Molecular biology and immunology of head and neck cancer

In recent years, our knowledge and understanding of head and neck squamous cell carcinoma (HNSCC) has expanded dramatically. New high-throughput sequencing technologies have accelerated these discoveries since the first reports of whole-exome sequencing of HNSCC tumors in 2011. In addition, the discovery of human papillomavirus in relationship with oropharyngeal squamous cell carcinoma has shifted our molecular understanding of the disease. New investigation into the role of immune evasion in HNSCC has also led to potential novel therapies based on immune-specific systemic therapies.

NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma

Using high-throughput analyses and the TRANSFAC database, we characterized TF signatures of head and neck squamous cell carcinoma (HNSCC) subgroups by inferential analysis of target gene expression, correcting for the effects of DNA methylation and copy number. Using this discovery pipeline, we determined that human papillomavirus-related (HPV+) and HPV- HNSCC differed significantly based on the activity levels of key TFs including AP1, STATs, NF-κB and p53. Immunohistochemical analysis confirmed that HPV- HNSCC is characterized by co-activated STAT3 and NF-κB pathways and functional studies demonstrate that this phenotype can be effectively targeted with combined anti-NF-κB and anti-STAT therapies. These discoveries correlate strongly with previous findings connecting STATs, NF-κB and AP1 in HNSCC. We identified five top-scoring pair biomarkers from STATs, NF-κB and AP1 pathways that distinguish HPV+ from HPV- HNSCC based on TF activity and validated these biomarkers on TCGA and on independent validation cohorts. We conclude that a novel approach to TF pathway analysis can provide insight into therapeutic targeting of patient subgroup for heterogeneous disease such as HNSCC.

Correcting transcription factor gene sets for copy number and promoter methylation variations

Gene set analysis provides a method to generate statistical inferences across sets of linked genes, primarily using high-throughput expression data. Common gene sets include biological pathways, operons, and targets of transcriptional regulators. In higher eukaryotes, especially when dealing with diseases with strong genetic and epigenetic components such as cancer, copy number loss and gene silencing through promoter methylation can eliminate the possibility that a gene is transcribed. This, in turn, can adversely affect the estimation of transcription factor or pathway activity from a set of target genes, as some of the targets may not be responsive to transcriptional regulation. Here we introduce a simple filtering approach that removes genes from consideration if they show copy number loss or promoter methylation, and demonstrate the improvement in inference of transcription factor activity in a simulated dataset based on the background expression observed in normal head and neck tissue.

Surgical salvage improves overall survival for patients with HPV-positive and HPV-negative recurrent locoregional and distant metastatic oropharyngeal cancer

BACKGROUND

Human papillomavirus (HPV) tumor status and surgical salvage are associated with improved prognosis for patients with recurrent oropharyngeal squamous cell carcinoma (OPSCC). Current data regarding types of surgery and the impact of surgery for patients with distant metastatic disease are limited.

METHODS

A retrospective analysis of patients with recurrent OPSCC from 2 institutions between 2000 and 2012 was performed. p16 immunohistochemistry and/or in situ hybridization, as clinically available, were used to determine HPV tumor status. Clinical characteristics, distribution of recurrence site, and treatment modalities were compared by HPV tumor status. Overall survival (OS) was examined using Kaplan-Meier and Cox proportional hazards methods.

RESULTS

The current study included 108 patients with 65 locoregional and 43 distant metastatic first recurrences. The majority of patients were HPV-positive (80 patients). HPV-positive tumor status was associated with longer time to disease recurrence (P<.01). Anatomic site distribution of disease recurrences did not differ by HPV tumor status. HPV-positive tumor status (adjusted HR [aHR], 0.23; 95% confidence interval [95% CI], 0.09-0.58 [P = .002]), longer time to disease recurrence (≥ 1 year; aHR, 0.36; 95% CI, 0.18-0.74 [P = .006]), and surgical salvage (aHR, 0.26; 95% CI, 0.12-0.61 [P = .002]) were found to be independently associated with OS after disease recurrence. Surgical salvage was independently associated with improved OS compared with nonsurgical treatment among patients with both locoregional (aHR, 0.15; 95% CI, 0.04-0.56 [P = .005]) and distant (aHR, 0.19; 95% CI, 0.05-0.75 [P = .018]) metastatic disease recurrences.

CONCLUSIONS

Surgical salvage was found to be associated with improved OS for patients with recurrent locoregional and distant metastatic OPSCC, independent of HPV tumor status. Further prospective data are needed to confirm the role of surgical salvage for distant metastases.

Sequencing the head and neck cancer genome: implications for therapy

Head and neck squamous cell carcinoma (HNSCC) is a disease with significant morbidity and mortality. The advancement of next-generation sequencing technologies now enables the landscape of genetic alterations in HNSCCs to be deciphered. In this review, we describe the mutation spectrum discovered in HNSCCs, especially human papilloma virus-associated and/or tobacco smoke exposure-associated HNSCCs. We also describe related research from two independent investigators and from the Cancer Genome Atlas. Emphasis is placed on the therapeutic implications of genes frequently altered in HNSCCs (i.e., TP53, PIK3CA, and NOTCH1) and their corresponding pathways, with a particular focus on recent findings of Notch signaling pathway activation in HNSCC. We also discuss the application of integrated genomic pathway-based analysis for precision cancer therapy in HNSCC.

Evaluation of prophylaxis treatment of Candida in alaryngeal patients with tracheoesophageal voice prostheses

OBJECTIVES/HYPOTHESIS

The objective of this study was to evaluate the effectiveness of nystatin and Biotène(®) mouthwash Oral Rinse for controlling Candida in total laryngectomy (TL) patients with a tracheosophageal voice prosthesis (TEP) because Biotène(®) mouthwash Oral Rinse is a less costly alternative to nystatin and requires less adherence time.

STUDY DESIGN

Randomized, unblinded, crossover trial.

METHODS

Twenty-one TL patients were randomized to receive nystatin followed by Biotène(®) mouthwash Oral Rinse, or the reverse order, after a basic oral-care phase (i.e., brushing teeth, cleaning dentures). A Provox(®) 2, 22.5 French TEP, which is an indwelling silicone voice prosthesis, was placed at the beginning of each phase. Patients were provided with oral care instructions at randomization and medication-specific instructions with each treatment's initiation. TEPs were processed and evaluated for Candida growth as colony-forming units (CFUs). Wilcoxon signed-rank tests were used for comparisons between treatments.

RESULTS

Fifteen patients were available for comparisons of Candida counts (6 received nystatin; 9 received Biotène(®) mouthwash first). Overall, the median log10 (CFUs) remained high regardless of treatment (no medication: 8.9; nystatin: 8.7; Biotène(®) mouthwash: 8.4). However, the median counts for both nystatin and Biotène(®) mouthwash Oral Rinse were lower than those for no medication (difference [Δ]:-0.9 and -0.3, respectively), although only nystatin was significantly lower (P = 0.02). There was no significant difference between the two treatments (P = 0.22). Overall, median medication-adherence was high (97%), and Biotène(®) mouthwash adherence was significantly higher than that of nystatin (Δ: 7.6%; P = 0.03).

CONCLUSION

Nystatin and Biotène(®) mouthwash Oral Rinse had similar CFU levels, with nystatin showing a significant improvement over usual oral care. Biotène(®) mouthwash is a less costly alternative to nystatin, with a less complex treatment protocol that might make it preferable to patients and clinicians.

LEVEL OF EVIDENCE

1b

Saliva and plasma quantitative polymerase chain reaction-based detection and surveillance of human papillomavirus-related head and neck cancer

IMPORTANCE

Human papillomavirus type 16 (HPV-16) is a major causative factor in oropharyngeal squamous cell carcinoma (OPSCC). The detection of primary OPSCC is often delayed owing to the challenging anatomy of the oropharynx.

OBJECTIVE

To investigate the feasibility of HPV-16 DNA detection in pretreatment and posttreatment plasma and saliva and its potential role as a marker of prognosis.

DESIGN, SETTING, AND PARTICIPANTS

This is a retrospective analysis of a prospectively collected cohort. Among a cohort of patients with oropharyngeal and unknown primary squamous cell carcinoma with known HPV-16 tumor status from the Johns Hopkins Medical Institutions and Greater Baltimore Medical Center (from 1999 through 2010), 93 patients were identified with a complete set of pretreatment and posttreatment plasma or saliva samples, of which 81 patients had HPV-16-positive tumors and 12 patients had HPV-16-negative tumors. Real-time quantitative polymerase chain reaction was used to detect HPV-16 E6 and E7 DNA in saliva and plasma samples.

MAIN OUTCOMES AND MEASURES

Main outcomes included sensitivity, specificity, negative predictive value of combined saliva and plasma pretreatment HPV-16 DNA status for detecting tumor HPV-16 status, as well as the association of posttreatment HPV DNA status with clinical outcomes, including recurrence-free survival and overall survival.

RESULTS

The median follow-up time was 49 months (range, 0.9-181.0 months). The sensitivity, specificity, negative predictive value, and positive predictive value of combined saliva and plasma pretreatment HPV-16 DNA status for detecting tumor HPV-16 status were 76%, 100%, 42%, and 100%, respectively. The sensitivities of pretreatment saliva or plasma alone were 52.8% and 67.3%, respectively. In a multivariable analysis, positive posttreatment saliva HPV status was associated with higher risk of recurrence (hazard ratio [HR], 10.7; 95% CI, 2.36-48.50) (P = .002). Overall survival was reduced among those with posttreatment HPV-positive status in saliva (HR, 25.9; 95% CI, 3.23-208.00) (P = .002) and those with HPV-positive status in either saliva or plasma but not among patients with HPV-positive status in plasma alone. The combined saliva and plasma posttreatment HPV-16 DNA status was 90.7% specific and 69.5% sensitive in predicting recurrence within 3 years.

