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1 - Vol 27, No.1, 2024
- doi:
- Editorial
- Prof Chuan-bin Guo
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- Chin J Dent Res 2024;27(1):29–38; doi:10.3290/j.cjdr.b5128515
- Review on the Role of IRF6 in the Pathogenesis of Non-syndromic Orofacial Clefts
- Si Di ZHANG, Yue YOU, Mei Lin YAO, Bing SHI, Zhong Lin JIA
- Non-syndromic orofacial clefts (NSOCs) are the most common craniofacial malformation. In the complex aetiology and pathogenesis of NSOCs, genetic factors play a crucial role and IRF6, located at chromosome 1q32.2, is the best documented NSOC susceptibility gene. IRF6 is a key factor in oral maxillofacial development and known to contribute the most in NSOCs. It is essential to conduct a complete review of the existing results on IRF6 to further understand its role in the pathogenesis of NSOCs. Thus, the present authors summarised the research progress on the mechanism of IRF6 in NSOCs from both genetic and functional perspectives in this review.
  
  Keywords: IRF6, genetics, non-syndromic orofacial cleft (NSOC)
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- Chin J Dent Res 2024;27(1):83–88; doi:10.3290/j.cjdr.b5128601
- Novel PTCH1 Mutation Causes Gorlin-Goltz Syndrome
- Hai Tang YUE, Hai Yan CAO, Miao HE
- Objective: To analyse the aetiology and pathogenesis of Gorlin-Goltz syndrome (GS; also known as nevoid basal cell carcinoma syndrome [NBCCS] or basal cell nevus syndrome [BCNS]) in a Chinese family.
  Methods: Whole-exome sequencing (WES) was performed on genomic DNA samples from the subjects in a family, followed by the investigation of pathogenesis via bioinformatic approaches and conformational analysis.
  Results: A novel heterozygous non-frameshift deletion patched 1 (PTCH1) [NM_000264: c.3512_3526del (p.1171_1176del)] was identified by WES and further validated by Sanger sequencing. Bioinformatic and conformational analysis showed that the mutation caused altered PTCH1 protein structure, which may be related to functional abnormalities.
  Conclusion: This study expands the mutation spectrum of PTCH1 in GS and facilitates the early diagnosis and screening of GS. PTCH1 [c.3512_3526del (p.1171_1176del)] may cause structural abnormalities and functional disabilities, leading to GS in families.
  
  Keywords: Gorlin-Goltz syndrome, mutation, nevoid basal cell carcinoma syndrome, PTCH1, whole-exome sequencing
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- Chin J Dent Res 2024;27(1):47–52; doi:10.3290/j.cjdr.b5128655
- Distinctive Craniofacial and Oral Anomalies in MN1 C-terminal Truncation Syndrome
- Jing Jia YU , Qiu Yi WU, Qiu Chi RAN, Ying Ya ZHAO, Lin Nan YU, Qing Xin CAO, Xi Meng CHEN, Wen Yang LI, Zhen Jin ZHAO
- MN1 C-terminal truncation (MCTT) syndrome was first reported in 2020 and only 28 patients have been recorded to date. Since MCTT syndrome is a newly defined and rare syndrome with many clinical features, the present study reviewed the manifestations and management of oral and dental anomalies. Gene variants of MCTT syndrome and their positive phenotypes were summarised. The phenotypes of variants in two exons differed from each other mainly in the craniomaxillofacial region, including brain MRI abnormalities and palatal morphology. Pathogenic mechanisms, especially in craniofacial and oral anomalies, were discussed. Appropriate treatments in the stomatology and respiratory departments could improve the symptoms of MCTT syndrome. The different sites of MN1 gene variants may influence the clinical symptoms and there may be racial differences in MCTT syndrome. We recommend oral and pulmonary evaluations for the multidisciplinary treatment of MCTT syndrome.
  
