Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma

Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (OPSCC) exhibits a different composition of epigenetic alterations. In this study, we identified differentially methylated regions (DMRs) with potential utility in screening for HPV-positive OPSCC. Genome wide DNA methylation was measured using methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) in 50 HPV-positive OPSCC tissues and 25 normal tissues. Fifty-one DMRs were defined with maximal methylation specificity to cancer samples. The Cancer Genome Atlas (TCGA) methylation array data was used to evaluate the performance of the proposed candidates. Supervised hierarchical clustering of 51 DMRs found that HPV-positive OPSCC had significantly higher DNA methylation levels compared to normal samples, and non-HPV-related head and neck squamous cell carcinoma (HNSCC). The methylation levels of all top 20 DNA methylation biomarkers in HPV-positive OPSCC were significantly higher than those in normal samples. Further confirmation using quantitative methylation specific PCR (QMSP) in an independent set of 24 HPV-related OPSCCs and 22 controls showed that 16 of the 20 candidates had significant higher methylation levels in HPV-positive OPSCC samples compared with controls. One candidate, OR6S1, had a sensitivity of 100%, while 17 candidates (KCNA3, EMBP1, CCDC181, DPP4, ITGA4, BEND4, ELMO1, SFMBT2, C1QL3, MIR129-2, NID2, HOXB4, ZNF439, ZNF93, VSTM2B, ZNF137P and ZNF773) had specificities of 100%. The prediction accuracy of the 20 candidates rang from 56.2% to 99.8% by receiver operating characteristic analysis. We have defined 20 highly specific DMRs in HPV-related OPSCC, which can potentially be applied to molecular-based detection tests and improve disease management.

Effects of a Comprehensive Performance Improvement Strategy on Postoperative Adverse Events in Head and Neck Surgery

Objectives

We aimed to demonstrate the efficacy of a multifaceted performance improvement regimen to reduce the incidence of adverse events following a spectrum of head and neck surgical procedures.

Methods

We conducted a chart review of patients who underwent a head and neck procedure between January 1, 2013, and October 30, 2015, at our institution, including 392 patients (450 procedures) before the quality improvement regimen was implemented (October 1, 2013) and 942 patients (1136 procedures) after implementation. Multivariate statistical models were used to investigate the association of clinical parameters and the intervention with postoperative adverse event rate.

Results

The incidence of adverse events decreased from 12.9% to 7.2% (95% CI, 2.46%-9.38%) after the intervention. Male sex (adjusted odds ratio [ORadj] = 1.57; 95% CI, 1.06-2.31) and the intervention (ORadj = 0.51; 95% CI, 0.35-0.74) were predictive of overall adverse event incidence by univariate and multivariate analyses. Although patient comorbid status, quantified with the Charlson Comorbidity Index, was not found to affect overall adverse event risk, each 1-point increase in index score was associated with a 17% relative increase (ORadj = 1.17; 95% CI, 1.03-1.33) in the odds of a high-grade adverse event.

Discussion

Comprehensive performance improvement programs can improve perioperative adverse event risk in head and neck surgery. Patient comorbid status and sex are considerations during assessment of the likelihood of high-grade and overall adverse event risk, respectively.

Implications for Practice

Given the cost of surgical complications, a comprehensive approach to perioperative risk mitigation is warranted.

Needle Biopsy of Routine Thyroid Nodules Should Be Performed Using a Capillary Action Technique with 24- to 27-Gauge Needles: A Systematic Review and Meta-Analysis

BACKGROUND

Fine-needle biopsy is the international standard for diagnostic evaluation of thyroid nodules. There is a lack of consensus regarding the optimal needle biopsy technique. The implementation of capillary action versus aspiration and the optimal needle gauge remain topics of debate.

METHODS

A systematic review of the Medline, Embase, and Cochrane databases was performed in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Articles evaluating the effects of capillary action versus aspiration and needle gauge on success rates of fine-needle biopsy of the thyroid were assessed for inclusion. The primary outcome of interest was the rate of non-diagnostic cytopathology.

RESULTS

Twenty-four articles with a collective 4428 nodules were ultimately included in the review. Twenty articles evaluated capillary action versus aspiration, and six evaluated needle gauge. All but two studies were prospective, most of which were blinded trials with or without randomization. Using a random-effects model, capillary action was associated with a statistically significant reduction in the relative risk of non-diagnostic cytopathology (relative risk = 0.57 [confidence interval 0.34-0.92]; p = 0.02). There was a nonsignificant trend in favor of smaller needle gauges.

CONCLUSION

Given the statistically significant deceased rate of non-diagnostic cytopathology with capillary action and the potential for increased pain and complications with larger needles without a proven benefit, needle biopsy of routine thyroid nodules should be performed without aspiration and with smaller needle gauges (24-27G).

Abstract 364: Differentially methylated super-enhancers regulate gene expression in human papillomavirus-related head and neck squamous cell carcinoma

Human papillomavirus-related head and neck squamous cell carcinoma (HPV+ HNSCC) is characterized by abundant gene expression changes, which cannot be explained by limited genetic alterations alone. We hypothesized that epigenetically regulated super-enhancers (SEs) are the drivers of aberrant gene expression in HPV+ HNSCC. We used integrated analysis of DNA methylation and gene expression data for cancer and noncancer oropharyngeal tissues to discover actionable SEs that regulate expression of target genes in HPV+ HNSCC. Since no SEs are currently defined for any HNSCC samples; we investigated 6196 SE elements that were obtained from the public domain for closely related tissues, including normal and tumor lung, and cervical cancer cell lines. We analyzed the methylation of these elements and gene expression of their nearby genes for 47 HPV+ HNSCC and their 25 noncancer controls. Overall, we found 122 differentially methylated SEs that had putative target (nearby) genes whose expression was correlated with enhancer methylation in HPV+ HNSCC. Of these, 107 were hypermethylated, and 15 were hypomethylated in tumors relative to normal samples. The pathway analysis revealed that the inferred SE-regulated genes were associated with pathways known to regulate carcinogenesis. Our data demonstrate that gene expression in HPV+ HNSCC may be regulated by epigenetic alterations in SE elements of related tissues.

Citation Format: Emily L. Flam, Dylan Z. Kelley, Elena Stavrovskaya, Ludmila Danilova, Theresa Guo, Michael Considine, Jiang Qian, Joseph A. Califano, Alexander V. Favorov, Elana J. Fertig, Daria A. Gaykalova. Differentially methylated super-enhancers regulate gene expression in human papillomavirus-related head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 364.

Abstract 3320: Discovery and development of DNA methylation biomarkers in human papillomavirus related oropharyngeal squamous cell carcinoma

Purpose: Human papillomavirus (HPV) related oropharyngeal squamous cell carcinoma (OPSCC) has an improved prognosis compared to cancers associated with tobacco and alcohol exposure, and also exhibits a different composition of epigenetic alterations. In this methylome-wide association study, we identified DNA methylation-based biomarkers with potential utility in screening for HPV positive OPSCC. Experimental Design: In the discovery stage, genome wide DNA methylation was measured using methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) in 50 HPV positive OPSCC tissues and 25 normal tissues. We defined 51 differentially methylated regions (DMRs) with maximal methylation specificity to cancer samples. We used TCGA methylation array data to evaluate the performance of the proposed candidates. Top 20 candidates were validated using quantitative methylation specific PCR (QMSP) in independent 24 HPV related OPSCCs and 22 controls. Results: Supervised hierarchical clustering of 51 DMRs based on TCGA methylation data found that HPV positive OPSCC had significantly higher DNA methylation levels compared to normal samples and head and neck squamous cell carcinoma (HNSCC) without HPV or with different tumor sites. The methylation levels of all top 20 candidates in HPV positive OPSCC were significantly higher than those in normal samples in TCGA data. 16 of these 20 candidates were found by QMSP to have significant higher methylation levels compared with controls. 2 candidates (CCDC181 and OR6S1) had a sensitivity of 100%, while 10 candidates (KCNA3, ITGA4, BEND4, ELMO1, SFMBT2, HOXB4, ZNF439, ZNF93, VSTM2B and ZNF773) had a specificity of 100%. Our 20 candidates were found by the receiver operating characteristic analysis to have a prediction accuracy ranging from 56.3% to 99.8%. Conclusions: This study discovered 20 epigenetic markers for detection of HPV related OPSCC, which can potentially be applied to develop a population based screening test and improve disease management.

Citation Format: Shuling Ren, Daria A. Gaykalova, Theresa W. Guo, Alexander V. Favorov, Elana J. Fertig, Zubair Khan, Peter M. DeJong, Mizuo Ando, Chao Liu, Akihiro Sakai, Takahito Fukusumi, Sunny Haft, Sayed Sadat, J Silvio Gutkind, Wayne M. Koch, Joseph A. Califano. Discovery and development of DNA methylation biomarkers in human papillomavirus related oropharyngeal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3320.

HEY1 is expressed independent of NOTCH1 and is associated with poor prognosis in head and neck squamous cell carcinoma

OBJECTIVES

Notch signaling is frequently altered in head and neck squamous cell carcinoma (HNSCC). However, the nature and clinical implications of this dysregulation are not well understood. We previously described an association of transcriptionally active NOTCH1 Intracellular Domain (NICD1) immunohistochemical (IHC) expression pattern with high-risk pathologic characteristics. Here we further characterize Notch signaling in HNSCC.

