scholarly journals OSmfs: An Online Interactive Tool to Evaluate Prognostic Markers for Myxofibrosarcoma

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1523
Author(s):  
Huimin Li ◽  
Longxiang Xie ◽  
Qiang Wang ◽  
Yifang Dang ◽  
Xiaoxiao Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Poor Prognosis ◽  
Analysis Data ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Prognostic Biomarkers ◽  
Rank Test ◽  
Web Tool ◽  
Kaplan Meier ◽  
Cox Analysis

Myxofibrosarcoma is a complex genetic disease with poor prognosis. However, more effective biomarkers that forebode poor prognosis in Myxofibrosarcoma remain to be determined. Herein, utilizing gene expression profiling data and clinical follow-up data of Myxofibrosarcoma cases in three independent cohorts with a total of 128 Myxofibrosarcoma samples from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we constructed an easy-to-use web tool, named Online consensus Survival analysis for Myxofibrosarcoma (OSmfs) to analyze the prognostic value of certain genes. Through retrieving the database, users generate a Kaplan–Meier plot with log-rank test and hazard ratio (HR) to assess prognostic-related genes or discover novel Myxofibrosarcoma prognostic biomarkers. The effectiveness and availability of OSmfs were validated using genes in ever reports predicting the prognosis of Myxofibrosarcoma patients. Furthermore, utilizing the cox analysis data and transcriptome data establishing OSmfs, seven genes were selected and considered as more potentially prognostic biomarkers through overlapping and ROC analysis. In conclusion, OSmfs is a promising web tool to evaluate the prognostic potency and reliability of genes in Myxofibrosarcoma, which may significantly contribute to the enrichment of novelly potential prognostic biomarkers and therapeutic targets for Myxofibrosarcoma.

scholarly journals Novel Epigenetic Eight-Gene Signature Predictive of Poor Prognosis and MSI-Like Phenotype in Human Metastatic Colorectal Carcinomas

Cancers ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 158
Author(s):  
Valentina Condelli ◽  
Giovanni Calice ◽  
Alessandra Cassano ◽  
Michele Basso ◽  
Maria Grazia Rodriquenz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Poor Prognosis ◽  
Cpg Island ◽  
Colon Adenocarcinoma ◽  
Gene Signature ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Cpg Island Methylator Phenotype ◽  
Prognostic Information ◽  
Global Methylation

Epigenetics is involved in tumor progression and drug resistance in human colorectal carcinoma (CRC). This study addressed the hypothesis that the DNA methylation profiling may predict the clinical behavior of metastatic CRCs (mCRCs). The global methylation profile of two human mCRC subgroups with significantly different outcome was analyzed and compared with gene expression and methylation data from The Cancer Genome Atlas COlon ADenocarcinoma (TCGA COAD) and the NCBI GENE expression Omnibus repository (GEO) GSE48684 mCRCs datasets to identify a prognostic signature of functionally methylated genes. A novel epigenetic signature of eight hypermethylated genes was characterized that was able to identify mCRCs with poor prognosis, which had a CpG-island methylator phenotype (CIMP)-high and microsatellite instability (MSI)-like phenotype. Interestingly, methylation events were enriched in genes located on the q-arm of chromosomes 13 and 20, two chromosomal regions with gain/loss alterations associated with adenoma-to-carcinoma progression. Finally, the expression of the eight-genes signature and MSI-enriching genes was confirmed in oxaliplatin- and irinotecan-resistant CRC cell lines. These data reveal that the hypermethylation of specific genes may provide prognostic information that is able to identify a subgroup of mCRCs with poor prognosis.

scholarly journals Functions and Clinical Significance of KLRG1 in the Development of Lung Adenocarcinoma and Immunotherapy

2020 ◽  
Author(s):  
Xiaodong Yang ◽  
Yuexin Zheng ◽  
Zhihai Han ◽  
xiliang zhang
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Lung Adenocarcinoma ◽  
Killer Cell ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Prognostic Biomarkers ◽  
Normal Lung ◽  
Using Data ◽  
Low Expression

