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Hnscc genomics

Esma Saada-Bouzid, Frederic Peyrade, Joel Guigay
PURPOSE OF REVIEW: The aim of this review is to summarize the current knowledge on the genomic characterization of squamous cell carcinomas of the head and neck (HNSCC) and discusses how these abnormalities could be incorporated into a therapeutic approach. RECENT FINDINGS: Tobacco and HPV infection, the two main risk factors of HNSCC, allow the definition of two groups with distinct anatomoclinical and genetic features. As tobacco and HPV infection are not exclusive, exposure to both risk factors is associated with an intermediate prognostic...
March 15, 2019: Current Opinion in Oncology
Yunbao Pan, Guohong Liu, Dujuan Wang, Yirong Li
Long non-coding RNA (lncRNA) can act as ceRNA to regulate the expression of target genes by sponging miRNAs, and therefore plays an essential role in tumor initiation and progression. However, functional roles and regulatory mechanisms of lncRNAs as ceRNAs in head and neck squamous cell carcinoma (HNSCC) remain to be determined. We downloaded RNA sequence profiles from The Cancer Genome Atlas (TCGA) database, and identified the differential RNAs by bioinformatics. Then we analyzed the biological processes of differential expressed RNAs (DER), and established their interaction networks and pathway analysis to find out potential biological effects of these DERs...
2019: Frontiers in Pharmacology
Gan-Guan Wei, Li Gao, Zheng-Yi Tang, Peng Lin, Li-Bin Liang, Jing-Jing Zeng, Gang Chen, Long-Cheng Zhang
The severe damage to health and social burden caused by head and neck squamous cell carcinoma (HNSCC) generated an urgent need to develop novel anti-cancer therapy. Currently, drug repositioning has risen in responses to the proper time as an efficient approach to invention of new anti-cancer therapies. In the present study, we aimed to screen candidate drugs for HNSCC by integrating HNSCC-related pathways from differentially expressed genes (DEGs) and drug-affected pathways from connectivity map (CMAP). We also endeavored to unveil the molecular mechanism of HNSCC through creating drug-target network and protein-to-protein (PPI) network of component DEGs in key overlapping pathways...
March 5, 2019: Pathology, Research and Practice
Yun Zhu, Xuehong Cao, Xiaomeng Zhang, Quan Chen, Lei Wen, Ping Wang
Purpose: To study the prognostic value of klotho ( KL) and its promoter DNA methylation in head and neck squamous cell carcinoma (HNSCC) and to assess their associations with the autophagy gene LC3 and the RNA transferase gene NSUN2. Materials and methods: Upper quartile normalized RNA-seq V2 RSEM values of KL mRNA and beta value for KL methylation were retrieved from The Cancer Genome Atlas HNSCC dataset. Kaplan-Meier survival curves were used to assess the associations of KL expression and methylation with patient survival; multivariate Cox proportional hazards regression models were used to estimate the HRs and their 95% CIs...
2019: Cancer Management and Research
Jinkyung Kim, Sung-Min Kang, Su Young Oh, Heon-Jin Lee, Inhan Lee, Jae-Chan Hwang, Su-Hyung Hong
NGFI-A binding protein 2 (NAB2) represses the transcriptional activation of early growth response protein-1 (EGR1), a tumor-suppressor. However, Epidermal Growth Factor (EGF) promotes tumor progression even with significant EGR1 upregulation. The molecular mechanism through which NAB2 is involved in cancer is largely unknown. Therefore, we evaluated how the NAB2-mediated suppression of EGR1 facilitates head and neck squamous cell carcinoma (HNSCC) cancer progression, in association with Sp1, which competes with EGR1 as a transcriptional regulator...
March 6, 2019: Cancers
Chongchang Zhou, Jinyun Li, Qun Li, Huigao Liu, Dong Ye, Zhenhua Wu, Zhisen Shen, Hongxia Deng
BACKGROUND: The purpose of the current study was to assess the association between HOXA9 (homeobox A9) promoter methylation and head and neck squamous cell carcinoma (HNSCC) and its diagnostic value. METHODS: Quantitative methylation-specific PCR (qMSP) was applied to measure HOXA9 promoter methylation levels in 145 paired HNSCC and corresponding normal tissue samples. Data from the Cancer Genome Atlas (TCGA) database (n = 578; 528 HNSCC and 50 normal) were also analyzed...
March 6, 2019: Journal of Clinical Laboratory Analysis
Shuang Bai, Ping Zhang, Jian-Cheng Zhang, Jun Shen, Xu Xiang, Ying-Bin Yan, Zhen-Qi Xu, Jun Zhang, Li Long, Chao Wang, Ping Shi, Li Yang, Wei Chen, Hao Liu
BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) has a poor prognosis that has not significantly improved in the past several decades. A prognostic-related signature was needed. METHODS: The Cancer Genome Atlas and GSE41613 databases were downloaded as a training and validation set, respectively. We identified 12 genes that demonstrated progression and prognostic value, and then, a gene signature was constructed. RESULTS: This classification could reflect distinct characteristics, phenotypically and molecularly, among HNSCC tumors...
