scholarly journals Six Metabolism Related mRNAs Predict the Prognosis of Patients With Hepatocellular Carcinoma

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiwen Wu ◽  
Tian Lan ◽  
Muqi Li ◽  
Junfeng Liu ◽  
Xukun Wu ◽  
...  

Background: Hepatocellular carcinoma (HCC) is one of the most common aggressive solid malignant tumors and current research regards HCC as a type of metabolic disease. This study aims to establish a metabolism-related mRNA signature model for risk assessment and prognosis prediction in HCC patients.Methods: HCC data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Enrichment Analysis (GSEA) website. Least absolute shrinkage and selection operator (LASSO) was used to screen out the candidate mRNAs and calculate the risk coefficient to establish the prognosis model. A high-risk group and low-risk group were separated for further study depending on their median risk score. The reliability of the prediction was evaluated in the validation cohort and the whole cohort.Results: A total of 548 differential mRNAs were identified from HCC samples (n = 374) and normal controls (n = 50), 45 of which were correlated with prognosis. A total of 373 samples met the screening criteria and there were randomly divided into the training cohort (n = 186) and the validation cohort (n = 187). In the training cohort, six metabolism-related mRNAs were used to construct a prognostic model with a LASSO regression model. Based on the risk model, the overall survival rate of the high-risk cohort was significantly lower than that of the low-risk cohort. The results of a time-ROC curve proved that the risk score (AUC = 0.849) had a higher prognostic value than the pathological grade, clinical stage, age or gender.Conclusion: The model constructed by the six metabolism-related mRNAs has a significant value for survival prediction and can be applied to guide the evaluation of HCC and the designation of clinical therapy.

2020 ◽  
Author(s):  
Qinqin Liu ◽  
Jing Li ◽  
Fei Liu ◽  
Weilin Yang ◽  
Jingjing Ding ◽  
...  

Abstract Background Hepatocellular carcinoma (HCC) is associated with dismal prognosis, and prediction of the prognosis of HCC can assist the therapeutic decisions. More and more studies showed that the texture parameters of images can reflect the heterogeneity of the tumor, and may have the potential to predict the prognosis of patients with HCC after surgical resection. The aim of the study was to investigate the prognostic value of computed tomography (CT) texture parameters for patients with HCC after hepatectomy, and try to develop a radiomics nomograms by combining clinicopathological factors with radiomics signature.Methods 544 eligible patients were enrolled in the retrospective study and randomly divided into training cohort (n=381) and validation cohort (n=163). The regions of interest (ROIs) of tumor is delineated, then the corresponding texture parameters are extracted. The texture parameters were selected by using the least absolute shrinkage and selection operator (LASSO) Cox model in training cohort, and the radiomics score (Rad-score) was generated. According to the cut-off value of the Rad-score calculated by the receiver operating characteristic (ROC) curve, the patients were divided into high-risk group and low-risk group. The prognosis of the two groups was compared and validated in the validation cohort. Univariate and multivariable analyses by COX proportional hazard regression model were used to select the prognostic factors of overall survival (OS). The radiomics nomogram for OS were established based on the radiomics signature and clinicopathological factors. The Concordance index (C-index), calibration plot and decision curve analysis (DCA) were used to evaluate the performance of the radiomics nomogram.Result 7 texture parameters associated with OS were selected in the training, and the radiomics signature was formulated based on the texture parameters. The patients were divided into high-risk group and low-risk group by the cut-off values of the Rad-score of OS. The 1-, 3- and 5-year OS rate was 71.0%, 45.5% and 35.5% in the high-risk group, respectively, and 91.7%, 82.1% and 78.7%, in the low-risk group, respectively, with significant difference (P <0.001). COX regression model found that Rad-score was an independent prognostic factor of OS. In addition, the radiomics nomogram was developed based on five variables: α‐fetoprotein (AFP), platelet lymphocyte ratio (PLR), largest tumor size, microvascular invasion (MVI) and Rad-score. The nomograms displayed good accuracy in predicting OS (C-index=0.747) in the training cohort and was confirmed in the validation cohort (C-index=0.777). The calibration plots also showed an excellent agreement between the actual and predicted survival probabilities. The DAC indicated that the radiomics nomogram showed better clinical usefulness than the clinicopathologic nomogram.Conclusion The radiomics signature is potential biomarkers of the prognosis of HCC after hepatectomy. Radiomics nomogram that integrated radiomics signature can provide more accurate estimate of OS for patients with HCC after hepatectomy.


