Identification of differentially-expressed genes between early-stage adenocarcinoma and squamous cell carcinoma lung cancer using meta-analysis methods

Wang, Tianjiao; Zhang, Lei; Tian, Pu; Tian, Suyan

doi:10.3892/ol.2017.5838

Cited by 12 publications

(13 citation statements)

References 43 publications

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“…According to the genecards database, DSC3 is directly related to lung cancer whereas these two genes are directly related to squamous cell carcinoma and adenocarcinoma. DSC3 was also identified in our previous studies (Tian & Suárez‐Fariñas, ; Wang, Zhang, Tian, & Tian, ). Moreover, Cui et al.…”

Section: Results and Conclusionsupporting

confidence: 78%

Classification of early‐stage non‐small cell lung cancer by weighing gene expression profiles with connectivity information

Zhang

Tian

2017

Biometrical J

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Pathway-based feature selection algorithms, which utilize biological information contained in pathways to guide which features/genes should be selected, have evolved quickly and become widespread in the field of bioinformatics. Based on how the pathway information is incorporated, we classify pathway-based feature selection algorithms into three major categories-penalty, stepwise forward, and weighting. Compared to the first two categories, the weighting methods have been underutilized even though they are usually the simplest ones. In this article, we constructed three different genes' connectivity information-based weights for each gene and then conducted feature selection upon the resulting weighted gene expression profiles. Using both simulations and a real-world application, we have demonstrated that when the data-driven connectivity information constructed from the data of specific disease under study is considered, the resulting weighted gene expression profiles slightly outperform the original expression profiles. In summary, a big challenge faced by the weighting method is how to estimate pathway knowledge-based weights more accurately and precisely. Only until the issue is conquered successfully will wide utilization of the weighting methods be impossible.

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Section: Results and Conclusionsupporting

confidence: 78%

Classification of early‐stage non‐small cell lung cancer by weighing gene expression profiles with connectivity information

Zhang

Tian

2017

Biometrical J

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“…Non-small cell lung cancer (NSCLC) is the major subtype of lung cancer, which is typically divided into two histological subtypes, lung adenocarcinoma (ADC) and lung squamous carcinoma (SCC) [ 2 ]. In addition to differences in morphology, the underlying mechanisms, molecular profiling and therapeutic methods are quite different [ 3 – 5 ]. Therefore, identifying differentially-expressed genes between ADC and SCC is useful to better understand their pathogenesis.…”

Section: Introductionmentioning

confidence: 99%

SOX30 is a key regulator of desmosomal gene suppressing tumor growth and metastasis in lung adenocarcinoma

Hao

Han

et al. 2018

J Exp Clin Cancer Res

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BackgroundThe expression of desmosomal genes in lung adenocarcinoma and lung squamous carcinoma is different. However, the regulatory mechanism of desmosomal gene expression in lung adenocarcinoma and lung squamous carcinoma remains unknown.MethodsThe correlation between expression of desmosomal gene expression and SOX30 expression were analyzed by bioinformatics. The expression of SOX30, DSP, JUP and DSC3 were detected in lung cancer cell lines, lung tissues of mice and patients’ tissues by qPCR, WB, Immunofluorescence and Immunohistochemistry. A chromatin Immunoprecipitation assay was used to investigate the mechanisms of the SOX30 regulation on desmosomal gene expression. In vitro proliferation, migration and invasion assays, and an in vivo nude mice model were utilized to assess the important role of desmosomal genes on SOX30-induced tumor suppression. A WB assay and TOP/FOP flash reporter assay was used to investigate the downstream pathway regulated by the SOX30-desmosomal gene axis. A chemical carcinogenic model of SOX30-knockout mice was generated to confirm the role of the SOX30-desmosomal gene axis in tumorigenesis.ResultsThe expression of desmosomal genes were upregulated by SOX30 in lung adenocarcinoma but not in lung squamous carcinoma. Further mechanism studies showed that SOX30 acts as a key transcriptional regulator of desmosomal genes by directly binding to the ACAAT motif of desmosomal genes promoter region and activating their transcription in lung adenocarcinoma. Knockdown of the expression of related desmosomal genes by miRNA significantly attenuated the inhibitory effect of SOX30 on cell proliferation, migration and invasion in vitro and on tumor growth and metastasis in vivo. In addition, knockout of SOX30 promotes lung tumor development and loss the inhibition of desmosomal genes on downstream Wnt and ERK signal in urethane-induced lung carcinogenesis in SOX30-knockout mice.ConclusionsOverall, these findings demonstrate for the first time that SOX30 acts as a master switch of desmosomal genes, inhibits lung adenocarcinoma cell proliferation, migration and invasion by activating the transcription of desmosomal genes. This study provides novel insights on the regulatory mechanism of desmosomal genes in lung adenocarcinoma.Electronic supplementary materialThe online version of this article (10.1186/s13046-018-0778-3) contains supplementary material, which is available to authorized users.