MATERIALS AND METHODS

IHC expression patterns and clinicopathologic associations of Notch pathway molecules were evaluated among 78 tumors with known NOTCH1 mutation status. IHC was performed for JAG1, a NOTCH1 activating ligand, and HEY1, an NICD1 transcriptional target and Notch pathway activation marker. IHC pattern and H-score (% staining × intensity) were recorded and compared to clinicopathologic characteristics and survival. Survival was analyzed using Kaplan Meier method and Cox proportional hazards models (HR).

RESULTS

JAG1 and NICD1 expression patterns were highly concordant among tumors without truncating NOTCH1 mutations (p < 0.001), but were dissimilar among tumors with truncating NOTCH1 mutations (p = 0.24). There was evidence for JAG1-independent NOTCH1 activation among seven tumors, all with wild-type NOTCH1. HEY1 expression was associated with neither JAG1 nor NICD1 expression, but was associated with NOTCH1 mutation status (p = 0.03). Twelve (16%) tumors expressed HEY1 but not NICD1. Higher HEY1 H-score was significantly associated with worse overall (adjusted hazard ratio [aHR] 2.0, 95% CI = 1.0-4.2) and disease-specific (aHR = 3.3, 95% CI = 1.4-7.9) survival, whereas JAG1 and NICD1 expression were not associated with survival.

CONCLUSIONS

These findings suggest both NOTCH1-dependent and -independent HEY1 regulation, and imply a previously unrecognized prognostic role for HEY1 in HNSCC.

Identification of potential biomarkers of head and neck squamous cell carcinoma using iTRAQ based quantitative proteomic approach

Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in India. Despite improvements in treatment strategy, the survival rates of HNSCC patients remain poor. Thus, it is necessary to identify biomarkers that can be used for early detection of disease. In this study, we employed iTRAQ-based quantitative mass spectrometry analysis to identify dysregulated proteins from a panel of head and neck squamous cell carcinoma (HNSCC) cell lines. We identified 2468 proteins, of which 496 proteins were found to be dysregulated in at least two out of three HNSCC cell lines compared to immortalized normal oral keratinocytes. We detected increased expression of replication protein A1 (RPA1) and heat shock protein family H (Hsp110) member 1 (HSPH1), in HNSCC cell lines compared to control. The differentially expressed proteins were further validated using parallel reaction monitoring (PRM) and western blot analysis in HNSCC cell lines. Immunohistochemistry-based validation using HNSCC tissue microarrays revealed overexpression of RPA1 and HSPH1 in 15.7% and 32.2% of the tested cases, respectively. Our study illustrates quantitative proteomics as a robust approach for identification of potential HNSCC biomarkers. The proteomic data has been submitted to ProteomeXchange Consortium (http://www.proteomecentral.proteomexchange.org) via the PRIDE public data repository accessible using the data identifier - PXD009241.

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance

Background

Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients’ treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors.

Methods

To determine the dynamics of these molecular changes, we obtained high throughput omics data (RNA-sequencing and DNA methylation) weekly during the development of cetuximab resistance in a head and neck cancer in vitro model. The CoGAPS unsupervised algorithm was used to determine the dynamics of the molecular changes associated with resistance during the time course of resistance development.

Results

CoGAPS was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically.

Conclusions

Genes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize the resistant phenotype. These genes include FGFR1, which was associated with EGFR inhibitors resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. This understanding of the time course progression of molecular changes in acquired resistance is important for the development of alternative treatment strategies that would introduce appropriate selection of new drugs to treat cancer before the resistant phenotype develops.

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0545-2) contains supplementary material, which is available to authorized users.

Positive Surgical Margins in the 10 Most Common Solid Cancers

A positive surgical margin (PSM) following cancer resection oftentimes necessitates adjuvant treatments and carries significant financial and prognostic implications. We sought to compare PSM rates for the ten most common solid cancers in the United States, and to assess trends over time. Over 10 million patients were identified in the National Cancer Data Base from 1998–2012, and 6.5 million had surgical margin data. PSM rates were compared between two time periods, 1998–2002 and 2008–2012. PSM was positively correlated with tumor category and grade. Ovarian and prostate cancers had the highest PSM prevalence in women and men, respectively. The highest PSM rates for cancers affecting both genders were seen for oral cavity tumors. PSM rates for breast cancer and lung and bronchus cancer in both men and women declined over the study period. PSM increases were seen for bladder, colon and rectum, and kidney and renal pelvis cancers. This large-scale analysis appraises the magnitude of PSM in the United States in order to focus future efforts on improving oncologic surgical care with the goal of optimizing value and improving patient outcomes.

MiR-124 acts as a tumor suppressor by inhibiting the expression of sphingosine kinase 1 and its downstream signaling in head and neck squamous cell carcinoma

By analyzing the expression profile of microRNAs in head and neck squamous cell carcinomas (HNSCC), we found that the expression level of miR-124 was 4.59-fold lower in tumors than in normal tissues. To understand its functions, we generated a miR-124-expressing subline (JHU-22^miR124) and a mock vector-transfected subline (JHU-22^vec) by transfecting the mimic of miR-124 into JHU-22 cancer cells. Restored expression of miR-124 in JHU-22^miR124 cells led to reduced cell proliferation, delayed colony formation, and decreased tumor growth, indicating a tumor-suppressive effect of miR-124. Subsequent target search revealed that the 3′-UTR of SphK1 mRNA carries a complementary site for the seed region of miR-124. SphK1 was also detected to be overexpressed in HNSCC cell lines, but down-expressed in JHU-22^miR124 cells and tumor xenografts. These results suggest that SphK1 is a target of miR-124. To confirm this finding, we constructed a 3′-UTR-Luc-SphK1 vector and a binding site-mutated luciferase reporter vector. Co-transfection of 3′-UTR-Luc-SphK1 with miR-124 expression vector exhibited a 9-fold decrease in luciferase activity compared with mutated vector, suggesting that miR-124 inhibits SphK1 activity directly. Further studies on downstream signaling demonstrated accumulation of ceramide, increased expression of the pro-apoptotic Bax, BAD and PARP, decreased expression of the anti-apoptotic Bcl-2 and Bcl-xL, and enhanced expression of cytochrome c and caspase proteins in JHU-22^miR124 compared with JHU-22^vec cells and tumor xenografts. We conclude that miR-124 acts as a tumor suppressor in HNSCC by directly inhibiting SphK1 activity and its downstream signals.

The NOTCH Pathway in Head and Neck Squamous Cell Carcinoma

Comprehensive genomic analyses have been performed for head and neck squamous cell carcinoma (HNSCC), revealing a significant rate of NOTCH1 mutations and identifying NOTCH1 as the second most frequently mutated gene after TP53. Most NOTCH1 mutations are considered inactivating, indicating that NOTCH1 is a tumor suppressor gene. On the other hand, cohorts from Asian populations with HNSCC have shown activating NOTCH1 mutations. HNSCC with NOTCH1 mutations have a worse prognosis than the NOTCH1 wild-type tumors. Additional data on other NOTCH family members have shown that NOTCH promotes HNSCC progression. NOTCH family members, including NOTCH pathway genes, are upregulated in HNSCC compared with normal tissues, and inhibition of the NOTCH pathway decreases cell proliferation and invasion. NOTCH activity in HNSCC is therefore contextual, and NOTCH in HNSCC is considered to have a bimodal role as a tumor suppressor and an oncogene. In this review, recent understandings of NOTCH pathway genes, including NOTCH genes, in HNSCC are described. In addition, the implications of NOTCH pathway alteration for HNSCC-specific NOTCH-targeted cancer therapy are explored.

Computational methods reveal novel functionalities of PIWI-interacting RNAs in human papillomavirus-induced head and neck squamous cell carcinoma

Human papillomavirus (HPV) infection is the fastest growing cause of head and neck squamous cell carcinoma (HNSCC) today, but its role in malignant transformation remains unclear. This study aimed to conduct a comprehensive investigation of PIWI-interacting RNA (piRNA) alterations and functionalities in HPV-induced HNSCC. Using 77 RNA-sequencing datasets from TCGA, we examined differential expression of piRNAs between HPV16(+) HNSCC and HPV(–) Normal samples, identifying a panel of 30 HPV-dysregulated piRNAs. We then computationally investigated the potential mechanistic significances of these transcripts in HPV-induced HNSCC, identifying our panel of piRNAs to associate with the protein PIWIL4 as well as the RTL family of retrotransposon-like genes, possibly through direct binding interactions. We also recognized several HPV-dysregulated transcripts for their correlations with well-documented mutations and copy number variations in HNSCC as well as HNSCC clinical variables, demonstrating the potential ability of our piRNAs to play important roles in large-scale modulation of HNSCC in addition to their direct, smaller-scale interactions in this malignancy. The differential expression of key piRNAs, including NONHSAT077364, NONHSAT102574, and NONHSAT128479, was verified in vitro by evaluating endogenous expression in HPV(+) cancer vs. HPV(–) normal cell lines. Overall, our novel study provides a rigorous investigation of piRNA dysregulation in HPV-related HNSCC, and lends critical insight into the idea that these small regulatory transcripts may play crucial and previously unidentified roles in tumor pathogenesis and progression.

