Metabolic signature of squamous cell carcinoma of the head and neck: Consequences of TP53 mutation and therapeutic perspectives

DNA-PK-Mediated Cytoplasmic DNA Sensing Stimulates Glycolysis to Promote Lung Squamous Cell Carcinoma Malignancy and Chemoresistance

Detection of cytoplasmic DNA is an essential biological mechanism that elicits IFN-dependent and immune-related responses. A better understanding of the mechanisms regulating cytoplasmic DNA sensing in tumor cells could help identify immunotherapeutic strategies to improve cancer treatment. Here we identified abundant cytoplasmic DNA accumulated in lung squamous cell carcinoma (LUSC) cells. DNA-PK, but not cGAS, functioned as a specific cytoplasmic DNA sensor to activate downstream ZAK/AKT/mTOR signaling, thereby enhancing the viability, motility, and chemoresistance of LUSC cells. DNA-PK-mediated cytoplasmic DNA sensing boosted glycolysis in LUSC cells, and blocking glycolysis abolished the tumor-promoting activity of cytoplasmic DNA. Elevated DNA-PK-mediated cytoplasmic DNA sensing was positively correlated with poor prognosis of human patients with LUSC. Targeting signaling activated by cytoplasmic DNA sensing with the ZAK inhibitor iZAK2 alone or in combination with STING agonist or anti-PD-1 antibody suppressed the tumor growth and improved the survival of mouse lung cancer models and human LUSC patient-derived xenografts model. Overall, these findings established DNA-PK-mediated cytoplasmic DNA sensing as a mechanism that supports LUSC malignancy and highlight the potential of targeting this pathway for treating LUSC.

SIGNIFICANCE

DNA-PK is a cytoplasmic DNA sensor that activates ZAK/AKT/mTOR signaling and boosts glycolysis to enhance malignancy and chemoresistance of lung squamous cell carcinoma.

Cancer cells co-opt nociceptive nerves to thrive in nutrient-poor environments and upon nutrient-starvation therapies

Although nutrient-starvation therapies can elicit strong anti-tumor effects in multiple carcinomas, it has been convincingly demonstrated that cancer cells exploit the tumor microenvironment to thrive in nutrient-poor environments. Here, we reveal that cancer cells can co-opt nociceptive nerves to thrive in nutrient-poor environments. Initially examining the low-glucose environment of oral mucosa carcinomas, we discovered that cancer cells employ ROS-triggered activation of c-Jun to secrete nerve growth factor (NGF), which conditions nociceptive nerves for calcitonin gene-related peptide (CGRP) production. The neurogenic CGRP subsequently induces cytoprotective autophagy in cancer cells through Rap1-mediated disruption of the mTOR-Raptor interaction. Both anti-glycolysis and anti-angiogenesis-based nutrient-starvation therapies aggravate the vicious cycle of cancer cells and nociceptive nerves and therapeutically benefit from blocking neurogenic CGRP with an FDA-approved antimigraine drug. Our study sheds light on the role of the nociceptive nerve as a microenvironmental accomplice of cancer progression in nutrient-poor environments and upon nutrient-starvation therapies.

Head and Neck Squamous Cell Carcinoma Subtypes Based on Immunologic and Hallmark Gene Sets in Tumor and Non-tumor Tissues

Background

Non-tumor tissue has a significant impact on the prognosis of head and neck squamous cell carcinoma (HNSCC). Previous studies for HNSCC have mainly focused on tumor tissue, greatly neglecting the role of non-tumor tissue. This study aimed to identify HNSCC subtypes and prognostic gene sets based on activity changes of immunologic and hallmark gene sets in tumor and adjacent non-tumor tissues to improve patient prognosis.

