Identification of methylated genes in salivary gland adenoid cystic carcinoma xenografts using global demethylation and methylation microarray screening

Shizhang Ling, Eleni M. Rettig, Marietta Tan, Xiaofei Chang, Zhiming Wang, Mariana Brait, Justin A. Bishop, Elana J. Fertig, Michael Considine, Michael J. Wick, Patrick K. Ha

Research output: Contribution to journalArticle

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Abstract

Salivary gland adenoid cystic carcinoma (ACC) is a rare head and neck malignancy without molecular biomarkers that can be used to predict the chemotherapeutic response or prognosis of ACC. The regulation of gene expression of oncogenes and tumor suppressor genes (TSGs) through DNA promoter methylation may play a role in the carcinogenesis of ACC. To identify differentially methylated genes in ACC, a global demethylating agent, 5-aza-2'-deoxycytidine (5-AZA) was utilized to unmask putative TSG silencing in ACC xenograft models in mice. Fresh xenografts were passaged, implanted in triplicate in mice that were treated with 5-AZA daily for 28 days. These xenografts were then evaluated for genome-wide DNA methylation patterns using the Illumina Infinium HumanMethylation27 BeadChip array. Validation of the 32 candidate genes was performed by bisulfite sequencing (BS-seq) in a separate cohort of 6 ACC primary tumors and 6 normal control salivary gland tissues. Hypermethylation was identified in the HCN2 gene promoter in all 6 control tissues, but hypomethylation was found in all 6 ACC tumor tissues. Quantitative validation of HCN2 promoter methylation level in the region detected by BS-seq was performed in a larger cohort of primary tumors (n=32) confirming significant HCN2 hypomethylation in ACCs compared with normal samples (n=10; p=0.04). HCN2 immunohistochemical staining was performed on an ACC tissue microarray. HCN2 staining intensity and H-score, but not percentage of the positively stained cells, were significantly stronger in normal tissues than those of ACC tissues. With our novel screening and sequencing methods, we identified several gene candidates that were methylated. The most significant of these genes, HCN2, was actually hypomethylated in tumors. However, promoter methylation status does not appear to be a major determinant of HCN2 expression in normal and ACC tissues. HCN2 hypomethylation is a biomarker of ACC and may play an important role in the carcinogenesis of ACC.

Original languageEnglish (US)
Pages (from-to)225-234
Number of pages10
JournalInternational Journal of Oncology
Volume49
Issue number1
DOIs
StatePublished - Jul 1 2016

Fingerprint

Adenoid Cystic Carcinoma
Salivary Glands
Heterografts
Methylation
Genes
decitabine
DNA Methylation
Neoplasms
Tumor Suppressor Genes
Carcinogenesis
Biomarkers
Staining and Labeling
Gene Expression Regulation
Gene Silencing
Oncogenes
Neck

Keywords

  • Adenoid cystic carcinoma
  • Beadchip array
  • Bisulfite sequencing
  • DNA methylation
  • Hyperpolarization-activated cation channel 2
  • Methylation-specific PCR
  • Oncogene
  • Salivary gland

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Identification of methylated genes in salivary gland adenoid cystic carcinoma xenografts using global demethylation and methylation microarray screening. / Ling, Shizhang; Rettig, Eleni M.; Tan, Marietta; Chang, Xiaofei; Wang, Zhiming; Brait, Mariana; Bishop, Justin A.; Fertig, Elana J.; Considine, Michael; Wick, Michael J.; Ha, Patrick K.

In: International Journal of Oncology, Vol. 49, No. 1, 01.07.2016, p. 225-234.

Research output: Contribution to journalArticle

Ling, Shizhang ; Rettig, Eleni M. ; Tan, Marietta ; Chang, Xiaofei ; Wang, Zhiming ; Brait, Mariana ; Bishop, Justin A. ; Fertig, Elana J. ; Considine, Michael ; Wick, Michael J. ; Ha, Patrick K. / Identification of methylated genes in salivary gland adenoid cystic carcinoma xenografts using global demethylation and methylation microarray screening. In: International Journal of Oncology. 2016 ; Vol. 49, No. 1. pp. 225-234.
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abstract = "Salivary gland adenoid cystic carcinoma (ACC) is a rare head and neck malignancy without molecular biomarkers that can be used to predict the chemotherapeutic response or prognosis of ACC. The regulation of gene expression of oncogenes and tumor suppressor genes (TSGs) through DNA promoter methylation may play a role in the carcinogenesis of ACC. To identify differentially methylated genes in ACC, a global demethylating agent, 5-aza-2'-deoxycytidine (5-AZA) was utilized to unmask putative TSG silencing in ACC xenograft models in mice. Fresh xenografts were passaged, implanted in triplicate in mice that were treated with 5-AZA daily for 28 days. These xenografts were then evaluated for genome-wide DNA methylation patterns using the Illumina Infinium HumanMethylation27 BeadChip array. Validation of the 32 candidate genes was performed by bisulfite sequencing (BS-seq) in a separate cohort of 6 ACC primary tumors and 6 normal control salivary gland tissues. Hypermethylation was identified in the HCN2 gene promoter in all 6 control tissues, but hypomethylation was found in all 6 ACC tumor tissues. Quantitative validation of HCN2 promoter methylation level in the region detected by BS-seq was performed in a larger cohort of primary tumors (n=32) confirming significant HCN2 hypomethylation in ACCs compared with normal samples (n=10; p=0.04). HCN2 immunohistochemical staining was performed on an ACC tissue microarray. HCN2 staining intensity and H-score, but not percentage of the positively stained cells, were significantly stronger in normal tissues than those of ACC tissues. With our novel screening and sequencing methods, we identified several gene candidates that were methylated. The most significant of these genes, HCN2, was actually hypomethylated in tumors. However, promoter methylation status does not appear to be a major determinant of HCN2 expression in normal and ACC tissues. HCN2 hypomethylation is a biomarker of ACC and may play an important role in the carcinogenesis of ACC.",
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AU - Tan, Marietta

AU - Chang, Xiaofei

AU - Wang, Zhiming

AU - Brait, Mariana

AU - Bishop, Justin A.

AU - Fertig, Elana J.

AU - Considine, Michael

AU - Wick, Michael J.

AU - Ha, Patrick K.

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KW - Oncogene

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