CONCLUSIONS AND RELEVANCE

Using a combination of pretreatment plasma and saliva can increase the sensitivity of pretreatment HPV-16 status as a tool for screening patients with HPV-16-positive OPSCC. In addition, analysis of HPV-16 DNA in saliva and plasma after primary treatment may allow for early detection of recurrence in patients with HPV-16-positive OPSCC.

Abstract 1384: Promoter methylation of tumor suppressor genes in convalescent saliva samples from patients with head and neck squamous cell carcinoma

Purpose: Silencing of tumor suppressor genes (TSGs) plays an important role in head and neck carcinogenesis. Methylation of CpG islands in the promoter regions of genes acts as a significant mechanism of epigenetic gene silencing. In this study, we assessed the feasibility of epigenetic alterations in TSGs in post-treatment DNA shed from the oral mucosa as a prognostic marker for persistent/recurrent head and neck cancer. A panel of four genes (KIF1A, EDNRB, p16, DCC) was evaluated in this study.

Experimental Design: Hypermethylation of the promoter regions was investigated by bisulfite modification and quantitative methylation-specific PCR (Q-MSP) which provides more objective and rapid estimation of gene methylation status. Fresh tumor samples and pre- and post-treatment salivary rinses were collected from 83 patients with HNSCC. Post-treatment saliva samples were collected once in every 3 months. In addition, 46 normal saliva and 16 normal mucosal samples from healthy individuals were obtained. Then we evaluated the correlation of the results with the clinical parameters.

Results: KIF1A, EDNRB, p16 and DCC genes were methylated in 94%, 95%, 37% and 84% of primary HNSCC tissues, respectively and were only methylated in 2%, 6.8%, 5% and 10% of the salivary rinses from normal subjects. In addition, KIF1A, EDNRB, p16 and DCC were methylated in 35%, 69%, 8.4% and 38.6% of pre-treatment salivary rinses from HNSCC patients, respectively. We evaluated whether methylation levels of these genes in the post treatment saliva may predict the recurrence/prognosis or the chance of cure after treatment. Our data indicate that these genes may be potential biomarkers for HNSCC detection and follow up. Sixteen of 83 patients had recurrent tumors and KIF1A+EDNRB+p16+DCC methylation was observed in 37.5% of the patients in this group. The three gene panel (KIF1A, EDNRB and DCC) was also observed in 37.5% of the recurrent group and 46% of the overall patients, respectively.

Conclusion: Methylation of the KIF1A, EDNRB and DCC gene promoters is a frequent event in HNSCC and these genes are not methylated in normal salivary rinses, demonstrating potential that they may act as biomarkers in detection strategies. Patients with presence of methylation in surveillance salivary rinses are at significant risk for recurrence. Quantitative measurement of salivary methylated DNA may have promise for surveillance and early detection of recurrence.

Citation Format: Semra Demokan, Jatinder Kaur, Alice Y. Chuang, Wojciech K. Mydlarz, Kavita M. Pattani, Wayne M. Koch, David Sidransky, Nejat Dalay, Joseph A. Califano. Promoter methylation of tumor suppressor genes in convalescent saliva samples from patients with head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1384. doi:10.1158/1538-7445.AM2014-1384

Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma

Purpose

Prior studies have demonstrated tumor-specific alternative splicing events in various solid tumor types. The role of alternative splicing in the development and progression of head and neck squamous cell carcinoma (HNSCC) is unclear. Our study queried exon-level expression to implicate splice variants in HNSCC tumors.

Experimental Design

We performed a comparative genome-wide analysis of 44 HNSCC tumors and 25 uvulopalatopharyngoplasty (UPPP) tissue samples at an exon expression level. In our comparison we ranked genes based upon a novel score—the Maximum-Minimum Exon Score (MMES) – designed to predict the likelihood of an alternative splicing event occurring. We validated predicted alternative splicing events using quantitative RT-PCR on an independent cohort.

Results

After MMES scoring of 17,422 genes, the top 900 genes with the highest scores underwent additional manual inspection of expression patterns in a graphical analysis. The genes LAMA3, DST, VEGFC, SDHA, RASIP1, and TP63 were selected for further validation studies because of a high frequency of alternative splicing suggested in our graphical analysis, and literature review showing their biological relevance and known splicing patterns. We confirmed TP63 as having dominant expression of the short DeltaNp63 isoform in HNSCC tumor samples, consistent with prior reports. Two of the six genes (LAMA3 and DST) validated by quantitative RT-PCR for tumor-specific alternative splicing events (Student's t test, P<0.001).

Conclusion

Alternative splicing events of oncologically relevant proteins occur in HNSCC. The number of genes expressing tumor-specific splice variants needs further elucidation, as does the functional significance of selective isoform expression.

Novel insight into mutational landscape of head and neck squamous cell carcinoma

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.

Impact of pharyngeal closure technique on fistula after salvage laryngectomy

IMPORTANCE

No consensus exists as to the best technique, or techniques, to optimize wound healing, decrease pharyngocutaneous fistula formation, and shorten both hospital length of stay and time to initiation of oral intake after salvage laryngectomy. We sought to combine the recent experience of multiple high-volume institutions, with different reconstructive preferences, in the management of pharyngeal closure technique for post-radiation therapy salvage total laryngectomy in an effort to bring clarity to this clinical challenge.

OBJECTIVE

To determine if the use of vascularized flaps in either an onlay or interposed fashion reduces the incidence or duration of pharyngocutaneous fistula after salvage laryngectomy compared with simple primary closure of the pharynx.

DESIGN

Multi-institutional retrospective review of all patients undergoing total laryngectomy after having received definitive radiation therapy with or without chemotherapy between January 2005 and January 2012, conducted at 7 academic medical centers.

SETTING

Academic, tertiary referral centers.

PATIENTS

The study population comprised 359 patients from 8 institutions. All patients had a history of laryngeal irradiation and underwent laryngectomy between 2005 and 2012. They were grouped as primary closure, pectoralis myofascial onlay flap, or interposed free tissue. All patients had a minimum of 4 months follow-up.

MAIN OUTCOMES AND MEASURES

Fistula incidence, severity, and predictors of fistula.

RESULTS

Of the 359 patients, fistula occurred in 94 (27%). For patients with fistula, hospital stay increased from 8.9 to 12.1 days (P < .001) and oral diet initiation was delayed from 10.5 days to 29.9 days (P < .001). Patients were grouped according to closure technique: primary closure (n = 99), pectoralis onlay flap (n = 40), and interposed free tissue (n = 220). Incidence of fistula with primary closure was 34%. For the interposed free flap group, the fistula rate was lower at 25% (P = .07). Incidence of fistula was the lowest for the pectoralis onlay group at 15% (P = .02). Multivariate analysis confirmed a significantly lower fistula rate with either flap technique. For patients who developed fistula, mean duration of fistula was significantly prolonged with primary closure (14.0 weeks) compared with pectoralis flap (9.0 weeks) and free flap (6.5 weeks).

CONCLUSIONS AND RELEVANCE

Pharyngocutaneous fistula remains a significant problem following salvage laryngectomy. Use of nonirradiated, vascularized flaps reduced the incidence and duration of fistula and should be considered during salvage laryngectomy.

Activation of the NOTCH pathway in head and neck cancer

NOTCH1 mutations have been reported to occur in 10% to 15% of head and neck squamous cell carcinomas (HNSCC). To determine the significance of these mutations, we embarked upon a comprehensive study of NOTCH signaling in a cohort of 44 HNSCC tumors and 25 normal mucosal samples through a set of expression, copy number, methylation, and mutation analyses. Copy number increases were identified in NOTCH pathway genes, including the NOTCH ligand JAG1. Gene set analysis defined a differential expression of the NOTCH signaling pathway in HNSCC relative to normal tissues. Analysis of individual pathway-related genes revealed overexpression of ligands JAG1 and JAG2 and receptor NOTCH3. In 32% of the HNSCC examined, activation of the downstream NOTCH effectors HES1/HEY1 was documented. Notably, exomic sequencing identified 5 novel inactivating NOTCH1 mutations in 4 of the 37 tumors analyzed, with none of these tumors exhibiting HES1/HEY1 overexpression. Our results revealed a bimodal pattern of NOTCH pathway alterations in HNSCC, with a smaller subset exhibiting inactivating NOTCH1 receptor mutations but a larger subset exhibiting other NOTCH1 pathway alterations, including increases in expression or gene copy number of the receptor or ligands as well as downstream pathway activation. Our results imply that therapies that target the NOTCH pathway may be more widely suitable for HNSCC treatment than appreciated currently.

Validation of nucleolar protein 4 as a novel methylated tumor suppressor gene in head and neck cancer

Methylation of CpG islands in the promoter region of genes acts as a significant mechanism of epigenetic gene silencing in head and neck cancer. In the present study, we assessed the association of epigenetic alterations of a panel of 12 genes [nucleolar protein 4 (NOL4), iroquois homeobox 1 (IRX1), SLC5A8, LRRC3B, FUSSEL18, EBF3, GBX2, HMX2, SEPT9, ALX3, SOCS3 and LHX6] with head and neck squamous cell carcinoma (HNSCC) via a candidate gene approach. After the initial screening of methylated CpG islands on the promoter regions by bisulfite sequencing using salivary rinse samples, only two genes had methylated CpG dinucleotides on their promoter regions in tumor samples and absence of methylated CpGs were found in normal salivary rinse samples after bisulfite modification and bisulfite sequencing. We then performed real-time quantitative methylation-specific PCR (QMSP) on 16 salivary rinse and 14 normal mucosal samples from healthy subjects and 33 HNSCC tumor samples for the two genes selected. After validation with QMSP, one gene, NOL4, was highly methylated (91%) in tumor samples and unmethylated in normal salivary rinses and minimally methylated in normal mucosal samples demonstrating cancer-specific methylation in HNSCC tissues. Although the IRX1 gene was observed as methylated in normal mucosal and salivary rinse samples, the methylation values of these normal samples were very low (<10%). In conclusion, we identified NOL4 as a highly specific promoter methylated gene associated with HNSCC. IRX1 may have potential as a biomarker for HNSCC and should be assessed in a larger cohort.

Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis

Head and neck squamous cell carcinoma (HNSCC) is largely divided into two groups based on their etiology, human papillomavirus (HPV)-positive and –negative. Global DNA methylation changes are known to drive oncogene and tumor suppressor expression in primary HNSCC of both types. However, significant heterogeneity in DNA methylation within the groups results in different transcriptional profiles and clinical outcomes. We applied a meta-pathway analysis to link gene expression changes to DNA methylation in distinguishing HNSCC subtypes. This approach isolated specific epigenetic changes controlling expression in HPV− HNSCC that distinguish it from HPV+ HNSCC. Analysis of genes identified Hedgehog pathway activation specific to HPV− HNSCC. We confirmed that GLI1, the primary Hedgehog target, showed higher expression in tumors compared to normal samples with HPV− tumors having the highest GLI1 expression, suggesting that increased expression of GLI1 is a potential driver in HPV− HNSCC. Our algorithm for integration of DNA methylation and gene expression can infer biologically significant molecular pathways that may be exploited as therapeutics targets. Our results suggest that therapeutics targeting the Hedgehog pathway may be of benefit in HPV− HNSCC. Similar integrative analysis of high-throughput coupled DNA methylation and expression datasets may yield novel insights into deregulated pathways in other cancers.

Recurrence patterns and management of oral cavity premalignant lesions

OBJECTIVE

To gain an understanding of head and neck mucosal premalignant recurrence and progression based on histology, treatment modality, and risk factors.

DESIGN

Retrospective chart review.

SETTING

Academic medical center.

PATIENTS

Patients who were followed or treated for oral cavity dysplasia/carcinoma in situ.

MAIN OUTCOMES MEASURES

Comparisons with clinical features, degree of dysplasia, anatomical location, rate of recurrences as well as malignant transformation and overall outcome were made.

RESULTS

Of the 136 patients who were included in the study, 20% (n = 27) initially presented with mild dysplasia, 39% (n = 53) with moderate dysplasia, 21% (n = 29) with severe dysplasia, and 20% (n = 27) with carcinoma in situ. Wide local excision (HR 0.54, p = 0.05) was associated with reduced local recurrence in comparison to observation. In comparison to observation, both wide local excision (HR 0.43, p = 0.04) and CO(2)/NO Yag laser treatment (HR 0.14, p = 0.02) of dysplastic lesions significantly reduced progression to cancer. Management of mild dysplasia included observation (n = 13), excision (n = 10) and laser therapy (n = 3). Six of the 13 observed patients suffered a premalignancy recurrence, whereas only 4 of the 13 patients who underwent excision/laser treatment experienced a recurrence. Similarly, 5/13 observed patients eventually progressed to malignancy in comparison to only 2/13 patients who underwent initial excision/laser treatment.

CONCLUSION

Wide excision and/or ablation of head and neck mucosal premalignancy is more effective than observation in preventing recurrence of premalignancy and progression to malignancy. Mild dysplasia has a potentially high rate of recurrence and progression to malignancy when observed, and may be treated by wide excision or ablation.

EDNRB and DCC salivary rinse hypermethylation has a similar performance as expert clinical examination in discrimination of oral cancer/dysplasia versus benign lesions

PURPOSE

Promoter hypermethylation has been recently proposed as a means for head and neck squamous cell carcinoma (HNSCC) detection in salivary rinses. In a prospective study of a high-risk population, we showed that endothelin receptor type B (EDNRB) promoter methylation in salivary rinses is a useful biomarker for oral cancer and premalignancy.

EXPERIMENTAL DESIGN

Using that cohort, we evaluated EDNRB methylation status and 8 additional genes. Clinical risk assessment by expert clinicians was conducted and compared with biomarker performance in the prediction of premalignant and malignant disease. Methylation status of 9 genes was analyzed in salivary rinses of 191 patients by quantitative methylation-specific PCR.

RESULTS

HOXA9, EDNRB, and deleted in colorectal cancer (DCC) methylation were associated (P = 0.012; P < 0.0001; P = 0.0005) with premalignant or malignant disease. On multivariable modeling, histological diagnosis was only independently associated with EDNRB (P = 0.0003) or DCC (P = 0.004) methylation. A subset of patients received clinical risk classification (CRC) by expert clinicians based on lesion examination. CRC, DCC, and EDNRB were associated with diagnosis of dysplasia/cancer on univariate (P = 0.008; P = 0.026; P = 0.046) and multivariate analysis (P = 0.012; P = 0.037; P = 0.047). CRC identified dysplasia/cancer with 56% of sensitivity and 66% of specificity with a similar area under curve [AUC; 0.61, 95% confidence interval (CI) = 0.60-0.81] when compared to EDNRB and DCC combined AUC (0.60, 95% CI = 0.51-0.69), sensitivity of 46% and specificity of 72%. A combination of EDNRB, DCC, and CRC was optimal AUC (0.67, 95% CI = 0.58-0.76).

CONCLUSIONS

EDNRB and/or DCC methylation in salivary rinses compares well to examination by an expert clinician in CRC of oral lesions. These salivary biomarkers may be particularly useful in oral premalignancy and malignancy screening in clinical care settings in which expert clinicians are not available.

Abstract 666: Validation of nucleolar protein 4 as a novel methylated tumor suppressor gene in head and neck cancer

Purpose: Methylation of CpG islands in the promoter region of genes acts as a significant mechanism of epigenetic gene silencing in head and neck cancer. In this study, we assessed the utility of epigenetic alterations of a panel of twelve genes (NOL4, IRX1, SLC5A8, LRRC3B, FUSSEL18, EBF3, GBX2, HMX2, SEPT9, ALX3, SOCS3, LHX6) previously reported.

Experimental Design: In this study we investigated methylation of the 12 gene promoters via a candidate gene approach. After the initial screening of methylated CpG islands on the promoter regions by bisulfite sequencing using salivary rinse samples, only two genes had methylated CpG dinucleotides on their promoter regions in tumor samples and absence of methylated CpGs were found in normal salivary rinse samples after bisulfite modification and bisulfite sequencing. We then performed quantitative methylation specific PCR (Q-MSP) on 16 salivary rinse and 14 normal mucosal samples from healthy people and 33 HNSCC tumor samples for two genes selected.

Results: After validation with QMSP, one gene, nucleolar protein 4 (NOL4), was highly methylated (91%) in tumor samples and unmethylated in normal salivary rinse samples and minimally methylated in normal mucosal samples demonstrating cancer specific methylation in HNSCC tissues. Although iroquois homeobox 1 (IRX1) gene was observed as methylated in normal mucosal and salivary rinse samples, indeed, the methylation values of these normal samples were very low (less than 10%).

Conclusions: We identified NOL4, as a highly specific promoter methylated gene was associated with HNSCC. IRX1 which may have a potential as a biomarker for HNSCC and should also be assessed in a larger cohort.

Citation Format: Semra Demokan, Alice Y. Chuang, Kavita M. Pattani, David Sidransky, Wayne Koch, Joseph A. Califano. Validation of nucleolar protein 4 as a novel methylated tumor suppressor gene in head and neck cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 666. doi:10.1158/1538-7445.AM2013-666

Abstract 3554: Promoter hypermethylation of zinc finger proteins is the novel epigenetic biomarkers of head and neck squamous cell carcinomas

Objective: Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer worldwide with five-year survival rate of 50% despite use of modern treatment modalities. We have employed a comprehensive genome-wide integrated analysis of epigenetic and transcriptional alteration in primary HNSCC tissues in order to discover novel biomarkers of this disease.

Experimental Design: A discovery cohort included 44 primary HNSCC and 25 normal mucosal samples was analyzed by Affymetrix GeneChip Human Exon 1.0 and Illumina Infinium Human Methylation 27 arrays. An independent validation cohort included 32 primary HNSCC and 15 normal mucosal samples to confirm differential methylation by bisulfate sequencing. A second validation cohort included salivary rinse and primary tissue from 59 HNSCC and 31 healthy patients. Detection of DNA methylation in bodily fluids and primary tissues from the later cohort was evaluated by quantitative methylation-specific PCR (qMSP).

Results: We have applied novel screening approach based on Cancer Outlier Profile Analysis (COPA) and Gene Set Enrichment Analysis (GSEA) to our array data for the discovery cohort. With use of this approach we determined 81 significant differentially expressed and 37 significant differentially methylated genes. Out of total 118 candidate genes we picked 36 tumor suppressing genes with strong correlation between hypermethylation and decrease of expression in tumor samples. 26 out of 36 genes (72%) demonstrated strong differential methylation in tumor samples that was confirmed on the independent validation cohort by bisulfate sequencing. Five of these 26 genes belong to Zinc Finger Proteins (ZNF) group. We analyzed the detection of the promoter methylation of ZNF14, ZNF160 and ZNF420 in salivary rinse of HNSCC and healthy patients. DNA methylation of at least one of ZNFs promoter was detected in HNSCC patients salivary rinses with sensitivity of 22% (95% CI: 12.3%-34.7%) and specificity 100% (95% CI: 89.9%-100%). Overall frequency and concordance of detection of DNA methylation from at least one ZNFs promoter in salivary rinse with signal found in primary tissues was 35.3% and 92.3%, respectively. ZNF methylation was strongly associated with oral cavity SCC (p = 0.0049).

Conclusions: Our new screening approach allowed the identification of at least 36 candidate tumor suppressor genes aberrantly methylated and transcriptionally suppressed in HNSCC. Promoter hypermethylation for three ZNF genes in salivary rinse was detected with 100% specificity to HNSCC and may be a valuable salivary rinse biomarker for HNSCC incidence and recurrence, especially among high-risk group population.