Abstract 05: Untangling the gene-epigenome networks: Timing of epigenetic regulation of gene expression in acquired cetuximab resistance gene programs

The current study performs time course RNA-seq and DNA methylation profiling to determine the complex interactions between gene expression and epigenetic changes in acquired therapeutic resistance. The genomics era provides widespread characterization of the genomic landscape of tumors and has enabled precision treatment strategies. Currently, epidermal growth factor receptor (EGFR) inhibitors are the only FDA-approved targeted therapy for clinical use in head and neck squamous cell carcinoma (HNSCC). EGFR inhibitors are only effective in a subset of each of these tumors. Moreover, patients with de novo sensitivity to EGFR inhibitors often subsequently acquire resistance and succumb to their tumors. Numerous genetic and epigenetic alterations occur in tumors with acquired resistance. However, their timing and function remain unknown. Therefore, we develop new computational techniques to find gene programs associated with the acquisition of resistance.

High-throughput transcriptional profiling enables unprecedented characterization of individual genes during cancer treatment. However, identifying and targeting mechanisms of EGFR resistance from these high-throughput data requires novel systems biology techniques that can discriminate altered cellular signaling pathways in response to cancer treatment. Therefore, we developed a new bioinformatics algorithm Coordinated Gene Activity in Pattern Sets (CoGAPS) to quantify multiplexed regulation and gene reuse in oncogenic signaling. To test this algorithm, we modified the HaCaT keratinocyte cell line model of premalignancy to simulate cancer cells with constitutive overexpression of wild-type EGFR and with activating mutations in HRAS and PIK3CA in a controlled genetic background. We apply CoGAPS to gene expression data from these models. This algorithm quantified relative changes in cellular signaling pathway activity in these data, not accessible to standard gene comparisons. Increases in CoGAPS pathway signatures from HRAS also occurred in gene expression data from the cetuximab resistant HNSCC cell line (1CC8) relative to its parental, sensitive cell line (UMSCC1).

Investigation of the mechanisms of acquired resistance has previously been limited by reliance on case-control comparisons between sensitive and resistant cells, such as the UMSCC1 and 1CC8 cell lines. Since activity in cellular signaling pathways evolves during cetuximab resistance, it is essential to extend these case-control paradigms to quantify the dynamics responsible for resistance. Therefore, we developed a novel time course analysis to determine the molecular mechanisms of acquired cetuximab resistance in HNSCC. Specifically, we treated the cetuximab sensitive SCC25 HNSCC cell line over generations with both cetuximab and PBS. This long-term treatment protocol models the progression of acquired therapeutic resistance, including controls for clonal selection unrelated to treatment. Overexpression of the previous HRAS gene program also occurs in gene expression data measured during acquired cetuximab resistance in SCC25. We also measure DNA methylation during this time course to find the driver of this aberrant signaling associated with resistance. We apply CoGAPS analysis to the time course data for both DNA methylation and gene expression. This analysis distinguished early gene expression changes from cetuximab treatment from longer-term epigenetic alterations to gene expression during acquired resistance. Epigenetic regulation of FGFR1 expression emerged as the dominant mechanism of acquired therapeutic resistance in this system. Thus, our integration of time course DNA methylation and gene expression data enables unprecedented inference of the timing of targetable gene-epigenome programs responsible for acquired resistance.

Citation Format: Genevieve Stein-O'Brien, Luciane T. Kagohara, Sijia Li, Manjusha Thakar, Ruchira Ranaweera, Michael Considine, Ludmila V. Danilova, Hiroyuki Ozawa, Joseph A. Califano, Daria A. Gaykalova, Michael F. Ochs, Christine H. Chung, Elana J. Fertig. Untangling the gene-epigenome networks: Timing of epigenetic regulation of gene expression in acquired cetuximab resistance gene programs [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; April 23-25, 2017; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(23_Suppl):Abstract nr 05.

The NOTCH4-HEY1 Pathway Induces Epithelial-Mesenchymal Transition in Head and Neck Squamous Cell Carcinoma

Purpose: Recently, several comprehensive genomic analyses demonstrated NOTCH1 and NOTCH3 mutations in head and neck squamous cell carcinoma (HNSCC) in approximately 20% of cases. Similar to other types of cancers, these studies also indicate that the NOTCH pathway is closely related to HNSCC progression. However, the role of NOTCH4 in HNSCC is less well understood.Experimental Design: We analyzed NOTCH4 pathway and downstream gene expression in the TCGA data set. To explore the functional role of NOTCH4, we performed in vitro proliferation, cisplatin viability, apoptosis, and cell-cycle assays. We also compared the relationships among NOTCH4, HEY1, and epithelial-mesenchymal transition (EMT)-related genes using the TCGA data set and in vitro assays.Results:HEY1 is specifically upregulated in HNSCC compared with normal tissues in the TCGA data set. NOTCH4 is more significantly related to HEY1 activation in HNSCC in comparison with other NOTCH receptors. NOTCH4 promotes cell proliferation, cisplatin resistance, inhibition of apoptosis, and cell-cycle dysregulation. Furthermore, NOTCH4 and HEY1 upregulation resulted in decreased E-cadherin expression and increased Vimentin, Fibronectin, TWIST1, and SOX2 expression. NOTCH4 and HEY1 expression was associated with an EMT phenotype as well as increased invasion and cell migration.Conclusions: In HNSCC, the NOTCH4-HEY1 pathway is specifically upregulated, induces proliferation and cisplatin resistance, and promotes EMT. Clin Cancer Res; 24(3); 619-33. ©2017 AACR.

Radiation Therapy for Oropharyngeal Squamous Cell Carcinoma: American Society of Clinical Oncology Endorsement of the American Society for Radiation Oncology Evidence-Based Clinical Practice Guideline

Purpose The American Society for Radiation Oncology (ASTRO) produced an evidence-based guideline on radiation therapy in oropharyngeal squamous cell carcinoma (OPSCC) that was determined to be relevant to the American Society of Clinical Oncology (ASCO) membership. After applying standard critical appraisal policy and endorsement procedures, ASCO chose to endorse the ASTRO guideline. Methods The ASTRO guideline was reviewed by ASCO content experts for clinical accuracy and by ASCO methodologists for developmental rigor. On favorable review, an ASCO Expert Panel was convened to review the guideline contents and recommendations. The ASCO guideline approval body, the Clinical Practice Guidelines Committee, approved the final endorsement. Results The ASCO Expert Panel determined that the ASTRO guideline recommendations, published in July 2017, are clear, thorough, and based upon the most relevant scientific evidence. ASCO endorsed the ASTRO guideline and added minor qualifying statements. Recommendations Recommendations for the addition of systemic therapy to definitive radiotherapy in the treatment of OPSCC, postoperative radiotherapy with and without systemic therapy following primary surgery of OPSCC, induction chemotherapy in the treatment of OPSCC, and the appropriate dose, fractionation, and volume regimens with and without systemic therapy in the treatment of OPSCC are outlined for a variety of disease stages and clinical scenarios. ASCO Endorsement Panel qualifying statements and minor modifications were made to the ASTRO recommendations. The staging system that is referenced in these guidelines is the American Joint Committee on Cancer Staging Manual, 7th edition. Additional information is available at: www.asco.org/head-neck-cancer-guidelines and www.asco.org/guidelineswiki .

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV⁺) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis. Cancer Res; 77(23); 6538-50. ©2017 AACR.

A comprehensive study of smoking-specific microRNA alterations in head and neck squamous cell carcinoma

OBJECTIVE

While tobacco smoking is a well-known risk factor for head and neck squamous cell carcinoma (HNSCC), the molecular mechanisms underlying tobacco-induced HNSCC remain unclear. This study sought to comprehensively identify microRNA (miRNA) alterations and evaluate their clinical relevance in smoking-induced HNSCC pathogenesis and progression.

MATERIALS AND METHODS

Using small RNA-sequencing data and clinical data from 145 HNSCC patients, we performed a series of differential expression and correlation analyses to identify a panel of tobacco-dysregulated miRNAs associated with key clinical characteristics in HNSCC. We then examined the expression patterns of these miRNAs in normal epithelial cell lines following exposure to cigarette smoke extract.

RESULTS

Our analyses revealed distinct panels of miRNAs to be dysregulated with smoking status and associated with additional clinical features, including tumor stage, metastasis, anatomic site, and patient survival. The differential expression of key miRNAs, including miR-101, miR-181b, miR-486, and miR-1301, was verified in cigarette-treated epithelial cell lines, suggesting their potential roles in the early development of smoking-related HNSCCs.

CONCLUSION

Specific alterations in miRNA expression may be traced to tobacco use and are associated with important HNSCC clinical characteristics. Future studies of these miRNAs may be valuable for furthering the understanding and targeted treatment of smoking-associated HNSCC.

