scholarly journals Transcription levels and prognostic significance of the NFI family members in human cancers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8816 ◽  
Author(s):  
Yuexian Li ◽  
Cheng Sun ◽  
Yonggang Tan ◽  
Lin Li ◽  
Heying Zhang ◽  
...  
Keyword(s):  
Head And Neck ◽  
Mrna Expression ◽  
Critical Role ◽  
Prognostic Significance ◽  
Family Members ◽  
Survival Outcomes ◽  
Expression Levels ◽  
Human Cancers ◽  
Study Results ◽  
Km Plotter

Background The nuclear factor I (NFI) is a family of transcription factors consisting of four distinct but closely related genes, NFIA, NFIB, NFIC and NFIX, which are important in the development of various tissues and organs in mammals. Recent study results have shown that NFI family may play a critical role in the progression of various human tumors and have been identified as key tumor suppressors and oncogenes for many cancers. However, the expression levels and distinctive prognostic values of the NFI family remain poorly explored in most cancers. Materials and Methods In the present study, the differences in mRNA expression of the NFI family in various cancers were investigated using the Oncomine and TCGA databases, and the mRNA expression, genetic alteration and DNA methylation of the NFI family members in various cancers were examined using cBioPortal for Cancer Genomics. In addition, the prognostic significance of the NFI family was assessed in multiple cancers using the Kaplan–Meier plotter (KM plotter) and SurvExpress databases. Results The mRNA expression levels in the NFI family were significantly downregulated in most cancers compared with normal tissues and DNA hypermethylation might downregulate the NFI family expression. Although NFIX expression was not downregulated in kidney, colorectal and prostate cancers. Furthermore, NFIB expression was upregulated in gastric cancer. Further survival analyses based on the KM plotter and SurvExpress databases showed dysregulations of the NFI genes were significantly correlated with survival outcomes in breast, lung, and head and neck cancers. Decreased expression levels of NFIA, NFIB and NFIC were associated with poor overall survival (OS) in head and neck cancer. Low mRNA expression of NFIA and NFIB was significantly associated with OS and first progression in lung adenocarcinoma, but not in lung squamous cell carcinoma. In addition, potential correlations between NFI family members and survival outcomes were also observed in liver, esophageal, kidney and cervical cancer. Conclusion The results from the present study indicated certain members of the NFI family could be promising therapeutic targets and novel prognostic biomarkers for human cancers.

scholarly journals High Expression of LTBP2 Contributes to Poor Prognosis in Colorectal Cancer Patients and Correlates with the Mesenchymal Colorectal Cancer Subtype

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Ying Huang ◽  
Guihua Wang ◽  
Chunmei Zhao ◽  
Rong Geng ◽  
Shu Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Protein Expression ◽  
Mrna Expression ◽  
Cell Lines ◽  
Critical Role ◽  
Prognostic Significance ◽  
Poor Overall Survival ◽  
Expression Levels ◽  
Mrna And Protein Expression

Colorectal cancer (CRC) is a complex and heterogeneous disease with four consensus molecular subtypes (CMS1-4). LTBP2 is a member of the fibrillin/LTBP super family and plays a critical role in tumorigenesis by activating TGF-β in the CMS4 CRC subtype. So far, the expression and prognostic significance of LTBP2 in CRC remains obscure. In this study, we aimed to analyze the mRNA and protein expression levels of LTBP2 in CRC tissues and then estimate their values as a potential prognostic biomarker. We detected the mRNA expression of LTBP2 in 28 cases of fresh CRC tissues and 4 CRC cell lines and the protein expression of LTBP2 in 483 samples of CRC tissues, matched tumor-adjacent tissues, and benign colorectal diseases. LTBP2 protein expression was then correlated to patients’ clinical features and overall survival. Both LTBP2 mRNA and protein expression levels in CRC tissues were remarkably superior to those in adjacent normal colorectal tissues (P=0.0071 and P<0.001, respectively), according to TCGA dataset of CRC. High LTBP2 protein expression was correlated with TNM stage (P<0.001), T stage (P<0.001), N stage (P<0.001), and M stage (P<0.001). High LTBP2 protein expression was related to poor overall survival in CRC patients and was an independent prognostic factor for CRC. LTBP2 mRNA expression was especially higher in the CMS4 subtype (P<0.001), which was confirmed in CRC cell lines. Our data suggested that LTBP2 may act as an oncogene in the development of colorectal cancer and have important significance in predicting CRC prognosis. LTBP2 could be a novel biomarker and potential therapeutic target for mesenchymal colorectal cancer and can improve the outcome of high-risk CRC.