Citation Format: Daria A. Gaykalova, Rajita Vatapalli, Yingying Wei, Hao Wang, Patrick Hennessey, Ryan Li, Chi Zhang, Marietta Tan, Zubair Khan, William Westra, Tanbir Khan, David Zaboli, Michael F. Ochs, Joseph A. Califano. Promoter hypermethylation of zinc finger proteins is the novel epigenetic biomarkers of head and neck squamous cell carcinomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3554. doi:10.1158/1538-7445.AM2013-3554

The gastrointestinal manifestations of telomere-mediated disease

Defects in telomere maintenance genes cause pathological telomere shortening, and manifest in syndromes which have prominent phenotypes in tissues of high turnover: the skin and bone marrow. Because the gastrointestinal (GI) epithelium is highly proliferative, we sought to determine whether telomere syndromes cause GI disease, and to define its prevalence, spectrum, and natural history. We queried subjects in the Johns Hopkins Telomere Syndrome Registry for evidence of luminal GI disease. In sixteen percent of Registry subjects (6 of 38), there was a history of significant GI pathology, and 43 additional cases were identified in the literature. Esophageal stenosis, enteropathy, and enterocolitis were the recurrent findings. In the intestinal mucosa, there was striking villous atrophy, extensive apoptosis, and anaphase bridging pointing to regenerative defects in the epithelial compartment. GI disease was often the first and most severe manifestation of telomere disease in young children. These findings indicate that telomere dysfunction disrupts the epithelial integrity in the human GI tract manifesting in recognizable disease processes. A high index of suspicion should facilitate diagnosis and management.

Identification of guanine nucleotide-binding protein γ-7 as an epigenetically silenced gene in head and neck cancer by gene expression profiling

Silencing of tumor suppressor genes plays a vital role in head and neck carcinogenesis. Aberrant hypermethylation in the promoter region of some known or putative tumor suppressor genes occurs frequently during the development of various types of cancer including head and neck squamous cell carcinoma (HNSCC). In this study we used an expanded mRNA expression profiling approach followed by microarray expression analysis to identify epigenetically inactivated genes in HNSCC. Two HNSCC cell lines were treated with 5-aza-2'-deoxycytidine followed by microarray analysis to identify epigenetically silenced genes in HNSCC. We found 1,960, 614 and 427 genes were upregulated in the HNSCC cell lines JHU-012, JHU-011 and the combination of both cell lines, respectively. HNSCC tumor and normal mucosal samples were used for gene profiling by a 47K mRNA gene expression array and we found 7,140 genes were downregulated in HNSCC tumors compared to normal mucosa, as determined by microarray analysis, and were integrated with cell line data. Integrative analysis defined 126 candidate genes, of which only seven genes showed differential methylation in tumors and no methylation in normal mucosa after bisulfite sequencing. Following validation by QMSP, one gene, guanine nucleotide-binding protein γ-7 (GNG7), was confirmed to be highly methylated in tumors and unmethylated in normal mucosal and salivary rinse samples demonstrating cancer-specific methylation in HNSCC tissues. TXNIP and TUSC2 were partially methylated in tumors and normal salivary rinses but unmethylated in normal mucosa. We concluded that GNG7 is a highly specific promoter methylated gene associated with HNSCC. In addition, TXNIP and TUSC2 are also potential biomarkers for HNSCC.

Suprabasin is hypomethylated and associated with metastasis in salivary adenoid cystic carcinoma

Background

Salivary gland adenoid cystic carcinoma (ACC) is a rare cancer, accounting for only 1% of all head and neck malignancies. ACC is well known for perineural invasion and distant metastasis, but its underlying molecular mechanisms of carcinogenesis are still unclear.

Principal Findings

Here, we show that a novel oncogenic candidate, suprabasin (SBSN), plays important roles in maintaining the anchorage-independent and anchorage-dependent cell proliferation in ACC by using SBSN shRNA stably transfected ACC cell line clones. SBSN is also important in maintaining the invasive/metastatic capability in ACC by Matrigel invasion assay. More interestingly, SBSN transcription is significantly upregulated by DNA demethylation induced by 5-aza-2′-deoxycytidine plus trichostatin A treatment and the DNA methylation levels of the SBSN CpG island located in the second intron were validated to be significantly hypomethylated in primary ACC samples versus normal salivary gland tissues.

Conclusions/Significance

Taken together, these results support SBSN as novel oncogene candidate in ACC, and the methylation changes could be a promising biomarker for ACC.

Multidisciplinary service utilization pattern by advanced head and neck cancer patients: a single institution study

Purpose. To analyze the patterns and associations of adjunctive service visits by head and neck cancer patients receiving primary, concurrent chemoradiation therapy. Methods. Retrospective chart review of patients receiving adjunctive support during a uniform chemoradiation regimen for stages III-IV head and neck squamous cell carcinoma. Univariate and multivariate models for each outcome were obtained from simple and multivariate linear regression analyses. Results. Fifty-two consecutive patients were assessed. Female gender, single marital status, and nonprivate insurance were factors associated with an increased number of social work visits. In a multivariate analysis, female gender and marital status were related to increased social work services. Female gender and stage IV disease were significant for increased nursing visits. In a multivariate analysis for nursing visits, living greater than 20 miles between home and hospital was a negative predictive factor. Conclusion. Treatment of advanced stage head and neck cancer with concurrent chemoradiation warrants a multidisciplinary approach. Female gender, single marital status, and stage IV disease were correlated with increased utilization of social work and nursing services. Distance over 20 miles from the center was a negative factor. This information may help guide the treatment team to allocate resources for the comprehensive care of patients.

Comparison of acute toxicities in two primary chemoradiation regimens in the treatment of advanced head and neck squamous cell carcinoma

PURPOSE

The optimal dosage and frequency of platinum-based chemoradiotherapy (CRT) regimen for treating advanced head and neck squamous cell carcinoma remains unresolved. This study aims to compare the toxicity and efficacy of weekly versus more dose-intensive cisplatin-based CRTs.

METHODS

We reviewed 155 stage III/IV head and neck squamous cell carcinoma patients with no evidence of distant metastasis treated with one of two CRT regimens from 2000 to 2010 at Greater Baltimore Medical Center. Twice-daily radiation was provided as a split course over a 45-day period. Regimen A consisted of concomitant cisplatin (30 mg/m2/1 h) weekly for 6 cycles; regimen B consisted of concomitant cisplatin (12 mg/m2/1 h) and 5-fluorouracil (600 mg/m2/20 h) on days 1 through 5 and days 29 through 33. Main outcome measures included acute toxicities (myelosuppression, neurotoxicity, nephrotoxicity, gastrointestinal dysfunction), unplanned hospitalizations, and disease control at 12 months.

RESULTS

Patients on regimen A were much less likely to experience ototoxicity due to their treatment (0% vs. 9.8%, P = 0.04). They were more likely to experience thrombocytopenia acutely (46% vs. 26%, P = 0.02), but the toxicity was not limiting (grade 1–2). No significant differences exist in the incidence of other toxicities or unplanned hospitalizations. At 1 year, 97% of patients on A vs. 86% of patients on regimen B were free of disease (P = 0.11).

CONCLUSIONS

With concurrent radiotherapy, low-dose, single-agent, weekly cisplatin is less likely than higher-dose daily cisplatin plus 5-fluorouracil provided at the beginning and end of treatment to be associated with ototoxicity. The preliminary data suggest at least equivalent efficacy, but longer follow-up is required.

Neck dissection through a facelift incision

OBJECTIVES/HYPOTHESIS

To determine the feasibility and safety of neck dissection through a facelift incision.

STUDY DESIGN

Prospective case series.

METHODS

Cadavers and live subjects underwent neck dissection using a facelift incision with and without endoscopic assistance. In the live facelift neck dissection (FLND), the preoperative surgical indications, staging, adjuvant therapy, intraoperative technical procedure, pathology reports on lymph nodes, and short-term outcomes were reviewed.

RESULTS

FLND was successfully performed in four cadavers and four live subjects, including selective (less than five neck levels removed) and comprehensive (levels I-V removed) neck dissections. All levels were accessible through this approach, with additional retraction required for levels I and IV. Endoscopic assistance was required in one neck dissection for adequate visualization. Short-term complications and number of excised lymph nodes were comparable to those from traditional neck dissection approaches.

CONCLUSIONS

Open neck dissection through a facelift incision is feasible and offers an alternate approach to traditional incisions. This can be performed without requiring robotic assistance and with endoscopic assistance only in certain cases. Endoscopic assistance can offer enhanced visualization of the surgical field and complement open direct approaches in neck dissection. Although FLND offers improved cosmetic outcomes when compared to those of traditional neck incisions, further study is required to determine its efficacy and indications.

Inhibition of TGF-β enhances the in vivo antitumor efficacy of EGF receptor-targeted therapy

EGF receptor (EGFR)-targeted monoclonal antibodies (mAb), such as cetuximab, execute their antitumor effect in vivo via blockade of receptor-ligand interactions and engagement of Fcγ receptors on immune effector cells that trigger antibody-dependent cell-mediated cytotoxicity (ADCC). We show that tumors counteract the in vivo antitumor activity of anti-EGFR mAbs by increasing tumor cell-autonomous expression of TGF-β. We show that TGF-β suppresses the expression of key molecular effectors of immune cell-mediated cytotoxicity, including Apo2L/TRAIL, CD95L/FasL, granzyme B, and IFN-γ. In addition to exerting an extrinsic inhibition of the cytotoxic function of immune effectors, TGF-β-mediated activation of AKT provides an intrinsic EGFR-independent survival signal that protects tumor cells from immune cell-mediated apoptosis. Treatment of mice-bearing xenografts of human head and neck squamous cell carcinoma with cetuximab resulted in emergence of resistant tumor cells that expressed relatively higher levels of TGF-β compared with untreated tumor-bearing mice. Although treatment with cetuximab alone forced the natural selection of TGF-β-overexpressing tumor cells in nonregressing tumors, combinatorial treatment with cetuximab and a TGF-β-blocking antibody prevented the emergence of such resistant tumor cells and induced complete tumor regression. Therefore, elevated levels of TGF-β in the tumor microenvironment enable tumor cells to evade ADCC and resist the antitumor activity of cetuximab in vivo. Our results show that TGF-β is a key molecular determinant of the de novo and acquired resistance of cancers to EGFR-targeted mAbs, and provide a rationale for combinatorial targeting of TGF-β to improve anti-EGFR-specific antibody therapy of EGFR-expressing cancers.

