scholarly journals miR-1301-3p is a Potential Prognostic Biomarker for Esophageal Carcinoma and Acts by Downregulating NBL1 Expression

2021 ◽  
Author(s):  
Jianting Du ◽  
Li-rong Xiao ◽  
Guobing Xu ◽  
Bin Zheng ◽  
Chun Chen
Keyword(s):  
Poor Prognosis ◽  
Target Gene ◽  
Target Genes ◽  
Expression Patterns ◽  
The Cancer Genome Atlas ◽  
Poor Overall Survival ◽  
Expression Levels ◽  
Potential Biomarker ◽  
Cancer Genome Atlas ◽  
Web Platform

Abstract Background: Esophageal cancer (ESCA) is one of the most aggressive and lethal human malignant cancers. It is associated with poor overall survival (OS) and ranks sixth among the causes of cancer-related mortalities. MiR-1301-3p plays vital roles in a majority of malignancies. The aim of this study was to investigate the correlation between miR-1301-3p/NBL1 axis and prognosis of ESCA patients.Methods: We compared the miR-1301-3p expression levels between ESCA and normal esophageal tissues using MiRNAseq data retrieved from The Cancer Genome Atlas (TCGA) database. We employed UALCAN web platform, starBase v3.0 database, R software and GEPIA web platform to perform statistical analysis and data visualization. We then used TargetScan Human, miRDB and DIANA Tools databases to predict the miR-1301-3p target genes. Finally, we analyzed the expression patterns of the target genes as well as their prognostic value in ESCA.Results: There was an overexpression of miR-1301-3p in most malignancies, including ESCA (P<0.001). The miR-1301-3p expression levels were significantly related to age and histologic grade in primary ESCA (P<0.05), with high expression of miR-1301-3p being significantly associated with poor prognosis (Hazard ratio [HR]=1.88, P=0.012). NBL1 was identified as a potential target gene for miR-1301-3p and a negatively correlation in expression levels between the two genes was observed (r=-0.282, P<0.001). Notably, NBL1 was significantly downregulated in ESCA (P<0.001) and its low expression was significantly associated with poor prognosis of ESCA patients (HR=0.53, P=0.0063).Conclusion: miR-1301-3p is a potential biomarker for predicting prognosis of ESCA patients. It may regulate ESCA progression by regulating NBL1 expression.

scholarly journals miR-1301-3p is a potential prognostic biomarker for esophageal carcinoma and acts by downregulating NBL1 expression

2021 ◽  
Author(s):  
Jianting Du ◽  
Li-rong Xiao ◽  
Guobing Xu ◽  
Bin Zheng ◽  
Chun Chen
Keyword(s):  
Poor Prognosis ◽  
Target Gene ◽  
Target Genes ◽  
Expression Patterns ◽  
The Cancer Genome Atlas ◽  
Poor Overall Survival ◽  
Expression Levels ◽  
Potential Biomarker ◽  
Cancer Genome Atlas ◽  
Web Platform

Abstract Background: Esophageal cancer (ESCA) is one of the most aggressive and lethal human malignant cancers. It is associated with poor overall survival (OS) and ranks sixth among the causes of cancer-related mortalities. MiR-1301-3p plays vital roles in a majority of malignancies. The aim of this study was to investigate the correlation between miR-1301-3p/NBL1 axis and prognosis of ESCA patients.Methods: We compared the miR-1301-3p expression levels between ESCA and normal esophageal tissues using MiRNAseq data retrieved from The Cancer Genome Atlas (TCGA) database. We employed UALCAN web platform, starBase v3.0 database, R software and GEPIA web platform to perform statistical analysis and data visualization. We then used TargetScan Human, miRDB and DIANA Tools databases to predict the miR-1301-3p target genes. Finally, we analyzed the expression patterns of the target genes as well as their prognostic value in ESCA.Results: There was an overexpression of miR-1301-3p in most malignancies, including ESCA (P<0.001). The miR-1301-3p expression levels were significantly related to age and histologic grade in primary ESCA (P<0.05), with high expression of miR-1301-3p being significantly associated with poor prognosis (Hazard ratio [HR]=1.88, P=0.012). NBL1 was identified as a potential target gene for miR-1301-3p and a negatively correlation in expression levels between the two genes was observed (r=-0.282, P<0.001). Notably, NBL1 was significantly downregulated in ESCA (P<0.001) and its low expression was significantly associated with poor prognosis of ESCA patients (HR=0.53, P=0.0063).Conclusion: miR-1301-3p is a potential biomarker for predicting prognosis of ESCA patients. It may regulate ESCA progression by regulating NBL1 expression.