Methods

In the study, we used gene set variation analysis (GSVA) to estimate the relative enrichment of gene sets over the sample population, and identified relevant subtypes of HNSCC by Cox regression analysis and the non-negative matrix factorization (NMF) method. The representative gene sets were identified by calculating the differential enrichment score of gene sets between each of the two subgroups, intersecting them, and screening them using univariate Cox regression analysis. The least absolute shrinkage and selection operator (LASSO) regression analysis was used to screen out potential prognostic gene sets and establish a risk model. Finally, genes encompassed in each prognostic gene set were obtained and subjected to enrichment analysis and protein–protein interaction (PPI) in tumor and non-tumor tissues.

Results

We identified three subtypes of HNSCC based on gene sets in tumor and non-tumor tissues, and patients with subtype 1 had a higher survival rate than subtypes 2 and 3. The subtypes were related to the survival status, pathological stage, and T stage of HNSCC patients. In total 450 differentially gene sets and 39 representative gene sets were obtained by calculating the differential enrichment score of gene sets between each of the two subgroups, intersecting them, and screening them using univariate Cox regression analysis. The prognostic model was constructed by LASSO regression analysis, including five prognostic gene sets. Kaplan-Meier analysis indicated that different risk groups and the five prognostic gene sets were associated with survival status in the model. Finally, enrichment analysis and PPI indicated that non-tumor and tumor tissues affect the prognosis of HNSCC patients in different ways.

Conclusion

In conclusion, we provide a novel insight for rational treatment strategies and precise prognostic assessments based on tumor and adjacent non-tumor tissues, suggesting that more emphasis should be placed on changes in adjacent non-tumor and tumor tissues, rather than just the tumor itself.

Metabolic Plasticity and Combinatorial Radiosensitisation Strategies in Human Papillomavirus-Positive Squamous Cell Carcinoma of the Head and Neck Cell Lines

Simple Summary

A subset of head and neck cancers (SCCHN) are caused by human papillomavirus (HPV). As these tumours tend to affect younger patients and are associated with favourable survival, there is a pressing need to find ways to reduce long-term treatment toxicity while maintaining oncological efficacy. We studied utilisation of metabolic pathways in HPV-positive SCCHN cells with the aim of exploiting such for potential therapeutic benefit. We found that these tumours maintained metabolic diversity, in contrast to what we have observed in traditional SCCHN cells associated with mutations in the TP53 gene. This, in turn, correlated with susceptibility to metabolic inhibitors, insofar as a combination of these agents acting on different metabolic pathways was required to augment the effects of ionising radiation (a mainstay of treatment for SCCHN). Notionally, this may provide a means of treatment de-intensification by facilitating radiation dose reduction to minimise the impact of treatment on long-term function.

Abstract

Background: A major objective in the management of human papillomavirus (HPV)-positive squamous cell carcinoma of the head and neck (SCCHN) is to reduce long-term functional ramifications while maintaining oncological outcomes. This study examined the metabolic profile of HPV-positive SCCHN and the potential role of anti-metabolic therapeutics to achieve radiosensitisation as a potential means to de-escalate radiation therapy. Methods: Three established HPV-positive SCCHN cell lines were studied (UM-SCC-104, UPCI:SCC154, and VU-SCC-147), together with a typical TP53 mutant HPV-negative SCCHN cell line (UM-SCC-81B) for comparison. Metabolic profiling was performed using extracellular flux analysis during specifically designed mitochondrial and glycolytic stress tests. Sensitivity to ionising radiation (IR) was evaluated using clonogenic assays following no treatment, or treatment with: 25 mM 2-deoxy-D-glucose (glycolytic inhibitor) alone; 20 mM metformin (electron transport chain inhibitor) alone; or 25 mM 2-deoxy-D-glucose and 20 mM metformin combined. Expression levels of p53 and reporters of p53 function (MDM2, p53, Phospho-p53 [Ser15], TIGAR and p21 [CDKN1A]) were examined by western blotting. Results: HPV-positive SCCHN cell lines exhibited a diverse metabolic phenotype, displaying robust mitochondrial and glycolytic reserve capacities. This metabolic profile, in turn, correlated with IR response following administration of anti-metabolic agents, in that both 2-deoxy-D-glucose and metformin were required to significantly potentiate the effects of IR in these cell lines. Conclusions: In contrast to our recently published data on HPV-negative SCCHN cells, which display relative glycolytic dependence, HPV-positive SCCHN cells can only be sensitised to IR using a complex anti-metabolic approach targeting both mitochondrial respiration and glycolysis, reflecting their metabolically diverse phenotype. Notionally, this may provide an attractive platform for treatment de-intensification in the clinical setting by facilitating IR dose reduction to minimise the impact of treatment on long-term function.