Dose-dependent activation of putative oncogene SBSN by BORIS

Testis-specific transcription factor BORIS (Brother of the Regulator of Imprinted Sites), a paralog and proposed functional antagonist of the widely expressed CTCF, is abnormally expressed in multiple tumor types and has been implicated in the epigenetic activation of cancer-testis antigens (CTAs). We have reported previously that suprabasin (SBSN), whose expression is restricted to the epidermis, is epigenetically derepressed in lung cancer. In this work, we establish that SBSN is a novel non-CTA target of BORIS epigenetic regulation. With the use of a doxycycline-inducible BORIS expressing vector, we demonstrate that relative BORIS dosage is critical for SBSN activation. At lower concentrations, BORIS induces demethylation of the SBSN CpG island and disruption and activation of chromatin around the SBSN transcription start site (TSS), resulting in a 35-fold increase in SBSN expression in the H358 human lung cancer cell line. Interestingly, increasing BORIS concentrations leads to a subsequent reduction in SBSN expression via chromatin repression. In a similar manner, increase in BORIS concentrations leads to eventual decrease of cell growth and colony formation. This is the first report demonstrating that different amount of BORIS defines its varied effects on the expression of a target gene via chromatin structure reorganization.

A phase II trial of cetuximab in high-risk premalignant lesions of the upper aerodigestive tract

5528

Background: High risk head and neck premalignancy includes patients with prior HNSCC and loss of heterozygosity (LOH). These patients demonstrate 30-60% rates of progression to malignancy despite conventional surgical excision. We performed a phase II trial using short term therapy with cetuximab, a humanized monoclonal antibody directed against EGFR, in the treatment of high risk premalignant lesions of the UADT. Methods: Inclusion criteria required; 1) presence of 3p, 9p21, or 17p LOH, and/or 2) surgically unresectable high grade premalignant lesions, and/or 3) high grade premalignancy after curative therapy for HNSCC. Patients received cetuximab 400 mg/m2 on week one followed by 250 mg/m2 on week 2-8 or observation, with the option for crossover to cetuximab for patients originally randomized to the observation arm. Histologic grade (1=benign, 2=mild dysplasia, 3=moderate dysplasia, 4=severe dysplasia/carcinoma in situ, 5=invasive cancer) and change in grade of dysplasia was evaluated. Results: 19 patients were enrolled. Two patients discontinued therapy due to toxicity. We noted a decrease in grade of dysplasia in the cetuximab treated group (-1.0) vs. the observation group (-0.2), (Wilcoxon test p value = 0.18). In the observation group, 0/5 patients (0%) underwent complete resolution of dysplasia; while 4/12 (33.3%) treated patients had no remaining dysplasia after therapy (p = 0.26), three of these patients had complete resolution of dysplastic changes after cetuximab therapy alone. Of these three patients, two have had no recurrence of leukoplakia or dysplasia at 1.5 and 2 years. One patient treated with oral cavity dysplasia has had no recurrence of dysplasia or lesions within the oral cavity, but developed a hypopharyngeal cancer at 1.5 years after trial completion. Of 5 patients randomized to observation, three underwent crossover to cetuximab therapy, and two of these three patients had complete resolution of dysplasia. Conclusions: EGFR blockade with cetuximab alone can result in significant, durable, and complete clinical and histological resolution of moderate to severe dysplasia in at least a subset of high risk patients.

Abstract 4041: Identification of GNG7 as an epigenetically silenced gene in head and neck cancer by gene expression profiling

Silencing of tumor suppressor genes plays a vital role in head and neck carcinogenesis. Aberrant hypermethylation in the promoter region of some known or putative tumor suppressor genes occurs frequently during the development of various cancers including head and neck squamous cell carcinoma (HNSCC). In this study we used an expanded mRNA expression profiling approach followed by microarray expression analysis to identify epigenetically inactivated genes in HNSCC. Two HNSCC cell lines were treated with 5-aza-2′-deoxycytidine followed by microarray analysis to identify epigenetically silenced genes in HNSCC. 1960, 614, and 427 genes were upregulated in HNSCC cell lines JHU-012, JHU-011 and the combination of both cell lines, respectively. HNSCC tumor and normal mucosal samples were used for gene profiling by a 47K mRNA gene expression array and we found, 7140 genes were downregulated in HNSCC tumors compared to normal mucosa as determined by microarray analysis and were integrated with cell line data. Integrative analysis defined 126 candidate genes, of which only seven genes showed differentially methylation in tumors and no methylation in normal mucosa after bisulfite sequencing. After validation by QMSP, one gene, GNG7, was confirmed as being highly methylated in tumors and unmethylated in normal mucosal and salivary rinse samples demonstrating cancer-specific methylation in HNSCC tissues. TXNIP and TUSC2 were partially methylated in tumors and normal salivary rinses but unmethylated in normal mucosa. We concluded GNG7 as a highly specific promoter methylated gene associated with HNSCC. In addition, TXNIP and TUSC2 are also potential biomarkers for HNSCC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4041. doi:1538-7445.AM2012-4041

Abstract 4097: Integrative analysis of epigenetic and transcriptional alterations in head and neck squamous cell carcinomas

Objective: Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide with a 50% patient survival rate 5 years post-diagnosis despite current therapeutic strategies. A direct comprehensive genome wide integrated analysis of epigenetic and transcriptional alteration in primary HNSCC has not been performed before. Such data would greatly enrich our knowledge about HNSCC biology and would be beneficial for the development of the individual targeted therapy. Experimental Design: 44 primary HNSCC and 25 normal mucosal samples were used in the Affymetrix GeneChip Human Exon 1.0 array and for the Illumina Infinium Human Methylation 27 array. To analyze the data we employed a novel screening approach based on Cancer Outlier Profile Analysis (COPA). With use of this approach we determined 81 significant differentially expressed and 37 significant differentially methylated genes with both oncogenic and tumor suppressing properties. Results: Out of total 118 candidate genes we picked 36 candidate tumor suppressing genes with strong correlation between hypermethylation and decrease of expression in tumor samples, such as BANK1, ADFP, MAPK4, ZNF71 and others. 20 genes out of total 36 were validated by bisulfite sequencing in a separate cohort of 32 primary HNSCC tumor and 16 normal mucosal tissues. Out of the total 20 genes, 13 demonstrated at least 40% difference in methylation, most notably for BANK1 81% of tumors were more methylated as compared to normals. 7 of these newly discovered genes out of the 36 belong to Zinc Finger Proteins (ZNF) group and they have never been reported as tumor suppressors in HNSCC before. Bisulfite sequencing and quantitative real time PCR (qRT-PCR) analysis of ZNFs revealed that they are strongly hypermethylated and underexpressed in HNSCC tumor samples. Conclusions: Our new screening approach allowed identification of 36 candidate tumor suppressor genes aberrantly methylated and transcriptionally suppressed in HNSCC. Validation of gene expression and methylation allowed the detection of ZNF genes whose downregulation may play a significant role in HNSCC tumor development.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4097. doi:1538-7445.AM2012-4097

Abstract 4095: Stimulation of blood based biomarker release in primary tumor models of the head and neck

Approximately 50,000 head and neck cancers (HNC) occur in the United States per year and are responsible for 11,000 deaths. Identification of early detection tumor biomarkers in bodily fluids has been the goal of many studies in recent years, however none have gained wide clinical acceptance. New approaches are needed to improve detection of biomarkers with higher sensitivity and specificity for HNC. Epigenetic changes, such as DNA methylation, are hallmarks of cancer and are potential biomarker candidates. Promoter methylation of DCC, KIF1A and EDNRB were shown by our group to be cancer specific in HNC. Proof of principal of techniques enhancing detection sensitivity in an animal model may allow us, in the future, to translate our results to human clinical trials. We aim to study methods to enhance the sensitivity of blood based biomarker detection in a head and neck tumorgraft model. The model proposed is based on acquisition of human HNC tumor tissue and implantation into immunodeficient mice. We exposed these mice to various stimulations that consist of low dose treatments, which would not be expected to cause much cell death or damage, nor considerable adverse effects. They comprise Radiation (1Gy), Cisplatin (2.5μg/g), Taxol (25μg/g), Cetuximab (15μg/g), Erlotinib (10μg/g). Every group consisted of 7 mice implanted with the same tumor that was grown until the same size: one mouse for each treatment and two control mice. Blood from a mouse without tumor was first analyzed to confirm that our detection was restricted to human DNA sequences. Thus far we have analyzed 5 tumors (5 groups). Following the exposures, promoter methylation levels of DCC, KIF1A and EDNRB were evaluated by quantitative methylation specific PCR (QMSP) in the tumor as well as in the serum. Although, high levels of methylation were observed in the tumors, we were not able to detect hypermethylation in the bloodstream of non-stimulated animals. In one of our groups, the mouse stimulated with Taxol showed sufficient biomarker release into the bloodstream to provide signal amplification of all 3 genes analyzed, under very stringent conditions of qPCR analysis. The corresponding tumor showed high levels of promoter methylation of DCC, KIF1A and EDNRB, however these were undetectable in the non-stimulated group, or those mice stimulated with any condition other than Taxol. We did not observe any changes in any of the other four groups analyzed; no epigenetic alteration was detectable in any serum samples, although observed in the tumor tissue. These preliminary data suggest that low dose of Taxol was able to increase the concentration of biomarkers circulating in the blood. Clinical applications of biomarker release include monitoring patients that are at high risk for disease recurrence, and detecting the presence of cancer cells before clinical symptoms appear. We will now expand our study to explore other experimental variables that facilitate biomarker release.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4095. doi:1538-7445.AM2012-4095

Comparison of promoter hypermethylation pattern in salivary rinses collected with and without an exfoliating brush from patients with HNSCC

BACKGROUND

Salivary rinses have been recently proposed as a valuable resource for the development of epigenetic biomarkers for detection and monitoring of head and neck squamous cell carcinoma (HNSCC). Both salivary rinses collected with and without an exfoliating brush from patients with HNSCC are used in detection of promoter hypermethylation, yet their correlation of promoter hypermethylation has not been evaluated. This study was to evaluate the concordance of promoter hypermethylation between salivary rinses collected with and without an exfoliating brush from patients with HNSCC. METHODOLGY: 57 paired salivary rinses collected with or without an exfoliating brush from identical HNSCC patients were evaluated for promoter hypermethylation status using Quantitative Methylation-Specific PCR. Target tumor suppressor gene promoter regions were selected based on our previous studies describing a panel for HNSCC screening and surveillance, including P16, CCNA1, DCC, TIMP3, MGMT, DAPK and MINT31.