Abstract 2424: The in-parallel whole-genome ChIP-Seq analysis of primary tissues, patient derived xenografts, and cancer cell lines from HPV-relative HNSCC samples

This project develops a novel experimental technique to perform ChIP-Seq (chromatin immunoprecipitation with massively parallel DNA sequencing) analysis of chromatin structure in primary tumor tissues from high risk HPV-related head and neck squamous cell carcinomas (HPV+ HNSCC). Recent data suggest that chromatin structure is the central regulator and predictor of cancer-specific expression and mutagenesis landscape of diseased cells. Genome-wide gene expression dysregulation in many tumors, including HPV+ HNSCC, are incompletely described by current knowledge. Methods for study of chromatin structure in primary tumor tissue are needed to better understand the role global epigenetic changes may play in these tumors. However, ChIP-Seq, which is the state-of-the-art method of elucidating chromatin structure, until now, has not been reliably performed on any HNSCC samples. Because chromatin structure is disrupted at room temperature, ChIP-Seq is especially complicated for primary patient tissues, which are primarily obtained as surgical waste after pathology review. Snap freezing of leftover waste surgical tissues and further tissue thawing for the analysis decreases chromatin structure integrity necessary for highly sensitive ChIP-Seq methodology, especially for tumor samples with chromatin structure deformed during carcinogenesis. To improve the chromatin structure integrity in tumor sample we added a xenografting step and minimized the exposure of cancer tissue to room temperature conditions after mouse surgery. We also minimized patient non-cancer tissue preservation at ambient temperature after patient surgery. We successfully performed ChIP-Seq for H3K4me3, H3K9me3, and H3K9ac on frozen uvulopalatopharyngoplasty (UPPP) primary tissues, frozen patient derived xenograft tissues, and freshly-cultured head and neck squamous cell carcinoma cell lines, revealing comparable success rates between tissue type and sample preservation techniques. ChIP-Seq techniques were performed and cross validated using tried and true qRT-PCR methods to demonstrate data reproducibility. The biological relevance of the ChIP-Seq data was confirmed through massive RNA-Seq analysis of 47 HPV+ HNSCC samples and 25 non-cancer controls. Analysis revealed that most H3K9ac and H3K9me3 enrichment is similar in primary tissues, regardless of disease status. Only small portion of them showed differential histone enrichment, which correlated with differential expression of corresponding genes. On the other hand, H3K4me3 showed strong tissue specificity and were found differentially enriched especially in tumor samples. The proposed experimental pipeline demonstrates high reproducibility between biological replicates, diversity of tissue models, and low dependence of ChIP-Seq analysis on tissue preservation techniques.

Citation Format: Dylan Z. Kelley, Emily L. Flam, Hildegard A. Wulf, Theresa Guo, Evgeny Izumchenko, Dzov A. Singman, Ludmila V. Danilova, Elena D. Stavrovskaya, Michael Considine, Justin A. Bishop, William H. Westra, Zubair Khan, Wayne M. Koch, David Sidransky, Sarah Wheelan, Joseph A. Califano, Alexander V. Favorov, Elana J. Fertig, Daria A. Gaykalova. The in-parallel whole-genome ChIP-Seq analysis of primary tissues, patient derived xenografts, and cancer cell lines from HPV-relative HNSCC samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2424. doi:10.1158/1538-7445.AM2017-2424

Abstract 4474: Functional characterization of alternatively spliced GSN in head and neck cancer

PURPOSE: Analyze the functional role of alternative splicing in HPV-related (HPV+) Head and Neck Squamous Cell Carcinoma (HNSCC) biology and oncogenesis.

HPV+ HNSCC incidence is rapidly increasing, while its oncogenic mechanisms, demographic, and clinico-pathological characteristics are largely uncharacterized and discrete from those of HPV- HNSCC. Investigation into the molecular biology of HPV pathogenesis in HNSCC may help with creation of more specific clinical tools for diagnosis and treatment, which are limited and lack accuracy. Alternative Splicing Events (ASEs), post-transcriptional modifications resulting in variant transcripts leading to alternative protein isoforms, have been under-investigated as putative causes of gene expression dysregulation in HPV+ HNSCC. Using RNA-Seq data, a genome-wide ASE discovery analysis was performed on a JHU HPV+ HNSCC cohort, which has expanded HPV+ HNSCC transcriptional characterization by identifying novel ASE biomarkers implicated in carcinogenic progression. Outlier Gene Set Analysis (OGSA) was used to identify genes with high rates of ASE and results were validated in TCGA samples from seven different cancer types. To verify the functional implications of differential isoform expression, vectors for knock-in and knock-down of WT-GSN and ASE-GSN isoforms were developed to evaluate changes in cell proliferation and invasion. ASE-GSN/WT-GSN ratio outliers were identified by OGSA in tumor samples from discovery JHU HPV+ HNSCC cohort, as well as in TCGA public domain data from HNSCC, Lung Squamous Cell Carcinoma, Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma, Bladder Urothelial Carcinoma, Breast Invasive Carcinoma, and Colon Adenocarcinoma. The increased ASE-GSN/WT-GSN ratio was also observed in a cohort of HPV+ Head and Neck Cancer Cell lines. SCC61 and UM-SCC-22B HNSCC cell lines were used to evaluate the function GSN ASEs in vitro. Overall expression levels of both GSN isoforms inversely correlated with cell proliferation whereas the high ratio of ASE-GSN to WT-GSN correlated with increased cellular invasion of stroma in vitro. Additionally, a decrease or increase in expression of one isoform is seen to cause a compensatory increase or decrease in the other isoform respectively. ASE-GSN outliers correlated with HPV+ cancers indicate that expression ratio between GSN isoforms is related to tumor behavior, which is reinforced in vitro where WT-GSN is inversely correlated and ASE-GSN is directly correlated to with cell invasion. These relationships suggest that both overall expression and balance between the two GSN isoforms are mediating factors in cell death or proliferation, while shorter ASE-GSN is more likely to indicate progression to cancer. Finally, we propose a mechanism for the role of GSN isoforms in apoptosis and metastasis, in which trends in expression between WT- and ASE-GSN isoforms can alternatively affect rates of apoptosis or metastatic ability.

Citation Format: Dylan Z. Kelley, Emily L. Flam, Theresa Guo, Craig Bohrson, Michael Considine, Ludmila V. Danilova, Justin A. Bishop, Chi Zhang, Wayne M. Koch, David Sidransky, William Westra, Sarah Wheelan, Liliana Florea, Elana J. Fertig, Joseph A. Califano, Daria A. Gaykalova. Functional characterization of alternatively spliced GSN in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4474. doi:10.1158/1538-7445.AM2017-4474

Abstract 3577: Splice expression variation analysis (SEVA) for differential gene isoform usage in cancer

Alternative splicing events (ASE) are a significant component of expression alterations in cancer, and have been demonstrated to be critically important in the development of malignant phenotypes in a variety of tumors. These alternative gene isoforms alter cell-signaling networks and serve as a hidden source of tumor-driving alterations not identified in multi-omics analyses. Recent studies have demonstrated that reads from RNA-seq data can infer gene isoforms expressed in a single sample. Therefore, RNA-seq data of tumors offers the opportunity to systematically evaluate expressed gene isoforms and identify splicing events in cancer samples.

To characterize a cancer specific ASEs landscape, it is essential to perform differential splice variant expression analysis to identify isoform variants that are unique to tumor samples compared to normal tissue. In spite of the breadth of ASE algorithms, few have been validated in primary tumor samples. Current methods for differential splice variant analysis compare mean expression of gene isoforms in sample groups. Because these variants are tumor-specific, ASEs are expected to have more variable exon junction expression than normal samples. Therefore, current differential ASE analysis algorithms from RNA-seq may not account for heterogeneous gene isoform usage in tumors. To address this, we introduce Splice Expression Variability Analysis (SEVA) to detect differential splice variation usage in tumor and normal samples and accounts for tumor heterogeneity. This algorithm compares the degree of variability of junction expression profiles within a population of normal samples relative to that in tumor samples.

The performance of SEVA was compared with two existing algorithms, EBSeq and DiffSplice, in simulated and real RNA-seq data. Simulated data suggest that SEVA is robust and computationally efficient relative to EBSeq and DiffSplice. In contrast to EBSeq and DiffSplice, SEVA was able to identify alternative splicing events independent of overall gene expression differences. Finally, additional validation was performed using RNA-seq data for primary tumor data from HPV-positive oropharynx squamous cell carcinoma (OPSCC) tumors and normal samples from both TCGA and an independent tumor cohort of 46 OPSCC tumors and 25 normal samples. In these tumor samples, SEVA finds cancer-specific ASEs in genes that are independent of their differential expression status. Moreover, SEVA finds approximately hundreds of splice variant candidates, manageable for experimental validation in contrast to the thousands of candidates found with EBSeq or DiffSplice. These candidates include experimentally validated splice variants in HNSCC from a previous microarray study. Based on performance in both simulated and real data, SEVA represents a robust algorithm that is well suited for differential ASE analysis, particularly in RNA-sequencing data from heterogeneous primary tumor samples.

