scholarly journals Comprehensive Analysis of the Clinical and Biological Significances of Endoplasmic Reticulum Stress in Diffuse Gliomas

Author(s):  
Ruoyu Huang ◽  
Guanzhang Li ◽  
Kuanyu Wang ◽  
Zhiliang Wang ◽  
Fan Zeng ◽  
...  

BackgroundAs a critical organelle for protein and lipid synthesis, the dysfunction of endoplasmic reticulum has a significant impact on multiple biological processes of cells. Thus, in this study, we constructed an ER stress-related risk signature to investigate the functional roles of ER stress in gliomas.MethodsA total of 626 samples from TCGA RNA-seq dataset (training cohort) and 310 samples from CGGA RNA-seq dataset (validation cohort) were enrolled in this study. Clinical information and genomic profiles were also obtained. The ER stress signature was developed by the LASSO regression model. The prognostic value of the risk signature was evaluated by Cox regression, Kaplan-Meier and ROC Curve analyses. Bioinformatics analysis and experiment in vitro were performed to explore the biological implication of this signature.ResultsWe found that the ER stress-related signature was tightly associated with major clinicopathological features and genomic alterations of gliomas. Kaplan-Meier curve and Cox regression analysis indicated that ER stress activation was an independent prognostic factor for patients with glioma. Besides, we also constructed an individualized prognosis prediction model through Nomogram and ROC Curve analysis. Bioinformatics analysis suggested that ER stress activation also promoted the malignant progression of glioma and participated in the regulation of tumor immune microenvironment, especially the infiltration of macrophages in M2 phase. These results were further validated in IHC analysis and cell biology experiments.ConclusionThe ER stress activation had a high prognostic value and could serve as a promising target for developing individualized treatment of glioma.

2021 ◽  
Author(s):  
Yen-ting Lin ◽  
Can-Xuan Li ◽  
Jie Chen

Abstract Background: Ferroptosis is a novel defined type of programmed cell death (PCD) with widespread functions involved in physical conditions or multiple diseases including malignancies. However, the relationship between ccRCC and ferroptosis-related regulators remains poorly known. Herein, we investigate the prognostic values and potential mechanisms of ferroptosis-related genes (FRGs) in ccRCC.Methods: Ferroptosis-related genes were obtained from FerrDb database, GeneCards database and previously published literatures. The gene expression profile of ferroptosis-related regulators and corresponding clinicopathological information were downloaded from The Cancer Genome Atlas (TCGA). Differentially expressed ferroptosis-related genes (DE-FRGs) were screened between ccRCC specimens and noncancerous specimens. Among these genes, prognostic DE-FRGs were identified using univariate COX analysis and LASSO regression analysis. Further multivariate COX regression was employed to identify prognosis-related hub DE-FRGs and establish a prognostic model. Results: We identified seven hub genes (HMGCR, MT1G, BID, EIF4A1, FOXM1, TFAP2C and CHAC1) from the DE-FRGs using univariate Cox regression analysis, LASSO and multivariate Cox regression analysis, and used them to establish a novel clinical predictive model in the TCGA train cohort (n = 374). Subsequently, we assessed the prognostic value of the model. Survival analysis showed that high-risk patients had a reduced overall survival (OS), the time-dependent receiver operating characteristic (ROC) curve analysis confirmed the signature's diagnostic performance. Additionally, multivariate Cox regression analysis suggested that the risk score was an independent prognostic factor. Additionally, we verified the prognostic performance of the risk model in the testing cohort (n=156), and the entire group (n=530) using Kaplan-Meier curve and ROC curve analyses. Functional analysis indicated that several carcinogenic pathways were enriched, and tumor-infiltrating immune cell abundances, and the expression levels of immunosuppressive molecules were different between two risk groups. Finally, external databases (ONCMINE, GEPIA, HPA, Kaplan-Meier plotter and cbioportal) were used to confirm the expression patterns, prognostic value, and genetic mutations of 7 hub FRGs in ccRCC.Conclusions: Collectively, we successfully constructed a novel ferroptosis-related risk signature that was significantly associated with the prognosis of ccRCC.


