Identification of key genes in the tumor microenvironment of lung adenocarcinoma

2021 ◽  
Vol 38 (7) ◽  
Author(s):  
Wenxing Long ◽  
Qing Li ◽  
Jianfang Zhang ◽  
Hui Xie
Keyword(s):  
Tumor Microenvironment ◽  
Lung Adenocarcinoma ◽  
Key Genes

scholarly journals CCR2 and PTPRC are regulators of Tumor Microenvironment and potential prognostic biomarkers of lung adenocarcinoma

2021 ◽  
Author(s):  
Chengbang Wang ◽  
Jie Wei ◽  
DaLang Fang
Keyword(s):  
Tumor Microenvironment ◽  
Lung Adenocarcinoma ◽  
Immune Cells ◽  
Cox Regression ◽  
Γδt Cells ◽  
Cox Regression Analysis ◽  
Immune State ◽  
Protein Protein Interaction ◽  
Intersection Analysis ◽  
Key Genes

Abstract Tumor microenvironment (TME) plays an essential role in lung adenocarcinoma (LUAD) development and metastasis. With the development of TME research, it has been proved that differences in tumor-infiltrating immune cells (TICs) and gene expression profile are related to the prognosis of cancer. Our study aimed to identify key genes affecting immune state in TME of LUAD. We downloaded the RNA-seq data of LUAD cases from the TCGA database. ImmuneScore, StromalScore and ESTIMATEScore of each LUAD sample were calculated using ESTIMATE algorithm. Based on the median of different scores, LUAD samples were divided into high and low score groups. Differentially expressed genes (DEGs) between groups were obtained, and univariate Cox regression analysis and protein-protein interaction (PPI) network were used to screen shared DEGs generating in the intersection analysis. CIBORSORT algorithm was performed to calculate the relative contents of TICs for each LUAD sample, and correlation analysis between TICs and key genes was used to determine the influence of key genes to the TME. Finally, CCR2 and PTPRC, affecting the immune status of TME and the prognosis of LUAD, were acquired. Analysis based on the CIBERSORT algorithm suggested that CCR2 and PTPRC were correlated with a variety of TICs, and closely related to the clinical characteristics of the LUAD patients. Our research showed that CCR2 and PTPRC may be potential prognostic markers in LUAD, which may affect function of γδT cells and other immune cells by participating in the regulation of TME immune state.

scholarly journals Identification of key genes associated with lung adenocarcinoma by bioinformatics analysis

2021 ◽  
Vol 104 (1) ◽  
pp. 003685042199727
Author(s):  
Xinyu Wang ◽  
Jiaojiao Yang ◽  
Xueren Gao
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Lung Adenocarcinoma ◽  
Cox Regression ◽  
Enrichment Analysis ◽  
Tumor Stage ◽  
Gene Expression Omnibus ◽  
Poor Overall Survival ◽  
Key Genes ◽  
Low Expression

Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer, comprising around 40% of all lung cancer. Until now, the pathogenesis of LUAD has not been fully elucidated. In the current study, we comprehensively analyzed the dysregulated genes in lung adenocarcinoma by mining public datasets. Two sets of gene expression datasets were obtained from the Gene Expression Omnibus (GEO) database. The dysregulated genes were identified by using the GEO2R online tool, and analyzed by R packages, Cytoscape software, STRING, and GPEIA online tools. A total of 275 common dysregulated genes were identified in two independent datasets, including 54 common up-regulated and 221 common down-regulated genes in LUAD. Gene Ontology (GO) enrichment analysis showed that these dysregulated genes were significantly enriched in 258 biological processes (BPs), 27 cellular components (CCs), and 21 molecular functions (MFs). Furthermore, protein-protein interaction (PPI) network analysis showed that PECAM1, ENG, KLF4, CDH5, and VWF were key genes. Survival analysis indicated that the low expression of ENG was associated with poor overall survival (OS) of LUAD patients. The low expression of PECAM1 was associated with poor OS and recurrence-free survival of LUAD patients. The cox regression model developed based on age, tumor stage, ENG, PECAM1 could effectively predict 5-year survival of LUAD patients. This study revealed some key genes, BPs, CCs, and MFs involved in LUAD, which would provide new insights into understanding the pathogenesis of LUAD. In addition, ENG and PECAM1 might serve as promising prognostic markers in LUAD.

