scholarly journals Diagnosis value of aberrantly expressed microRNA profiles in lung squamous cell carcinoma: a study based on the Cancer Genome Atlas

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4101 ◽  
Author(s):  
Sheng Yang ◽  
Jing Sui ◽  
Geyu Liang
Keyword(s):  
Lung Cancer ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Bioinformatics Analysis ◽  
Lung Squamous Cell Carcinoma ◽  
Clinical Information ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Background Lung cancer is considered as one of the most frequent and deadly cancers with high mortality all around the world. It is critical to find new biomarkers for early diagnosis of lung cancer, especially lung squamous cell carcinoma (LUSC). The Cancer Genome Atlas (TCGA) is a database which provides both cancer and clinical information. This study is a comprehensive analysis of a novel diagnostic biomarker for LUSC, based on TCGA. Methods and Results The present study investigated LUSC-specific key microRNAs (miRNAs) from large-scale samples in TCGA. According to exclusion criteria and inclusion criteria, the expression profiles of miRNAs with related clinical information of 332 LUSC patients were obtained. Most aberrantly expressed miRNAs were identified between tumor and normal samples. Forty-two LUSC-specific intersection miRNAs (fold change >2, p < 0.05) were obtained by an integrative computational method, among them six miRNAs were found to be aberrantly expressed concerning characteristics of patients (gender, lymphatic metastasis, patient outcome assessment) through Student t-test. Five miRNAs correlated with overall survival (log-rank p < 0.05) were obtained through the univariate Cox proportional hazards regression model and Mantel–Haenszel test. Then, five miRNAs were randomly selected to validate the expression in 47 LUSC patient tissues using quantitative real-time polymerase chain reaction. The results showed that the test findings were consistent with the TCGA findings. Also, the diagnostic value of the specific key miRNAs was determined by areas under receiver operating characteristic curves. Finally, 577 interaction mRNAs as the targets of 42 LUSC-specific intersection miRNAs were selected for further bioinformatics analysis. Conclusion This study indicates that this novel microRNA expression signature may be a useful biomarker of the diagnosis for LUSC patients, based on bioinformatics analysis.

A seven long-noncoding RNA signature predicts prognosis of lung squamous cell carcinoma

2020 ◽  
Vol 14 (1) ◽  
pp. 53-63
Author(s):  
Shuai Li ◽  
Yue Teng ◽  
Min-Jie Yuan ◽  
Ting-Ting Ma ◽  
Jian Ma ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Noncoding Rna ◽  
Lung Squamous Cell Carcinoma ◽  
Mapk Signaling ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Aim: This study profiled differentially expressed long noncoding RNAs (lncRNAs) in lung squamous cell carcinoma (LSCC) to predict LSCC overall survival (OS) using The Cancer Genome Atlas data. Materials & methods: The RNA-seq and clinical dataset of 475 LSCC patients was retrieved from The Cancer Genome Atlas database and statistically analyzed. Results: There were 67 upregulated and 32 downregulated lncRNAs in LSCCs and 12 lncRNAs associated with OS. The seven-lncRNA signature was associated with poor OS and RP11-150O12.6 and CTA-384D8.35 were associated with better OS (p < 0.001). The seven lncRNAs-mRNA interaction network analysis showed their association with 187 protein-coding genes for cancer development, cell migration, adhesion, proliferation, apoptosis, angiogenesis and the MAPK signaling pathways. Conclusion: This seven-lncRNA signature is useful to predict LSCC OS.

scholarly journals ZCCHC24 is a Prognostic-related Biomarker and Correlated with Immune Infiltrates in Gastric Cancer and Lung Squamous Cell Carcinoma