Abstract Background. As a marker of differentiation, Killer cell lectin like receptor G1 (KLRG1) plays an inhibitory role in human NK cells and T cells. However, its clinical role remains inexplicit. This work intended to investigate the predictive ability of KLRG1 in lung adenocarcinoma (LUAD) after immune-checkpoint inhibitor therapy, as well as to explore the role of a possible KLRG1 molecular mechanism on LUAD development.Methods. Using data from the Gene Expression Omnibus, the Cancer Genome Atlas and the Genotype-Tissue Expression, we compared the expression of KLRG1 and its related genes Bruton tyrosine kinase (BTK), C-C motif chemokine receptor 2 (CCR2), Scm polycomb group protein like 4 (SCML4) in LUAD and normal lung tissues. We further established a stable LUAD cell line with KLRG1 knockdown and investigate the effect of KLRG1 knockdown on tumor cell proliferation. We also studied the prognostic value of the four factors in terms of overall survival (OS) in LUAD. Using data from the Gene Expression Omnibus, we further investigated the expression of KLRG1 in the patients with different responses after immunotherapy.Results. The expression of KLRG1, BTK, CCR2 and SCML4 was significantly downregulated in LUAD tissues compared to normal controls. Knockdown of KLRG1 promoted the proliferation of A549 tumor cells. And low expression of these four factors was all associated with unfavorable overall survival in patients with LUAD. Furthermore, low expression of KLRG1 also correlated with poor responses in LUAD patients after immunotherapy.Conclusion. Based on these findings, we infer that KLRG1 had significant correlation with immunotherapy response. Meanwhile, KLRG1, BTK, CCR2 and SCML4 might serve as valuable prognostic biomarkers in LUAD. Key pointsKLRG1 inhibits the progress of LUAD.KLRG1 had significant correlation with immunotherapy response.KLRG1, BTK, CCR2 and SCML4 might serve as valuable prognostic biomarkers in LUAD.

scholarly journals Unveiling Prognostics Biomarkers of Tyrosine Metabolism Reprogramming in Liver Cancer by Cross-platform Gene Expression Analyses

2020 ◽  
Author(s):  
Tran Ngoc Nguyen ◽  
Ha Quy Nguyen ◽  
Duc-Hau Le
Keyword(s):  
Gene Expression ◽  
Normal Liver ◽  
Tyrosine Aminotransferase ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Enzymatic Reactions ◽  
Kaplan Meier ◽  
Catabolic Genes ◽  
Tyrosine Metabolism ◽  
Cross Platform

AbstractTyrosine is mainly degraded in the liver by a series of enzymatic reactions. Abnormal expression of the tyrosine catabolic enzyme tyrosine aminotransferase (TAT) has been reported in patients with hepatocellular carcinoma (HCC). Despite this, aberration in tyrosine metabolism has not been investigated in cancer development. In this work, we conduct comprehensive cross-platform study to obtain foundation for discoveries of potential therapeutics and preventative biomarkers of HCC. We explore data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine and Kaplan Meier plotter (KM plotter) and performed integrated analyses to evaluate the clinical significance and prognostic values of the tyrosine catabolic genes in HCC. We find that five tyrosine catabolic enzymes are downregulated in HCC compared to normal liver at mRNA and protein level. Moreover, low expression of these enzymes correlates with poorer survival in patients with HCC. Notably, we identify pathways and upstream regulators that might involve in tyrosine catabolic reprogramming and further drive HCC development. In total, our results underscore tyrosine metabolism alteration in HCC and lay foundation for incorporating these pathway components in therapeutics and preventative strategies.

OScc: an online survival analysis web server to evaluate the prognostic value of biomarkers in cervical cancer

2019 ◽  
Vol 15 (32) ◽  
pp. 3693-3699 ◽  
Author(s):  
Qiang Wang ◽  
Lu Zhang ◽  
Zhongyi Yan ◽  
Longxiang Xie ◽  
Yang An ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Web Server ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Prognostic Biomarkers ◽  
P Value ◽  
Kaplan Meier ◽  
Cancer Genome Atlas ◽  
The Web

Aim: To establish a web server that can mutually validate prognostic biomarkers of cervical cancer. Methods: Four datasets including expression profiling and relative clinical follow-up data were collected from Gene Expression Omnibus and The Cancer Genome Atlas. The web server was developed by R software. Results: The web server was named OScc including 690 patients and can be accessed at http://bioinfo.henu.edu.cn/CESC/CESCList.jsp . The Kaplan–Meier survival curves with log-rank p-value and hazard ratio will be generated of interested gene in OScc. Compared with previous predictive tools, OScc had the advantages of registration-free, larger sample size and subgroup analysis. Conclusion: The OScc is highly valuable to perform the preliminary assessment and validation of new or interested prognostic biomarkers for cervical cancer.

