1
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Radhakrishna U, Nath SK, Uppala LV, Veerappa A, Forray A, Muvvala SB, Metpally RP, Crist RC, Berrettini WH, Mausi LM, Vishweswaraiah S, Bahado-Singh RO. Placental microRNA methylome signatures may serve as biomarkers and therapeutic targets for prenatally opioid-exposed infants with neonatal opioid withdrawal syndrome. Front Genet 2023; 14:1215472. [PMID: 37434949 PMCID: PMC10332887 DOI: 10.3389/fgene.2023.1215472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction: The neonate exposed to opioids in utero faces a constellation of withdrawal symptoms postpartum commonly called neonatal opioid withdrawal syndrome (NOWS). The incidence of NOWS has increased in recent years due to the opioid epidemic. MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. Epigenetic variations in microRNAs (miRNAs) and their impact on addiction-related processes is a rapidly evolving area of research. Methods: The Illumina Infinium Methylation EPIC BeadChip was used to analyze DNA methylation levels of miRNA-encoding genes in 96 human placental tissues to identify miRNA gene methylation profiles as-sociated with NOWS: 32 from mothers whose prenatally opioid-exposed infants required pharmacologic management for NOWS, 32 from mothers whose prenatally opioid-exposed infants did not require treat-ment for NOWS, and 32 unexposed controls. Results: The study identified 46 significantly differentially methylated (FDR p-value ≤ 0.05) CpGs associated with 47 unique miRNAs, with a receiver operating characteristic (ROC) area under the curve (AUC) ≥0.75 including 28 hypomethylated and 18 hypermethylated CpGs as potentially associated with NOWS. These dysregulated microRNA methylation patterns may be a contributing factor to NOWS pathogenesis. Conclusion: This is the first study to analyze miRNA methylation profiles in NOWS infants and illustrates the unique role miRNAs might have in diagnosing and treating the disease. Furthermore, these data may provide a step toward feasible precision medicine for NOWS babies as well.
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Affiliation(s)
- Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Lavanya V. Uppala
- College of Information Science and Technology, Peter Kiewit Institute, The University of Nebraska at Omaha, Omaha, NE, United States
| | - Avinash Veerappa
- Department of Genetics, Cell Biology and Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Ariadna Forray
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Srinivas B. Muvvala
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Danville, PA, United States
| | - Richard C. Crist
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Wade H. Berrettini
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
- Geisinger Clinic, Danville, PA, United States
| | - Lori M. Mausi
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
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2
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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: 5] [Impact Index Per Article: 5.0] [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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3
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Zhang B, Zhang Y, Wu S, Ma D, Ma J. DNA methylation profile of lip tissue from congenital nonsyndromic cleft lip and palate patients by whole-genome bisulfite sequencing. Birth Defects Res 2023; 115:205-217. [PMID: 36210532 PMCID: PMC10092010 DOI: 10.1002/bdr2.2102] [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: 06/22/2022] [Revised: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 01/29/2023]
Abstract
Congenital nonsyndromic cleft lip and palate (NSCLP) is one of the most common malformations worldwide. DNA methylation has been implicated in many diseases. However, its involvement in lip tissue from NSCLP is not well understood. This study aimed to investigate the role of dysregulated DNA methylation in NSCLP. DNA methylation profile was determined in eight injured and five self-normal lip tissue samples from children with NSCLP by whole-genome bisulfite sequencing. A total of 2,711 differentially methylated regions (DMRs), corresponding to 1,231 genes were identified. Given the important role of promoter methylation in regulating gene expression, the promoter DMR-related genes were considered. Bioinformatics analysis demonstrated that some of them showed potential associations with NSCLP. Therefore, the well-known NSCLP susceptibility gene, GLI family zinc finger 2 (GLI2) with an unknown role in its DNA methylation in NSCLP, was selected for further analysis. The promoter hypomethylation and higher mRNA expression level of GLI2 were observed in injured lip tissues by verification in additional samples. Moreover, dual luciferase reporter assay indicated that promoter hypermethylation of GLI2 inhibited its transcription. Overall, this study suggested that abnormal DNA methylation in lip tissue may be correlated with the pathogenesis of congenital NSCLP.
