenterNijmegen, Netherlands.,Department of Oral Health Sciences, University Hospitals-KU LeuvenLeuven, Belgium
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