  Keywords: craniofacial and oral anomalies, MN1 C-terminal truncation syndrome, MN1 gene variant.
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- Chin J Dent Res 2024;27(1):101–109; doi:10.3290/j.cjdr.b5128671
- Hub Genes, Possible Pathways and Predicted Drugs in Hereditary Gingival Fibromatosis by Bioinformatics Analysis
- Rong Xia YANG, Fan SHI, Shu Ning DU, Xin Yu LUO, Wan Qing WANG, Zhi Lu YUAN, Dong CHEN
- Objective: To explore potential pathogenic processes and possible treatments using unbiased and reliable bioinformatic tools.
  Methods: Gene expression profiles of control and hepatocyte growth factor (HGF) samples were downloaded from CNP0000995. Analysis of differentially expressed genes (DEGs) was conducted using R software (version 4.2.1, R Foundation, Vienna, Austria). Functional enrichment analyses were performed using the Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) databases, then the proteinprotein interaction (PPI) network was constructed to screen the top 10 hub genes. Finally, five genes related to cell junctions were selected to build gene-miRNA interactions and predict small-molecule drugs.
  Results: A total of 342 downregulated genes and 188 upregulated genes were detected. Candidate pathways include the extracellular matrix (ECM) receptor interaction pathway, the TGF-β signalling pathway and the cell adhesion molecule (CAM) pathway, which were discovered through KEGG and GSEA enrichment studies. GO analyses revealed that these DEGs were significantly enriched in cell adhesion, the adherens junction and focal adhesion. Five hub genes (CDH1, SNAP25, RAC2, APOE and ITGB4) associated with cell adhesion were identified through PPI analysis. Finally, the gene-miRNA regulatory network identified three target miRNAs: hsa-miR-7110-5p, hsa-miR-149-3p and hsa-miR-1207-5p. Based on the gene expression profile, the small-molecule drugs zebularine, ecuronium and prostratin were selected for their demonstrated binding activity when docked with the mentioned molecules.
  Conclusion: This study offered some novel insights into molecular pathways and identified five hub genes associated with cell adhesion. Based on these hub genes, three potential therapeutic miRNAs and small-molecule drugs were predicted, which are expected to provide guidance for the treatment of patients with HGF.
  
  Keywords: CDH1, cell-cell junction, hereditary gingival fibromatosis, MiRNA, small-molecule drugs
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- Chin J Dent Res 2024;27(1):89–99; doi:10.3290/j.cjdr.b5128703
- Clinical and Genetic Analysis of Multiple Idiopathic Cervical Root Resorption
- Yu Meng WANG, Wen Yan RUAN, Dan Dan CHI, Xiao Hong DUAN
- Objective: To explore the genetic background and clinical phenotypes of multiple idiopathic cervical root resorption (MICRR) in a Chinese family.
  Methods: The proband and his three family members were clinically examined and had radiographs taken with a radiovisiography (RVG) system and CBCT to define the diagnosis of MICRR. Genomic DNA (gDNA) was extracted from peripheral blood samples of the patient, his father, mother and younger sister for whole exome sequencing (WES). The pathogenicity of rare variants with minor allele frequency (MAF) less than 0.005 were analysed following possible inheritance patterns, predicted results from 12 software programs, the American College of Medical Genetics (ACMG) 2015 criteria, and information from ClinVar, OMIM and HGMD databases as well as gene function.
  Results: The proband presented the typical MICRR phenotypes such as thin cervical pulp wall and apple core–like lesions in radiographs. Following the recessive inheritance pattern, WES analysis identified SHROOM2, SYTL5, MAGED1 and FLNA with a higher chance of causing MICRR. Four genes with compound heterozygous variants and another 27 genes with de novo variants either in autosomal-dominant or autosomal-recessive pattern were also found to have the potential pathogenicity.
  Conclusion: A total of 35 novel potential pathogenic genes were found to be associated with MICRR from a Chinese family through WES. The new genetic background of MICRR may be helpful for clinical and molecular diagnosis.
  
  Keywords: de novo variants, multiple idiopathic cervical root resorption, pathogenic variant filtering, whole-exome sequencing
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- Chin J Dent Res 2024;27(1):39–46; doi:10.3290/j.cjdr.b5136729
- Characteristic and Import Mechanism of Protein Nuclear Translocation
- Zi Yan SUN, Zhi Peng FAN
- Coordination and information exchange among the various organelles ensure the precise and orderly functioning of eukaryotic cells. Interaction between the cytoplasm and nucleoplasm is crucial for many physiological processes. Macromolecular protein transport into the nucleus requires assistance from the nuclear transport system. These proteins typically contain a nuclear localisation sequence that guides them to enter the nucleus. Understanding the mechanism of nuclear import of macromolecular proteins is important for comprehending cellular processes. Investigation of disease-related alterations can facilitate the development of novel therapeutic strategies and provide additional evidence for clinical trials. This review provides an overview of the proteins involved in nuclear transport and the mechanisms underlying macromolecular
  protein transport.
  
  Keywords: karyopherin, nuclear import, nuclear localisation sequence, nuclear pore complex, nucleocytoplasmic transport
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- Chin J Dent Res 2024;27(1):75–82; doi:10.3290/j.cjdr.b5136733
- Knowledge Mapping of Cowden Syndrome: a Bibliometric Analysis
- Qiao PENG, Ning DUAN, Xiang WANG, Wen Mei WANG
- Objective: To provide a comprehensive overview of the current knowledge structure and research hotspots of Cowden syndrome via bibliometrics.
  Methods: The articles and reviews related to Cowden syndrome were included from the Web of Science Core Collection (WoSCC) database. VOSviewer, CiteSpace and GraphPad Prism were used to conduct the bibliometric analysis.
  Results: The number of papers focusing on Cowden syndrome was relatively low initially but increased rapidly from 1997 to 1999, and then maintained small-scale fluctuation. A total of 1,557 papers from 65 countries/regions and 1,762 institutions were identified. The USA was the most productive country, and Ohio State University was the most productive institution. In terms of the number of publications, Human Molecular Genetics ranked first, and Cancer Research was the most frequently cited journal. Eng was the most productive author, and Liaw was the most co-cited author. Phosphatase and tensin homologue (PTEN), germline mutations, gene, cancer, mutations, tumour suppressor gene and breast were high-frequency key words in this field.
  Conclusion: This study was the first comprehensive bibliometric overview of the current state and development of Cowden disease. The mutation of PTEN and associated cancers, especially breast, thyroid and endometrial cancer, could be the focus of future research in this field.
  