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Affiliation(s)
- Bowen Zhang
- Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, ENT Institute, Fudan University, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Youmeng Zhang
- Department of Stomatology Stomatology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Siyi Wu
- Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, ENT Institute, Fudan University, Shanghai, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jing Ma
- Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, ENT Institute, Fudan University, Shanghai, China
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Germline Variants in Angiogenesis-Related Genes Contribute to Clinical Outcome in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14071844. [PMID: 35406617 PMCID: PMC8997703 DOI: 10.3390/cancers14071844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary A high risk of relapse and treatment resistance are among the major challenges in locally advanced head and neck squamous cell carcinoma (HNSCC). Data show that common germline alterations in genes regulating angiogenesis may modulate treatment sensitivity, cancer progression, and prognosis, but relatively little is known about their role in HNSCC. Thus, our goal was to examine the effect of variation in these genes on survival outcomes in HNSCC patients receiving radiotherapy and cisplatin-based chemoradiotherapy. We identified genetic variants significantly affecting therapy results, constituting independent prognostic factors in these patients. Our results suggest that some polymorphisms in angiogenesis genes may be determinants of treatment efficacy and tumor aggressiveness in HNSCC, which may be of importance in standard therapy. These findings emphasize the potential value of the host genetic profile related to angiogenesis in assessing the risk of treatment failure. Abstract Fibroblast growth factor (FGF)/FGF receptor (FGFR), and platelet-derived growth factor (PDGF)/PDGF receptor (PDGFR) systems, as well as some matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs), are involved in various steps of angiogenesis. Data indicate that common germline variations in angiogenesis-regulating genes may modulate therapy results and cancer progression. However, whether these variants affect clinical outcome in head and neck squamous cell carcinoma (HNSCC) is unclear. Hence, we assessed the relationship between FGF/FGFR, PDGF/PDGFR, MMP, and TIMP genetic variants and treatment outcomes in HNSCC patients receiving radiotherapy (RT) alone or combined with cisplatin-based chemotherapy. In multivariate analysis, FGF2 rs1048201 CC homozygotes showed a higher risk of death (p = 0.039), while PDGFRA rs2228230 T was strongly associated with an increased risk of locoregional relapse (HR 2.49, p = 0.001) in the combination treatment subgroup. In the RT alone subset, MMP2 rs243865 TT carriers had a higher risk of locoregional recurrence (HR 2.92, p = 0.019), whereas PDGFRB rs246395 CC homozygotes were at increased risk of metastasis (HR 3.06, p = 0.041). The MMP2 rs7201 C and TIMP2 rs7501477 T were associated with a risk of locoregional failure in the entire cohort (p = 0.032 and 0.045, respectively). Furthermore, rs1048201, rs2228230, rs246395, rs243865, rs7201, and rs7201/rs7501477 were independent indicators of an unfavorable outcome. This study demonstrates that the FGF2, PDGFRA, PDGFRB, MMP2, and TIMP2 variants may contribute to treatment failure and poor prognosis in HNSCC.
