Defining the relationship of salivary gland malignancies to novel cell subpopulations in human salivary glands using single nucleus RNA-sequencing

Salivary glands have essential roles in maintaining oral health, mastication, taste and speech, by secreting saliva. Salivary glands are composed of several types of cells, and each cell type is predicted to be involved in the carcinogenesis of different types of cancers including adenoid cystic carcinoma (ACC), acinic cell carcinoma (AciCC), salivary duct carcinoma (SDC), myoepithelial carcinoma (MECA) and other histology. In our study, we performed single nucleus RNA-seq on three human salivary gland samples to clarify the gene expression profile of each complex cellular component of the salivary glands and related these expression patterns to expression found in salivary gland cancers (SGC) to infer cell of origin. By single nucleus RNA-seq, salivary gland cells were stratified into four clusters: acinar cells, ductal cells 1, ductal cells 2 and myoepithelial cells/stromal cells. The localization of each cell group was verified by IHC of each cluster marker gene, and one group of ductal cells was found to represent intercalated ductal cells labeled with HES1. Furthermore, in comparison with SGC RNA-seq data, acinar cell markers were upregulated in AciCC, but downregulated in ACC and ductal cell markers were upregulated in SDC but downregulated in MECA, suggesting that markers of origin are highly expressed in some SGC. Cell type expressions in specific SGC histology are similar to those found in normal salivary gland populations, indicating a potential etiologic relationship.

Computational and AI-driven 3D structural analysis of human papillomavirus (HPV) oncoproteins E5, E6, and E7 reveal significant divergence of HPV E5 between low-risk and high-risk genotypes

There are over 220 identified genotypes of Human papillomavirus (HPV), and the HPV genome encodes 3 major oncogenes, E5, E6, and E7. Conservation and divergence in protein sequence and function between low-risk versus high-risk oncogenic HPV genotypes has not been fully characterized. Here, we used modern computational and structural folding algorithms to perform a comparative analysis of HPV E5, E6, and E7 between multiple low risk and high risk genotypes. We first identified significantly greater sequence divergence in E5 between low- and high-risk genotypes compared to E6 and E7. Next, we used AlphaFold to model the structure of papillomavirus proteins and complexes with high confidence, including some with no established consensus structure. We observed that HPV E5, but not E6 or E7, had a dramatically different 3D structure between low-risk and high-risk genotypes. To our knowledge, this is the first comparative analysis of HPV proteins using Alphafold artificial intelligence (AI) system. The marked differences in E5 sequence and structure in high-risk HPVs may contribute in important and underappreciated ways to the development of HPV-associated cancers.

Transoral Surgery in HPV-Positive Oropharyngeal Carcinoma: Oncologic Outcomes in the Veterans Affairs System

OBJECTIVES

Most transoral robotic surgery (TORS) literature for HPV-positive oropharyngeal squamous cell carcinoma (HPV-OPC) derives from high-volume tertiary-care centers. This study aims to describe long-term recurrence and survival outcomes among Veterans Health Administration patients.

MATERIALS AND METHODS

Using the US Veterans Affairs database, we identified patients with HPV-OPC treated with TORS between January 2010 and December 2016. Patients were stratified in risk categories: low (0-1 metastatic nodes, negative margins), intermediate (close margins, 2-4 metastatic nodes, lymphovascular or perineural invasion, pT3-pT4 tumor), or high (positive margins, extranodal extension (ENE), and/or ≥5 metastatic nodes). Primary outcomes included overall survival (OS), disease-specific survival (DSS), and recurrence-free survival (RFS).

RESULTS

The cohort included 161 patients of which 29 (18%) were low-risk, 45 (28%) intermediate-risk, and 87 (54%) high-risk. ENE was present in 41% of node-positive cases and 24% had positive margins. Median follow-up was 5.6 years (95% CI, 3.0-9.3). The 5-year DSS for low, intermediate, and high-risk groups were: 100%, 90.0% (95% CI, 75.4-96.1%), and 88.7% (95% CI, 78.3-94.2%). Pathologic features associated with poor DSS on univariable analysis included pT3-T4 tumors (HR 3.81, 95% CI, 1.31-11; p = 0.01), ≥5 metastatic nodes (HR 3.41, 95% CI, 1.20-11; p = 0.02), and ENE (HR 3.53, 95% CI, 1.06-12; p = 0.04). Higher 5-year cumulative incidences of recurrence were observed in more advanced tumors (pT3-T4, 33% [95% CI, 14-54%] versus pT1-T2, 13% [95% CI, 8-19%]; p = 0.01).

CONCLUSIONS

In this nationwide study, patients with HPV-OPC treated with TORS followed by adjuvant therapy at Veterans Affairs Medical Centers demonstrated favorable survival outcomes comparable to those reported in high-volume academic centers and clinical trials.

LEVEL OF EVIDENCE

4 Laryngoscope, 134:207-214, 2024.

A Network Landscape of HPVOPC Reveals Methylation Alterations as Significant Drivers of Gene Expression via an Immune-Mediated GPCR Signal

HPV-associated oropharynx carcinoma (HPVOPC) tumors have a relatively low mutational burden. Elucidating the relative contributions of other tumor alterations, such as DNA methylation alterations, alternative splicing events (ASE), and copy number variation (CNV), could provide a deeper understanding of carcinogenesis drivers in this disease. We applied network propagation analysis to multiple classes of tumor alterations in a discovery cohort of 46 primary HPVOPC tumors and 25 cancer-unaffected controls and validated our findings with TCGA data. We identified significant overlap between differential gene expression networks and all alteration classes, and this association was highest for methylation and lowest for CNV. Significant overlap was seen for gene clusters of G protein-coupled receptor (GPCR) pathways. HPV16-human protein interaction analysis identified an enriched cluster defined by an immune-mediated GPCR signal, including CXCR3 cytokines CXCL9, CXCL10, and CXCL11. CXCR3 was found to be expressed in primary HPVOPC, and scRNA-seq analysis demonstrated CXCR3 ligands to be highly expressed in M2 macrophages. In vivo models demonstrated decreased tumor growth with antagonism of the CXCR3 receptor in immunodeficient but not immunocompetent mice, suggesting that the CXCR3 axis can drive tumor proliferation in an autocrine fashion, but the effect is tempered by an intact immune system. In conclusion, methylation, ASE, and SNV alterations are highly associated with network gene expression changes in HPVOPC, suggesting that ASE and methylation alterations have an important role in driving the oncogenic phenotype. Network analysis identifies GPCR networks, specifically the CXCR3 chemokine axis, as modulators of tumor-immune interactions that may have proliferative effects on primary tumors as well as a role for immunosurveillance; however, CXCR3 inhibition should be used with caution, as these agents may both inhibit and stimulate tumor growth considering the competing effects of this cytokine axis. Further investigation is needed to explore opportunities for targeted therapy in this setting.

Direct reprogramming of oral epithelial progenitor cells to cancer stem cells at single cell resolution in vivo

Tumor initiation represents the initial step in tumorigenesis during which normal progenitor cells undergo cell fate transition to cancer. Most studies investigating cancer-driving mechanisms in solid tumors rely on analyses of established malignant lesions, and thus cannot directly capture processes underlying the reprogramming of normal progenitor cells into cancer cells. Here, using spatiotemporally controlled oncogene expression in a genetically engineered system we demonstrate that concomitant YAP activation and HPV E6-E7 -mediated inhibition of tumor suppressive pathways is sufficient to rapidly reprogram oral epithelial progenitor cells (OEPCs) into cancer stem cells (CSCs). Single cell analyses of these nascent CSCs revealed hallmark transcriptional programs driving tumor initiation. Importantly, these CSC-enriched expression signatures distinguish normal tissue from malignant head and neck tumors and are associated with poor patient survival. Elucidating mechanisms underlying OEPC to CSC reprogramming may offer new insights to halt the conversion of premalignant cells into invasive carcinoma.

HIGHLIGHTS

YAP and HPV E6-E7 reprogram oral epithelial progenitor cells into cancer stem cells. Single cell analyses reveal the transcriptional architecture of tumor initiation.CSC transcriptional programs distinguish normal tissue from carcinoma.CSC signatures are associated with poor head and neck cancer survival.

Abstract Figure

Human papillomavirus E5 suppresses immunity via inhibition of the immunoproteasome and STING pathway

The role that human papillomavirus (HPV) oncogenes play in suppressing responses to immunotherapy in cancer deserves further investigation. In particular, the effects of HPV E5 remain poorly understood relative to E6 and E7. Here, we demonstrate that HPV E5 is a negative regulator of anti-viral interferon (IFN) response pathways, antigen processing, and antigen presentation. Using head and neck cancer as a model, we identify that E5 decreases expression and function of the immunoproteasome and that the immunoproteasome, but not the constitutive proteasome, is associated with improved overall survival in patients. Moreover, immunopeptidome analysis reveals that HPV E5 restricts the repertoire of antigens presented on the cell surface, likely contributing to immune escape. Mechanistically, we discover a direct interaction between E5 and stimulator of interferon genes (STING), which suppresses downstream IFN signaling. Taken together, these findings identify a powerful molecular mechanism by which HPV E5 limits immune detection and mediates resistance to immunotherapy.

