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Comprehensive Analysis of a Novel Immune-Related Gene Signature in Lung Adenocarcinoma. J Clin Med 2022; 11:jcm11206154. [PMID: 36294477 PMCID: PMC9605017 DOI: 10.3390/jcm11206154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022] Open
Abstract
Lung cancer is the major cause of cancer-related deaths around the world. Lung adenocarcinoma (LUAD), the most common subtype of lung cancer, contributed to the majority of mortalities and showed different clinical outcomes in prognosis. Tumor-infiltrated immune cells at the tumor site are associated with better survival and immunotherapy response. Thus, it is essential to further investigate the molecular mechanisms and new prognostic biomarkers of lung adenocarcinoma development and progression. In this study, a six-gene signature (CR2, FGF5, INSL4, RAET1L, AGER, and TNFRSF13C) was established to predict the prognosis of LUAD patients, as well as predictive value. The prognostic risk model was also significantly associated with the infiltration of immune cells in LUAD microenvironments. To sum up, a novel immune-related six-gene signature (CR2, FGF5, INSL4, RAET1L, AGER, and TNFRSF13C) was identified that could predict LUAD survival and is highly related to B cells and dendritic cells, which may provide a theoretical basis of personalized treatment for targeted immunotherapy.
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Pu Z, Liu J, Liu Z, Peng F, Zhu Y, Wang X, He J, Yi P, Hu X, Fan X, Chen J. STING pathway contributes to the prognosis of hepatocellular carcinoma and identification of prognostic gene signatures correlated to tumor microenvironment. Cancer Cell Int 2022; 22:314. [PMID: 36224658 PMCID: PMC9554977 DOI: 10.1186/s12935-022-02734-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most malignant solid tumors worldwide. Recent evidence shows that the stimulator of interferon genes (STING) pathway is essential for anti-tumor immunity via inducing the production of downstream inflammatory cytokines. However, its impact on the prognosis and tumor microenvironment of HCC was still limited known. Methods We obtained gene expression profiles of HCC from GEO, TCGA, and ICGC databases, and immune-related genes (IRGs) from the ImmPort database. Multivariate Cox regression was performed to identify independent prognostic factors. Nomogram was established to predict survival probability for individual patients. Kaplan–Meier curve was used to evaluate the survival difference. Afterward, ESTIMATE, TISCH, and TIMER databases were combined to assess the immune cell infiltration. Furthermore, the qPCR, western blotting, and immunohistochemistry were done to evaluate gene expression, and in vitro cell models were built to determine cell migratory ability. Results We found that gene markers of NLRC3, STING1, TBK1, TRIM21, and XRCC6 within STING pathway were independent prognostic factors in HCC patients. Underlying the finding, a predictive nomogram was constructed in TCGA-training cohort and further validated in TCGA-all and ICGC datasets, showing credible performance. Experimentally, up-regulated TBK1 promotes the ability of HCC cell migration. Next, the survival-related immune-related co-expressed gene signatures (IRCGS) (VAV1, RHOA, and ZC3HAV1) were determined in HCC cohorts and their expression was verified in human HCC cells and clinical samples. Furthermore, survival-related IRCGS was associated with the infiltration of various immune cell subtypes in HCC, the transcriptional expression of prominent immune checkpoints, and immunotherapeutic response. Conclusion Collectively, we constructed a novel prognostic nomogram model for predicting the survival probability of individual HCC patients. Moreover, an immune-related prognostic gene signature was determined. Both might function as potential therapeutic targets for HCC treatment in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02734-4.
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Affiliation(s)
- Zhangya Pu
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.,Department of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang Province, China
| | - Jinghua Liu
- Department of Hepatobiliary Surgery, Linyi People's Hospital, Linyi, Shandong, China
| | - Zelong Liu
- Division of Interventional Ultrasound, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Fang Peng
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.,NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, 41800, Hunan Province, China
| | - Yuanyuan Zhu
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.,NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, 41800, Hunan Province, China
| | - Xiaofang Wang
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China
| | - Jiayan He
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang Province, China
| | - Panpan Yi
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China
| | - Xingwang Hu
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.
| | - Xuegong Fan
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.
| | - Jiang Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang Province, China.
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Wu P, Shi J, Wang Z, Sun W, Zhang H. Evaluate the immune-related eRNA models and signature score to predict the response to immunotherapy in thyroid carcinoma. Cancer Cell Int 2022; 22:307. [PMID: 36217201 PMCID: PMC9549686 DOI: 10.1186/s12935-022-02722-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The functional alterations of eRNAs have been reported to be correlated with tumorigenesis. However, the roles of eRNAs in thyroid cancer (THCA) remain still unclear. This study aimed to construct an immune-related eRNA prognostic signature that could effectively predict the survival and prognosis for THCA. METHODS The Weighted Gene Co-Expression Network Analysis (WGCNA) was performed to identify THCA-specific immune-related hub genes and immune-related eRNAs were obtained using Pearson correlation analysis. Univariate and least absolute shrinkage and selection operator (LASSO) Cox regression were conducted to construct an immune-related eRNA prognostic signature in training cohort, and the predictive capability was verified in test cohort and entire cohort. Kaplan-Meier analysis, principal component analysis (PCA), receiver operating characteristic (ROC) curves, and nomogram were used to validate the risk signature. Furthermore, CIBERSORT, ESTIMATE and ssGSEA were analyzed to explore the tumor immune microenvironment (TIME) of the risk signature, and the response of potential immunotherapeutic were also discussed. RESULTS A total of 125 immune-related eRNAs were obtained and 16 immune-related eRNAs were significantly correlated with overall survival (OS). A 9-immune-related eRNA prognostic signature was constructed, and the risk score was identified as an independent predictor. High-risk groups were associated with a poorer OS. Immune microenvironment analysis indicated that low risk score was correlated with higher immuneScore, high immune cell infiltration, and the better response of immunotherapy. Additionally, we also detected 9 immune-related eRNA expression levels in sixty-two matched tumorous and non-tumorous tissues using qRT-PCR analysis. CONCLUSION Our immune-related eRNA risk signature that was an independent prognostic factor was strongly correlated with the immune microenvironment and may be promising for the clinical prediction of prognosis and immunotherapeutic responses in THCA patients.
