Fifteen hub genes associated with progression and prognosis of clear cell renal cell carcinoma identified by coexpression analysis

Renal cell carcinoma (RCC) is the most common type of renal tumor, and the clear cell renal cell carcinoma (ccRCC) is the most frequent subtype. In this study, our aim is to identify potential biomarkers that could effectively predict the prognosis and progression of ccRCC. First, we used The Cancer Genome Atlas (TCGA) RNA-sequencing (RNA-seq) data of ccRCC to identify 2370 differentially expressed genes (DEGs). Second, the DEGs were used to construct a coexpression network by weighted gene coexpression network analysis (WGCNA). Moreover, we identified the yellow module, which was strongly related to the histologic grade and pathological stage of ccRCC. Then, the functional annotation of the yellow module and single-samples gene-set enrichment analysis of DEGs were performed and mainly enriched in cell cycle. Subsequently, 18 candidate hub genes were screened through WGCNA and protein–protein interaction (PPI) network analysis. After verification of TCGA’s ccRCC data set, Gene Expression Omnibus (GEO) data set (GSE73731) and tissue validation, we finally identified 15 hub genes that can actually predict the progression of ccRCC. In addition, by using survival analysis, we found that patients of ccRCC with high expression of each hub gene were more likely to have poor prognosis than those with low expression. The receiver operating characteristic curve showed that each hub gene could effectively distinguish between localized and advanced ccRCC. In summary, our study indicates that 15 hub genes have great predictive value for the prognosis and progression of ccRCC, and may contribute to the exploration of the pathogenesis of ccRCC.     

伴HBV感染性肝癌调控枢纽基因筛选与初步鉴定

慢性乙型肝炎病毒(Hepatitis B virus,HBV)感染引起的原发性肝癌涉及多种基因、转录本和蛋白质的相互作用及调控。从单个基因的角度来看,某个基因的表达量的改变只能对肝癌发生发展的局部作出解释而无法从整体行为进行深入和全面的探索,无法满足高度复杂性的调控研究需要。筛选乙肝相关性肝癌的基因芯片数据获取差异表达基因后,应用加权基因共表达网络分析算法构建基因共表达网络,识别与肝癌发生相关的模块,利用可视化筛选枢纽基因,并针对枢纽基因进行基因本体富集分析和初步验证。富集分析和文献挖掘一致发现,某些枢纽基因确实与多种癌症的发生与发展存在显著的关联。权重基因共表达网络分析方法被证明是一个高效的系统生物学方法,应用该方法发现了新的HBV相关性肝癌枢纽基因。经实验验证,发现枢纽基因SHARPIN促进细胞迁移。该研究对肝癌发生的调控机制以及发现HBV慢性感染导致肝癌的新型诊断标志物和(或)药物作用靶点提供了新的视野。     

Identification of EPHX2 and RMI2 as two novel key genes in cervical squamous cell carcinoma by an integrated bioinformatic analysis

Cervical cancer is the fourth most common malignancy in women worldwide and cervical squamous cell carcinoma (CESC) is the most common histological type of cervical cancer. The dysregulation of genes plays a significant role in cancer. In the present study, we screened out differentially expressed genes (DEGs) of CESC in the GSE63514 data set from the Gene Expression Omnibus database. An integrated bioinformatics analysis was used to select hub genes, as well as to investigate their related prognostic signature, functional annotation, methylation mechanism, and candidate molecular drugs. As a result, a total of 1907 DEGs were identified (944 were upregulated and 963 were downregulated). In the protein–protein interaction network, three hub modules and 30 hub genes were identified. And two hub modules and 116 hub genes were screened out from four CESC-related modules by the weighted gene coexpression network analysis. The gene ontology term enrichment analysis and Kyoto encyclopedia of genes and genomes pathway analysis were performed to better understand functions and pathways. Genes with a significant prognostic value were found by prognostic signature analysis. And there were five genes (EPHX2, CHAF1B, KIAA1524, CDC45, and RMI2) identified as significant CESC-associated genes after expression validation and survival analysis. Among them, EPHX2 and RMI2 were noted as two novel key genes for the CESC-associated methylation and expression. In addition, four candidate small molecule drugs for CESC (camptothecin, resveratrol, vorinostat, and trichostatin A) were defined. Further studies are required to explore these significant CESC-associated genes for their potentiality in diagnosis, prognosis, and targeted therapy.     