Adjuvant Radiotherapy in Surgically Treated HPV-Positive Oropharyngeal Carcinoma with Adverse Pathological Features

Purpose: HPV-positive oropharyngeal carcinoma (HPV-OPC) is increasingly treated with primary surgery. The National Comprehensive Cancer Network (NCCN) recommends adjuvant therapy for surgically treated HPV-OPC displaying adverse pathological features (AF). We evaluated adjuvant radiotherapy patterns and outcomes in surgically treated AF-positive HPV-OPC (AF-HPV-OPC). Methods: The National Cancer Database was interrogated for patients ≥ 18 years with early-stage HPV-OPC from 2010 to 2017 who underwent definitive resection. Patients that had an NCCN-defined AF indication for adjuvant radiotherapy were assessed, including positive surgical margins (PSM), extranodal extension (ENE), lymphovascular invasion, and level 4/5 cervical lymph nodes. Overall survival (OS) was evaluated using Cox proportional hazards models and Kaplan−Meier analysis in whole and propensity score matched (PM) cohorts. Results: Of 15,036 patients meeting inclusion criteria, 55.7% were positive for at least one AF. Presence of any AF was associated with worse OS (hazard ratio (HR) = 1.56, p < 0.001). In isolation, each AF was associated with worse OS. On PM analysis, insurance status, T2 category, Charlson-Deyo comorbidity score, ENE (HR = 1.81, p < 0.001), and PSM (HR = 1.58, p = 0.002) were associated with worse OS. Median 3-year OS was 92.0% among AF-HPV-OPC patients undergoing adjuvant radiotherapy and 84.2% for those who did not receive adjuvant radiotherapy (p < 0.001, n = 1678). The overall rate of patients with AF-HPV-OPC who did not receive adjuvant radiotherapy was 13% and increased from 10% in 2010 to 17% in 2017 (ptrend = 0.007). Conclusions: In patients with AF-HPV-OPC, adjuvant radiotherapy is associated with improved survival. In the era of de-escalation therapy for HPV-OPC, our findings demonstrate the persistent prognostic benefit of post-operative radiotherapy in the setting of commonly identified adverse features. Ongoing clinical trials will better elucidate optimized patient selection for de-escalated therapy.

Lymphatic-preserving treatment sequencing with immune checkpoint inhibition unleashes cDC1-dependent antitumor immunity in HNSCC

Despite the promise of immune checkpoint inhibition (ICI), therapeutic responses remain limited. This raises the possibility that standard of care treatments delivered in concert may compromise the tumor response. To address this, we employ tobacco-signature head and neck squamous cell carcinoma murine models in which we map tumor-draining lymphatics and develop models for regional lymphablation with surgery or radiation. We find that lymphablation eliminates the tumor ICI response, worsening overall survival and repolarizing the tumor- and peripheral-immune compartments. Mechanistically, within tumor-draining lymphatics, we observe an upregulation of conventional type I dendritic cells and type I interferon signaling and show that both are necessary for the ICI response and lost with lymphablation. Ultimately, we provide a mechanistic understanding of how standard oncologic therapies targeting regional lymphatics impact the tumor response to immune-oncology therapy in order to define rational, lymphatic-preserving treatment sequences that mobilize systemic antitumor immunity, achieve optimal tumor responses, control regional metastatic disease, and confer durable antitumor immunity.

The association of active and passive tobacco smoke exposure with chronic rhinosinusitis symptom severity: A cross-sectional study

BACKGROUND

 Chronic rhinosinusitis (CRS) causes a great deal of morbidity. There are a multitude of causal factors, though their precise contribution to symptom severity has yet to be defined.  We hypothesized that exposure to both primary and secondhand tobacco smoke would correlate with more severe symptoms of CRS.

METHODS

This is a prospective cross-sectional study performed at an academic tertiary care medical center from 2010 to 2013. A total of 85 consecutive patients with chronic sinusitis were screened; 70 with medically refractory CRS requiring functional Endoscopic sinus surgery (FESS) were enrolled. Recent tobacco exposure was assessed using serum cotinine levels. Sinonasal mucosa was biopsied to assess ciliary architecture. Demographics, medical history, tobacco and environmental exposures, and computed tomography (CT) imaging were also collected. Two quality of life (QOL) surveys were administered: one disease specific, Sinonasal Outcomes Test-20 (SNOT-20), and one general, Short Form-12 (SF-12). Results were correlated with the aforementioned exposures.

RESULTS

 The 70 patients had an average age of 46 years, and 42% were male.  Variables that correlated with worse SNOT-20 scores included serum cotinine (r = 0.43, p = 0.002), number of cigarettes smoked daily (r = 0.27, p = 0.03), and number of secondhand cigarettes exposed to per day (r = 0.29, p = 0.04). There were no significant correlations between SNOT-20 scores and Lund-MacKay or axonemal ultrastructural abnormalities (AUA)-ciliary scores. The two five-variable models best predicted disease-specific QOL.

CONCLUSIONS

 Increased amounts of serum cotinine and primary and secondhand smoke exposure were associated with worse sinonasal QOL. This study establishes an objective relationship between smoke exposure and patient-perceived severity of CRS, emphasizing the importance of tobacco cessation counseling as part of management.

Quality improvement intervention to reduce time to postoperative radiation in head and neck free flap patients

BACKGROUND

Best-practice guidelines for head and neck cancer patients advise postoperative radiation therapy (PORT) initiation within 6 weeks of surgery. We report our institutional experience improving timeliness of adjuvant radiation in free-flap patients.

METHODS

Thirty-nine patients met inclusion criteria in the 2017-2019 study period. We divided into "Early" (n = 19) and "Late" (n = 20) time-period groups to compare performance over time. The primary endpoint was time to PORT initiation, with success defined as <6 weeks.

RESULTS

The number of patients achieving timely PORT improved from 10.5% in the Early group to 50.0% in the Late group (p = 0.014). Patients undergoing concurrent adjuvant chemoradiation were more likely to meet the PORT target in the Late group (p = 0.012).

CONCLUSIONS

We ascribe this quality improvement in free-flap patients to increased communication among multidisciplinary care teams, proactive consultation referrals, and a targeted patient-navigator intervention. Though work is needed to further improve performance, insight gained from our experience may benefit other teams.

A Hospital-Wide Intervention to Improve Compliance With TNM Cancer Staging Documentation

BACKGROUND

Accurate oncologic staging meeting clinical practice guidelines is essential for guideline adherence, quality assessment, and survival outcomes. However, timely and uniform documentation in the electronic health record (EHR) at the time of diagnosis is a challenge for providers. This quality improvement project aimed to increase provider compliance of timely clinical TNM (cTNM) or pathologic TNM (pTNM) staging for newly diagnosed oncologic patients.

METHODS

Providers in the following site-specific oncologic teams were included: head and neck, skin, breast, genitourinary, gastrointestinal, lung and thoracic, gynecologic, colorectal, and bone marrow transplant. Interventions to facilitate timely cTNM and pTNM staging included standardized EHR-based workflows, learning modules, stakeholder meetings, and individualized provider training sessions. For most teams, staging was considered compliant if it was completed in the EHR within the first 7 days of the calendar month after the date of the patient visit. Factors associated with staging compliance were analyzed using logistic regression models.

RESULTS

From January 1, 2014, to December 31, 2018, 7,787 preintervention and 5,152 postintervention new patient visits occurred. During the preintervention period, staging was compliant in 5.6% of patients compared with 67.4% of patients after intervention (P<.001). In the final month of the postintervention period, the overall staging compliance rate was 78.1%. At most recent tracking, staging compliance was 95%, 97%, and 93% in December 2019, January 2020, and February 2020, respectively. Logistic regression found that increasing years of provider experience was associated with decreased staging compliance.

CONCLUSIONS

High rates of staging compliance in complex multidisciplinary academic oncologic practice models can be achieved via comprehensive quality improvement and structured initiatives. This approach serves as a model for improving oncologic documentation systems to facilitate clinical decision-making and multidisciplinary coordination of care.

End of treatment cone-beam computed tomography (CBCT) is predictive of radiation response and overall survival in oropharyngeal squamous cell carcinoma

BACKGROUND

Image guidance in radiation oncology has resulted in significant improvements in the accuracy and precision of radiation therapy (RT). Recently, the resolution and quality of cone beam computed tomography (CBCT) for image guidance has increased so that tumor masses and lymph nodes are readily detectable and measurable. During treatment of head and neck squamous cell carcinoma (HNSCC), on-board CBCT setup imaging is routinely obtained; however, this CBCT imaging data is not utilized to predict patient outcomes. Here, we analyzed whether changes in CBCT measurements obtained during a course of radiation therapy correlate with responses on routine 3-month follow-up diagnostic imaging and overall survival (OS).