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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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6
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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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7
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Li A, Jia P, Mallik S, Fei R, Yoshioka H, Suzuki A, Iwata J, Zhao Z. Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. Brief Bioinform 2021; 21:1465-1478. [PMID: 31589286 DOI: 10.1093/bib/bbz082] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/03/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022] Open
Abstract
Cleft palate (CP) is the second most common congenital birth defect. The etiology of CP is complicated, with involvement of various genetic and environmental factors. To investigate the gene regulatory mechanisms, we designed a powerful regulatory analytical approach to identify the conserved regulatory networks in humans and mice, from which we identified critical microRNAs (miRNAs), target genes and regulatory motifs (miRNA-TF-gene) related to CP. Using our manually curated genes and miRNAs with evidence in CP in humans and mice, we constructed miRNA and transcription factor (TF) co-regulation networks for both humans and mice. A consensus regulatory loop (miR17/miR20a-FOXE1-PDGFRA) and eight miRNAs (miR-140, miR-17, miR-18a, miR-19a, miR-19b, miR-20a, miR-451a and miR-92a) were discovered in both humans and mice. The role of miR-140, which had the strongest association with CP, was investigated in both human and mouse palate cells. The overexpression of miR-140-5p, but not miR-140-3p, significantly inhibited cell proliferation. We further examined whether miR-140 overexpression could suppress the expression of its predicted target genes (BMP2, FGF9, PAX9 and PDGFRA). Our results indicated that miR-140-5p overexpression suppressed the expression of BMP2 and FGF9 in cultured human palate cells and Fgf9 and Pdgfra in cultured mouse palate cells. In summary, our conserved miRNA-TF-gene regulatory network approach is effective in detecting consensus miRNAs, motifs, and regulatory mechanisms in human and mouse CP.
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Affiliation(s)
- Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,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
| | - Peilin Jia
- 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
| | - Rong Fei
- 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
| | - 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, 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, 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, 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.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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8
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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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9
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Yoshioka H, Ramakrishnan SS, Suzuki A, Iwata J. Phenytoin Inhibits Cell Proliferation through microRNA-196a-5p in Mouse Lip Mesenchymal Cells. Int J Mol Sci 2021; 22:1746. [PMID: 33572377 PMCID: PMC7916186 DOI: 10.3390/ijms22041746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/22/2023] Open
Abstract
Cleft lip (CL) is one of the most common birth defects. It is caused by either genetic mutations or environmental factors. Recent studies suggest that environmental factors influence the expression of noncoding RNAs [e.g., microRNA (miRNA)], which can regulate the expression of genes crucial for cellular functions. In this study, we examined which miRNAs are associated with CL. Among 10 candidate miRNAs (miR-98-3p, miR-101a-3p, miR-101b-3p, miR-141-3p, miR-144-3p, miR-181a-5p, miR-196a-5p, miR-196b-5p, miR-200a-3p, and miR-710) identified through our bioinformatic analysis of CL-associated genes, overexpression of miR-181a-5p, miR-196a-5p, miR-196b-5p, and miR-710 inhibited cell proliferation through suppression of genes associated with CL in cultured mouse embryonic lip mesenchymal cells (MELM cells) and O9-1 cells, a mouse cranial neural crest cell line. In addition, we found that phenytoin, an inducer of CL, decreased cell proliferation through miR-196a-5p induction. Notably, treatment with a specific inhibitor for miR-196a-5p restored cell proliferation through normalization of expression of CL-associated genes in the cells treated with phenytoin. Taken together, our results suggest that phenytoin induces CL through miR-196a-5p induction, which suppresses the expression of CL-associated genes.
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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; (H.Y.); (S.S.R.); (A.S.)
- 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; (H.Y.); (S.S.R.); (A.S.)
- 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; (H.Y.); (S.S.R.); (A.S.)
- 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; (H.Y.); (S.S.R.); (A.S.)
