Head And Neck Squamous Cell Carcinoma Cohort Research Articles

Abstract B057: Base-error model (BEM) for improved detection of ctDNA in lymph samples of HPV-negative head and neck cancer patients

Abstract Introduction: Previously we demonstrated that ctDNA present in lymphatic exudate collected via surgical drains (“lymph”) outperformed plasma for detecting minimal residual disease (MRD) in head and neck squamous cell carcinoma (HNSCC) patients through a targeted sequencing (TS) approach. However, artifacts introduced during library preparation and sequencing remain challenges to sensitive low allelic fraction mutation detection. To enhance the performance of the TS approach, we characterized the background noise in lymph samples and developed a base-error model (BEM) that reduces sequencing artifacts and maximizes ctDNA signal. Methods: Lymph and blood were collected from 44 HPV-negative HNSCC patients postoperatively at 24 hours along with resected tumor. Cell-free DNA was extracted from lymph and sequenced using a custom TS panel with unique molecular identifiers (UMI). Somatic mutations were identified by tumor and blood exome sequencing (200x). Five patients had <2 mutations in tumor and were excluded. Two patients were censored due to lack of clinical data, yielding 17 patients with disease recurrence (REC) and 20 with no evidence of disease (NED) with >1 year of follow-up. Tumor-specific variants were force-called in lymph using a custom pipeline. A BEM of each tumor variant was built using a series of high-quality lymph reference samples to quantify the background noise. BEM was fit by Weibull distribution if more than 5 non-zero non-reference alleles were observed at a tumor variant position across the reference samples. Otherwise, Gaussian distribution was used to fit BEM. Force-called variants were considered artifacts if the variant allele fraction (VAF) was not greater than BEM cutoff controlled by false discovery rate. Patients were considered MRD positive if the mean VAF was greater than the estimated limit of detection. The Kaplan-Meier (KM) estimator with log-rank test and Cox proportional-hazards model were used for survival analyses. Results: Background noise was observed in reference lymph samples across all 12 nucleotide substitution classes. Out of 299 single nucleotide variants (SNVs), 94 were determined as artifacts by BEM. Among the artifacts, 77 were C/G to A/T mutations, indicating that the majority of recurrent background artifact in TS is likely the result of oxidative damage. The artifacts had VAFs ranging from 0.004% to 0.12% with median of 0.02%. Incorporation of BEM in lymph TS showed significantly improved specificity (sensitivity (SN) = 71%, specificity (SP) = 65%; p = 0.027, Hazard ratio (HR) = 3.07) compared to the same cohort without BEM (SN = 76%, SP = 30%, p = 0.60, HR = 1.34). Conclusions: BEM is a sensitive and robust method to improve ctDNA detection accuracy in TS. We demonstrated its utility in improving recurrence prediction in a HNSCC cohort. Given its advantages, we envision that BEM will prove useful as a general strategy for deep sequencing applications requiring precise digital quantification of low frequency alleles in TS. Citation Format: Zhuosheng Gu, Maciej Pacula, Seka Lazare, Noah Earland, Marra S. Francis, Adam Harmon, Megan Long, Aadel A. Chaudhuri, Jose P. Zevallos, Wendy Winckler. Base-error model (BEM) for improved detection of ctDNA in lymph samples of HPV-negative head and neck cancer patients [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B057.

Small Nucleolar RNAs in Head and Neck Squamous Cell Carcinomas.

Small nucleolar RNAs (snoRNAs), a distinct class of noncoding RNAs, encompass highly diverse structures and have a range of 60 to 300 nucleotides in length. About 90% of human snoRNAs are intronic and embedded within introns of their host gene transcripts. Most snoRNAs enriched in specific tissue correlate in abundance with their parental host genes. Advancements in high-throughput sequencing have facilitated the discovery of dysregulated snoRNA expression in numerous human malignancies including head and neck squamous cell carcinoma (HNSCC). Hundreds of differentially expressed snoRNAs have been identified in HNSCC tissues. Among 1,524 snoRNA genes in a 567 HNSCC cohort, 113 snoRNAs were found to be survival related. As for snoRNA's roles in HNSCC, based on the available evidence, dysregulated snoRNAs are closely associated with the carcinogenesis and development of HNSCC. Upregulated snoRNAs have been shown to augment the expression of other oncogenes or activate the Wnt/β-catenin signaling pathway, thereby promoting tumor cell viability, glycolysis, migration, and the epithelial-mesenchymal transition while inhibiting apoptosis in vitro. In vivo animal studies have further elucidated the functional roles of snoRNAs. Knockdown of host genes of these snoRNAs suppressed the Wnt/β-catenin signaling pathway and restrained tumor proliferation and aggressiveness in mice. The putative mechanisms underlying these observations are associated with the biological functions of snoRNAs, primarily involving microRNA-like functions through the generation of microRNA-like fragments and regulation of alternative splicing to yield diverse transcripts. While most of the snoRNAs are upregulated in HNSCC, 4 downregulated snoRNAs have been identified and annotated. SNORA36B (implicated in the regulation of DNA templates) and U3 (chr17, influencing cell proliferation) may serve as protective factors associated with prolonged overall survival. This review describes the viable structures of snoRNAs, endeavors to refine snoRNA sequencing technology, and summarizes snoRNAs' expression profile as well as their role in HNSCC progression for potential diagnostic and therapeutic strategies for HNSCC management.