Identification of gene coexpression modules,hub genes,and pathways related to spinal cord injury using integrated bioinformatics methods

Spinal cord injury (SCI) is characterized by dramatic neurons loss and axonal regeneration suppression. The underlying mechanism associated with SCI-induced immune suppression is still unclear. Weighted gene coexpression network analysis (WGCNA) is now widely applied for the identification of the coexpressed modules, hub genes, and pathways associated with clinic traits of diseases. We performed this study to identify hub genes associated with SCI development. Gene Expression Omnibus (GEO) data sets GSE45006 and GSE20907 were downloaded and the significant correlativity and connectivity between them were detected using WGCNA. Three significant consensus modules, including 567 eigengenes, were identified from the master GSE45006 data following the preconditions of approximate scale-free topology for WGCNA. Further bioinformatics analysis showed these eigengenes were involved in inflammatory and immune responses in SCI. Three hub genes Rac2, Itgb2, and Tyrobp and one pathway “natural killer cell-mediated cytotoxicity” were identified following short time-series expression miner, protein-protein interaction network, and functional enrichment analysis. Gradually upregulated expression patterns of Rac2, Itgb2, and Tyrobp genes at 0, 3, 7, and 14 days after SCI were confirmed based on GSE45006 and GSE20907 data set. Finally, we found that Rac2, Itgb2, and Tyrobp genes might take crucial roles in SCI development through the “natural killer cell–mediated cytotoxicity” pathway.     

血清miRNAs作为食管鳞癌新的生物标志物

食管鳞癌是我国最常见的恶性肿瘤之一。由于缺乏有效的早期诊断方法,大多数食管鳞癌患者在确诊时已到中晚期并预后不良。MicroRNAs(miRNAs)是一类可通过抑制其特异性靶基因表达从而调控食管鳞癌发生发展的非编码内源性小RNA。相比于传统的生物标志物(例如mRNA和蛋白质),miRNAs更加稳定并易于筛选及精确地定量分析,从而成为理想的新一代癌症早期诊断和预后评估的生物标志物。近来的研究结果显示,食管鳞癌病人血清中的一些miRNAs表达水平的变化与病情诊断及预后的结果显著相关。文章综述了食管鳞癌病人血清中miRNAs的变化规律,讨论了检测这些miRNAs的表达水平变化作为一种新的方法应用于食管鳞癌的早期诊断和预后评估的可能性。值得注意的是,不同的血清miRNAs的检测方法所产生的结果是不完全一致的,文章还对这些差异产生的原因进行了讨论。     

DNA methylation biomarkers for head and neck squamous cell carcinoma

DNA methylation plays an important role in the etiology and pathogenesis of head and neck squamous cell carcinoma (HNSCC). The current study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) by a comprehensive bioinformatics analysis. In addition, we screened for DEGs affected by DNA methylation modification and further investigated their prognostic values for HNSCC. We included microarray data of DNA methylation (GSE25093 and GSE33202) and gene expression (GSE23036 and GSE58911) from Gene Expression Omnibus. Aberrantly methylated-DEGs were analyzed with R software. The Cancer Genome Atlas (TCGA) RNA sequencing and DNA methylation (Illumina HumanMethylation450) databases were utilized for validation. In total, 27 aberrantly methylated genes accompanied by altered expression were identified. After confirmation by The Cancer Genome Atlas (TCGA) database, 2 hypermethylated-low-expression genes (FAM135B and ZNF610) and 2 hypomethylated-high-expression genes (HOXA9 and DCC) were identified. A receiver operating characteristic (ROC) curve confirmed the diagnostic value of these four methylated genes for HNSCC. Multivariate Cox proportional hazards analysis showed that FAM135B methylation was a favorable independent prognostic biomarker for overall survival of HNSCC patients.     

Mining TCGA database for screening and identification of hub genes in kidney renal clear cell carcinoma microenvironment

To evaluate the diagnosis and prognosis of the tumor microenvironment (immunization and stromal cells) in kidney renal clear cell carcinoma (KIRC), KIRC cases selected from The Cancer Genome Atlas database were divided into two groups according to the ESTIMATE algorithm-derived immune scores. Our data suggested that the Von Hippel-Lindau mutations and pathologic grades are associated with immune scores. Importat ntly, we identified 173 differential expression genes (DEGs) associated with prognosis in patients with KIRC. Consequently, Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed on these DEGs, which included immune response, defense response, intrinsic to the plasma membrane, positive regulation of immune system process, and cytokine binding. Next, the protein-protein interaction network of DEGs and the most significant module was constructed. Five hub genes were identified and analyzed using biological analysis. The survival analysis of the hub genes showed that KIRC patients with high gene expression of C2, MXRA8, TNFSF13B, and X-linked inhibitor of apoptosis protein-associated factor 1 (XAF1) had worse overall survival, and MXRA8, TNFSF13B, and XAF1 alteration were significantly associated with disease-free survival (DFS). In addition, high gene expression of XAF1 alteration showed better DFS. Conclusion: we identified a list of microenvironment-related genes that are useful for understanding the molecular mechanisms and prognosis of KIRC.     

