Mutational profiles of persistent/recurrent laryngeal squamous cell carcinoma

Multi-kinase compensation rescues EGFR knockout in a cell line model of head and neck squamous cell carcinoma

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) is a debilitating disease with poor survival rates. While the epidermal growth factor receptor (EGFR)-targeting antibody Cetuximab is approved for treatment, responses are limited and the molecular mechanisms driving resistance remain incompletely understood.

METHODS

To better understand how cells survive without EGFR activity, we developed an EGFR knockout derivative of the UM-SCC-92 cell line using CRISPR/Cas9 technology. We then characterized changes to the transcriptome with RNAseq and changes in response to kinase inhibitors with resazurin cell viability assays. Finally, we tested if inhibitors with activity in the EGFR knockout model also had synergistic activity in combination with EGFR inhibitors in either wild type UM-SCC-92 cells or a known Cetuximab-resistant model.

RESULTS

Functional and molecular analysis showed that knockout cells had decreased cell proliferation, upregulation of FGFR1 expression, and an enhanced mesenchymal phenotype. In fact, expression of common EMT genes including VIM, SNAIL1, ZEB1 and TWIST1 were all upregulated in the EGFR knockout. Surprisingly, EGFR knockout cells were resistant to FGFR inhibitor monotherapies, but sensitive to combinations of FGFR and either XIAP or IGF-1R inhibitors. Accordingly, both wild type UM-SCC-92 and Cetuximab-resistant UM-SCC-104 cells with were sensitive to combined inhibition of EGFR, FGFR and either XIAP or IGF-1R.

CONCLUSIONS

These data offer insights into EGFR inhibitor resistance and show that resistance to EGFR knockout likely occurs through a complex network of kinases. Future studies of cetuximab-resistant HNSCC tumors are warranted to determine if this EMT phenotype and/or multi-kinase resistance is observed in patients.

NOTCH1 mutation associates with impaired immune response and decreased relapse-free survival in patients with resected T1-2N0 laryngeal cancer

Background

Patients with early-stage laryngeal cancer, even stage T1-2N0, are at considerable risk of recurrence and death. The genetic and immunologic characteristics of recurrent laryngeal cancer remain unclear.

Methods

A total of 52 T1-2N0 laryngeal cancer patients were enrolled. Of these, 42 tissue samples were performed by targeted DNA sequencing, and 21 cases were performed by NanoString immuno-oncology targeted RNA sequencing to identify the distinct molecular bases and immunologic features associated with relapse in patients with early laryngeal cancer, respectively.

Results

To the best to our knowledge, we present for the first time an overview of the genomic mutation spectrum of early-stage laryngeal cancers. A total of 469 genomic alterations were detected in 211 distinct cancer-relevant genes, and the genes found to be mutated in more than five patients (>10%) included tumor protein p53 (TP53, 78.5%), FAT atypical cadherin 1 (FAT1, 26%), LDL receptor related protein 1B (LRP1B, 19%), cyclin dependent kinase inhibitor 2A (CDKN2A, 17%), tet methylcytosine dioxygenase 2 (TET2, 17%), notch receptor 1 (NOTCH1, 12%) and neuregulin 1 (NRG1, 12%). Recurrent laryngeal cancer demonstrated a higher tumor mutation burden (TMB), as well as higher LRP1B mutation and NOTCH1 mutation rates. Univariate and multivariate analyses revealed that high TMB (TMB-H) and NOTCH1 mutation are independent genetic factors that are significantly associated with shorter relapse-free survival (RFS). Simultaneously, the results of the transcriptome analysis presented recurrent tumors with NOTCH1 mutation displayed upregulation of the cell cycle pathway, along with decreased B cells score, T cells score, immune signature score and tumor-infiltrating lymphocytes (TILs) score. The Cancer Genome Atlas (TCGA)-laryngeal cancer dataset also revealed weakened immune response and impaired adhesion functions in NOTCH1-mutant patients.

