scholarly journals Transcriptome Analysis of lncRNA-mRNA Interactions in the Non-Small Cell Lung Cancer

2020 ◽  
Author(s):  
Bin Liu ◽  
Jing Li ◽  
JiMan Li ◽  
GuangYuan Liu ◽  
YongSheng Wang
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Biological Function ◽  
Therapeutic Targets ◽  
Small Cell ◽  
Differentially Expressed ◽  
Clinical Samples ◽  
Small Cell Lung ◽  
Normal Tissues

Abstract As a serious malignancy with high incidence and fatality, non-small cell lung cancer (NSCLC) has affected millions of people each year worldwide. However, the 5-year survival rate of NSCLC is still not satisfactory. Therefore, it is particularly imperative and necessary to explore the underlying molecular mechanisms of NSCLC to contribute to the potential therapeutic targets and strategies. Six clinical samples including three normal tissues and three cancer tissues obtained from patients diagnosed with NSCLC were sequenced through Illumina Hiseq2500 sequencer. Differentially expressed lncRNAs and mRNAs analysis were implemented using the edgeR, and the function of differentially expressed lncRNAs and mRNAs were analyzed with GO and KEGG enrichment analysis. Then, top 10 dysregulated lncRNAs and mRNAs were screened out. Finally, the co-expression, biological function and pathway networks of dysregulated lncRNA with the predicted target genes were constructed. Differentially expressed lncRNAs and mRNAs could distinguish cancerous tissues from normal tissues. The functions and KEGG pathway of differentially expressed lncRNAs and mRNAs mainly were enriched in immune response, metabolism, phagosome, cytokine receptor interaction and IL-17 signaling pathway. The co-expression network revealed that top ten dysregulated lncRNAs were interacted with IGH gene cluster. Furthermore, the biological function and pathway network also indicated that dysregulated lncRNAs were involved in immune process. The results demonstrated that the biologic function of dysregulated lncRNAs that may be involved in immune process. Our data provides a foundation of the biologic significances of lncRNAs to contribute to the therapeutic targets and strategies for NSCLC to promote the survival for patients.

scholarly journals Analysis of Long Non-Coding RNA Expression Profiles in Non-Small Cell Lung Cancer

2016 ◽  
Vol 38 (6) ◽  
pp. 2389-2400 ◽  
Author(s):  
Li Wang ◽  
Zhenhong Chen ◽  
Li An ◽  
Yajuan Wang ◽  
Zhijian Zhang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Expression Profiles ◽  
Small Cell ◽  
Differentially Expressed ◽  
Expression Level ◽  
Small Cell Lung ◽  
Normal Tissues ◽  
Nsclc Patients

Background/Aims: Long non-coding RNAs (lncRNAs) play an important role in tumorigenesis. However, the role of lncRNA expression in human Non-small cell lung cancer (NSCLC) biology, prognosis and molecular classification remains unknown. Methods: We established the IncRNA profile in NSCLC by re-annotation of microarrays from the Gene expression omnibus database. Quantitative real-time PCR was used to determine expression of LINC00342. Results: 6066 differentially expressed IncRNAs were identified and we found a novel IncRNA, LINC00342 was significantly up-regulated in NSCLC tissues compared with normal tissues. We confirmed the over-expression of LINC00342 in a cohort of NSCLC patients and found LINC00342 expression level was positively correlated with lymph node metastasis and TNM stages. Furthermore, in a large online database of 1942 NSCLC patients, high expression of LINC00342 indicated poor Overall survival (HR = 1.28, 95% CI: 1.13-1.45) and post progression survival (HR = 1.43, 95% CI: 1.09-1.88). Bioinformatics analyses showed that LINC00342 was co-expressed with different protein-coding genes in NSCLC and normal tissues. Additionally, gene set enrichment analyses found that PTEN and P53 pathways genes were enriched in the groups with higher LINC00342 expression level. By small interfering RNAs mediated silence of LINC00342, proliferation ability was significantly inhibited in lung cancer cell line. Conclusion: To summary, our findings indicate that a set of IncRNAs are differentially expressed in NSCLC and we characterized a novel IncRNA, LINC00342 which is significantly up-regulated in NSCLC and could be a prognostic biomarker.

Chemokines as Therapeutic Targets in Non-Small Cell Lung Cancer

2002 ◽  
Vol 2 (3) ◽  
pp. 403-417 ◽  
Author(s):  
Bentham Science Publisher E.S. White ◽  
Bentham Science Publisher R.M. Strieter ◽  
Bentham Science Publisher D.A. Arenberg
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Therapeutic Targets ◽  
Small Cell ◽  
Small Cell Lung

scholarly journals RNA-Based Assay for Next-Generation Sequencing of Clinically Relevant Gene Fusions in Non-Small Cell Lung Cancer

Cancers ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 139
Author(s):  
Caterina De Luca ◽  
Francesco Pepe ◽  
Antonino Iaccarino ◽  
Pasquale Pisapia ◽  
Luisella Righi ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Limit Of Detection ◽  
Predictive Biomarkers ◽  
Small Cell ◽  
Clinical Samples ◽  
Gene Fusions ◽  
Small Cell Lung ◽  
Relevant Gene

