scholarly journals The Oncogenic Roles of PTTG1 and PTTG2 Genes and Pseudogene PTTG3P in Head and Neck Squamous Cell Carcinomas

Diagnostics ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 606 ◽  
Author(s):  
Inga Grzechowiak ◽  
Justyna Graś ◽  
Dominika Szymańska ◽  
Martyna Biernacka ◽  
Kacper Guglas ◽  
...  
Keyword(s):  
Dna Repair ◽  
Oxidative Phosphorylation ◽  
Head And Neck ◽  
Squamous Cell ◽  
Enrichment Analysis ◽  
Tp53 Gene ◽  
Squamous Cell Carcinomas ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Expression Levels

Background: Head and neck squamous cell carcinomas are a group of heterogeneous diseases that occur in the mouth, pharynx and larynx and are characterized by poor prognosis. A low overall survival rate leads to a need to develop biomarkers for early head and neck squamous cell carcinomas detection, accurate prognosis and appropriate selection of therapy. Therefore, in this paper, we investigate the biological role of the PTTG3P pseudogene and associated genes PTTG1 and PTTG2 and their potential use as biomarkers. Methods: Based on TCGA data and the UALCAN database, PTTG3P, PTTG1 and PTTG2 expression profiles and clinicopathological features with TP53 gene status as well as expression levels of correlated genes were analyzed in patients’ tissue samples. The selected genes were classified according to their biological function using the PANTHER tool. Gene Set Enrichment Analysis software was used for functional enrichment analysis. All statistical analyses were performed using GraphPad Prism 5. Results: In head and neck squamous cell carcinomas, significant up-regulation of the PTTG3P pseudogene, PTTG1 and PTTG2 genes’ expression between normal and cancer samples were observed. Moreover, the expression of PTTG3P, PTTG1 and PTTG2 depends on the type of mutation in TP53 gene, and they correlate with genes from p53 pathway. PTTG3P expression was significantly correlated with PTTG1 as well as PTTG2, as was PTTG1 expression with PTTG2. Significant differences between expression levels of PTTG3P, PTTG1 and PTTG2 in head and neck squamous cell carcinomas patients were also observed in clinicopathological contexts. The contexts taken into consideration included: T-stage for PTTG3P; grade for PTTG3, PTTG1 and PTTG2; perineural invasion and lymph node neck dissection for PTTG1 and HPV p16 status for PTTG3P, PTTG1 and PTTG2. A significantly longer disease-free survival for patients with low expressions of PTTG3P and PTTG2, as compared to high expression groups, was also observed. Gene Set Enrichment Analysis indicated that the PTTG3 high-expressing group of patients have the most deregulated genes connected with DNA repair, oxidative phosphorylation and peroxisome pathways. For PTTG1, altered genes are from DNA repair groups, Myc targets, E2F targets and oxidative phosphorylation pathways, while for PTTG2, changes in E2F targets, G2M checkpoints and oxidative phosphorylation pathways are indicated. Conclusions: PTTG3P and PTTG2 can be used as a prognostic biomarker in head and neck squamous cell carcinomas diagnostics. Moreover, patients with high expressions of PTTG3P, PTTG1 or PTTG2 have worse outcomes due to upregulation of oncogenic pathways and more aggressive phenotypes.

scholarly journals Increased Expression of FN1 in Head and Neck Squamous Cell Carcinoma Predicts Poor Prognosis

2021 ◽  
Author(s):  
Hung-Sheng Shih ◽  
Li-Yu Hung ◽  
Ming-Yu Hsieh
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Neck Squamous Cell Carcinoma ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Kaplan Meier

