scholarly journals Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma Are Molecularly Distinct

Cancers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 105
Author(s):  
Alana Sorgini ◽  
Hugh Andrew Jinwook Kim ◽  
Peter Y. F. Zeng ◽  
Mushfiq Hassan Shaikh ◽  
Neil Mundi ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Laryngeal Squamous Cell Carcinoma ◽  
Response To Therapy ◽  
The Cancer Genome Atlas ◽  
Glottic Cancer ◽  
Neural Pathways ◽  
Cancer Genome Atlas ◽  
Tcga Dataset

Laryngeal squamous cell carcinoma (LSCC) from different subsites have distinct presentations and prognosis. In this study, we carried out a multiomic comparison of LSCC subsites. The Cancer Genome Atlas (TCGA) LSCC cohort was analyzed in the R statistical environment for differences between supraglottic and glottic cancers in single nucleotide variations (SNVs), copy number alterations (CNAs), mRNA abundance, protein abundance, pathway overrepresentation, tumor microenvironment (TME), hypoxia status, and patient outcome. Supraglottic cancers had significantly higher overall and smoking-associated SNV mutational load. Pathway analysis revealed upregulation of muscle related pathways in glottic cancer and neural pathways in supraglottic cancer. Proteins involved in cancer relevant signaling pathways including PI3K/Akt/mTOR, the cell cycle, and PDL1 were differentially abundant between subsites. Glottic and supraglottic tumors have different molecular profiles, which may partially account for differences in presentation and response to therapy.

scholarly journals Integrative Analysis of TP53INP2 in Head and Neck Squamous Cell Carcinoma

2021 ◽  
Vol 12 ◽  
Author(s):  
Ruoyan Cao ◽  
Suyang Liu ◽  
Jiayu Zhang ◽  
Xianyue Ren ◽  
Xijuan Chen ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Hormone Receptors ◽  
Neck Squamous Cell Carcinoma ◽  
The Cancer Genome Atlas ◽  
Number Variation ◽  
Cancer Genome Atlas ◽  
Tcga Dataset

TP53INP2 plays an important role in regulating gene transcription and starvation-induced autophagy, however, its function in head and neck squamous cell carcinoma (HNSCC) remains unclear. Therefore, we assessed the expression and prognostic value of TP53INP2. In addition, RNAseq, miRNAseq, copy number variation, and mutation profiles from The Cancer Genome Atlas (TCGA) dataset were applied to evaluate the distinctive genomic patterns related to TP53INP2 expression. We found that TP53INP2 expression was lower in HNSCC compared with normal controls. Patients with higher TP53INP2 expression had longer survival time. Knockdown of TP53INP2 promoted cell viability. Functional analysis exhibited that TP53INP2 was linked to DNA replication, DNA repair, cell cycle, and multiple metabolic pathways. Moreover, TP53INP2 might affect the expression of multiple genes via enhancing the transcriptional activity of nuclear hormone receptors. A competing endogenous RNA (ceRNA) network consisting of 33 lncRNAs, eight miRNAs, and 13 mRNAs was constructed based on the expression of TP53INP2. Taken together, our study highlights the potential value of TP53INP2 in predicting the survival of HNSCC and its important role in the genesis and development of HNSCC.

scholarly journals Transcriptome Analysis Identifies ALCAM Overexpression as a Prognosis Biomarker in Laryngeal Squamous Cell Carcinoma

Cancers ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 470 ◽  
Author(s):  
Pedro Nicolau-Neto ◽  
Paulo Thiago de Souza-Santos ◽  
Mariana Severo Ramundo ◽  
Priscila Valverde ◽  
Ivanir Martins ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Transcriptome Analysis ◽  
Laryngeal Squamous Cell Carcinoma ◽  
The Cancer Genome Atlas ◽  
Adjacent Mucosa ◽  
Cancer Genome Atlas ◽  
Validation Set ◽  
Worse Prognosis

Background: Laryngeal squamous cell carcinoma (LSCC) is one of the most incident tumors in the world, especially in developing countries, such as Brazil. Different from other tumors, LSCC prognosis did not improve during the past four decades. Therefore, the objective of this study was to develop biomarkers that can predict LSCC patient’s prognosis. Results: Transcriptome analysis pointed out 287 overexpressed genes in LSCC in comparison to adjacent mucosa. Among these, a gene-pattern signature was created with 24 genes associated with prognosis. The Bayesian clustering of both Brazil and The Cancer Genome Atlas (TCGA) data pointed out clusters of samples possessing significative differences in the prognosis, and the expression panel of three genes (ALCAM, GBP6, and ME1) was capable to distinguish patients with worse prognosis with an accuracy of 97%. Survival analyses with TCGA data highlighted ALCAM gene expression as an independent prognostic factor for LSCC. This was further confirmed through immunohistochemistry, using a validation set of Brazilian patients. ALCAM expression was not associated with prognosis for other head and neck tumor sites. Conclusion: ALCAM overexpression seems to be an independent prognosis biomarker for LSCC patients.

