An integrative analysis of genome‐wide methylation and expression in ameloblastoma: A pilot study
Objective DNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally aggressive with a high level of recurrence. A delay in treatment can lead to severe facial disfigurement. To the best of our knowledge, this i...
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| Published in | Oral diseases Vol. 27; no. 6; pp. 1455 - 1467 |
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| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Denmark
Wiley Subscription Services, Inc
01.09.2021
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1354-523X 1601-0825 1601-0825 |
| DOI | 10.1111/odi.13666 |
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| Abstract | Objective
DNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally aggressive with a high level of recurrence. A delay in treatment can lead to severe facial disfigurement. To the best of our knowledge, this is the first integrated analysis of DNA methylation and gene expression in ameloblastoma with the aim to identify genes that may be regulated by DNA methylation.
Materials and Methods
We used an Infinium MethylationEPIC array to measure genome‐wide methylation and the Illumina HiSeq platform to obtain gene expression data in ameloblastoma tissues from five patients and dental follicles from three healthy subjects. An integration analysis was performed using City of Hope CpG Island Analysis Pipeline software.
Results
We identified 25,255 differentially methylated CpG sites and 17 differentially methylated CpG islands; six of the islands were negatively correlated with the expression of BAIAP2, DUSP6, FGFR2, FOXF2, NID2, and PAK6. Pyrosequencing and immunostaining techniques were further used to validate FGFR2, NID2, and PAK6.
Conclusions
This analysis identifies a group of novel genes that may be regulated by DNA methylation and will possibly lead to new insights into the pathology and invasion mechanism of ameloblastoma. |
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| AbstractList | Objective
DNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally aggressive with a high level of recurrence. A delay in treatment can lead to severe facial disfigurement. To the best of our knowledge, this is the first integrated analysis of DNA methylation and gene expression in ameloblastoma with the aim to identify genes that may be regulated by DNA methylation.
Materials and Methods
We used an Infinium MethylationEPIC array to measure genome‐wide methylation and the Illumina HiSeq platform to obtain gene expression data in ameloblastoma tissues from five patients and dental follicles from three healthy subjects. An integration analysis was performed using City of Hope CpG Island Analysis Pipeline software.
Results
We identified 25,255 differentially methylated CpG sites and 17 differentially methylated CpG islands; six of the islands were negatively correlated with the expression of BAIAP2, DUSP6, FGFR2, FOXF2, NID2, and PAK6. Pyrosequencing and immunostaining techniques were further used to validate FGFR2, NID2, and PAK6.
Conclusions
This analysis identifies a group of novel genes that may be regulated by DNA methylation and will possibly lead to new insights into the pathology and invasion mechanism of ameloblastoma. DNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally aggressive with a high level of recurrence. A delay in treatment can lead to severe facial disfigurement. To the best of our knowledge, this is the first integrated analysis of DNA methylation and gene expression in ameloblastoma with the aim to identify genes that may be regulated by DNA methylation.OBJECTIVEDNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally aggressive with a high level of recurrence. A delay in treatment can lead to severe facial disfigurement. To the best of our knowledge, this is the first integrated analysis of DNA methylation and gene expression in ameloblastoma with the aim to identify genes that may be regulated by DNA methylation.We used an Infinium MethylationEPIC array to measure genome-wide methylation and the Illumina HiSeq platform to obtain gene expression data in ameloblastoma tissues from five patients and dental follicles from three healthy subjects. An integration analysis was performed using City of Hope CpG Island Analysis Pipeline software.MATERIALS AND METHODSWe used an Infinium MethylationEPIC array to measure genome-wide methylation and the Illumina HiSeq platform to obtain gene expression data in ameloblastoma tissues from five patients and dental follicles from three healthy subjects. An integration analysis was performed using City of Hope CpG Island Analysis Pipeline software.We identified 25,255 differentially methylated CpG sites and 17 differentially methylated CpG islands; six of the islands were negatively correlated with the expression of BAIAP2, DUSP6, FGFR2, FOXF2, NID2, and PAK6. Pyrosequencing and immunostaining techniques were further used to validate FGFR2, NID2, and PAK6.RESULTSWe identified 25,255 differentially methylated CpG sites and 17 