Circular RNAs expression profiles in plasma exosomes from early‐stage lung adenocarcinoma and the potential biomarkers

2019 ◽  
Vol 121 (3) ◽  
pp. 2525-2533 ◽  
Author(s):  
Falin Chen ◽  
Chunli Huang ◽  
Qiumei Wu ◽  
Lili Jiang ◽  
Shaoting Chen ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Early Stage ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Potential Biomarkers

scholarly journals A circular RNAs dataset landscape reveals potential signatures for the detection and prognosis of early-stage lung adenocarcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhiying Chen ◽  
Jiahui Wei ◽  
Min Li ◽  
Yongjuan Zhao
Keyword(s):  
Functional Analysis ◽  
Survival Analysis ◽  
Lung Adenocarcinoma ◽  
Target Genes ◽  
Interaction Analysis ◽  
Early Stage ◽  
Gene Interaction ◽  
Gene Expression Omnibus ◽  
Circular Rnas ◽  
Cerna Network

Abstract Background This study aimed to identify potential circular ribonucleic acid (circRNA) signatures involved in the pathogenesis of early-stage lung adenocarcinoma (LAC). Methods The circRNA sequencing dataset of early-stage LAC was downloaded from the Gene Expression Omnibus database. First, the differentially expressed circRNAs (DEcircRNAs) between tumour and non-tumour tissues were screened. Then, the corresponding miRNAs and their target genes were predicted. In addition, prognosis-related genes were identified using survival analysis and further used to build a network of competitive endogenous RNAs (ceRNAs; DEcircRNA–miRNA–mRNA). Finally, the functional analysis and drug–gene interaction analysis of mRNAs in the ceRNA network was performed. Results A total of 35 DEcircRNAs (30 up-regulated and 5 down-regulated circRNAs) were identified. Moreover, 135 DEcircRNA–miRNA and 674 miRNA–mRNA pairs were predicted. The survival analysis of these target mRNAs revealed that 60 genes were significantly associated with survival outcomes in early-stage LAC. Of these, high levels of PSMA 5 and low levels of NAMPT, CPT 2 and TNFSF11 exhibited favourable prognoses. In addition, the DEcircRNA–miRNA–mRNA network was constructed, containing 5 miRNA–circRNA (hsa_circ_0092283/hsa-miR-762/hsa-miR-4685-5p; hsa_circ_0070610/hsa-let-7a-2-3p/hsa-miR-3622a-3p; hsa_circ_0062682/hsa-miR-4268) and 60 miRNA–mRNA pairs. Functional analysis of the genes in the ceRNA network showed that they were primarily enriched in the Wnt signalling pathway. Moreover, PSMA 5, NAMPT, CPT 2 and TNFSF11 had strong correlations with different drugs. Conclusion Three circRNAs (hsa_circ_0062682, hsa_circ_0092283 and hsa_circ_0070610) might be potential novel targets for the diagnosis of early-stage LAC.

scholarly journals Exploring potential biomarkers for lung adenocarcinoma using LC-MS/MS metabolomics

2020 ◽  
Vol 48 (4) ◽  
pp. 030006051989721
Author(s):  
Liang Mo ◽  
Bing Wei ◽  
Renji Liang ◽  
Zhi Yang ◽  
Shouzhi Xie ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Carbon Metabolism ◽  
Lung Tumor ◽  
Early Stage ◽  
Characteristic Curve ◽  
Central Carbon Metabolism ◽  
Tissue Samples ◽  
Diagnosis And Prognosis ◽  
Central Carbon ◽  
Potential Biomarkers

Background The average 5-year survival rate of lung adenocarcinoma patients is only 15% to 17%, which is primarily due to late-stage diagnosis and a lack of specific prognostic evaluations that can recommend effective therapies. Additionally, there is no clinically recognized biomarker that is effective for early-stage diagnosis. Methods Tissue samples from 10 lung adenocarcinoma patients (both tumor and non-tumor tissues) and 10 benign lung tumor samples were collected. The significantly differentially represented metabolites from the three groups were analyzed by liquid chromatography and tandem mass spectrometry. Results Pathway analysis indicated that central carbon metabolism was the top altered pathway in lung adenocarcinoma, while protein digestion and absorption, and central carbon metabolism were the top altered pathways in benign lung tumors. Receiver operating characteristic curve analysis revealed that adenosine 3′-monophosphate, creatine, glycerol, and 14 other differential metabolites were potential sensitive and specific biomarkers for the diagnosis and prognosis of lung adenocarcinoma. Conclusion Our findings suggest that the metabolomics approach may be a useful method to detect potential biomarkers in lung adenocarcinoma patients.

scholarly journals CircKEAP1 serves as a ceRNA to suppress lung adenocarcinoma progression by activating KEAP1 signal pathway