Citation Format: Bahman Afsari, Theresa Guo, Michael Considine, Dylan Kelley, Emily Flam, Liliana Florea, Patrick Ha, Donald Geman, Michael F. Ochs, Joseph A. Califano, Daria A. Gaykalova, Alexander V. Favorov, Elana J. Fertig. Splice expression variation analysis (SEVA) for differential gene isoform usage in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3577. doi:10.1158/1538-7445.AM2017-3577

Abstract 86: Time course analysis of gene expression and epigenetic interactions in acquired cetuximab resistance in head and neck squamous cell carcinoma

The current study performs time course genomics and epigenomics profiling to determine the complex dynamics of interactions between gene expression and epigenetic changes that alter cellular signaling and drive acquired therapeutic resistance. Targeted therapeutic agents block the activity of specific molecules critical for tumor progression. Cetuximab is a monoclonal antibody against EGFR currently used in the treatment of head and neck squamous cell carcinoma (HNSCC) and metastatic colorectal cancers. Similar to many targeted therapeutics, cetuximab improves survival for a brief period of two years, after which most patients acquire resistance resulting in tumor progression or recurrence. The mechanisms that alter cellular signaling pathways and cause resistance are poorly understood. We hypothesize that the molecular alterations that precede the resistance phenotype are more likely to be responsible for the resistance than the widespread alterations observed once the resistance is established. To test this hypothesis, we develop a novel time course experimental and bioinformatics model of acquired resistance. Specifically, this protocol enables weekly profiling of RNA, DNA, and proliferation as cetuximab resistance developed in vitro. We apply the CoGAPS bioinformatics algorithm to perform integrated analysis of gene expression and DNA methylation. This analysis distinguishes signatures of sustained activation of cellular pathways in response to treatment from signatures of clonal expansion associated with acquired cetuximab resistance. Despite identifying massive changes in gene expression driven by therapeutic response, only the expression changes associated with the acquired resistance, and not response to treatment, have corresponding epigenetic signatures. The genomic signature associated with acquired resistance is enriched for gene targets of the AP-2 family of transcription factors. In a previous study, we found that these gene targets were overexpressed after short-term treatment in cetuximab sensitive cell lines and HNSCC tumors. Our data suggest that this family of transcription factors serves as a feedback mechanism to maintain homeostasis to growth factors receptor signaling. As a result, AP-2 transcription factors serve as a natural mechanism to cause subsequent therapeutic resistance without addition of genetic alterations. Further investigation is needed to determine the role of AP-2 transcription factors in acquired cetuximab resistance.

Citation Format: Luciane T. Kagohara, Genevieve Stein-O'Brien, Sijia Li, Manjusha Thakar, Ruchira Ranaweera, Michael Considine, Joseph A. Califano, Christine H. Chung, Daria Gaykalova, Elana J. Fertig. Time course analysis of gene expression and epigenetic interactions in acquired cetuximab resistance in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 86. doi:10.1158/1538-7445.AM2017-86

Abstract 1332: NOTCH - HEY1 pathway induces EMT in head and neck squamous cell carcinoma

Background

Head and neck squamous cell carcinoma (HNSCC) is noted to have a NOTCH mutation rate of 20% within the Cancer Genome Atlas (TCGA) dataset consistent with tumor suppressor gene status. However, NOTCH genes are also upregulated in wild type HNSCC and show signs of downstream activation in a substantial proportion of HNSCC. In this study, we aimed to further explore the potential for NOTCH pathways to be activated in HNSCC.

Material and Methods

mRNA sequence of TCGA data includes 520 HNSCC tumors and 46 normal tissues. We used 447 HNSCC excluding 73 tumors with NOTCH mutations. The activated groups of NOTCH downstream genes were defined as tumors with expression 1 standard deviation above the mean of normal tissue. We used four HNSCC cell lines (SKN3, Cal27, SCC61, SCC090) to ascertain the results of the TCGA analysis in vitro.

Result

In TCGA analysis, HEY1 activated HNSCC had significant more expression of NOTCH pathway genes. In particular NOTCH4 had the most significant correlation with HEY1 activation among NOTCH receptors. To confirm this result in vitro, HEY1 expression was compared between si-control and si-NOTCH4 of SKN3, Cal27, SCC61 and SCC090. As expected, HEY1 expression in all si-NOTCH4 treated cell lines were significant decreased. Next, we examined the relationship about NOTCH4 and an epithelial mesenchymal transition phenotype (EMT). Using TCGA data, we found that mesenchymal marker genes were significantly increased in high NOTCH4 group. In vitro experiments, si-NOTCH4 cells decreased mesenchymal marker gene expression such as Fibronectin and TWIST1. We also examined HEY1 function. Similar to NOTCH4, it was found that HEY1 is significantly related to EMT in silico and in vitro.

Conclusion

The NOTCH4-HEY1 pathway is significantly upregulated in HNSCC and induces EMT.

Citation Format: Takahito Fukusumi, Theresa W. Guo, Shuling Ren, Akihiro Sakai, Mizuo Ando, Sunny Haft, Chao Liu, Joseph A. Califano. NOTCH - HEY1 pathway induces EMT in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1332. doi:10.1158/1538-7445.AM2017-1332

Abstract 3353: An epigenetic biomarker panel in HPV related oropharyngeal squamous cell carcinoma

HPV related head and neck squamous cell carcinoma (HNSCC) is known to occur in a separate patient population in comparison to tobacco related HNSCC, and also exhibits less mutational, genetic, and chromosomal alterations, and a different composition of epigenetic alterations. In particular, HPV is present in up to 70% of oropharyngeal squamous cell carcinoma (OPSCC), and is driving the increase in incidence rates of OPSCC. Given the precedent for successful screening for cervical cancer, it is attractive to consider similar population based screening for HPV related OPSCC. Here, we developed an epigenetic biomarker panel that can be combined with high risk HPV DNA detection with potential utility in screening. We performed high throughput qMBD-seq analysis on 50 primary HPV positive OPSCC samples and 25 UPPP normal samples. Subsequently, we performed an outlier analysis and ranking strategy of 100 bp segmented regions within this discovery cohort and defined 20 differentially methylated regions to be used as biomarkers for detection. Simultaneously, we validated these 20 biomarker candidates using TCGA methylation array dataset and found that the methylation levels of these 20 candidates in HPV positive OPSCC were significantly higher than those in normal samples. Moreover, we created QMSP assays for these genes, and validated EMBP1 and KCNA3 in a separate validation cohort including tissue and saliva from 46 HPV related OPSCC and 25 normal controls. The sensitivity and specificity values for EMBP1, KCNA3 or both in tissue and saliva are shown. EMBP1 has a high sensitivity in tissue and a high specificity in saliva, while KCNA3 has a high specificity in both tissue and saliva. A panel including both genes has an extremely high sensitivity. Ultimately, we defined a panel of two differentially methylation regions that has a high sensitivity in tissue. This study might serve as a diagnostic biomarker development trial for HPV OPSCC detection with potential application for development of a population based screening test.

Sensitivity and specificity for HPV related OPSCC in tissue and salivaTissueTissueSalivaSalivaGeneSensitivitySpecificitySensitivitySpecificityEMBP197.7%83.3%13.3%94.7%KCNA376.7%92.0%13.3%94.7%EMBP1& KCNA3100.0%84.0%13.0%84.2%

Citation Format: Shuling Ren, Daria A. Gaykalova, Theresa Guo, Zubair Khan, Mizuo Ando, Sunny Haft, Joseph A. Califano. An epigenetic biomarker panel in HPV related oropharyngeal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3353. doi:10.1158/1538-7445.AM2017-3353

Abstract 4800: A next-gen animal model to Study PIK3CA-mTOR driven HPV-related oral malignancies

The rising incidence of HPV-associated malignancies, especially for head and neck squamous cell carcinoma (HNSCC), has highlighted the urgent need to understand the role of HPV-16 E6/E7 oncogenes in cancer initiation and progression. For that propose we decided to generate a doxycycline inducible E6/E7 transgenic mouse targeting E6/E7 onco-proteins to the basal epithelia layer, including the stem cell compartment, through a doxycycline inducible cytokeratin 5 promoter (cK5-rtTA). This system allows to turn on the expression of HPV genes after birth, minimizing the negative effect that viral E6/E7 expression may have during embryonic development, and mimicking the natural infection process that usually happens in adults after initiation of sexual activities. Interestingly, we found that after doxycycline induction, both E6 and E7 were highly expressed, resulting in a clear increase in the number of proliferative cells even in the suprabasal layers, which results in rapid epidermal hyperplasia. However, in our animal mouse model HPV-16 E6/E7 expression alone was not sufficient to induce spontaneous squamous carcinomas (SCC). Due that we decided to challenge the oncogenic role of HPV using a classical chemical carcinogenesis protocol (DMBA-TPA). These mice develop SCC rapidly after a single exposure to a skin carcinogen, DMBA, which was increased by the prolonged exposure to a tumor promoter, TPA. These data suggest that only few oncogenic hits may be sufficient to induce cancer in humans already infected with HPV-16 E6/E7. Then, we decided to elucidate whether or not a few genomic alterations in combination with HPV-16 expression may be sufficient to induce cancer. One of the most frequent mutations in HNSCC, including HPV-associated cancers, are those affecting the PI3K-mTOR pathway. Based on that, we engineered a genetically defined mouse model combining HPV-16 E6/E7 and PIk3CAH1047R expression under the control of a cytokeratin 14 promoter driven tamoxifen-regulated Cre recombinase (cK14-CreERTM). Surprisingly, we found that upon tamoxifen activation mice develop oral cancer in only few weeks. Furthermore, our HPV-related cancer mouse models exhibited a marker increase of mTOR activation which is a key oncogenic driver in malignant progression to SCC. Remarkably, rapamycin, an mTOR inhibitor, was able to block tumor development, supporting the potential clinical use of direct and indirect mTOR inhibitors as a molecular targeted approach for prevention of HPV-associated malignancies.

Citation Format: Juan Luis Callejas-Valera, Ramiro Iglesias-Bartolome, Panomwat Amornphimoltham, Julia Palacios-Garcia, Daniel Martin, Joseph A. Califano, Alfredo A. Molinolo, J.Silvio  Gutkind. A next-gen animal model to Study PIK3CA-mTOR driven HPV-related oral malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4800. doi:10.1158/1538-7445.AM2017-4800

Corrigendum: A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma

This corrects the article DOI: 10.1038/srep36132.