2020 ◽  
Vol 7 ◽  
Author(s):  
Muqi Li ◽  
Minni Liang ◽  
Tian Lan ◽  
Xiwen Wu ◽  
Wenxuan Xie ◽  
...  

BackgroundLong non-coding RNA (LncRNA) plays an important role in the occurrence and development of hepatocellular carcinoma (HCC). This study aims to establish an immune-related LncRNA model for risk assessment and prognosis prediction in HCC patients.MethodsHepatocellular carcinoma patient samples with complete clinical data and corresponding whole transcriptome expression were obtained from the Cancer Genome Atlas (TCGA). Immune-related genes were acquired from the Gene Set Enrichment Analysis (GSEA) website and matched with LncRNA in the TCGA to get immune-related LncRNA. Least Absolute Shrinkage and Selection Operator (LASSO) regression was used for screening the candidate LncRNAs and calculating the risk coefficient to establish the prognosis model. Patients were divided into a high-risk group and a low-risk group depending on the median risk score. The reliability of the prediction was evaluated in the validation cohort and the whole cohort. GSEA and principal component analysis were used for function evaluation.ResultsA total of 319 samples met the screening criteria and were randomly distributed across the training cohort and the validation cohort. After comparison with the IMMUNE_RESPONSE gene set and the IMMUNE_SYSTEM_PROCESS gene set, a total of 3094 immune-related LncRNAs were screened. Ultimately, four immune-related LncRNAs were used to construct a formula using LASSO regression. According to the formula, the low-risk group showed a higher survival rate than the high-risk group in the validation cohort and the whole cohort. The receiver operating characteristic curves data demonstrated that the risk score was more specific than other traditional clinical characteristics in predicting the 5-year survival rate for HCC.ConclusionThe four-immune-related-LncRNA model can be used for survival prediction in HCC and guide clinical therapy.


2021 ◽  
Vol 12 ◽  
Author(s):  
Quanxiao Li ◽  
Limin Jin ◽  
Meng Jin

Hepatocellular carcinoma (HCC) is the most common form of liver cancer with limited therapeutic options and low survival rate. The hypoxic microenvironment plays a vital role in progression, metabolism, and prognosis of malignancies. Therefore, this study aims to develop and validate a hypoxia gene signature for risk stratification and prognosis prediction of HCC patients. The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases were used as a training cohort, and one Gene Expression Omnibus database (GSE14520) was served as an external validation cohort. Our results showed that eight hypoxia-related genes (HRGs) were identified by the least absolute shrinkage and selection operator analysis to develop the hypoxia gene signature and demarcated HCC patients into the high- and low-risk groups. In TCGA, ICGC, and GSE14520 datasets, patients in the high-risk group had worse overall survival outcomes than those in the low-risk group (all log-rank P &lt; 0.001). Besides, the risk score derived from the hypoxia gene signature could serve as an independent prognostic factor for HCC patients in the three independent datasets. Finally, a nomogram including the gene signature and tumor-node-metastasis stage was constructed to serve clinical practice. In the present study, a novel hypoxia signature risk model could reflect individual risk classification and provide therapeutic targets for patients with HCC. The prognostic nomogram may help predict individualized survival.


2021 ◽  
Vol 12 ◽  
Author(s):  
Xingte Chen ◽  
Lei Wang ◽  
Liang Hong ◽  
Zhixiong Su ◽  
Xiaohong Zhong ◽  
...  