MATERIALS/METHODS

Patients with oropharyngeal primary tumors who received radiation therapy between 2015 and 2018 were included. Anatomical measurements were collected of largest nodal conglomerate (LNC) at CT simulation, end of radiation treatment (EOT CBCT), and routine 3-month post-RT imaging. At each timepoint anteroposterior (AP), mediolateral (ML) and craniocaudal (CC) measurements were obtained and used to create a 2-dimensional (2D) maximum.

RESULTS

CBCT data from 64 node positive patients were analyzed. The largest nodal 2D maximum and CC measurements on EOT CBCT showed a statistically significant correlation with complete response on 3-month post-RT imaging (r = 0.313, p = 0.02 and r = 0.318, p = 0.02, respectively). Furthermore, patients who experienced a 30% or greater reduction in the CC dimension had improved OS (Binary Chi-Square HR 4.85, p = 0.028).

CONCLUSION

Decreased size of pathologic lymph nodes measured using CBCT setup imaging during a radiation course correlates with long term therapeutic response and overall survival of HNSCC patients. These results indicate that CBCT setup imaging may have utility as an early predictor of treatment response in oropharyngeal HNSCC.

Role of B Cells in Responses to Checkpoint Blockade Immunotherapy and Overall Survival of Cancer Patients

The role of B cells in the tumor microenvironment and B-cell-mediated antitumor immune responses remains relatively understudied. Recent seminal studies have discovered that B cells and associated tertiary lymphoid structures correlate with responses to checkpoint blockade immunotherapy and are prognostic for overall survival of cancer patients. B-cell subsets have remarkable functional diversity and include professional antigen-presenting cells, regulatory cells, memory populations, and antibody-producing plasma cells. Importantly, secreted antibodies can independently activate innate immune responses and induce the cancer immunity cycle. Thus, B cells and B-cell-mediated antibody responses comprise the largely underappreciated second arm of the adaptive immune system and certainly deserve further attention in the field of oncology. Here, we review the known functions of B cells in the tumor microenvironment, the contribution of B cells to the antitumor activity of immunotherapies, and the role of B cells in the overall survival of cancer patients.

Patterns of failure after definitive treatment for T4a larynx cancer in the Veterans Affairs Health System

e18006

Background: Both chemoradiotherapy (CRT) and total laryngectomy (TL) with adjuvant therapy are curative-intent treatment options for patients with T4a larynx cancer. Disease recurrence is a known negative prognosicator, but differences in recurrence patterns and the subsequent survival associations are not well characterized. To address this knowledge gap, we present long-term recurrence and survival outcomes from a novel longitudinal data source. Methods: Retrospective study of non-metastatic T4a larynx cancer patients diagnosed between 2000-2017 who underwent curative-intent treatment (TL with adjuvant therapy or primary CRT) from the VA Informatics and Computing Infrastructure database. Adjuvant therapy consisted of either postoperative radiotherapy (RT) or CRT. Fine-Gray and Cox models were used to evaluate primary outcomes – time to locoregional recurrence and distant recurrence. Secondary outcomes included overall survival (OS), cancer-specific survival (CSS), non-cancer specific survival (NCSS), and disease-free survival (DFS). These multivariable models accounted for age, race, alcohol history, smoking status, education and income, Charlson-Deyo score, N-classification, and tumor subsite. Results: The study included 1,114 patients with a median follow-up time of 63.3 months among those alive at last follow up. In the TL group, adjuvant RT was used in 69% and adjuvant CRT was used in 31%. Median time to first recurrence was 24.4 months with overall incidence of 28.5% locoregional and 9.5% distant recurrence. Primary CRT patients had higher rates of locoregional (37.2 vs. 22.9%) and distant recurrence (13.3 vs. 7.0%) (p < 0.0001). Median OS was 27.3 months for CRT (95% CI: 23.6-32.4 months) and 47.5 months (95% CI: 39.6-52.1 months) for TL. Median DFS was 14.1 months for CRT (95% CI:12.5-17.2 months) and 37.9 months (95% CI 31.2-47.5 months) for TL. On multivariable analysis compared to CRT, TL was associated with longer time to locoregional (HR 0.50, 95% CI:0.40-0.61) and distant recurrence (HR 0.50, 95% CI:0.34-0.73). Having N+ disease increased risk of distant recurrence (HR 2.20, 95% CI:1.42-3.41). TL was associated with improved OS (HR 0.78, 95% CI:0.67 – 0.91), CSS (HR 0.73, 95% CI:0.59 – 0.89), and DFS (HR 0.58, 95% CI 0.49-0.69) compared to CRT; NCSS was equivalent between groups (HR 1.09, 95% CI:0.88-1.35). Of the CRT patients with locoregional failures, 67/163 (41.1%) were salvaged with surgery. Conclusions: In this cohort of T4a larynx cancer patients, surgical management demonstrated favorable recurrence and survival results. TL with adjuvant therapy was associated with significantly lower incidence of both locoregional and distant recurrence and increased OS, CSS and DFS compared to CRT. Lower probability of disease recurrence, in addition to a survival advantage, should be considered as an important advantage to up-front surgery.

Transoral robotic surgery for human papillomavirus-associated oropharynx squamous cell carcinoma: Recurrence and survival in the Veterans Affairs health system

6054

Background: Most transoral robotic surgery (TORS) literature comes from single and multi-institutional studies at tertiary-care academic intuitions. Long-term outcomes for patients with HPV-mediated oropharyngeal squamous cell carcinoma (HPV-OPSCC) treated with upfront TORS in other hospital settings across the United States are largely unknown. We present long-term recurrence and survival outcomes from a novel Veterans Health Administration (VHA) longitudinal dataset that includes patient-level data. Methods: Retrospective analysis of national VHA patients with p16-positive OPSCC diagnosed between January 2010 and December 2016, treated with TORS primary tumor resection with neck dissection. Outcome measures included: Cancer-specific survival (CSS), progression free survival (PFS), overall survival (OS), recurrence, extranodal extension (ENE), positive surgical margin (PSM), and adjuvant therapy regimen. Results: One hundred sixty-one patients were included of whom 29 (18%) were low-risk [0-1 metastatic lymph nodes, negative margins]; 45 (28%) intermediate-risk [close surgical margins, 2 to 4 metastatic nodes, LVI or PNI, pathologic T3 or T4 tumor]; and 87 (54%) high-risk [PSM, ENE, and/or ≥ 5 metastatic nodes]. ENE was present in 41% of cases and 24% of cases had positive surgical margins. Median follow-up was 5.6 years (95% CI 3.0-9.3). The 5-year CSS rates for low, intermediate, and high-risk groups were: 100%, 90.0% (95% CI 75.4-96.1%), and 88.7% (78.3-94.2%). On univariable analysis, pathologic factors associated with inferior CSS were: pT3-T4 tumor category (HR 3.81, 95% CI 1.31-11; p = 0.01), presence of more than four metastatic lymph nodes (HR 3.41, 95% CI 1.20-11; p = 0.02), and ENE (HR 3.53, 95% CI 1.06-12; p = 0.04). Close or PSM were not associated with CSS (HR 0.67, 95% CI 0.21 – 2.14; p = 0.50). In the low-risk group, 48% avoided adjuvant therapy and although there were five recurrences, none died from cancer. The intermediate-risk group was treated with adjuvant radiation in 64% of cases, and chemoradiation in 29% of cases; and there were five locoregional recurrences and three distant recurrences. Adjuvant chemoradiation was used in 68% of high-risk cases. Of the seven total patients with distant recurrences, six died of their disease. Conclusions: Our findings in this national cohort of Veterans with HPV-OPSCC demonstrate that TORS followed by adjuvant therapy yields favorable survival outcomes. Tumor-category, ENE, and more than four nodal metastases were the strongest adverse features in our data, and surgical margins did not have a significant impact on survival. Further investigations with large cohorts and prospective clinical trials are needed to elucidate the true oncologic implications of high-risk features and to identify patients best suited for de-intensified treatment.

High rates of postoperative radiotherapy delay in head and neck cancer before and after Medicaid expansion

BACKGROUND

The objective is to study the effect of Medicaid expansion on postoperative radiation therapy (PORT) delay in patients with head and neck squamous cell carcinoma (HNSCC).

METHODS

Patients from the National Cancer Database with HNSCC undergoing curative-intent surgery in the 2 years before and after Medicaid expansion were analyzed (n = 11 717) using the difference-in-differences technique to study the effect on PORT delay.

RESULTS

The rate of PORT delay before and after expansion was 66.0% and 66.9%, respectively. Medicaid patients had more frequent PORT delay than privately insured patients (pre-expansion 77.2% vs. 59.4%, p < 0.001; post-expansion 76.5% vs. 60.9%, p < 0.001). Medicaid expansion had no effect on PORT delay [hazard ratio 0.95, 95% confidence interval 0.81-1.12]. Supplemental analyses revealed that pathologic stage, number of treating facilities, and comorbidities were among several factors associated with PORT delay in the cohort.

CONCLUSION

PORT delay is unacceptably frequent. Improvement in timely adjuvant therapy requires more than Medicaid expansion.