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Affiliation(s)
- Pu Wu
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Jinyuan Shi
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Zhiyuan Wang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China.
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Li S, Zhang Q, Weng L, Li J. Construction of an immune-related signature for predicting the ischemic events in patients undergoing carotid endarterectomy. Front Genet 2022; 13:1014264. [PMID: 36299596 PMCID: PMC9592116 DOI: 10.3389/fgene.2022.1014264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/29/2022] [Indexed: 01/25/2023] Open
Abstract
Background: Inflammatory responses have drawn more attention to atherosclerosis; however, the immune-related genes (IRGs) as a prognostic factor in atherosclerotic plaque remain to be fully elucidated. Here, the purpose of this study was to investigate whether the IRGs could be identified as a reliable biomarker for predicting ischemic events in patients undergoing carotid endarterectomy (CEA). Methods: Two datasets GSE97210 and GSE21545 were downloaded from the Gene Expression Omnibus (GEO) database. The dataset GSE97210 was used to explore the significant pathways and differentially expressed IRGs (DEIRGs) between plaques and controls, which were further screened to identify the prognostic DEIRGs in the GSE21545 dataset. The identification of molecular subgroups with the prognostic gene expression patterns was achieved through nonnegative matrix factorization (NMF) clustering. Functional analyses including GO, KEGG, GSVA, and GSEA analyses, and immune analyses including xCell and ssGSEA algorithms were conducted to elucidate the underlying mechanisms. The prognostic risk model was constructed using the LASSO algorithm and multivariate Cox regression analysis. Results: A total of 796 DEIRGs (including 588 upregulated and 208 downregulated) were identified. Nine prognostic DEIRGs were further screened with univariate Cox regression analysis. Two clusters with different prognosis were grouped based on the prognostic DEIRGs. Immune infiltration analysis shows that cluster 2 with a better prognosis presented with a higher immune response than cluster 1. A prognostic model based on seven IRGs (IL2RA, NR4A2, DES, ERAP2, SLPI, RASGRP1, and AGTR2) was developed and verified. Consistent with the immune analysis of the cluster, the immune infiltration in the low-risk group with a better prognosis was also more active than that in the high-risk group. Finally, a nomogram based on the seven genes was constructed, which might have future implications in clinical care. Conclusion: The expression of immune-related genes is correlated with the immune microenvironment of atherosclerotic patients and could be applied to predict the ischemic events in patients undergoing CEA accurately.
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Affiliation(s)
- Shifu Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
| | - Qian Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
| | - Ling Weng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China,Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China,Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Jian Li,
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Cao J, Tu DY, Zhou J, Jiang GQ, Jin SJ, Su BB, Tang H, Tang YH, Wang AQ, Wang Q, Liu RJ, Zhang C, Bai DS. Comprehensive analysis of the clinical significance, immune infiltration, and biological role of MARCH ligases in HCC. Front Immunol 2022; 13:997265. [PMID: 36263042 PMCID: PMC9573977 DOI: 10.3389/fimmu.2022.997265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
The membrane‐associated RING‐CH (MARCH) family, a member of the E3 ubiquitin ligases, has been confirmed by a growing number of studies to be associated with immune function and has been highlighted as a potential immunotherapy target. In our research, hepatocellular carcinoma (HCC) patients were divided into C1 and C2 MARCH ligase-related patterns by the non-negative matrix factorization (NMF) algorithm. Multiple analyses revealed that the MARCH ligase-related cluster was related to prognosis, clinicopathological characteristics, and the tumor immune microenvironment (TIME). Next, the signature (risk score) of the MARCH prognosis was constructed, including eight genes associated with the MARCH ligase (CYP2C9, G6PD, SLC1A5, SPP1, ANXA10, CDC20, PON1, and FTCD). The risk score showed accuracy and stability. We found that the correlations between risk score and TIME, tumor mutation burden (TMB), prognosis, and clinicopathological characteristics were significant. Additionally, the risk score also had important guiding significance for HCC treatment, including chemotherapy, immunotherapy, and transarterial chemoembolization (TACE).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Chi Zhang
- *Correspondence: Dou-sheng Bai, ; Chi Zhang,
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Clinical and Prognostic Value of PPIA, SQSTM1, and CCL20 in Hepatocellular Carcinoma Patients by Single-Cell Transcriptome Analysis. Cells 2022; 11:cells11193078. [PMID: 36231045 PMCID: PMC9563471 DOI: 10.3390/cells11193078] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most malignant and poor-prognosis subtype of primary liver cancer. The scRNA-seq approach provides unique insight into tumor cell behavior at the single-cell level. Cytokine signaling in the immune system plays an important role in tumorigenesis and has both pro-tumorigenic and anti-tumorigenic functions. A biomarker of cytokine signaling in immune-related genes (CSIRG) is urgently required to assess HCC patient diagnosis and treatment. By analyzing the expression profiles of HCC single cells, TCGA, and ICGC data, we discovered that three important CSIRG (PPIA, SQSTM1, and CCL20) were linked to the overall survival of HCC patients. Cancer status and three hub CSIRG were taken into account while creating a risk nomogram. The nomogram had a high level of predictability and accuracy. Based on the CSIRG risk score, a distinct pattern of somatic tumor mutational burden (TMB) was detected between the two groups. The enrichment of the pyrimidine metabolism pathway, purine metabolism pathway, and lysosome pathway in HCC was linked to the CSIRG high-risk scores. Overall, scRNA-seq and bulk RNA-seq were used to create a strong CSIRG signature for HCC diagnosis.