scholarly journals Comprehensive analysis of inhibitor of differentiation/DNA-binding gene family in lung cancer using bioinformatics methods

2020 ◽  
Vol 40 (2) ◽  
Author(s):  
Suming Xu ◽  
Yaoqin Wang ◽  
Yanhong Li ◽  
Lei Zhang ◽  
Chunfang Wang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Transcription Factor ◽  
Dna Binding ◽  
Mrna Expression ◽  
Family Members ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Genetic Mutations ◽  
Expression Levels ◽  
Mrna Expression Levels

Abstract The inhibitor of differentiation/DNA-binding (ID) is a member of the helix–loop–helix (HLH) transcription factor family, and plays a role in tumorigenesis, invasiveness and angiogenesis. The aims were to investigate the expression patterns and prognostic values of individual ID family members in lung cancer, and the potential functional roles. The expression levels of ID family were assessed using the Oncomine online database and GEPIA database. Furthermore, the prognostic value of ID family members was evaluated using the Kaplan–Meier plotter database. The genetic mutations of ID family members were investigated using the cBioPortal database. Moreover, enrichment analysis was performed using STRING database and Funrich software. It was found that all the ID family members were significantly down-regulated in lung cancer. Prognostic results indicated that low mRNA expression levels of ID1 or increased mRNA expression levels of ID2/3/4 were associated with improved overall survival, first progression and post progression survival. Additionally, genetic mutations of ID family members were identified in lung cancer, and it was suggested that amplification and deep deletion were the main mutation types. Furthermore, functional enrichment analysis results suggested that ID1/2/4 were significantly enriched in ‘regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism’ for biological process, ‘transcription factor activity’ for molecular function and ‘HLH domain’ for protein domain. However, it was found that ID3 was not enriched in the above functions. The aberrant expression of ID family members may affect the occurrence and prognosis of lung cancer, and may be related to cell metabolism and transcriptional regulation.

scholarly journals The prognostic value of long noncoding RNA SNHG16 on clinical outcomes in human cancers: a systematic review and meta-analysis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Chenghao Zhang ◽  
Xiaolei Ren ◽  
Jieyu He ◽  
Wanchun Wang ◽  
Chao Tu ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Prognostic Value ◽  
Meta Analysis ◽  
Clinicopathological Features ◽  
Survival Outcomes ◽  
Tumor Type ◽  
Free Survival ◽  
Expression Levels ◽  
Human Cancers ◽  
Tcga Dataset

Abstract Background Cancer has been a worldwide health problem with a high risk of morbidity and mortality, however ideal biomarkers for effective screening and diagnosis of cancer patients are still lacking. Small nucleolar RNA host gene 16 (SNHG16) is newly identified lncRNA with abnormal expression in several human malignancies. However, its prognostic value remains controversial. This meta-analysis aimed to synthesize available data to clarify the association between SNHG16 expression levels and clinical prognosis value in multiple cancers. Methods Extensive literature retrieval was conducted to identify eligible studies, and data regarding SNHG16 expression levels on survival outcomes and clinicopathological features were extracted and pooled for calculation of the hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (CIs). Forest plots were applied to show the association between SNHG16 expression and survival prognosis. Additionally, The Cancer Genome Atlas (TCGA) dataset was screened and extracted for validation of the results in this meta-analysis. Results A total of eight studies comprising 568 patients were included in the final meta-analysis according to the inclusion and exclusion criteria. In the pooled analysis, high SNHG16 expression significantly predicted worse overall survival (OS) in various cancers (HR = 1.87, 95% CI 1.54–2.26, P < 0.001), and recurrence-free survival (RFS) in bladder cancer (HR = 1.68, 95% CI 1.01–2.79, P = 0.045). Meanwhile, stratified analyses revealed that the survival analysis method, tumor type, sample size, and cut-off value did not alter the predictive value of SNHG16 for OS in cancer patients. In addition, compared to the low SNHG16 expression group, patients with high SNHG16 expression were more prone to worse clinicopathological features, such as larger tumor size, advanced clinical stage, lymph node metastasis (LNM) and distant metastasis (DM). Exploration of TCGA dataset further validated that the upregulated SNHG16 expression predicted unfavorable OS and disease-free survival (DFS) in cancer patients. Conclusions The present study implicated that aberrant expression of lncRNA SNHG16 was strongly associated with clinical survival outcomes in various cancers, and therefore might serve as a promising biomarker for predicting prognosis of human cancers.

