scholarly journals Bioinformatic Analysis: The Role of LINC00634 in Colorectal Carcinoma

2021 ◽  
Author(s):  
Fang Liu ◽  
Fengyihuan Fu ◽  
Yuqiang Nie
Keyword(s):  
Esophageal Cancer ◽  
Regression Analysis ◽  
Prognostic Factors ◽  
Colorectal Carcinoma ◽  
Roc Curve ◽  
Cox Regression ◽  
Survival Outcomes ◽  
Immune Infiltration ◽  
The Relationship

Abstract Background: LINC00634 is highly expressed in esophageal cancer, and its depletion can suppress the viability and induce the apoptosis of esophageal cancer cells. However, there is a lack of studies that examine the relationship between LINC00634 expression and the clinicopathological features, survival outcomes, prognostic factors and tumor immune cell infiltration of colorectal carcinoma (CRC) patients.Objective: We aim at investigating the role of LINC00634 in colorectal carcinoma.Methods: We obtained data from the TCGA (The Cancer Genome Atlas) public database, GTEx (Genotype-Tissue Expression) database and clinical samples. Wilcoxon rank-sum test, Kruskal-Wallis test and logistic regression analysis were employed to assess the relationship between LINC00634 expression and the clinicopathological characteristics of CRC patients. Receiver operating characteristic (ROC) curve was constructed to evaluate the ability of LINC00634 for distinguishing between CRC patients and normal subjects based on the area under the curve (AUC) score. Univariate and multivariate analyses were conducted to evaluate the association between prognostic factors and survival outcomes. Kaplan-Meier curves and Cox regression analysis were employed to determine the contribution of LINC00634 expression to the prognosis of colorectal carcinoma patients. Immune infiltration analysis and Gene Set Enrichment Analysis (GSEA) were conducted to identify the significantly involved functions of LINC00634. Finally, a nomogram was constructed for internal verification based on the Cox regression data.Results: The expression of LINC00634 was upregulated in CRC patients, and markedly associated with N stage, residual tumor, pathological stage, and overall survival (OS) event. ROC curve showed that LINC00634 had strong diagnostic and prognostic abilities (AUC=0.74). The high expression of LINC00634 could predict poor disease specific survival (DSS; P=0.008) and poor overroll survival (OS;P<0.01). The expression of LINC00634 was independently associated with OS in CRC patients (P=0.019). GSEA and immune infiltration analysis demonstrated that LINC00634 expression was involved in gene transcription, epigenetic regulation and the functions of certain types of immune infiltrating cells. The c-index of the nomogram was 0.772 (95％CI: 0.744-0.799).Conclusions: Our study reveals that LINC00634 can serve as a potential prognostic biomarker for CRC patients.

scholarly journals Expression Status and Prognostic Value of m6A RNA Methylation Regulators in Lung Adenocarcinoma

2020 ◽  
Author(s):  
Rui Wang ◽  
Zian Feng ◽  
Jie Hu ◽  
Xiaodong He ◽  
Zuojun Shen
Keyword(s):  
Regression Analysis ◽  
Survival Analysis ◽  
Roc Curve ◽  
Cox Regression ◽  
Risk Group ◽  
Cox Regression Analysis ◽  
Rna Methylation ◽  
Kaplan Meier ◽  
Prediction Efficiency