2009 ◽  
Vol 16 (1) ◽  
pp. 62-67 ◽  
Author(s):  
Valentina Zipoli ◽  
Benedetta Goretti ◽  
Bahia Hakiki ◽  
Gianfranco Siracusa ◽  
Sandro Sorbi ◽  
...  

Significant cognitive impairment has been found in 20—30% of patients with clinically isolated syndromes suggestive of multiple sclerosis. In this study we aimed to assess the prognostic value of the presence of cognitive impairment for the conversion to multiple sclerosis in patients with clinically isolated syndromes. All patients with clinically isolated syndromes consecutively referred to our centre since 2002 and who had been followed-up for at least one year underwent cognitive assessment through the Rao’s Battery and the Stroop test. Possible predictors of conversion to clinically definite multiple sclerosis were evaluated through the Kaplan Meier curves and Cox regression analysis. A total of 56 patients (41 women; age 33.2 ± 8.5 years; expanded disability scale score 1.2 ± 0.7) were recruited. At baseline, 32 patients (57%) fulfilled McDonald’s criteria for dissemination in space. During the follow-up (3.5 ± 2.3 years), 26 patients (46%) converted to a diagnosis of multiple sclerosis. In particular, 64% of patients failing ≥ 2 tests and 88% of patients failing ≥ 3 tests converted to multiple sclerosis. In the Cox regression model, the failure of at least three tests (HR 3.3; 95% CI 1.4—8.1; p = 0.003) and the presence of McDonald’s dissemination in space at baseline (HR 3.8; 95% CI 1.5—9.7; p = 0.005), were found to be predictors for conversion to multiple sclerosis. We conclude that cognitive impairment is detectable in a sizable proportion of patients with clinically isolated syndromes. In these subjects cognitive impairment has a prognostic value in predicting conversion to multiple sclerosis and may therefore play a role in therapeutic decision making.


2019 ◽  
Vol 28 (4) ◽  
pp. 439-447 ◽  
Author(s):  
Yan Jiao ◽  
Yanqing Li ◽  
Bai Ji ◽  
Hongqiao Cai ◽  
Yahui Liu

Background and Aims: Emerging studies indicate that long noncoding RNAs (lncRNAs) play a role as prognostic markers in many cancers, including liver cancer. Here, we focused on the lncRNA lung cancer-associated transcript 1 (LUCAT1) for liver cancer prognosis. Methods: RNA-seq and phenotype data were downloaded from the Cancer Genome Atlas (TCGA). Chisquare tests were used to evaluate the correlations between LUCAT1 expression and clinical features. Survival analysis and Cox regression analysis were used to compare different LUCAT1 expression groups (optimal cutoff value determined by ROC). The log-rank test was used to calculate the p-value of the Kaplan-Meier curves. A ROC curve was used to evaluate the diagnostic value. Gene Set Enrichment Analysis (GSEA) was performed, and competing endogenous RNA (ceRNA) networks were constructed to explore the potential mechanism. Results: Data mining of the TCGA -Liver Hepatocellular Carcinoma (LIHC) RNA-seq data of 371 patients showed the overexpression of LUCAT1 in cancerous tissue. High LUCAT1 expression was associated with age (p=0.007), histologic grade (p=0.009), T classification (p=0.022), and survival status (p=0.002). High LUCAT1 patients had a poorer overall survival and relapse-free survival than low LUCAT1 patients. Multivariate analysis identified LUCAT1 as an independent risk factor for poor survival. The ROC curve indicated modest diagnostic performance. GSEA revealed the related signaling pathways, and the ceRNA network uncovered the underlying mechanism. Conclusion: High LUCAT1 expression is an independent prognostic factor for liver cancer.