Plasma metabolic phenotypes of HPV-associated vs smoking-associated head and neck cancer and patient survival

BACKGROUND

Metabolic differences between human papillomavirus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) and smoking-associated HNSCC may partially explain differences in prognosis. The former relies on mitochondrial oxidative phosphorylation (OXPHOS) while the latter relies on glycolysis. These differences have not been studied in blood.

METHODS

We extracted metabolites using untargeted liquid chromatography high-resolution mass spectrometry from pretreatment plasma in a cohort of 55 HPV-associated and 82 smoking-associated HNSCC subjects. Metabolic pathway enrichment analysis of differentially expressed metabolites produced pathway-based signatures. Significant pathways (P<0.05) were reduced via principal components analysis and assessed with overall survival via Cox models. We classified each subject as glycolytic or OXPHOS phenotype and assessed it with survival.

RESULTS

Of 2,410 analyzed metabolites, 191 were differentially expressed. Relative to smoking-associated HNSCC, bile acid biosynthesis (P<0.0001) and octadecatrienoic acid beta-oxidation (P=0.01), were upregulated in HPV-associated HNSCC, while galactose metabolism (P=0.001) and vitamin B6 metabolism (P=0.01) were downregulated; the first two suggest an OXPHOS phenotype while the latter two suggest glycolytic. First principal components of bile acid biosynthesis (HR=0.52 per standard deviation, 95% CI:0.38-0.72, P<0.001) and octadecatrienoic acid beta-oxidation (HR=0.54 per sd, 95% CI:0.38-0.78, P<0.001) were significantly associated with overall survival independent of HPV and smoking. The glycolytic vs OXPHOS phenotype was also independently associated with survival (HR=3.17, 95% CI:1.07-9.35; P=0.04).

CONCLUSIONS

Plasma metabolites related to glycolysis and mitochondrial OXPHOS may be biomarkers of HNSCC patient prognosis independent of HPV or smoking. Future investigations should determine if they predict treatment efficacy.

IMPACT

Blood metabolomics may be a useful marker to aid HNSCC patient prognosis.

Association Between Vitamin D Exposure and Head and Neck Cancer: A Systematic Review With Meta-Analysis

Background

Vitamin D deficiency is a well-described preventable cause of many cancers; the association of vitamin D use with the development of head and neck cancer (HNC) is not clear. We aim to conduct a systematic review of the studies assessing the relation between vitamin D exposure and the prevention and prognosis of the HNC using meta-analysis.

Methods

PubMed, EMBASE, Cochrane Library, Web of Science up to 1 January 2021, and reference lists of related studies were searched. We extracted observational studies reporting the association between vitamin D (vitamin D receptor gene polymorphisms, 25-hydroxyvitamin D concentrations, and vitamin D intake) and the outcomes of interest (HNC incidence and HNC mortality) in HNC patients aged 18 or older. Fixed effects models were used to calculate pooled effect sizes and 95% confidence intervals (CIs) by RevMan (version 5.3).