March 6, 2019: Head & Neck
Ksenija Božinović, Ivan Sabol, Emil Dediol, Nina Milutin Gašperov, Spomenka Manojlović, Zuzana Vojtechova, Ruth Tachezy, Magdalena Grce
Head and neck cancer is the sixth most common malignancy worldwide, predominantly developing from squamous cell epithelia (HNSCC). The main HNSCC risk factors are tobacco, excessive alcohol use, and the presence of human papillomavirus (HPV). HPV positive (+) cancers are etiologically different from other HNSCC and often show better prognosis. The current knowledge regarding HNSCC miRNA profiles is still incomplete especially in the context of HPV+ cancer. Thus, we analyzed 61 freshly collected primary oral (OSCC) and oropharyngeal (OPSCC) SCC samples...
February 19, 2019: Scientific Reports
Anthony Saleh, Hui Cheng, Scott E Martin, Han Si, Pinar Ormanaglu, Sophie G Carlson, Paul E Clavijo, Xinping Yang, Rita Das, Shaleeka Cornelius, Jamie Coupar, Douglas B Chepeha, Ludmila Danilova, Thomas M Harris, Michael B Prystowsky, Geoffrey Childs, Richard V Smith, Gordon Robertson, Steven Jm Jones, Andrew D Cherniack, Sang-Soo Kim, Antonina Rait, Kathleen F Pirollo, Esther H Chang, Zhong Chen, Carter Van Waes
PURPOSE: To identify deregulated and inhibitory microRNAs (miRNA, miR), and generate novel mimics for replacement nanomedicine for head and neck squamous cell carcinomas (HNSCC). EXPERIMENTAL DESIGN: We integrated miRNA and mRNA expression, copy number variation, and DNA methylation results from The Cancer Genome Atlas (TCGA), with a functional genome-wide screen. RESULTS: We reveal that the miR-30 family is commonly repressed, and all 5 members sharing these seed sequence similarly inhibit HNSCC proliferation in vitro...
February 5, 2019: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Julius Moratin, Stefan Hartmann, Roman C Brands, Dominik Horn, Andreas Fuchs, Grit Mutzbauer, Axel Seher, Claus Scholz, Urs D A Müller-Richter, Christian Linz
OBJECTIVES: Locoregional disease recurrence and metastatic events are the leading causes of death and the most important prognostic factors in patients with head and neck squamous cell carcinoma (HNSCC). A major goal of oncology is the identification of clinical and molecular parameters to evaluate the individual risk of recurrence. MicroRNAs (miRNAs) have been shown to correlate well with tumor size and differentiation. Therefore, they are candidate biomarkers for estimating clinical outcomes...
March 2019: Journal of Cranio-maxillo-facial Surgery
Neeraja M Krishnan, Mohanraj I, Janani Hariharan, Binay Panda
PURPOSE: With large amounts of multidimensional molecular data on cancers generated and deposited into public repositories such as The Cancer Genome Atlas and International Cancer Genome Consortium, a cancer type agnostic and integrative platform will help to identify signatures with clinical relevance. We devised such a platform and showcase it by identifying a molecular signature for patients with metastatic and recurrent (MR) head and neck squamous cell carcinoma (HNSCC). METHODS: We devised a statistical framework accompanied by a graphical user interface-driven application, Clinical Association of Functionally Established MOlecular CHAnges ( CAFE MOCHA; https://github...
December 2018: JCO Clinical Cancer Informatics
Guo-Rung You, Ann-Joy Cheng, Li-Yu Lee, Yu-Chen Huang, Hsuan Liu, Yin-Ju Chen, Joseph T Chang
BACKGROUND: Radiotherapy is an indispensable treatment modality in head and neck cancer (HNC), while radioresistance is the major cause of treatment failure. The aim of this study is to identify a prognostic molecular signature associated with radio-resistance in HNC for further clinical applications. METHODS: Affymetrix cDNA microarrays were used to globally survey different transcriptomes between HNC cell lines and isogenic radioresistant sublines. The KEGG and Partek bioinformatic analytical methods were used to assess functional pathways associated with radioresistance...
January 14, 2019: BMC Cancer
Farhad Ghasemi, Stephenie D Prokopec, Danielle MacNeil, Neil Mundi, Steven F Gameiro, Christopher Howlett, William Stecho, Paul Plantinga, Nicole Pinto, Kara M Ruicci, Mohammed Imran Khan, John Yoo, Kevin Fung, Axel Sahovaler, David A Palma, Eric Winquist, Joe S Mymryk, John W Barrett, Paul C Boutros, Anthony C Nichols
Smoking has historically been recognized as a negative prognostic factor in head and neck squamous cell carcinoma (HNSCC). This study aimed to assess the mutational differences between heavy smokers (>20 pack years) and never smokers among the HNSCC patients within The Cancer Genome Atlas (TCGA). Single nucleotide variation and copy number aberration differences between heavy smokers and never smokers were compared within human papillomavirus-positive (HPV-positive) (n = 67) and HPV-negative (n = 431) TCGA cohorts with HNSCC, and the impact of these mutations on survival were assessed...