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Yang X, Yu Y, Wang Z, Wu P, Su X, Wu Z, Gan J, Zhang D. NOX4 has the potential to be a biomarker associated with colon cancer ferroptosis and immune infiltration based on bioinformatics analysis. Front Oncol 2022; 12:968043. [PMID: 36249057 PMCID: PMC9554470 DOI: 10.3389/fonc.2022.968043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
Background Colon cancer (CC) is a common tumor, but its pathogenesis is still not well understood. Competitive endogenous RNA (ceRNA) theory, ferroptosis and tumor immune infiltration may be the mechanisms of the development of cancer. The purpose of the study is to seek genes connected with both immunity and ferroptosis, and provide important molecular basis for early noninvasive diagnosis and immunotherapy of CC. Methods We extracted messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) data of CC from The Cancer Genome Atlas database (TCGA), identified the differentially expressed mRNA (DEmRNA), miRNA (DEmiRNA) and lncRNA (DElncRNA), then constructed a ceRNA network. Venn overlap analysis was used to identify genes associated with immunity and ferroptosis in ceRNA network. The expression and prognosis of target genes were analyzed via Gene Expression Profiling Interactive Analysis (GEPIA) and PrognoScan database, and we analysed the related functions and signaling pathways of target genes by enrichment analysis. The correlation between target genes and tumor immune infiltrating was explored by CIBERSORT and spearman correlation analysis. Finally, the expression of target genes was detected via quantitative reverse transcription-PCR (qRT-PCR) in CC and normal colon tissues. Results Results showed that there were 4 DElncRNA, 4 DEmiRNA and 126 DEmRNA in ceRNA network. NADPH oxidase 4 protein (NOX4) was a DEmRNA associated with immunity and ferroptosis in ceRNA network. NOX4 was highly expressed in CC and connected with unfavourable prognosis. NOX4 was obviously enriched in pathways connected with carcinogenesis and significantly correlated with six kinds of immune cells. Immune checkpoints and NOX4 spearman correlation analysis showed that the expression of NOX4 was positively related to programmed cell death protein 1 (PD-1)-PDCD1, programmed cell death-Ligand 1 (PD-L1)-CD274 and cytotoxic T-lymphocyte-associated protein 4 (CTLA4). Conclusions To conclude, our study suggests that NOX4 is associated with both ferroptosis and tumor immunity, and might be a biomarker associated with the carcinogenesis, prognosis of CC and a potential target of CC immunotherapy.
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Affiliation(s)
- Xiaoping Yang
- Key Laboratory of Digestive Diseases of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Yi Yu
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, China
| | - Zirui Wang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Pingfan Wu
- Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People’s Liberation Army, Lanzhou, China
| | - Xiaolu Su
- Department of Pathology, Lanzhou University Second Hospital, Lanzhou, China
| | - Zhiping Wu
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, China
| | - Jianxin Gan
- Department of general surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Dekui Zhang
- Key Laboratory of Digestive Diseases of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, China
- *Correspondence: Dekui Zhang,
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Hong J, Cai X. Construction of a Novel Oxidative Stress Response-Related Gene Signature for Predicting the Prognosis and Therapeutic Responses in Hepatocellular Carcinoma. DISEASE MARKERS 2022; 2022:6201987. [PMID: 36133439 PMCID: PMC9484914 DOI: 10.1155/2022/6201987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC) is a highly heterogeneous malignancy with poor outcomes, and the assessment of its prognosis as well as its response to therapy is still challenging. In this study, we aimed to construct an oxidative stress response-related genes-(OSRGs-) based gene signature for predicting prognosis and estimating treatment response in patients with HCC. We integrated the transcriptomic data and clinicopathological information of HCC patients from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. LASSO Cox regression analysis was utilized to establish an integrated multigene signature in the TCGA cohort, and its prediction performance was validated in the ICGC cohort. The CIBERSORT algorithm was employed to evaluate immune cell infiltration. The response rate to immune checkpoint inhibition (ICI) therapy was assessed using a TIDE platform. Drug activity data from the Cancer Genome Project and NCI-60 human cancer cell lines were used to predict sensitivity to chemotherapy. We successfully established a gene signature comprising G6PD, MT3, CBX2, CDKN2B, CCNA2, MAPT, EZH2, and SLC7A11. The risk score of each patient, which was determined by the multigene signature, was identified as an independent prognostic marker. The immune cell infiltration patterns, response rates to ICI therapy, and the estimated sensitivity of 89 chemotherapeutic drugs were associated with risk scores. Individual prognostic genes were also associated with susceptibility to various FDA-approved drugs. Our study indicates that a comprehensive transcriptomic analysis of OSRGs can provide a reliable molecular model to predict prognosis and therapeutic response in patients with HCC.
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Affiliation(s)
- Junjie Hong
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xiujun Cai
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
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Immunotherapeutic Value of Transcription Factor 19 (TCF19) Associated with Renal Clear Cell Carcinoma: A Comprehensive Analysis of 33 Human Cancer Cases. JOURNAL OF ONCOLOGY 2022; 2022:1488165. [PMID: 36111242 PMCID: PMC9470357 DOI: 10.1155/2022/1488165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022]
Abstract
Background We aimed to study the relationship between transcription factor 19 (TCF19) and cancer immunotherapy in the 33 types of human cancers. Methods The Cancer Genome Atlas database was analyzed to obtain the gene expression data and clinical characteristics for the cases of 33 types of cancers. GSE67501, GSE78220, and IMvigor 210 were included in the immunotherapy cohorts. Relevant data were obtained by analyzing the gene expression database. The prognostic value of TCF19 was determined by analyzing various clinical parameters, such as survival duration, age, the stage of the tumor, and sex of the patients. The single-sample gene set enrichment analysis method was used to determine the activity of TCF19 and the method was also used to assess the differences between the TCF19 transcriptome and protein levels. The correlation between TCF19 and various immune processes and elements such as immunosuppressants, stimulants, and major histocompatibility complexes were analyzed to gain insights into the role of TCF19. The coherent paths associated with the process of TCF19 signal transduction and the influence of TCF19 on immunotherapy biomarkers have also been discussed herein. Finally, three independent immunotherapy methods were used to understand the relationship between TCF19 and immunotherapy response. Results It was observed that TCF19 was not significantly influenced by the age (5/33), sex (3/33), or tumor stage (3/21) of cancer patients. But the results revealed that TCF19 exhibited a potential prognostic value and could predict the survival rate of the patients. In some cases of this study, the activity and expression of TCF19 were taken at the same level (7/33). Conclusion TCF19 is strongly related to immune cell infiltration, immunomodulators, and immunotherapy markers. Our study demonstrated that high expression levels of TCF19 are strongly linked with the immune-related pathways. Nevertheless, it is noteworthy that TCF19 is not significantly associated with immunotherapy response.