Background: Aging is a well-studied concept, but no studies have comprehensively analyzed the association between aging-related genes (AGs) and hepatocellular carcinoma (HCC) prognosis.Methods: Gene candidates were selected from differentially expressed genes and prognostic genes in The Cancer Genome Atlas (TCGA) database. A gene risk score for overall survival prediction was established using the least absolute shrinkage and selection operator (LASSO) regression analysis, and this was validated using data from the International Cancer Genome Consortium (ICGC) database. Functional analysis was conducted using gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes analysis, gene set enrichment analysis, and immune microenvironment and tumor stemness analyses.Results: Initially, 72 AGs from the TCGA database were screened as differentially expressed between normal and tumor tissues and as genes associated with HCC prognosis. Then, seven AGs (POLA1, CDK1, SOCS2, HDAC1, MAPT, RAE1, and EEF1E1) were identified using the LASSO regression analysis. The seven AGs were used to develop a risk score in the training set, and the risk was validated to have a significant prognostic value in the ICGC set (p &lt; 0.05). Patients with high risk scores had lower tumor differentiation, higher stage, and worse prognosis (all p &lt; 0.05). Multivariate Cox regression analyses also confirmed that the risk score was an independent prognostic factor for HCC in both the TCGA and ICGC sets (all p &lt; 0.05). Further analysis showed that a high risk score was correlated with the downregulation of metabolism and tumor immunity.Conclusion: The risk score predicts HCC prognosis and could thus be used as a biomarker not only for predicting HCC prognosis but also for deciding on treatment.


2021 ◽  
Vol 11 ◽  
Author(s):  
Qianwen Cheng ◽  
Li Cai ◽  
Yuyang Zhang ◽  
Lei Chen ◽  
Yu Hu ◽  
...  

Background: To investigate the prognostic value of circulating plasma cells (CPC) and establish novel nomograms to predict individual progression-free survival (PFS) as well as overall survival (OS) of patients with newly diagnosed multiple myeloma (NDMM).Methods: One hundred ninetyone NDMM patients in Wuhan Union Hospital from 2017.10 to 2020.8 were included in the study. The entire cohort was randomly divided into a training (n = 130) and a validation cohort (n = 61). Univariate and multivariate analyses were performed on the training cohort to establish nomograms for the prediction of survival outcomes, and the nomograms were validated by calibration curves.Results: When the cut-off value was 0.038%, CPC could well distinguish patients with higher tumor burden and lower response rates (P &lt; 0.05), and could be used as an independent predictor of PFS and OS. Nomograms predicting PFS and OS were developed according to CPC, lactate dehydrogenase (LDH) and creatinine. The C-index and the area under receiver operating characteristic curves (AUC) of the nomograms showed excellent individually predictive effects in training cohort, validation cohort or entire cohort. Patients with total points of the nomograms ≤ 60.7 for PFS and 75.8 for OS could be defined as low-risk group and the remaining as high-risk group. The 2-year PFS and OS rates of patients in low-risk group was significantly higher than those in high-risk group (p &lt; 0.001).Conclusions: CPC is an independent prognostic factor for NDMM patients. The proposed nomograms could provide individualized PFS and OS prediction and risk stratification.


2021 ◽  
Author(s):  
Yong Lv ◽  
ShuGuang Jin ◽  
Bo Xiang

Abstract BackgroundTreatment of neuroblastoma is evolving toward precision medicine. LncRNAs can be used as prognostic biomarkers in many types of cancer.MethodsBased on the RNA-seq data from GSE49710, we built a lncRNAs-based risk score using the least absolute shrinkage and selection operation (LASSO) regression. Cox regression, receiver operating characteristic curves were used to evaluate the association of the LASSO risk score with overall survival. Nomograms were created and then validated in an external cohort from TARGET database. Gene set enrichment analysis was performed to identify the significantly changed biological pathways. ResultsThe 16-lncRNAs-based LASSO risk score was used to separate patients into high-risk and low-risk groups. In GSE49710 cohort, the high-risk group exhibited a poorer OS than those in the low-risk group (P<0.001). Moreover, multivariate Cox regression analysis demonstrated that LASSO risk score was an independent risk factor (HR=6.201;95%CI:2.536-15.16). The similar prognostic powers of the 16-lncRNAs were also achieved in the external cohort and in stratified analysis. In addition, a nomogram was established and worked well both in the internal validation cohort (C-index=0.831) and external validation cohort (C-index=0.773). The calibration plot indicated the good clinical utility of the nomogram. Gene set enrichment analysis (GSEA) indicated that high-risk group was related with cancer recurrence, metastasis and inflammatory associated pathways.ConclusionThe lncRNA-based LASSO risk score is a promising and potential prognostic tool in predicting the survival of patients with neuroblastoma. The nomogram combined the lncRNAs and clinical parameters allows for accurate risk assessment in guiding clinical management.