Disruption of the HER3-PI3K-mTOR oncogenic signaling axis and PD-1 blockade as a multimodal precision immunotherapy in head and neck cancer

Immune checkpoint blockade (ICB) therapy has revolutionized head and neck squamous cell carcinoma (HNSCC) treatment, but <20% of patients achieve durable responses. Persistent activation of the PI3K/AKT/mTOR signaling circuitry represents a key oncogenic driver in HNSCC; however, the potential immunosuppressive effects of PI3K/AKT/mTOR inhibitors may limit the benefit of their combination with ICB. Here we employ an unbiased kinome-wide siRNA screen to reveal that HER3, is essential for the proliferation of most HNSCC cells that do not harbor PIK3CA mutations. Indeed, we find that persistent tyrosine phosphorylation of HER3 and PI3K recruitment underlies aberrant PI3K/AKT/mTOR signaling in PIK3CA wild type HNSCCs. Remarkably, antibody-mediated HER3 blockade exerts a potent anti-tumor effect by suppressing HER3-PI3K-AKT-mTOR oncogenic signaling and concomitantly reversing the immune suppressive tumor microenvironment. Ultimately, we show that HER3 inhibition and PD-1 blockade may provide a multimodal precision immunotherapeutic approach for PIK3CA wild type HNSCC, aimed at achieving durable cancer remission.

Reciprocal activation of HEY1 and NOTCH4 under SOX2 control promotes EMT in head and neck squamous cell carcinoma

Several comprehensive studies have demonstrated that the NOTCH pathway is altered in a bimodal manner in head and neck squamous cell carcinoma (HNSCC). In a previous study, it was found that the NOTCH4/HEY1 pathway was specifically upregulated in HNSCC and promoted epithelial-mesenchymal transition (EMT), and that HEY1 activation supported SOX2 expression. However, the interactions in this pathway have not yet been fully elucidated. The present study investigated the NOTCH4/HEY1/SOX2 axis in HNSCC using in vitro models and the Cancer Genome Atlas (TCGA) database. To explore the association, reporter and ChIP RT-qPCR assays using SOX2-overexpressing (SOX2-OE) cells were performed. The association between NOTCH4 and HEY1 was examined in the same manner using HEY1-overexpressing (HEY1-OE) cells. The results of the in vitro experiments indicated that HEY1 promoted EMT in the HNSCC cells. Furthermore, the overexpression of HEY1 also promoted sphere formation and increased murine xenograft tumorigenicity. Reporter assays and ChIP RT-qPCR experiments indicated that SOX2 regulated HEY1 expression via direct binding of the HEY1 promoter. HEY1 expression significantly correlated with SOX2 expression in primary lung SCC and other SCCs using the TCGA database. HEY1 also regulated NOTCH4 expression to create a positive reciprocal feedback loop. On the whole, the present study demonstrates that HEY1 expression in HNSCC is regulated via the promotion of SOX2 and promotes EMT. The NOTCH4/HEY1 pathway is specifically upregulated via a positive reciprocal feedback loop mediated by the HEY1-medaited regulation of NOTCH4 transcription, and SOX2 correlates with HEY1 expression in SCC from other primary sites.

Improving documentation of cancer staging at an academic cancer center utilizing an EMR-based system with public accountability

197

Background: Accurate TNM staging of malignancy is essential to quality care of cancer patients but maintaining consistent documentation of appropriate staging remains a challenge. We identified documentation of TNM staging at our institution to be below target levels. We sought to improve documentation of staging in all patients at our cancer center with a diagnosis of malignancy by implementing both automated and manual reminders through our electronic medical record (EMR) software (Epic), as well as by using team accountability. Methods: We defined an expectation that all patients seen at UC San Diego Moores Cancer Center with a billing diagnosis of malignancy would have TNM staging documented in the EMR within 1 month of their initial visit. The project started in 1/2016, with a phased rollout to individual teams, including education and outreach prior to the start of performance tracking. We used the AJCC staging module in Epic and focused on all new patient visits with a billing diagnosis of malignancy. Providers were asked to add this diagnosis to the problem list and then document the stage using the AJCC staging module in EPIC. We tracked compliance by individual provider and by team and emailed performance reports to all providers on a monthly basis. To facilitate compliance, we initiated automatic Epic messages to providers for an unstaged cancer diagnosis on the problem list and followed up with a personal email from administrative staff if documentation was not completed in a timely manner. Results: At the initiation of this project, there was no standardized documentation of cancer staging. The project was phased in with the skin cancer and head and neck cancers teams in phase I. Compliance in the initial month of measurement was 28%. Within 3 months of implementation of the project, compliance was over 50%, and within 27 months, over 90%. Compliance has remained > 90% since. For 3/2020, 368 patients were eligible for staging and 98% were staged within a month of their visit. Conclusions: Documentation of TNM staging of malignancy was significantly improved by both automated and personal reminders with a vital component of team accountability. Further efforts to improve the current practice and culture of documentation for diagnosed cancer patients remains a crucial aspect of quality and safety.

HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers

The dominant paradigm for HPV carcinogenesis includes integration into the host genome followed by expression of E6 and E7 (E6/E7). We explored an alternative carcinogenic pathway characterized by episomal E2, E4, and E5 (E2/E4/E5) expression. Half of HPV positive cervical and pharyngeal cancers comprised a subtype with increase in expression of E2/E4/E5, as well as association with lack of integration into the host genome. Models of the E2/E4/E5 carcinogenesis show p53 dependent enhanced proliferation in vitro, as well as increased susceptibility to induction of cancer in vivo. Whole genomic expression analysis of the E2/E4/E5 pharyngeal cancer subtype is defined by activation of the fibroblast growth factor receptor (FGFR) pathway and this subtype is susceptible to combination FGFR and mTOR inhibition, with implications for targeted therapy.

Elective neck dissection for T3/T4 cN0 sinonasal squamous cell carcinoma

BACKGROUND

In locally advanced sinonasal squamous cell carcinoma (SNSCC), management of the clinically node-negative (cN0) neck is variable and elective neck dissection (END) remains controversial.

METHODS

Patients with surgically treated T3/T4 cN0 M0 SNSCC were identified using the NCDB. Overall survival (OS) was assessed by Cox proportional hazard analysis in propensity score-matched cohorts. Factors associated with END were evaluated with logistic regression.

RESULTS

Two hundred twenty patients underwent END (19.6%). END did not correlated with OS in propensity score-matched cohorts (HR 0.971, 95% CI 0.677-1.392), a maxillary sinus tumor subgroup (HR 1.089, 95% CI 0.742-1.599), or by radiation status [radiation: (HR 0.802, 95% CI 0.584-1.102); no radiation: (HR 0.852, 95% CI 0.502-1.445)]. The occult metastasis rate in the END cohort was 12.7%.

CONCLUSION

END did not significantly improve OS in this study. Further information on disease-free survival is necessary to determine its role in advanced-stage SNSCC.

Identifying predictors of HPV-related head and neck squamous cell carcinoma progression and survival through patient-derived models

Therapeutic innovation for human papilloma virus-related (HPV+) head and neck squamous cell carcinomas (HNSCCs) is impaired by inadequate preclinical models and the absence of accurate biomarkers. Our study establishes the first well-characterized panel of patient-derived xenografts (PDXs) and organoids from HPV+ HNSCCs while determining fidelity of the models to the distinguishing genetic features of this cancer type. Despite low engraftment rates, whole exome sequencing showed that PDXs retain multiple distinguishing features of HPV+ HNSCC lost in existing cell lines, including PIK3CA mutations, TRAF3 deletion and the absence of EGFR amplifications. Engrafted HPV+ tumors frequently contained NOTCH1 mutations, thus providing new models for a negatively prognostic alteration in this disease. Genotype-phenotype associations in the models were then tested for prediction of tumor progression and survival in published clinical cohorts. Observation of high tumor mutational burdens (TMBs) in the faster-growing models facilitated identification of a novel association between TMB and local progression in both HPV+ and HPV- patients that was prognostic in HPV- cases. In addition, reduced E7 and p16^INK4A levels found in a PDX from an outlier case with lethal outcome led to detection of similar profiles among recurrent HPV+ HNSCCs. Transcriptional data from the Cancer Genome Atlas was used to demonstrate that the lower E2F target gene expression predicted by reduced E7 levels has potential as a biomarker of disease recurrence risk. Our findings bridge a critical gap in preclinical models for HPV+ HNSCCs and simultaneously reveal novel potential applications of quantifying mutational burden and viral oncogene functions for biomarker development.

