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Last Updated: 09/17/20

Yale Head and Neck Cancer SPORE: Overcoming Treatment Resistance in Head and Neck Cancer

Barbara Burtness, MD

Principal Investigator: Barbara Burtness, MD


Barbara Burtness, MD
Professor of Medicine
Head and Neck Cancer Disease Aligned Research Team Leader
Co-Leader, Developmental Therapeutics Program
Yale Cancer Center
Yale School of Medicine
333 Cedar Street
New Haven, CT, 06520-8028
Phone: 203-737-7636


Head and neck squamous cell carcinoma (HNSCC) is the seventh most common cancer globally. Current treatments are morbid, even for patients who are cured, and there are over 13,000 deaths in the US from HNSCC annually. HPV-negative HNSCC is commonly resistant to DNA damaging therapy, EGFR inhibition and immunotherapy. HPV-associated tumors are highly treatment-responsive, but 20-30 percent recur. Even with immune checkpoint inhibition, the majority of these patients succumb. The Yale Head and Neck SPORE (YHN-SPORE) represents highly translational researchers with deep disease-based expertise who leverage the extraordinary scientific strength at Yale Cancer Center, in collaboration with investigators at Fox Chase Cancer Center and the University of North Carolina Lineburger Cancer Center, to improve treatment for patients with this terrible malignancy. YHN-SPORE investigators have significantly impacted the field of HNSCC through training, and translational and clinical research. Basic scientists bring rigorous methodology to bear.

The YHN-SPORE seeks to address critical barriers to cure of HNSCC due to resistance to immune, DNA damaging and targeted therapy through these specific aims: Aim 1: To overcome resistance to EGFR inhibition in HNSCC by targeting active conformations of ErbB family members; Aim 2: To advance rational synthetic lethal combination therapy to the clinic in HPV-negative HNSCC; Aim 3: To advance combination demethylating therapy with immune checkpoint inhibition to the clinic for HPV-mediated HNSCC, with mechanistic studies and characterization of immune response; Aim 4: To bolster the foundation for HNSCC research through our Administrative, Biospecimen and Biostatistics/Bioinformatics cores, to engage institutional resources and the wider SPORE community; and Aim 5: To advance new research and to foster the next generation of HNSCC translational researchers through a Developmental Research Program, a Career Enhancement Program, and interaction and collaboration with the wider SPORE and HNSCC research communities. The overarching theme of the 3 coordinated projects is overcoming treatment resistance, spanning mechanistic insights into resistance to current treatment modalities and immunotherapy; translational validation; human endpoints to underpin future trials of novel strategies to circumvent resistance; mechanistic confirmation in correlative studies; and clinical trials in HPV-negative and HPV-driven HNSCC. Anticipated translational outcomes of the YHN-SPORE are: (1) conformationally sensitive inhibitors to overcome resistance to EGFR inhibition in HNSCC; (2) clinical safety and pharmacodynamic data combined aurora A kinase/WEE1 inhibition in HPV-negative HNSCC; (3) proof-of-concept and immuno-profiling data to support development of combined demethylation and immunotherapy in HPV-mediated HNSCC; (4) novel models and genomically-characterized tumors to enable HNSCC translational research; and (5) a diverse group of young investigators who will emerge as the generation who cure HNSCC.

PROJECT 1: Improved Targeting of EGFR Family Members in Squamous Cell Carcinomas of the Head and Neck

Mark Lemmon (Basic Co-leader)
Joseph Contessa (Clinical Co-leader)

The epidermal growth factor receptor (EGFR) remains the only validated molecular target in head and neck squamous cell carcinoma (HNSCC), mediating cell survival signaling and resistance to radiation therapy. despite the success of EGFR targeted therapies such as cetuximab, therapeutic resistance to EGFR targeting ultimately develops. A significant challenge for improving EGFR targeted therapies is to identify and clinically validate actionable mechanisms of therapeutic resistance. In this proposal, we have designed a strategy that iterates between basic science investigations, preclinical testing, and clinical specimen testing to elucidate the mechanism of cetuximab resistance in HNSCC. Using an in vitro approach for analyzing cetuximab resistance, we identified upregulation of a targetable autocrine ligand, NRG-1, as a target mechanism of resistance. We have modeled this resistance both in cell lines and in vivo, using mouse xenograft studies, and have shown that it can be reversed therapeutically by using an ErbB3-targeted antibody therapeutic (CDX-3379) – which can restore responses to cetuximab and radiation therapy. We have also observed NRG-1-induced resistance to small molecule EGFR kinase inhibitors in cancer cells, and have studied the mechanistic origin of this resistance at a structural level. We propose to exploit this new knowledge to advance small molecular approaches for targeting EGFR family members in HNSCC. In parallel with these studies, we will study clinical specimens from an ongoing phase II HNSCC trial of afatinib plus cetuximab, plus two ECOG trials of cetuximab, to investigate resistance mechanisms in the clinic. We will also develop patient-derived xenografts (PDX) models from the ongoing clinical trial to test hypotheses for resistance mechanisms and to assess effectiveness of new strategies devised to overcome it.