Mature tertiary lymphoid structures in lung adenocarcinoma are associated with better progression free survival

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S149-S149
Author(s):  
R Obeng ◽  
V Parihar ◽  
D Alexis ◽  
M Behera ◽  
T Owonikoko ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Lung Adenocarcinoma ◽  
Progression Free Survival ◽  
Germinal Centers ◽  
Disease Stage ◽  
Free Survival ◽  
Formalin Fixed Paraffin Embedded ◽  
Tertiary Lymphoid Structures ◽  
Lymphoid Structures ◽  
Lymphoid Aggregates

Abstract Introduction/Objective The presence of inducible lymphoid structures known as tertiary lymphoid structures in the tumor microenvironment has been shown to correlate with positive clinical outcome. However, the maturation states of lymphoid aggregates in lung adenocarcinoma are not completely understood. Methods/Case Report Seventy tumor samples from 69 patients diagnosed with lung adenocarcinoma (Stages I to III) between 2013 and 2015 were included in the study. The presence and maturation states of the lymphoid structures within the tumors were evaluated by conventional and 26 samples were further analyzed by multiplexed immunohistochemistry of formalin fixed paraffin embedded tissues and then quantified. Mature lymphoid follicles containing germinal centers were identified by the presence of CD21+ and BCL-6+ cells in an organized configuration within tight clusters of T and B cells. Results (if a Case Study enter NA) Samples with fully mature lymphoid structures (germinal centers) had larger tumors and higher disease stage. The number of mature lymphoid structures correlated with the total number of lymphoid aggregates present in the tumor microenvironment. Additionally, tumor samples with ≥10 mature lymphoid structures had more primary follicles. While there was no difference in overall survival, progression free survival was significantly longer in patients who had ≥10 mature lymphoid structures in comparison with patients who had <10 mature structures. Conclusion In conclusion, a spectrum of lymphoid aggregates in different stages of maturation are present in lung adenocarcinoma. An increase in the number of mature lymphoid structures may be associated with progression free survival in patients with lung adenocarcinoma.

scholarly journals Integrated analysis reveals key genes with prognostic value in lung adenocarcinoma

2018 ◽  
Vol Volume 10 ◽  
pp. 6097-6108 ◽  
Author(s):  
Ying-Jian Song ◽  
Juan Tan ◽  
Xin-Huai Gao ◽  
Li-Xin Wang
Keyword(s):  
Lung Adenocarcinoma ◽  
Prognostic Value ◽  
Integrated Analysis ◽  
Key Genes

scholarly journals Modulatory Effects of Circadian Rhythms in the Lung Adenocarcinoma Tumor Microenvironment

2021 ◽  
Author(s):  
Qianzhun Huang ◽  
Xiaoyang Su ◽  
Ning Fang ◽  
Jian Huang
Keyword(s):  
Tumor Microenvironment ◽  
Circadian Rhythms ◽  
Lung Adenocarcinoma ◽  
Circadian Clock ◽  
Drug Sensitivity ◽  
Molecular Mechanisms ◽  
Clock Genes ◽  
Functional Enrichment ◽  
Expression Levels ◽  
Circadian Clock Genes

Abstract Background: Dysregulated circadian dynamic balance is strongly associated with cancer development. However, biological functions of circadian rhythms in lung adenocarcinoma (LUAD) have not been elucidated. This study aimed at valuating the modulatory effects of circadian rhythms in the LUAD tumor microenvironment.Methods: Multiple open-source bioinformatics research platforms are used to comprehensively elucidate the expression level, prognosis, potential biological function, drug sensitivity, and immune microenvironment of circadian clock genes in LUAD.Results: Most circadian clock genes in LUAD are dysregulated and are strongly correlated with patient prognosis, and missense mutations at splicing sites of these genes. Besides, these genes are closely associated with some well-known cancer-related marker pathways, which are mainly involved in the inhibition of the Apoptosis, Cell cycle, and DNA Damage Response Pathway. Furthermore, functional enrichment analysis revealedthat circadian clock genes regulate transcription factor activities and circadian rhythms in LUAD tissues. As for drug sensitivity, high expression of CLOCK, CRY1, and NR1D2 as well as suppressedPER2 and CRY2 expression levels are associated with drug resistance. The expression levels of circadian clock genes in LUAD correlate with immune infiltration and are involved in the regulation of immunosuppression.Conclusions: Our multi-omics analysis provides a more comprehensive understanding of the molecular mechanisms of the circadian clock genes in LUAD and provides new insights for a more precise screening of prognostic biomarkers and immunotherapy.

Long non-coding RNA C5orf64 is a potential indicator for tumor microenvironment and mutation pattern remodeling in lung adenocarcinoma

Genomics ◽  
2021 ◽  
Vol 113 (1) ◽  
pp. 291-304
Author(s):  
Zhaofei Pang ◽  
Xiaowei Chen ◽  
Yu Wang ◽  
Yadong Wang ◽  
Tao Yan ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Lung Adenocarcinoma ◽  
Non Coding Rna ◽  
Potential Indicator ◽  
Mutation Pattern ◽  
Long Non Coding Rna
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