January 10, 2019: JCI Insight
Ling-Ying Wei, Jang-Jaer Lee, Chiou-Yueh Yeh, Chia-Ju Yang, Sang-Heng Kok, Jenq-Yuh Ko, Feng-Chiao Tsai, Jean-San Chia
OBJECTIVES: Crosstalk between cancer cells and carcinoma-associated fibroblasts (CAFs) is known to be involved in various aspects of tumor biology, including during invasion. Using oral squamous cell carcinoma (OSCC) cells as a model, we examined whether and how CAFs respond to inflammatory signals to influence cancer cell migration and invasion. MATERIALS AND METHODS: Chemokine signatures within the human HNSCC datasets from The Cancer Genome Atlas (TCGA) were analyzed together with tissue assessment using immunohistochemical staining (IHC) and real-time PCR...
January 2019: Oral Oncology
Musaffe Tuna, Christopher I Amos, Gordon B Mills
Smoking and alcohol intake are major risk factors in head and neck squamous cell carcinomas (HNSCCs). Although the link between TP53 mutation and smoking has been well established, very little is known about the link between acquired uniparental disomy (aUPD) and smoking and/or alcohol consumption or other clinical characteristics. We used TCGA genomic data to investigate whether smoking, alcohol intake, clinical and demographic variables, HPV status and TP53 mutation are associated with aUPD at specific chromosomal regions...
January 4, 2019: Neoplasia: An International Journal for Oncology Research
Tuna Toptan, Marion G Brusadelli, Brian Turpin, David P Witte, Jordi Surrallés, Eunike Velleuer, Martin Schramm, Ralf Dietrich, Ruud H Brakenhoff, Patrick S Moore, Yuan Chang, Susanne I Wells
Fanconi anemia is a rare genome instability disorder with extreme susceptibility to squamous cell carcinoma of the head and neck and anogenital tract. In patients with this inherited disorder, the risk of head and neck cancer is 800-fold higher than in the general population, a finding which might suggest a viral etiology. Here, we analyzed the possible contribution of human polyomaviruses to FA-associated head and neck squamous cell carcinoma (HNSCC) by a pan-polyomavirus immunohistochemistry test which detects the T antigens of all known human polyomaviruses...
2018: PloS One
Xue Xu, Mengzhi Li, Jun Hu, Zheng Chen, Jinyu Yu, Yan Dong, Chengtao Sun, Junqing Han
Aim: The aim of this study is to identify a gene prognostic signature for the head-and-neck squamous cell carcinoma (HNSCC). HNSCC is one of the most common malignancies worldwide; however, the molecular mechanisms underlying the malignancy are unclear. Materials and Methods: We analyzed the gene expression profiles of GSE2379, GSE53819, and GSE59102 derived from the gene expression omnibus, and the cancer genome atlas (TCGA) HNSC databases. The R software was used to identify the differentially expressed genes (DEGs) between HNSCC tissues and normal controls...
2018: Journal of Cancer Research and Therapeutics
Saisai Tian, Guofeng Meng, Weidong Zhang
Background: Transcriptional dysregulation is one of the most important features of cancer genesis and progression. Applying gene expression dysregulation information to predict the development of cancers is useful for cancer diagnosis. However, previous studies mainly focused on the relationship between a single gene and cancer. Prognostic prediction using combined gene models remains limited. Materials and methods: Gene expression profiles were downloaded from The Cancer Genome Atlas and the data sets were randomly divided into training data sets and test data sets...
2019: Cancer Management and Research
Robert Hollows, Wenbin Wei, Jean-Baptiste Cazier, Hisham Mehanna, Gabriella Parry, Graham Halford, Paul Murray
BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is more prevalent in men than women and this disparity cannot be fully explained by known risk factors. Recent studies have shown that loss of Y chromosome (LoY) confers an increased risk of solid cancer and reduces life expectancy in men. METHODS: Using publicly available data from The Cancer Genome Atlas, we investigated the prevalence of LoY and its association with clinicopathological features in male HNSCC...
December 23, 2018: Head & Neck
Ariel L Hernandez, Ying Wang, Hilary L Somerset, Stephen B Keysar, Dara L Aisner, Carrie Marshall, Daniel W Bowles, Sana D Karam, David Raben, Antonio Jimeno, Marileila Varella-Garcia, Xiao-Jing Wang
Reports regarding the frequency of SMAD4 loss in human head and neck squamous cell carcinoma (HNSCC) vary significantly. We have shown that SMAD4 deletion contributes to HNSCC initiation and progression. Therefore, accurately detecting genetic SMAD4 loss is critical to determine prognosis and therapeutic interventions in personalized medicine. We developed a SMAD4 fluorescence in situ hybridization (FISH) assay to identify chromosomal SMAD4 loss at the single cell level of primary HNSCC specimens and patient derived xenograft (PDX) tumors derived from HNSCCs...
December 21, 2018: Molecular Carcinogenesis
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