PRINCIPAL FINDINGS

In salivary rinses collected with and without brush, frequent methylation was detected in P16 (8.8% vs. 5.2%), CCNA1 (26.3% vs. 22.8%), DCC (33.3% vs. 29.8%), TIMP3 (31.6% vs. 36.8%), MGMT (29.8% vs. 38.6%), DAPK (14.0% vs. 19.2%), and MINT31 (10.5% vs. 8.8%). Spearman's rank correlation coefficient showed a positive correlation between salivary rinses collected with and without brush for P16 (ρ = 0.79), CCNA1 (ρ = 0.61), DCC (ρ = 0.58), TIMP3 (ρ = 0.10), MGMT (ρ = 0.70), DAPK (ρ = 0.51) and MINT31 (ρ = 0.72) (P<0.01). The percent agreement of promoter methylation between salivary rinses with brush and without brush were 96.5% for P16, 82.5% for CCNA1, 78.9% for DCC, 59.7% for TIMP3, 84.2% for MGMT, 84.2% for DAPK, and 94.7% for MINT31.

CONCLUSIONS

Our study demonstrated strong correlations of gene promoter hypermethylation between salivary rinses collected with and without an exfoliating brush. Salivary rinse collection without using an exfoliating brush may offer a cost effective, rapid, non-invasive, and reliable means for development of epigenetic salivary rinse biomarkers.

Serum microRNA biomarkers for detection of non-small cell lung cancer

Non small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality world-wide and the majority of cases are diagnosed at late stages of disease. There is currently no cost-effective screening test for NSCLC, and the development of such a test is a public health imperative. Recent studies have suggested that chest computed tomography screening of patients at high risk of lung cancer can increase survival from disease, however, the cost effectiveness of such screening has not been established. In this Phase I/II biomarker study we examined the feasibility of using serum miRNA as biomarkers of NSCLC using RT-qPCR to examine the expression of 180 miRNAs in sera from 30 treatment naive NSCLC patients and 20 healthy controls. Receiver operating characteristic curves (ROC) and area under the curve were used to identify differentially expressed miRNA pairs that could distinguish NSCLC from healthy controls. Selected miRNA candidates were further validated in sera from an additional 55 NSCLC patients and 75 healthy controls. Examination of miRNA expression levels in serum from a multi-institutional cohort of 50 subjects (30 NSCLC patients and 20 healthy controls) identified differentially expressed miRNAs. A combination of two differentially expressed miRNAs miR-15b and miR-27b, was able to discriminate NSCLC from healthy controls with sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 100% in the training set. Upon further testing on additional 130 subjects (55 NSCLC and 75 healthy controls), this miRNA pair predicted NSCLC with a specificity of 84% (95% CI 0.73–0.91), sensitivity of 100% (95% CI; 0.93–1.0), NPV of 100%, and PPV of 82%. These data provide evidence that serum miRNAs have the potential to be sensitive, cost-effective biomarkers for the early detection of NSCLC. Further testing in a Phase III biomarker study in is necessary for validation of these results.

Detection of TIMP3 promoter hypermethylation in salivary rinse as an independent predictor of local recurrence-free survival in head and neck cancer

PURPOSE

To validate a panel of methylation-based salivary rinse biomarkers (P16, CCNA1, DCC, TIMP3, MGMT, DAPK, and MINT31) previously shown to be independently associated with poor overall survival and local recurrence in a larger, separate cohort of patients with head and neck squamous cell carcinoma (HNSCC).

EXPERIMENTAL DESIGN

One hundred ninety-seven patients were included. All pretreatment saliva DNA samples were evaluated for the methylation status of the gene promoters by quantitative methylation-specific PCR. The main outcome measures were overall survival, local recurrence-free survival, and disease-free survival.

RESULTS

In univariate analyses, the detection of hypermethylation of CCNA1, MGMT, and MINT31 was significantly associated with poor overall survival; the detection of hypermethylation of TIMP3 was significantly associated with local recurrence-free survival; and the detection of hypermethylation of MINT31 was significantly associated with poor disease-free survival. In multivariate analyses, detection of hypermethylation at any single marker was not predictive of overall survival in patients with HNSCC; detection of hypermethylation of TIMP3 in salivary rinse had an independent, significant association with local recurrence-free survival (HR = 2.51; 95% CI: 1.10-5.68); and none of the studied markers was significantly associated with disease-free survival.

CONCLUSION

The detection of promoter hypermethylation of the seven genes in salivary rinse as an independent prognostic indicator of overall survival in patients with HNSCC was not validated. Detection of promoter hypermethylation of TIMP3 in pretreatment salivary rinse is independently associated with local recurrence-free survival in patients with HNSCC and may be a valuable salivary rinse biomarker for HNSCC recurrence.

Tissue imprint for molecular mapping of deep surgical margins in patients with head and neck squamous cell carcinoma

BACKGROUND

Tissue imprinting can generate molecular marker maps of tumor cells at deep surgical margins. The purpose of this study was to evaluate the feasibility of this method for detection of residual head and neck squamous cell carcinoma (HNSCC).

METHODS

Paired fresh tissue and nitrocellulose membrane imprints of tumor and deep margins were collected from 17 HNSCC resections. DNA was amplified using quantitative methylation-specific polymerase chain reaction (qMSP) for p16, DCC, KIF1A, and EDNRB. Levels of methylation in tumors and deep margins were compared.

RESULTS

DNA from imprints was adequate for qMSP. Hypermethylation of target genes was present in 12 of 17 tumors and in 8 deep margins. Methylation level was better from margin imprints than tissue. During follow-up (median, 13 months), local or regional recurrences occurred in 6 cases of which 5 had molecularly positive margins.

CONCLUSION

Tissue imprinting is feasible for molecular detection of residual tumor at deep surgical margins and may correlate with locoregional recurrence.

Prescription medication abuse and illegitimate internet-based pharmacies

Abuse of controlled prescription medications in the United States exceeds that of all illicit drugs combined except marijuana and has grown considerably in the past decade. Although available through traditional channels, controlled prescription medications can also be purchased on the Internet without a prescription. This issue has gained the attention of federal regulators, law enforcement, and the media, but physician awareness of the problem is scarce. This article describes the nature of the problem and its magnitude, discusses the challenges to federal and private efforts to combat illegitimate online pharmacies, and outlines strategies for physicians to recognize and minimize the unwarranted effects of the availability of these medications on the Internet.

Promoter methylation and loss of p16(INK4a) gene expression in head and neck cancer

BACKGROUND

Silencing of tumor suppressor genes plays a vital role in head and neck carcinogenesis. In this study we aimed to evaluate aberrant p16(INK4a) gene promoter methylation in patients with head and neck cancer.

METHODS

Methylation of the gene was investigated by bisulfite modification/methylation-specific polymerase chain reaction and gene expression levels were analyzed by quantitative reverse transcription-polymerase chain reaction in tumors and matched normal tissue samples from Turkish patients with head and neck cancer.

RESULTS

The promoter region of the p16(INK4a) gene was methylated in 67.5% and 28.6% of the primary tumors and the corresponding normal tissue, respectively. This difference was highly significant. In concordance, p16(INK4a) gene expression was downregulated in 67.5% of the tumor samples. Methylation and the absence of expression in the tumors were observed in 48% of the patients.

CONCLUSIONS

Our data indicate that methylation of the p16(INK4a) gene is a frequent event in primary head and neck cancer and that it plays a major role in the silencing of p16(INK4a) gene expression during tumor development.

Abstract PR3: Exome sequencing of head and neck squamous cell carcinoma reveals a higher frequency of mutations in TP53 among African Americans

This abstract will be presented as a proffered talk on Wednesday, September 21, in Plenary Session 8.

African American (AA) and Puerto Rican (PR) men have a higher oral (OSCC) and head and neck squamous cell carcinoma (HNSCC) burden than White men in the United States (US), but the biological basis for these differences are poorly understood. Overall Five-Year relative survival rates for patients diagnosed with oral cavity cancer increased from 53% in 1975 to 63% in 2005 across all races in the US, an increase that parallels a decline in smoking among males during the same period of time. However, the disparity in overall survival rates between Whites and African American patients has remained, practically unchanged from 1975 (19%) to 2005 (18%). The survival disparity difference in HNSCC among AA may be due, among other factors, to a higher prevalence of genetic alterations.

To gain an initial profile of the disparities in genetic alterations between Whites and Non-Whites HNSCC patients we performed a secondary analysis on a convenience sample from an exome-sequencing project that was undertaken at Johns Hopkins School of Medicine. For this project we sequenced ∼18,000 protein-encoding genes in tumors from 17 HNSCC patients which comprised the Discovery set. DNA was purified from these tumors as well as matched non-neoplastic tissue and used to generate libraries suitable for massively parallel sequencing. After capture of the coding sequences with a SureSelect (Agilent) the DNA was sequenced using an Illumina GAIIx/HiSeq instrument. The average coverage of each base in the targeted regions was 77-fold and 92.6% of targeted bases were represented by at least 10 reads in this platform.