2021 ◽  
Author(s):  
Liu-qing Zhou ◽  
Jie-yu Zhou ◽  
Yao Hu

Abstract Background: N6-methyladenosine (m6A) modifications play an essential role in tumorigenesis. m6A modifications are known to modulate RNAs, including mRNAs and lncRNAs. However, the prognostic role of m6A-related lncRNAs in head and neck squamous cell carcinoma (HNSCC) is poorly understood.Methods: Based on LASSO Cox regression, enrichment analysis, univariate and multivariate Cox regression analysis, a risk prognostic model, and consensus clustering analysis, we analyzed the 12 m6A-related lncRNAs in HNSCC samples data using the data from The Cancer Genome Atlas (TCGA) database.Results: We found twelve m6A-related lncRNAs in the training cohort and validated in all cohorts by Kaplan-Meier and Cox regression analyses, and revealing their independent prognostic value in HNSCC. Moreover, ROC analysis was conducted, confirming the strong predictive ability of this signature for HNSCC prognosis. GSEA and detailed immune infiltration analyses revealed specific pathways associated with m6A-related lncRNAs.Conclusions: In this study, a novel risk model including twelve genes (SAP30L-AS1, AC022098.1, LINC01475, AC090587.2, AC008115.3, AC015911.3, AL122035.2, AC010226.1, AL513190.1, ZNF32-AS1, AL035587.1 and AL031716.1) was built. It could accurately predict HNSCC prognosis and provide potential prediction outcome and new therapeutic target for HNSCC patients.


2020 ◽  
Author(s):  
Xianfeng Zhang ◽  
Xianjun Zhang ◽  
Xinguo Li ◽  
Hongbing Bao ◽  
Guang Li ◽  
...  

Abstract Background: Nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) was over-expressed in some tumors, including hepatocellular carcinoma (HCC). However, the clinical significance of NUCKS1 in HCC was still unclear. The aim of this study was to explore the expression and prognostic value of NUCKS1 in HCC. Methods: Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the relative mRNA expression of NUCKS1 in HCC tissues and corresponding adjacent normal tissues. The relationship between NUCKS1 expression and clinical characteristics of patients was analyzed by c2 test. Kaplan-Meier method and cox regression analysis were applied to estimate the prognostic value of NUCKS1 in HCC. Results: Compared with normal tissues, the relative mRNA expression level of NUCKS1 was significantly up-regulated in HCC tissues (P < 0.001). And high NUCKS1 expression was closely associated with tumor differentiation, TNM stage, vascular invasion and metastasis (P < 0.05). Kaplan-Meier analysis revealed that the overall survival of HCC patients with low expression of NUCKS1 was obviously longer than those with high NUCKS1 expression (log rank test, P = 0.001). NUCKS1 was an independent prognostic factor of HCC patients via univariate and multivariate cox regression analyses.Conclusions: NUCKS1 may be correlated with the progression of HCC and may serve as a potential factor for the prognosis of this disease.


2020 ◽  
Author(s):  
Rui Wang ◽  
Zian Feng ◽  
Jie Hu ◽  
Xiaodong He ◽  
Zuojun Shen

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.


2017 ◽  
Vol 35 (4_suppl) ◽  
pp. 551-551 ◽  
Author(s):  
Jae Hyun Kim ◽  
Seun Ja Park

551 Background: Inflammatory response plays an important role in the pathogenesis of cancer. Some evidence has suggested that elevations in the neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are associated with decreased survival in various types of cancer. In this study, we aimed to evaluate the prognostic value of the NLR and PLR in patients with colorectal cancer (CRC). Methods: Between August 1995 and December 2010, medical records from a total of 2,004 patients with CRC were retrospectively reviewed. The values of simple inflammatory markers including NLR and PLR in predicting the long-term outcomes of these patients were evaluated using Kaplan-Meier curves and multivariate Cox regression models. Results: The median follow-up duration was 42 months (interquartile range, 19 – 69). The estimation of NLR and PLR was based on the time of diagnosis. In multivariate Cox regression analysis, high NLR ( ≥ 2.6) [hazard ratio (HR) 2.251, 95% confidence interval (CI) 1.570-3.228, p < 0.001] and high PLR ( ≥ 155) [HR 1.473, 95% CI 1.019 – 2.128, p = 0.039] were independent risk factors predicting poor overall survival (OS) in CRC patients. Combined high NLR and PLR was also an independent risk factor predicting poor OS in patients with CRC [HR 2.316, 95% CI 1.529 – 3.508, p < 0.001]. Conclusions: In this study, we identified that high NLR ( ≥ 2.6), high PLR ( ≥ 155), and combined high NLR and PLR are useful prognostic factors to predict OS in CRC patients.