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60
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Che Y, Wang G, Xia Q. CDK2AP1 influences immune infiltrates and serves as a prognostic indicator for hepatocellular carcinoma. Front Genet 2022; 13:937310. [PMID: 36105112 PMCID: PMC9465009 DOI: 10.3389/fgene.2022.937310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a tumor with high malignancy and poor 5-years survival rate. Excellent tumor markers are very important for early clinical diagnosis and prognosis evaluation. Previous studies have shown that CDK2AP1 (Cyclin-dependent kinase 2-associated protein 1) is involved in cell-cycle and epigenetic regulation. In the present study, we assess CDK2AP1 expression, prognostic value, immunomodulatory and possible influencing pathways in HCC.Method: The Cancer Genome Atlas (TCGA) database was used to analyse gene expression, clinicopathology and prognosis. The protein level of CDK2AP1 in HCC tissues was detected in the Human Protein Atlas (HPA) database. The immune score in HCC to CDKAP1 expression were analyzed using ESTIMATE. Furthermore, we use Tumor IMmune Estimation Resource (TIMER) database to study CDK2AP1 expression and Immune Infiltration Levels in HCC. Co-expressed genes of CDK2AP1 were predicted and elaborated by LinkedOmics.Results: In normal liver tissues, the expression of CDK2AP1 was significantly lower than tumor tissues, and was correlated with the level of clinical stage and histologic grade in HCC patients. Patients with high expression of CDK2AP1 have a poor prognosis than patients with low CDK2AP1 expression. CDK2AP1 expression level exhibits significantly positive correlations with the number of infiltrating B cells, CD4+ T cells, CD8+ T cells, Macrophages, Neutrophils, and DCs in HCC tissues. KEGG enrichment analysis showed that the related pathways affected by CDK2AP1 mainly include: Fc gamma R-mediated phagocytosis, Th1 and Th2 cell differentiation, Cell cycle, etc. Both in vitro and in vivo experiments confirmed that CDK2AP1 promotes the proliferation and metastasis in hepatocellular carcinoma. Our results highlight the role of CDK2AP1 as an important prognostic indicator and immunotherapy target for HCC patients.Conclusion: We found CDK2AP1 as a new prognostic biomarker for HCC, which could help explain changes in the biological processes and immune environment lead to liver cancer development. Therefore, CDK2AP1 is a potential new target for HCC therapy.
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Affiliation(s)
- Yibin Che
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ge Wang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China
- Shanghai Institute of Transplantation, Shanghai, China
- *Correspondence: Qiang Xia,
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Guo C, Tang Y, Yang Z, Li G, Zhang Y. Hallmark-guided subtypes of hepatocellular carcinoma for the identification of immune-related gene classifiers in the prediction of prognosis, treatment efficacy, and drug candidates. Front Immunol 2022; 13:958161. [PMID: 36032071 PMCID: PMC9399518 DOI: 10.3389/fimmu.2022.958161] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC), accounting for ~90% of all primary liver cancer, is a prevalent malignancy worldwide. The intratumor heterogeneity of its causative etiology, histology, molecular landscape, and immune phenotype makes it difficult to precisely recognize individuals with high mortality risk or tumor-intrinsic treatment resistance, especially immunotherapy. Herein, we comprehensively evaluated the activities of cancer hallmark gene sets and their correlations with the prognosis of HCC patients using gene set variation analysis (GSVA) and identified two HCC subtypes with distinct prognostic outcomes. Based on these subtypes, seven immune-related genes (TMPRSS6, SPP1, S100A9, EPO, BIRC5, PLXNA1, and CDK4) were used to construct a novel prognostic gene signature [hallmark-guided subtypes-based immunologic signature (HGSIS)] via multiple statistical approaches. The HGSIS-integrated nomogram suggested an enhanced predictive performance. Interestingly, oncogenic hallmark pathways were significantly enriched in the high-risk group and positively associated with the risk score. Distinct mutational landscapes and immune profiles were observed between different risk groups. Moreover, immunophenoscore (IPS) and tumor immune dysfunction and exclusion (TIDE) analysis showed different sensitivities of HGSIS risk groups for immune therapy efficacy, and the pRRophetic algorithm indicated distinguishable responses for targeted/chemotherapies in different groups. KIF2C was picked out as the key target concerning HGSIS, and the top 10 small molecules were predicted to bind to the active site of KIF2C via molecular docking, which might be further used for candidate drug discovery of HCC. Taken together, our study offers novel insights for clinically significant subtype recognition, and the proposed signature may be a helpful guide for clinicians to improve the treatment regimens.
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Affiliation(s)
- Chengbin Guo
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yuqin Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhao Yang
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Gen Li
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Yongqiang Zhang, ; Gen Li,
| | - Yongqiang Zhang
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Yongqiang Zhang, ; Gen Li,
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Risk predictive model based on three immune-related gene pairs to assess prognosis and therapeutic sensitivity for hepatocellular carcinoma. World J Surg Oncol 2022; 20:252. [PMID: 35932027 PMCID: PMC9354375 DOI: 10.1186/s12957-022-02681-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) as a common tumor has a poor prognosis. Recently, a combination of atezolizumab and bevacizumab has been recommended as the preferred regimen for advanced HCC. However, the overall response rate of this therapy is low. There is an urgent need to identify sensitive individuals for this precise therapy among HCC patients. METHODS The Wilcox test was used to screen the differentially expressed immune-related genes by combining the TCGA cohort and the Immunology Database. Univariate and multivariate Cox regression analysis were used to screen the immune gene pairs concerning prognosis. A predictive model was constructed using LASSO Cox regression analysis, and correlation analysis was conducted between the signature and clinical characteristics. ICGC cohort and GSE14520 were applied for external validations of the predictive risk model. The relationship between immune cell infiltration, TMB, MSI, therapeutic sensitivity of immune checkpoint inhibitors, targeted drugs, and the risk model were assessed by bioinformatics analysis in HCC patients. RESULTS A risk predictive model consisting of 3 immune-related gene pairs was constructed and the risk score was proved as an independent prognostic factor for HCC patients combining the TCGA cohort. This predictive model exhibited a positive correlation with tumor size (p < 0.01) and tumor stage (TNM) (p < 0.001) in the chi-square test. The predictive power was verified by external validations (ICGC and GSE14520). The risk score clearly correlated with immune cell infiltration, MSI, immune checkpoints, and markers of angiogenesis. CONCLUSIONS Our research established a risk predictive model based on 3 immune-related gene pairs and explored its relationship with immune characteristics, which might help to assess the prognosis and treatment sensitivity to immune and targeted therapy of HCC patients.