Genomic Landscape of Squamous Cell Carcinoma of the Lung

2013 ◽  
pp. 348-353
Author(s):  
Daniel Morgensztern ◽  
Siddhartha Devarakonda ◽  
Ramaswamy Govindan
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Molecular Targets ◽  
The Cancer Genome Atlas ◽  
Molecular Alterations ◽  
The Past ◽  
Genomic Landscape ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Outcomes with standard therapy for patients with advanced squamous cell carcinoma (SQCC) of the lung have not improved significantly over the past decade using a predominantly empiric approach. Recent advances in pulmonary adenocarcinomas (ACs) have allowed the subdivision according to molecular subsets and the identification of specific molecular alterations that predict significant benefit from specific targeted therapies. Genomic alterations reported by The Cancer Genome Atlas (TCGA) Project identified a number of molecular targets that need to be studied systematically to improve the overall survival of patients with SQCC of the lung.

scholarly journals FOXL2 expression might be a novel prognostic biomarker in patients with laryngeal squamous cell carcinoma

2020 ◽  
Vol 48 (4) ◽  
pp. 030006052091925
Author(s):  
Jun Ge ◽  
Li Jiang ◽  
Yuke Tian ◽  
Min Zheng ◽  
Meiling Huang ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Laryngeal Squamous Cell Carcinoma ◽  
Prognostic Biomarker ◽  
Dna Amplification ◽  
Progression Free Survival ◽  
Genetic Alterations ◽  
The Cancer Genome Atlas ◽  
Gene Body

Objectives This study aimed to explore the expression profile of the Forkhead box protein L2 gene ( FOXL2) and to determine its prognostic value and associated epigenetic and genetic alterations in patients with laryngeal squamous cell carcinoma (LSCC). Materials and methods Data for a subset of patients with LSCC (N = 116) were extracted from the head and neck squamous cell carcinoma dataset of The Cancer Genome Atlas and analyzed in relation to FOXL2 expression and survival. Results Aberrant FOXL2 expression was an independent prognostic factor for progression-free survival (PFS) (hazard ratio (HR): 2.63, 95% confidence interval (CI): 1.34–5.18) and overall survival (OS) (HR: 2.39, 95%CI: 1.28–4.46). Two gene-body CpG sites (cg10554436 and cg23637494) were moderately and positively correlated with FOXL2 expression. DNA amplification (+2/+1) was common (82/115, 71%) in LSCC, and FOXL2 expression was significantly upregulated in the high-amplification group (+2) compared with copy-neutral (0) cases. Conclusion Aberrant FOXL2 expression may be a novel prognostic biomarker for PFS and OS among patients with LSCC. FOXL2 upregulation may be related to gene-body hypermethylation and DNA amplification.

scholarly journals The Study of the Expression of CGB1 and CGB2 in Human Cancer Tissues

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1082
Author(s):  
Piotr Białas ◽  
Aleksandra Śliwa ◽  
Anna Szczerba ◽  
Anna Jankowska
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Human Cancer ◽  
Germ Cell Tumors ◽  
Lung Squamous Cell Carcinoma ◽  
Cervical Squamous Cell Carcinoma ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Cancer Tissues

Human chorionic gonadotropin (hCG) is a well-known hormone produced by the trophoblast during pregnancy as well as by both trophoblastic and non-trophoblastic tumors. hCG is built from two subunits: α (hCGα) and β (hCGβ). The hormone-specific β subunit is encoded by six allelic genes: CGB3, CGB5, CGB6, CGB7, CGB8, and CGB9, mapped to the 19q13.32 locus. This gene cluster also encompasses the CGB1 and CGB2 genes, which were originally considered to be pseudogenes, but as documented by several studies are transcriptionally active. Even though the protein products of these genes have not yet been identified, based on The Cancer Genome Atlas (TCGA) database analysis we showed that the mutual presence of CGB1 and CGB2 transcripts is a characteristic feature of cancers of different origin, including bladder urothelial carcinoma, cervical squamous cell carcinoma, esophageal carcinoma, head and neck squamous cell carcinoma, ovarian serous cystadenocarcinoma, lung squamous cell carcinoma, pancreatic adenocarcinoma, rectum adenocacinoma, testis germ cell tumors, thymoma, uterine corpus endometrial carcinoma and uterine carcinosarcoma.

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