Abstract Background: N6-methyladenosine (m6A) RNA modification is the most abundant modification method in mRNA, and it plays an important role in the occurrence and development of many cancers. However, data on the role of m6A RNA methylation regulators in lung adenocarcinoma (LUAD) are still lacking. This paper mainly discusses the role of m6A RNA methylation regulators in LUAD, to identify novel prognostic biomarkers.Methods: The gene expression data of 19 m6A methylation regulator in LUAD patients and its relevant clinical parameters were extracted from The Cancer Genome Atlas (TCGA) database. The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm were performed to construct a risk signature and evaluated its prognostic prediction efficiency by using the receiver operating characteristic (ROC) curve. The risk score of each patient was calculated according to the risk signature, and LUAD patients were divided into high-risk group and low-risk group. Kaplan-Meier survival analysis and Cox regression analysis were used to identify the independent prognostic significance of risk signature. Finally, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were used to explore the differential signaling pathways and cellular processes between the two groups.Results: The expression of 15 m6A RNA methylation regulators in LUAD tissues was significantly different than that in normal tissues. YTHDF3, YTHDF2, KIAA1429, HNRNPA2B1, RBM15, METTL3, HNRNPC, YTHDF1, IGF2BP2, IGF2BP3, IGF2BP1 were significantly up-regulated in LUAD, and the expressions of FTO, ZC3H13, WTAP, and METL14 were significantly down-regulated. We selected IGF2BP1, HNRNPC, and HNRNPA2B1 to construct the risk signature. ROC curve indicated the area under the curve (AUC) was 0.659, which means the risk signature had a good prediction efficiency. The results of Kaplan-Meier survival analysis and Cox regression analysis showed that the risk score can be used as an independent prognostic factor for LUAD.Conclusions: The m6A RNA methylation regulators IGF2BP1, HNRNPC, and HNRNPA2B1 have a significant correlation with the clinicopathological characteristics of LUAD, which may be a promising prognostic feature and clinical treatment target.

scholarly journals NMB as a Novel Prognostic Biomarker in Colorectal Cancer Correlating with Immune Infiltrates

2022 ◽  
Author(s):  
Jiaxin Fan ◽  
Chaowei Liang ◽  
Jiajia Wang ◽  
Chaojie Liang ◽  
Jiansheng Guo
Keyword(s):  
Colorectal Cancer ◽  
T Cells ◽  
Regression Analysis ◽  
Survival Rate ◽  
Signaling Pathway ◽  
Risk Score ◽  
Roc Curve ◽  
The Relationship ◽  
Geo Database

Abstract Background:Neuromedin B(NMB) is associated with the occurrence and development of a variety of cancers, However, the role of NMB in colorectal cancer is lacking in further studies.Methods:Transcriptome data and clinical data of CRC were downloaded and analyzed from the TCGA database and GEO database to study the differential expression of NMB. We analyzed the relationship between NMB expression and survival in patients with colorectal cancer using 8 public datasets from the Gene Expression Integration (GEO) database and the TCGA database. Meta-analysis was performed on the analysis results of TCGA and GEO data to determine the role of NMB in CRC. The receiver operating characteristic (ROC) curve was used to evaluate the accuracy of NMB in predicting survival rate in CRC patients. Wilcox. Test and Kruskal. Tests were used to study the relationship between clinicopathological features and the expression of NMB. Cox regression analysis was used to analyze the effect of NMB expression on survival. Gene collection enrichment analysis (GSEA) was performed using the TCGA database to screen the signaling pathway regulated by NMB. The Linkedomics platform was used to identify NMB co-expressed genes and explore the potential mechanisms of NMB mediation. Tumor Immune Estimation Resource (TIMER) site database was used to analyze the relationship between NMB expression level and immune infiltration. Related genes were identified by co-expression analysis, and four genes (NDUFB10, SERF2, DPP7, and NAPRT) were screened out as a prognostic signature. The relationship between risk score and OS were studied to explore the predictive value of risk score for CRC. Nomogram was constructed to predict 1 - and 3-year survival in colorectal cancer patients.Results:NMB was highly expressed in colorectal cancer, suggested a poor prognosis. The ROC curve proved that NMB had a high accuracy in predicting the survival rate of CRC patients. Multivariate regression analysis demonstrated that NMB was an independent predictor of survival in patients with CRC.GSEA identified the pathways involved in NMB regulation, including the P53 Signaling pathway, VEGF Signaling pathway, JAK-STAT Signaling pathway, MAPK Signaling pathway,mTOR Signaling pathway, TGF-BETA Signaling pathway, and WNT Signaling pathway, etc. Then,6512 co-expressed genes were identified through the Linkedomics Platform to investigate the potential mechanisms of NMB regulation, including Hepatocellular carcinoma cell cycle, EGF/EGFR Signaling Pathway, VEGFA-VEGFR2 Signaling Pathway, etc. We also conclude that NMB is correlated with T cells CD8, T cells CD4 memory resting, Macrophages M0. Different mutational forms of NMB were associated with the immune infiltration of 6 leukocytes. We determined the relationship between NMB and immune marker sets in colorectal cancer, such as CCR7, CD3E, CTLA4, HAVCR2, HLA-DPB1. The predictive ability of the risk score was significantly better than that of T, N, and M stages. A new nomogram for predicting the 1-year and 3-year OS of CRC patients was constructed, showing good reliability and accuracy for improved treatment decisions. In addition, NMB may contribute to drug resistance in CRC.Conclusion:NMB is highly expressed in CRC and provides a potential biomarker for the diagnosis and prognosis of CRC.