Screening and identification of autophagy-related biomarkers for oral squamous cell carcinoma (OSCC) via integrated bioinformatics analysis

Increasing evidences have showed that autophagy played a significant role in oral squamous cell carcinoma (OSCC). Purpose of our study was to explore the prognostic value of autophagy-related genes (ATGs) and screen autophagy-related biomarkers for OSCC. RNA-seq and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database following extracting ATG expression profiles. Then, differentially expressed analysis was performed in R software and a risk score model according to ATGs was established. Moreover, comprehensive bioinformatics analyses were used to screen autophagy-related biomarkers which were later verified in OSCC tissues and cell lines. A total of 232 ATGs were extracted, and 37 genes were differentially expressed in OSCC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that these genes were mainly located in autophagosome membrane and associated with autophagy. Furthermore, the risk score on basis of ATGs was identified as potential independent prognostic biomarker. Moreover, ATG12 and BID were identified as potential autophagy-related biomarkers of OSCC. This study successfully constructed a risk model, and the risk score could predict the prognosis of OSCC patients accurately. Moreover, ATG12 and BID were identified as two potential independent prognostic autophagy-related biomarkers and might provide new OSCC therapeutic targets.     

Ectopic coexpression of keratin 8 and 18 promotes invasion of transformed keratinocytes and is induced in patients with cutaneous squamous cell carcinoma

Cutaneous squamous cell carcinoma (cSCC) results from transformation of epidermal keratinocytes. Invasion of transformed keratinocytes through the basement membrane into the dermis results in invasive cSCC with substantial metastatic potential. To better understand the mechanisms for invasion and metastasis, we compared the protein expression profiles of a non-metastatic transformed mouse keratinocyte line and its metastatic derivative. Keratin 8 (Krt8) and Krt18, not seen in normal keratinocytes, were coexpressed and formed Krt8/18 filaments in the metastatic line. The metastatic line efficiently invaded an artificial basement membrane in vitro owing to the Krt8/18-coexpression, since coexpression of exogenous Krt8/18 in the non-invasive parental line conferred invasiveness. To test whether the Krt8/18-coexpression is induced and is involved in cSCC invasion, we examined specimens from 21 pre-invasive and 24 invasive cSCC patients by immunohistochemistry, and the ectopic Krt8/18-coexpression was almost exclusively found in invasive cSCC. Further studies are needed to examine the clinical significance of ectopic Krt8/18-coexpression in cSCC.     

Identification of potential core genes and pathways predicting pathogenesis in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the most common subtype of head and neck cancer; however, its pathogenesis and potential therapeutic targets remain largely unknown. In the present study, we analyzed three gene expression profiles and screened differentially expressed genes (DEGs) between HNSCC and normal tissues. The DEGs were subjected to gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), protein–protein interaction (PPI), and survival analyses, while the connectivity map (CMap) database was used to predict candidate small molecules that may reverse the biological state of HNSCC. Finally, we measured the expression of the most relevant core gene in vitro and examined the effect of the top predicted potential drug against the proliferation of HNSCC cell lines. Among the 208 DEGs and ten hub genes identified, CDK1 and CDC45 were associated with unfavorable HNSCC prognosis, and three potential small molecule drugs for treating HNSCC were identified. Increased CDK1 expression was confirmed in HNSCC cells, and menadione, the top predicted potential drug, exerted significant inhibitory effects against HNSCC cell proliferation and markedly reversed CDK1 expression. Together, the findings of the present study suggest that the ten hub genes and pathways identified may be closely related to HNSCC pathogenesis. In particular, CDK1 and CDC45 overexpression could be reliable biomarkers for predicting unfavorable prognosis in patients with HNSCC, while the new candidate small molecules identified by CMap analysis provide new avenues for the development of potential drugs to treat HNSCC.     

YAP and TAZ are essential for basal and squamous cell carcinoma initiation

YAP and TAZ are key downstream regulators of the Hippo pathway, regulating cell proliferation and differentiation. YAP and TAZ activation has been reported in different cancer types. However, it remains unclear whether they are required for the initiation of major skin malignancies like basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). Here, we analyze the expression of YAP and TAZ in these skin cancers and evaluate cancer initiation in knockout mouse models. We show that YAP and TAZ are nuclear and highly expressed in different BCC types in both human and mice. Further, we find that cells with nuclear YAP and TAZ localize to the invasive front in well‐differentiated SCC, whereas nuclear YAP is homogeneously expressed in spindle cell carcinoma undergoing EMT. We also show that mouse BCC and SCC are enriched for YAP gene signatures. Finally, we find that the conditional deletion of YAP and TAZ in mouse models of BCC and SCC prevents tumor formation. Thus, YAP and TAZ are key determinants of skin cancer initiation, suggesting that targeting the YAP and TAZ signaling pathway might be beneficial for the treatment of skin cancers.     