- 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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10
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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: 13] [Impact Index Per Article: 3.3] [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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11
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Jiang G, Xiao G, Luo C, Tang Z, Teng Z, Peng X. Correlation Between SNPs at the 3'UTR of the FGF2 Gene and Their Interaction with Environmental Factors in Han Chinese Diabetic Peripheral Neuropathy Patients. J Mol Neurosci 2020; 71:203-214. [PMID: 32613556 DOI: 10.1007/s12031-020-01641-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 06/19/2020] [Indexed: 12/12/2022]
Abstract
FGF2 is a neurotrophic factor that can act as a key regulatory molecule of neuroprotection, neurogenesis, and angiogenesis in various injuries. To explore the genetic background of the FGF2 gene on DPN development, this study analyzed the correlation between SNPs in the 3'UTR of the FGF2 gene and their interaction with environmental factors in DPN patients of Han Chinese nationality. Sanger sequencing was used to analyze the FGF2 genotypes at the rs1048201, rs3804158, rs41348645, rs6854081, rs3747676, rs7683093, rs1476215, and rs1476217 loci in 150 DPN patients, 150 NDPN patients, and 150 healthy control patients. Plasma FGF2 levels were measured in all subjects by using ELISAs. Subjects carrying the T allele at the rs1048201 locus in the FGF2 gene had a significantly lower risk of developing DPN compared with subjects carrying the C allele (OR = 0.43, 95% CI = 0.33-0.56, p < 0.01). Subjects with the G genotype at the rs6854081 locus had an exceptionally higher risk of developing DPN than subjects with the T allele (OR = 1.66, 95% CI = 1.39-1.89, p < 0.01). Individuals harboring the G allele at the rs7683093 locus had a markedly higher risk of DPN than patients with the C allele (OR = 1.63, 95% CI = 1.36-1.87, p < 0.01). Finally, individuals having the A genotype at the rs1476215 locus had a significantly higher risk of DPN than individuals carrying the T allele (OR = 1.82, 95% CI = 1.53-2.02, p < 0.01). There was an interaction between age and alcohol consumption and the SNP rs7683093. SNPs at rs1048201, rs6854081, rs7683093, and rs1476215 in the FGF2 3'UTR were strongly associated with plasma levels of FGF2 (p < 0.05). SNPs at the rs1048201, rs6854081, rs7683093, and rs1476215 loci in the FGF2 gene were significantly associated with the risk of DPN. A possible mechanism is that these SNPs affect the expression level of FGF2 by interrupting the binding of microRNAs to target sites in the 3'UTR.
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Affiliation(s)
- Guangyuan Jiang
- Department of Neurosurgery, The Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Gang Xiao
- Department of Neurosurgery, The Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Chao Luo
- Department of Neurosurgery, The Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Zhaohua Tang
- Departmen of neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhipeng Teng
- Department of Neurosurgery, The Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Xing Peng
- Department of Neurosurgery, The Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, China.
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12
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Paiva KBS, Maas CS, dos Santos PM, Granjeiro JM, Letra A. Extracellular Matrix Composition and Remodeling: Current Perspectives on Secondary Palate Formation, Cleft Lip/Palate, and Palatal Reconstruction. Front Cell Dev Biol 2019; 7:340. [PMID: 31921852 PMCID: PMC6923686 DOI: 10.3389/fcell.2019.00340] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/29/2019] [Indexed: 12/13/2022] Open
Abstract
Craniofacial development comprises a complex process in humans in which failures or disturbances frequently lead to congenital anomalies. Cleft lip with/without palate (CL/P) is a common congenital anomaly that occurs due to variations in craniofacial development genes, and may occur as part of a syndrome, or more commonly in isolated forms (non-syndromic). The etiology of CL/P is multifactorial with genes, environmental factors, and their potential interactions contributing to the condition. Rehabilitation of CL/P patients requires a multidisciplinary team to perform the multiple surgical, dental, and psychological interventions required throughout the patient's life. Despite progress, lip/palatal reconstruction is still a major treatment challenge. Genetic mutations and polymorphisms in several genes, including extracellular matrix (ECM) genes, soluble factors, and enzymes responsible for ECM remodeling (e.g., metalloproteinases), have been suggested to play a role in the etiology of CL/P; hence, these may be considered likely targets for the development of new preventive and/or therapeutic strategies. In this context, investigations are being conducted on new therapeutic approaches based on tissue bioengineering, associating stem cells with biomaterials, signaling molecules, and innovative technologies. In this review, we discuss the role of genes involved in ECM composition and remodeling during secondary palate formation and pathogenesis and genetic etiology of CL/P. We also discuss potential therapeutic approaches using bioactive molecules and principles of tissue bioengineering for state-of-the-art CL/P repair and palatal reconstruction.