Conclusions

Genomic instability and impaired immune response are key features of the immunosurveillance escape and recurrence of early laryngeal cancer after surgery. These findings revealed immunophenotypic attenuation in recurrent tumors and provided valuable information for improving the management of these high-risk patients. Due to the small number of patients in this study, these differences need to be further validated in a larger cohort.

PET measured hypoxia and MRI parameters in re-irradiated head and neck squamous cell carcinomas: findings of a prospective pilot study

Background: Tumor hypoxia measured by dedicated tracers like [ ¹⁸F]fluoromisonidazole (FMISO) is a well-established prognostic factor in head and neck squamous cell carcinomas (HNSCC) treated with definitive chemoradiation (CRT). However, prevalence and characteristics of positron emission tomography (PET) measured hypoxia in patients with relapse after previous irradiation is missing. Here we report imaging findings of a prospective pilot study in HNSCC patients treated with re-irradiation.

Methods: In 8 patients with recurrent HNSCC, diagnosed at a median of 18 months after initial radiotherapy/CRT, [ ¹⁸F]fluorodeoxyglucose (FDG)-PET/CT (n=8) and FMISO-PET/MRI (n=7) or FMISO-PET/CT (n=1) were performed. Static FMISO-PET was performed after 180 min. MRI sequences in PET/MRI included diffusion-weighted imaging with apparent diffusion coefficient (ADC) values and contrast enhanced T1w imaging (StarVIBE). Lesions (primary tumor recurrence, 4; cervical lymph node, 1; both, 3) were delineated on FDG-PET and FMISO-PET data using a background-adapted threshold-based method. SUV _max and SUV _mean in FDG- and FMISO-PET were derived, as well as maximum tumor-to-muscle ratio (TMR _max) and hypoxic volume with 1.6-fold muscle SUV _mean (HV _1.6) in FMISO-PET. Intensity of lesional contrast enhancement was rated relative to contralateral normal tissue. Average ADC values were derived from a 2D region of interest in the tumor.

Results: In FMISO-PET, median TMR _max was 1.7 (range: 1.1-1.8). Median HV _1.6 was 0.05 ml (range: 0-7.3 ml). Only in 2/8 patients, HV _1.6 was ≥1.0 ml. In FDG-PET, median SUV _max was 9.3 (range: 5.0-20.1). On contrast enhanced imaging four lesions showed decreased and four lesions increased contrast enhancement compared to non-pathologic reference tissue. Median average ADC was 1,060 ×10 ⁶ mm ²/s (range: 840-1,400 ×10 ⁶ mm ²/s).

Conclusions: This pilot study implies that hypoxia detectable by FMISO-PET may not be as prevalent as expected among loco-regional recurrent, HPV negative HNSCC. ADC values were only mildly reduced, and contrast enhancement was variable. The results require confirmation in larger sample sizes.

Development and validation of a novel metabolic signature for predicting prognosis in patients with laryngeal cancer

PURPOSE

Despite advances in the development of treatments for laryngeal cancer (LC), including surgical treatments and radio-chemotherapy, the survival rate of LC remains low. Therefore, novel metabolic signatures are urgently needed to evaluate the prognosis of LC patients.

METHODS

Differentially expressed metabolic genes were extracted via bioinformatics analysis from the raw data of The Cancer Genome Atlas and Gene Expression Omnibus (GEO) databases. Univariate Cox regression and LASSO analyses were performed to identify metabolic genes that were significantly correlated with overall survival (OS). Using the Kaplan-Meier analysis and receiver operating characteristics, the prognostic power of candidate signatures was evaluated in the two databases. Gene Set Enrichment Analysis (GSEA) was performed to explore significant signaling pathways and underlying mechanisms in the high- and low-risk groups.