scholarly journals Riemerella anatipestifer infection in ducks induces IL-17A production, but not IL-23p19

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rochelle A. Flores ◽  
Cherry P. Fernandez-Colorado ◽  
Fahmida Afrin ◽  
Paula Leona T. Cammayo ◽  
Suk Kim ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Proinflammatory Cytokines ◽  
Post Infection ◽  
Proinflammatory Cytokine ◽  
Th17 Cells ◽  
Critical Role ◽  
Splenic Lymphocytes ◽  
Expression Levels ◽  
Time Points ◽  
Mrna Expression Analysis

Abstract R. anatipestifer (RA) is one of the most harmful bacterial pathogens affecting the duck industry, and infection is associated with the production of proinflammatory cytokines, including IL-17A. Another proinflammatory cytokine, IL-23, is critical for the development of Th17 cells, which produce IL-17. However, IL-23 roles have not been studied in this infection. Here, we describe the identification and mRNA expression analysis of duck IL-23p19 (duIL-23p19) in splenic lymphocytes and macrophages stimulated with killed RA and in spleens of RA-infected ducks. Expression of duIL-23p19 transcript identified in this study was relatively high in livers of healthy ducks and was upregulated in mitogen-activated splenic lymphocytes as well as in splenic lymphocytes and macrophages stimulated with killed RA. In spleens of RA-infected ducks, expression levels of duIL-23p19 transcript were unchanged at all time points except on days 4 and 7 post-infection; however, duIL-17A and IL-17F expression levels were upregulated in both spleens of RA-infected ducks and splenic lymphocytes and macrophages stimulated with killed RA. In sera collected at 24 h after this infection, duIL-23p19 expression levels were unchanged, whereas IL-17A significantly upregulated. These results suggest that IL-23p19 does not play a critical role in the IL-17A response in early stages of RA-infected ducks.

scholarly journals Prognostic significance of Wilms tumor 1 mRNA expression levels in peripheral blood and bone marrow in patients with myelodysplastic syndromes

2016 ◽  
Vol 17 (1) ◽  
pp. 21-32 ◽  
Author(s):  
Sumiko Kobayashi ◽  
Yasunori Ueda ◽  
Yasuhito Nannya ◽  
Hirohiko Shibayama ◽  
Hideto Tamura ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Mrna Expression ◽  
Myelodysplastic Syndromes ◽  
Peripheral Blood ◽  
Wilms Tumor ◽  
Prognostic Significance ◽  
Expression Levels ◽  
Wilms Tumor 1 ◽  
Mrna Expression Levels

scholarly journals Expression and prognostic significance of MT1 isoforms in clear cell renal cell carcinoma

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 280
Author(s):  
Xiaohua Niu ◽  
Ling Deng ◽  
Chaoming Tang ◽  
Dexiang Zhuo
Keyword(s):  
Mrna Expression ◽  
Survival Time ◽  
Renal Cell ◽  
Clear Cell ◽  
Cell Cancer ◽  
Tumor Biology ◽  
Prognostic Significance ◽  
High Expression ◽  
Expression Levels ◽  
Mrna Expression Levels

Metallothioneins (MTs), a family of low-weight cysteine-rich proteins, play key roles in tumor biology, such as proliferation, differentiation, apoptosis, and drug resistance. Clinical studies have demonstrated that deregulation of MTs in various types of solid cancers. However, a comprehensive overview of MT1 isoforms expression and clinical relevance in clear cell renal cell cancer (ccRCC) is lacking. The present study explored mRNA expression levels and prognostic values of MT1 isoforms in ccRCC tissues using The Cancer Genome Atlas (TCGA), Gene Expression Profiling and Interactive Analysis (GEPIA) and Oncomine database. The study observed that mRNA expression levels of six members of MT1 isoforms decreased in renal cancer tumor tissues compared with normal tissues. We further found that high-expression of MT1G, MT1H, MT1F and MT1X was related with poor overall survival time in ccRCC patients and high-expression of MT1G, MT1F and MT1X were inversely associated with disease-free survival time in ccRCC patients. Based on the correlation analysis, MT1G was identified to be co-expressed with MT1H and MT1F in ccRCC tissues. These findings suggested that MT1 isoforms mRNA may serve as diagnostic and prognostic markers for ccRCC.

scholarly journals Association of mRNA expression levels of Cullin family members with prognosis in breast cancer