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Affiliation(s)
- Katiúcia Batista Silva Paiva
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Clara Soeiro Maas
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Pâmella Monique dos Santos
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - José Mauro Granjeiro
- Clinical Research Laboratory in Dentistry, Federal Fluminense University, Niterói, Brazil
- Directory of Life Sciences Applied Metrology, National Institute of Metrology, Quality and Technology, Duque de Caxias, Brazil
| | - Ariadne Letra
- Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston, TX, United States
- Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX, United States
- Department of Diagnostic and Biomedical Sciences, UTHealth School of Dentistry at Houston, Houston, TX, United States
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13
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Bioinformatics analysis of regulatory elements of the CD151 gene and insilico docking of CD151 with diallyl sulfide. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Rosero Salazar DH, Carvajal Monroy PL, Wagener FADTG, Von den Hoff JW. Orofacial Muscles: Embryonic Development and Regeneration after Injury. J Dent Res 2019; 99:125-132. [PMID: 31675262 PMCID: PMC6977159 DOI: 10.1177/0022034519883673] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Orofacial congenital defects such as cleft lip and/or palate are associated with impaired muscle regeneration and fibrosis after surgery. Also, other orofacial reconstructions or trauma may end up in defective muscle regeneration and fibrosis. The aim of this review is to discuss current knowledge on the development and regeneration of orofacial muscles in comparison to trunk and limb muscles. The orofacial muscles include the tongue muscles and the branchiomeric muscles in the lower face. Their main functions are chewing, swallowing, and speech. All orofacial muscles originate from the mesoderm of the pharyngeal arches under the control of cranial neural crest cells. Research in vertebrate models indicates that the molecular regulation of orofacial muscle development is different from that of trunk and limb muscles. In addition, the regenerative ability of orofacial muscles is lower, and they develop more fibrosis than other skeletal muscles. Therefore, specific approaches need to be developed to stimulate orofacial muscle regeneration. Regeneration may be stimulated by growth factors such fibroblast growth factors and hepatocyte growth factor, while fibrosis may be reduced by targeting the transforming growth factor β1 (TGFβ1)/myofibroblast axis. New approaches that combine these 2 aspects will improve the surgical treatment of orofacial muscle defects.
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Affiliation(s)
- D H Rosero Salazar
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - P L Carvajal Monroy
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, the Netherlands.,Department of Oral and Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - F A D T G Wagener
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - J W Von den Hoff
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, the Netherlands
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15
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Gajera M, Desai N, Suzuki A, Li A, Zhang M, Jun G, Jia P, Zhao Z, Iwata J. MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip. BMC Med Genomics 2019; 12:70. [PMID: 31122291 PMCID: PMC6533741 DOI: 10.1186/s12920-019-0535-2] [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] [Received: 09/26/2018] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Background The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex and involves the contribution of genetic and environmental factors. Although many candidate genes have been identified, the regulation and interaction of these genes in CL/P remain unclear. In addition, the contribution of microRNAs (miRNAs), non-coding RNAs that regulate the expression of multiple genes, to the etiology of CL/P is largely unknown. Methods To identify the signatures of causative biological pathways for human CL/P, we conducted a systematic literature review for human CL/P candidate genes and subsequent bioinformatics analyses. Functional enrichment analyses of the candidate CL/P genes were conducted using the pathway databases GO and KEGG. The miRNA-mediated post-transcriptional regulation of the CL/P candidate genes was analyzed with miRanda, PITA, and TargetScan, and miRTarbase. Genotype-phenotype