The majority of patients (82%) in the Discovery setwere White and the remainder were African American (18%). All the African American patients were smokers. The majority of the AA patients were males (60%), over 60 yrs old (80%) with an oropharyngeal cancer (40%). Using stringent criteria for analysis of these data we identified 249 somatic mutations. The range of confirmed mutations per tumor was 2 to 78, with a mean and standard deviation of 19 ± 16.5 mutations per tumor.

We selected genes for further analysis if they or closely related genes were altered in at least two of the 17 tumors sequenced. The genes included were PIK3AP1, RIMBP2, SI, NRXN2, NRXN3, EPHA7, RASA1, RXFP3, PIK3CA, HRAS, TP53, CDKN2A, NOTCH1, and FBXW7. We then analyzed the sequences of these genes in additional HNSCC and their corresponding normal tissues. In total, somatic mutations in TP53, NOTCH1, CDKN2A, PIK3CA, FBXW7, and HRAS were identified in 47%, 15%, 9%, 6%, 5% and 4% of patients, respectively. Most of the mutations (84%) were observed in White patients. There was no significant difference in the number of mutations per patient in White (14.6) vs African American (13.7) patients. Breaking down the somatic mutations by race we found that the mutations among African Americans was higher (73%) for TP53, when compared to Whites (55%) or to previously observed frequency of TP53 mutations in HNSCC. The mutations in NOTCH1, CDKN2A, PIK3CA had similar mutation frequency in African Americans and in White patients. African American patients did not have somatic mutations in FBXW7 and HRAS.

This is the first exome sequencing study to report HNSCC mutation disparities in African Americans. Although the number of HNSCC African American patients examined in this project is small, the results of this study provide evidence that HNSCCs, although morphologically similar, are comprised of distinct diseases at the molecular level. These results should be examined in a larger cohort of African American patients. Our preliminary findings that HNSCCs have few directly targetable mutations has implications for controlling this disease in the future. In particular, it suggests that prevention, careful surveillance of patients at risk, and early detection are the optimal approaches for reducing cancer health disparities in this disease.

Citation Information: Cancer Epidemiol Biomarkers Prev 2011;20(10 Suppl):PR3.

Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. To explore the genetic origins of this cancer, we used whole-exome sequencing and gene copy number analyses to study 32 primary tumors. Tumors from patients with a history of tobacco use had more mutations than did tumors from patients who did not use tobacco, and tumors that were negative for human papillomavirus (HPV) had more mutations than did HPV-positive tumors. Six of the genes that were mutated in multiple tumors were assessed in up to 88 additional HNSCCs. In addition to previously described mutations in TP53, CDKN2A, PIK3CA, and HRAS, we identified mutations in FBXW7 and NOTCH1. Nearly 40% of the 28 mutations identified in NOTCH1 were predicted to truncate the gene product, suggesting that NOTCH1 may function as a tumor suppressor gene rather than an oncogene in this tumor type.

Value of chest CT in the diagnosis and management of tracheobronchial foreign bodies

BACKGROUND

The aim of the present study was to investigate the value of chest multidetector computed tomography (CT) in the evaluation of children with suspected foreign body aspiration.

METHODS

Chest CT was performed in 45 consecutive children with suspected foreign body aspiration, and plain chest X-ray was conducted at the same time. Multiplanar reformatted imaging was carried out after multidetector CT. Rigid bronchoscopy and removal of the foreign body was performed under general anesthesia.

RESULTS

All 42 patients (100%) with tracheobronchial foreign bodies were identified on chest CT. Three patients avoided unnecessary operations due to negative CT scans. For the patients with tracheobronchial foreign bodies, the occurrence of unilateral hyperlucent lung and post-obstructive lobar or segmental infiltrates on plain chest X-ray was 42.9% (18/42) and 4.8% (2/42), respectively. Twenty-two of the 42 patients (52.4%) had no abnormalities on plain X-ray. The difference between multidetector CT and plain X-ray results was statistically significant (P < 0.001). Surgical plans were designed and appropriate foreign body forceps were selected based on the CT scans. All foreign bodies were removed successfully, and no severe complications were observed. The location, shape, and volume of the foreign bodies found at surgery were consistent with the CT images.

CONCLUSIONS

The diagnosis of foreign body aspiration of the airway in children can be accomplished by using chest multidetector CT. It is often useful in delineating the exact shape, location, volume and form of a bronchial foreign body and can help the surgeon plan for operative bronchoscopy and safe removal of the foreign body.

Detection of promoter hypermethylation in salivary rinses as a biomarker for head and neck squamous cell carcinoma surveillance

PURPOSE

Hypermethylation of tumor suppressor gene promoters has been found in head and neck squamous carcinoma (HNSCC) and other solid tumors. We evaluated these alterations in pretreatment salivary rinses from HNSCC patients by using real-time quantitative methylation-specific PCR (Q-MSP).

EXPERIMENTAL DESIGN

Pretreatment saliva DNA samples from HNSCC patients were evaluated for patterns of hypermethylation by using Q-MSP. Target tumor suppressor gene promoter regions were selected based on a previous study describing a screening panel for HNSCC in a high-risk population subjects. The selected genes were: DAPK, DCC, MINT-31, TIMP-3, p16, MGMT, CCNA1.

RESULTS

We analyzed the panel in a cohort of 61 HNSCC patients. Thirty-three of the analyzed patients (54.1%) showed methylation of at least one of the selected genes in the saliva DNA. Pretreatment methylated saliva DNA was not significantly associated with tumor site (P = 0.209) nor clinical stage (P = 0.299). However, local disease control and overall survival were significantly lower in patients presenting hypermethylation in saliva rinses (P = 0.010 and P = 0.015, respectively). Multivariate analysis confirmed that this hypermethylation pattern remained as an independent prognostic factor for local recurrence (HR = 12.2; 95% CI = 1.8-80.6; P = 0.010) and overall survival (HR = 2.8; 95% CI = 1.2-6.5; P = 0.016).

CONCLUSIONS

We were able to confirm an elevated rate of promoter hypermethylation in HNSCC saliva of patients by using a panel of gene promoters previously described as methylated specifically in HNSCC. Detection of hypermethylation in pretreatment saliva DNA seems to be predictive of local recurrence and overall survival. This finding has potential to influence treatment and surveillance of HNSCC patients.

A new American Joint Committee on Cancer staging system for cutaneous squamous cell carcinoma: creation and rationale for inclusion of tumor (T) characteristics

BACKGROUND

The incidence of cutaneous squamous cell carcinoma (cSCC) is increasing. Although most patients achieve complete remission with surgical treatment, those with advanced disease have a poor prognosis. The American Joint Committee on Cancer (AJCC) is responsible for the staging criteria for all cancers. For the past 20 years, the AJCC cancer staging manual has grouped all nonmelanoma skin cancers, including cSCC, together for the purposes of staging. However, based on new evidence, the AJCC has determined that cSCC should have a separate staging system in the 7th edition AJCC staging manual.

OBJECTIVE

We sought to present the rationale for and characteristics of the new AJCC staging system specific to cSCC tumor characteristics (T).

METHODS

The Nonmelanoma Skin Cancer Task Force of AJCC reviewed relevant data and reached expert consensus in creating the 7th edition AJCC staging system for cSCC. Emphasis was placed on prospectively accumulated data and multivariate analyses. Concordance with head and neck cancer staging system was also achieved.

RESULTS

A new AJCC cSCC T classification is presented. The T classification is determined by tumor diameter, invasion into cranial bone, and high-risk features, including anatomic location, tumor thickness and level, differentiation, and perineural invasion.

LIMITATIONS

The data available for analysis are still suboptimal, with limited prospective outcomes trials and few multivariate analyses.

CONCLUSIONS

The new AJCC staging system for cSCC incorporates tumor-specific (T) staging features and will encourage coordinated, consistent collection of data that will be the basis of improved prognostic systems in the future.

Promoter methylation in head and neck squamous cell carcinoma cell lines is significantly different than methylation in primary tumors and xenografts

Studies designed to identify novel methylation events related to cancer often employ cancer cell lines in the discovery phase of the experiments and have a relatively low rate of discovery of cancer-related methylation events. An alternative algorithm for discovery of novel methylation in cancer uses primary tumor-derived xenografts instead of cell lines as the primary source of nucleic acid for evaluation. We evaluated DNA extracted from primary head and neck squamous cell carcinomas (HNSCC), xenografts grown from these primary tumors in nude mice, HNSCC-derived cell lines, normal oral mucosal samples, and minimally transformed oral keratinocyte-derived cell lines using Illumina Infinum Humanmethylation 27 genome-wide methylation microarrays. We found >2,200 statistically significant methylation differences between cancer cell lines and primary tumors and when comparing normal oral mucosa to keratinocyte cell lines. We found no statistically significant promoter methylation differences between primary tumor xenografts and primary tumors. This study demonstrates that tumor-derived xenografts are highly accurate representations of promoter methylation in primary tumors and that cancer derived cell lines have significant drawbacks for discovery of promoter methylation alterations in primary tumors. These findings also support use of primary tumor xenografts for the study of methylation in cancer, drug discovery, and the development of personalized cancer treatments.

An epigenetic marker panel for detection of lung cancer using cell-free serum DNA

PURPOSE

We investigated the feasibility of detecting aberrant DNA methylation of some novel and known genes in the serum of lung cancer patients.

EXPERIMENTAL DESIGN

To determine the analytic sensitivity, we examined the tumor and the matched serum DNA for aberrant methylation of 15 gene promoters from 10 patients with primary lung tumors by using quantitative methylation-specific PCR. We then tested this 15-gene set to identify the more useful DNA methylation changes in the serum of a limited number of lung cancer patients and controls. In an independent set, we tested the six most promising genes (APC, CDH1, MGMT, DCC, RASSF1A, and AIM1) for further elucidation of the diagnostic application of this panel of markers.

