scholarly journals The clinical value of lncRNA NEAT1 in digestive system malignancies: A comprehensive investigation based on 57 microarray and RNA-seq datasets

Oncotarget ◽  
2017 ◽  
Vol 8 (11) ◽  
pp. 17665-17683 ◽  
Author(s):  
Dan-Dan Xiong ◽  
Zhen-Bo Feng ◽  
Wei-Luan Cen ◽  
Jing-Jing Zeng ◽  
Lu Liang ◽  
...  
Keyword(s):  
Digestive System ◽  
Rna Seq ◽  
Clinical Value ◽  
Comprehensive Investigation ◽  
Lncrna Neat1

scholarly journals Potential Targets and Clinical Value of MiR-224-5p in Cancers of the Digestive Tract

2017 ◽  
Vol 44 (2) ◽  
pp. 682-700 ◽  
Author(s):  
Lu Zhang ◽  
Lan-shan Huang ◽  
Gang Chen ◽  
Zhen-bo Feng
Keyword(s):  
Digestive Tract ◽  
Digestive System ◽  
Kegg Pathway ◽  
Univariate Analysis ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Clinical Value ◽  
Go Annotation ◽  
Pathway Enrichment ◽  
Target Mrnas

Background/Aims: MicroRNAs participate in various biological processes in malignant tumors. However, the mechanisms of miR-224-5p in digestive system cancers are not fully understood. A comprehensive investigation of the clinical value and potential targets of miR-224-5p in cancers of the digestive tract is necessary. Methods: Expression profiling data and related-prognostic data of miR-224-5p were acquired from Gene Expression Omnibus, The Cancer Genome Atlas, ArrayExpress, and published literature. The potential target mRNAs of miR-224-5p were predicted using bioinformatics methods and finally annotated using Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Results: MiR-224-5p is up-regulated in digestive system cancers (SMD=0.69, 95% CI: 0.43-0.96, P<0.0001) and exhibits a moderate diagnostic ability (AUC=0.84, 95% CI: 0.80-0.87). Our data also demonstrated that miR-224-5p is statistically significantly correlated with overall survival univariate analysis (HR=1.69, 95% CI: 1.15-2.49, P=0.007) and multivariate analysis (HR=2.39, 95% CI: 1.74-3.30, P<0.0001). In total, 388 potential miR-224-5p target mRNAs were predicted by bioinformatics methods. GO annotation analysis revealed that the top terms of miR-224-5p in biological process, cellular component and molecular function were system development, neuron part, and transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding, respectively. Moreover, eight pathways were identified in KEGG pathway enrichment analysis. Conclusions: MiR-224-5p is up-regulated and has the potential to become a diagnostic and prognostic biomarker in digestive system cancers. MiR-224-5p might play vital roles in cancers of the digestive tract but the exact molecular mechanisms need further study and verification.

scholarly journals Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative

2018 ◽  
pp. 1-18 ◽  
Author(s):  
Christian Brueffer ◽  
Johan Vallon-Christersson ◽  
Dorthe Grabau ◽  
Anna Ehinger ◽  
Jari Häkkinen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Endocrine Therapy ◽  
Single Gene ◽  
Growth Factor Receptor ◽  
Population Based ◽  
Classification Performance ◽  
Error Rates ◽  
Classification Error ◽  
Rna Seq ◽  
Clinical Value

Purpose In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification. Methods In total, 3,678 patients with BC were studied. For 405 tumors, a comprehensive multi-rater histopathologic evaluation was performed. Using RNA-seq data, single-gene classifiers and multigene classifiers (MGCs) were trained on consensus histopathology labels. Trained classifiers were tested on a prospective population-based series of 3,273 BCs that included a median follow-up of 52 months (Sweden Cancerome Analysis Network—Breast [SCAN-B], ClinicalTrials.gov identifier: NCT02306096), and results were evaluated by agreement statistics and Kaplan-Meier and Cox survival analyses. Results Pathologist concordance was high for ER, PgR, and HER2 (average κ, 0.920, 0.891, and 0.899, respectively) but moderate for Ki67 and NHG (average κ, 0.734 and 0.581). Concordance between RNA-seq classifiers and histopathology for the independent cohort of 3,273 was similar to interpathologist concordance. Patients with discordant classifications, predicted as hormone responsive by histopathology but non–hormone responsive by MGC, had significantly inferior overall survival compared with patients who had concordant results. This extended to patients who received no adjuvant therapy (hazard ratio [HR], 3.19; 95% CI, 1.19 to 8.57), or endocrine therapy alone (HR, 2.64; 95% CI, 1.55 to 4.51). For cases identified as hormone responsive by histopathology and who received endocrine therapy alone, the MGC hormone-responsive classifier remained significant after multivariable adjustment (HR, 2.45; 95% CI, 1.39 to 4.34). Conclusion Classification error rates for RNA-seq–based classifiers for the five key BC biomarkers generally were equivalent to conventional histopathology. However, RNA-seq classifiers provided added clinical value in particular for tumors determined by histopathology to be hormone responsive but by RNA-seq to be hormone insensitive.

scholarly journals Cell-type diversity and regionalized gene expression in the planarian intestine

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
David J Forsthoefel ◽  
Nicholas I Cejda ◽  
Umair W Khan ◽  
Phillip A Newmark
Keyword(s):  
Gene Expression ◽  
Hedgehog Signaling ◽  
Digestive System ◽  
Cell Types ◽  
Goblet Cells ◽  
Proper Function ◽  
Rna Seq ◽  
Digestive Physiology ◽  
Gli 1 ◽  
Laser Capture

Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.

scholarly journals Overexpression of RAB34 Associates With Tumor Aggressiveness and Immune Infiltration in Glioma