2020 ◽  
Author(s):  
Yanbo Wang ◽  
Fenghai Ren ◽  
Dawei Sun ◽  
Jing Liu ◽  
BenKun Liu ◽  
...  
Keyword(s):  
Tumor Growth ◽  
Lung Adenocarcinoma ◽  
Expression Profiles ◽  
Signal Pathway ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Tumor Tissues ◽  
Rna Immunoprecipitation

Abstract BackgroundCircular RNAs (circRNAs) are widely expressed noncoding RNAs, and plays a key role in the biological function of competitive endogenous RNA (ceRNA) network in various human diseases, especially in cancer. However, the regulatory roles of circRNAs in lung adenocarcinoma (LUAD) remains largely unknown. MethodsThe expression profiles of circRNAs in LUAD tissues and adjacent non-tumor tissues were analyzed by Agilent Arraystar Human CircRNA microarray. The level and prognostic values of circKEAP1 in tissues and cancer cell lines were determined by quantitative real-time PCR. Then, the effects of circKEAP1 on tumor growth were investigated by functional experiments in vitro and in vivo. Mechanistically, dual luciferase reporter assay, RNA pull-down and RNA immunoprecipitation experiments were performed to confirm the interaction between circKEAP1 and miR-141-3p in LUAD.ResultsWe found circKEAP1 was significantly downregulated in LUAD tissues, and repressed tumor growth both in vitro and in vivo. Mechanistically, circKEAP1 competitively binds to miR-141-3p and relive miR-141-3p repression for its target gene KEAP1, which activated the KEAP1/NRF2 signal pathway, and finally suppress the cell proliferation.ConclusionsOur findings suggest that circKEAP1 inhibits LUAD progression through circKEAP1/miR-141-3p/KEAP1 axis and it may serve as a new target for treatment of LUAD patients.

scholarly journals Screening Circular RNA Related to Vascular Endothelial Proliferation, Migration and Angiogenesis in Spinal Cord Injury by RNA Sequencing

2020 ◽  
Author(s):  
Xin Ye ◽  
Yilei Chen ◽  
Jiasheng Wang ◽  
Jian Chen ◽  
Ying Yao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spinal Cord ◽  
Spinal Cord Injury ◽  
Early Stage ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Circular Rnas ◽  
Vascular Endothelial ◽  
Endothelial Proliferation ◽  
Cord Injury

Abstract Background: Traumatic spinal cord injury (SCI) causes high rates of worldwide morbidity because of the complex secondary injury. Circular RNAs (circRNAs) are a novel class of endogenous non-coding RNAs, which have recently been recognized as important regulators of gene expression and pathological processes. In this study, we have attempted to elucidate the expression profiles of circRNAs in a mouse model of SCI and comprehensively understand vascular endothelial proliferation, migration and angiogenesis in the early stage of secondary injury.Methods: Deep RNA sequencing (RNA-seq) and bioinformatic analysis including GO enrichment analysis, KEGG pathway analysis and circRNA-miRNA-mRNA network construction were performed to investigate the expression patterns of circRNAs in mouse spinal cord after SCI (n= 3 per group) for three days and explore the differentially expressed circRNAs related to vascular endothelial proliferation, migration and angiogenesis. Results: Total of 1288 circRNAs were altered (>2-fold change, p<0.05) in the spinal cord after SCI, including 991 were upregulated and 297 were downregulated. Meanwhile we constructed a circRNA-mRNA network to predict their functions for circRNAs can act as “miRNA sponges”,. We next analyzed the altered circRNAs related to vascular endothelial proliferation, migration and angiogenesis by GO and KEGG analyses. 121 circRNAs were found to correlating to vascular endothelial proliferation，migration and angiogenesis in spinal cord after SCI. Conclusions: Our results reveal that circRNAs locally regulate their related protein-gene expression and play key roles in the vascular endothelial proliferation, migration and angiogenesis of SCI.

scholarly journals Mutational Pattern in Multiple Pulmonary Nodules Are Associated With Early Stage Lung Adenocarcinoma

2021 ◽  
Vol 10 ◽  
Author(s):  
Shao-wei Dong ◽  
Rong Li ◽  
Zhiqiang Cheng ◽  
Dong-cheng Liu ◽  
Jinquan Xia ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Lung Adenocarcinoma ◽  
Signaling Pathways ◽  
Structural Changes ◽  
Early Stage ◽  
Expression Profiles ◽  
Single Gene ◽  
Gene Expression Profiles ◽  
Pulmonary Nodules ◽  
Multiple Pulmonary Nodules

The clinical significance of mutation in multiple pulmonary nodules is largely limited by single gene mutation-directed analysis and lack of validation of gene expression profiles. New analytic strategy is urgently needed for comprehensive understanding of genomic data in multiple pulmonary nodules. In this study, we performed whole exome sequencing in 16 multiple lung nodules and 5 adjacent normal tissues from 4 patients with multiple pulmonary nodules and decoded the mutation information from a perspective of cellular functions and signaling pathways. Mutated genes as well as mutation patterns shared in more than two lesions were identified and characterized. We found that the number of mutations or mutated genes and the extent of protein structural changes caused by different mutations is positively correlated with the degree of malignancy. Moreover, the mutated genes in the nodules are associated with the molecular functions or signaling pathways related to cell proliferation and survival. We showed a developing pattern of quantity (the number of mutations/mutated genes) and quality (the extent of protein structural changes) in multiple pulmonary nodules. The mutation and mutated genes in multiple pulmonary nodules are associated with cell proliferation and survival related signaling pathways. This study provides a new perspective for comprehension of genomic mutational data and might shed new light on deciphering molecular evolution of early stage lung adenocarcinoma.