Results

Sixteen studies with a total of 81,908 participants were enrolled in our meta-analysis. Based on the pooled genomic analysis, comparing with participants with the genotypes of Ff + FF or FF, the pooled odds ratio (OR) of participants with the genotype of ff was 0.77 (95% CI: 0.61 to 0.97) and 0.75 (0.58 to 0.97), respectively. A similar trend was noted when comparing tt with Tt + TT or TT, in which OR (95% CI) was 0.70 (0.55 to 0.90) and 0.72 (0.55 to 0.95). No significant association was identified between BsmI polymorphism and HNC. Furthermore, the OR of HNC incidence was 0.77 (0.65 to 0.92) for participants with vitamin D intake over the ones with a regular diet. High concentrations of circulated 25-hydroxyvitamin D (25-OHD) significantly decreased by 32% of HNC incidence (OR (95% CI): 0.68 (0.59 to 0.78)) and increased HNC survival (pooled hazard ratio 1.13, 1.05 to 1.22) during a 4-5 years follow-up. High concentrations of circulating 25-OHD in patients with HNC led to a decreased risk of mortality to 0.75 (0.60 to 0.94) as the follow-up extends to 8-12 years.

Conclusions

Elevated activities of vitamin D by diet intake, genomic polymorphisms, or circulated 25-OHD may protect people from HNC and improve the prognosis of patients with HNC.

Systematic Review Registration

PROSPERO, identifier CRD42020176002 (https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=176002).

Significance of TP53 mutation in treatment and prognosis in head and neck squamous cell carcinoma

Background:TP53 is ranked as the most common mutated gene in head and neck squamous cell carcinoma (HNSCC). Results: The status of TP53 mutation was investigated on International Cancer Genome Consortium and The Cancer Genome Atlas database and TP53-related differentially expressed genes were screened out from transcriptome data and mutation information. A TP53-related prognostic gene signature (TIMP4, ONECUT2, CGNL1, DMRTA2 and NKX2.3) was constructed based on Cox regression analysis and LASSO algorithm. Univariate and multivariate analyses were carried out to identify promising prognosticators for HNSCC. Conclusion: Our findings provide a well-rounded landscape of TP53 mutation in HNSCC and pave the groundwork for developing innovative and effective cancer treatment methods for HNSCC.

MicroRNA-3666 Suppresses Cell Growth in Head and Neck Squamous Cell Carcinoma Through Inhibition of PFKFB3-Mediated Warburg Effect

Purpose

MicroRNA-3666 (miR-3666) is aberrantly expressed and plays critical roles in numerous human tumors. However, the expression pattern, biological role, and mechanisms of action of miR-3666 in head and neck squamous cell carcinoma (HNSCC) remain unknown. Therefore, we attempted to determine the expression status and function of miR-3666 in HNSCC and to explore the underlying mechanisms in detail.

Methods

In this study, quantitative real-time polymerase chain reaction was carried out to measure the expression of miR-3666 HNSCC tissues. A series of experiments, including a Cell Counting Kit-8 assay, colony formation assay, BrdU incorporation and apoptosis analysis, were applied to test whether miR-3666 affects the growth of HNSCC cells. Glucose uptake and lactate production measurements and extracellular acidification and oxygen consumption rate assays were conducted to determine the effect of miR-3666 on glycolysis.

Results

We found that miR-3666 showed a decreased expression in HNSCC tissues. Further functional studies demonstrated that miR-3666 inhibited the growth of HNSCC cells by suppressing cell proliferation and promoting apoptosis. Bioinformatics analysis and luciferase reporter assays identified phosphofructokinase-2/fructose-2,6-bisphosphatase 3 (PFKFB3), a key enzyme regulating glycolysis, as a direct target of miR-3666. Through inhibition of PFKFB3, miR-3666 decreased glycolysis in HNSCC cells by reducing the production of F2,6BP. Importantly, glycolysis suppression caused by miR-3666 was found to be required for its inhibitory effect on HNSCC cell growth.

Conclusion

Our data suggest that miR-3666 functions as a tumor suppressor by decreasing the rate of glycolysis through inhibition of PFKFB3 activity, and this miRNA may present a potential candidate for HNSCC therapy.