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Yu Z, Yang H, Song K, Fu P, Shen J, Xu M, Xu H. Construction of an immune-related gene signature for the prognosis and diagnosis of glioblastoma multiforme. Front Oncol 2022; 12:938679. [PMID: 35982954 PMCID: PMC9379258 DOI: 10.3389/fonc.2022.938679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/04/2022] [Indexed: 12/30/2022] Open
Abstract
Background Increasing evidence has suggested that inflammation is related to tumorigenesis and tumor progression. However, the roles of immune-related genes in the occurrence, development, and prognosis of glioblastoma multiforme (GBM) remain to be studied. Methods The GBM-related RNA sequencing (RNA-seq), survival, and clinical data were acquired from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Chinese Glioma Genome Atlas (CGGA), and Gene Expression Omnibus (GEO) databases. Immune-related genes were obtained from the Molecular Signatures Database (MSigDB). Differently expressed immune-related genes (DE-IRGs) between GBM and normal samples were identified. Prognostic genes associated with GBM were selected by Kaplan–Meier survival analysis, Least Absolute Shrinkage and Selection Operator (LASSO)-penalized Cox regression analysis, and multivariate Cox analysis. An immune-related gene signature was developed and validated in TCGA and CGGA databases separately. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to explore biological functions of the signature. The correlation between immune cell infiltration and the signature was analyzed by single-sample gene set enrichment analysis (ssGSEA), and the diagnostic value was investigated. The gene set enrichment analysis (GSEA) was performed to explore the potential function of the signature genes in GBM, and the protein–protein interaction (PPI) network was constructed. Results Three DE-IRGs [Pentraxin 3 (PTX3), TNFSF9, and bone morphogenetic protein 2 (BMP2)] were used to construct an immune-related gene signature. Receiver operating characteristic (ROC) curves and Cox analyses confirmed that the 3-gene-based prognostic signature was a good independent prognostic factor for GBM patients. We found that the signature was mainly involved in immune-related biological processes and pathways, and multiple immune cells were disordered between the high- and low-risk groups. GSEA suggested that PTX3 and TNFSF9 were mainly correlated with interleukin (IL)-17 signaling pathway, nuclear factor kappa B (NF-κB) signaling pathway, tumor necrosis factor (TNF) signaling pathway, and Toll-like receptor signaling pathway, and the PPI network indicated that they could interact directly or indirectly with inflammatory pathway proteins. Quantitative real-time PCR (qRT-PCR) indicated that the three genes were significantly different between target tissues. Conclusion The signature with three immune-related genes might be an independent prognostic factor for GBM patients and could be associated with the immune cell infiltration of GBM patients.
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Affiliation(s)
- Ziye Yu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Huan Yang
- Department of Nursing, Huashan Hospital, Fudan University, Shanghai, China
| | - Kun Song
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengfei Fu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingjing Shen
- Department of Anesthesiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ming Xu
- Department of Anesthesiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Hongzhi Xu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Center for Neurological Disorders Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Hongzhi Xu,
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Yu L, Liu X, Wang X, Yan H, Pu Q, Xie Y, Du J, Yang Z. Glycometabolism-related gene signature of hepatocellular carcinoma predicts prognosis and guides immunotherapy. Front Cell Dev Biol 2022; 10:940551. [PMID: 35938165 PMCID: PMC9354664 DOI: 10.3389/fcell.2022.940551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/29/2022] [Indexed: 12/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a severe cancer endangering human health. We constructed a novel glycometabolism-related risk score to predict prognosis and immunotherapy strategies in HCC patients. The HCC data sets were obtained from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database, and the glycometabolism-related gene sets were obtained from the Molecular Signature Database. The least absolute contraction and selection operator (LASSO) regression model was used to construct a risk score based on glycometabolism-related genes. A simple visual nomogram model with clinical indicators was constructed and its effectiveness in calibration, accuracy, and clinical value was evaluated. We also explored the correlation between glycometabolism-related risk scores and molecular pathways, immune cells, and functions. Patients in the low-risk group responded better to anti-CTLA-4 immune checkpoint treatment and benefited from immune checkpoint inhibitor (ICI) therapy. The study found that glycometabolism-related risk score can effectively distinguish the prognosis, molecular and immune-related characteristics of HCC patients, and may provide a new strategy for individualized treatment.