differentially methylated CpG islands; six of the islands were negatively correlated with the expression of BAIAP2, DUSP6, FGFR2, FOXF2, NID2, and PAK6. Pyrosequencing and immunostaining techniques were further used to validate FGFR2, NID2, and PAK6.This analysis identifies a group of novel genes that may be regulated by DNA methylation and will possibly lead to new insights into the pathology and invasion mechanism of ameloblastoma.CONCLUSIONSThis analysis identifies a group of novel genes that may be regulated by DNA methylation and will possibly lead to new insights into the pathology and invasion mechanism of ameloblastoma. ObjectiveDNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally aggressive with a high level of recurrence. A delay in treatment can lead to severe facial disfigurement. To the best of our knowledge, this is the first integrated analysis of DNA methylation and gene expression in ameloblastoma with the aim to identify genes that may be regulated by DNA methylation.Materials and MethodsWe used an Infinium MethylationEPIC array to measure genome‐wide methylation and the Illumina HiSeq platform to obtain gene expression data in ameloblastoma tissues from five patients and dental follicles from three healthy subjects. An integration analysis was performed using City of Hope CpG Island Analysis Pipeline software.ResultsWe identified 25,255 differentially methylated CpG sites and 17 differentially methylated CpG islands; six of the islands were negatively correlated with the expression of BAIAP2, DUSP6, FGFR2, FOXF2, NID2, and PAK6. Pyrosequencing and immunostaining techniques were further used to validate FGFR2, NID2, and PAK6.ConclusionsThis analysis identifies a group of novel genes that may be regulated by DNA methylation and will possibly lead to new insights into the pathology and invasion mechanism of ameloblastoma. DNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally aggressive with a high level of recurrence. A delay in treatment can lead to severe facial disfigurement. To the best of our knowledge, this is the first integrated analysis of DNA methylation and gene expression in ameloblastoma with the aim to identify genes that may be regulated by DNA methylation. We used an Infinium MethylationEPIC array to measure genome-wide methylation and the Illumina HiSeq platform to obtain gene expression data in ameloblastoma tissues from five patients and dental follicles from three healthy subjects. An integration analysis was performed using City of Hope CpG Island Analysis Pipeline software. We identified 25,255 differentially methylated CpG sites and 17 differentially methylated CpG islands; six of the islands were negatively correlated with the expression of BAIAP2, DUSP6, FGFR2, FOXF2, NID2, and PAK6. Pyrosequencing and immunostaining techniques were further used to validate FGFR2, NID2, and PAK6. This analysis identifies a group of novel genes that may be regulated by DNA methylation and will possibly lead to new insights into the pathology and invasion mechanism of ameloblastoma. |
| Author | Chaiwongkot, Arkom Sanguansin, Sirima Kitkumthorn, Nakarin Kengkarn, Sudaporn Klongnoi, Boworn Pongpanich, Monnat |
| Author_xml | – sequence: 1 givenname: Monnat surname: Pongpanich fullname: Pongpanich, Monnat organization: Chulalongkorn University – sequence: 2 givenname: Sirima surname: Sanguansin fullname: Sanguansin, Sirima organization: Mahidol University – sequence: 3 givenname: Sudaporn surname: Kengkarn fullname: Kengkarn, Sudaporn organization: Rangsit University – sequence: 4 givenname: Arkom surname: Chaiwongkot fullname: Chaiwongkot, Arkom organization: Chulalongkorn University – sequence: 5 givenname: Boworn surname: Klongnoi fullname: Klongnoi, Boworn organization: Mahidol University – sequence: 6 givenname: Nakarin orcidid: 0000-0003-0616-6039 surname: Kitkumthorn fullname: Kitkumthorn, Nakarin email: Nakarinkit@gmail.com organization: Mahidol University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33022811$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_1016_j_oraloncology_2023_106651 crossref_primary_10_1177_00220345241282256 crossref_primary_10_1007_s12017_024_08795_0 crossref_primary_10_1097_PAS_0000000000002293 crossref_primary_10_1016_j_modpat_2025_100717 |
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DNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally... DNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally aggressive... ObjectiveDNA methylation regulates the expression of various genes involved in tumorigenesis. Ameloblastoma is a benign odontogenic jaw tumor. It is locally... |
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| SubjectTerms | Ameloblastoma Ameloblastoma - genetics CpG Islands Deoxyribonucleic acid DNA DNA Methylation Fibroblast growth factor receptor 2 Follicles Gene expression Genomes Humans integrative analysis Jaw Neoplasm Recurrence, Local Pilot Projects Tumorigenesis |
| Title | An integrative analysis of genome‐wide methylation and expression in ameloblastoma: A pilot study |
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