Suprabasin Is Hypomethylated and Associated with Metastasis in Salivary Adenoid Cystic Carcinoma

Shao, Chunbo; Tan, Marietta; Bishop, Justin A.; Liu, Jia; Bai, Weiliang; Gaykalova, Daria A.; Ogawa, Takenori; Vikani, Ami R.; Agrawal, Yuri; Li, Ryan J.; Kim, Myoung Sook; Westra, William H.; Sidransky, David; Califano, Joseph A.; Ha, Patrick K.

doi:10.1371/journal.pone.0048582

Cited by 37 publications

(50 citation statements)

References 34 publications

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“…DNA was then purified using standard phenol-chloroform extraction and ethanol precipitation methods as previously described [31], [32]. DNA was resuspended in LoTE buffer (EDTA 2.5 mM and Tris-HCl 10 mM, pH 7.5).…”

Section: Methodsmentioning

confidence: 99%

Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma

et al. 2014

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Development of head and neck squamous cell carcinoma (HNSCC) is characterized by accumulation of mutations in several oncogenes and tumor suppressor genes. We have formerly described the mutation pattern of HNSCC and described NOTCH signaling pathway alterations. Given the complexity of the HNSCC, here we extend the previous study to understand the overall HNSCC mutation context and to discover additional genetic alterations. We performed high depth targeted exon sequencing of 51 highly actionable cancer-related genes with a high frequency of mutation across many cancer types, including head and neck. DNA from primary tumor tissues and matched normal tissues was analyzed for 37 HNSCC patients. We identified 26 non-synonymous or stop-gained mutations targeting 11 of 51 selected genes. These genes were mutated in 17 out of 37 (46%) studied HNSCC patients. Smokers harbored 3.2-fold more mutations than non-smokers. Importantly, TP53 was mutated in 30%, NOTCH1 in 8% and FGFR3 in 5% of HNSCC. HPV negative patients harbored 4-fold more TP53 mutations than HPV positive patients. These data confirm prior reports of the HNSCC mutational profile. Additionally, we detected mutations in two new genes, CEBPA and FES, which have not been previously reported in HNSCC. These data extend the spectrum of HNSCC mutations and define novel mutation targets in HNSCC carcinogenesis, especially for smokers and HNSCC without HPV infection.

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Section: Methodsmentioning

confidence: 99%

Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma

et al. 2014

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“…Although SBSN is reported to be upregulated in tumor endothelial cells (88), salivary adenoid cystic carcinoma (89) and in differentiating keratinocytes (90), there is little known about the expression and role of CALML5 and KRT1 in tumor pathophysiology, and their further investigation is warranted.…”

Section: Discussionmentioning

confidence: 99%

In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

Azimi

Kaufman

Ali

et al. 2016

CGP

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“…The presence of cancer in each tumor tissue sample was histologically confirmed in slides taken before and after sample harvesting. After four rounds of proteinase K exposure during two overnight periods, phenol/chloroform extraction and ethanol precipitation was performed as previously described 24 . DNA from margin imprints were immediately eluted, digested and extracted by the same procedure.…”

Section: Methodsmentioning

confidence: 99%

Correlation of gene methylation in surgical margin imprints with locoregional recurrence in head and neck squamous cell carcinoma

Hayashi

Roh

et al. 2015

Cancer

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Background Securing negative surgical margins is a critical goal for head and neck surgery. Local recurrence occurs even in some cases with histologically negative surgical margins. Minimal residual tumor cells may lead to locoregional recurrence despite clear histologic margins reported at the time of resection of head and neck squamous cell carcinoma (HNSCC). In order to identify subclinical residual disease, we analyzed deep margin imprint samples collected on one layer nitrocellulose sheets. Methods Bisulfite treated DNA from 73 eligible cases was amplified by quantitative methylation-specific polymerase chain reaction (QMSP) targeting 6 genes (DCC, EDNRB, HOXA9, KIF1A, NID2, NR2B). QMSP values were dichotomized as positive or negative. Associations between the QMSP status of deep margin samples and clinical outcomes were evaluated. Results Two gene methylation combinations among DCC, EDNRB and HOXA9 were associated with decreased locoregional recurrence-free survival (LRFS), recurrence-free survival (RFS) and overall survival (OS). The methylated gene combination EDNRB and HOXA9 in margin imprints was the most powerful predictor of poor LRFS (HR=3.31, 95% CI=1.30-8.46; P=0.012), independent of standard histological factors. In addition, methylation of EDNRB/HOXA9 showed a trend toward reduced RFS (HR=2.74, 95% CI=0.90-8.33; P=0.075) and OS (HR=5.78, 95% CI=0.75-44.7; P=0.093) by multivariable analysis. Conclusion A panel of gene methylation targets in deep surgical margin imprints provides a potential predictive marker of post-operative locoregional recurrence. Intra-operative use of molecular margin-imprint analysis might assist surgeons to obtain rigorously negative surgical margins and improve the outcome of head and neck surgery.

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Suprabasin Is Hypomethylated and Associated with Metastasis in Salivary Adenoid Cystic Carcinoma

Cited by 37 publications

References 34 publications

Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma

Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma

In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

Correlation of gene methylation in surgical margin imprints with locoregional recurrence in head and neck squamous cell carcinoma

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