Bioinformatics and functional analyses of key genes in smoking‑associated lung adenocarcinoma

Zhou, Dajie; Sun, Yilin; Jia, Yanfei; Liu, Duanrui; Wang, Jing; Chen, Xiaowei; Zhang, Yujie

doi:10.3892/ol.2019.10733

Cited by 13 publications

(14 citation statements)

References 43 publications

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“…In other cancers, bioinformatic studies using the Human Genome Atlas has identified NTS as a clinically significant differentially expressed gene in determining survival in oral squamous cell carcinoma [32]. NTSR1 mRNA expression appeared to be an important survival factor in smoking-associated lung adenocarcinoma [33]. Additionally, NTS has been identified as a hub differentially expressed gene in recurrence of lower-grade brain glioma [34].…”

Section: Discussionmentioning

confidence: 99%

Characterisation of the Expression of Neurotensin and Its Receptors in Human Colorectal Cancer and Its Clinical Implications

et al. 2020

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Introduction: Colorectal Cancer (CRC) accounts for 9% of cancer deaths globally. Hormonal pathways play important roles in some cancers. This study investigated the association of CRC expression of neurotensin (NTS), NTS receptors 1 and 3 (NTSR1 and NTSR3) and clinical outcomes. Methods: A prospective cohort study which quantifies the protein expression of NTS, NTSR1 and NTSR3 in human CRCs using immunohistochemistry. Expression levels were then compared with clinico-pathological outcome including histological grade, overall survival (OS) and disease-free survival (DFS). Results: Sixty-four patients were enrolled with median follow-up of 44.0 months. There was significantly higher expression of NTS in cancer tissue in CRC with higher T stages (p < 0.01), N stages (p = 0.03), and AJCC clinical stages (p = 0.04). There was significantly higher expression of NTS, NTSR1 and NTSR3 in cancer tissue compared to surrounding normal epithelium (median H-score 163.5 vs 97.3, p < 0.01). There was significantly shorter DFS in individuals with CRC with high levels of NTS compared to lower levels of NTS (35.8 months 95% CI 28.7–42.8 months vs 46.4 months 95% CI 42.2–50.5 months, respectively, p = 0.02). Above median NTS expression in cancer tissue was a significant risk factor for disease recurrence (HR 4.10, 95% CI 1.14–14.7, p = 0.03). Discussion: The expression of NTS and its receptors has the potential to be utilised as a predictive and prognostic marker in colorectal cancer for postoperative selection for adjuvant therapy and identify individuals for novel therapies targeting the neurotensinergic pathways. Conclusions: High NTS expression appears to be associated with more advanced CRC and worse DFS.

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Section: Discussionmentioning

confidence: 99%

Characterisation of the Expression of Neurotensin and Its Receptors in Human Colorectal Cancer and Its Clinical Implications

et al. 2020

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“…At the genetic level, smokers and nonsmokers were accurately identi ed in LA based on a support vector machine (SVM) classi cation model constructed from 27 characteristic genes with signi cant enrichment of cancer proteoglycan and Ras signaling pathway [24] . It was suggested that 7 mRNAs including CYP17A1, PKHD1L1, RPE65, NTSR1, FETUB, IGFBP1 and G6PC might be used as prognostic indicators in smokers with LA [9] . However, very few researchers focus on the development from normal lung tissue to LA tissue in smokers.…”

Section: Discussionmentioning

confidence: 99%

“…Besides, it was found that aberrant activation of mast cells and CD4 + memory T cells also contributed to LA development and progression. However, the signaling pathways and driver genes in smoking-associated lung adenocarcinoma remain uncertain [9] . In the last few decades, we mainly focused on the effect of smoking between lung cancer patients and normal people.…”

Section: Introductionmentioning

confidence: 99%

COL1A1, COL1A2, COL3A1 and DCN are Potential Biomarkers to Predict Progression from Smokers to Suffering from Lung Adenocarcinoma