Abstract A01: HPV+ oral cancer PDXs identify prognostic utility for E2F target gene expression and mutation burden

Barriers to advancing therapy for HPV-related (HPV+) head and neck squamous cell carcinomas (HNSCCs) include a paucity of preclinical models and difficulty prospectively identifying the minority of cases with lethal potential. This study therefore sought to establish HPV+ patient-derived models with high genetic fidelity and use them to help identify aggressive molecular subtypes of HPV+ HNSCC. Using whole-exome sequence and viral transcript analysis, nine stably passaged patient-derived xenogafts (PDXs) were found to avoid typical artifacts in HPV+ cell lines, which include loss of canonical PIK3CA mutants, gains in 3q copy number, and increased viral integration. Notably, the models contained markedly increased rates of alteration in Notch pathway genes and in H3K4 methyltransferases than would be predicted by The Cancer Genome Atlas (TCGA). Although phenotypic correlates of these alterations were not overtly apparent in the models, analysis of their growth features uncovered strong positive associations of tumor mutational burden (TMB) with in vivo growth rate and in vitro organoid propagation capacity. This observation led to identification of a novel association in TCGA between TMB and both reduced local progression and survival of early HPV-negative HNSCCs, which was further validated in esophageal squamous cell carcinomas. Although TMB failed to be prognostic in the HPV+ HNSCCs, insight into high-risk HPV+ molecular features was provided by a PDX from an unusual case that suffered lethal relapse shortly after definitive therapy. Reduced viral E7 and p16INK4A expression was identified both in this model and in early lethal HPV+ cases in TCGA as well as those in a second HPV+ HNSCC cohort (JHU). The lower E7 and p16INK4A levels here suggested a diminished imprint of viral oncogene function upon cell cycle regulation in lethal cases. Hierarchical clustering of the cohorts using a broad E2F target gene expression panel revealed a distinctive pattern of E2F target dysregulation in the clusters that captured the early lethal cases. A subset of ten transcripts optimally predicted survival independent of stage in both TCGA and JHU cohorts. This analysis of the largest panel of HPV+ HNSCC PDXs described to date identified robust models for PIK3CA activation, Notch pathway dysregulation, and altered H3K4 methylation in this disease. At the same time, it defined novel clinical correlates of TMB and E2F target expression pattern that have potential utility in guiding risk stratification, biomarker development, and trial design.

Citation Format: Nicole D. Facompre, Pavithra Rajagopalan, Alexander T. Pearson, Kathleen T. Montone, Claire D. James, Frederico O. Gleber-Netto, Hiroshi Nakagawa, Elizabeth A. White, Anil K. Rustgi, Joseph A. Califano, Curtis R. Pickering, Bradley Windle, Iaian M. Morgan, Phyllis A. Gimotty, Devraj Basu. HPV+ oral cancer PDXs identify prognostic utility for E2F target gene expression and mutation burden [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr A01.

An Analysis of 1-Year Charges for Head and Neck Cancer: Targets for Value-Based Interventions

OBJECTIVE

To identify the dominant clinical factors associated with increased 1-year charges in treating head and neck cancer.

STUDY DESIGN

Retrospective review.

SETTING

Single academic institution.

SUBJECTS AND METHODS

We retrospectively reviewed 1-year charges for 196 consecutive patients with head and neck cancer (HNC) who were treated exclusively at our institution. We analyzed charges by department as well as factors associated with increased charges per multivariable regression.

RESULTS

The mean age was 59.6 years (SD, 14.9). Most of the population was male (64%), white (70%), and commercially insured (46%). The most common primary sites were the oropharynx (25%; 76%, HPV positive), skin (19%), and thyroid (17%). Eighty-three percent of total charges were due to standard-of-care treatment for HNC: surgery ($16 million), radiation therapy ($22 million), or chemotherapy ($11 million). The median total charge per patient was $212,484 (interquartile range, $78,630-$475,823). Multivariable regression demonstrated that the following were associated with increased charges: nasopharynx subsite ($250,929 [95% CI, $93,290-$408,569]; effect size in US dollars, P = .002), advanced stage (American Joint Committee on Cancer, seventh edition; $80,331 [$22,726-$137,936], P = .007), therapeutic surgery ($281,893 [$117,371-$446,415], P = .001), chemotherapy ($183,331 [$125,497-$241,165], P < .001), radiation ($203,397 [$143,454-$263,341], P < .001), surgical complication requiring return to the operating room ($147,247 [$37,240-$257,254], P = .009), emergency department visits ($89,050 [$23,811-$154,289], P = .008), and admissions ($140,894 [$82,895-$198,893], P < .001; constant, -$233,927 [-$410,790 to -$57,064]). The top quartile accrued 55% of the total charges.

CONCLUSION

Radiation, followed by surgery and chemotherapy, were the most expensive components of HNC care. In this analysis, we identified the dominant clinical factors associated with increased charges.

Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing

Alternative mRNA splicing increases protein diversity, and alternative splicing events (ASEs) drive oncogenesis in multiple tumor types. However, the driving alterations that underlie the broad dysregulation of ASEs are incompletely defined. Using head and neck squamous cell carcinoma (HNSCC) as a model, we hypothesized that the genomic alteration of genes associated with the spliceosome may broadly induce ASEs across a broad range of target genes, driving an oncogenic phenotype. We identified 319 spliceosome genes and employed a discovery pipeline to identify 13 candidate spliceosome genes altered in HNSCC using The Cancer Genome Atlas (TCGA) HNSCC data. Phenotypic screens identified amplified and overexpressed CPSF1 as a target gene alteration that was validated in proliferation, colony formation, and apoptosis assays in cell line and xenograft systems as well as in primary HNSCC. We employed knockdown and overexpression assays followed by identification of ASEs regulated by CPSF1 overexpression to identify changes in ASEs, and the expression of these ASEs was validated using RNA from cell line models. Alterations in expression of spliceosome genes, including CPSF1, may contribute to HNSCC by mediating aberrant ASE expression.

Meta-analysis of risk of occult lymph node metastasis in the irradiated, clinically N0 neck

BACKGROUND

Recurrent head and neck squamous cell carcinoma (HNSCC) after radiation is associated with poor survival, and management of the clinically negative (N0) neck during salvage surgery is controversial.

METHODS

Studies were selected according to preferred reporting items for systematic reviews and meta-analyses guidelines. Inclusion criteria were patients with HNSCC, prior radiation to the lateral neck nodal basin, undergoing salvage surgery for local recurrence, persistence or second primary, and N0 at time of salvage. Eleven studies with a total of 382 patients met inclusion criteria.

RESULTS

The rate of occult metastasis was 15.4%. The pooled rate of occult nodal metastasis was 16.2% for oral cavity, 12.9% for oropharynx, 23.7% for hypopharynx, and 27.3% for supraglottic or transglottic tumors. There was a significantly higher relative risk of occult metastasis for locally advanced tumors.

CONCLUSION

Elective neck dissection at time of salvage surgery should be considered based on subsite, T classification, and prior history of nodal metastasis.

Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma

BACKGROUND

We aimed to use genomic data for optimizing polymerase chain reaction (PCR) primer/probe sets for detection of human papillomavirus (HPV)-16 in body fluids of patients with HPV-related head and neck squamous cell carcinoma (HPV-HNSCC).

METHODS

We used genomic HPV-HNSCC sequencing data from a single institutional and a TCGA cohort. Optimized primer/probe sets were designed and tested for analytical performance in CaSki HPV-16 genome and confirmed in salivary rinse samples from patients with HPV-HNSCC.

RESULTS

The highest read density was observed between E5 and L2 regions. The E1 region contained a region that was universally present. Among candidate PCR primer/probe sets created, six reliably detected 30 HPV-16 copy number. In a CLIA certified laboratory setting, the combination of two novel primer/probe with E7 sets improved performance in salivary rinse samples with a sensitivity of 96% and specificity of 100%.

CONCLUSIONS

PCR-based detection of HPV-16 DNA in HPV-HNSCC can be improved using rational genomic design.

B Cells Improve Overall Survival in HPV-Associated Squamous Cell Carcinomas and Are Activated by Radiation and PD-1 Blockade

PURPOSE

To characterize the role of B cells on human papilloma virus (HPV)-associated cancer patient outcomes and determine the effects of radiation and PD-1 blockade on B-cell populations.

EXPERIMENTAL DESIGN

Tumor RNA-sequencing data from over 800 patients with head and neck squamous cell carcinoma (HNSCC) and cervical cancer, including a prospective validation cohort, was analyzed to study the impact of B-cell gene expression on overall survival (OS). A novel murine model of HPV⁺ HNSCC was used to study the effects of PD-1 blockade and radiotherapy on B-cell activation, differentiation, and clonality including analysis by single-cell RNA-sequencing and B-cell receptor (BCR)-sequencing. Human protein microarray was then used to quantify B-cell-mediated IgG and IgM antibodies to over 16,000 proteins in the serum of patients treated on a clinical trial with PD-1 blockade.

RESULTS

RNA-sequencing identified CD19 and IGJ as novel B-cell prognostic biomarkers for 3-year OS (HR, 0.545; P < 0.001). PD-1 blockade and radiotherapy enhance development of memory B cells, plasma cells, and antigen-specific B cells. BCR-sequencing found that radiotherapy enhances B-cell clonality, decreases CDR3 length, and induces B-cell somatic hypermutation. Single-cell RNA-sequencing identified dramatic increases in B-cell germinal center formation after PD-1 blockade and radiotherapy. Human proteome array revealed enhanced IgG and IgM antibody responses in patients who derived clinical benefit but not those with progressive disease after treatment with PD-1 blockade.

