CCR2 and PTPRC are regulators of tumor microenvironment and potential prognostic biomarkers of lung adenocarcinoma

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.

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Modulatory Effects of Circadian Rhythms in the Lung Adenocarcinoma Tumor Microenvironment

10.21203/rs.3.rs-838444/v1 ◽

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.

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Identification of CDKN3 and UBE2C mRNAs as Prognostic Biomarkers in Early-Stage Lung Adenocarcinoma Using Bioinformatics Strategy

Iranian Red Crescent Medical Journal ◽

10.5812/ircmj.86174 ◽

2019 ◽

Vol In Press (In Press) ◽

Author(s):

Qiang Chen ◽

Lutong Xu ◽

Jing Hu ◽

Tonglian Wang ◽

Kang Zhang ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Early Stage ◽

Prognostic Biomarkers

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High expression of MCM10 is predictive of poor outcomes in lung adenocarcinoma

PeerJ ◽

10.7717/peerj.10560 ◽

2021 ◽

Vol 9 ◽

pp. e10560

Author(s):

Mingrui Shao ◽

Shize Yang ◽

Siyuan Dong

Keyword(s):

Lung Adenocarcinoma ◽

Complex Disease ◽

Enrichment Analysis ◽

Integrated Approach ◽

Replication Initiation ◽

Prognostic Biomarkers ◽

Normal Lung ◽

Pathway Enrichment Analysis ◽

Therapeutic Value

Backgrounds Lung adenocarcinoma is a complex disease that results in over 1.8 million deaths a year. Recent advancements in treating and managing lung adenocarcinoma have led to modest decreases in associated mortality rates, owing in part to the multifactorial etiology of the disease. Novel prognostic biomarkers are needed to accurately stage the disease and act as the basis of adjuvant treatments. Material and Methods The microarray datasets GSE75037, GSE31210 and GSE32863 were downloaded from the Gene Expression Omnibus (GEO) database to identify prognostic biomarkers for lung adenocarcinoma and therapy. The differentially expressed genes (DEGs) were identified by GEO2R. Functional and pathway enrichment analysis were performed by Kyoto Encyclopedia of Genes and Genomes and Gene Ontology (GO). Validation was performed based on 72 pairs of lung adenocarcinoma and adjacent normal lung tissues. Results Results showed that the DEGs were mainly focused on cell cycle and DNA replication initiation. Forty-one hub genes were identified and further analyzed by CytoScape. Here, we provide evidence which suggests MCM10 is a potential target with prognostic, diagnostic and therapeutic value. We base this on an integrated approach of comprehensive bioinformatics analysis and in vitro validation using the A549 lung adenocarcinoma cell line. We show that MCM10 overexpression correlates with a poor prognosis, while silencing of this gene decreases aberrant growth by 2-fold. Finally, evaluation of 72 clinical biopsy samples suggests that overexpression of MCM10 in the lung adenocarcinoma highly correlates with larger tumor size. Together, this work suggests that MCM10 may be a clinically relevant gene with both predictive and therapeutic value in lung adenocarcinoma.

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

Genomics ◽

10.1016/j.ygeno.2020.12.010 ◽

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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Identification of immune-related gene signature predicting survival in the tumor microenvironment of lung adenocarcinoma

Immunogenetics ◽

10.1007/s00251-020-01189-z ◽

2020 ◽

Vol 72 (9-10) ◽

pp. 455-465

Author(s):

Mengnan Zhao ◽

Ming Li ◽

Zhencong Chen ◽

Yunyi Bian ◽

Yuansheng Zheng ◽

...

Keyword(s):

Tumor Microenvironment ◽

Lung Adenocarcinoma ◽

Gene Signature ◽

Related Gene ◽

Immune Related Gene

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Identification of a 5-Gene Metabolic Signature for Predicting Prognosis Based on an Integrated Analysis of Tumor Microenvironment in Lung Adenocarcinoma

Journal of Oncology ◽

10.1155/2020/5310793 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12 ◽

Cited By ~ 1

Author(s):

Xiaolin Yu ◽

Xiaomei Zhang ◽

Yanxia Zhang

Keyword(s):

Tumor Microenvironment ◽

Confidence Interval ◽

Lung Adenocarcinoma ◽

Cox Regression ◽

External Validation ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Integrated Analysis ◽

Lasso Regression ◽

The Status

Lung adenocarcinoma (LUAD) is a common subtype of lung cancer with a depressing survival rate. The reprogramming of tumor metabolism was identified as a new hallmark of cancer in tumor microenvironment (TME), and we made a comprehensive exploration to reveal the prognostic role of the metabolic-related genes. Transcriptome profiling data of LUAD were, respectively, downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. Based on the extracted metabolic-related genes, a novel 5-gene metabolic prognostic signature (including GNPNAT1, LPGAT1, TYMS, LDHA, and PTGES) was constructed by univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression. This signature confirmed its robustness and accuracy by external validation in multiple databases. It could be an independent risk factor for LUAD, and the nomograms possessed moderately accurate performance with the C-index of 0.755 (95% confidence interval: 0.706–0.804) and 0.691 (95% confidence interval: 0.636–0.746) in training set and testing set. This signature could reveal the metabolic features according to the results of gene set enrichment analysis (GSEA) and meanwhile monitor the status of TME through ESTIMATE scores and the infiltration levels of immune cells. In conclusion, this gene signature is a cost-effective tool which could indicate the status of TME to provide more clues in the exploration of new diagnostic and therapeutic strategy.

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