TP53 mutations in head and neck cancer cells determine the Warburg phenotypic switch creating metabolic vulnerabilities and therapeutic opportunities for stratified therapies

Patients with mutated TP53 have been identified as having comparatively poor outcomes compared to those retaining wild-type p53 in many cancers, including squamous cell carcinomas of the head and neck (SCCHN). We have examined the role of p53 in regulation of metabolism in SCCHN cells and find that loss of p53 function determines the Warburg effect in these cells. Moreover, this metabolic adaptation to loss of p53 function creates an Achilles' heel for tumour cells that can be exploited for potential therapeutic benefit. Specifically, cells lacking normal wild-type p53 function, whether through mutation or RNAi-mediated downregulation, display a lack of metabolic flexibility, becoming more dependent on glycolysis and losing the ability to increase energy production from oxidative phosphorylation. Thus, cells that have compromised p53 function can be sensitised to ionizing radiation by pre-treatment with a glycolytic inhibitor. These results demonstrate the deterministic role of p53 in regulating energy metabolism and provide proof of principle evidence for an opportunity for patient stratification based on p53 status that can be exploited therapeutically using current standard of care treatment with ionising radiation.

Application of Machine Learning in Developing a Novelty Five-Pseudogene Signature to Predict Prognosis of Head and Neck Squamous Cell Carcinoma: A New Aspect of "Junk Genes" in Biomedical Practice

Head and neck squamous cell carcinoma (HNSCC) is the sixth malignancy, which is characterized by poor prognosis or high mortality because of the lack of predicting markers. Aberrant cancer pseudogenes have been found predictive for prognosis. We aim to identify a pseudogene-based prognosis signature for HNSCC by machine learning. RNA-seq data were downloaded from The Cancer Genome Atlas, and 700 differentially-expressed pseudogenes were identified. The survival-related pseudogenes were screened through COX-regression analysis, which includes univariate regression, least absolute shrinkage and selection operator regression, and multivariate regression, and a five-pseudogene signature was constructed. The value of prediction for the signature was validated in multiple subgroups in terms of survival. Gene set enrichment analysis (GSEA) and coexpression analysis were used to determine the underlying biological functions. Seven hundred dysregulated pseudogenes were identified, and the five-pseudogene signature can distinguish the low-risk and high-risk patients for both training and testing sets and predicted prognosis with high sensitivity and specificity. Furthermore, the signature was applicable to patients of different genders, ages, stages, and grades. Coexpression analysis revealed that the five-pseudogene is associated with immune system. GSEA showed cancer-related biological process and pathways the five-pseudogene involved in. The five-pseudogene signature is not only a novel marker for prognosis but also a promising signature for monitoring therapeutic schedule. Therefore, our findings may have potential clinical significance.

Expression scoring of a small-nucleolar-RNA signature identified by machine learning serves as a prognostic predictor for head and neck cancer

Head and neck squamous cell carcinoma (HNSCC) is a common malignancy with high mortality and poor prognosis due to a lack of predictive markers. Increasing evidence has demonstrated small nucleolar RNAs (snoRNAs) play an important role in tumorigenesis. The aim of this study was to identify a prognostic snoRNA signature of HNSCC. Survival-related snoRNAs were screened by Cox regression analysis (univariate, least absolute shrinkage and selection operator, and multivariate). The predictive value was validated in different subgroups. The biological functions were explored by coexpression analysis and gene set enrichment analysis (GSEA). One hundred and thirteen survival-related snoRNAs were identified, and a five-snoRNA signature predicted prognosis with high sensitivity and specificity. Furthermore, the signature was applicable to patients of different sexes, ages, stages, grades, and anatomic subdivisions. Coexpression analysis and GSEA revealed the five-snoRNA are involved in regulating malignant phenotype and DNA/RNA editing. This five-snoRNA signature is not only a promising predictor of prognosis and survival but also a potential biomarker for patient stratification management.