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“…Homogeneous treatment strategies have been traditionally implemented for the two fundamentally different subtypes in clinical practice, resulting in poor response to treatment. Therefore, a better understanding of their biological pattern is critical for finding subtype-specific diagnosis and treatment strategies [ 14 ]. The aim of this study is to identify epigenetic pattern in LUSC on a genome-wide scale.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide DNA methylation profiling reveals novel epigenetic signatures in squamous cell lung cancer

Shi

Wáng

et al. 2017

BMC Genomics

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BackgroundEpigenetic alterations are strongly associated with the development of cancer. The aim of this study was to identify epigenetic pattern in squamous cell lung cancer (LUSC) on a genome-wide scale.ResultsHere we performed DNA methylation profiling on 24 LUSC and paired non-tumor lung (NTL) tissues by Illumina Human Methylation 450 K BeadArrays, and identified 5214 differentially methylated probes. By integrating DNA methylation and mRNA expression data, 449 aberrantly methylated genes accompanied with altered expression were identified. Ingenuity Pathway analysis highlighted these genes which were closely related to the carcinogenesis of LUSC, such as ERK family, NFKB signaling pathway, Hedgehog signaling pathway, providing new clues for understanding the molecular mechanisms of LUSC pathogenesis. To verify the results of high-throughput screening, we used 56 paired independent tissues for clinical validation by pyrosequencing. Subsequently, another 343 tumor tissues from the Cancer Genome Atlas (TCGA) database were utilized for further validation. Then, we identified a panel of DNA methylation biomarkers (CLDN1, TP63, TBX5, TCF21, ADHFE1 and HNF1B) in LUSC. Furthermore, we performed receiver operating characteristics (ROC) analysis to assess the performance of biomarkers individually, suggesting that they could be suitable as potential diagnostic biomarkers for LUSC. Moreover, hierarchical clustering analysis of the DNA methylation data identified two tumor subgroups, one of which showed increased DNA methylation.ConclusionsCollectively, these results suggest that DNA methylation plays critical roles in lung tumorigenesis and may potentially be proposed as a diagnostic biomarker.Trial registration ChiCTR-RCC-12002830 Date of registration: 2012–12-17.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4223-3) contains supplementary material, which is available to authorized users.

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Identification of differentially-expressed genes between early-stage adenocarcinoma and squamous cell carcinoma lung cancer using meta-analysis methods

Cited by 12 publications

References 43 publications

Classification of early‐stage non‐small cell lung cancer by weighing gene expression profiles with connectivity information

Classification of early‐stage non‐small cell lung cancer by weighing gene expression profiles with connectivity information

SOX30 is a key regulator of desmosomal gene suppressing tumor growth and metastasis in lung adenocarcinoma

Genome-wide DNA methylation profiling reveals novel epigenetic signatures in squamous cell lung cancer

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