  Keywords: bibliometric analysis, Cowden syndrome, germline mutation, PTEN
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- Chin J Dent Res 2024;27(1):65–73; doi:10.3290/j.cjdr.b5136745
- Integrative Multi-omics Analysis Identifies Genetic Variants Contributing to Non-syndromic Cleft Lip with or without Cleft Palate
- Shu LOU, Jing YANG, Gui Rong ZHU, Dan Dan LI, Lan MA, Lin WANG, Yong Chu PAN
- Objective: To provide novel insights into the aetiology of non-syndromic cleft lip with or without cleft palate (NSCL/P) by integrating multi-omics data and exploring susceptibility genes associated with NSCL/P.
  Methods: A two-stage genome-wide association study (GWAS) of NSCL/P was performed, involving a total of 1,069 cases and 1,724 controls. Using promoter capture Hi-C (pCHi-C) datasets in human embryonic stem cells (hESC) and chromatin immunoprecipitation sequencing (ChIP-seq) in craniofacial tissues, we filtered out single nucleotide polymorphisms (SNPs) with active cis-regulation and their target genes. Additionally, we employed expression quantitative trait loci (eQTL) analysis to identify candidate genes.
  Results: Thirteen SNPs were identified as cis-regulation units associated with the risk of NSCL/P. Five of these were proven to be active in chromatin states in early human craniofacial development (rs7218002: odds ratio [OR] 1.50, P = 8.14E-08; rs835367: OR 0.78, P = 3.48E-05; rs77022994: OR 0.55, P = 1.05E-04; rs961470: OR 0.73, P = 1.38E-04; rs17314727: OR 0.73, P = 1.85E-04). Additionally, pCHi-C and eQTL analysis prioritised three candidate genes (rs7218002: NTN1, rs835367: FGGY, LINC01135). NTN1 and FGGY were expressed in mouse orofacial development. Deficiencies in NTN1, FGGY and LINC01135 were associated with cleft palate and cleft lip, abnormal facial shape and bifid uvula, and abnormality of the face, respectively.
  Conclusion: Our study identified five SNPs (rs7218002, rs835367, rs77022994, rs961470 and rs17314727) and three susceptibility genes (NTN1, FGGY and LINC01135) associated with NSCL/P. These findings contribute to a better understanding of the genetic factors involved.
  
  Keywords: ChIP-seq, expression quantitative trait loci, non-syndromic cleft lip, pCHi-C
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- Chin J Dent Res 2024;27(1):53–63; doi:10.3290/j.cjdr.b5136761
- FAM20A-Associated Amelogenesis Imperfecta: Gene Variants with Functional Verification and Histological Features
- Jia Nan DING, Miao YU, Hao Chen LIU, Kai SUN, Jing WANG, Xiang Liang XU,Yang LIU, Dong HAN
- Objective: To investigate FAM20A gene variants and histological features of amelogenesis imperfecta and to further explore the functional impact of these variants.
  Methods: Whole-exome sequencing (WES) and Sanger sequencing were used to identify pathogenic gene variants in three Chinese families with amelogenesis imperfecta. Bioinformatics analysis, in vitro histological examinations and experiments were conducted to study the functional impact of gene variants, and the histological features of enamel, keratinised oral mucosa and dental follicle.
  Results: The authors identified two nonsense variants c. 406C > T (p.Arg136*) and c.826C > T (p.Arg176*) in a compound heterozygous state in family 1, two novel frameshift variants c.936dupC (p.Val313Argfs*67) and c.1483dupC (p.Leu495Profs*44) in a compound heterozygous state in family 2, and a novel homozygous frameshift variant c.530_531insGGTC (p.Ser178Valfs*21) in family 3. The enamel structure was abnormal, and psammomatoid calcifications were identified in both the gingival mucosa and dental follicle. The bioinformatics and subcellular localisation analyses indicated these variants to be pathogenic. The secondary and tertiary structure analysis speculated that these five variants would cause structural damage to FAM20A protein.
  Conclusion: The present results broaden the variant spectrum and clinical and histological findings of diseases associated with FAM20A, and provide useful information for future genetic counselling and functional investigation.
  
  Keywords: amelogenesis imperfecta, FAM20A, frameshift variants, mutations, nonsense variants
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