Smoking status regulates a novel panel of PIWI-interacting RNAs in head and neck squamous cell carcinoma

OBJECTIVE

Smoking remains a primary etiological factor in head and neck squamous cell carcinoma (HNSCC). Given that non-coding RNAs (ncRNAs), including PIWI-interacting RNAs (piRNAs), have emerged as mediators of initiation and progression in head and neck malignancies, we undertook a global study of piRNA expression patterns in smoking-associated HNSCC.

MATERIALS AND METHODS

Using RNA-sequencing data from 256 current smoker and lifelong nonsmoker samples in The Cancer Genome Atlas (TCGA), we analyzed the differential expression patterns of 27,127 piRNAs across patient cohorts stratified by tobacco use, with HPV16 status and tumor status taken into account. We correlated their expression to clinical characteristics and to smoking-induced alterations of PIWI proteins, the functional counterparts of piRNAs. Finally, we correlated our identified piRNAs and PIWI proteins to known chromosomal aberrations in HNSCC to understand their wider-ranging genomic effects.

RESULTS AND CONCLUSION

Our analyses implicated a 13-member piRNA panel in smoking-related HNSCC, among which NONHSAT123636 and NONHSAT113708 associated with tumor stage, NONHSAT067200 with patient survival, and NONHSAT081250 with smoking-altered PIWIL1 protein expression. 6 piRNAs as well as PIWIL1 correlated with genomic alterations common to HNSCC, including TP53 mutation, TP53-3p co-occurrence, and 3q26, 8q24, and 11q13 amplification. Collectively, our findings provide novel insights into the etiology-specific piRNA landscape of smoking-induced HNSCC.

Favorable Swallowing Outcomes following Vagus Nerve Sacrifice for Vagal Schwannoma Resection

Objective To determine the impact of unilateral vagal sacrifice for vagal schwannoma on postoperative swallowing function. Study Design Case series, chart review. Setting Academic medical institution. Subjects and Methods Ten patients underwent vagus nerve sacrifice for vagal schwannoma resection. Archived pathology records dating from 1985 through 2012 at our institution were retrospectively queried for cases of vagal schwannoma with vagus nerve sacrifice. Medical records were abstracted for demographic and disease information as well as cranial nerve and swallowing function. Preoperative and postoperative cranial nerve function, subjective and objective measures of swallowing function, Functional Oral Intake Scale (FOIS) level, and need for vocal fold medialization were variables collected. Data were analyzed with summary statistics. Results The patients who underwent vagal sacrifice for vagal schwannoma at our institution had a mean age of 42.3 years (median, 44 years; range, 15-63 years) and follow-up of 35.6 months (median, 9 months; range, 1-115 months). Most presented with no preoperative cranial nerve deficit or difficulty swallowing. Immediately postoperatively, 90% had a vagus nerve deficit, but 50% had no subjective difficulty swallowing, and 70% had a FOIS level of 7 at postoperative hospital discharge. Within 1 month after surgery, 70% had normal swallowing function according to a modified barium swallow study. A full diet was tolerated by mouth within an average of 2.7 days (median, 2 days; range, 1-6 days) after surgery in this cohort. Seventy percent required vocal fold medialization postoperatively for incomplete glottic closure. Conclusion Vagal nerve sacrifice during resection of vagal schwannoma can be performed with normal postoperative swallowing function.

The Molecular Biology of Mucosal Field Cancerization of the Head and Neck

Field cancerization was first described in 1953 as histologically altered epithelium surrounding tumor samples taken from the upper aerodigestive tract. Since then, the term has been used to describe multiple patches of pre-malignant disease, a higher-than-expected prevalence of multiple local second primary tumors, and the presence of synchronous distant tumors within the upper aerodigestive tract. Molecular techniques such as karyotype analysis, microsatellite analysis, p53 mutation screening, and X-chromosome inactivation studies have further refined the relationship among these lesions. While there are differences in the techniques used to identify the clonal origins of the lesions, these studies indicate that there is often lateral clonal spread of pre-malignant or malignant disease, and a significant portion of local second primary tumors are in fact genetically related. Distant second primary tumors found in the esophagus are often not related to concurrent head and neck cancer, whereas synchronous squamous lung tumors with a head and neck primary are often, in fact, metastases, rather than independently arising malignancies. These observations help to explain the high incidence of recurrent disease, despite excision or other therapy—pre-malignant or malignant clones often have the ability to migrate and persist outside of the field of treatment. Therefore, alternative means of prevention or therapy that can affect the entire head and neck region may be of benefit to such patients. Future studies will further refine the relationship among these lesions and perhaps identify key molecular alterations to be used as targets for gene therapy.

A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma

Despite advances in clinical management, 5-year survival rate in patients with late-stage head and neck squamous cell carcinoma (HNSCC) has not improved significantly over the past decade. Targeted therapies have emerged as one of the most promising approaches to treat several malignancies. Though tyrosine phosphorylation accounts for a minority of total phosphorylation, it is critical for activation of signaling pathways and plays a significant role in driving cancers. To identify activated tyrosine kinase signaling pathways in HNSCC, we compared the phosphotyrosine profiles of a panel of HNSCC cell lines to a normal oral keratinocyte cell line. Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A) was one of the kinases hyperphosphorylated at Tyr-321 in all HNSCC cell lines. Inhibition of DYRK1A resulted in an increased apoptosis and decrease in invasion and colony formation ability of HNSCC cell lines. Further, administration of the small molecular inhibitor against DYRK1A in mice bearing HNSCC xenograft tumors induced regression of tumor growth. Immunohistochemical labeling of DYRK1A in primary tumor tissues using tissue microarrays revealed strong to moderate staining of DYRK1A in 97.5% (39/40) of HNSCC tissues analyzed. Taken together our results suggest that DYRK1A could be a novel therapeutic target in HNSCC.

mTOR inhibition prevents rapid-onset of carcinogen-induced malignancies in a novel inducible HPV-16 E6/E7 mouse model

The rising incidence of human papillomavirus (HPV)-associated malignancies, especially for oropharyngeal cancers, has highlighted the urgent need to understand how the interplay between high-risk HPV oncogenes and carcinogenic exposure results in squamous cell carcinoma (SCC) development. Here, we describe an inducible mouse model expressing high risk HPV-16 E6/E7 oncoproteins in adults, bypassing the impact of these viral genes during development. HPV-16 E6/E7 genes were targeted to the basal squamous epithelia in transgenic mice using a doxycycline inducible cytokeratin 5 promoter (cK5-rtTA) system. After doxycycline induction, both E6 and E7 were highly expressed, resulting in rapid epidermal hyperplasia with a remarkable expansion of the proliferative cell compartment to the suprabasal layers. Surprisingly, in spite of the massive growth of epithelial cells and their stem cell progenitors, HPV-E6/E7 expression was not sufficient to trigger mTOR activation, a key oncogenic driver in HPV-associated malignancies, and malignant progression to SCC. However, these mice develop SCC rapidly after a single exposure to a skin carcinogen, DMBA, which was increased by the prolonged exposure to a tumor promoter, 12-O-tetradecanoylphorbol-13-acetate (TPA). Thus, only few oncogenic hits may be sufficient to induce cancer in E6/E7 expressing cells. All HPV-E6/E7 expressing SCC lesions exhibited increased mTOR activation. Remarkably, rapamycin, an mTOR inhibitor, abolished tumor development when administered to HPV-E6/E7 mice prior to DMBA exposure. Our findings revealed that mTOR inhibition protects HPV-E6/E7 expressing tissues form SCC development upon carcinogen exposure, thus supporting the potential clinical use of mTOR inhibitors as a molecular targeted approach for prevention of HPV-associated malignancies.

Short Hospital Stay After Neck Dissection

OBJECTIVE: Cervical lymphadenectomy is a common adjunctive therapy for the treatment of head and neck malignancies. Postoperative care of otherwise healthy patients with isolated neck dissection or in combination with other procedures often requires limited nursing attention after the first postoperative day. At our institution, patients are often taught to manage their drains and discharged home. Therefore, we sought to characterize the subset of patients who will require only overnight hospital care after neck dissection.

STUDY DESIGN: We retrospectively reviewed our experience in a tertiary academic medical center over the past 6 years with patients who underwent neck dissection, isolated or with other procedures, and were sent home by postoperative day 1.

RESULTS: In all, 23 of 260 patients were identified (8.8%). Two patients were noted to have postoperative seromas, with no other complications noted.

CONCLUSION: We conclude that short hospital stay after neck dissection is reasonable for the motivated patient without significant comorbidities.

SIGNIFICANCE: This is the first study to examine the feasibility of short hospital stay after neck dissection.

The role of pre-operative CT-guided FNAB for parapharyngeal space tumors

Objective

To determine the role of computed tomography (CT)-guided fine needle aspiration biopsy (FNAB) in surgical planning for parapharyngeal space (PPS) tumors.

Design and Setting

Chart review of 49 consecutive patients with surgically treated PPS tumors from 1995 to 2005.

Results

Twenty-nine patients had CT-guided FNAB. A cytopathologic diagnosis that was the same as final pathology was rendered in 14 (48%) patients; suggestive but not conclusive in 6 (21%) patients; discordant in 3 (10%) patients; and 6 (21%) patients had a nondiagnostic result. Fourteen of 15 patients who had a final histopathologic finding of pleomorphic adenoma had a correct or highly suggestive preoperative FNAB diagnosis. The positive predictive value for CT-guided FNAB to identify benign tumors is 90%, (18 of 20) but to identify malignant PPS tumors is 75% (3 of 4).