2021 ◽  
Author(s):  
Jiahuang Huang ◽  
Qinhui Zhang ◽  
Wei Li ◽  
Jianchang Shu
Keyword(s):  
Gastric Cancer ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Immune Cell ◽  
Lung Squamous Cell Carcinoma ◽  
The Cancer Genome Atlas ◽  
Immune Cell Infiltration ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Abstract Background: ZCCHC24 is one of alternative splicing factors which affect immune cell infiltration, but the mechanisms whereby it drives immune infiltration in cancer remain uncertain. Methods: ZCCHC24 expression was analyzed via the Oncomine database and Tumor Immune Estimation Resource (TIMER) site. We evaluated the influence of ZCCHC24 on clinical prognosis using Kaplan-Meier plotter, the PrognoScan database and Gene Expression Profiling Interactive Analysis (GEPIA). The correlations between ZCCHC24 and cancer immune infiltrates was investigated via TIMER. In addition, correlations between ZCCHC24 expression and gene marker sets of immune infiltrates were analyzed by TIMER and GEPIA.Results: ZCCHC24 significantly impacts the prognosis of diverse cancers via The Cancer Genome Atlas (TCGA). elevated ZCCHC24 expression was significantly correlated with poor OS and progression-free survival (PFS) in gastric cancers (OS HR = 2.11, P = 6.3e-12; PFS HR = 2.03, P = 3.1e-11). Moreover, ZCCHC24 significantly impacts the prognosis of diverse cancers via The Cancer Genome Atlas (TCGA). Specifically, high ZCCHC24 expression was correlated with worse OS and PFS in Stage, T stage, N stage, M stage, Lauren classification and differentiation of gastric cancer patients. ZCCHC24 expression was positively correlated with infiltrating levels of CD4+ T，CD8+ T cells, Macrophages, Neutrophils and dendritic cells (DCs) in stomach adenocarcinoma (STAD) and lung squamous cell carcinoma (LUSC). ZCCHC24 expression showed strong correlations with diverse immune marker sets in STAD and LUSC.Conclusions: These findings suggest that ZCCHC24 is a key factor which governs immune cell recruitment to gastric cancer and lung squamous cell carcinoma, potentially playing a vital role in governing immune cell infiltration and thus representing a valuable prognostic biomarker in gastric cancer and lung squamous cell carcinoma patients.

scholarly journals UBE2D1 RNA Expression Was an Independent Unfavorable Prognostic Indicator in Lung Adenocarcinoma, but Not in Lung Squamous Cell Carcinoma

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Liyan Hou ◽  
Yingbo Li ◽  
Ying Wang ◽  
Dongqiang Xu ◽  
Hailing Cui ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Squamous Cell Carcinoma ◽  
Lung Adenocarcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Survival Data ◽  
Lung Squamous Cell Carcinoma ◽  
Prognostic Indicator ◽  
The Cancer Genome Atlas ◽  
Rna Expression

In this study, we investigated the potential prognostic value of ubiquitin-conjugating enzyme E2D1 (UBE2D1) RNA expression in different histological subtypes of non-small-cell lung cancer (NSCLC). A retrospective study was performed by using molecular, clinicopathological, and survival data in the Cancer Genome Atlas (TCGA)—Lung Cancer. Results showed that both lung adenocarcinoma (LUAD) (N=514) and lung squamous cell carcinoma (LUSC) (N=502) tissues had significantly elevated UBE2D1 RNA expression compared to the normal tissues (p<0.001 and p=0.036, respectively). UBE2D1 RNA expression was significantly higher in LUAD than in LUSC tissues. Increased UBE2D1 RNA expression was independently associated with shorter OS (HR: 1.359, 95% CI: 1.031–1.791, p=0.029) and RFS (HR: 1.842, 95% CI: 1.353–2.508, p<0.001) in LUAD patients, but not in LUSC patients. DNA amplification was common in LUAD patients (88/551, 16.0%) and was associated with significantly upregulated UBE2D1 RNA expression. Based on these findings, we infer that UBE2D1 RNA expression might only serve as an independent prognostic indicator of unfavorable OS and RFS in LUAD, but not in LUSC.

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.

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