scholarly journals MicroRNA-497-5p Is Downregulated in Hepatocellular Carcinoma and Associated with Tumorigenesis and Poor Prognosis in Patients

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Lin-Lin Tian ◽  
Bin Qian ◽  
Xiao-Hui Jiang ◽  
Yu-Shan Liu ◽  
Tong Chen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cancer Progression ◽  
Poor Prognosis ◽  
Target Genes ◽  
Progression Free Survival ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Rank Test ◽  
Tumor Diameter ◽  
Expression Levels

Background. MicroRNAs (miRNAs) have been demonstrated to exhibit important regulatory roles in multiple malignancies, including hepatocellular carcinoma (HCC). hsa-miR-497-5p was reported to involve in cancer progression and poor prognosis in many kinds of tumors. However, the expression and its clinical significance of hsa-miR-497-5p in HCC remain unclear. Methods. In the present study, we investigated the expression of hsa-miR-497-5p in HCC and analyzed the correction of clinical features with prognosis. The expression levels of hsa-miR-497-5p and potential target genes were analyzed in HCC and adjacent noncancerous tissues using The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) datasets. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to analyze hsa-miR-497-5p levels in 328 HCC tissues and 30 paired adjacent noncancer tissues. Overall survival (OS) and progression-free survival (PFS) of patients with HCC were assessed using the Kaplan-Meier method and the log-rank test. Results. The hsa-miR-497-5p expression levels were decreased, and its target genes ACTG1, CSNK1D, PPP1CC, and BIRC5 were upregulated in HCC tissues compared with normal tissues. Lower levels of hsa-miR-497-5p expression and higher levels of the four target genes were significantly associated with higher tumor diameter. Moreover, patients with lower hsa-miR-497-5p expression and higher target genes levels had shorter OS. Conclusion. The expression levels of hsa-miR-497-5p may play an important regulatory role in HCC and are closely correlated with HCC progression and poor prognosis in patients. The hsa-miR-497-5p may be a specific therapeutic target for the treatment of HCC.

scholarly journals High Vimentin Expression Predicts a Poor Prognosis and Progression in Colorectal Cancer: A Study with Meta-Analysis and TCGA Database

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Le Du ◽  
Jingchuan Li ◽  
Lei Lei ◽  
Hongjuan He ◽  
Erfei Chen ◽  
...  
Keyword(s):  
Multivariate Analysis ◽  
Poor Prognosis ◽  
Meta Analysis ◽  
Univariate Analysis ◽  
Disease Free Survival ◽  
The Cancer Genome Atlas ◽  
Poor Overall Survival ◽  
Vimentin Expression ◽  
Cancer Genome Atlas ◽  
N Stage

The aim of this study was to evaluate the role of vimentin expression in the prognosis and progression of CRC. Meta-analysis was conducted to investigate the correlations between vimentin and prognosis and clinicopathological features in CRC. Literatures were searched by PubMed, Embase, ClinicalKey, CNKI, VIP, and WanFang databases. The Cancer Genome Atlas (TCGA) database was used to assess the association of vimentin expression with survival rate in CRC. Eleven reports with 1969 cases were included in the meta-analysis. The results showed that positive vimentin expression predicted a poor overall survival (OS) in the univariate analysis (HR: 2.087, 95%CI: 1.660-2.625) and multivariate analysis (HR: 1.633, 95%CI: 1.223-2.181). Vimentin overexpression also conferred worse disease-free survival (DFS) in the univariate analysis (HR: 2.069, 95%CI: 1.024-4.179) and multivariate analysis (HR: 2.802, 95%CI: 1.421-5.527). Moreover, upregulated vimentin is related to lymph node metastasis (OR: 2.288, 95%CI: 1.159-4.517), TNM stages (OR: 1.957, 95%CI: 1.333-2.873), and N stage (OR: 2.316, 95%CI: 1.482-3.620). Analysis of TCGA database indicated that elevated vimentin predicated a shorter OS (p=0.033). Our findings reveal that upregulated vimentin contributes to the progression and poor prognosis of CRC. Vimentin may be a prognostic biomarker and therapeutic target in patients with CRC.