CONCLUSIONS

These findings establish a key role for B cells in patient outcomes and responses to PD-1 blockade in HPV-associated squamous cell carcinomas and demonstrate the need for additional diagnostics and therapeutics targeting B cells.

Targeting Viral DNA and Promoter Hypermethylation in Salivary Rinses for Recurrent HPV-Positive Oropharyngeal Cancer

OBJECTIVE

The incidence and survivorship of human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) are increasing. Presence of HPV DNA and epigenetic alterations in salivary rinses are independently associated with clinical prognosis. We evaluated the utility of a combined panel in detecting disease recurrence during surveillance. We also assessed the assay's applicability in screening for HPV+ OPSCC.

STUDY DESIGN

Retrospective cohort study.

SETTING

Two tertiary academic hospitals.

SUBJECTS AND METHODS

Forty-nine patients with posttreatment OPSCC were enrolled. Separately, 21 treatment-naive patients and 40 controls were included in the screening analysis. Salivary rinses were obtained from these cohorts and biomarker levels were quantified. Receiver operative characteristic (ROC) curves and multivariate logistic models were used to assess performance of biomarker combinations.

RESULTS

Eight patients (16.3%) in the posttreatment cohort developed locoregional recurrence. Recurrence was associated with alcohol use (odds ratio [OR], 6.12; 95% confidence interval [CI], 0.26-3.79) and advanced nodal disease (OR, 2.21; 95% CI, 1.52-3.01). A panel of HPV DNA and methylated EDNRB improved detection of recurrent disease (area under the curve [AUC], 0.88) compared to single markers (AUC, 0.69-0.78). Positive biomarkers preceded clinical detection by 2.4 ± 1.6 months and was associated with nearly 40-fold risk of recurrence (OR, 36.4; 95% CI, 1.15-45.22). Within the screening analysis, single biomarkers demonstrated moderate sensitivity and specificity (AUC, 0.59-0.83) in the detection of primary disease. A panel combining HPV DNA markers with methylated EDNRB and methylated PAX5 improved AUC to 0.93.

CONCLUSION

Detection of high-risk HPV DNA or aberrant hypermethylation in oral rinses is associated with presence and recurrence of OPSCC. Targeting both markers in saliva may have utility in long-term surveillance.

Cannabinoids Promote Progression of HPV-Positive Head and Neck Squamous Cell Carcinoma via p38 MAPK Activation

PURPOSE

Human papillomavirus (HPV)-related head and neck squamous cell carcinoma (HNSCC) is associated with daily marijuana use and is also increasing in parallel with increased marijuana use in the United States. Our study is designed to define the interaction between cannabinoids and HPV-positive HNSCC.

EXPERIMENTAL DESIGN

The expression of cannabinoid receptors CNR1 and CNR2 was analyzed using The Cancer Genome Atlas (TCGA) HNSCC data. We used agonists, antagonists, siRNAs, or shRNA-based models to explore the roles of CNR1 and CNR2 in HPV-positive HNSCC cell lines and animal models. Cannabinoid downstream pathways involved were determined by Western blotting and analyzed in a primary HPV HNSCC cohort with single-sample gene set enrichment analysis (ssGSEA) and the OncoGenome Positioning System (Onco-GPS).

RESULTS

In TCGA cohort, the expression of CNR1 and CNR2 was elevated in HPV-positive HNSCC compared with HPV-negative HNSCC, and knockdown of CNR1/CNR2 expression inhibited proliferation in HPV-positive HNSCC cell lines. Specific CNR1 and CNR2 activation as well as nonselective cannabinoid receptor activation in cell lines and animal models promoted cell growth, migration, and inhibited apoptosis through p38 MAPK pathway activation. CNR1/CNR2 antagonists suppressed cell proliferation and migration and induced apoptosis. Using whole-genome expression analysis in a primary HPV HNSCC cohort, we identified specific p38 MAPK pathway activation signature in tumors from HPV HNSCC patients with objective measurement of concurrent cannabinoid exposure.

CONCLUSIONS

Cannabinoids can promote progression of HPV-positive HNSCC through p38 MAPK pathway activation.

HPV16 E5 Mediates Resistance to PD-L1 Blockade and Can Be Targeted with Rimantadine in Head and Neck Cancer

There is a critical need to understand mechanisms of resistance and to develop combinatorial strategies to improve responses to checkpoint blockade immunotherapy (CBI). Here, we uncover a novel mechanism by which the human papillomavirus (HPV) inhibits the activity of CBI in head and neck squamous cell carcinoma (HNSCC). Using orthotopic HNSCC models, we show that radiation combined with anti-PD-L1 immunotherapy significantly enhanced local control, CD8⁺ memory T cells, and induced preferential T-cell homing via modulation of vascular endothelial cells. However, the HPV E5 oncoprotein suppressed immune responses by downregulating expression of major histocompatibility complex and interfering with antigen presentation in murine models and patient tumors. Furthermore, tumors expressing HPV E5 were rendered entirely resistant to anti-PD-L1 immunotherapy, and patients with high expression of HPV16 E5 had worse survival. The antiviral E5 inhibitor rimantadine demonstrated remarkable single-agent antitumor activity. This is the first report that describes HPV E5 as a mediator of resistance to anti-PD-1/PD-L1 immunotherapy and demonstrates the antitumor activity of rimantadine. These results have broad clinical relevance beyond HNSCC to other HPV-associated malignancies and reveal a powerful mechanism of HPV-mediated immunosuppression, which can be exploited to improve response rates to checkpoint blockade. SIGNIFICANCE: This study identifies a novel mechanism of resistance to anti-PD-1/PD-L1 immunotherapy mediated by HPV E5, which can be exploited using the HPV E5 inhibitor rimantadine to improve outcomes for head and neck cancer patients. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/4/732/F1.large.jpg.

A novel splice variant of LOXL2 promotes progression of human papillomavirus-negative head and neck squamous cell carcinoma

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) is one of the most frequently diagnosed cancers worldwide. LOXL2 demonstrates alternative splicing events in patients with human papillomavirus (HPV)-negative HNSCC. The current study explored the role of a dominant LOXL2 variant in HPV-negative HNSCC.

METHODS

Expression of the LOXL2 variant was analyzed using The Cancer Genome Atlas cohorts and validated using quantitative reverse transcriptase-polymerase chain reaction in a separate primary tumor set. The authors defined the effect of LOXL2 splice variants in assays for cell proliferation using a cell viability assay and colony formation assay. Cell migration and invasion were examined using a cell scratch assay and transwell cell migration and invasion assay in LOXL2 splice variant gain and loss of expression cells. Western blot analysis and gene set enrichment analysis were used to explore the potential mechanism of the LOXL2 splice variant in HPV-negative HNSCC.

RESULTS

Expression of a novel LOXL2 variant was found to be upregulated in The Cancer Genome Atlas HPV-negative HNSCC, and confirmed in the separate primary tumor validation set. Analyses of loss and gain of function demonstrated that this LOXL2 variant enhanced proliferation, migration, and invasion in HPV-negative HNSCC cells and activated the FAK/AKT pathway. A total of 837 upregulated and 820 downregulated genes and 526 upregulated and 124 downregulated pathways associated with LOXL2 variant expression were identified using gene set enrichment analysis, which helped in developing a better understanding of the networks activated by this LOXL2 variant in patients with HPV-negative HNSCC.

CONCLUSIONS

The novel LOXL2 variant can promote the progression of HPV-negative HNSCC, in part through FAK/AKT pathway activation, which may provide a new potential therapeutic target among patients with HPV-negative HNSCC.

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer

Current literature suggests that epigenetically regulated super-enhancers (SEs) are drivers of aberrant gene expression in cancers. Many tumor types are still missing chromatin data to define cancer-specific SEs and their role in carcinogenesis. In this work, we develop a simple pipeline, which can utilize chromatin data from etiologically similar tumors to discover tissue-specific SEs and their target genes using gene expression and DNA methylation data. As an example, we applied our pipeline to human papillomavirus-related oropharyngeal squamous cell carcinoma (HPV + OPSCC). This tumor type is characterized by abundant gene expression changes, which cannot be explained by genetic alterations alone. Chromatin data are still limited for this disease, so we used 3627 SE elements from public domain data for closely related tissues, including normal and tumor lung, and cervical cancer cell lines. We integrated the available DNA methylation and gene expression data for HPV + OPSCC samples to filter the candidate SEs to identify functional SEs and their affected targets, which are essential for cancer development. Overall, we found 159 differentially methylated SEs, including 87 SEs that actively regulate expression of 150 nearby genes (211 SE-gene pairs) in HPV + OPSCC. Of these, 132 SE-gene pairs were validated in a related TCGA cohort. Pathway analysis revealed that the SE-regulated genes were associated with pathways known to regulate nasopharyngeal, breast, melanoma, and bladder carcinogenesis and are regulated by the epigenetic landscape in those cancers. Thus, we propose that gene expression in HPV + OPSCC may be controlled by epigenetic alterations in SE elements, which are common between related tissues. Our pipeline can utilize a diversity of data inputs and can be further adapted to SE analysis of diseased and non-diseased tissues from different organisms.