2020 ◽  
Author(s):  
Dawei Wang ◽  
Youchen Ye ◽  
Tingting Qu ◽  
Zhifang Zhao ◽  
Zenghui Gu ◽  
...  

Abstract Background Osteosarcoma is the most common primary malignant tumor of skeleton in adolescence. Histone deacetylase 2 (HDAC2), a member of class I histone deacetylase, is putatively involved in tumorigenesis of human malignancies. This study aimed to evaluate the expression pattern and prognostic value of HDAC2 in osteosarcoma.Methods Four datasets were obtained from the gene expression omnibus (GEO) database to explore the expression and prognostic value of HDAC2. Level 3 mRNA expression profiles and clinical data were obtained in The Cancer Genome Atlas (TCGA) for validation. Expression pattern of HDAC2 were illustrated in GSE16088, GSE36001 and GSE42352. The prognostic value of HDAC2 was evaluated and validated by Kaplan-Meier analyses, receiver operating characteristic (ROC), concordance index (C-index) and calibration curve in GSE21257 and TCGA. Multivariate Cox regression analysis, nomogram, and decision curve analysis (DCA) were performed to assess the prognosis predictive capability. Protein-protein interaction (PPI) and gene set enrichment analysis (GSEA) were applied to further understand the molecular network and regulatory mechanisms.Results HDAC2 expression was significantly increased in osteosarcoma tissues. High HDAC2 expression was associated with tumor metastasis and chemotherapy efficacy. Kaplan-Meier analysis demonstrated that high HDAC2 predicted worse overall survival. The ROC curve showed good performance in survival prediction. Cox regression demonstrated that HDAC2 could be an independent prognostic indicator. GSEA revealed patients with high HDAC2 expression were enriched with multiple ontological signatures.Conclusions Elevated expression of HDAC2 may identify an aggressive subgroup in osteosarcoma and serve as an independent prognostic indicator in these patients.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2004-2004
Author(s):  
Athanasios Galanopoulos ◽  
Christos K. Kontos ◽  
Nora-Athina Viniou ◽  
Ioannis Kotsianidis ◽  
Vassiliki Pappa ◽  
...  

