A Novel Autophagy-Related IncRNAs Signature for Prognostic Prediction and Clinical Value in Patients With Pancreatic Cancer

Deng, Zhengdong; Li, Xiangyu; Shi, Yuanxin; Lü, Yun; Yao, Wei; Wang, Jianming

doi:10.3389/fcell.2020.606817

Cited by 29 publications

(28 citation statements)

References 34 publications

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“…It can expedite the proliferation and migration of gastric cancer cells through IGF2BP3-involved ZEB1 mediated self-stabilization and PI3K/AKT signaling pathway [22,25]. LINC01559 can also accelerate the progression of cancer through the YAP protein, or by promoting autophagy in pancreatic cancer cells [23,45]. We found that patients with high expression of LINC01559 had poor survival rates.…”

Section: Discussionmentioning

confidence: 77%

Long Non-Coding RNA LINC01559 Exerts Oncogenic Role Via Enhancing Autophagy in Lung Adenocarcinoma

Zhao

Wan

Guo

et al. 2021

Preprint

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Background: Long non-coding RNAs (lncRNAs) have been verified to play fatal role in regulating the progression of lung adenocarcinoma (LUAD). Although lncRNAs play important role in regulating the autophagy of tumor cells, the function and molecular mechanism of LINC01559 in regulating lung cancer development remain to be elucidated. Method and materials: In this study, we used bioinformatics to screen out autophagy-related lncRNAs from TCGA-LUAD repository, and the least absolute shrinkage and selection operator (LASSO) regression was applied to establish the clinical characteristics and survival of autophagy-related lncRNAs in LUAD patients was analyzed. Finally, we selected the most significant differences lncRNA, LINC01559, to verify its function in regulating LUAD progression.Results: we found high expression of LINC01559 indicates lymph node metastasis and poor prognosis. Besides, LINC01559 promotes lung cancer cell proliferation and migration in vitro, by enhancing autophagy signal pathway. Conclusion: We revealed a novel prognostic model based on autophagy-related lncRNAs, and provide a new therapeutic target and for patients with lung adenocarcinoma with LINC01559.

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Section: Discussionmentioning

confidence: 77%

Long Non-Coding RNA LINC01559 Exerts Oncogenic Role Via Enhancing Autophagy in Lung Adenocarcinoma

Zhao

Wan

Guo

et al. 2021

Preprint

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“…In addition, combining transcriptomic data with genomic sequencing, mutational landscape, immune infiltrate or genetic alteration can identify additional subtypes with clinical relevance (Bailey et al, 2016;Connor et al, 2017;Brunton et al, 2020;Rashid et al, 2020). More importantly than predicting patient prognosis and disease aggressiveness, recent studies find that transcriptomic data is also good at predicting chemotherapy sensitivity for PDAC (Deng et al, 2020;Nicolle et al, 2021;Nishiwada et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

An EMT-Related Gene Signature for Predicting Response to Adjuvant Chemotherapy in Pancreatic Ductal Adenocarcinoma

Feng

Lou

et al. 2021

Front. Cell Dev. Biol.

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BackgroundFor pancreatic ductal adenocarcinoma (PDAC) patients, chemotherapy failure is the major reason for postoperative recurrence and poor outcomes. Establishment of novel biomarkers and models for predicting chemotherapeutic efficacy may provide survival benefits by tailoring treatments.MethodsUnivariate cox regression analysis was employed to identify EMT-related genes with prognostic potential for DFS. These genes were subsequently submitted to LASSO regression analysis and multivariate cox regression analysis to identify an optimal gene signature in TCGA training cohort. The predictive accuracy was assessed by Kaplan–Meier (K-M), receiver operating characteristic (ROC) and calibration curves and was validated in PACA-CA cohort and our local cohort. Pathway enrichment and function annotation analyses were conducted to illuminate the biological implication of this risk signature.ResultsLASSO and multivariate Cox regression analyses selected an 8-gene signature comprised DLX2, FGF9, IL6R, ITGB6, MYC, LGR5, S100A2, and TNFSF12. The signature had the capability to classify PDAC patients with different DFS, both in the training and validation cohorts. It provided improved DFS prediction compared with clinical indicators. This signature was associated with several cancer-related pathways. In addition, the signature could also predict the response to immune-checkpoint inhibitors (ICIs)-based immunotherapy.ConclusionWe established a novel EMT-related gene signature that was capable of predicting therapeutic response to adjuvant chemotherapy and immunotherapy. This signature might facilitate individualized treatment and appropriate management of PDAC patients.