The key premise of the proposal is that understanding mechanisms of resistance to cetuximab will open up new therapeutic opportunities — allowing us to develop approaches that can still inhibit EGFR when cetuximab fails, and to develop approaches to target other molecules that activate EGFR in a cetuximab-insensitive way (such as ErbB3). Our three Specific Aims are:

  1. To elucidate and model mechanisms of cetuximab resistance in HNSCC, and to test CDX-3379 as a new ErbB3 targeted approach for enhancing systemic and/or radiation therapy in HNSCC.
  2. To develop new structure/mechanism-guided strategies for successful ErbB-receptor targeting with small molecule tyrosine kinase inhibitors (TKIs) in HNSCC.
  3. To identify biomarkers of therapeutic response to ErbB-targeted therapies using clinical trial samples, and to establish parallel patient-derived tumor models to evaluate mechanisms of resistance to ErbB-targeted therapies in HNSCC.

PROJECT 2:  Synthetic Lethal Therapy for HPV-Negative Head and Neck Cancer

Erica Golemis (Basic Co-leader)
Barbara Burtness (Clinical Co-leader)

HPV-negative head and neck squamous cell carcinomas (HNSCC) typically lose G1/S cell cycle checkpoints, with most tumors having mutations in TP53, and many also mutating other tumor suppressors such as CDKN2A. Such tumors become dependent on checkpoints associated with G2/M to repair DNA damage arising from replication stress and other genomic insults. This dependency suggests a tumor-selective vulnerability to synthetic lethal strategies controlling progress through G2/M. In extensive preliminary data, we show that AZD1775/adavosertib, an inhibitor of the G2/M checkpoint kinase WEE1, potently sensitizes TP53mut HNSCC cell lines to inhibition of Aurora A kinase (AURKA). WEE1 induces an inhibitory Y15-phosphorylation of CDK1, blocking M-phase entry and thus blunting the cytotoxic effects AURKA inhibition. WEE1 inhibition abrogates this arrest, accelerating mitotic entry for cells bearing highly disruptive spindle abnormalities and other defects arising from AURKA inhibition, resulting in mitotic catastrophe and apoptosis. We found combined AURKA/WEE1 inhibition is potent in HNSCC xenografts, while well-tolerated in normal tissue and cells. We have extended this concept, identifying additional promising drug combinations between WEE1 and other G2/M regulatory kinases (PLK1 and CHK1). Notably, the limited number of cells surviving synthetic lethal treatment are characterized by aneuploidy and other defects suggesting they may have increased tumor mutation burden (TMB), express neoantigens, and upregulated inflammatory signaling associated with sensitivity to immune checkpoint inhibition.

This project will take this observation directly to the clinic. We will conduct a pre-operative window phase I and expansion clinical trial of the late generation, high potency selective AURKA inhibitor VIC1911 with adavosertib combination, establishing pharmacodynamic proof of concept, identifying biomarkers for patient selection in future studies, and placing synergistic combinations in context of genomic alteration and treatment resistance. In Aim 1, we will evaluate mechanisms of combination lethality, and use single cell sequencing and Luminex profiling to query TMB, predict neoantigens, and measure inflammatory signaling. Aim 2 will query the effect of classes of common HNSCC TP53 and CDKN2A mutations, and cisplatin resistance, on response to a WEE1-AURKA inhibitor combination, using defined cell line models and patient derived xenografts (PDXs). In Aim 3, we will perform a pre-operative window trial to establish recommended phase 2 doses, determine activity and establish pharmacodynamic proof of concept, and to evaluate putative predictive biomarkers for response to combination WEE1/AURKA inhibition in HNSCC.