association analysis was conducted using GWAS. The functional significance of the candidate miRNAs was evaluated experimentally in cell proliferation and target gene regulation assays in human lip fibroblasts. Results Through an extensive search of the main biomedical databases, we mined 177 genes with mutations or association/linkage reported in individuals with CL/P, and considered them as candidate genes for human CL/P. The genotype-phenotype association study revealed that mutations in 12 genes (ABCA4, ADAM3A, FOXE1, IRF6, MSX2, MTHFR, NTN1, PAX7, TP63, TPM1, VAX1, and WNT9B) were significantly associated with CL/P. In addition, our bioinformatics analysis predicted 16 microRNAs (miRNAs) to be post-transcriptional regulators of CL/P genes. To validate the bioinformatics results, the top six candidate miRNAs (miR-124-3p, miR-369-3p, miR-374a-5p, miR-374b-5p, miR-497-5p, and miR-655-3p) were evaluated by cell proliferation/survival assays and miRNA-gene regulation assays in cultured human lip fibroblasts. We found that miR-497-5p and miR-655-3p significantly suppressed cell proliferation in these cells. Furthermore, the expression of the predicted miRNA-target genes was significantly downregulated by either miR-497-5p or miR-655-3p mimic. Conclusion Expression of miR-497-5p and miR-655-3p suppresses cell proliferation through the regulation of human CL/P-candidate genes. This study provides insights into the role of miRNAs in the etiology of CL/P and suggests possible strategies for the diagnosis of CL/P. Electronic supplementary material The online version of this article (10.1186/s12920-019-0535-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mona Gajera
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Neha Desai
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Akiko Suzuki
- Department of Diagnostic & 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
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Musi Zhang
- Department of Diagnostic & 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
| | - Goo Jun
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, 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
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, 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
| | - Junichi Iwata
- Department of Diagnostic & 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.
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16
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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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17
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Li L, Zhang S, Wei L, Wang Z, Ma W, Liu F, Qian Y. FGF2 and FGFR2 in patients with idiopathic pulmonary fibrosis and lung cancer. Oncol Lett 2018; 16:2490-2494. [PMID: 30013642 PMCID: PMC6036565 DOI: 10.3892/ol.2018.8903] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/01/2018] [Indexed: 01/04/2023] Open
Abstract
The aim of this study was to investigate the expression of FGF2 and FGFR2 in patients with idiopathic pulmonary fibrosis (IPF) and lung cancer (LC) as well as their clinical significance. Reverse transcription-quantitative PCR (RT-qPCR) and western blotting were used to detect FGF2 and FGFR2 expression in LC and adjacent normal tissues of LC patients and lavage fluid of idiopathic pulmonary fibers patients and normal controls (confirmed by bronchoalveolar lavage examination). The expression levels of FGF2 mRNA and protein in the non-small cell LC tissues were significantly higher than those in the adjacent normal tissues (P<0.001). The expression level of FGF2 protein in lavage fluid of patients with IPF was higher than that of the control group (P<0.001). The expression level of FGFR2 mRNA in the non-small cell LC tissues was significantly higher than that in the adjacent normal tissues (P<0.001). The expression level of FGFR2 protein in the non-small cell LC tissues was higher than that in the adjacent normal lung tissues (P<0.001). The expression levels of FGF2 mRNA and FGFR2 mRNA in cancer tissues were not significantly correlated with age, sex and history of smoking (P>0.05), but were significantly correlated with lymph node metastasis, tumor differentiation and TNM staging. FGF2 and FGFR2 proteins were highly expressed in cancer tissues of LC patients and lavage fluid of patients with IPF. The expression of FGF2 mRNA and FGFR2 mRNA was correlated with lymph node metastasis and TNM stage. The high expression levels of FGF2 mRNA and FGFR2 mRNA were associated with tumor metastasis and poor prognosis of LC patients.