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 Overexpression of B7-H3 Is Associated With Poor Prognosis in Laryngeal Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Yixuan Li ◽  
Qian Cai ◽  
Ximing Shen ◽  
Xiaoting Chen ◽  
Zhong Guan
Keyword(s):  
Gene Expression ◽  
Laryngeal Cancer ◽  
Poor Prognosis ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Expression Level ◽  
Normal Tissues ◽  
Qrt Pcr ◽  
Node Metastasis ◽  
B7 Family

The immune checkpoint molecule, B7-H3, which belongs to the B7 family, has been shown to be overexpressed in various cancers. Its role in tumors is not well defined, and many studies suggest that it is associated with poor clinical outcomes. The effect of B7-H3 on laryngeal cancer has not been reported. This study investigated the expression of B7-H3 in laryngeal squamous cell carcinoma (LSCC), and its relationship with clinicopathological factors and prognosis of LSCC patients. The gene expression quantification data and clinical data of LSCC retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were analyzed to determine the diagnostic and prognostic roles of B7-H3. Quantitative real-time polymerase chain reaction (qRT-PCR) was then performed to determine the gene expression level of B7-H3 between LSCC tissues and paired normal adjacent tissues. In addition, TCGA RNA-seq data was analyzed to evaluate the expression level of B7 family genes. Next, the protein expression of B7-H3 and CD8 in LSCC was determined using immunohistochemistry and immunofluorescence. qRT-PCR results showed that the expression level of B7-H3 mRNA was significantly higher in LSCC tissues than in adjacent normal tissues. Similar results were obtained from the TCGA analysis. The expression of B7-H3 was significantly associated with T stage, lymph node metastasis, and pathological tumor node metastasis (TNM) stage, and it was also an independent factor influencing the overall survival time (OS) of patients with LSCC. In addition, B7-H3 was negatively correlated with CD8+T cells. These results show that B7-H3 is upregulated in LSCC. Therefore, B7-H3 may serve as a biomarker of poor prognosis and a promising therapeutic target in LSCC.

scholarly journals Prognostic Value of Genes Related with Tumor Microenvironment in Ovarian Cancer

2020 ◽  
Author(s):  
Shimei Li ◽  
Jiyi Yao ◽  
Shen Zhang ◽  
Xinchuan Zhou ◽  
Xinbao Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Tumor Microenvironment ◽  
Poor Prognosis ◽  
External Validation ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Gene Expression Signatures ◽  
Poor Outcomes ◽  
Geo Database

Abstract Background Ovarian cancer (OV) is the fifth leading cause of cancer death among females. Growing evidence supports a key role of tumor microenvironment in growth, progress, and metastasis of OV. However, the impacts of gene expression signatures related with OV microenvironment on prognosis have not been well-established . This study aimed to apply ESTIMATE algorithm to extract genes related with tumor microenvironment that predicted poor outcomes in OV patients. Methods The gene expression profile of OV samples were downloaded from The Cancer Genome Atlas (TCGA) database. The immune scores and stromal scores of 469 OV samples were available based on the ESTIMATE algorithm. To better understand impacts of gene expression signatures related with OV microenvironment on prognosis, these samples were categorized based on their ESTIMATE scores into high and low score groups. A different OV cohort from the Gene Expression Omnibus (GEO) database was used for external validation. Results The molecular subtypes in OV patients were correlated with stromal scores, in which the mesenchymal subtype had the highest stromal scores (p < 0.0001). Poor prognosis were found in patients (especially for patients with overall survivals (OS) < 5 years) with higher stromal score (p = 0.0376). 449 differentially expressed genes (DEGs) in stromal scores group were identified and 26 DEGs were significantly associated with poor prognosis in OV patients (p < 0.05). Eventually, 6 genes have further validated to be significantly associated with poor outcomes in 40 patients from a different OV cohort of GEO database (p < 0.05). Conclusion In this study, several genes related with tumor microenvironment that predicted poor prognosis in OV patients were extracted. In addition, some previously overlooked genes could be potential prognostic biomarkers for OV.

scholarly journals Identification of Genes in Patients for Predicting Ulcerative Colitis-Associated Colorectal Cancer

2020 ◽  
Author(s):  
hongyun wei ◽  
qian zhang ◽  
xiaosa chi ◽  
xiaohui yang ◽  
zibin tian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Ulcerative Colitis ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Rank Test ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Limma Package ◽  
Public Datasets