scholarly journals FXYD5 is a Marker for Poor Prognosis and a Potential Driver for Metastasis in Ovarian Carcinomas

2015 ◽  
Vol 14 ◽  
pp. CIN.S30565 ◽  
Author(s):  
Pichai Raman ◽  
Timothy Purwin ◽  
Richard Pestell ◽  
Aydin Tozeren
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Poor Prognosis ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Ovarian Carcinomas ◽  
Tissue Arrays ◽  
Cancer Genome Atlas ◽  
Underlying Causes ◽  
Web Platform

Ovarian cancer (OC) is a leading cause of cancer mortality, but aside from a few well-studied mutations, very little is known about its underlying causes. As such, we performed survival analysis on ovarian copy number amplifications and gene expression datasets presented by The Cancer Genome Atlas in order to identify potential drivers and markers of aggressive OC. Additionally, two independent datasets from the Gene Expression Omnibus web platform were used to validate the identified markers. Based on our analysis, we identified FXYD5, a glycoprotein known to reduce cell adhesion, as a potential driver of metastasis and a significant predictor of mortality in OC. As a marker of poor outcome, the protein has effective antibodies against it for use in tissue arrays. FXYD5 bridges together a wide variety of cancers, including ovarian, breast cancer stage II, thyroid, colorectal, pancreatic, and head and neck cancers for metastasis studies.

scholarly journals DDX17 promotes hepatocellular carcinoma progression via inhibiting Klf4 transcriptional activity

2019 ◽  
Vol 10 (11) ◽  
Author(s):  
Ying Xue ◽  
Xuebing Jia ◽  
Changcan Li ◽  
Ke Zhang ◽  
Lei Li ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Target Gene ◽  
Target Genes ◽  
The Cancer Genome Atlas ◽  
Gene Expressions ◽  
Pathological Characteristics ◽  
Dead Box ◽  
Cancer Genome Atlas ◽  
First Time

Abstract DEAD box RNA helicase 17 (DDX17) is a transcriptional regulator of several transcription factors, which is more appreciated than its role in RNA metabolism. However, prognostic value and biofunction of DDX17 in HCC remain unclear. Illuminating the mechanism underlying the regulating HCC progression by DDX17 may contribute to therapeutic strategies. In our study, we report for the first time that DDX17 was overexpressed in HCC specimens by using The Cancer Genome Atlas (TCGA) and immunohistochemistry (IHC) and correlated to clinical pathological characteristics and patients’ survival. In vitro, DDX17 was ascertained to alter HCC migratory and invasive capacities after overexpression and knockdown in HCC cell lines. Moreover, by performing co-immunoprecipitation (Co-IP) and GST-pull down assay, the physical association between DDX17 and Klf4 was discovered and validated. Additionally, DDX17 could modulate expressions of Klf4 target genes including E-cadherin, MMP2 by inhibiting the promoter activity. The potent correlation between DDX17 and Klf4 target gene expressions was further appraised by a same set of 30 HCC tissues. Besides, we discovered that DDX17 could not deploy its function in regulating Klf4 target gene expressions and HCC progression in Klf4-depletion condition. Intriguingly, DDX17 failed to interact with Klf4 once the zinc-finger domain was deleted and inhibited the binding of Klf4 on MMP-2 promoter. Collectively, our study enucleates novel mechanism of DDX17-mediated oncogenesis by suppressing the transcriptional activity of Klf4 thus is likely to be a therapeutic target in HCC.