scholarly journals Role of the TGFβ/PDCD4/AP-1 Signaling Pathway in Nasopharyngeal Carcinoma and Its Relationship to Prognosis

2017 ◽  
Vol 43 (4) ◽  
pp. 1392-1401 ◽  
Author(s):  
Jie Ma ◽  
Shu-Hong Xuan ◽  
Yan Li ◽  
Zhi-Ping Zhang ◽  
Xin-Hua Li
Keyword(s):  
Regression Analysis ◽  
Prognostic Factors ◽  
Nasopharyngeal Carcinoma ◽  
Cox Regression ◽  
Advanced Tumor Stage ◽  
Cox Regression Analysis ◽  
Normal Tissues ◽  
Kaplan Meier ◽  
Low Expression

Background: The objective of the present study was to evaluate the role of the TGFβ/PDCD4/AP-1 pathway in nasopharyngeal carcinoma (NPC) and its relationship to NPC prognosis. Methods: NPC tissues collected from 66 NPC patients were compared to 17 nasopharyngeal mucosa biopsy specimens collected as normal tissues. Immunohistochemical staining was performed to assess expression of transforming growth factor-β receptor I (TGFβRI), programmed cell death 4 (PDCD4) and activator protein-1 (AP-1). The Kaplan-Meier method was applied to evaluate NPC patient overall survival (OS) and progression-free-survival (PFS). Cox regression analysis was used to estimate independent prognostic factors for NPC. The human NPC cell line CNE2 was selected and treated with SB431542, an inhibitor of TGFβRI; expression of TGFβRI and PDCD4 in CNE2 cells was determined by western blotting. NPC tissues showed higher expression of TGFβRI and AP-1 but lower expression of PDCD4 than normal tissues (all P < 0.05). Results: The results of Kaplan-Meier analysis showed that TGFβRI-positive patients and AP-1-positive patients had shorter OS and PFS than TGFβRI-negative patients and AP-1-negative patients; additionally, PDCD4-positive patients had higher OS and PFS than PDCD4-negative patients. Cox regression analysis revealed that advanced tumor stage, overexpression of TGFβRI and AP-1, and low expression of PDCD4 were unfavorable factors influencing OS and PFS in NPC patients. Compared with the control group, expression of TGFβRI decreased and that of PDCD4 increased significantly in CNE2 cells treated with the inhibitor (all P < 0.05). These findings indicate that the TGFβ/PDCD4/AP-1 pathway may be associated with NPC development and progression. Conclusion: High expression of TGFβRI and AP-1 and low expression of PDCD4 may be unfavorable prognostic factors for NPC.

scholarly journals Identification of a New Prognostic Risk Signature of Clear Cell Renal Cell Carcinoma Based on N6-Methyladenosine RNA Methylation Regulators

2021 ◽  
Vol 2021 ◽  
pp. 1-23
Author(s):  
Yan Zhang ◽  
Yao Yao ◽  
Xiaochen Qi ◽  
Jianyi Li ◽  
Meihong Liu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Regression Analysis ◽  
Roc Curve ◽  
Cox Regression ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma ◽  
Cox Regression Analysis ◽  
Rna Methylation ◽  
M6a Rna Methylation