RESULTS

Promoter hypermethylation of at least one of the genes studied was detected in all 10 lung primary tumors. In majority of cases, aberrant methylation in serum DNA was accompanied by methylation in the matched tumor samples. In the independent set, using a single gene that had 100% specificity (DCC), 35.5% (95% CI: 25-47) of the 76 lung cancer patients were correctly identified. For patients without methylated DCC, addition of a logistic regression score that was based on the five remaining genes improved sensitivity from 35.5% to 75% (95% CI: 64-84) but decreased the specificity from 100% to 73% (95% CI: 54-88).

CONCLUSION

This approach needs to be evaluated in a larger test set to determine the role of this gene set in early detection and surveillance of lung cancer.

The role of MAGEA2 in head and neck cancer

OBJECTIVE

To examine the role of MAGEA2 in the tumorigenesis of head and neck squamous cell carcinoma (HNSCC).

DESIGN

Primary tissue microarray data and quantitative reverse transcription-polymerase chain reaction (RT-PCR) showed that MAGEA2 is differentially overexpressed in HNSCC. Functional analyses were then performed using MAGEA2 transfections and small-interfering RNA knockdowns with subsequent anchorage-dependent growth studies and cell cycle analyses. Quantitative RT-PCR was used to evaluate expression changes in p53 downstream targets after transfection of MAGEA2 into normal upper aerodigestive cell lines.

RESULTS

MAGEA2 is differentially overexpressed in HNSCC. In addition, MAGEA2 promotes growth in normal oral keratinocytes, whereas knockdown of MAGEA2 in HNSCC cells decreases growth. Using the HCT116 p53 wt and null cell line system, transfection of MAGEA2 induced growth in the p53 wt cell line while providing no growth advantage in the p53 mutant cells. Subsequently, transfection of MAGEA2 induced a decrease in messenger RNA expression of the p53 downstream targets CDKN1A and BAX and decreased G1 arrest in cells allowed to remain confluent for longer than 48 hours.

CONCLUSIONS

These data suggest that MAGEA2 is differentially expressed in HNSCC and functions, in part, through the p53 pathway by increasing cellular proliferation and abrogating cell cycle arrest. This improved understanding of MAGEA2 function and expression patterns will potentially allow for the improved ability to use MAGEA2 for detection, surveillance, and targeted therapeutics.

Cigarette smoke induces promoter methylation of single-stranded DNA-binding protein 2 in human esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is the sixth most frequent cause of cancer death in the world, and cigarette smoke is a key factor in esophageal carcinogenesis. To identify molecular changes during cigarette smoke-induced ESCC, we examined the methylation status of 13 gene promoters in the human immortalized, nontumorigenic esophageal epithelial cell line (Het-1A) that were exposed to mainstream (MSE) or sidestream cigarette smoke extract (SSE) for 6 months in culture. The promoter of sequence-specific single-stranded DNA-binding protein 2 (SSBP2) was methylated in the Het-1A cells exposed to MSE (MSE-Het-1A). Promoter methylation (86%, 56/70) and downregulation of SSBP2 expression were frequently detected in tumor tissues from ESCC patients. In addition, reintroduction of SSBP2 in an ESCC cell line (TE1) that does not express SSBP2 and in the MSE-Het-1A cells inhibited expression of LRP6 and Dvl3, which are mediators of the Wnt signaling pathway. SSBP2 expression markedly decreased the colony-forming ability of ESCC cell lines and significantly inhibited cell growth of the MSE-Het-1A cells. Our results indicate that cigarette smoking is a cause of SSBP2 promoter methylation and that SSBP2 harbors a tumor suppressive role in ESCC through inhibition of the Wnt signaling pathway.

BORIS binding to the promoters of cancer testis antigens, MAGEA2, MAGEA3, and MAGEA4, is associated with their transcriptional activation in lung cancer

PURPOSE

Aim of this study was to determine whether BORIS (Brother of the Regulator of Imprinted Sites) is a regulator of MAGEA2, MAGEA3, and MAGEA4 genes in lung cancer.

EXPERIMENTAL DESIGN

Changes in expression of MAGEA genes upon BORIS induction/knockdown were studied. Recruitment of BORIS and changes in histone modifications at their promoters upon BORIS induction were analyzed. Luciferase assays were used to study their activation by BORIS. Changes in methylation at these promoters upon BORIS induction were evaluated.

RESULTS

Alteration of BORIS expression by induction/knockdown directly correlated with expression of MAGEA genes. BORIS was enriched at their promoters in H1299 cells, which show high expression of these cancer testis antigens (CTA), compared with normal human bronchial epithelial (NHBE) cells which show low expression of the target CTAs. BORIS induction in A549 cells resulted in increased amounts of BORIS and activating histone modifications at their promoters along with a corresponding increase in their expression. Similarly, BORIS binding at these promoters in H1299 correlates with enrichment of activating modifications, whereas absence of BORIS binding in NHBE is associated with enrichment of repressive marks. BORIS induction of MAGEA3 was associated with promoter demethylation, but no methylation changes were noted with activation of MAGEA2 and MAGEA4.

CONCLUSIONS

These data suggest that BORIS positively regulates these CTAs by binding and inducing a shift to a more open chromatin conformation with promoter demethylation for MAGEA3 or independent of promoter demethylation in case of MAGEA2 and MAGEA4 and may be a key effector involved in their derepression in lung cancer.

Integrated, genome-wide screening for hypomethylated oncogenes in salivary gland adenoid cystic carcinoma

PURPOSE

Salivary gland adenoid cystic carcinoma (ACC) is a rare malignancy that is poorly understood. To look for relevant oncogene candidates under the control of promoter methylation, an integrated, genome-wide screen was conducted.

EXPERIMENTAL DESIGN

Global demethylation of normal salivary gland cell strains using 5-aza-2'-deoxycytidine (5-aza-dC) and trichostatin A (TSA), followed by expression array analysis was conducted. ACC-specific expression profiling was generated using expression microarray analysis of primary ACC and normal samples. Next, the two profiles were integrated to identify a subset of genes for further validation of promoter demethylation in ACC versus normal. Finally, promising candidates were further validated for mRNA, protein, and promoter methylation levels in larger ACC cohorts. Functional validation was then conducted in cancer cell lines.

RESULTS

We found 159 genes that were significantly re-expressed after 5-aza-dC/TSA treatment and overexpressed in ACC. After initial validation, eight candidates showed hypomethylation in ACC: AQP1, CECR1, C1QR1, CTAG2, P53AIP1, TDRD12, BEX1, and DYNLT3. Aquaporin 1 (AQP1) showed the most significant hypomethylation and was further validated. AQP1 hypomethylation in ACC was confirmed with two independent cohorts. Of note, there was significant overexpression of AQP1 in both mRNA and protein in the paraffin-embedded ACC cohort. Furthermore, AQP1 was upregulated in 5-aza-dC/TSA-treated SACC83. Finally, AQP1 promoted cell proliferation and colony formation in SACC83.

CONCLUSIONS

Our integrated, genome-wide screening method proved to be an effective strategy for detecting novel oncogenes in ACC. AQP1 is a promising oncogene candidate for ACC and is transcriptionally regulated by promoter hypomethylation.

Abstract 2042: Cancer-specific transcription factor BORIS has different effects on expression of its target genes via chromatin structure alterations

BORIS (Brother of the Regulator of Imprinted Sites), the paralog of insulator CTCF, is male germ line-specific transcription factor. BORIS and CTCF are highly structurally similar and share the same DNA sequence recognition sites. However, unlike widely expressed CTCF, BORIS is repressed in normal tissues and expressed only in testis and in several types of human cancers including head and neck cancers, lung cancers, melanomas and in tumor-derived cell lines. Suprabasin (SBSN) is a protein that is normally expressed only in suprabasal layer of epidermis, and was defined as a potential oncogene in non small cell lung carcinoma.

BORIS has been implicated in the activation of cancer-testis antigens (CTA) genes, such as MAGEA1 and NY-ESO-1. Additionally, BORIS is shown to bind hypermethylated DNA sites and alter the DNA methylation state of MAGEA1 promoter. BORIS shows abundant expression in a variety of cancers and its importance in tumorigenesis has been reported. However, there are controversial reports about the role of BORIS on tumorigenesis.

Using cell proliferation assays, immunoprecipitation, qPCR, qRT-PCR, QMSP and other techniques we show that SBSN is a newly discovered target of BORIS epigenetic regulation. Induction of low concentrations of BORIS leads to activation of the chromatin around SBSN transcription start site resulting in its 18-35 fold increase in expression in human cancer cell lines, including lung cancer. We have demonstrate that high BORIS concentrations can lead to subsequent repression of SBSN by 2-3 folds via chromatin repression (5-10 fold decrease in presence of active histone modifications, evaluated by ChIP and qPCR) and via DNA hypermethylation (4 folds increase, by QMSP). In a similar manner, overexpression of BORIS leads to eventual repression of other well-known BORIS targets, including NY-ESO-1 and H19. We also show that BORIS induces cell growth at low concentration and inhibits cell growth and colony formation at high concentrations.

Our data indicate that BORIS has different effects on target genes depending on its abundance around binding sites. Thus, low BORIS concentration leads to strong target activation and cell proliferation, while higher concentrations leads to repression of the target genes and cell growth inhibition. These data explain the enigmatic controversy of published materials about role of BORIS effect on tumorigenesis. Preliminary data also suggests that there are a group of transcription factors similar to BORIS that can recognize DNA methylation status of the binding sites. Therefore, they might have both stimulating and repressing effects on epigenetic regulation of target genes expression depending on the factor abundance.

Molecular analysis of epigenetic mechanisms of action of BORIS and BORIS-like transcription factors might be beneficial for further development of cancer therapeutics.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2042. doi:10.1158/1538-7445.AM2011-2042