Development and Validation of a Cholesterol-related Gene Signature for Prognostic Assessment in Head and Neck Squamous Cell Carcinoma.

This study seeks to develop a prognostic risk signature for head and neck squamous cell carcinoma (HNSCC) based on cholesterol-related genes (CholRG), aiming to enhance prognostic accuracy in clinical practice. HNSCC poses significant challenges due to its aggressive behavior and limited response to standard treatments, resulting in elevated morbidity and mortality rates.In order to improve prognostic prediction in HNSCC, our study is inspired by the realization that cholesterol metabolism plays a critical role in accelerating the progression of cancer. To this end, we are developing a unique risk signature using CholRG. The aim of this study was to create a CholRG-based risk signature to predict HNSCC prognosis, aiding in clinical decision-making accurately. The TCGA HNSCC dataset, along with GSE41613 and GSE65858, was obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases, respectively. A CholRG-based risk signature was then developed and validated across various independent HNSCC cohorts. Moreover, a nomogram model incorporating CholRG-based risk signature was established. Additionally, functional enrichment analysis was conducted, and the immune landscapes of the high- and low-risk groups were compared. Finally, in vitro experiments were performed using lipid-based transfection to deliver siRNAs targeting ACAT1 to SCC1 and SCC23 cell lines, further examining the effects of ACAT1 knockdown on these cells. Utilizing RNA-seq, microarray, and clinical data from public databases, we constructed and validated a CholRG-based risk signature that includes key genes such as ACAT1, CYP19A1, CYP27A1, FAXDC2, INSIG2, PRKAA2, and SEC14L2, which can effectively predict the clinical outcome of HNSCC. Additionally, our findings were reinforced by a nomogram model that integrates the risk score with clinical variables for more clinically practical prognostic assessment. In addition, patients at high risk show hypoxia and increased oncogenic pathways such as mTORC1 signaling, as well as a suppressed immune microenvironment marked by a reduction in the infiltration of important immune cells. Notably, in vitro experiments showed that ACAT1 depletion significantly suppressed the proliferation, colony formation, and invasion capabilities of HNSCC cells, confirming ACAT1's role in promoting malignancy. Collectively, our study not only underscores the importance of cholesterol metabolism in HNSCC pathogenesis but also highlights the CholRG-based risk signature as a promising tool for enhancing prognostic accuracy and personalizing therapeutic strategies.

Enfortumab vedotin and pembrolizumab as first-line treatment in recurrent or metastatic head and neck squamous cell carcinoma: A cohort of the EV-202 trial.

TPS148 Background: Novel treatment strategies are needed to treat recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) given the poor durability of response and prognosis with standard therapy. In KEYNOTE-048, among patients with R/M HNSCC and PD-L1 combined positive score (CPS) ≥1, first-line (1L) treatment with pembrolizumab demonstrated a median overall survival (OS) of 12.3 months. Nectin-4 is widely expressed in a variety of solid tumors, including bladder cancers and HNSCC. Enfortumab vedotin (EV) is a Nectin-4–directed antibody–drug conjugate approved for use in previously treated (EV monotherapy) or 1L (EV + pembrolizumab) locally advanced or metastatic urothelial carcinoma (la/mUC). EV + pembrolizumab showed superior OS and progression-free survival (PFS) vs chemotherapy in 1L la/mUC. EV-202 is a multicenter, open-label, phase 2 study (NCT04225117) evaluating the efficacy and safety of EV in multiple tumor-specific cohorts. In the previously treated R/M head and neck cancer cohort, 11 of 46 patients (23.9%) had a confirmed objective response with EV monotherapy; median PFS was 3.9 months (Swiecicki P, et al. ASCO 2023. Poster #6017). We hypothesize that EV + pembrolizumab may demonstrate benefit as a 1L therapy in patients with R/M HNSCC and CPS ≥1. Methods: Patients in the R/M HNSCC cohort of EV-202 have histologically or cytologically confirmed HNSCC, an ECOG performance status 0 or 1, no prior systemic therapy administered in the R/M setting (with the exception of systemic therapy completed >6 months prior if given as part of treatment for locally advanced disease), and CPS ≥1. A total of 40 patients are expected to be enrolled. An interim analysis will be conducted when 20 patients are evaluable for tumor response; 5 responders will be needed to proceed. Of 40 total patients, 14 must demonstrate response to claim promising antitumor activity. Patients will receive EV 1.25 mg/kg intravenously on days 1 and 8 and 200 mg of pembrolizumab intravenously on day 1 of each 21-day cycle until discontinuation, for reasons including disease progression or toxicity. Disease assessments will be performed 9 weeks from the first dose and every 6 weeks thereafter until disease progression, start of subsequent anticancer therapy, death, consent withdrawal, loss to follow-up, or study end, whichever occurs first. The primary endpoint is investigator-assessed, confirmed ORR per RECIST v1.1. Secondary endpoints include investigator-assessed duration of response, disease control rate, PFS, OS, and safety/tolerability. Analyses will also be evaluated per iRECIST. Exploratory analyses will include pharmacokinetics, immunogenicity, quality of life, and assessment of biomarkers that may correlate with treatment outcome, including Nectin-4 expression. Recruitment for this cohort began in November 2023 and is ongoing. Clinical trial information: NCT04225117 .

Therapeutic Targeting of the GLS1-c-Myc Positive Feedback Loop Suppresses Glutaminolysis and Inhibits Progression of Head and Neck Cancer.