2021 ◽  
Vol 2021 ◽  
pp. 1-24
Author(s):  
Junyu Huo ◽  
Liqun Wu ◽  
Yunjin Zang

Background. An increasing number of reports have found that immune-related genes (IRGs) have a significant impact on the prognosis of a variety of cancers, but the prognostic value of IRGs in gastric cancer (GC) has not been fully elucidated. Methods. Univariate Cox regression analysis was adopted for the identification of prognostic IRGs in three independent cohorts (GSE62254, n = 300 ; GSE15459, n = 191 ; and GSE26901, n = 109 ). After obtaining the intersecting prognostic genes, the three independent cohorts were merged into a training cohort ( n = 600 ) to establish a prognostic model. The risk score was determined using multivariate Cox and LASSO regression analyses. Patients were classified into low-risk and high-risk groups according to the median risk score. The risk score performance was validated externally in the three independent cohorts (GSE26253, n = 432 ; GSE84437, n = 431 ; and TCGA, n = 336 ). Immune cell infiltration (ICI) was quantified by the CIBERSORT method. Results. A risk score comprising nine genes showed high accuracy for the prediction of the overall survival (OS) of patients with GC in the training cohort ( AUC > 0.7 ). The risk of death was found to have a positive correlation with the risk score. The univariate and multivariate Cox regression analyses revealed that the risk score was an independent indicator of the prognosis of patients with GC ( p < 0.001 ). External validation confirmed the universal applicability of the risk score. The low-risk group presented a lower infiltration level of M2 macrophages than the high-risk group ( p < 0.001 ), and the prognosis of patients with GC with a higher infiltration level of M2 macrophages was poor ( p = 0.011 ). According to clinical correlation analysis, compared with patients with the diffuse and mixed type of GC, those with the Lauren classification intestinal GC type had a significantly lower risk score ( p = 0.00085 ). The patients’ risk score increased with the progression of the clinicopathological stage. Conclusion. In this study, we constructed and validated a robust prognostic signature for GC, which may help improve the prognostic assessment system and treatment strategy for GC.


2020 ◽  
Vol 11 ◽  
Author(s):  
Yu Jia ◽  
Yan Chen ◽  
Jiansheng Liu

Autophagy plays a vital role in hepatocellular carcinoma (HCC) pathogenesis. Long non-coding RNAs (lncRNAs) are considered regulators of autophagy, and the aim of the present study was to investigate the prognostic value of autophagy-related lncRNA (ARlncRNA) and develop a new prognostic signature to predict the 1-year and 3-year overall survival (OS) of HCC patients. Transcriptome and clinical survival information of HCC patients was obtained from The Cancer Genome Atlas database. A set of ARlncRNAs was identified by co-expression analysis, from which seven ARlncRNAs (AC005229.4, AL365203.2, AL117336.3, AC099850.3, ELFN1-AS1, LUCAT1, and AL031985.3) were selected for use as a predictive signature. Risk scores were derived for each patient, who were then divided into high-risk and low-risk groups according to the median risk value. The OS of high-risk patients was significantly lower than that of low-risk patients (P &lt; 0.0001). The 1- and 3-year time-dependent ROC curves were used to evaluate the predictive ability of the risk score (AUC = 0.785 of 1 year, 0.710 of 3 years), and its predictive ability was found to be better than TNM stage. Moreover, the risk score was significantly, linearly related to pathological grade and TNM stage (P &lt; 0.05). Overall, a novel nomogram to predict the 1-year and 3-year OS of HCC patients was developed, which shows good reliability and accuracy, for use in improved treatment decision-making.


BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chen Han ◽  
Cong Zhang ◽  
Huixia Wang ◽  
Kexin Li ◽  
Lianmei Zhao

Abstract Background Stomach adenocarcinoma (STAD), which accounts for approximately 95% of gastric cancer types, is a malignancy cancer with high morbidity and mortality. Tumor angiogenesis plays important roles in the progression and pathogenesis of STAD, in which long noncoding RNAs (lncRNAs) have been verified to be crucial for angiogenesis. Our study sought to construct a prognostic signature of angiogenesis-related lncRNAs (ARLncs) to accurately predict the survival time of STAD. Methods The RNA-sequencing dataset and corresponding clinical data of STAD were acquired from The Cancer Genome Atlas (TCGA). ARLnc sets were obtained from the Ensemble genome database and Molecular Signatures Database (MSigDB, Angiogenesis M14493, INTegrin pathway M160). A ARLnc-related prognostic signature was then constructed via univariate Cox and multivariate Cox regression analysis in the training cohort. Survival analysis and Cox regression were performed to assess the performance of the prognostic signature between low- and high-risk groups, which was validated in the validation cohort. Furthermore, a nomogram that combined the clinical pathological characteristics and risk score conducted to predict the overall survival (OS) of STAD. In addition, ARLnc-mRNA coexpression pairs were constructed with Pearson’s correlation analysis and visualized to infer the functional annotation of the ARLncs by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The expression of four ARLncs in STAD and their correlation with the angiogenesis markers, CD34 and CD105, were also validated by RT–qPCR in a clinical cohort. Results A prognostic prediction signature including four ARLncs (PVT1, LINC01315, AC245041.1, and AC037198.1) was identified and constructed. The OS of patients in the high-risk group was significantly lower than that of patients in the low-risk group (p < 0.001). The values of the time-dependent area under the curve (AUC) for the ARLnc signature for 1-, 3-, and 5- year OS were 0.683, 0.739, and 0.618 in the training cohort and 0.671, 0.646, and 0.680 in the validation cohort, respectively. Univariate and multivariate Cox regression analyses indicated that the ARLnc signature was an independent prognostic factor for STAD patients (p < 0.001). Furthermore, the nomogram and calibration curve showed accurate prediction of the survival time based on the risk score. In addition, 262 mRNAs were screened for coexpression with four ARLncs, and GO analysis showed that mRNAs were mainly involved in biological processes, including angiogenesis, cell adhesion, wound healing, and extracellular matrix organization. Furthermore, correlation analysis showed that there was a positive correlation between risk score and the expression of the angiogenesis markers, CD34 and CD105, in TCGA datasets and our clinical sample cohort. Conclusion Our study constructed a prognostic signature consisting of four ARLnc genes, which was closely related to the survival of STAD patients, showing high efficacy of the prognostic signature. Thus, the present study provided a novel biomarker and promising therapeutic strategy for patients with STAD.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Junjie Guo ◽  
Xiaoyang Li ◽  
Shen Shen ◽  
Xuejian Wu

AbstractCancer immunotherapy is a promising therapeutic approach, but the prognostic value of immune-related genes in osteosarcoma (OS) is unknown. Here, Target-OS RNA-seq data were analyzed to detect differentially expressed genes (DEGs) between OS subgroups, followed by functional enrichment analysis. Cox proportional risk regression was performed for each immune-related gene, and a risk score model to predict the prognosis of patients with OS was constructed. The risk scores were calculated using the risk signature to divide the training set into high-risk and low-risk groups, and validation was performed with GSE21257. We identified two immune-associated clusters, C1 and C2. C1 was closely related to immunity, and the immune score was significantly higher in C1 than in C2. Furthermore, we validated 6 immune cell hub genes related to the prognosis of OS: CD8A, KIR2DL1, CD79A, APBB1IP, GAL, and PLD3. Survival analysis revealed that the prognosis of the high-risk group was significantly worse than that of the low-risk group. We also explored whether the 6-gene prognostic risk model was effective for survival prediction. In conclusion, the constructed a risk score model based on immune-related genes and the survival of patients with OS could be a potential tool for targeted therapy.


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