Conclusion

CT-guided FNAB of PPS tumors is helpful to predict the nature of the PPS tumors (especially benign), which allows the surgeon and patient to plan for treatment, accordingly.

Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma

The Cancer Genome Atlas (TCGA) sequencing analysis of head and neck squamous cell carcinoma (HNSCC) recently reported on gene fusions, however, few human papillomavirus (HPV) positive samples were included, and the functional relevance of identified fusions was not explored. We therefore performed an independent analysis of gene fusions in HPV-positive oropharyngeal SCC (OPSCC). RNA sequencing was performed on 47 HPV-positive OPSCC primary tumors and 25 normal mucosal samples from cancer unaffected controls on an Illumina TruSeq platform. MapSplice2 was used for alignment and identification of fusion candidates. Putative fusions with less than five spanning reads, detected in normal tissues, or that mapped to the same gene were filtered out. Selected fusions were validated by RT-PCR and Sanger sequencing. Within 47 HPV-positive OPSCC tumors, 282 gene fusions were identified. Most fusions (85.1%) occurred in a single tumor, and the remaining fusions recurred in 2-16 tumors. Gene fusions were associated with significant up regulation of 16 genes (including EGFR and ERBB4) and down regulation of four genes (PTPRT, ZNF750, DLG2, SLCO5A1). Expression of these genes followed similar patterns of up regulation and down regulation in tumors without these fusions compared to normal tissue. Five of six gene fusions selected for validation were confirmed through RT-PCR and sequencing. This integrative analysis provides a method of prioritizing functionally relevant gene fusions that may be expanded to other tumor types. These results demonstrate that gene fusions may be one mechanism by which functionally relevant genes are altered in HPV-positive OPSCC.

Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas

To explore the potential of tumor-specific DNA as a biomarker for head and neck squamous cell carcinomas (HNSCC), we queried DNA from saliva or plasma of 93 HNSCC patients. We searched for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n = 10) and 95% (n = 37), respectively. When segregated by site, tumor DNA was detected in 100% (n = 15), 91% (n = 22), 100% (n = 7), and 100% (n = 3) of patients with tumors of the oral cavity, oropharynx, larynx, and hypopharynx, respectively. In saliva, tumor DNA was found in 100% of patients with oral cavity cancers and in 47 to 70% of patients with cancers of the other sites. In plasma, tumor DNA was found in 80% of patients with oral cavity cancers, and in 86 to 100% of patients with cancers of the other sites. Thus, saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in saliva was found postsurgically in three patients before clinical diagnosis of recurrence, but in none of the five patients without recurrence. Tumor DNA in the saliva and plasma appears to be a potentially valuable biomarker for detection of HNSCC.

A synthetic-lethality RNAi screen reveals an ERK-mTOR co-targeting pro-apoptotic switch in PIK3CA+ oral cancers

mTOR inhibition has emerged as a promising strategy for head and neck squamous cell carcinomas (HNSCC) treatment. However, most targeted therapies ultimately develop resistance due to the activation of adaptive survival signaling mechanisms limiting the activity of targeted agents. Thus, co-targeting key adaptive mechanisms may enable more effective cancer cell killing. Here, we performed a synthetic lethality screen using shRNA libraries to identify druggable candidates for combinatorial signal inhibition. We found that the ERK pathway was the most highly represented. Combination of rapamycin with trametinib, a MEK1/2 inhibitor, demonstrated strong synergism in HNSCC-derived cells in vitro and in vivo, including HNSCC cells expressing the HRAS and PIK3CA oncogenes. Interestingly, cleaved caspase-3 was potently induced by the combination therapy in PIK3CA+ cells in vitro and tumor xenografts. Moreover, ectopic expression of PIK3CA mutations into PIK3CA- HNSCC cells sensitized them to the pro-apoptotic activity of the combination therapy. These findings indicate that co-targeting the mTOR/ERK pathways may provide a suitable precision strategy for HNSCC treatment. Moreover, PIK3CA+ HNSCC are particularly prone to undergo apoptosis after mTOR and ERK inhibition, thereby providing a potential biomarker of predictive value for the selection of patients that may benefit from this combination therapy.

Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination

The goal of this study was to discover a minimally invasive pathway-specific biomarker that is immune to normal cell mRNA contamination for diagnosing head and neck squamous cell carcinoma (HNSCC). Using Elsevier's MedScan natural language processing component of the Pathway Studio software and the TRANSFAC database, we produced a curated set of genes regulated by the signaling networks driving the development of HNSCC. The network and its gene targets provided prior probabilities for gene expression, which guided our CoGAPS matrix factorization algorithm to isolate patterns related to HNSCC signaling activity from a microarray-based study. Using patterns that distinguished normal from tumor samples, we identified a reduced set of genes to analyze with Top Scoring Pair in order to produce a potential biomarker for HNSCC. Our proposed biomarker comprises targets of the transcription factor (TF) HIF1A and the FOXO family of TFs coupled with genes that show remarkable stability across all normal tissues. Based on validation with novel data from The Cancer Genome Atlas (TCGA), measured by RNAseq, and bootstrap sampling, the biomarker for normal vs. tumor has an accuracy of 0.77, a Matthews correlation coefficient of 0.54, and an area under the curve (AUC) of 0.82.

Dysregulation of splicing proteins in head and neck squamous cell carcinoma

Signaling plays an important role in regulating all cellular pathways. Altered signaling is one of the hallmarks of cancers. Phosphoproteomics enables interrogation of kinase mediated signaling pathways in biological systems. In cancers, this approach can be utilized to identify aberrantly activated pathways that potentially drive proliferation and tumorigenesis. To identify signaling alterations in head and neck squamous cell carcinoma (HNSCC), we carried out proteomic and phosphoproteomic analysis of HNSCC cell lines using a combination of tandem mass tag (TMT) labeling approach and titanium dioxide-based enrichment. We identified 4,920 phosphosites corresponding to 2,212 proteins in six HNSCC cell lines compared to a normal oral cell line. Our data indicated significant enrichment of proteins associated with splicing. We observed hyperphosphorylation of SRSF protein kinase 2 (SRPK2) and its downstream substrates in HNSCC cell lines. SRPK2 is a splicing kinase, known to phosphorylate serine/arginine (SR) rich domain proteins and regulate splicing process in eukaryotes. Although genome-wide studies have reported the contribution of alternative splicing events of several genes in the progression of cancer, the involvement of splicing kinases in HNSCC is not known. In this study, we studied the role of SRPK2 in HNSCC. Inhibition of SRPK2 resulted in significant decrease in colony forming and invasive ability in a panel of HNSCC cell lines. Our results indicate that phosphorylation of SRPK2 plays a crucial role in the regulation of splicing process in HNSCC and that splicing kinases can be developed as a new class of therapeutic target in HNSCC.

Serum biomarkers for detection of head and neck squamous cell carcinoma

BACKGROUND

Detection of hypermethylated circulating tumor DNA has the potential to be a minimally invasive, low cost, and reproducible method for cancer detection.

METHODS

We evaluated serum from 100 patients with known head and neck squamous cell carcinoma (HNSCC) and 50 healthy control patients for 3 previously described methylation targets, endothelin receptor type B (EDNRB), cyclin-dependent kinase inhibitor 2A (CDKN2A or p16), and deleted in colorectal carcinoma (DCC), using quantitative methylation specific polymerase chain reaction (qMSPCR).

RESULTS

EDNRB hypermethylation was identified in the serum of 10% of the patients with HNSCC but in none of the control patients. DCC hypermethylation was detected in 2 serum samples from patients with cancer that also amplified EDNRB and one of these samples also had p16 hypermethylation. EDNRB hypermethylation was statistically significant by Fisher's exact test (p = .03) when comparing HNSCC to controls.

CONCLUSIONS

Serum EDNRB hypermethylation is a highly specific but not sensitive serum biomarker for HNSCC.

Cetuximab activity in dysplastic lesions of the upper aerodigestive tract

BACKGROUND

High risk head and neck mucosal premalignancy has a malignant conversion rate of up to 40%, despite adequate surgical therapy. Epidermal Growth Factor Receptor (EGFR) blocking agents, including cetuximab, have shown activity in head and neck squamous cell carcinoma (HNSCC) and have potential for therapy in high risk premalignancy.

METHODS

We conducted a randomized, prospective, phase II clinical trial to determine the effects of cetuximab on patients with high risk premalignancy. Patients were randomized to treatment with cetuximab 400mg/m(2) on week one followed by 250mg/m(2) on week 2-8 or observation, with the option for crossover to cetuximab therapy for patients originally randomized to the observation arm.

RESULTS

Two of 19 enrolled patients did not complete therapy due to treatment toxicity. Analysis of 17 patients who completed the trial regimen show a trend toward a larger mean decrease in grade of dysplasia in the cetuximab treated group (-1.0) vs. the observation group (-0.2) (P=0.082, one-sided exact Wilcoxon rank sum test). However, in the observation group, none of the 5 patients (0%) achieved complete resolution of dysplasia; while 4 of 12 (33.3%) cetuximab treated patients had no remaining dysplasia after therapy.

CONCLUSIONS

Treatment of high risk premalignancy of the upper aerodigestive tract with cetuximab alone may result in significant, durable, and complete clinical and histological resolution of moderate to severe dysplasia in at least a subset of high risk patients. These results warrant further investigation in larger studies with increased statistical power.

Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients

Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance of HNSCC. In this work, a comprehensive genome-wide analysis of epigenetic alterations in primary HNSCC tumors was employed in conjunction with cancer-specific outlier statistics to define novel biomarker genes which are differentially methylated in HNSCC. The 37 identified biomarker candidates were top-scoring outlier genes with prominent differential methylation in tumors, but with no signal in normal tissues. These putative candidates were validated in independent HNSCC cohorts from our institution and TCGA (The Cancer Genome Atlas). Using the top candidates, ZNF14, ZNF160, and ZNF420, an assay was developed for detection of HNSCC cancer in primary tissue and saliva samples with 100% specificity when compared to normal control samples. Given the high detection specificity, the analysis of ZNF DNA methylation in combination with other DNA methylation biomarkers may be useful in the clinical setting for HNSCC detection and surveillance, particularly in high-risk patients. Several additional candidates identified through this work can be further investigated toward future development of a multi-gene panel of biomarkers for the surveillance and detection of HNSCC.

Reduction of Pharyngocutaneous Fistulae in Laryngectomy Patients by a Comprehensive Performance Improvement Intervention

Objective

Pharyngocutaneous fistula is a common complication in laryngectomy patients, particularly in previously irradiated cases. We initiated a comprehensive performance improvement intervention in all head and neck surgery patients intended to reduce postoperative infection and fistulae rates. We report our review of outcomes within laryngectomy patients.

Study Design

Case series with chart review.

Setting

Academic tertiary referral center.

Subjects

Nineteen laryngectomy patients at risk of postoperative fistula formation.

Methods

We reviewed the medical records of all patients who had undergone laryngectomy procedures between January 2013 and April 2014. Clinicodemographic data were obtained, including history of diabetes, prior radiation therapy, type of reconstruction performed for closure of the pharyngeal defect, and the presence or absence of postoperative fistula.

Results

The study population comprised 19 laryngectomy patients. Prior to implementation of our performance improvement intervention, 8 of 11 (73%) patients undergoing laryngectomy developed postoperative fistulae. After intervention, 0 of 8 patients developed fistulae ( P = .002). Prior radiation, diabetes mellitus, and overall stage were not associated with a reduction in fistula rate ( P > .05).

Conclusion

Comprehensive uniform application of a standard antibiotic prophylaxis, surgical technique, perioperative care, and treatment of comorbid conditions can significantly reduce and potentially eliminate fistulae in laryngectomy patients who are especially at risk.

Chronic exposure to chewing tobacco selects for overexpression of stearoyl-CoA desaturase in normal oral keratinocytes

Chewing tobacco is a common practice in certain socio-economic sections of southern Asia, particularly in the Indian subcontinent and has been well associated with head and neck squamous cell carcinoma. The molecular mechanisms of chewing tobacco which leads to malignancy remains unclear. In large majority of studies, short-term exposure to tobacco has been evaluated. From a biological perspective, however, long-term (chronic) exposure to tobacco mimics the pathogenesis of oral cancer more closely. We developed a cell line model to investigate the chronic effects of chewing tobacco. Chronic exposure to tobacco resulted in higher cellular proliferation and invasive ability of the normal oral keratinocytes (OKF6/TERT1). We carried out quantitative proteomic analysis of OKF6/TERT1 cells chronically treated with chewing tobacco compared to the untreated cells. We identified a total of 3,636 proteins among which expression of 408 proteins were found to be significantly altered. Among the overexpressed proteins, stearoyl-CoA desaturase (SCD) was found to be 2.6-fold overexpressed in the tobacco treated cells. Silencing/inhibition of SCD using its specific siRNA or inhibitor led to a decrease in cellular proliferation, invasion and colony forming ability of not only the tobacco treated cells but also in a panel of head and neck cancer cell lines. These findings suggest that chronic exposure to chewing tobacco induced carcinogenesis in non-malignant oral epithelial cells and SCD plays an essential role in this process. The current study provides evidence that SCD can act as a potential therapeutic target in head and neck squamous cell carcinoma, especially in patients who are users of tobacco.

Tadalafil augments tumor specific immunity in patients with head and neck squamous cell carcinoma

PURPOSE

To determine if phosphodiesterase 5 (PDE5) inhibitors can augment immune function in patients with head and neck cancer through inhibition of myeloid-derived suppressor cells (MDSC).

EXPERIMENTAL DESIGN

We performed a randomized, prospective, double blinded, placebo controlled, phase II clinical trial to determine the in vivo effects of systemic PDE5 inhibition on immune function in patients with head and neck squamous cell carcinoma (HNSCC).

RESULTS

Tadalafil augmented immune response, increasing ex vivo T-cell expansion to a mean 2.4-fold increase compared with 1.1-fold in control patients (P = 0.01), reducing peripheral MDSC numbers to mean 0.81-fold change compared with a 1.26-fold change in control patients (P = 0.001), and increasing general immunity as measured by delayed type hypersensitivity response (P = 0.002). Tumor-specific immunity in response to HNSCC tumor lysate was augmented in tadalafil-treated patients (P = 0.04).

CONCLUSIONS

These findings demonstrate that tadalafil augments general and tumor-specific immunity in patients with HNSCC and has therapeutic potential in HNSCC. Evasion of immune surveillance and suppression of systemic and tumor-specific immunity is a significant feature of head and neck cancer development. This study demonstrates that a PDE5 inhibitor, tadalafil, can reverse tumor-specific immune suppression in patients with head and neck cancer, with potential for therapeutic application.

Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma

Dysregulation of protein expression is associated with most diseases including cancer. MS-based proteomic analysis is widely employed as a tool to study protein dysregulation in cancers. Proteins that are differentially expressed in head and neck squamous cell carcinoma (HNSCC) cell lines compared to the normal oral cell line could serve as biomarkers for patient stratification. To understand the proteomic complexity in HNSCC, we carried out iTRAQ-based MS analysis on a panel of HNSCC cell lines in addition to a normal oral keratinocyte cell line. LC-MS/MS analysis of total proteome of the HNSCC cell lines led to the identification of 3263 proteins, of which 185 proteins were overexpressed and 190 proteins were downregulated more than twofold in at least two of the three HNSCC cell lines studied. Among the overexpressed proteins, 23 proteins were related to DNA replication and repair. These included high-mobility group box 2 (HMGB2) protein, which was overexpressed in all three HNSCC lines studied. Overexpression of HMGB2 has been reported in various cancers, yet its role in HNSCC remains unclear. Immunohistochemical labeling of HMGB2 in a panel of HNSCC tumors using tissue microarrays revealed overexpression in 77% (54 of 70) of tumors. The HMGB proteins are known to bind to DNA structure resulting from cisplatin-DNA adducts and affect the chemosensitivity of cells. We observed that siRNA-mediated silencing of HMGB2 increased the sensitivity of the HNSCC cell lines to cisplatin and 5-FU. We hypothesize that targeting HMGB2 could enhance the efficacy of existing chemotherapeutic regimens for treatment of HNSCC. All MS data have been deposited in the ProteomeXchange with identifier PXD000737 (http://proteomecentral.proteomexchange.org/dataset/PXD000737).

Abstract 4807: Discovery of novel alternative splicing events in human papillomavirus-related oropharyngeal squamous cell carcinoma

Although the overall incidence of head and neck squamous cell cancers have decreased in the past 30 years, the incidence oropharyngeal squamous cell carcinoma (OPSCC) related to human papillomavirus (HPV) has actually been rising. Clinically, HPV-related tumors show improved response to treatment and longer overall survival. Recent genomic sequencing data also suggests that HPV-related tumors represent a biologically distinct entity, harboring significantly fewer mutations than non-HPV-related head and neck tumors. The paucity of genetic alterations in HPV-related OPSCC has limited our understanding of its underlying biology and our ability to identify targetable pathways for therapy. Thus, we sought to use RNA sequencing to study post-transcriptional changes in HPV-related OPSCC, primarily alternative splicing events (ASEs). ASEs have been shown to play an important role in carcinogenesis in other cancer types leading to protein expression changes in the absences of genetic alterations at the DNA level.

RNA sequencing data was obtained using an Illumina platform in a cohort of 47 HPV-related OPSCC primary tumors and 25 normal mucosa tissue samples from uvulopalatopharyngoplasty surgical specimens. We developed a novel algorithm for the identification of ASEs which utilized outlier analysis to identify differential expression of these splicing events in tumors compared to normal tissues. Our analysis identified 3522 putative alternative splicing events occurring in tumor samples. These ASEs were ranked based on presence of outlier over-expression and under-expression in tumors. The top 200 candidates for over-expression and under-expression were selected for further validation. Differential expression of these candidate ASEs was confirmed using integrated genome viewer (IGV). Additional validation was performed using RT-PCR in the original tumor and normal tissue cohort. These were further validated in publically available TCGA RNA sequencing data. An independent cohort of normal and tissue samples was collected, and differential ASE expression was confirmed using RT-PCR. These methods identified several ASEs that offer insight into the molecular biology of HPV-related OPSCC. This pipeline represents a robust and validated algorithm for identification and prioritizing biologically significant ASEs using RNA sequencing data that may be adapted for analysis in other tumor types.

Citation Format: Theresa Guo, Daria Gaykalova, Michael Considine, Justin A. Bishop, William H. Westra, Zubair Khan, Elana Fertig, Joseph A. Califano. Discovery of novel alternative splicing events in human papillomavirus-related oropharyngeal squamous cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4807. doi:10.1158/1538-7445.AM2015-4807