Head and neck squamous cell carcinoma (HNSCC) is addicted to glutaminolysis. Targeting this metabolic dependency has emerged as a potential therapeutic approach for HNSCC. In this study, we conducted a bioinformatic analysis of The Cancer Genome Atlas HNSCC cohort that revealed a robust correlation between expression of MYC (encoding the protein c-Myc) and glutaminase 1 (GLS1), which catalyzes the first step in glutaminolysis. Intriguingly, disruption of GLS1 signaling in HNSCC cells by genetic depletion or CB-839 treatment resulted in a reduction in c-Myc protein stability via a ubiquitin-specific peptidase 1-dependent ubiquitin-proteasome pathway. On the other hand, c-Myc directly binds to the promoter region of GLS1 and upregulates its transcription. Notably, the GLS1-c-Myc pathway enhanced acetyl-coenzyme A carboxylase-dependent Slug acetylation, prompting cancer cell invasion and metastasis. Thus, the GLS1-c-Myc axis emerged as a positive feedback loop critical for driving the aggressiveness of HNSCC. Therapeutically, combining CB-839 with the c-Myc inhibitor MYCi975 strongly suppressed GLS1-c-Myc signaling, resulting in a superior antitumor effect compared with either single agent in an orthotopic mouse model of HNSCC. These findings hold promise for the development of effective therapies for patients with HNSCC, addressing an urgent need arising from the significant incidence and high metastatic rate of the disease. Significance: GLS1 and c-Myc form a positive feedback loop that promotes head and neck cancer metastasis and can be targeted as a promising therapeutic strategy for this disease.

Dendritic cell-related hub genes in head-and-neck squamous cell carcinoma: implications for prognosis and immunotherapy.

In the context of head-and-neck squamous cell carcinoma (HNSCC), dendritic cells (DCs) assume pivotal responsibilities, acting as architects of antigen presentation and conductors of immune checkpoint modulation. In this study, we aimed to identify hub genes associated with DCs in HNSCC and explore their prognostic significance and implications for immunotherapy. Integrated clinical datasets from The Cancer Genome Atlas (TCGA)-HNSCC and GSE65858 cohorts underwent meticulous analysis. Employing weighted gene co-expression network analysis (WGCNA), we delineated candidate genes pertinent to DCs. Through the application of random survival forest and least absolute shrinkage and selection operator (LASSO) Cox's regression, we derived key genes of significance. Lisa (epigenetic Landscape In Silico deletion Analysis and the second descendent of MARGE) highlighted transcription factors, with Dual-luciferase assays confirming their regulatory role. Furthermore, immunotherapeutic sensitivity was assessed utilizing the Tumor Immune Dysfunction and Exclusion online tool. This study illuminated the functional intricacies of HNSCC DC subsets to tailor innovative therapeutic strategies. We leveraged clinical data from the TCGA-HNSCC and GSE65858 cohorts. We subjected the data to advanced analysis, including WGCNA, which revealed 222 DC-related candidate genes. Following this, a discerning approach utilizing random survival forest analysis and LASSO Cox's regression unveiled seven genes associated with the prognostic impact of DCs, notably ACP2 and CPVL, associated with poor overall survival. Differential gene expression analysis between ACP2 + and ACP2 - DC cells revealed 208 differential expressed genes. Lisa analysis identified the top five significant transcription factors as STAT1, SPI1, SMAD1, CEBPB, and IRF1. The correlation between STAT1 and ACP2 was confirmed through quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Dual-luciferase assays in HEK293T cells. Additionally, TP53 and FAT1 mutations were more common in high-risk DC subgroups. Importantly, the sensitivity to immunotherapy differed among the risk clusters. The low-risk cohorts were anticipated to exhibit favorable responses to immunotherapy, marked by heightened expressions of immune system-related markers. In contrast, the high-risk group displayed augmented proportions of immunosuppressive cells, suggesting a less conducive environment for immunotherapeutic interventions. Our research may yield a robust DC-based prognostic system for HNSCC; this will aid personalized treatment and improve clinical outcomes as the battle against this challenging cancer continues.

Integrative machine learning and neural networks for identifying PANoptosis-related lncRNA molecular subtypes and constructing a predictive model for head and neck squamous cell carcinoma.

PANoptosis is considered a novel type of cell death that plays important roles in tumor progression. In this study, we applied machine learning algorithms to explore the relationships between PANoptosis-related lncRNAs (PRLs) and head and neck squamous cell carcinoma (HNSCC) and established a neural network model for prognostic prediction. Information about the HNSCC cohort was downloaded from the TCGA database, and the differentially expressed prognostic PRLs between tumor and normal samples were assessed in patients with different tumor subtypes via nonnegative matrix factorization (NMF) analysis. Subsequently, five kinds of machine-learning algorithms were used to select the core PRLs across the subtypes, and the interactive features were pooled into a neural network model to establish a PRL-related risk score (PLRS) system. Survival differences were compared via Kaplan‒Meier analysis, and the predictive effects were assessed with the areas under the ROCs. Moreover, functional enrichment analysis, immune infiltration, tumor mutation burden (TMB) and clinical therapeutic response were also conducted to further evaluate the novel predictive model. A total of 347 PRLs were identified, 225 of which were differentially expressed between tumor and normal samples. Patients were divided into two clusters via NMF analysis, in which cluster 1 had a better prognosis and more immune cells and functional infiltrates. With the application of five machine learning algorithms, we selected 13 interactive PRLs to construct the predictive model. The AUCs for the ROCs in the entire set were 0.735, 0.740 and 0.723, respectively. Patients in the low-PLRS group exhibited a better prognosis, greater immune cell enrichment, greater immune function activation, lower TMB and greater sensitivity to immunotherapy. In this study, we established a novel neural network prognostic model to predict survival and identify tumor subtypes in HNSCC patients. This novel assessment system is useful for prediction, providing ideas for clinical treatment.