Abstract BackgroundUlcerative colitis (UC) has been considered as a risk factor for colorectal cancer (CRC). However, effective biomarkers for predicting UC-associated CRC are lacking. Therefore, it is necessary to screen biomarkers associated with UC-related CRC, which could be used to evaluate UC-associated CRC early, and provide possible mechanisms involved in UC-associated CRC. Efficient bioinformatics analysis could help us to explore potential biomarkers.MethodsTwo public datasets, including 44 UC without CRC samples and 17 UC-associated CRC samples were chosen from Gene Expression Omnibus (GEO) database. Sva package was used to remove batch effects, and then we screened out differentially expressed genes (DEGs) with limma package. STRING and Cytoscape were used to achieve protein-protein interaction (PPI) network analysis. The survival curves between high and low gene expression were performed by log rank test based on the cancer genome atlas (TCGA) program. The expression of three identified hub genes was validated based on Oncomine. To validate the expression of three hub genes, we compared the expression of three hub genes between normal and colorectal cancer based on Oncomine.Results405 DEGs were identified, including 256 down-regulated genes and 149 up-regulated genes in UC-associated CRC tissues. 16 hub genes were identified. And among them, RPL6, RPL7, and RPL35 were related to poor prognosis of patients in survival analysis. Higher expression of RPL6, RPL7, and RPL35 was validated in CRC tissues based on Oncomine.ConclusionsOur study showed that overexpressed RPL6, RPL7, and RPL 35 may be potential tumor oncogenes and could act as a prognostic factor in clinical diagnosis and treatment.

scholarly journals Identification and Validation of a Novel Immune-Related Four-lncRNA Signature for Lung Adenocarcinoma

2021 ◽  
Vol 12 ◽  
Author(s):  
Jixin Wang ◽  
Xiangjun Yin ◽  
Yin-Qiang Zhang ◽  
Xuming Ji
Keyword(s):  
Gene Expression ◽  
Lung Adenocarcinoma ◽  
Immune Cell ◽  
Cox Regression ◽  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Lasso Regression ◽  
Kaplan Meier

Lung adenocarcinoma (LUAD) is a major subtype of lung cancer, the prognosis of patients with which is associated with both lncRNAs and cancer immunity. In this study, we collected gene expression data of 585 LUAD patients from The Cancer Genome Atlas (TCGA) database and 605 subjects from the Gene Expression Omnibus (GEO) database. LUAD patients were divided into high and low immune-cell-infiltrated groups according to the single sample gene set enrichment analysis (ssGSEA) algorithm to identify differentially expressed genes (DEGs). Based on the 49 immune-related DE lncRNAs, a four-lncRNA prognostic signature was constructed by applying least absolute shrinkage and selection operator (LASSO) regression, univariate Cox regression, and stepwise multivariate Cox regression in sequence. Kaplan–Meier curve, ROC analysis, and the testing GEO datasets verified the effectiveness of the signature in predicting overall survival (OS). Univariate Cox regression and multivariate Cox regression suggested that the signature was an independent prognostic factor. The correlation analysis revealed that the infiltration immune cell subtypes were related to these lncRNAs.

scholarly journals Prediction of Poor Prognosis of HCC by Early Warning Model for Co-Expression of miRNA and mRNA Based on Bioinformatics Analysis

2020 ◽  
Vol 19 ◽  
pp. 153303382095935
Author(s):  
Zi-jian Su ◽  
Chun-cheng Lin ◽  
Jian-hui Pan ◽  
Jian-hua Zhang ◽  
Tao Han ◽  
...  
Keyword(s):  
High Risk ◽  
Poor Prognosis ◽  
Target Genes ◽  
Risk Model ◽  
Prognostic Significance ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Venn Diagram ◽  
Kaplan Meier ◽  
Cox Analysis

Objective: Hepatocellular Carcinoma (HCC) has the highest mortality rate worldwide with the intractability of its extremely complicated pathogenesis and unclear mechanism. The limited survival highlights the need for the further detection of prognosis for HCC. MicroRNAs (miRNAs) and messenger RNAs (mRNAs) have been identified as regulatory factors and target genes in human cancers, while some studies also found post-transcriptional modification plays a crucial role in the occurrence and development of HCC. The present study aimed to elucidate the prognostic significance of miRNA and mRNA models in HCC. Methods: Data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases. The miRNA and mRNA expressions were tested by the Wilcoxon and used funrich software to predict mRNA that might be related to miRNA. Then we determined the intersection with overlapped mRNA and miRNA Venn diagram, and screened out hub gene by using Degree algorithm in Cytoscape software. The COX models, with TCGA data as the training set and ICGC data as the test set, were constructed. All patients were divided into high-risk and low-risk groups. Data on overall survival of different groups were collected and analyzed by Kaplan-Meier method, and independent risk factors affecting prognosis were assessed by Cox analysis. Results: The miRNA and mRNA polygenic risk model showed a good true positive rate. Kaplan-Meier curve and Cox analysis suggested that the high-risk group was associated with poor prognosis, and the risk score could be used as an independent risk factor for HCC. Conclusion: Tumor risk models constructed in this study could effectively predict the prognosis of patients, which is expected to provide a reference for the prognostic stratification and treatment strategy development of HCC.

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