scholarly journals Identification of novel autophagy-related lncRNAs associated with a poor prognosis of colon adenocarcinoma through bioinformatics analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dejun Wu ◽  
Zhenhua Yin ◽  
Yisheng Ji ◽  
Lin Li ◽  
Yunxin Li ◽  
...  
Keyword(s):  
High Risk ◽  
Poor Prognosis ◽  
Notch Pathway ◽  
Colon Adenocarcinoma ◽  
High Risk Group ◽  
The Cancer Genome Atlas ◽  
Future Research ◽  
Risk Patients ◽  
Cancer Genome Atlas ◽  
Immune Score

AbstractLncRNAs play a pivotal role in tumorigenesis and development. However, the potential involvement of lncRNAs in colon adenocarcinoma (COAD) needs to be further explored. All the data used in this study were obtained from The Cancer Genome Atlas database, and all analyses were conducted using R software. Basing on the seven prognosis-related lncRNAs finally selected, we developed a prognosis-predicting model with powerful effectiveness (training cohort, 1 year: AUC = 0.70, 95% Cl = 0.57–0.78; 3 years: AUC = 0.71, 95% Cl = 0.6–0.8; 5 years: AUC = 0.76, 95% Cl = 0.66–0.87; validation cohort, 1 year: AUC = 0.70, 95% Cl = 0.58–0.8; 3 years: AUC = 0.73, 95% Cl = 0.63–0.82; 5 years: AUC = 0.68, 95% Cl = 0.5–0.85). The VEGF and Notch pathway were analyzed through GSEA analysis, and low immune and stromal scores were found in high-risk patients (immune score, cor =  − 0.15, P < 0.001; stromal score, cor =  − 0.18, P < 0.001) , which may partially explain the poor prognosis of patients in the high-risk group. We screened lncRNAs that are significantly associated with the survival of patients with COAD and possibly participate in autophagy regulation. This study may provide direction for future research.

scholarly journals Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Peirong Li ◽  
Tongbing Su ◽  
Deshuang Zhang ◽  
Weihong Wang ◽  
Xiaoyun Xin ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Leaf Development ◽  
Target Genes ◽  
Expression Patterns ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Leaf Morphogenesis ◽  
Expression Levels ◽  
Parental Lines

AbstractHeterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.

scholarly journals Radiosensitivity index emerges as a potential biomarker for combined radiotherapy and immunotherapy

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Yang-Hong Dai ◽  
Ying-Fu Wang ◽  
Po-Chien Shen ◽  
Cheng-Hsiang Lo ◽  
Jen-Fu Yang ◽  
...  
Keyword(s):  
Dna Repair ◽  
Interferon Γ ◽  
The Cancer Genome Atlas ◽  
Differential Analysis ◽  
Macrophage Polarisation ◽  
Molecular Features ◽  
Kaplan Meier ◽  
M1 Macrophage ◽  
Potential Biomarker ◽  
Cancer Genome Atlas

AbstractIn the era of immunotherapy, there lacks of a reliable genomic predictor to identify optimal patient populations in combined radiotherapy and immunotherapy (CRI). The purpose of this study is to investigate whether genomic scores defining radiosensitivity are associated with immune response. Genomic data from Merged Microarray-Acquired dataset (MMD) were established and the Cancer Genome Atlas (TCGA) were obtained. Based on rank-based regression model including 10 genes, radiosensitivity index (RSI) was calculated. A total of 12832 primary tumours across 11 major cancer types were analysed for the association with DNA repair, cellular stemness, macrophage polarisation, and immune subtypes. Additional 585 metastatic tissues were extracted from MET500. RSI was stratified into RSI-Low and RSI-High by a cutpoint of 0.46. Proteomic differential analysis was used to identify significant proteins according to RSI categories. Gene Set Variance Analysis (GSVA) was applied to measure the genomic pathway activity (18 genes for T-cell inflamed activity). Kaplan-Meier analysis was performed for survival analysis. RSI was significantly associated with homologous DNA repair, cancer stemness and immune-related molecular features. Lower RSI was associated with higher fraction of M1 macrophage. Differential proteomic analysis identified significantly higher TAP2 expression in RSI-Low colorectal tumours. In the TCGA cohort, dominant interferon-γ (IFN-γ) response was characterised by low RSI and predicted better response to programmed cell death 1 (PD-1) blockade. In conclusion, in addition to radiation response, our study identified RSI to be associated with various immune-related features and predicted response to PD-1 blockade, thus, highlighting its potential as a candidate biomarker for CRI.