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“…ROC curves of 1, 3, and 5 years were plotted with the survivalROC R package. Then, we conducted the performance comparison of the signature in our study (referred to as TP53Sig) with eight recently published signatures: 6-mRNA signature from Hou’s study (referred to as HouSig) [ 18 ], 4-mRNA signature from Meng’s study (referred to as MengSig) [ 19 ], 8-mRNA signature from Meng’s study (referred to as MengSig) [ 20 ], 5-mRNA signature from Wu’s study (referred to as WuSig) [ 21 ], 7-mRNA signature from Wu’s study (referred to as WuSig) [ 22 ], 10-mRNA signature from Yue’s study (referred to as YueSig) [ 23 ], 2-mRNA signature from Zhou’s study (referred to as ZhouSig) [ 24 ] and 6-LncRNA signature from Deng’s study (referred to as DengSig) [ 25 ]. ROC curves of 3 years were plotted and AUC values were calculated using the survivalROC R package.…”

Section: Methodsmentioning

confidence: 99%

A novel tp53-associated nomogram to predict the overall survival in patients with pancreatic cancer

Liu

Chen

et al. 2021

BMC Cancer

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Background Gene mutations play critical roles in tumorigenesis and cancer development. Our study aimed to screen survival-related mutations and explore a novel gene signature to predict the overall survival in pancreatic cancer. Methods Somatic mutation data from three cohorts were used to identify the common survival-related gene mutation with Kaplan-Meier curves. RNA-sequencing data were used to explore the signature for survival prediction. First, Weighted Gene Co-expression Network Analysis was conducted to identify candidate genes. Then, the ICGC-PACA-CA cohort was applied as the training set and the TCGA-PAAD cohort was used as the external validation set. A TP53-associated signature calculating the risk score of every patient was developed with univariate Cox, least absolute shrinkage and selection operator, and stepwise regression analysis. Kaplan-Meier and receiver operating characteristic curves were plotted to verify the accuracy. The independence of the signature was confirmed by the multivariate Cox regression analysis. Finally, a prognostic nomogram including 359 patients was constructed based on the combined expression data and the risk scores. Results TP53 mutation was screened to be the robust and survival-related mutation type, and was associated with immune cell infiltration. Two thousand, four hundred fifty-five genes included in the six modules generated in the WGCNA were screened as candidate survival related TP53-associated genes. A seven-gene signature was constructed: Risk score = (0.1254 × ERRFI1) - (0.1365 × IL6R) - (0.4400 × PPP1R10) - (0.3397 × PTOV1-AS2) + (0.1544 × SCEL) - (0.4412 × SSX2IP) – (0.2231 × TXNL4A). Area Under Curves of 1-, 3-, and 5-year ROC curves were 0.731, 0.808, and 0.873 in the training set and 0.703, 0.677, and 0.737 in the validation set. A prognostic nomogram including 359 patients was constructed and well-calibrated, with the Area Under Curves of 1-, 3-, and 5-year ROC curves as 0.713, 0.753, and 0.823. Conclusions The TP53-associated signature exhibited good prognostic efficacy in predicting the overall survival of PC patients.

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A Novel Autophagy-Related IncRNAs Signature for Prognostic Prediction and Clinical Value in Patients With Pancreatic Cancer

Cited by 29 publications

References 34 publications

Long Non-Coding RNA LINC01559 Exerts Oncogenic Role Via Enhancing Autophagy in Lung Adenocarcinoma

Long Non-Coding RNA LINC01559 Exerts Oncogenic Role Via Enhancing Autophagy in Lung Adenocarcinoma

An EMT-Related Gene Signature for Predicting Response to Adjuvant Chemotherapy in Pancreatic Ductal Adenocarcinoma

A novel tp53-associated nomogram to predict the overall survival in patients with pancreatic cancer

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