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Affiliation(s)
- Lihua Yu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaoli Liu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xinhui Wang
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Huiwen Yan
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Qing Pu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Xie
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- First Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Juan Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Juan Du, ; Zhiyun Yang,
| | - Zhiyun Yang
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Juan Du, ; Zhiyun Yang,
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Zhang Y, Pang S, Sun B, Zhang M, Jiao X, Lai L, Qian Y, Yang N, Yang W. ELOVLs Predict Distinct Prognosis Value and Immunotherapy Efficacy In Patients With Hepatocellular Carcinoma. Front Oncol 2022; 12:884066. [PMID: 35912257 PMCID: PMC9334671 DOI: 10.3389/fonc.2022.884066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a primary malignancy of the liver with high prevalence worldwide and poor prognosis. It has been verified that elongation of very-long-chain fatty acids gene family (ELOVLs), a group of genes that responsible for elongation of saturated and polyunsaturated fatty acids, participate in the pathogenesis and development of multiplex disease including cancers. However, the functions and prognosis of ELOVLs in HCC are still indistinguishable. Methods First, we searched the mRNA expression and survival data of ELOVLs in patients with HCC via the data of The Cancer Genome Atlas (TCGA). The prognosis value of ELOVLs on HCC was assessed by Kaplan–Meier plotter and Cox regression analysis. reverse transcription quantitative- polymerase chain reaction (RT-qPCR), Western blot (WB), and immunohistochemistry were applied to assess the specific mRNA and protein expression of ELOVLs in HCC clinical specimens of our cohort. Then, the functional enrichment of ELOVL1 especially the pathways relating to the immune was conducted utilizing the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) analysis. Additionally, TIMER, CIBERSOR, and tumor immune dysfunction and exclusion (TIDE) were employed to evaluate the relationship between ELOVL1 and immune responses. Last, the correlation of ELOVL1 with genome heterogeneity [microsatellite instability (MSI), tumor mutational burden (TMB), mutant-allele tumor heterogeneity (MATH), homologous recombination deficiency (HRD), purity, ploidy, loss of heterozygosity (LOH), and neoantigens] and mutational landscape were also evaluated basing on the date in TCGA. Results Significant expression alteration was observed in ELOVLs family at the pan-cancer level. In liver cancer, ELOVL1 and ELOVL3 were strongly associated with poor prognosis of HCC by survival analysis and differential expression analysis. Immunohistochemistry microarray, WB, and RT-qPCR confirmed that ELOVL1 but not ELOVL3 played an important role in HCC. Mechanistically, functional network analysis revealed that ELOVL1 might be involved in the immune response. ELOVL1 could affect immune cell infiltration and immune checkpoint markers such as PD-1 and CTLA4 in HCC. Meanwhile, high expression of ELOVL1 would be insensitive to immunotherapy. Correlation analysis of immunotherapy markers showed that ELOVL1 has been associated with MSI, TMB, and oncogene mutations such as TP53. Conclusion ELOVLs play distinct prognostic value in HCC. ELOVL1 could predict the poor prognosis and might be a potential indicator of immunotherapy efficacy in HCC patients.
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Affiliation(s)
- Yu Zhang
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shujie Pang
- Department V of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Bo Sun
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Minbo Zhang
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoxiao Jiao
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Linying Lai
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yiting Qian
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ning Yang
- Department V of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- *Correspondence: Ning Yang, ; Wenzhuo Yang,
| | - Wenzhuo Yang
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Ning Yang, ; Wenzhuo Yang,
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Construction of a Novel Clinical Stage-Related Gene Signature for Predicting Outcome and Immune Response in Hepatocellular Carcinoma. J Immunol Res 2022; 2022:6535009. [PMID: 35865652 PMCID: PMC9296277 DOI: 10.1155/2022/6535009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Hepatocellular carcinoma (HCC) with high heterogeneity is one of the most frequent malignant tumors. However, there were no studies to create a clinical stage-related gene signature for HCC patients. Differentially expressed genes (DEGs) associated with clinical stage of HCC were analyzed based on TCGA datasets. Functional enrichment analysis was carried out by the use of stage-related DEGs. Then, the least absolute shrinkage and selection operator (LASSO) regression and univariate Cox regression were performed to reduce the overfit and the number of genes for further analysis. Next, survival and ROC assays were carried out to demonstrate the model using TCGA. Functional analysis and immune microenvironment analysis related to stage-related DEGs were performed. Reverse transcriptase polymerase chain reaction (RT-PCR) and Cell Counting Kit-8 (CCK-8) assays were applied to examine the expression and function of PNCK in HCC. In this research, there were 21 DEGs between HCC specimens with stage (I-II) and HCC specimens with stage (III-IV), including 20 increased genes and 1 decreased genes. A novel seven-gene signature (including PITX2, PNCK, GLIS1, SCNN1G, MMP1, ZNF488, and SHISA9) was created for the prediction of outcomes of HCC patients. The ROC curves confirmed the prognostic value of the new model. Cox assays demonstrated that the seven-gene signature can independently forecast overall survival. The immune analysis revealed that patients with low risk score exhibited more immune activities. Moreover, we confirmed that PNCK expressions were distinctly increased in HCC, and its silence suppressed the proliferation of HCC cells. Overall, our research offered a robust and reliable gene signature which displayed an important value in the prediction of overall survival of HCC patients and might deliver more effective personalized therapies.
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Guo Y, Yang J, Gao H, Tian X, Zhang X, Kan Q. Development and Verification of a Combined Immune- and Metabolism-Related Prognostic Signature for Hepatocellular Carcinoma. Front Immunol 2022; 13:927635. [PMID: 35874741 PMCID: PMC9304746 DOI: 10.3389/fimmu.2022.927635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/10/2022] [Indexed: 12/09/2022] Open
Abstract
Immune escape and metabolic reprogramming are becoming important characteristics of tumor biology, which play critical roles in tumor initiation and progression. However, the integrative analysis of immune and metabolic characteristics for the tumor microenvironment in hepatocellular carcinoma (HCC) remains unclear. Herein, by univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses, a prognostic signature associated with tumor microenvironment was established based on five immune- and metabolism-related genes (IMRGs), which was fully verified and evaluated in both internal and external cohorts. The C-index was superior to previously published HCC signatures, indicating the robustness and reliability of IMRGs prognostic signature. A nomogram was built based on IMRGs prognostic signature and various clinical parameters, such as age and T stage. The AUCs of nomogram at 1-, 3-, and 5-year (AUC = 0.829, 0.749, 0.749) were slightly better than that of IMRGs signature (AUC = 0.809, 0.734, 0.711). The relationship of risk score (RS) with immune checkpoint expressions, immunophenoscore (IPS), as well as microsatellite instability (MSI) together accurately predicted the treatment efficacy. Collectively, the IMRGs signature might have the potential to better predict prognostic risk, evaluate immunotherapy efficacy, and help personalize immunotherapy for HCC patients.
