A seven-lncRNA signature predicts overall survival in esophageal squamous cell carcinoma

Mao, Yu; Fu, Zhanzhao; Zhang, Yunjie; Liu, Dong; Zhang, Yanqiu; Zhang, Qiang; Li, Xin; Liu, Jia

doi:10.1038/s41598-018-27307-2

Cited by 63 publications

(60 citation statements)

References 30 publications

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“…As the sixth leading cause of cancer‐associated death, esophageal cancer results in approximately 400 000 mortalities globally every year . In Asian countries, ESCC remains the predominant histologic type of esophageal cancer . Despite incremental advancement in diagnostics and therapeutics, its prognosis remains poor with a 5‐year survival rate of 15%‐25% .…”

Section: Introductionmentioning

confidence: 99%

Circulating exosomes from esophageal squamous cell carcinoma mediate the generation of B10 and PD‐1^high Breg cells

et al. 2019

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As one of the most frequently diagnosed cancers, esophageal squamous cell carcinoma (ESCC) remains the leading cause of malignancy‐related death worldwide. Many studies have focused on the potential role of cancer cells in educating B cells during cancer progression. Here, we aim to explore the role of circulating exosomes from ESCC in the generation of two main regulatory B (Breg) subsets, including interleukin‐10+ Bregs (B10) and programmed cell death (PD)‐1high Bregs. Firstly, we observed an elevated percentage of B10 cells in peripheral blood of ESCC patients compared with healthy controls. Then we isolated and characterized exosomes from the peripheral blood of ESCC patients and an ESCC cell line. Exosomes from ESCC patients and the ESCC cell line suppressed the proliferation of B cells and induced the augmentation of B10 and PD‐1high Breg cells. By comparing the long non‐coding RNA and mRNA expression profiles in exosomes from ESCC patients or healthy controls, we identified a series of differentially expressed genes. Finally, we undertook gene annotation and pathway enrichment analyses on differentially expressed genes to explore the potential mechanism underlying the modulatory role of cancer exosomes in B cells. Our findings contribute to the study on B cell‐mediated ESCC immunosuppression and shed light on the possible application of exosomes in anticancer therapies.

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Section: Introductionmentioning

confidence: 99%

Circulating exosomes from esophageal squamous cell carcinoma mediate the generation of B10 and PD‐1^high Breg cells

et al. 2019

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“…Long non-coding RNAs (lncRNAs) are closely associated with tumor development and influence the prognosis of patients with tumors (19)(20)(21). The previous studies have indicated the predictive ability of lncRNA signatures for the prognosis of ESCC including our previous study (22)(23)(24). In addition, some studies also revealed that lncRNA was associated with the MetS or related metabolism disorder (25,26).…”

Section: Introductionmentioning

confidence: 85%

The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma

et al. 2020

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Background: Metabolic syndrome (MetS) is associated with the development of esophageal squamous cell carcinoma (ESCC), and long non-coding RNAs (lncRNAs) are involved in a variety of mechanisms of MetS and tumor. This study will explore the prognostic effect of MetS and the associated lncRNA signature on ESCC.Methods: Our previous RNA-chip data (GSE53624, GSE53622) for 179 ESCC patients were reanalyzed according to MetS. The recurrence-free survival (RFS) was collected for these patients. The status of the MetS-related tumor microenvironment was analyzed with the CIBERSORT and ESTIMATE algorithms. A lncRNA signature was established with univariate and multivariate Cox proportional hazards regression (PHR) analysis and verified using the Kaplan-Meier survival curve analysis and time-dependent receiver operating characteristic (ROC) curves. A clinical predictive model was constructed based on multiple risk factors, evaluated using C-indexes and calibration curves, and verified using data from the GEO and TCGA databases. Results:The results showed that MetS was an independent risk factor for ESCC patients conferring low OS and RFS. Tumor microenvironment analysis indicated that patients with MetS have high stromal scores and M2 macrophage infiltration. A six-lncRNA signature was established by 60 ESCC patients randomly selected from GSE53624 and identified with an effective predictive ability in validation cohorts (59 patients from GSE53624 and 60 patients from GSE53622), subgroup analysis, and ESCC patients from TCGA. MetS and the six-lncRNA signature could be regarded as independent risk factors and enhanced predictive ability in the clinical predictive model. Conclusions:Our results indicated that MetS was associated with poor prognosis in ESCC patients, and the possible mechanism was related to changes in the tumor microenvironment. MetS and the six-lncRNA signature could also serve as independent risk factors with available clinical application value.