As the most prevalent internal eukaryotic modification, N6-methyladenosine (m6A) is installed by methyltransferases, removed by demethylases, and recognized by readers. However, there are few studies on the role of m6A in clear cell renal cell carcinoma (ccRCC). In this study, we researched the RNA-seq transcriptome data of ccRCC in the TCGA dataset and used bioinformatics analyses to detect the relationship between m6A RNA methylation regulators and ccRCC. First, we compared the expression of 18 m6A RNA methylation regulators in ccRCC patients and normal tissues. Then, data from ccRCC patients were divided into two clusters by consensus clustering. LASSO Cox regression analysis was used to build a risk signature to predict the prognosis of patients with ccRCC. An ROC curve, univariate Cox regression analysis, and multivariate Cox regression analysis were used to verify this risk signature’s predictive ability. Then, we internally validated this signature by random sampling. Finally, we explored the role of the genes in the signature in some common pathways. Gene distribution between the two subgroups was different; cluster 2 was gender-related and had a worse prognosis. IGF2BP3, IGF2BP2, HNRNPA2B1, and METTL14 were chosen to build the risk signature. The overall survival of the high- and low-risk groups was significantly different ( p = 7.47 e − 12 ). The ROC curve also indicated that the risk signature had a decent predictive significance ( AUC = 0.72 ). These results imply that the risk signature has a potential value for ccRCC treatment.

scholarly journals The Role of CBLL1 in the Prognosis and Immune Infiltration of Pan-Cancer

2020 ◽  
Author(s):  
Qiang Guo ◽  
Dan Li ◽  
Yanmei Ji ◽  
Jialong Guo
Keyword(s):  
Mrna Expression ◽  
Immune Cells ◽  
Cox Regression ◽  
Expression Level ◽  
Cox Regression Analysis ◽  
Immune Infiltration ◽  
The Relationship ◽  
Pan Cancer ◽  
Ucsc Database

Abstract ObjectiveThis study aims to explore the role of CBLL1 in pan-carcinoma and tumor immune infiltrates. MethodsDownload mRNA expression, mutation and clinical data in UCSC database, to analyze the relationship between CBLL1 expression and clinicopathological vlaue, and immune microenvironment in pan-cancer. CIBERSORT was used to analyze the relationship between CBLL1 expression and the infiltration of pan-carcinoma immune cells. The mRNA expression data of UCSC database were used to analyze the correlation between CBLL1 expression and pan-cancer immunomodulations, checkpoints and receptor molecules. ResultsThe levels of CBLL1 mRNA expression in pan-cancer tissues were abnormal. The level of CBLL1 is related to the age, race, clinical stage and treatment effect of patients with pan-carcinoma and associated with the prognosis of patients with KIRC, LUSC, THCA, THYM, MESO, PRAD, STAD, and UVM. Univariate COX regression analysis showed that expression of CBLL1 was a risk factor for poor prognosis in patients with KICH, KIRC, LAML, THYM, KIRC, PCPG, OV, PRAD, STAD, GBM and UVM. The expression level of CBLL1 was correlated with BLCA, BRCA, COAD, LAML, LGG, LUAD, LUSC, SARC, STAD, THCA, THYM and UVM tumor mutational burden, and with ACC, BRCA, CESC, COAD, DLBC, HNSC, PRAD, READ, SARC, STAD, TGCT, THCA and UCEC microsatellite instability. The expression level of CBLL1 was correlated with cancer stromal cells and immune cells. The expression of CBLL1 is related to pan-cancer immunomodulators, checkpoints and receptor molecules. ConclusionCBLL1 is abnormally expressed in patients with pan-carcinoma, which is expected to be a biomarker for prognosis, mutation and immune infiltration in patients with pan-carcinoma.

scholarly journals Identification of Prognostic RBPs in Osteosarcoma

2021 ◽  
Vol 20 ◽  
pp. 153303382110049
Author(s):  
Bei Li ◽  
Long Fang ◽  
Baolong Wang ◽  
Zengkun Yang ◽  
Tingbao Zhao
Keyword(s):  
Regression Analysis ◽  
Prognostic Factors ◽  
Differential Expression ◽  
Ribosome Biogenesis ◽  
Rna Binding ◽  
Cox Regression ◽  
Rna Binding Proteins ◽  
Malignant Tumors ◽  
Differential Expression Analysis ◽  
Cox Regression Analysis