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Affiliation(s)
- Yuanyuan Guo
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Jing Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Hua Gao
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
- *Correspondence: Xin Tian, ; Xiaojian Zhang, ; Quancheng Kan,
| | - Xiaojian Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
- *Correspondence: Xin Tian, ; Xiaojian Zhang, ; Quancheng Kan,
| | - Quancheng Kan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
- *Correspondence: Xin Tian, ; Xiaojian Zhang, ; Quancheng Kan,
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Liu J, Lu J, Li W, Mao W, Lu Y. Machine Learning Screens Potential Drugs Targeting a Prognostic Gene Signature Associated With Proliferation in Hepatocellular Carcinoma. Front Genet 2022; 13:900380. [PMID: 35836576 PMCID: PMC9273781 DOI: 10.3389/fgene.2022.900380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Background: This study aimed to screen potential drugs targeting a new prognostic gene signature associated with proliferation in hepatocellular carcinoma (HCC). Methods: CRISPR Library and TCGA datasets were used to explore differentially expressed genes (DEGs) related to the proliferation of HCC cells. Differential gene expression analysis, univariate COX regression analysis, random forest algorithm and multiple combinatorial screening were used to construct a prognostic gene signature. Then the predictive power of the gene signature was validated in the TCGA and ICGC datasets. Furthermore, potential drugs targeting this gene signature were screened. Results: A total of 640 DEGs related to HCC proliferation were identified. Using univariate Cox analysis and random forest algorithm, 10 hub genes were screened. Subsequently, using multiplex combinatorial screening, five hub genes (FARSB, NOP58, CCT4, DHX37 and YARS) were identified. Taking the median risk score as a cutoff value, HCC patients were divided into high- and low-risk groups. Kaplan-Meier analysis performed in the training set showed that the overall survival of the high-risk group was worse than that of the low-risk group (p < 0.001). The ROC curve showed a good predictive efficiency of the risk score (AUC > 0.699). The risk score was related to gene mutation, cancer cell stemness and immune function changes. Prediction of immunotherapy suggetsted the IC50s of immune checkpoint inhibitors including A-443654, ABT-888, AG-014699, ATRA, AUY-922, and AZ-628 in the high-risk group were lower than those in the low-risk group, while the IC50s of AMG-706, A-770041, AICAR, AKT inhibitor VIII, Axitinib, and AZD-0530 in the high-risk group were higher than those in the low-risk group. Drug sensitivity analysis indicated that FARSB was positively correlated with Hydroxyurea, Vorinostat, Nelarabine, and Lomustine, while negatively correlated with JNJ-42756493. DHX37 was positively correlated with Raltitrexed, Cytarabine, Cisplatin, Tiotepa, and Triethylene Melamine. YARS was positively correlated with Axitinib, Fluphenazine and Megestrol acetate. NOP58 was positively correlated with Vorinostat and 6-thioguanine. CCT4 was positively correlated with Nerabine. Conclusion: The five-gene signature associated with proliferation can be used for survival prediction and risk stratification for HCC patients. Potential drugs targeting this gene signature deserve further attention in the treatment of HCC.
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Affiliation(s)
- Jun Liu
- Department of Clinical Laboratory, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Medical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Jianjun Lu
- Department of Medical Affairs, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Wenjie Mao
- Emergency Department, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Yamin Lu
- Department of Clinical Laboratory, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
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Hou Y, Zhang R, Zong J, Wang W, Zhou M, Yan Z, Li T, Gan W, Lv S, Zeng Z, Yang M. Comprehensive Analysis of a Cancer-Immunity Cycle-Based Signature for Predicting Prognosis and Immunotherapy Response in Patients With Colorectal Cancer. Front Immunol 2022; 13:892512. [PMID: 35711437 PMCID: PMC9193226 DOI: 10.3389/fimmu.2022.892512] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/02/2022] [Indexed: 12/31/2022] Open
Abstract
Immune checkpoint blockade (ICB) has been recognized as a promising immunotherapy for colorectal cancer (CRC); however, most patients have little or no clinical benefit. This study aimed to develop a novel cancer-immunity cycle–based signature to stratify prognosis of patients with CRC and predict efficacy of immunotherapy. CRC samples from The Cancer Genome Atlas (TCGA) were used as the training set, while the RNA data from Gene Expression Omnibus (GEO) data sets and real-time quantitative PCR (RT-qPCR) data from paired frozen tissues were used for validation. We built a least absolute shrinkage and selection operator (LASSO)-Cox regression model of the cancer-immunity cycle–related gene signature in CRC. Patients who scored low on the risk scale had a better prognosis than those who scored high. Notably, the signature was an independent prognostic factor in multivariate analyses, and to improve prognostic classification and forecast accuracy for individual patients, a scoring nomogram was created. The comprehensive results revealed that the low-risk patients exhibited a higher degree of immune infiltration, a higher immunoreactivity phenotype, stronger expression of immune checkpoint–associated genes, and a superior response to ICB therapy. Furthermore, the risk model was closely related to the response to multiple chemotherapeutic drugs. Overall, we developed a reliable cancer-immunity cycle–based risk model to predict the prognosis, the molecular and immune status, and the immune benefit from ICB therapy, which may contribute greatly to accurate stratification and precise immunotherapy for patients with CRC.
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Affiliation(s)
- Yufang Hou
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rixin Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinbao Zong
- Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China.,Qingdao Hospital of Traditional Chinese Medicine, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Weiqi Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingxuan Zhou
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Yan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tiegang Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenqiang Gan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Silin Lv
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zifan Zeng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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A novel epithelial-mesenchymal transition gene signature for the immune status and prognosis of hepatocellular carcinoma. Hepatol Int 2022; 16:906-917. [PMID: 35699863 PMCID: PMC9349121 DOI: 10.1007/s12072-022-10354-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/06/2022] [Indexed: 12/11/2022]
Abstract
Background This study clarified whether EMT-related genes can predict immunotherapy efficacy and overall survival in patients with HCC. Methods The RNA-sequencing profiles and patient information of 370 samples were derived from the Cancer Genome Atlas (TCGA) dataset, and EMT-related genes were obtained from the Molecular Signatures database. The signature model was constructed using the least absolute shrinkage and selection operator Cox regression analysis in TCGA cohort. Validation data were obtained from the International Cancer Genome Consortium (ICGC) dataset of patients with HCC. Kaplan–Meier analysis and multivariate Cox analyses were employed to estimate the prognostic value. Immune status and tumor microenvironment were estimated using a single-sample gene set enrichment analysis (ssGSEA). The expression of prognostic genes was verified using qRT-PCR analysis of HCC cell lines. Results A signature model was constructed using EMT-related genes to determine HCC prognosis, based on which patients were divided into high-risk and low-risk groups. The risk score, as an independent factor, was related to tumor stage, grade, and immune cells infiltration. The results indicated that the most prognostic genes were highly expressed in the HCC cell lines, but GADD45B was down-regulated. Enrichment analysis suggested that immunoglobulin receptor binding and material metabolism were essential in the prognostic signature. Conclusion Our novel prognostic signature model has a vital impact on immune status and prognosis, significantly helping the decision-making related to the diagnosis and treatment of patients with HCC. Supplementary Information The online version contains supplementary material available at 10.1007/s12072-022-10354-3.