A ferroptosis-related gene signature for overall survival prediction and immune infiltration in lung squamous cell carcinoma

Background: Ferroptosis is associated with cancer initiation and progression. However, the molecular mechanism and prognostic value of ferroptosis-related genes in lung squamous cell carcinoma (LUSC) are poorly understood.Methods: The mRNA expression profiles, methylation data, and clinical information of patients with LUSC were downloaded from TCGA and GEO database. Ferroptosis-related differentially expressed genes (DEGs) were identified between cancerous and non-cancerous tissues, and their prognostic value was systemically investigated by bioinformatic analyses.Results: A ferroptosis-related gene signature (ALOX5, TFRC, PHKG2, FADS2, NOX1) was constructed using multivariate Cox regression analysis and represented as a risk score. Overall survival (OS) probability was significantly lower in the high-risk group than in the low-risk group (P<0.001), and receiver operating characteristic curve showed a good predictive capacity (AUC = 0.739). The risk score was an independent prognostic factor for LUSC. A nomogram was constructed to predict the OS probabilities at 1, 3, and 5 years. High-risk score was associated with increased immune infiltration, lower methylation levels, higher immune checkpoint genes expression levels, and better chemotherapy response. Cell adhesion molecules, focal adhesion, and extracellular matrix receptor interaction were the main pathways in the high-risk group. The signature was validated using the TCGA test cohort, entire TCGA cohort, {"type":"entrez-geo","attrs":{"text":"GSE30219","term_id":"30219"}}GSE30219, {"type":"entrez-geo","attrs":{"text":"GSE157010","term_id":"157010"}}GSE157010, {"type":"entrez-geo","attrs":{"text":"GSE73403","term_id":"73403"}}GSE73403, and {"type":"entrez-geo","attrs":{"text":"GSE4573","term_id":"4573"}}GSE4573 datasets. The gene disorders in patients with LUSC were validated using real-time PCR and single-cell RNA sequencing analysis.Conclusions: A ferroptosis-related gene signature was constructed to predict OS probability in LUSC. This could facilitate novel therapeutic methods and guide individualized therapy.     

Plasma microRNA profiling highlights miR-1260b and miR-720 as novel diagnostic and prognostic biomarkers of esophageal squamous cell carcinoma

This paper was designed to explore the value of miRNAs as diagnostic biomarkers that may facilitate the early detection of esophageal squamous cell carcinoma (ESCC). Plasma miRNA profiles were defined via an array-based approach using samples from ESCC patients and healthy controls (n=5 each). Differentially expressed miRNAs in these samples were validated via qPCR in ESCC patients (n=96) and healthy controls (n=51), and the relationship between ESCC patient plasma miR-1260b and miR-720 levels and clinicopathological characteristics were additionally examined. In total, 12 plasma miRNAs that were differentially expressed between ESCC patients and healthy controls were identified via miRNA. Six of these miRNAs were subsequently validated, revealing that both miR-1260b and miR-720 were significantly differentially abundant in ESCC patients and controls, with miR-1260b being significantly upregulated in ESCC patients relative to controls (2.24, 1.41 respectively, P<0.001), while the opposite was observed with respect to miR-720 (0.66, 2.27 respectively, P=0.001). The use of both miR-720 and miR-1260b as a combined diagnostic tool was highly efficacious, yielding an AUC of 0.814, a sensitivity of 86.3%, and a specificity of 73.2% as a means of detecting ESCC patients. Elevated plasma miR-1260b level was also associated with a poorer patient prognosis when compared to patients with a low plasma miRNA level (P=0.021). This study has successfully developed a plasma miRNA biomarker signature of ESCC that may offer value as a diagnostic or prognostic tool when evaluating patients with ESCC.     

食管鳞癌相关基因与预后及临床病理关系的研究进展

食管鳞癌是一种多因素的疾病,除了环境因素可以影响食管癌发生和发展,分子水平的基因改变是近年研究的热点。近年基因芯片技术的发展,已发现众多基因,如β-catenin、wnt1、p53、cyclinD1以及EGFR等基因表达的改变与食管鳞癌的发生、发展或预后相关,从而可更好地寻找判断预后的分子指标,具有广阔的应用前景,但其与影响食管鳞癌预后的众多因素之间的关系及其与临床病理的关系以及应用,仍需进一步研究。     

食管鳞癌相关基因与预后及临床病理关系的研究进展

食管鳞癌是一种多因素的疾病,除了环境因素可以影响食管癌发生和发展,分子水平的基因改变是近年研究的热点。近年基因芯片技术的发展,已发现众多基因,如β-catenin、wnt1、p53、cyclinD1以及EGFR等基因表达的改变与食管鳞癌的发生、发展或预后相关,从而可更好地寻找判断预后的分子指标,具有广阔的应用前景,但其与影响食管鳞癌预后的众多因素之间的关系及其与临床病理的关系以及应用,仍需进一步研究。