Enfortumab vedotin and pembrolizumab as first-line treatment in recurrent or metastatic head and neck squamous cell carcinoma: A cohort of the EV-202 trial.

TPS6116 Background: Novel treatment strategies are needed to treat recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) given the poor durability of response and prognosis with standard therapy. In KEYNOTE-048, among patients with R/M HNSCC and PD-L1 combined positive score (CPS) ≥1, first-line (1L) treatment with pembrolizumab demonstrated a median overall survival (OS) of 12.3 months. Nectin-4 is widely expressed in a variety of solid tumors, including bladder cancers and HNSCC. Enfortumab vedotin (EV) is a Nectin-4–directed antibody–drug conjugate approved for use in previously treated (EV monotherapy) or 1L (EV + pembrolizumab) locally advanced or metastatic urothelial carcinoma (la/mUC). EV + pembrolizumab showed superior OS and progression-free survival (PFS) vs chemotherapy in 1L la/mUC. EV-202 is a multicenter, open-label, phase 2 study (NCT04225117) evaluating the efficacy and safety of EV in multiple tumor-specific cohorts. In the previously treated R/M head and neck cancer cohort, 11 of 46 patients (23.9%) had a confirmed objective response with EV monotherapy; median PFS was 3.9 months (Swiecicki P, et al. ASCO 2023. Poster #6017). We hypothesize that EV + pembrolizumab may demonstrate benefit as a 1L therapy in patients with R/M HNSCC and CPS ≥1. Methods: Patients in the R/M HNSCC cohort of EV-202 have histologically or cytologically confirmed HNSCC, an ECOG performance status 0 or 1, no prior systemic therapy administered in the R/M setting (with the exception of systemic therapy completed >6 months prior if given as part of treatment for locally advanced disease), and CPS ≥1. A total of 40 patients are expected to be enrolled. An interim analysis will be conducted when 20 patients are evaluable for tumor response; 5 responders will be needed to proceed. Of 40 total patients, 14 must demonstrate response to claim promising antitumor activity. Patients will receive EV 1.25 mg/kg intravenously on days 1 and 8 and 200 mg of pembrolizumab intravenously on day 1 of each 21-day cycle until discontinuation, for reasons including disease progression or toxicity. Disease assessments will be performed 9 weeks from the first dose and every 6 weeks thereafter until disease progression, start of subsequent anticancer therapy, death, consent withdrawal, loss to follow-up, or study end, whichever occurs first. The primary endpoint is investigator-assessed, confirmed ORR per RECIST v1.1. Secondary endpoints include investigator-assessed duration of response, disease control rate, PFS, OS, and safety/tolerability. Analyses will also be evaluated per iRECIST. Exploratory analyses will include pharmacokinetics, immunogenicity, quality of life, and assessment of biomarkers that may correlate with treatment outcome, including Nectin-4 expression. Recruitment for this cohort began in November 2023 and is ongoing. Clinical trial information: NCT04225117 .

The expression of immune co-stimulators as a prognostic predictor of head and neck squamous cell carcinomas and oral squamous cell carcinomas

Background/purposeT cells require second immune checkpoint molecules for activation and immune memory after antigen presentation. We found that inducible co-stimulator (ICOS) has been a favorable prognostic factor amongst B7 immune checkpoint co-stimulators (ICSs) families in head and neck squamous cell carcinoma (HNSCC) and oral SCC (OSCC). Materials and methodsThis study analyzed the expression of non-B7 tumor necrosis factor (TNF) superfamily ICSs in the Cancer Genome Atlas (TCGA) HNSCC cohort, our OSCC cohort, and TCGA pan-cancer datasets. The correlation in expression, prognosis, and immune status was assessed. ResultsThe higher expression of CD27, CD30, CD40L, death domain 3 (DR3), and OX40, presumably on the T cell surface, defined better overall survival of HNSCC patients. Besides, CD27, CD30, CD40L, and OX40 were highly correlated with ICOS expression in tumors. CD27, CD40L, and DR3 expression are higher in HPV+ HNSCC tumors than in HPV- tumors. The combined expression level of CD27/OX40 or CD27/CD40L/OX40 enables the potent survival prediction of small, less nodal involvement, early stage, and HPV + tumor subsets. Tumors expressing high CD27, CD30, CD40L, ICOS, and OX40 exhibited enhanced immune cell infiltration. The high correlation in the expression of these ICSs was also noted in the vast majority of tumor types in TCGA datasets. ConclusionThe findings of this study not only confirm the potential of the concordant stimulation of CD27, CD30, CD40L, ICOS, and OX40 as a crucial strategy in cancer immunotherapy but also inspire further exploration into the field, highlighting the promising future of cancer treatment.