Acoustic Nanomotors for Detection of Human Papillomavirus-Associated Head and Neck Cancer

OBJECTIVE

Human papillomavirus (HPV)-associated oropharyngeal cancer (OPC) is a lethal disease with increasing incidence; however, technologies for early detection are limited. Nanomotors are synthetic nanostructures that can be powered by different mechanisms and functionalized for specific applications, such as biosensing. The objective of this investigation was to demonstrate an in vitro proof of concept for a novel nanomotor-based cancer detection approach toward in vivo detection of HPV-OPC.

STUDY DESIGN

In vitro cell line incubated with ultrasound-propelled nanomotors.

SETTING

Basic science and engineering laboratories.

SUBJECTS AND METHODS

Ultrasound-powered gold nanowire nanomotors were functionalized with graphene oxide and dye-labeled single-stranded DNA for the specific intracellular detection of HPV16 E6 mRNA transcripts. Nanomotors were incubated with HPV-positive or HPV-negative human OPC cells under static conditions or with an applied ultrasound field for 15 minutes. The resulting intracellular fluorescence was assessed with fluorescence microscopy and analysis software.

RESULTS

Nanomotors incubated with RNA extracted from HPV-positive OPC cells resulted in 60.7% of maximal fluorescence recovery, while incubation with RNA extracted from HPV-negative cells produced negligible fluorescence. Nanomotor incubation with intact HPV-negative cells produced minimal fluorescence (0.01 au), while incubation with HPV-positive cells produced a detectable signal (0.43 au) under static conditions and had 2.3-times greater intensity when powered with ultrasound.

CONCLUSION

Acoustically powered nanomotors can successfully identify HPV16 E6 mRNA transcripts extracellularly and within intact cells. This work represents the first step toward a novel, practical approach to address the challenge of visually detecting HPV-OPC in real time.

Impact of margin status on survival after surgery for sinonasal squamous cell carcinoma

BACKGROUND

Sinonasal squamous cell carcinoma (SNSCC) is the most common malignancy of the paranasal sinuses. Surgery is the mainstay of treatment, yet positive surgical margins (PSM) are common and the prognostic impact on overall survival (OS) is mixed. Given the heterogeneity of impact of PSM on OS within the literature, we hypothesized that extent of tumor extirpation (microscopic PSM vs macroscopic PSM) may play a role in OS.

METHODS

Patients with SNSCC were identified in the National Cancer Database (NCDB, n = 7808). Of these, 4543 patients underwent surgery, 3265 patients underwent nonsurgical therapy. Kaplan-Meier curves were used to compare OS between negative surgical margin (NSM), micro-PSM, and macro-PSM cohorts vs patients undergoing primary nonsurgical therapy in a propensity-score-matched analysis. Multivariable analysis of factors associated with macro-PSM was also performed.

RESULTS

One thousand thirty-three (22.0%) of the surgery patients had PSM, and approximately half (n = 521, 50.6%) of these had macro-PSM. When compared with nonsurgical treatment, propensity-score-matched results demonstrated improved OS in patients with NSM and micro-PSM (p < 0.001), but macro-PSM patients did not demonstrate improvement (p = 0.20). Tumor within the paranasal sinuses and advanced nodal classification (N2/N3) (odds ratio [OR], 1.18; p = 0.02; and OR, 15.09; p = 005, respectively) was associated with increased odds of macro-PSM on multivariable analysis.

CONCLUSION

We demonstrate that the degree of tumor extirpation correlates with OS. Macro-PSM did not confer a benefit to OS when compared with nonsurgical therapy, and factors including tumor location and advanced nodal status affect whether surgery will result in macro-PSM. Given these findings, informed, shared decisionmaking between patient and surgeon regarding nonsurgical alternatives should occur before electing to proceed with surgery in SNSCC.

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer

Motivation

Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in normal tissues, which have stable regulation of gene splicing. Pathological conditions, such as cancer, can have broken regulation of splicing that increases the heterogeneity of the expression of splice variants. Inferring events with such differential heterogeneity in gene isoform usage requires new statistical approaches.

Results

We introduce Splice Expression Variability Analysis (SEVA) to model increased heterogeneity of splice variant usage between conditions (e.g. tumor and normal samples). SEVA uses a rank-based multivariate statistic that compares the variability of junction expression profiles within one condition to the variability within another. Simulated data show that SEVA is unique in modeling heterogeneity of gene isoform usage, and benchmark SEVA's performance against EBSeq, DiffSplice and rMATS that model differential isoform usage instead of heterogeneity. We confirm the accuracy of SEVA in identifying known splice variants in head and neck cancer and perform cross-study validation of novel splice variants. A novel comparison of splice variant heterogeneity between subtypes of head and neck cancer demonstrated unanticipated similarity between the heterogeneity of gene isoform usage in HPV-positive and HPV-negative subtypes and anticipated increased heterogeneity among HPV-negative samples with mutations in genes that regulate the splice variant machinery. These results show that SEVA accurately models differential heterogeneity of gene isoform usage from RNA-seq data.

Availability and implementation

SEVA is implemented in the R/Bioconductor package GSReg.

Contact

bahman@jhu.edu or favorov@sensi.org or ejfertig@jhmi.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers

The original version of this Article contained an error in the author affiliations. Trey Ideker was incorrectly associated with 'Department of Medicine (Oncology), Stanford University School of Medicine, 875 Blake Wilbur Dr, Palo Alto, CA 94304, USA.' This has now been corrected in both the PDF and HTML versions of the Article.

Comparison of Tumor Classifications for Cutaneous Squamous Cell Carcinoma of the Head and Neck in the 7th vs 8th Edition of the AJCC Cancer Staging Manual

Importance

Previous studies have shown that the AJCC Cancer Staging Manual, 7th edition (AJCC 7), tumor classification for cutaneous squamous cell carcinoma (CSCC) failed to accurately stratify disease-related outcomes. The recently released 8th edition (AJCC 8) features a revised tumor classification for only head and neck CSCC (HNCSCC).

Objective

To compare AJCC 7 and AJCC 8 tumor classifications for HNCSCC and to validate AJCC 8.

Design, Setting, and Participants

This was a 10-year retrospective cohort study (2000-2009) at an academic tertiary care center reviewing 680 primary HNCSCC tumors in 459 patients.

Main Outcomes and Measures

Primary HNCSCC tumors were reviewed for disease-related outcomes (DROs): local recurrence (LR), nodal metastasis (NM), and disease-specific death (DSD). Tumors were stratified by AJCC 7 and AJCC 8 tumor classification. Distinctiveness (outcome differences between categories), homogeneity (outcome similarity within categories), and monotonicity (outcome worsening with increasing categories) were assessed for both classifications.

Results

Most of the 459 patients were white (451 [98.3%]) and male (312 [68.0%]). AJCC 8 high tumor categories (T3/T4) accounted for 121 (17.8%) of total cases but 50 of 71 DROs (70.4%) (22 of 34 of LRs [64.7%], 17 of 24 NMs [70.8%], and 11 of 13 of DSDs [84.6%]). This was a significant improvement over AJCC 7, where only 12 of 71 DROs (16.9%) (4 of 34 LRs [11.8%], 3 of 24 NMs [12.5%], and 5 of 13 DSDs [38.5%]) occurred in T3/T4 categories. However, AJCC 8 T2 and T3 were indistinct, with overlapping 95% CIs for 10-year cumulative incidences of LR, NM, and DSD. The 10-year cumulative incidence of DROs in the 119 AJCC 8 T3 cases were 19.7% (95% CI, 13.0%-29.7%) for LR, 14.1% (95% CI, 9.7%-20.7%) for NM, and 9.3% (95% CI, 6.8%-14.0% for DSD).

Conclusions and Relevance

AJCC 8 demonstrates superior homogeneity and monotonicity compared with AJCC 7. It now may be possible for AJCC 8 HNCSCC T2, T3, and T4 cases to be recorded and tracked by tumor registries because they represented a 23.1% subset in this study, which includes nearly all poor outcomes (85.9%). Further work is needed to validate AJCC 8 with population-level data and to compare AJCC 8 performance against alternative tumor classifications.