PROJECT 3: Demethylation of HPV-associated head and neck cancer to trigger APOBEC synthetic lethality and enhance immune response

Karen Anderson (Basic Co-leader)
Wendell Yarbrough (Clinical Co-leader)

Human papillomavirus (HPV)-associated neck squamous cell carcinoma (HNSCC) represents an increasing proportion of HNSCC. The incidence of HPV+ HNSCC has dramatically increased over the last 2 decades and in 2012 surpassed uterine cervical cancer as the most common HPV-related malignancy in the U.S. Despite the HPV vaccine, it is estimated that the “epidemic” of HNSCC caused by HPV will not diminish until 2060. HPV+ HNSCCs occur in younger individuals and prognosis for patients with these tumors is better compared to patients with classical HNSCC; however, ~25% of patients recur with few effective therapeutic options. Based on observed hypermethylation of HPV+ HNSCC from TCGA, and understanding that HPV uses hypermethylation to impede the innate immune response, effects of the demethylating agent, 5-azacytidine (5- azaC), were tested on HPV+ HNSCC. We found that HPV+ HNSCC cells in culture and xenografts are sensitive to 5-azaC, and that 5-azaC caused double strand breaks (DSB) that were not observed after 5-azaC therapy in HPV-negative HNSCC, even with much higher doses. We found that following 5-azaC therapy, APOlipoprotein B mRNA-Editing enzyme Catalytic polypeptide 3B (APOBEC3B) was associated with chromatin in HPV+ HNSCC, but not HPV-negative cells. CRISPR knockdown of A3B prevented DSB and protected cells from 5-azaC-induced death. Despite being required for DSBs and cellular toxicity caused by 5- azaC, A3B was also required for clonogenic survival of untreated HPV+ HNSCC. These data showing that A3B is required for survival of HPV+ HNSCC cells, but that following demethylation A3B mediates toxicity and DSB. In addition, 5-azaC therapy increased type I interferon signaling as measured by increased expression of interferon-stimulated genes. These exciting pre-clinical data led to a window trial of 5days of 5-azaC. Analysis of tumor specimens confirmed in vitro data showing that 5-azaC resulted in cellular toxicity. Immunofluorescent staining of an HPV+ patient tumors pre- and post-5-azaC showed a marked increase in tumor-associated lymphocytes, possibly driven through activation of type I interferon combined with increased expression of neoantigens. In this YHN-SPORE project, we hypothesize 5-azaC therapy will enhance response to nivolumab through its ability to cause cell death, increase neoantigen expression, increase A3B-driven mutational load, and enhance T cell infiltration through increased type I interferon signaling. These hypotheses will be tested using established and novel in vitro assays, as well as through examination of pre- and post-therapy tumor specimens from a 3-armed clinical trial. In Aim 1, tumor specimens from the SPORE window trial will be analyzed to determine effects of 5-azaC, nivolumab, or the combination on cell death, cell proliferation, immune infiltration and immune activation. Aim 2 will employ standard and novel assays to explore the role of A3B in cellular toxicity exposed by 5-azaC therapy. In Aim 3, we will determine effects of 5-azaC on activators of immune recognition and response in the presence or absence of nivolumab.

Administrative Core

Barbara Burtness (Director)
Ed Kaftan (Co-Director)

The Administrative Core (Core A) will be directed by Dr. Barbara Burtness, Principal Investigator of the Yale Head and Neck SPORE in Lung Cancer (YHN-SPORE), and co-directed by Dr. Edward Kaftan. Drs. Erica Golemis and Wendell Yarbrough will serve as Site Leaders for Fox Chase Cancer Center and University of North Carolina, respectively. Careful oversight by the Administrative Core will be critical to ensure the success of the YHN-SPORE. The Administrative Core will serve as the central coordination point for all YHN-SPORE investigators, with responsibility for strategic and scientific direction, and monitoring progress of all projects and cores towards the translational goals of the SPORE. The Core Director and Co-Directors will have responsibility for leading the SPORE, setting translational research priorities, identifying new translational research opportunities, monitoring the progress of all projects, cores and developmental projects and determining changes in direction of projects, cores and translational research as needed. Interactions among YHN-SPORE investigators will be facilitated by Core A to accelerate the translation of laboratory findings to the bedside through rational and rigorous translational and clinical studies. If required, the Core A Director will manage conflicts among SPORE investigators. As a team, the Core personnel will provide financial oversight, maintain communication among project and core leaders and coordinate bi-weekly meetings, quarterly meetings of the Executive Committee, annual meetings of the Internal/External Advisory boards and an annual YHN-SPORE retreat. In addition to these functions, the Core will be the primary interface with the NCI, Fox Chase Cancer Center, University of North Carolina, head and neck or other disease- or pathway-focused SPOREs, Yale Cancer Center and Yale School of Medicine, and will coordinate outreach efforts, including publications (internal and external), website development, seminars, and patient/research advocacy activities. Through these administrative activities, Core A will be essential to the organization of the YHN-SPORE program, to advancing science to overcome treatment resistance in head and neck cancer, developing models and approaches to advance the field, and mentoring a new generation of head and neck cancer translational researchers.