Abstract Introduction - Aims: Several prognostic scoring systems have been developed for patients with myelodysplastic syndromes (MDS), including the International Prognostic System (IPSS), the WHO Prognostic Scoring System (WPSS) and the Revised IPSS (IPSS-R). We evaluated the prognostic value of the IPSS-R on an independent group of 2,582 Greek patients with MDS, registered in the Hellenic National MDS Registry. The aim of this multicenter study was to validate the IPSS-R as a predictor for leukemia-free survival (LFS) and overall survival (OS), in newly-diagnosed MDS patients and to compare its prognostic significance with that of IPSS and WPSS. Moreover, to investigate the predictive value of IPSS-R in association with other recognized prognostic variables, such as patient's age, baseline serum lactate dehydrogenase (LDH), and ferritin concentrations, IPSS, WPSS, Eastern Cooperative Oncology Group (ECOG) performance status, transfusion dependency, and response to first-line treatment. Methods: Clinicopathological data from 2,582 MDS patients, diagnosed between 1/2000 - 1/2015 and registered in the Hellenic National MDS Registry were analyzed. Patients with MDS/MPN were excluded. Data included age, gender, date of diagnosis, clinical characteristics, WHO-2008 classification, laboratory parameters, transfusion dependency, bone marrow aspirate and biopsy morphology, cytogenetic findings, and type of treatment. LFS was calculated from the date of initial diagnosis of MDS until bone marrow blast increased to ≥20% [transformation to acute myeloid leukemia (AML), according to the WHO classification], or last contact. OS was defined as the time from MDS diagnosis to death, or last contact. Patients alive and not having developed AML until last follow-up were censored for OS and LFS, respectively. Kaplan-Meier survival analysis and Cox regression analysis were performed with regard to LFS and OS. Differences between Kaplan-Meier curves were evaluated using the Mantel-Cox (log-rank) test. All significant variables identified by univariate Cox regression analysis and clinical factors important for MDS were used to build the multivariate Cox regression models. Multivariate Cox regression analysis included only those patients for whom the status of all variables was known, and comprised age, serum LDH, and ferritin levels, transfusion dependency, response to first-line treatment, IPSS, WPSS, and IPSS-R. Confidence intervals (CI) were estimated at the 95% level; all tests were two-sided, accepting p<0.05 as indicative of a statistically significant difference. All statistical analyses were performed with the statistical software SPSS (version 21). Results: 1,623 male (62.9%) and 959 female MDS patients with a median age of 74 years at diagnosis were included in the current study. Complete follow-up information was available for 2,376 patients. The estimated median OS was 58 months (95% CI = 52.9 - 63.1 months). For 1,974 patients, data used in the calculation of all three scoring systems were complete, thus allowing risk score calculation and comparison of the three risk assessment systems. Median OS was significantly different in patient subgroups classified according to IPSS, WPSS, and IPSS-R, as shown by the Kaplan-Meier survival analysis (p<0.001). Fig. 1 shows Kaplan-Meier OS curves of MDS patients stratified according to IPSS-R (p<0.001). Moreover, the comparison of the prognostic value of the IPSS, WPSS, and IPSS-R revealed that the IPSS-R was significantly superior to both, WPSS and IPSS (p<0.001 in all cases). Multivariate Cox regression analysis demonstrated that the high prognostic value of IPSS-R, in terms of LFS and OS, was independent of patient's age, serum LDH, and ferritin concentration, ECOG performance status, and transfusion dependency (p<0.001). Interestingly, besides IPSS-R, patient age and transfusion dependency retain their small - yet significant - prognostic impact in the multiparametric models, thus implying that these two parameters could add prognostic value to the IPSS-R. Conclusions: Our data support the notion that all three prognostic scores are very useful predictors for both, LFS and OS in MDS, yet IPSS-R is superior to IPSS and WPSS as a prognostic tool, with regard to OS. Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Junsheng Li ◽  
Qian Zhang ◽  
Peicong Ge ◽  
Chaofan Zeng ◽  
Fa Lin ◽  
...  

Objective. The overall survival of patients with recurrent glioblastoma (rGBM) is quite different, so clinical outcome prediction is necessary to guide personalized clinical treatment for patients with rGBM. The expression level of lncRNA FAM225B was analyzed to determine its prognostic value in rGBMs. Methods. We collected 109 samples of Chinese Glioma Genome Atlas (CGGA) RNA sequencing dataset and divided into training set and validation set. Then, we analyzed the expression of FAM225B, clinical characteristics, and overall survival (OS) information. Kaplan-Meier survival analysis was used to estimate the OS distributions. The prognostic value of FAM225B in rGBMs was tested by univariate and multivariate Cox regression analyses. Moreover, we analyzed the biological processes and signaling pathways of FAM225B. Results. We found that FAM225B was upregulated in rGBMs ( P = 0.0009 ). The expression of FAM225B increased with the grades of gliomas ( P < 0.0001 ). The OS of rGBMs in the low-expression group was significantly longer than that in the high-expression group ( P = 0.0041 ). Similar result was found in the training set ( P = 0.0340 ) and verified in the validation set ( P = 0.0292 ). In multivariate Cox regression analysis, FAM225B was identified to be an independent prognostic factor for rGBMs ( P = 0.003 ). Biological process and KEGG pathway analyses implied FAM225B mainly played a functional role on transcription, regulation of transcription, cell migration, focal adhesion, etc. Conclusions. FAM225B is expected to be as a new prognostic biomarker for the identification of rGBM patients with poor outcome. And our study provided a potential therapeutic target for rGBMs.


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