Gene fusions represent novel predictive biomarkers for advanced non-small cell lung cancer (NSCLC). In this study, we validated a narrow NGS gene panel able to cover therapeutically-relevant gene fusions and splicing events in advanced-stage NSCLC patients. To this aim, we first assessed minimal complementary DNA (cDNA) input and the limit of detection (LoD) in different cell lines. Then, to evaluate the feasibility of applying our panel to routine clinical samples, we retrospectively selected archived lung adenocarcinoma histological and cytological (cell blocks) samples. Overall, our SiRe RNA fusion panel was able to detect all fusions and a splicing event harbored in a RNA pool diluted up to 2 ng/µL. It also successfully analyzed 46 (95.8%) out of 48 samples. Among these, 43 (93.5%) out of 46 samples reproduced the same results as those obtained with conventional techniques. Intriguingly, the three discordant results were confirmed by a CE-IVD automated real-time polymerase chain reaction (RT-PCR) analysis (Easy PGX platform, Diatech Pharmacogenetics, Jesi, Italy). Based on these findings, we conclude that our new SiRe RNA fusion panel is a valid and robust tool for the detection of clinically relevant gene fusions and splicing events in advanced NSCLC.

scholarly journals Differentially expressed and activated proteins associated with non small cell lung cancer tissues

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
E. Nigro ◽  
E. Imperlini ◽  
O. Scudiero ◽  
M.L. Monaco ◽  
R. Polito ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Small Cell ◽  
Differentially Expressed ◽  
Small Cell Lung ◽  
Cancer Tissues

scholarly journals Co-expression Network and Prognosis Analyses of Pyroptosis-related Genes in Non-small Cell Lung Cancer

2021 ◽  
Author(s):  
Zixiao Liu ◽  
Xudong Liu ◽  
Yu Zhang ◽  
Yongjie Zhou ◽  
Shuaibin Lian ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Hydrophobic Interactions ◽  
Tumor Staging ◽  
Lung Squamous Cell Carcinoma ◽  
Small Cell ◽  
Differentially Expressed ◽  
Small Cell Lung ◽  
Nsclc Patients

Abstract Lung cancer is very difficult to diagnose in the its early stages because of its initial asymptomatic characteristics. In recent years, pyrolysis has been shown identified as a novel type of programmed cell death with inflammation mediated by the gasdermin family. In this study, 33 differentially-expressed pyroptosis-related genes were commonly identified in both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients. Tumor-related gasdermin family genes that were significantly differentially expressed in non-small cell lung cancer (NSCLC) tissues were identified by our co-expression network analysis. Among them, the mRNA level of GSDMB gene had significant impacts on tumor staging and survival rates of NSCLC patients. Therefore, this gene is a potential new therapeutic target for the treatment of NSCLC. In addition, the high expression levels of GSDMC/D were significantly correlated with the low overall survival (OS), progression-free survival (FP) and post-progression survival (PPS) of NSCLC patients. Therefore, this gene is a potential oncogene for NSCLC. Furthermore, four small molecules (erastin, cefotiam, metanephrine, and vorinostat) that could most significantly reverse the NSCLC gene expression were identified. They interacted with GSDMB proteins mainly through H-bonds and hydrophobic interactions. This study provides new therapeutic targets and prognostic makers for NSCLC patients.

scholarly journals Identification of LOC338963 and AP3B2 as Potential Biomarkers for Lambert-Eaton Myasthenic Syndrome

2021 ◽  
Author(s):  
Fei Yang ◽  
Feng Jing ◽  
Yang Li ◽  
Shanshan Kong ◽  
Shimin Zhang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Expression Profiles ◽  
Small Cell ◽  
Differentially Expressed ◽  
Healthy Controls ◽  
Small Cell Lung ◽  
Qrt Pcr ◽  
Myasthenic Syndrome

Abstract Background: Lambert-Eaton myasthenic syndrome (LEMS) is a rare neuromuscular junction disorder associated with muscle weakness and small-cell lung cancer. Here, we used microarray analysis to identify long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) that might serve as biomarkers for LEMS.Methods: Plasma lncRNA and mRNA expression profiles of three patients with paraneoplastic LEMS and three healthy controls were analyzed using Arraystar Human lncRNA Microarray v4.0. Differentially expressed lncRNAs and adjacent mRNAs were analyzed jointly, and candidates were verified in individual samples by quantitative real-time polymerase chain reaction (qRT-PCR). The identified lncRNAs and mRNAs were evaluated in nine patients with paraneoplastic LEMS, eight patients with non-tumor LEMS, and four patients with small cell lung cancer (SCLC). Results: A total of 320 lncRNAs were differentially expressed in patients with paraneoplastic LEMS compared to healthy controls (fold change >1.5, P < 0.05), and nine were further evaluated. One of the identified lncRNAS, LOC338963 (NR_031439), is known to regulated the expression of the mRNA AP3B2, and both were upregulated more than 2-fold in patients with paraneoplastic LEMS compared to healthy controls. Furthermore, qRT-PCR analysis revealed significant upregulation of LOC338963 (NR_031439) and AP3B2 expression in patients with paraneoplastic LEMS compared to those with either non-tumor LEMS (2.37- and 5.06-fold, respectively) or SCLC (4.36- and 14.97-fold, respectively).Conclusions: Plasma LOC338963 (NR_031439) and AP3B2 were found to be upregulated in LEMS and might be used as diagnostic biomarkers for this disease.

scholarly journals Tyrosine kinases Tie1 and Tie2 are differentially expressed in non-small cell lung cancer.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Tyrosine Kinases ◽  
The United States ◽  
Small Cell ◽  
Differentially Expressed ◽  
Small Cell Lung ◽  
Genes Encoding ◽  
Epidermal Growth

Non-small cell lung cancer (NSCLC) is the leading cause of cancer death in the United States (1). We mined published microarray data (2, 3, 4) to identify differentially expressed genes in NSCLC. We found that the genes encoding the tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1 - Tie1, and its counterpart Tie2 - were both among the genes whose expression was most quantitatively different in tumors from patients with NSCLC as compared to the lung. Tie1 and Tie2 may be important for initiation or progression of non-small cell lung cancer in humans.

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