Abstract LB414: Novel ALK/PIK3CA cooperativity in head and neck squamous cell carcinoma (HNSCC) progression

Abstract Recent genomic characterization studies have demonstrated the genetic heterogeneity of head and neck squamous cell carcinoma (HNSCC). Yet, most of these genetic aberrations remain undruggable. Anaplastic Lymphoma Kinase (ALK) is somatically mutated in ~3.6% of HNSCC (18/504 cases, TCGA-HNSCC Firehose cohort, USA), and the majority of these ALK-mutated HNSCC cases are of advanced stage diseases. Here, we hypothesized that ALK mutations might plausibly contribute to HNSCC progression and could be potentially druggable. Unexpectedly, analysis of HNSCC genomic events revealed a novel co-occurrence relationship between ALK and PIK3CA genomic aberrations in TCGA-HNSCC Firehose cohort (Odds Ratio=2.41; N=522 samples with CNV data), with subsequent validation in an independent metastatic MSK-MetTropism HNSCC cohort (Odds Ratio=5.12; N=412). Consistent with this newly identified co-occurrence relationship, we showed that all 7 HNSCC-relevant ALK point mutations were potent drivers for HNSCC invasiveness and clonogenic growth only in corroboration with PIK3CA aberrations in HNSCC cell models, highlighting the functional importance of this novel ALK/PIK3CA cooperativity in HNSCC, likely reminiscent of ALK/MYCN cooperativity in neuroblastoma. Further, by clonogenic assay, we demonstrated pharmacologic vulnerabilities of all 7 ALK point mutations (including extracellular domain mutations) to ALK targeting by ceritinib in FaDu cell background with endogenous PIK3CA amplification. Strikingly, we were able to capture, for the first time, spontaneous emergence of a druggable ALK somatic mutation directly from a PIK3CA-altered HNSCC patient-derived culture (PDC) upon forced acquisition of anoikis-resistance ex vivo (PDC-25-AR), demonstrating co-evolution of ALK/PIK3CA aberrations in HNSCC likely associated with cancer progression. Patient-derived culture-xenograft (PDCx) of PDC-25-AR displayed remarkable sensitivity to ALK targeting, PI3K targeting, as well as their combination, with induction of apoptosis in these tumors compared to vehicle control. In conclusion, ALK aberrations corroborate with PIK3CA aberrations to promote HNSCC progression, yet, these events are potentially druggable in advanced HNSCC. Citation Format: Lan Wang, Helen Hoi-Yin Chan, Angel Yee Lok Fung, Yuen-Keng Ng, Patrick Kwok-Shing Ng, Yuxiong Su, Jason Ying Kuen Chan, Peony Hiu Yan Poon, Thomas Chun Kit Yeung, Chi Man Tsang, Hoi-Lam Ngan, Wenying Piao, Yuchen Liu, Jack Nimitz Smith, Tin Yu Samuel Law, Ee Ling Kong, Melissa Sue Ann Chan, Chun Ho Law, Sze-Man Chan, Zoey Wing Yee Liu, Joshua Chung-Hymn Ng, Gordon B. Mills, Vivian W.Y. Lui. Novel ALK/PIK3CA cooperativity in head and neck squamous cell carcinoma (HNSCC) progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB414.

Abstract 6110: Computational exploration of genomic differences in Black patients treated with chemoradiation for head and neck squamous cell carcinoma (HNSCC)

Abstract Background: Black patients treated with chemoradiation for head and neck squamous cell carcinoma (HNSCC) experience significantly worse survival outcomes than White patients treated with the same modality. Our group aims to explore potential sociodemographic and biological factors undermining this differing response to therapy. Here, we present our computational findings of genomic differences in Black compared with White HNSCC patients receiving chemoradiation. Methods: We obtained gene expression, phenotype, and clinical datasets for the Cancer Genome Atlas (TCGA) HNSCC cohort from the UCSC Xena web browser. Of the 528 HNSCC patients, 131 (Black=13, White=118) of those receiving chemoradiation had gene expression, phenotype, and clinical data available. Our analysis included anatomic sites involving the oral cavity, hypopharynx, and larynx, and excluded the oropharynx. We performed differential gene expression analysis in Black compared with White (reference population) patients via edgeR in R studio (-log2FC < -1 or log2FC >1; p value < 0.05; FDR < 0.05). The Database for Annotation, Visualization, and Integrated Discovery (DAVID) webtool was used to identify significantly enriched molecular processes and pathways. Results: 462 genes were found to be significantly differentially expressed between Black and White HNSCC patients receiving chemoradiation. Of these genes, 198 were found to be higher in Black patients, and the most significant included JPH3, PCSK1N, DCUN1D5, CRYGS, and CCL7 (p < 0.005, FDR < 0.005). 264 were found to be lower in Black patients, with the most significant being KBTBD12, CMYA5, NEFH, LDB3, PYGM (p < 0.005, FDR < 0.005). Genes found to be higher in Black patients showed enrichment for processes such as EGFR tyrosine kinase inhibitor resistance (p < 0.005), drug metabolism (p < 0.005), and chemical carcinogenesis (p < 0.005). Genes found to be lower in Black patients showed enrichment for muscle-related processes such as myogenesis (p < 0.005), actin-binding (p < 0.005), muscle protein (p < 0.005), and hypertrophic cardiomyopathy (p < 0.005). Conclusion: In conclusion, using TCGA, we identified differentially expressed genes between Black and White HNSCC patients receiving chemoradiation. Moreover, these findings suggest that biological processes may differ in Black compared with White patients receiving chemoradiation, and this may dictate differing response to therapy. Additional studies will involve further computational analysis using other datasets for validation. Citation Format: Chayil C. Lattimore, Caretia J. Washington, Dejana Braithwaite, Shama D. Karanth, Kristianna M. Fredenburg. Computational exploration of genomic differences in Black patients treated with chemoradiation for head and neck squamous cell carcinoma (HNSCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6110.