RESULTS

Thirteen metabolism genes showed superior ability to predict OS for LC when compared to clinical variables, and patients in the high-risk group showed significantly poorer OS than those in the low-risk group. The area under the curve of receiver operating curves for 5- and 3-year OS was 0.929 and 0.899, respectively, which were better than the OS obtained with clinicopathological variables. Similar results obtained in the GEO cohort indicated that this gene signature could differentiate between LC patients with and without recurrence.

CONCLUSION

To our knowledge, this study is the first to report that the 13 metabolic genes could serve as an independent biomarker for LC, which could provide vital prognostic information and prediction for personalized treatment of LC.

Prognostic Significance of Oxidation Pathway Mutations in Recurrent Laryngeal Squamous Cell Carcinoma

Simple Summary

Organ preservation protocols have become first line therapy for the majority of advanced laryngeal cancers. Unfortunately, up to one third of patients will develop recurrent disease requiring salvage surgery. These tumors tend to display aggressive features when compared to primary disease. The aim of this study is to identify genomic alterations associated with poor prognosis in the recurrent setting to guide precision therapy and identify potential targetable pathways. Here we show that mutations in the oxidation pathway, specifically the KEAP1-NFR2 pathway, predict survival in a cohort of patients undergoing salvage laryngectomy.

Abstract

Organ preservation protocols are commonly used as first line therapy for advanced laryngeal cancer. Recurrence thereafter is associated with poor survival. The aim of this study is to identify genetic alterations associated with survival among patients with recurrent laryngeal cancer undergoing salvage laryngectomy. Sixty-two patients were sequenced using a targeted panel, of which twenty-two also underwent transcriptome sequencing. Alterations were grouped based on biologic pathways and survival outcomes were assessed using Kaplan-Meier analysis and multivariate cox regression. Select pathways were evaluated against The Cancer Genome Atlas (TCGA) data. Patients with mutations in the Oxidation pathway had significantly worse five-year disease specific survival (1% vs. 76%, p = 0.02), while mutations in the HN-Immunity pathway were associated with improved five-year disease specific survival (100% vs. 62%, p = 0.02). Multivariate analysis showed mutations in the Oxidation pathway remained an independent predictor of disease specific survival (HR 3.2, 95% CI 1.1–9.2, p = 0.03). Transcriptome analysis of recurrent tumors demonstrated that alterations in the Oxidation pathway were associated a positive Ragnum hypoxia signature score, consistent with enhanced pathway activity. Further, TCGA analyses demonstrated the prognostic value of oxidation pathway alterations in previously untreated disease. Alterations in the Oxidation pathway are associated with survival among patients with recurrent laryngeal cancer. These prognostic genetic biomarkers may inform precision medicine protocols and identify putatively targetable pathways to improve survival in this cohort.

Five genes as a novel signature for predicting the prognosis of patients with laryngeal cancer

In this study, we purpose to investigate a novel five-gene signature for predicting the prognosis of patients with laryngeal cancer. The laryngeal cancer datasets were obtained from The Cancer Genome Atlas (TCGA). Both univariate and multivariate Cox regression analysis was applied to screening for prognostic differential expressed genes (DEGs), and a novel gene signature was obtained. The performance of this Cox regression model was tested by receiver operating characteristic (ROC) curves and area under the curve (AUC). Further survival analysis for each of the five genes was carried out through the Kaplan-Meier curve and Log-rank test. Totally, 622 DEGs were screened from the TCGA datasets in this study. We construct a five-gene signature through Cox survival analysis. Patients were divided into low- and high-risk groups depending on the median risk score, and a significant difference of the 5-year overall survival was found between these two groups (P < .05). ROC curves verified that this five-gene signature had good performance to predict the prognosis of laryngeal cancer (AUC = 0.862, P < .05). In conclusion, the five-gene signature consist of EMP1, HOXB9, DPY19L2P1, MMP1, and KLHDC7B might be applied as an independent prognosis predictor of laryngeal cancer.