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Wang X, Wu P, Fu Y, Yang R, Li C, Chen Y, He A, Chen X, Ma D, Ma J, Zhang T. The circular RNA expression profile of human auricle cartilage and the role of circCOL1A2 in isolated microtia. Cell Signal 2024; 115:111017. [PMID: 38123043 DOI: 10.1016/j.cellsig.2023.111017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/24/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Microtia is one of the most common craniofacial birth defects worldwide, and its primary clinical manifestation is auricle deformity. Epigenetic factors are known to contribute to the etiology of microtia, yet the involvement of circular RNAs (circRNAs) in human auricle development and their association with microtia remains poorly understood. In this study, we aimed to analyze differentially expressed circRNAs and explore their functional implications in isolated microtia. By employing circRNA microarray analysis and bioinformatics approaches, we identified 340 differentially expressed circRNAs in auricle cartilage of patients with isolated microtia, comprising 152 upregulated and 188 downregulated circRNAs. A circRNA-mRNA co-expression network was constructed, followed by gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Subsequently, we selected four significantly upregulated circRNAs from the co-expression network based on their association with cartilage development and validated their expressions in 30 isolated microtia and 30 control clinical auricle cartilage samples. Among these circRNAs, circCOL1A2, the most significantly upregulated circRNA, was selected as a representative circRNA for investigating its role in isolated microtia. Overexpression of circCOL1A2 significantly inhibited chondrocyte proliferation and chondrogenic differentiation of human mesenchymal stem cells. Additionally, circCOL1A2 upregulated Dermatan Sulfate Epimerase Like (DSEL) expression by sponging miR-637 through the competing endogenous RNA (ceRNA) mechanism. Notably, the downregulation of DSEL attenuated the inhibitory effect of circCOL1A2 overexpression on cell proliferation and chondrogenic differentiation. Collectively, these findings highlight the involvement of circCOL1A2 in the pathogenesis of isolated microtia and emphasize the potential significance of dysregulated circRNAs in disease development.
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Affiliation(s)
- Xin Wang
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Peixuan Wu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Yaoyao Fu
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Run Yang
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, China.
| | - Chenlong Li
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Ying Chen
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Aijuan He
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Xin Chen
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, 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 200032, China.
| | - Jing Ma
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, China.
| | - Tianyu Zhang
- ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital, Fudan University, Shanghai 200031, China; NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai 200031, China.
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Sun P, Gu L, Yu Q, Luan F. Pathogenic Genes for Congenital Microtia: A Bioinformatics Analysis. J Craniofac Surg 2023; 34:2560-2562. [PMID: 37643078 DOI: 10.1097/scs.0000000000009620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/20/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE The purpose of this study is to accurately find the pathogenic genes of congenital microtia, so as to lay a theoretical foundation for genetic screening, diagnosis, and gene therapy of congenital microtia in the further stage. METHODS In this study, the authors used public data from the Mouse Genome Informatics database. The authors used the String database ( https://string-db.org/ ) to construct the Protein-Protein Interaction network. Then Gene Ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed for the pathogenic genes. RESULTS The authors searched the Mouse Genome Informatics database and found 84 pathogenic genes of congenital microtia. The Protein-Protein Interaction network for pathogenic genes was constructed, which contained 81 nodes and 148 lines with MCM5, CDT1, POLA1, CDC45, CDC6, EFTUD2, ORC1, ORC4, ORC6, and TCOF1 . The authors conducted a Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis on pathogenic genes, and the results showed that pathogenic genes were involved in O-mannan biosynthesis, cell cycle, RNA polymerase, and other signaling pathways. CONCLUSIONS The authors' results indicated that the occurrence of congenital microtia is attributed to a variety of genes. Furthermore, the interactions of pathogenic genes were further elucidated by using a bioinformatics approach. This study will help to reveal the pathogenesis of congenital microtia and lay the foundation for accurate diagnosis and treatment of congenital microtia in the future.
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Affiliation(s)
- Pengfei Sun
- Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Luosha Gu
- Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Qian Yu
- Department of Dermatologic Surgery, Shandong Provincial Hospital for Skin Disease & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medial University & Shandong Academy of Medical Sciences, Shandong
| | - Fang Luan
- Department of Plastic Surgery, Zibo Central Hospital, Shandong, China
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Liu B, Liu W, Zhao S, Ma L, Zang T, Huang C, Shu K, Gao H, Tang X. Transcriptome sequencing of facial adipose tissue reveals alterations in mRNAs of hemifacial microsomia. Front Pediatr 2023; 11:1099841. [PMID: 36861077 PMCID: PMC9968928 DOI: 10.3389/fped.2023.1099841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Hemifacial microsomia (HFM) is a common congenital malformation of the craniofacial region, including mandibular hypoplasia, microtia, facial palsy and soft tissue deficiencies. However, it remains unclear which specific genes are involved in the pathogenesis of HFM. By identifying differentially expressed genes (DEGs) in deficient facial adipose tissue from HFM patients, we hope to provide a new insight into disease mechanisms from the transcriptome perspective. RNA sequencing (RNA-Seq) was performed with 10 facial adipose tissues from patients of HFM and healthy controls. Differentially expressed genes in HFM were validated by quantitative real-time PCR (qPCR). Functional annotations of the DEGs were analyzed with DESeq2 R package (1.20.0). A total of 1,244 genes were identified as DEGs between HFM patients and matched controls. Bioinformatic analysis predicted that the increased expression of HOXB2 and HAND2 were associated with facial deformity of HFM. Knockdown and overexpression of HOXB2 were achieved with lentiviral vectors. Cell proliferation, migration, and invasion assay was performed with adipose-derived stem cells (ADSC) to confirm the phenotype of HOXB2. We also found that PI3K-Akt signaling pathway and human papillomavirus infection were activated in HFM. In conclusion, we discovered potential genes, pathways and networks in HFM facial adipose tissue, which contributes to a better understanding of the pathogenesis of HFM.