Abstract 3061: A positive feedback loop between GLS1 and c-Myc drives tumor aggressiveness

Abstract Both GLS1 and c-Myc are upregulated in head and neck squamous cell carcinoma (HNSCC) primary tumors and further increased in metastatic tumors. However, the regulation between these two molecules remains largely unknown. GLS1 is a critical enzyme that regulates glutamate, which plays an important role in cancer metabolism that supports cancer growth and survival. Our bioinformatic analysis of the TCGA HNSCC cohort revealed a strong correlation between c-Myc and GLS1 expression. We describe the importance of c-Myc in regulating GLS1 and vice versa. c-Myc protein directly binds to the promoter of the GLS1 gene and upregulates its expression at the transcriptional level. Interestingly, blocking GLS1 signaling in HNSCC cells by lentiviral shRNA knockdown or CB-839 treatment downregulates USP1, one of the best characterized human DUBs, which in turn reduces c-Myc protein stability via the ubiquitin-proteasome pathway. The GLS1-c-Myc axis thus represents a novel positive feedback loop that is critical for driving the aggressiveness of HNSCC. As the treatment of HNSCC remains a major challenge, these novel findings provide the molecular basis for combining GLS1-specific inhibitors with c-Myc-targeted therapy for the treatment of HNSCC patients. Citation Format: Jianqiang Yang, Fanghui Chen, Fan Yang, Yong Teng. A positive feedback loop between GLS1 and c-Myc drives tumor aggressiveness [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3061.

Combined IL6 and CCR2 blockade potentiates antitumor activity of NK cells in HPV-negative head and neck cancer

BackgroundWhile T cell-activating immunotherapies against recurrent head and neck squamous cell carcinoma (HNSCC) have shown impressive results in clinical trials, they are often ineffective in the majority of patients. NK cells are potential targets for immunotherapeutic intervention; however, the setback in monalizumab-based therapy in HNSCC highlights the need for an alternative treatment to enhance their antitumor activity.MethodsSingle-cell RNA sequencing (scRNA-seq) and TCGA HNSCC datasets were used to identify key molecular alterations in NK cells. Representative HPV-positive ( +) and HPV-negative ( −) HNSCC cell lines and orthotopic mouse models were used to validate the bioinformatic findings. Changes in immune cells were examined by flow cytometry and immunofluorescence.ResultsThrough integration of scRNA-seq data with TCGA data, we found that the impact of IL6/IL6R and CCL2/CCR2 signaling pathways on evasion of immune attack by NK cells is more pronounced in the HPV − HNSCC cohort compared to the HPV + HNSCC cohort. In orthotopic mouse models, blocking IL6 with a neutralizing antibody suppressed HPV − but not HPV + tumors, which was accompanied by increased tumor infiltration and proliferation of CD161+ NK cells. Notably, combining the CCR2 chemokine receptor antagonist RS504393 with IL6 blockade resulted in a more pronounced antitumor effect that was associated with more activated intratumoral NK cells in HPV − HNSCC compared to either agent alone.ConclusionsThese findings demonstrate that dual blockade of IL6 and CCR2 pathways effectively enhances the antitumor activity of NK cells in HPV-negative HNSCC, providing a novel strategy for treating this type of cancer.

LINC02454-CCT complex interaction is essential for telomerase activity and cell proliferation in head and neck squamous cell carcinoma

Telomerase activity is upregulated in head and neck squamous cell carcinoma (HNSCC), yet its regulatory mechanisms remain unclear. Here, we identified a cancer-specific lncRNA (LINC02454) associated with poor prognosis by using LncRNA chip of our HNSCC cohorts and external datasets. Through employing negative-stain transmission electron microscopy (NS-TEM), we discovered an interaction between LINC02454 and CCT complex which would augment telomerase activity for maintaining telomere homeostasis. Supporting this, in the telomerase repeat amplification protocol (TRAP) assay and quantitative fluorescence in situ hybridization (Q-FISH) analysis, LINC02454 depletion significantly reduced telomerase activity and shortened telomere length. Consistently, pathways related to telomerase, mitosis, and apoptosis were significantly impacted upon LINC02454 knockdown in RNAseq analysis. Functionally, LINC02454-deficient cells exhibited a more significant senescence phenotype in β-galactosidase staining, cell cycle, and apoptosis assays. We further confirmed the role of LINC02454 in HNSCC proliferation through a combination of in vitro and in vivo experiments. The therapeutic potential of targeting LINC02454 was verified by adenovirus-shRNA approach in HNSCC patient-derived xenograft (PDX) models. In summary, our findings provided valuable insights into the molecular mechanisms of HNSCC tumorigenesis and potential targets for future treatment modalities.

DNA-methylome-derived epigenetic fingerprint as an immunophenotype indicator of durable clinical immunotherapeutic benefits in head and neck squamous cell carcinoma.