Abstract Background: A few recent studies have addressed the function of FN1 (Fibronectin 1) in head and neck cancer. The clinical information from 500 HNSCC (Head and neck squamous cell carcinoma) patients with FN1 gene expression data set was published by The Cancer Genome Atlas (TCGA). The correlation between clinicopathologic characteristics and FN1 expression was analyzed by Logistic regression and Wilcoxon signed rank test. Survival function was performed employing Kaplan-Meier estimator, and the relationship between clinicopathological characteristics, prognostic outcome, and FN1 expression were examined by using Cox regression analysis. As Gene set enrichment analysis (GSEA) was performed, we investigated the correlation between FN1 expression and immune cell infiltrates with single-sample gene set enrichment analysis (ssGSEA). Results: Patients with high FN1 expression revealed a significantly decreased overall survival (OS), and disease-specific survival (DSS) than those with low FN1 expression in Kaplan-Meier survival analyses. According to the above results, univariate and multivariate analysis revealed that patients with high FN1 expression had lower OS than those with low FN1 expression.Conclusions: The findings of this research provide insights for FN1 may be potential prognostic biomarkers for diagnosis as well as therapeutic targets in HNSCC patients.

scholarly journals Upregulated Glycolysis Correlates With Clinical and Transcriptomic Significances in Head and Neck Squamous Cell Carcinoma

2021 ◽  
Author(s):  
Hideyuki Takahashi ◽  
Reika Kawabata-Iwakawa ◽  
Shota Ida ◽  
Ikko Mito ◽  
Hiroe Tada ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Enrichment Analysis ◽  
Janus Kinase ◽  
Gene Set Enrichment Analysis ◽  
Neck Squamous Cell Carcinoma ◽  
Tumor Type ◽  
High Group

Abstract Altered metabolism is an emerging hallmark of cancer. Cancer cells preferentially utilize glycolysis for energy production, termed “aerobic glycolysis.” In this study, we performed a comprehensive analysis of the glycolysis status in the tumor microenvironment (TME) of head and neck squamous cell carcinoma (HNSCC) using data from The Cancer Genome Atlas database. We first divided 520 patients with HNSCC into two groups based on the mRNA expression of 16 glycolysis-related genes. The glycolysis-high signature positively correlated with human papillomavirus-negative tumor type, advanced T factor, and unfavorable prognosis. The gene set enrichment analysis revealed upregulation of several pathways, including interferon-alpha response, myc targets, hypoxia, epithelial-mesenchymal transition, transforming growth factor-β signaling, and interleukin 6-Janus kinase-signal transducer and activator of transcription 3 signaling, in the glycolysis-high group. Immune cell enrichment analysis revealed decreased infiltration of T cells, dendritic cells, and B cells in the glycolysis-high group, suggesting impaired tumor antigen presentation, T cell activation, and antibody production in TME. Moreover, the expression of TGFB1, CD274, and PDCD1LG2, which facilitate immunosuppression in the TME, was upregulated in the glycolysis-high group. Collectively, these findings suggest the potential of glycolysis monitoring as a biomarker for tumor progression and immunosuppression in the TME of HNSCC.

scholarly journals Immune-related miRNA signature identifies prognosis and immune landscape in head and neck squamous cell carcinomas

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Bo Ma ◽  
Hui Li ◽  
Jia Qiao ◽  
Tao Meng ◽  
Riyue Yu
Keyword(s):  
Head And Neck ◽  
Squamous Cell ◽  
Cox Regression ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Immune Checkpoints ◽  
Cox Regression Analysis ◽  
Immunosuppressive Microenvironment ◽  
Selection Operator

Abstract Background: Head and neck squamous cell carcinoma (HNSCC) is recognised as an immune active cancer, but little is known about the role of microRNAs (miRNAs) in it. In the present study, we aim to determine a prognostic and immune-related miRNAs signature (IRMS) in HNSCC. Methods: Spearman correlation analysis was used to screen out prognostic immune-related miRNAs based on single-sample gene set enrichment analysis (ssGSEA). Least absolute shrinkage and selection operator (LASSO) Cox regression model was used to establish IRMS in HNSCC. Then, the influence of the IRMS on HNSCC was comprehensively analysed. Results: We obtained 11 prognostic immune-related miRNAs based on ssGSEA. Then an IRMS integrated with six miRNAs was established through LASSO Cox regression analysis. The stratification survival analysis indicated that IRMS was independent from other characteristics and performed favourably in the overall survival (OS) prediction. The function annotation suggested that IRMS was highly associated with the immune-related response biological processes and pathways which are so important for tumorigenesis of HNSCC. Moreover, the nomogram demonstrated that our model was identified as an independent prognostic factor. In addition, we found that IRMS was significantly correlated with the immune infiltration and expression of critical immune checkpoints, indicating that the poor prognosis might be caused partly by immunosuppressive microenvironment. Conclusion: We established a novel IRMS, which exhibited a potent prognostic value and could be representative of immune status in HNSCC.