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Affiliation(s)
- Bingyang Liu
- Department of Craniomaxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Liu
- Department of Craniomaxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanbaga Zhao
- Department of Craniomaxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lunkun Ma
- Department of Craniomaxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianying Zang
- Department of Craniomaxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Changjin Huang
- Department of Craniomaxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kaiyi Shu
- Department of Craniomaxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hengbin Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xiaojun Tang
- Department of Craniomaxillofacial Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Ronkainen J, Heiskala A, Vehmeijer FO, Lowry E, Caramaschi D, Estrada Gutierrez G, Heiss JA, Hummel N, Keikkala E, Kvist T, Kupsco A, Melton PE, Pesce G, Soomro MH, Vives-Usano M, Baiz N, Binder E, Czamara D, Guxens M, Mustaniemi S, London SJ, Rauschert S, Vääräsmäki M, Vrijheid M, Ziegler AG, Annesi-Maesano I, Bustamante M, Huang RC, Hummel S, Just AC, Kajantie E, Lahti J, Lawlor D, Räikkönen K, Järvelin MR, Felix JF, Sebert S. Maternal haemoglobin levels in pregnancy and child DNA methylation: a study in the pregnancy and childhood epigenetics consortium. Epigenetics 2022; 17:19-31. [PMID: 33331245 PMCID: PMC8813068 DOI: 10.1080/15592294.2020.1864171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/26/2020] [Accepted: 12/08/2020] [Indexed: 01/05/2023] Open
Abstract
Altered maternal haemoglobin levels during pregnancy are associated with pre-clinical and clinical conditions affecting the fetus. Evidence from animal models suggests that these associations may be partially explained by differential DNA methylation in the newborn with possible long-term consequences. To test this in humans, we meta-analyzed the epigenome-wide associations of maternal haemoglobin levels during pregnancy with offspring DNA methylation in 3,967 newborn cord blood and 1,534 children and 1,962 adolescent whole-blood samples derived from 10 cohorts. DNA methylation was measured using Illumina Infinium Methylation 450K or MethylationEPIC arrays covering 450,000 and 850,000 methylation sites, respectively. There was no statistical support for the association of maternal haemoglobin levels with offspring DNA methylation either at individual methylation sites or clustered in regions. For most participants, maternal haemoglobin levels were within the normal range in the current study, whereas adverse perinatal outcomes often arise at the extremes. Thus, this study does not rule out the possibility that associations with offspring DNA methylation might be seen in studies with more extreme maternal haemoglobin levels.
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Affiliation(s)
- Justiina Ronkainen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Anni Heiskala
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Florianne O.L. Vehmeijer
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Estelle Lowry
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- School of Natural and Built Environment, Queen’s University Belfast, Belfast, Northern Ireland
| | - Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
| | | | - Jonathan A. Heiss
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nadine Hummel
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Elina Keikkala
- Department of Obstetrics and Gynecology, PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
| | - Tuomas Kvist
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, USA
| | - Allison Kupsco
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Phillip E. Melton
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Giancarlo Pesce
- Sorbonne Université, Institut Pierre Louis D’épidémiologie Et De Santé Publique (IPLESP), Paris, France
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Institut National De La Santé Et De La Recherche Médicale (INSERM) UMR-S 1136, Institut Pierre Louis D’épidémiologie Et De Santé Publique (IPLESP), Team EPAR, Paris, France
| | - Munawar H. Soomro
- Sorbonne Université, Institut Pierre Louis D’épidémiologie Et De Santé Publique (IPLESP), Paris, France
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Institut National De La Santé Et De La Recherche Médicale (INSERM) UMR-S 1136, Institut Pierre Louis D’épidémiologie Et De Santé Publique (IPLESP), Team EPAR, Paris, France
| | - Marta Vives-Usano
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
| | - Nour Baiz
- Sorbonne Université, Institut Pierre Louis D’épidémiologie Et De Santé Publique (IPLESP), Paris, France
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Institut National De La Santé Et De La Recherche Médicale (INSERM) UMR-S 1136, Institut Pierre Louis D’épidémiologie Et De Santé Publique (IPLESP), Team EPAR, Paris, France
| | - Elisabeth Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Mònica Guxens
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Centre, Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Sanna Mustaniemi
- Department of Obstetrics and Gynecology, PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
| | - Stephanie J. London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, WashingtonDC, USA
| | | | - Marja Vääräsmäki
- Department of Obstetrics and Gynecology, PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
| | - Martine Vrijheid
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anette-G. Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum Rechts Der Isar, Munich-Neuherberg, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München, Munich-Neuherberg, Germany
| | - Isabella Annesi-Maesano
- Sorbonne Université, Institut Pierre Louis D’épidémiologie Et De Santé Publique (IPLESP), Paris, France
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Institut National De La Santé Et De La Recherche Médicale (INSERM) UMR-S 1136, Institut Pierre Louis D’épidémiologie Et De Santé Publique (IPLESP), Team EPAR, Paris, France
| | - Mariona Bustamante
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Australia
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum Rechts Der Isar, Munich-Neuherberg, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München, Munich-Neuherberg, Germany
| | - Allan C. Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eero Kajantie
- Department of Obstetrics and Gynecology, PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
| | - Deborah Lawlor
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Janine F. Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department for Genomics of Common Diseases, School of Medicine, Imperial College London, LondonUK
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