Biospecimen Core

David Rimm (Director)
Denise Connolly (Co-Director)

The Biospecimen Core B is designed to support all aspects of this SPORE grant that need to use or analyze biospecimens. We have 4 specific aims that are designed to span the needs of the projects and include potential future work, including the DRPs and CDPs. Our aims include: Aim 1: To collect, store and distribute human biospecimens with complete clinical, pathological, and demographic annotation. Aim 2: To conduct or assist in the collection, maintenance and distribution of HNSCC cell lines. Aim 3: To conduct or assist in preparation for genomic analyses of biospecimens. And, Aim 4: To conduct or assist in the in situ molecular pathology analyses of biospecimens. In the body of the proposal we expand on our capacities and preliminary data for each aim. We also illustrate how the core will meet the needs of the relevant specific aims of each project. Overall, we look forward to serving as a key tissue provider and analysis facility to allow the SPORE project to seamlessly generate data from the Yale and Fox Chase Cancer Center tissue resources.

Bioinformatics and Biostatistics Core

Jeffrey Townsend (Director)
Eric Ross (Co-Director)

The goal of the Biostatistics and Bioinformatics Core (Core C) is to address the statistical design and analysis needs of the Yale SPORE in Head and Neck Cancer (YHN-SPORE) Projects, the Cores, the Developmental Research Program (DRP), and the Career Development Program (CDP). To accomplish this goal we have assembled a highly interactive team of cancer biostatisticians and bioinformaticians who will work collaboratively with basic, clinical, translational, and population science researchers to advance the frontiers of cancer medicine. The specific aims of the Biostatistics and Bioinformatics Core are:

Aim 1: Provide collaboration and consulting in the design, execution, monitoring and analysis of basic, translational, population, and clinical studies for YHN-SPORE.

Aim 2: Oversee and coordinate the collection, management, and analysis of data. Ensure that data collected on all YHN-SPORE studies are of high quality, are evaluated with bioinformatic and statistical rigor, are accessible within SPORE-affiliated collaborative groups, ultimately enabling the widest accessibility that is appropriate given publication and privacy concerns.

For Aim 1, the Core will work closely with the investigators to analyze clinical trial and pre-clinical data, next generation sequencing data, and bioinformatics data mining. Services provided by the Core will range from planning and design activities to consulting on specific analytic questions. The Core will address the analytic and informatics questions arising from the YHN-SPORE projects. The Core will rigorously design and monitor clinical trials for safety, efficacy and futility. The Core will schedule regular meetings with the YHN-SPORE investigators, and maintain an open-door policy for any biostatistical and bioinformatics questions. The Core will conduct interim and final analyses, develop new statistical and bioinformatics methodology as needed, provide timely suggestions to YHN-SPORE investigators, and thus play an important role in the entire study. Biostatistics and Bioinformatics is also a key partner in the YHN-SPORE with representation on their Senior Leadership Team and participation in all core meetings. For Aim 2, The Core will work with the Yale Cancer Center (YCC), Yale Center for Analytical Sciences (YCAS), Fox Chase Cancer Center (FCCC) and its quantitative cores to facilitate communication among YHN-SPORE researchers, creating and implementing web-accessible databases for collecting, storing and accessing the various types of data (e.g. laboratory, clinical, population, and genomic data) that will be generated for the YHN-SPORE projects. The Core is highly integrated with the projects, and will have regular meetings with project investigators, as well as YCAS data managers, to evaluate the data generated from the studies and ensure accurate and up-to-date data management.