scholarly journals Transcriptomic Analysis Implicates Necroptosis in Disease Progression and Prognosis in Myelodysplastic Syndromes

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3006-3006
Author(s):  
Guillermo Montalban-Bravo ◽  
Caleb Class ◽  
Irene Ganan-Gomez ◽  
Rashmi Kanagal-Shamanna ◽  
Koji Sasaki ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Innate Immunity ◽  
Cell Death ◽  
Research Funding ◽  
Somatic Mutations ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Expression Levels ◽  
Cd34 Cells

INTRODUCTION: Myelodysplastic syndromes (MDS) are characterized by ineffective hematopoiesis and cytopenias due to uncontrolled programmed cell death. The presence of pro-inflammatory cytokines and constitutive activation of innate immunity signals in MDS cells suggest inflammatory cell death, such as necroptosis, may be responsible for disease phenotype. There is no data evaluating the association of RIPK1, RIPK3 and MLKL with response and prognosis in MDS. METHODS: We evaluated 64 bone marrow samples from 55 patients with MDS or chronic myelomonocytic leukemia (CMML) obtained prior to (n=46) or after (n=18) therapy with hypomethylating agents (HMAs). RNA from sorted bone marrow CD34+ cells was isolated and subject to amplification and RNA-seq. Gene co-expression was evaluated using Spearman correlation. Pathway enrichment analysis was performed using gene set enrichment analysis, with the fgsea library in R. Sequencing data was obtained by use of a 81-gene targeted PCR-based next generation sequencing (NGS) platform. Previously described somatic mutations registered at the Catalogue of Somatic Mutations in Cancer (COSMIC: http://cancer.sanger.ac.uk/cosmic) were considered as potential driver mutations. RESULTS: Compared to healthy controls, MLKL (CMML vs controls: 2.09 log2FC, p=0.0013; MDS vs control: 1.89 log2FC, p=0.003), but not RIPK1 or RIPK3, were significantly upregulated in patients with MDS and CMML (Figure 1A-C). No differences in the level of expression of RIPK1, MLKL or RIPK3 were observed based on the mutation context or burden. No significant difference in RIPK1, RIPK3 or MLKL expression levels was observed based on presence of cytogenetic abnormalities (RIPK1: 0.10 log2FC, p=0.6; RIPK3: -0.39 log2FC, p=0.40; MLKL: 0.34 log2FC, p=0.30). Higher expression levels of MLKL were associated with lower hemoglobin levels at the time of diagnosis (-0.19 log2FC per 1g/dL increase of Hgb, p=0.03) (Figure 1D). Exposure to HMA therapy was associated with a trend to decreased expression of MLKL (-0.52 log2FC, p=0.08) when all post-HMA therapy samples were evaluated. Among patient matched samples, significant reduction in MLKL levels was observed after HMA therapy (-1.06 log2FC, p=0.05). The degree of reduction in expression levels was greater among non-responders (-2.89 log2FC, p=0.06) compared to responders (-0.78, log2FC, p=0.06). Expression levels of RIPK1 at the time of diagnosis predicted for shorter survival for patients with high RIPK1 levels, defined as a log expression higher than median mRNA expression values, (median OS 10.7 vs 24.2 months, HR 1.92, 95% CI 1.00-3.67, p=0.049 by Cox proportional hazards) (Figure 1E). A multivariate analysis for overall survival using both IPSS-R risk and RIPK1 expression levels demonstrated that high RIPK1 expression was an independent adverse prognostic factor in MDS patients (HR 6.83, 95% CI 1.74-26.8, p=0.006). A total of 359 genes were significantly correlated with RIPK1 levels in MDS CD34+ cells (Spearman's method q<0.2). Among these, 21 genes were positively correlated with RIPK1 expression, while 17 genes were negative correlated (Spearman's correlation, q<0.1). Gene set enrichment analysis identified 373 gene sets that significantly correlated with RIPK1 expression. Upregulated genes were associated with molecular signals associated with innate immunity and inflammatory signaling including TNF-α signaling via NFkB, NFkB signaling, the IFN-g pathway, and RIG-I-like receptor (RLRs) signaling genes (Figure 1F). CONCLUSIONS: This data provides further support for a role of necroptosis in MDS, and potentially response to HMAs and prognosis. This data also indicates that RIPK1/RIPK3/MLKL are potential therapeutic targets in MDS. Figure 1 Disclosures Sasaki: Otsuka: Honoraria; Pfizer: Consultancy. Bueso-Ramos:Incyte: Consultancy. Kantarjian:Cyclacel: Research Funding; Jazz Pharma: Research Funding; AbbVie: Honoraria, Research Funding; Astex: Research Funding; Amgen: Honoraria, Research Funding; Actinium: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Research Funding; Immunogen: Research Funding; Daiichi-Sankyo: Research Funding; Pfizer: Honoraria, Research Funding; Novartis: Research Funding; Ariad: Research Funding; Agios: Honoraria, Research Funding; Takeda: Honoraria. Garcia-Manero:Amphivena: Consultancy, Research Funding; Helsinn: Research Funding; Novartis: Research Funding; AbbVie: Research Funding; Celgene: Consultancy, Research Funding; Astex: Consultancy, Research Funding; Onconova: Research Funding; H3 Biomedicine: Research Funding; Merck: Research Funding.