Identifying adverse molecular features of HPV+ head and neck cancers using patient-derived models

6057

Background: Advancing therapy for human papilloma virus-related (HPV+) head and neck squamous cell carcinoma (HNSCC) is hindered by inadequate preclinical models and risk stratification tools. This study addresses both barriers by characterizing a panel of patient-derived xenografts (PDXs) that includes nine new models of HPV+ disease. Methods: Exome-sequenced genetic features of the PDXs were compared to their growth properties and the outcomes of their patients of origin. Genetic traits with potential prognostic utility were validated in multiple retrospective patient cohorts. Results: The HPV+ PDXs avoided known artifacts in HPV+ cell lines, including 3q amplifications and loss of PIK3CA mutants, while enriching for alterations in H3K4 methyltransferases and Notch pathway genes. A positive association emerged between PDX tumor mutational burden (TMB) and their growth efficiency both in vivo and as organoids. This finding led to identification in The Cancer Genome Atlas (TCGA) of an association between high TMB and worse survival of early-stage HPV-negative cancers but not HPV+ ones. Insight into aggressive HPV+ disease came from a PDX established from a patient before lethal relapse. The reduced levels of viral E7 and p16INK4A present in this model were also detected in early lethal HPV+ cases in TCGA as well as the recurrences in a second HPV+ HNSCC cohort (JHU). This observation suggested a diminished contribution of viral oncogenes to cell cycle dysregulation in aggressive cases. To evaluate this possibility, hierarchical clustering of both cohorts was performed based on expression of E2F target genes. This analysis discovered a distinct cell cycle-related transcriptional pattern in the clusters of cases containing the recurrences and early lethal events. Furthermore, a subset of these transcripts proved to be stage-independent predictors of survival for the HPV+ HNSCCs in both TCGA and JHU cohorts. Conclusions: Characterizing the most HPV+ patient-derived models described to date revealed novel prognostic utility for E2F target expression in HPV+ HNSCCs and TMB in HPV-negative HNSCCs. These features have potential for application to risk stratification, biomarker development, and trial design.

Locally advanced high-risk HPV related oropharyngeal squamous cell carcinoma (OPSCC); have we forgotten it is a different disease?

HPV related OPSCC has a distinct behavior and improved outcome. As immunotherapy has recently evolved into a new standard for advanced (SCCHN), trials for high-risk SCCHN have trended to encompass both HPV related and unrelated diseases. In this invited editorial, we question the wisdom of this approach and argue for the design of trials focused specifically on HPV related locally advanced oropharyngeal squamous cell carcinoma as a unique disease entity.

Mutation of chromatin regulators and focal hotspot alterations characterize human papillomavirus-positive oropharyngeal squamous cell carcinoma

BACKGROUND

Human papillomavirus (HPV)-associated oropharyngeal cancer is a disease clinically and biologically distinct from smoking-related head and neck squamous cell carcinoma (HNSCC). Despite its rapidly increasing incidence, the mutational landscape of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) remains understudied.

METHODS

This article presents the first mutational analysis of the 46 HPV+ OPSCC tumors within the newly expanded cohort of 530 HNSCC tumors from The Cancer Genome Atlas. A separate exome sequencing analysis was also performed for 46 HPV+ OPSCCs matched to their normal lymphocyte controls from the Johns Hopkins University cohort.

RESULTS

There was a strikingly high 33% frequency of mutations within genes associated with chromatin regulation, including mutations in lysine methyltransferase 2C (KMT2C), lysine methyltransferase 2D (KMT2D), nuclear receptor binding SET domain protein 1 (NSD1), CREB binding protein (CREBBP), E1A-associated protein p300 (EP300), and CCCTC-binding factor (CTCF). In addition, the commonly altered genes phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA) and fibroblast growth factor receptor 3 (FGFR3) showed distinct domain-specific hotspot mutations in comparison with their HPV- counterparts. PIK3CA showed a uniquely high rate of mutations within the helicase domain, and FGFR3 contained a predominance of hotspot S249C alterations that were not found in HPV- HNSCC.

CONCLUSIONS

This analysis represents one of the largest studies to date of HPV+ OPSCC and lends novel insight into the genetic landscape of this biologically distinct disease, including a high rate of mutations in histone- and chromatin-modifying genes, which may offer novel therapeutic targets.

Immune Modulation of Head and Neck Squamous Cell Carcinoma and the Tumor Microenvironment by Conventional Therapeutics

Head and neck squamous cell carcinoma (HNSCC) accounts for more than 600,000 cases and 380,000 deaths annually worldwide. Although human papillomavirus (HPV)-associated HNSCCs have better overall survival compared with HPV-negative HNSCC, loco-regional recurrence remains a significant cause of mortality and additional combinatorial strategies are needed to improve outcomes. The primary conventional therapies to treat HNSCC are surgery, radiation, and chemotherapies; however, multiple other targeted systemic options are used and being tested including cetuximab, bevacizumab, mTOR inhibitors, and metformin. In 2016, the first checkpoint blockade immunotherapy was approved for recurrent or metastatic HNSCC refractory to platinum-based chemotherapy. This immunotherapy approval confirmed the critical importance of the immune system and immunomodulation in HNSCC pathogenesis, response to treatment, and disease control. However, although immuno-oncology agents are rapidly expanding, the role that the immune system plays in the mechanism of action and clinical efficacy of standard conventional therapies is likely underappreciated. In this article, we focus on how conventional and targeted therapies may directly modulate the immune system and the tumor microenvironment to better understand the effects and combinatorial potential of these therapies in the context and era of immunotherapy.

Prognostic Role of p16 in Nonoropharyngeal Head and Neck Cancer

Background

Previous studies have reported conflicting information regarding the prognostic role of p16 in nonoropharyngeal head and neck squamous cell carcinoma (HNSCC).

Methods

Using the US Veterans Affairs database, we analyzed 1448 patients with locoregionally advanced HNSCC and known p16 status diagnosed between 2005 and 2015 and treated with surgery, radiotherapy, or chemoradiotherapy. Tumor p16 status was determined through manual review of pathology reports of primary tumor specimens. Oropharyngeal (n = 1061) or nonoropharyngeal (n = 387; hypopharyngeal, laryngeal, or oral cavity) tumor site was determined from tumor registry data and manually reviewed for accuracy. We used multivariable Cox regression to analyze the effect of p16 status on overall survival (OS), cancer-specific survival (CSS), and competing mortality (CM) for oropharyngeal or nonoropharyngeal tumor sites. All statistical tests were two-sided.

Results

In multivariable models adjusting for treatment, stage, age, comorbidity, and body mass index, patients with p16-positive tumors had improved OS, CSS, and CM compared with patients with p16-negative tumors in both oropharyngeal (OS: hazard ratio [HR] = 0.53, 95% confidence interval [CI] = 0.40 to 0.71, P < .001; CSS: HR = 0.50, 95% CI = 0.35 to 0.73, P < .001; CM: HR = 0.59, 95% CI = 0.38 to 0.93, P = .02) and nonoropharyngeal primary sites (OS: HR = 0.41, 95% CI = 0.25 to 0.69, P < .001; CSS: HR = 0.37, 95% CI = 0.18 to 0.77, P = .008; CM: HR = 0.46, 95% CI = 0.23 to 0.95, P = .04). The prognostic impact of p16 status did not statistically significantly differ by primary tumor site for OS, CSS, or CM (Pinteraction > .05).

Conclusions

Our findings support the hypothesis that p16 has a similar prognostic role in both nonoropharyngeal and oropharyngeal cancer. Consideration should be given to increased testing for p16 in laryngeal, hypopharyngeal, and oral cavity primaries.

Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma

We have recently performed the characterization of alternative splicing events (ASEs) in head and neck squamous cell carcinoma, which allows dysregulation of protein expression common for cancer cells. Such analysis demonstrated a high ASE prevalence among tumor samples, including tumor-specific alternative splicing in the GSN gene.In vitro studies confirmed that overall expression of either ASE-GSN or wild-type GSN (WT-GSN) isoform inversely correlated with cell proliferation, whereas the high ratio of ASE-GSN to WT-GSN correlated with increased cellular invasion. Additionally, a change in expression of either isoform caused compensatory changes in expression of the other isoform. Our results suggest that the overall expression and the balance between GSN isoforms are mediating factors in proliferation, while increased overall expression of ASE-GSN is specific to cancer tissues. As a result, we propose ASE-GSN can serve not only as a biomarker of disease and disease progression, but also as a neoantigen for head and neck squamous cell carcinoma treatment, for which only a limited number of disease-specific targeted therapies currently exist.

Testican 1 (SPOCK1) and protein tyrosine phosphatase, receptor type S (PTPRS) show significant increase in saliva of tobacco users with oral cancer

Objectives:

To identify potential candidate proteins which are secretory in nature and present at a higher abundance in oral cancer patients with tobacco habits.

Methods:

Conditioned media of tobacco-treated and -untreated non-neoplastic oral keratinocytes were analyzed using iTRAQ-based mass spectrometry. Hypersecreted proteins; SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 (SPOCK1); prosaposin (PSAP); and protein tyrosine phosphatase, receptor type S (PTPRS) were validated by enzyme-linked immunosorbent assay (ELISA) using saliva samples from oral cancer patients who are tobacco users.

Results:

Proteomic analysis of tobacco-treated and -untreated cells led to the identification of 2873 proteins. Among these, 378 proteins showed high abundance and 253 proteins showed low abundance (2-fold cutoff) in conditioned-media of tobacco-treated cells. ELISA-based validation showed significantly higher levels of SPOCK1, PSAP, and PTPRS in oral cancer patients with tobacco chewing habits compared to healthy controls. However, PSAP showed low specificity compared to SPOCK1 and PTPRS.

Conclusions:

This study indicates significantly increased levels of SPOCK1, PSAP, and PTPRS in saliva of oral cancer patients with tobacco habits. These protein biomarkers might be useful to identify tobacco users with high risk of developing oral cancers.