Cancer immunotherapy provides durable response and improves survival in a subset of head and neck squamous cell carcinoma (HNSC) patients, which may due to discriminative tumor microenvironment (TME). Epigenetic regulations play critical roles in HNSC tumorigenesis, progression, and activation of functional immune cells. This study aims to identify an epigenetic signature as an immunophenotype indicator of durable clinical immunotherapeutic benefits in HNSC patients. Unsupervised consensus clustering approach was applied to distinguish immunophenotypes based on five immune signatures in The Cancer Genome Atlas (TCGA) HNSC cohort. Two immunophenotypes (immune 'Hot' and immune 'Cold') that had different TME features, diverse prognosis, and distinct DNA methylation patterns were recognized. Immunophenotype-related methylated signatures (IPMS) were identified by the least absolute shrinkage and selector operation algorithm. Additionally, the IPMS score by deconvolution algorithm was constructed as an immunophenotype classifier to predict clinical outcomes and immunotherapeutic response. The 'Hot' HNSC immunophenotype had higher immunoactivity and better overall survival (p = 0.00055) compared to the 'Cold' tumors. The immunophenotypes had distinct DNA methylation patterns, which was closely associated with HNSC tumorigenesis and functional immune cell infiltration. 311 immunophenotype-related methylated CpG sites (IRMCs) was identified from TCGA-HNSC dataset. IPMS score model achieved a strong clinical predictive performance for classifying immunophenotypes. The area under the curve value (AUC) of the IPMS score model reached 85.9% and 89.8% in TCGA train and test datasets, respectively, and robustness was verified in five HNSC validation datasets. It was also validated as an immunophenotype classifier for predicting durable clinical benefits (DCB) in lung cancer patients who received anti-PD-1/PD-L1 immunotherapy (p = 0.017) and TCGA-SKCM patients who received distinct immunotherapy (p = 0.033). This study systematically analyzed DNA methylation patterns in distinct immunophenotypes to identify IPMS with clinical prognostic potential for personalized epigenetic anticancer approaches in HNSC patients. The IPMS score model may serve as a reliable epigenome prognostic tool for clinical immunophenotyping to guide immunotherapeutic strategies in HNSC.

Association of cuproptosis-related signature with the prognosis of patients with head and neck squamous cell carcinoma

Patients with head and neck squamous cell carcinoma (HNSCC) have a poor prognosis because of their high recurrence and metastasis rates. Cuproptosis is a novel type of copper-dependent cell death that differs from apoptosis, necroptosis, and cytosolic scorch death. We designed and validated an individualized cuproptosis-related gene (CRG) signature for risk evaluation and prognostic prediction in HNSCC patients. Ninety differentially expressed CRGs were found in HNSCC. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses were performed to investigate the functional involvement of CRGs in the Cancer Genome Atlas (TCGA) HNSCC cohort. A CRG signature was created using 10 genes after univariate and multivariate analysis. Kaplan Meier (KM) analysis showed that the survival rate of the high-risk group was significantly lower than that of the low-risk group. Multivariate regression analysis identified risk scores based on prognostic characteristics as independent prognostic indicators of HNSCC. Moreover, risk models are related to tumor mutational burden (TMB), tumor-infiltrating immune cells (TICs), immune checkpoints, clinical characteristics, and antitumor drug susceptibility. Furthermore, we found that CuCl2 treatment promoted cuproptosis in HNSCC cells, and that the expression levels of cuproptosis-related genes were altered by different doses of CuCl2. In summary, understanding the detailed molecular mechanisms of cuproptosis and its impact on overall survival (OS), and identifying potential therapeutic targets for HNSCC will provide potential insights for treatment. Communicated by Ramaswamy H. Sarma

TSPO is a potential independent prognostic factor associated with cellular respiration and p16 in head and neck squamous cell carcinoma.

Treatment resistance and relapse are common problems in head and neck squamous cell carcinoma (HNSCC). Except for p16, no clinically accepted prognostic biomarkers are available for HNSCC. New biomarkers predictive of recurrence and survival are crucial for optimal treatment planning and patient outcome. High translocator protein (TSPO) levels have been associated with poor survival in cancer, but the role of TSPO has not been extensively evaluated in HNSCC. TSPO expression was determined in a large population-based tissue microarray cohort including 611 patients with HNSCC and evaluated for survival in several clinicopathological subgroups. A TCGA HNSCC cohort was used to further analyze the role of TSPO in HNSCC. TSPO expression was downregulated in more aggressive tumors. Low TSPO expression associated with worse 5-year survival and was an independent prognostic factor for disease-specific survival. Subgroup analyses showed that low TSPO expression associated with worse survival particularly in p16-positive oropharyngeal cancer. In silico analyses supported the prognostic role of TSPO. Cellular respiration had the highest significance in pathway analyses for genes expressed positively with TSPO. Decreased TSPO expression associates with poor prognosis in HNSCC. TSPO is a prognostic biomarker in HNSCC to potentially guide treatment stratification especially in p16-positive oropharyngeal cancer.

HPV-negative head and neck cancers with adverse pathological features carry specific molecular changes that are associated with survival.