Nucleotide Excision Repair Proteins and Risk of Head and Neck Squamous Cell Carcinomas in a Chinese Population

2020 ◽  
Author(s):  
Pengyu Ren ◽  
Xiaorong Niu ◽  
Ruimin Zhao ◽  
Zichen Chen ◽  
Hao Dai ◽  
...  
Keyword(s):  
Head And Neck ◽  
Nucleotide Excision Repair ◽  
Squamous Cell ◽  
Chinese Population ◽  
Excision Repair ◽  
Squamous Cell Carcinomas ◽  
Expression Levels ◽  
Increased Risk ◽  
Nucleotide Excision ◽  
Drinking Status

Abstract Background Nucleotide excision repair (NER) is pivotal in the development of smoking-related malignancies. We hypothesize that expression levels of NER proteins are associated with risk of the head and neck squamous cell carcinomas (HNSCCs) in a Chinese population. Methods To test this hypothesis, we conducted a case-control study of 337 HNSCC patients and 285 cancer-free controls by measuring the expression levels of nine core NER proteins in cultured peripheral lymphocytes. Results Compared with the controls, cases had statistically significantly lower expression levels of XPA (P=0.001). After dividing the subjects by controls’ medians of expression levels, we found an association between an increased risk of HNSCCs and low XPA expression levels [adjusted ORs and 95% CIs:1.42 and 1.03-1.96; Ptrend=0.031]. We identified a multiplicative interaction between smoking as well as drinking status and XPA expression levels (P = 0.005 and 0.044, respectively). Finally, the sensitivity of the expanded model with protein expression levels, in addition to demographic variables, on HNSCCs risk was significantly improved, especially among ever smokers and ever drinkers. Conclusions Reduced XPA expression levels were associated with an increased risk of HNSCCs in a Chinese population.

scholarly journals DNA repair gene expression is increased in HPV positive head and neck squamous cell carcinomas

Virology ◽  
2020 ◽  
Vol 548 ◽  
pp. 174-181
Author(s):  
Andrew J. Holcomb ◽  
Laura Brown ◽  
Ossama Tawfik ◽  
Rashna Madan ◽  
Yelizaveta Shnayder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Head And Neck ◽  
Squamous Cell ◽  
Squamous Cell Carcinomas ◽  
Repair Gene ◽  
Dna Repair Gene

scholarly journals A Novel Prognostic Index Based on the Analysis of Glycolysis-Related Genes in Head and Neck Squamous Cell Carcinomas

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Yuchao Liu ◽  
Shihua Yin
Keyword(s):  
Head And Neck ◽  
Squamous Cell ◽  
Prognostic Significance ◽  
Prognostic Index ◽  
Enrichment Analysis ◽  
Prognostic Indicator ◽  
Low Risk ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Risk Patients