Osteosarcoma often occurs in children and adolescents and causes poor prognosis. The role of RNA-binding proteins (RBPs) in malignant tumors has been elucidated in recent years. Our study aims to identify key RBPs in osteosarcoma that could be prognostic factors and treatment targets. GSE33382 dataset was downloaded from Gene Expression Omnibus (GEO) database. RBPs extraction and differential expression analysis was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed to explore the biological function of differential expression RBPs. Moreover, we constructed Protein-protein interaction (PPI) network and obtained key modules. Key RBPs were identified by univariate Cox regression analysis and multiple stepwise Cox regression analysis combined with the clinical information from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Risk score model was generated and validated by GSE16091 dataset. A total of 38 differential expression RBPs was identified. Go and KEGG results indicated these RBPs were significantly involved in ribosome biogenesis and mRNA surveillance pathway. COX regression analysis showed DDX24, DDX21, WARS and IGF2BP2 could be prognostic factors in osteosarcoma. Spearman’s correlation analysis suggested that WARS might be important in osteosarcoma immune infiltration. In conclusion, DDX24, DDX21, WARS and IGF2BP2 might play key role in osteosarcoma, which could be therapuetic targets for osteosarcoma treatment.

scholarly journals LDH, CRP and ALB predict nucleic acid turn negative within 14 days in symptomatic patients with COVID-19

2021 ◽  
pp. 003693302199424
Author(s):  
Gaoli Liu ◽  
Bicheng Zhang ◽  
Shaowen Zhang ◽  
Haifeng Hu ◽  
TingTing Liu
Keyword(s):  
Logistic Regression ◽  
Regression Analysis ◽  
Nucleic Acid ◽  
Hospital Stay ◽  
Prognostic Marker ◽  
Roc Curve ◽  
Prognostic Value ◽  
Statistical Significance ◽  
Biochemical Indicators ◽  
The Relationship

Aims To search for biochemical indicators that can identify symptomatic patients with COVID-19 whose nucleic acid could turn negative within 14 days, and assess the prognostic value of these biochemical indicators in patients with COVID-19. Patients and methods We collected the clinical data of patients with COVID-19 admitted to our hospital, by using logistic regression analysis and AUC curves, explored the relationship between biochemical indicators and nucleic acid positive duration, the severity of COVID-19, and hospital stay respectively. Results A total of two hundred and thirty-three patients with COVID-19 were enrolled in the study. We found patients whose nucleic acid turned negative within 14 days had lower LDH, CRP and higher ALB ( P < 0.05). ROC curve results indicated that lower LDH, TP, CRP and higher ALB predicted the nucleic acid of patients turned negative within 14 days with statistical significance( P < 0.05), AST, LDH, CRP and PCT predicted the severe COVID-19 with statistical significance, and CRP predicted hospital stay >31days with statistical significance ( P < 0.05). After verification, the probability of nucleic acid turning negative within 14 days in patients with low LDH (<256 U/L), CRP (<44.5 mg/L) and high ALB (>35.8 g/L) was about 4 times higher than that in patients with high LDH, CRP and low ALB ( P < 0.05). Conclusions LDH, CRP and ALB are useful prognostic marker for predicting nucleic acid turn negative within 14 days in symptomatic patients with COVID-19.

FAM196B promotes proliferation and migration via regulating epithelial-mesenchymal transition in esophageal cancer

2021 ◽  
pp. 1-8
Author(s):  
Haifeng Xia ◽  
Fang Hu ◽  
Liangbin Pan ◽  
Chengcheng Xu ◽  
Haitao Huang ◽  
...  
Keyword(s):  
Esophageal Cancer ◽  
Western Blot ◽  
Cox Regression ◽  
Epithelial Mesenchymal Transition ◽  
Mesenchymal Transition ◽  
Cox Regression Analysis ◽  
Ec Cells ◽  
And Migration ◽  
Proliferation And Migration