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Affiliation(s)
- Li Li
- Department of Respiratory Disease, Baoshan Branch, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, P.R. China.,Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, P.R. China
| | - Sufang Zhang
- Department of Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, P.R. China
| | - Lei Wei
- Department of Respiratory Disease, Baoshan Branch, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, P.R. China.,Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, P.R. China
| | - Zhongfu Wang
- Department of Respiratory Disease, Baoshan Branch, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, P.R. China.,Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, P.R. China
| | - Wei Ma
- Department of Respiratory Disease, Baoshan Branch, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, P.R. China.,Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, P.R. China
| | - Fangying Liu
- Department of Respiratory Disease, Baoshan Branch, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, P.R. China.,Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, P.R. China
| | - Yechang Qian
- Department of Respiratory Disease, Baoshan Branch, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, P.R. China.,Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, P.R. China
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18
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Ishorst N, Francheschelli P, Böhmer AC, Khan MFJ, Heilmann-Heimbach S, Fricker N, Little J, Steegers-Theunissen RPM, Peterlin B, Nowak S, Martini M, Kruse T, Dunsche A, Kreusch T, Gölz L, Aldhorae K, Halboub E, Reutter H, Mossey P, Nöthen MM, Rubini M, Ludwig KU, Knapp M, Mangold E. Nonsyndromic cleft palate: An association study at GWAS candidate loci in a multiethnic sample. Birth Defects Res 2018; 110:871-882. [PMID: 29498243 DOI: 10.1002/bdr2.1213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/19/2018] [Accepted: 02/07/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Nonsyndromic cleft palate only (nsCPO) is a common and multifactorial form of orofacial clefting. In contrast to successes achieved for the other common form of orofacial clefting, that is, nonsyndromic cleft lip with/without cleft palate (nsCL/P), genome wide association studies (GWAS) of nsCPO have identified only one genome wide significant locus. Aim of the present study was to investigate whether common variants contribute to nsCPO and, if so, to identify novel risk loci. METHODS We genotyped 33 SNPs at 27 candidate loci from 2 previously published nsCPO GWAS in an independent multiethnic sample. It included: (i) a family-based sample of European ancestry (n = 212); and (ii) two case/control samples of Central European (n = 94/339) and Arabian ancestry (n = 38/231), respectively. A separate association analysis was performed for each genotyped dataset, and meta-analyses were performed. RESULTS After association analysis and meta-analyses, none of the 33 SNPs showed genome-wide significance. Two variants showed nominally significant association in the imputed GWAS dataset and exhibited a further decrease in p-value in a European and an overall meta-analysis including imputed GWAS data, respectively (rs395572: PMetaEU = 3.16 × 10-4 ; rs6809420: PMetaAll = 2.80 × 10-4 ). CONCLUSION Our findings suggest that there is a limited contribution of common variants to nsCPO. However, the individual effect sizes might be too small for detection of further associations in the present sample sizes. Rare variants may play a more substantial role in nsCPO than in nsCL/P, for which GWAS of smaller sample sizes have identified genome-wide significant loci. Whole-exome/genome sequencing studies of nsCPO are now warranted.
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Affiliation(s)
- Nina Ishorst
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Paola Francheschelli
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Anne C Böhmer
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Mohammad Faisal J Khan
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Stefanie Heilmann-Heimbach
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Nadine Fricker
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Julian Little
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Regine P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, Department of Pediatrics, Division Neonatology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Borut Peterlin
- Department of Obstetrics & Gynecology, Clinical Institute of Medical Genetics, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Stefanie Nowak
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Markus Martini
- Department of Oral and Maxillo-Facial-Plastic Surgery, University of Bonn, Bonn, Germany
| | - Teresa Kruse
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Anton Dunsche
- Department of Oral and Maxillo-Facial Surgery, Clinics Karlsruhe, Karlsruhe, Germany
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord-Heidberg, Hamburg, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Khalid Aldhorae
- Orthodontic Department, College of Dentistry, Thamar University, Thamar, Yemen
| | - Esam Halboub
- Department of Maxillofacial Surgery and Diagnostic Sciences, Devision of Oral Medicine and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Neonatology, Children's Hospital, University of Bonn, Bonn, Germany
| | - Peter Mossey
- Dental Hospital, University of Dundee, Dundee, United Kingdom
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michele Rubini
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Kerstin U Ludwig
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
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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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