Adverse pathological features following surgery in head and neck squamous cell carcinoma (HNSCC) are strongly associated with survival and guide adjuvant therapy. We investigated molecular changes associated with these features. We downloaded data from the Cancer Genome Atlas and Cancer Proteome Atlas HNSCC cohorts. We compared tumors positive versus negative for perineural invasion (PNI), lymphovascular invasion (LVI), extracapsular spread (ECS), and positive margins (PSM), with multivariable analysis. All pathological features were associated with poor survival, as were the following molecular changes: low cyclin E1 (HR = 1.7) and high PKC-alpha (HR = 1.8) in tumors with PNI; six of 13 protein abundance changes with LVI; greater tumor hypoxia and high Raptor (HR = 2.0) and Rictor (HR = 1.6) with ECS; and low p38 (HR = 2.3), high fibronectin (HR = 1.6), low annexin A1 (HR = 3.1), and high caspase-9 (HR = 1.6) abundances with PSM. Pathological features in HNSCC carry specific molecular changes that may explain their poor prognostic associations.

Abstract PR013: Association of a polymorphic variant in JMJD1C with response to chemoradiotherapy in rectal cancer and head and neck cancer: Implications for a diverse population

Abstract Neoadjuvant chemoradiotherapy (nCRT) is the standard treatment for locally advanced rectal cancer (LARC). Although nCRT has improved outcomes for many patients, ~70-80% of patients show poor or no response, and CRT is toxic. No biomarker exists that can predict which patients may benefit from nCRT. CRT efficacy arises from unrepaired double-strand breaks (DSBs). Recent work has suggested that dynamic changes in lysine modification of chromatin regulate DSB repair. This study investigated the association of germline single nucleotide polymorphisms (SNPs) in lysine-modifying genes with DSB repair and CRT outcomes in LARC. The LARC patients (n=84) were segregated into poor (PoR) and complete (CR) responders using the Neoadjuvant Rectal score. Blood DNA was sequenced to identified SNPs, matched LARC patient-derived cells were tested for sensitivity to DNA damage, and results correlated. Significant SNP-response correlations were confirmed in an independent cohort of CRT-treated head and neck squamous cell carcinoma (HNSCC) patients who had received chemoradiation (n=90). The HNSCC patients were segregated into 3 groups based on response: disease-free (n=30), recurrent disease (n=28), and never-disease free (n=32). Isogenic HNSCC lines with either the wildtype (WT) or SNP were generated using CRISPR/Cas9 technology, and bulk RNA sequencing and immunofluorescence-based studies were performed to assess pathways affected. LARC CRs were significantly enriched versus PoRs for a germline SNP in the lysine H3K9 demethylase, JMJD1C, resulting in a missense variant (discovery (n=30, p<0.00001), validation (n=54, p=0.001); Fisher’s Exact). In the HNSCC cohort, the JMJD1C SNP was significantly associated with no recurrence (p=0.0003, Fisher’s Exact). LARC patient-derived cell lines carrying the SNP were significantly more sensitive to DSB damage versus those carrying the WT (n=12, p<0.001, Mann-Whitney). Cells bearing the SNP were significantly enriched for altered mRNA levels of genes associated with DNA repair compared with WT cells (q-value<0.05). On irradiation, the SNP cells showed robust activation of DSB repair (γH2AX, BRCA1 foci, JMJD1C nuclear localization) versus the WT cells. Finally, analysis of the JMJD1C SNP frequency in large population datasets found that while it was abundant in European Americans (EAs), it is relatively rare in African Americans (AAs) (EA= 0.3139 vs. AA=0.072; gnomAD population). This study provides novel insight into a SNP in a lysine-modifying gene affecting DSB repair that may serve as a predictive biomarker for CRT response in 2 different cancer types. Our data suggest that host genetics impact DSB repair and warrant further investigation to better understand disparities in response to CRT. Future research will further explore the racial/ethnic disparities in tumor recurrence and confirm results in in vitro and in vivo models of cancer, and in large patient datasets. Citation Format: Adria Hasan, Elena Demidova, Philip Czyzewicz, Shreya Shah, Karthik Devarajan, Thomas J. Galloway, Margret B. Einarson, Barbara Burtness, Erica A. Golemis, Joshua E. Meyer, Sanjeevani Arora. Association of a polymorphic variant in JMJD1C with response to chemoradiotherapy in rectal cancer and head and neck cancer: Implications for a diverse population [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr PR013.

Constructing a T-Cell Receptor-Related Gene Signature for Prognostic Stratification and Therapeutic Guidance in Head and Neck Squamous Cell Carcinoma

Backgroud: The stratification of head and neck squamous cell carcinoma (HNSCC) patients based on prognostic differences is critical for therapeutic guidance. This study was designed to construct a predictive signature derived from T-cell receptor-related genes (TCRRGs) to forecast the clinical outcomes in HNSCC. Methods: We sourced gene expression profiles from The Cancer Genome Atlas (TCGA) HNSCC dataset, GSE41613, and GSE65858 datasets. Utilizing consensus clustering analysis, we identified two distinct HNSCC clusters according to TCRRG expression. A TCRRG-based signature was subsequently developed and validated across diverse independent HNSCC cohorts. Moreover, we established a nomogram model based on TCRRGs. We further explored differences in immune landscapes between high- and low-risk groups. Results: The TCGA HNSCC dataset was stratified into two clusters, displaying marked variations in both overall survival (OS) and immune cell infiltration. Furthermore, we developed a robust prognostic signature based on TCRRG utilizing the TCGA HNSCC train cohort, and its prognostic efficacy was validated in the TCGA HNSCC test cohort, GSE41613, and GSE65858. Importantly, the high-risk group was characterized by a suppressive immune microenvironment, in contrast to the low-risk group. Our study successfully developed a robust TCRRG-based signature that accurately predicts clinical outcomes in HNSCC, offering valuable strategies for improved treatments.