Medicine ◽  
2019 ◽  
Vol 98 (31) ◽  
pp. e16625 ◽  
Author(s):  
Aiyu Liu ◽  
Shizhen Zhang ◽  
Yanwen Shen ◽  
Rui Lei ◽  
Yannan Wang
Keyword(s):  
Breast Cancer ◽  
Mrna Expression ◽  
Family Members ◽  
Expression Levels ◽  
Mrna Expression Levels

scholarly journals Prognostic values of E2F mRNA expression in human gastric cancer

2018 ◽  
Vol 38 (6) ◽  
Author(s):  
Theasha Manicum ◽  
Fubiao Ni ◽  
Yiming Ye ◽  
Xuhui Fan ◽  
Bi-Cheng Chen
Keyword(s):  
Gastric Cancer ◽  
Transcription Factors ◽  
Mrna Expression ◽  
Prognostic Significance ◽  
Family Members ◽  
Incidence Rates ◽  
Human Gastric Cancer ◽  
Kaplan Meier ◽  
E2f Transcription Factors ◽  
Transcription Activators

Gastric cancer (GC) is the second most frequent cause of cancer-related mortality in the world, with Eastern Asia having the highest incidence rates. E2F is a family of transcription factor proteins that has a variety of functions, which include control of cell cycle, cell differentiation, DNA damage response and cell death. E2F transcription factors are divided into two subfamilies: transcription activators (E2F transcription factors 1 (E2F1), 2 (E2F2) and 3a (E2F3a)) and repressors (E2F3b, E2F transcription factors 4 (E2F4), 5 (E2F5), 6 (E2F6), 7 (E2F7) and 8 (E2F8)). Studies have demonstrated that E2F had prognostic significance in a number of cancers. However, the entirety of the prognostic roles of E2F mRNA expression in GC has not yet been apparently determined. In the present study, the prognostic value of individual family members of E2F mRNA expression for overall survival (OS) was evaluated by using online Kaplan–Meier Plotter (KM Plotter) database. Our result demonstrated that high expressions of three family members of E2F (E2F1, E2F3, E2F4) mRNA were significantly associated with unfavourable OS in all GC patients. However, increased expressions of E2F2, E2F5, E2F6 and E2F7 were significantly associated with favourable OS, especially for higher clinical stages in GC patients. These results provided a better insight into the prognostic functions of E2F mRNA genes in GC. Although the results should be further verified in clinical trials, our findings may be a favourable prognostic predictor for the development of newer therapeutic drugs in the treatment of GC.

scholarly journals Distinct Prognostic Values of Phospholipase C Beta Family Members for Non-Small Cell Lung Carcinoma

2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Tengfang Zhang ◽  
Xiaowei Song ◽  
Xiwen Liao ◽  
Xiangkun Wang ◽  
Guangzhi Zhu ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Phospholipase C ◽  
Small Cell Lung Carcinoma ◽  
Expression Patterns ◽  
Family Members ◽  
Small Cell ◽  
Small Cell Lung ◽  
Cell Lung Carcinoma ◽  
Expression Levels ◽  
Nsclc Patients

Background. Non-small cell lung cancer (NSCLC) is a main cause of cancer-related mortality worldwide. The relationships of the phospholipase C beta (PLCB) enzymes, which are encoded by the genes PLCB1, PLCB2, PLCB3, and PLCB4, with NSCLC have not been investigated. Therefore, the aim of the present study was to identify any correlations between NSCLC prognosis and the expression patterns of PLCB family members.Materials and Methods. The prognostic values of the PLCB gene family members in NSCLC patients were evaluated using the “Kaplan–Meier plotter” database, which includes updated gene expression data and survival information of a total of 1,926 NSCLC patients. The GeneMANIA plugin of Cytoscape software was used to evaluate the relationships of the four PLCB family members at the gene and protein levels. Gene ontology enrichment analysis and KEGG pathway analysis were performed using the Database for Annotation, Visualization, and Integrated Discovery.Results. High mRNA expression levels of PLCB1, PLCB2, and PLCB3 were significantly associated with poor overall survival (OS) of all NSCLC patients and significantly associated with poor prognosis of adenocarcinoma. In contrast, high mRNA expression of PLCB4 was associated with better OS of adenocarcinoma patients. In addition, the expression levels of the PLCB family members were correlated to smoking status, clinical stage, and patient sex but not radiotherapy and chemotherapy outcomes.Conclusions. PLCB1, PLCB2, PLCB3, and PLCB4 appear to be potential biomarkers for the prognosis of patients with NSCLC. The prognostic values of the PLCB genes require further investigations.

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