scholarly journals HSP105 Recruits Protein Phosphatase 2A To Dephosphorylate β-Catenin

2015 ◽  
Vol 35 (8) ◽  
pp. 1390-1400 ◽  
Author(s):  
Nancy Yu ◽  
Michael Kakunda ◽  
Victoria Pham ◽  
Jennie R. Lill ◽  
Pan Du ◽  
...  
Keyword(s):  
Protein Phosphatase ◽  
Target Gene ◽  
Target Genes ◽  
Glycogen Synthase ◽  
Protein Phosphatase 2A ◽  
Breast Cancer Patients ◽  
Poor Overall Survival ◽  
Protein Levels ◽  
Phosphatase 2A ◽  
Unidentified Component

The Wnt/β-catenin pathway causes accumulation of β-catenin in the cytoplasm and its subsequent translocation into the nucleus to initiate the transcription of the target genes. Without Wnt stimulation, β-catenin forms a complex with axin (axis inhibitor), adenomatous polyposis coli (APC), casein kinase 1α (CK1α), and glycogen synthase kinase 3β (GSK3β) and undergoes phosphorylation-dependent ubiquitination. Phosphatases, such as protein phosphatase 2A (PP2A), interestingly, also are components of this degradation complex; therefore, a balance must be reached between phosphorylation and dephosphorylation. How this balance is regulated is largely unknown. Here we show that a heat shock protein, HSP105, is a previously unidentified component of the β-catenin degradation complex. HSP105 is required for Wnt signaling, since depletion of HSP105 compromises β-catenin accumulation and target gene transcription upon Wnt stimulation. Mechanistically, HSP105 depletion disrupts the integration of PP2A into the β-catenin degradation complex, favoring the hyperphosphorylation and degradation of β-catenin. HSP105 is overexpressed in many types of tumors, correlating with increased nuclear β-catenin protein levels and Wnt target gene upregulation. Furthermore, overexpression of HSP105 is a prognostic biomarker that correlates with poor overall survival in breast cancer patients as well as melanoma patients participating in the BRIM2 clinical study.

scholarly journals High RPS27A Expression Predicts Poor Prognosis in Patients With HPV Type 16 Cervical Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Qiming Wang ◽  
Yan Cai ◽  
Xuewen Fu ◽  
Liang Chen
Keyword(s):  
Cervical Cancer ◽  
Poor Prognosis ◽  
Biological Significance ◽  
Enrichment Analysis ◽  
Hpv Infection ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Protein Protein Interaction ◽  
Cervical Cancer Cells ◽  
Cancer Genome Atlas

In recent years, the incidence and the mortality rate of cervical cancer have been gradually increasing, becoming one of the major causes of cancer-related death in women. In particular, patients with advanced and recurrent cervical cancers present a very poor prognosis. In addition, the vast majority of cervical cancer cases are caused by human papillomavirus (HPV) infection, of which HPV16 infection is the main cause and squamous cell carcinoma is the main presenting type. In this study, we performed screening of differentially expressed genes (DEGs) based on The Cancer Genome Atlas (TCGA) database and GSE6791, constructed a protein–protein interaction (PPI) network to screen 34 hub genes, filtered to the remaining 10 genes using the CytoHubba plug-in, and used survival analysis to determine that RPS27A was most associated with the prognosis of cervical cancer patients and has prognostic and predictive value for cervical cancer. The most significant biological functions and pathways of RPS27A enrichment were subsequently investigated with gene set enrichment analysis (GSEA), and integration of TCGA and GTEx database analyses revealed that RPS27A was significantly expressed in most cancer types. In this study, our analysis revealed that RPS27A can be used as a prognostic biomarker for HPV16 cervical cancer and has biological significance for the growth of cervical cancer cells.

Sign in / Sign up

Export Citation Format

Share Document