Aims. The preferential dependence on glycolysis as a pathway of energy metabolism is a hallmark of cancer cells. However, the prognostic significance of glycolysis-related genes in head and neck squamous cell carcinoma (HNSCC) remains obscure. The purpose of this study was to identify glycolysis-related genes of prognostic value in HNSCC. Results. Transcriptional and clinical data of 544 HNSCC samples were obtained from The Cancer Genome Atlas (TCGA) dataset. By gene set enrichment analysis (GSEA) and by employing a univariate and subsequently a stepwise multivariate Cox proportional regression model, eight glycolysis-related genes of prognostic significance in HNSCC (KIF2A, JMJD8, HMMR, STC2, HK1, EXT2, GPR8, and STC1) were identified. The patients were clustered into two groups (high and low risk) based on the expression of these genes. High-risk patients had significantly a shorter overall survival than low-risk patients. Furthermore, a new prognostic indicator based on selected glycolysis-related genes was developed by multivariate Cox analysis that proved to be a better predictor of patient outcome compared to other clinical factors. Conclusion. Our findings provide new insights into the role of glycolysis in HNSCC. The identified genes predict the patient prognosis and might substantially contribute to the development of individualized treatments.

OC-0483: DNA repair defects in squamous cell carcinomas of the head and neck

2014 ◽  
Vol 111 ◽  
pp. S189
Author(s):  
C. Vens ◽  
C. Verhagen ◽  
D. Vossen ◽  
F. Hageman ◽  
K. Borgmann ◽  
...  
Keyword(s):  
Dna Repair ◽  
Head And Neck ◽  
Squamous Cell ◽  
Squamous Cell Carcinomas

scholarly journals The Landscape of Transmembrane Protein Family Members in Head and Neck Cancers: Their Biological Role and Diagnostic Utility

Cancers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 4737
Author(s):  
Oliwia Koteluk ◽  
Antonina Bielicka ◽  
Żaneta Lemańska ◽  
Kacper Jóźwiak ◽  
Weronika Klawiter ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Immune Cell ◽  
Patient Survival ◽  
Gene Set Enrichment Analysis ◽  
Neck Squamous Cell Carcinoma ◽  
Expression Levels

Background: Transmembrane proteins (TMEM) constitute a large family of proteins spanning the entirety of the lipid bilayer. However, there is still a lack of knowledge about their function or mechanism of action. In this study, we analyzed the expression of selected TMEM genes in patients with head and neck squamous cell carcinoma (HNSCC) to learn their role in tumor formation and metastasis. Materials and Methods: Using TCGA data, we analyzed the expression levels of different TMEMs in both normal and tumor samples and compared those two groups depending on clinical-pathological parameters. We selected four TMEMs whose expression was highly correlated with patient survival status and subjected them to further analysis. The pathway analysis using REACTOME and the gene set enrichment analysis (GSEA) were performed to evaluate the association of those TMEMs with genes involved in hallmarks of cancer as well as in oncogenic and immune-related pathways. In addition, the fractions of different immune cell subpopulations depending on TMEM expression were estimated in analyzed patients. The results for selected TMEMs were validated using GEO data. All analyses were performed using the R package, Statistica, and Graphpad Prism. Results: We demonstrated that 73% of the analyzed TMEMs were dysregulated in HNSCC and depended on tumor localization, smoking, alcohol consumption, or HPV infection. The expression levels of ANO1, TMEM156, TMEM173, and TMEM213 correlated with patient survival. The four TMEMs were also upregulated in HPV-positive patients. The elevated expression of those TMEMs correlated with the enrichment of genes involved in cancer-related processes, including immune response. Specifically, overexpression of TMEM156 and TMEM173 was associated with immune cell mobilization and better survival rates, while the elevated ANO1 expression was linked with metastasis formation and worse survival. Conclusions: In this work, we performed a panel of in silico analyses to discover the role of TMEMs in head and neck squamous cell carcinoma. We found that ANO1, TMEM156, TMEM173, and TMEM213 correlated with clinical status and immune responses in HNSCC patients, pointing them as biomarkers for a better prognosis and treatment. This is the first study describing such the role of TMEMs in HNSCC. Future clinical trials should confirm the potential of those genes as targets for personalized therapy of HNSCC.

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