Three differential expression profiles of miRNAs as potential biomarkers for lung adenocarcinoma

2018 ◽  
Vol 507 (1-4) ◽  
pp. 377-382 ◽  
Author(s):  
Rongjiong Zheng ◽  
Wenjie Mao ◽  
Zhennan Du ◽  
Jun Zhang ◽  
Mingming Wang ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Differential Expression ◽  
Expression Profiles ◽  
Potential Biomarkers

TRIM58 is a prognostic biomarker remodeling tumor microenvironment in KRAS-driven lung adenocarcinoma

2021 ◽  
Author(s):  
Xiaowei Chen ◽  
Yu Wang ◽  
Xiao Qu ◽  
Fenglong Bie ◽  
Yadong Wang ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Lung Adenocarcinoma ◽  
Prognostic Biomarker ◽  
Expression Profiles ◽  
The Cancer Genome Atlas ◽  
Follicular Helper ◽  
Follicular Helper T Cell ◽  
Cancer Genome Atlas ◽  
Genome Atlas ◽  
Potential Biomarkers

Aim: To comprehensively analyze the expression profiles of ubiquitin-related genes (URGs) and determine potential biomarkers in KRAS-driven lung adenocarcinoma (LUAD). Materials & methods: Differential expression analyses were performed between KRAS-wild and KRAS-mutant LUAD samples from The Cancer Genome Atlas database, and 34 URGs were screened out. ESTIMATE and CIBERSORT methods were used to calculate the ratio of immune and stromal components. Results & conclusion: TRIM58 was positively correlated with abundances of M2 macrophages and resting mast cells and negatively correlated with follicular helper T-cell abundances in KRAS-driven LUAD. TRIM58 was a potential prognosis-associated indicator for tumor microenvironment modulation and played a key role in TME-specific AS landscapes alterations in KRAS-driven LUAD.

scholarly journals Identifying and Validating Potential Biomarkers of Early Stage Lung Adenocarcinoma Diagnosis and Prognosis

2021 ◽  
Vol 11 ◽  
Author(s):  
Yingji Chen ◽  
Longyu Jin ◽  
Zhibin Jiang ◽  
Suo Liu ◽  
Wei Feng
Keyword(s):  
Cell Proliferation ◽  
Lung Adenocarcinoma ◽  
Early Stage ◽  
Ppi Network ◽  
Hub Genes ◽  
Promote Cell Proliferation ◽  
Protein Protein Interaction ◽  
Elevated Expression ◽  
Potential Biomarkers

BackgroundLung adenocarcinoma (LUAD) is the most common pathological type of lung cancer. At present, most patients with LUAD are diagnosed at an advanced stage, and the prognosis of advanced LUAD is poor. Hence, we aimed to identify novel biomarkers for the diagnosis and treatment of early stage LUAD and to explore their predictive value.MethodsThe microarray datasets GSE63459, GSE27262, and GSE33532 were searched, and the differentially expressed genes (DEGs) were obtained using GEO2R. The DEGs were subjected to gene ontology (GO) and pathway enrichment analyses using METASCAPE. A protein–protein interaction (PPI) network was plotted with STRING and visualized by Cytoscape. Module analysis of the PPI network was performed using MCODE. Overall survival (OS) analysis and analysis of the mRNA expression levels of genes identified by MCODE were performed with UALCAN. Western blot analysis of hub genes in LUAD patients, MTS assays, and clonogenic assays were performed to test the effects of the hub genes on cell proliferation in vitro.ResultsA total of 341 DEGs were obtained, which were mainly enriched in terms related to blood vessel development, growth factor binding, and extracellular matrix organization. A PPI network consisting of 300 nodes and 1140 edges was constructed, and a significant module including 15 genes was identified. Elevated expression of ASPM, CCNB2, CDCA5, PRC1, KIAA0101, and UBE2T was associated with poor OS in LUAD patients. In the protein level, the hub gene was overexpressed in LUAD patients. In vitro experiments showed that knockdown of the hub genes in the LUAD cell lines could promote cell proliferation.ConclusionsDEGs are potential biomarkers for early stage lung adenocarcinoma and could have utility for the diagnosis and predicting treatment efficacy.

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