2021 ◽  
Author(s):  
Peng Hou ◽  
Quan Wan ◽  
Qing Wang ◽  
Xuechao Wu ◽  
Xiaojie Lu
Keyword(s):  
Epithelial To Mesenchymal Transition ◽  
The Cancer Genome Atlas ◽  
Immune Checkpoints ◽  
Migration And Invasion ◽  
Rna Seq ◽  
Clinical Value ◽  
Mesenchymal Transition ◽  
Immune Infiltration ◽  
Genome Atlas

Abstract Background: RAB34 is aberrantly expressed in various cancers and exhibits oncogenic properties. However, its function in glioma remains largely unclear. Herein, we investigated the clinical value and biological functions of RAB34 in glioma.Methods: In this study, we collected 697 RNA-seq data from The Cancer Genome Atlas (TCGA) dataset and 325 RNA-seq data from Chinese Glioma Genome Atlas (CGGA) dataset. CCK-8 and EdU assays were employed to assess cell proliferation ability. The transwell assay was utilized to explore cell migration and invasion capacities. Western blot coupled with qRT-PCR were employed to determine the protein, as well as RNA contents. The statistical analyses along with the graphical work were mainly implemented in the R software.Results: RAB34 expression was positively related to the glioma tumor grade, and predicted poor outcomes for glioma patients. RAB34 expression was significantly upregulated in classical and mesenchymal subtypes, and IDH wild-type gliomas. Additionally, RAB34 expression was regulated by promoter DNA methylation. Moreover, RAB34 expression was remarkably correlated with inflammatory activities, immune infiltration, and immune checkpoints in glioma. In vitro experiments demonstrated that inhibition of RAB34 restrained the growth, migration, as well as invasion of glioma cells, and reversed the epithelial-to-mesenchymal transition (EMT) process. Conclusion: Our findings established RAB34 as a novel progression-related biomarker and a possible immunotherapy target for glioma.

scholarly journals Overexpression of RAB34 associates with tumor aggressiveness and immune infiltration in glioma

2021 ◽  
Author(s):  
Peng Hou ◽  
Quan Wan ◽  
Qing Wang ◽  
Xuechao Wu ◽  
Xiaojie Lu
Keyword(s):  
Epithelial To Mesenchymal Transition ◽  
The Cancer Genome Atlas ◽  
Immune Checkpoints ◽  
Migration And Invasion ◽  
Rna Seq ◽  
Clinical Value ◽  
Mesenchymal Transition ◽  
Immune Infiltration ◽  
Genome Atlas

Abstract Background RAB34 is aberrantly expressed in various cancers and exhibits oncogenic properties. However, its function in glioma remains largely unclear. Herein, we investigated the clinical value and biological functions of RAB34 in glioma. Methods In this study, we collected 697 RNA-seq data from The Cancer Genome Atlas (TCGA) dataset and 325 RNA-seq data from Chinese Glioma Genome Atlas (CGGA) dataset. CCK-8 and EdU assays were employed to assess cell proliferation ability. The transwell assay was utilized to explore cell migration and invasion capacities. Western blot coupled with qRT-PCR were employed to determine the protein, as well as RNA contents. The statistical analyses along with the graphical work were mainly implemented in the R software. Results RAB34 expression was positively related to the glioma tumor grade, and predicted poor outcomes for glioma patients. RAB34 expression was significantly upregulated in classical and mesenchymal subtypes, and IDH wild-type gliomas. Additionally, RAB34 expression was regulated by promoter DNA methylation. Moreover, RAB34 expression was remarkably correlated with inflammatory activities, immune infiltration, and immune checkpoints in glioma. In vitro experiments demonstrated that inhibition of RAB34 restrained the growth, migration, as well as invasion of glioma cells, and reversed the epithelial-to-mesenchymal transition (EMT) process. Conclusion Our findings established RAB34 as a novel progression-related biomarker and a possible immunotherapy target for glioma.

scholarly journals Re-Clustering and Profiling of Digestive System Tumors According to Microenvironment Components

2021 ◽  
Vol 10 ◽  
Author(s):  
Yongwei Wang ◽  
Sen Guo ◽  
Zhihong Chen ◽  
Bing Bai ◽  
Shuo Wang ◽  
...  
Keyword(s):  
Digestive System ◽  
Poor Response ◽  
Response Prediction ◽  
Immune Checkpoint Blockade ◽  
Clinical Value ◽  
R Language ◽  
Survival Status ◽  
New Strategy ◽  
Cancer Genome Atlas ◽  
System Tumor

BackgroundImmunotherapy has become the most promising therapy in digestive system tumors besides conventional chemotherapy and radiotherapy. But only a few patients can benefit from different types of immunotherapies, such as immune checkpoint blockade (ICB). To identify these ICB-susceptible patients, methods are urgently needed to screen and profile subgroups of patients with different responsiveness to ICB.MethodsThis study carried out analysis on patients with digestive system tumors that were obtained from Cancer Genome Atlas (TCGA) cohorts. The analyses were mainly performed using GraphPad Prism 7 and R language.ResultsWe have quantified the microenvironmental components of eight digestive system tumor patients in TCGA cohorts and evaluated their clinical value. We re-clustered patients based on their microenvironment composition and divided these patients into six clusters. The differences between these six clusters were profiled, including survival conditions, enriched biological processes, genomic mutations, and microenvironment traits. Cluster 3 was the most immune-related cluster, exhibiting a high infiltration of non-tumor components and poor survival status, along with an inhibitory immune status, and we found that patients with high stromal score indicated a poor response in ICB cohort.ConclusionsOur research provides a new strategy based on the microenvironment components for the reclassification of digestive system tumors, which could provide guidance for prognosis judgment and treatment response prediction like ICB.

Sign in / Sign up

Export Citation Format

Share Document