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“…Genes associated with survival in the univariate Cox and KM analyses were collected to perform the least absolute shrinkage and selection operator (LASSO) regression using R package GLMNET (https://CRAN.R-project.org/package=glmnet). LASSO regression aids in selection of appropriate variables to simplify the final signature and avoid over‐fitting. The penalty regularization parameter λ, which control the complexity of the signature, was obtained at minimum partial likelihood deviance .…”

Section: Methodsmentioning

confidence: 99%

“… LASSO regression aids in selection of appropriate variables to simplify the final signature and avoid over‐fitting. The penalty regularization parameter λ, which control the complexity of the signature, was obtained at minimum partial likelihood deviance . Further, R package Survminer (https://CRAN.R-project.org/package=survminer) was used to construct the final multivariate Cox survival risk model .…”

Section: Methodsmentioning

confidence: 99%

A risk signature‐based on metastasis‐associated genes to predict survival of patients with osteosarcoma

Shi

Zhuang

et al. 2020

J of Cellular Biochemistry

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Osteosarcoma (OS) is the most common primary solid malignant bone tumor, and its metastasis is a prominent cause of high mortality in patients. In this study, a prognosis risk signature was constructed based on metastasis-associated genes. Four microarrays datasets with clinical information were downloaded from Gene Expression Omnibus, and 256 metastasis-associated genes were identified by limma package. Further, a protein-protein interaction network was constructed, and survival analysis was performed using data from the Therapeutically Applicable Research to Generate Effective Treatments data matrix, identifying 19 genes correlated with prognosis. Six genes were selected by the least absolute shrinkage and selection operator regression for multivariate cox analysis. Finally, a three-gene (MYC, CPE, and LY86) risk signature was constructed, and datasets GSE21257 and GSE16091 were used to validate the prediction efficiency of the signature. The survival times of low-and highrisk groups were significantly different in the training set and validation set.Additionally, gene set enrichment analysis revealed that the genes in the signature may affect the cell cycle, gap junctions, and interleukin-6 production. Therefore, the three-gene survival risk signature could potentially predict the prognosis of patients with OS. Further, proteins encoded by CPE and LY86 may provide novel insights into the prediction of OS prognosis and therapeutic targets.differentially expressed genes, metastasis, osteosarcoma, risk signature, survival analysis 1 | INTRODUCTION Osteosarcoma (OS), characterized by malignant mesenchymal cells producing an osteoid matrix and fibrillary stroma, is the most common osseous aggressive cancer in children and juveniles and commonly arises at the terminus of the long bones, including distal femurs, proximal tibias, and proximal humor. 1 According to the National Cancer Institute Surveillance, Epidemiology, and End Results program, the frequency of OS has increased by 0.3% per year over the last decade. 2 With the intensification of chemotherapeutic regimens, the 5-year survival rate of OS patients without metastasis has been improved to 60%-70%. 3 By contrast, the survival rate is only 0%-30% in patients with OS with metastasis, 4 indicating that OS metastasis is associated poor longterm prognosis. However, metastasis-associated molecules Yi Shi and Ronghan He contributed equally to this work.

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A seven-lncRNA signature predicts overall survival in esophageal squamous cell carcinoma

Cited by 63 publications

References 30 publications

Circulating exosomes from esophageal squamous cell carcinoma mediate the generation of B10 and PD‐1^high Breg cells

Circulating exosomes from esophageal squamous cell carcinoma mediate the generation of B10 and PD‐1^high Breg cells

The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma

A risk signature‐based on metastasis‐associated genes to predict survival of patients with osteosarcoma

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A seven-lncRNA signature predicts overall survival in esophageal squamous cell carcinoma

Cited by 63 publications

References 30 publications

Circulating exosomes from esophageal squamous cell carcinoma mediate the generation of B10 and PD‐1high Breg cells

Circulating exosomes from esophageal squamous cell carcinoma mediate the generation of B10 and PD‐1high Breg cells

The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma

A risk signature‐based on metastasis‐associated genes to predict survival of patients with osteosarcoma

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Circulating exosomes from esophageal squamous cell carcinoma mediate the generation of B10 and PD‐1^high Breg cells

Circulating exosomes from esophageal squamous cell carcinoma mediate the generation of B10 and PD‐1^high Breg cells