Correlation between ER, PR, P53, Ki67 expression, and high-risk HPV infection in patients with different levels of cervical intraepithelial neoplasia

This study was designed to investigate the correlation between high-risk human papillomavirus (HPV) infection and the expression of IHC markers (ER, PR, p53, Ki67) in patients with different grades of cervical intraepithelial neoplasia (CIN). It was a retrospective study, which was conducted from June 2016 to June 2018. 140 specimens of CIN were collected from the pathology department of a certain hospital that included 40 specimens of CIN1, 50 specimens of CIN2 and 50 specimens of CIN3. The expression of ER, PR, P53 and Ki67 were determined by immunohistochemistry. The high-risk HPV infections were detected by PCR fluorescence quantification and were given the correlation analysis. In the 140 specimens, the positive rates of HPV16 and HPV18 in CIN1 specimens were 27.5% and 25.0% respectively, and in CIN2 specimens were 64.0% and 60.0% respectively, and in CIN3 specimens were 90.0% and 92.0% respectively, the difference were statistically significant (p<0.05). There were no significant correlation (p<0.05) between HPV16 and HPV18 positive rate and patient age, tissue differentiation, and tumor size. With the increased of CIN grade, the positive rate of ER, PR, P53 and Ki67 expression in specimen were also increased significantly, and the difference were statistically significant (p<0.05). Pearson correlation analysis showed there were positive correlation (p<0.05) between the positive rates of HPV16 and HPV18 and the positive rates of ER, PR, P53 and Ki67. With the increase of CIN level, the positive rates of high-risk HPV infection as well as ER, PR, P53 and Ki67 are increased, and they have positive correlation.

Wild type- and mutant p53 proteins in mitochondrial dysfunction: emerging insights in cancer disease

Deregulated cell metabolism is one of the cancer hallmarks. Mitochondrial DNA mutations and enzyme defects, aberrant tumor suppressor or oncogenic activities cause mitochondrial dysfunction leading to deregulated cellular energetics. The tumor suppressor protein, p53 is a tetrameric transcription factor that in response to diverse genotoxic and non-genotoxic insults activates a plethora of target genes to preserve genome integrity. In the last two decades the discovery of cytoplasmic p53 localization focused intense research on its extra-nuclear functions. The ability of p53 to induce apoptosis acting directly at mitochondria and the related mechanisms of p53 localization and translocation in the cytoplasm have been investigated. A role of cytoplasmic p53 in autophagy, pentose phosphate pathway, fatty acid synthesis and oxidation, and drug response has been proposed. TP53 gene is mutated in more than half of human cancers. In parallel to loss of tumor suppressive functions, mutant p53 proteins often gain new tumorigenic activities (GOF, gain of function). It has been recently shown that mutant p53 proteins mediate metabolic changes thereby promoting cancer development and metastases. Here we review the contribution of either wild-type p53 or mutant p53 proteins to the fine-tuning of mitochondrial metabolism of both normal and cancer cells. Greater knowledge at the mechanistic level might provide insights to develop new cancer therapeutic approaches.

Diagnostic accuracy and prognostic applications of CYFRA 21-1 in head and neck cancer: A systematic review and meta-analysis

Cytokeratin fraction 21–1 (CYFRA 21–1) has been widely studied as an important biomarker in non-small cell lung cancer for both diagnosis and prognosis. Many studies have also assessed the clinical applications of CYFRA 21–1 in head and neck cancer, but the diagnostic and prognostic values of CYFRA 21–1 are not yet fully established. This pooled analysis aims at evaluating the diagnostic accuracy and prognostic applications of CYFRA 21–1 in patients with head and neck cancer. A systematic retrieval of literatures was conducted without time or language restrictions by searching PubMed, EMBASE, Web of Science, Cochrane library and China National Knowledge Infrastructure. Twenty studies were eligible for systematic review, of which 14 conformed for diagnostic analysis and 7 for prognostic analysis. The pooled sensitivity and specificity of CYFRA 21–1 analysis were 0.53 (95% CI: 0.39–0.67) and 0.97 (95% CI: 0.93–0.99), respectively. A high level of CYFRA 21–1 was significantly correlated with shorter overall survival (HR 1.33, 95% CI: 1.13–1.56) and disease-free survival (HR 1.48; 95%CI: 1.10–1.97). Current evidence indicates that the level of CYFRA 21–1 in the serum could be used as an indicator for monitoring tumor status and evaluating its curative effects.