BACKGROUND: EC (esophageal cancer) is a common cancer among people in the world. The molecular mechanism of FAM196B (family with sequence similarity 196 member B) in EC is still unclear. This article aimed to clarify the role of FAM196B in EC. METHODS: The expression of FAM196B in EC tissues was detected using qRT-PCR. The prognosis of FAM196B in EC patients was determined by log-rank kaplan-Meier survival analysis and Cox regression analysis. Furthermore, shRNA was used to knockdown the expression of FAM196B in EC cell lines. MTT, wound healing assays and western blot were used to determine the role of FAM196B in EC cells. RESULTS: In our research, we found that the expression of FAM196B was up-regulated in EC tissues. The increased expression of FAM196B was significantly correlated with differentiation, lymph node metastasis, stage, and poor survival. The proliferation and migration of EC cells were inhibited after FAM196B-shRNA transfection in vitro and vivo. The western blot result showed that FAM196B could regulate EMT. CONCLUSION: These results suggested that FAM196B severs as an oncogene and promotes cell proliferation and migration in EC. In addition, FAM196B may be a potential therapeutic target for EC patients.

The Role of an Actual Brand Positioning: An Analysis of Digital Advertisements

2021 ◽  
pp. 1-10
Author(s):  
June Won ◽  
J. Lucy Lee
Keyword(s):  
Regression Analysis ◽  
Content Analysis ◽  
Brand Positioning ◽  
Focus Group Interviews ◽  
Mediating Role ◽  
Percentage Difference ◽  
Performance Tradition ◽  
Group Interviews ◽  
The Relationship

The purpose of this study was to: (a) investigate the actual positions in digital communications; (b) assess the relationship between position-congruity among intended positions (i.e., how a firm desires to be perceived by consumers), actual brand positions, and perceived brand positions (i.e., the perceptions that customers have in their minds); and (c) understand the role of actual positioning (AP) in the positioning process. Multiple methods (one-on-one and focus group interviews, content analysis) were applied to analyze positions. Brand managers, golf consumers, and digital advertisements in Golf Digest magazine were sampled. Content analysis, frequencies and percentages, percentage difference, and regression analysis were performed for all positions for each research brand. The results revealed that: (a) tangibility-based positions (88.5%: great quality, innovation) outnumbered intangibility-based ones (11.5%: tour performance, tradition) in digital AP, (b) there was no positive correlation between the degree of congruence between intended and AP and the degree of congruence between intended and perceived positioning, and (c) the AP mediated between intended and perceived positioning in the brand positioning model. The study provides empirical evidence for the mediating role of AP and suggests modifications to the previous positioning process.

scholarly journals High Expression of PRMT6 Associated With Prognosis and Immune Infiltration in Glioma

2020 ◽  
Author(s):  
Yi Yang ◽  
Zhenshuang Wang ◽  
Shengrong Long ◽  
Jinhai Huang ◽  
Chengran Xu ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Clinical Work ◽  
High Expression ◽  
Clinical Indicators ◽  
Immune Infiltration ◽  
Tumor Tissues ◽  
Potential Biomarker ◽  
Patient Prognosis ◽  
The Relationship

Abstract Background: Gliomas are characterised by easy invasion of surrounding tissues, high mortality and poor prognosis. Moreover, with the increase of grade, the prognosis of glioma is increasingly poor and not optimistic. Therefore, biological markers for glioma are needed in clinical work, which can be utilized to detect and evaluate the situation and prognosis of glioma patients. Many studies have found that the protein arginine methyltransferase 6 (PRMT6) expression is elevated in various tumors and is associated with patient prognosis. However, the role of PRMT6 in glioma has not been reported or analyzed. Methods: In this study, we used a variety of tumor related databases to analyze the mechanism of PRMT6 in tumors, especially gliomas, from the perspective of bioinformatics, and carried out relevant experimental verification with tumor tissues extracted from patients during surgery. In addition, we analyzed the relationship between PRMT6 expression and immune infiltration and immune-related cells, and discussed the possible mechanisms. We also discussed the role of PRMT6 expression in glioma from the perspectives of mutation, clinical indicators, enrichment analysis, and immunohistochemical results. Results: PRMT6 is significantly differentially expressed in a variety of tumors and is associated with survival and prognosis. Especially in gliomas, the expression of PRMT6 gradually increased with the increase of grade. In addition, PRMT6 can be used as an independent prognostic risk factor in the nomogram and has been verified in a variety of databases. Conclusions: Our results indicate that high expression of PRMT6 is a potential biomarker for predicting glioma prognosis and progression.

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