Chen

Wang

et al. 2020

Preprint

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Background: To explore novel related genes and potential biomarkers that predict progression from smokers to lung adenocarcinoma (LA). Methods: Three datasets from GEO (Gene Expression Omnibus) database were used to identify differentially expressed genes (DEGs) between LA tissue (LAT) and normal tumor adjacent tissue (TAT). The overlap of DEGs could be found and enriched in gene oncology (GO) and pathways to discover the potential biological mechanisms. Protein-protein interaction (PPI) network was applied to find the relationship among proteins. Survival analysis contributed to the definiteness of key genes. The expression of key genes in LA patients who smoke was verified. Furthermore, genetic alterations, co-expression and pathways of key genes were explored. To obtain more information, key genes were further analyzed in immune infiltration, drug target and the distribution of single cell in LA. Results: 245 DEGs were revealed in 3 datasets from GEO. In Kaplan Meier plotter, we found that high expression of COL1A1, COL1A2 and COL3A1 was associated with poorer survival while low expression of DCN was contributed to poorer survival in LAs who smoke. Thus, three up-regulated genes (COL1A1, COL1A2, COL3A1) and one down-regulated gene (DCN) were defined as key genes. Their genetic alterations were more common in female LA smokers and co-expression genes/proteins of them mainly functioned at extracellular matrix. Furthermore, COL1A1, COL1A2, COL3A1 genes had a common targeted drug called Collagenase clostridium histolyticum (DB00048) and DCN gene had a targeted drug called Tromethamine (DB03754). In the Single Cell Expression Atlas of EMBL-EBL, COL3A1 gene was specifically highly expressed in female LA patients with brain metastasis. Conclusions: COL1A1, COL1A2, COL3A1 and DCN could be regarded as novel potential biomarkers that predict progression from smokers to lung adenocarcinoma.

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“…The functional features of the CMT-related genes were examined by R software [ 20 , 21 ] and KOBAS 3.0 [ 22 , 23 ]. To understand the CMT-related genes underlying biological processes, Gene Ontology analyses (GO; http://geneontology.org ) were conducted using R software (version 3.6.2).…”

Section: Methodsmentioning

confidence: 99%

Identification of Candidate Genes Associated with Charcot-Marie-Tooth Disease by Network and Pathway Analysis

Zhong

Luo

et al. 2020

BioMed Research International

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Charcot-Marie-Tooth Disease (CMT) is the most common clinical genetic disease of the peripheral nervous system. Although many studies have focused on elucidating the pathogenesis of CMT, few focuses on achieving a systematic analysis of biology to decode the underlying pathological molecular mechanisms and the mechanism of its disease remains to be elucidated. So our study may provide further useful insights into the molecular mechanisms of CMT based on a systematic bioinformatics analysis. In the current study, by reviewing the literatures deposited in PUBMED, we identified 100 genes genetically related to CMT. Then, the functional features of the CMT-related genes were examined by R software and KOBAS, and the selected biological process crosstalk was visualized with the software Cytoscape. Moreover, CMT specific molecular network analysis was conducted by the Molecular Complex Detection (MCODE) Algorithm. The biological function enrichment analysis suggested that myelin sheath, axon, peripheral nervous system, mitochondrial function, various metabolic processes, and autophagy played important roles in CMT development. Aminoacyl-tRNA biosynthesis, metabolic pathways, and vasopressin-regulated water reabsorption were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway network, suggesting that these pathways may play key roles in CMT occurrence and development. According to the crosstalk, the biological processes could be roughly divided into a correlative module and two separate modules. MCODE clusters showed that in top 3 clusters, 13 of CMT-related genes were included in the network and 30 candidate genes were discovered which might be potentially related to CMT. The study may help to update the new understanding of the pathogenesis of CMT and expand the potential genes of CMT for further exploration.

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Bioinformatics and functional analyses of key genes in smoking‑associated lung adenocarcinoma

Cited by 13 publications

References 43 publications

Characterisation of the Expression of Neurotensin and Its Receptors in Human Colorectal Cancer and Its Clinical Implications

Characterisation of the Expression of Neurotensin and Its Receptors in Human Colorectal Cancer and Its Clinical Implications

COL1A1, COL1A2, COL3A1 and DCN are Potential Biomarkers to Predict Progression from Smokers to Suffering from Lung Adenocarcinoma

Identification of Candidate Genes Associated with Charcot-Marie-Tooth Disease by Network and Pathway Analysis

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