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NOL12 as an Oncogenic Biomarker Promotes Hepatocellular Carcinoma Growth and Metastasis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6891155. [PMID: 35693698 PMCID: PMC9184182 DOI: 10.1155/2022/6891155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy with a poor prognosis worldwide. However, the pathogenesis of HCC remains poorly understood. In this study, we found that NOL12 was significantly overexpressed in independent HCC datasets from TCGA database. We confirmed that the expression level of NOL12 was upregulated in human HCC tissues and cell lines by RT-qPCR. High expression of NOL12 is associated with worse reduced overall survival (OS), high pathological grade, node metastasis, and advanced clinical stage in patients with HCC. Moreover, knockdown of NOL12 dramatically inhibits the proliferation and metastasis of HCC cells in vitro and in vivo. CIBERSORTx analysis revealed that twelve types of tumor-infiltrating immune cells (TICs) are correlated with NOL12 expression. The risk signature based on 8 NOL12-related genes is an independent prognostic factor for patients with HCC. The OS rate of patients in the low-risk score group was better than that in the high-risk score group. In addition, the total tumor mutation burden (TMB) in the high-risk score group increased significantly, and the risk scores could be used as an alternative indicator of immune checkpoint inhibitor (ICI) response. In conclusion, our findings indicated that NOL12 might be involved in the progression of HCC and can be used as a potential therapeutic target. Moreover, the NOL12-related risk signature may have predictive relevance with regard to ICI therapy.
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Ma S, Wang F, Wang N, Jin J, Ba Y, Ji H, Du J, Hu S. Multiomics Data Analysis and Identification of Immune-Related Prognostic Signatures With Potential Implications in Prognosis and Immune Checkpoint Blockade Therapy of Glioblastoma. Front Neurol 2022; 13:886913. [PMID: 35669882 PMCID: PMC9165649 DOI: 10.3389/fneur.2022.886913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022] Open
Abstract
Background In recent years, glioblastoma multiforme (GBM) has been a concern of many researchers, as it is one of the main drivers of cancer-related deaths worldwide. GBM in general usually does not responding well to immunotherapy due to its unique microenvironment. Methods To uncover any further informative immune-related prognostic signatures, we explored the immune-related distinction in the genetic or epigenetic features of the three types (expression profile, somatic mutation, and DNA methylation). Twenty eight immune-related hub genes were identified by Weighted Gene Co-Expression Network Analysis (WGCNA). The findings showed that three genes (IL1R1, TNFSF12, and VDR) were identified to construct an immune-related prognostic model (IRPM) by lasso regression. Then, we used three hub genes to construct an IRPM for GBM and clarify the immunity, mutation, and methylation characteristics. Results Survival analysis of patients undergoing anti-program cell death protein 1 (anti-PD-1) therapy showed that overall survival was superior in the low-risk group than in the high-risk group. The high-risk group had an association with epithelial-mesenchymal transition (EMT), high immune cell infiltration, immune activation, a low mutation number, and high methylation, while the low-risk group was adverse status. Conclusions In conclusion, IRPM is a promising tool to distinguish the prognosis of patients and molecular and immune characteristics in GBM, and the IRPM risk score can be used to predict patient sensitivity to checkpoint inhibitor blockade therapy. Thus, three immune-related signatures will guide us in improving treatment strategies and developing objective diagnostic tools.
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Affiliation(s)
- Shuai Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Neurosurgery, Emergency Medicine Center, Zhejiang Provincial People's Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
| | - Fang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Nan Wang
- Department of Neurosurgery, Emergency Medicine Center, Zhejiang Provincial People's Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
| | - Jiaqi Jin
- Department of Neurosurgery, Emergency Medicine Center, Zhejiang Provincial People's Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
| | - Yixu Ba
- Department of Neurosurgery, Emergency Medicine Center, Zhejiang Provincial People's Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
| | - Hang Ji
- Department of Neurosurgery, Emergency Medicine Center, Zhejiang Provincial People's Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
| | - Jianyang Du
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Jianyang Du
| | - Shaoshan Hu
- Department of Neurosurgery, Emergency Medicine Center, Zhejiang Provincial People's Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
- *Correspondence: Shaoshan Hu ;
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73
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Wang H, Shao R, Liu W, Peng S, Bai S, Fu B, Zhao C, Lu Y. Integrative analysis identifies CXCL11 as an immune-related prognostic biomarker correlated with cell proliferation and immune infiltration in multiple myeloma microenvironment. Cancer Cell Int 2022; 22:187. [PMID: 35568859 PMCID: PMC9107742 DOI: 10.1186/s12935-022-02608-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/02/2022] [Indexed: 02/07/2023] Open
Abstract
Purpose The interaction between tumor cells and tumor microenvironment (TME) has an important impact on progression and prognosis of multiple myeloma (MM), and has been proven to be promising therapeutic targets. This study intended to explore the relationship between TME and prognosis and identify valuable biomarkers of MM. Methods The transcriptomic and clinical information of MM retrieved from the Gene Expression Omnibus (GEO) were used to establish the model. The curve of Kaplan–Meier survival and the time-dependent receiver operating characteristic (ROC) were used to appraise the predictive ability. A nomogram was established for clinical application. Furthermore, the CIBERSORT algorithm was used to investigate the relation between IRGPI with the infiltration of immune cells. We also used histology, as well as in vitro and in vivo experiments to validate these findings. Results The results demonstrated an immune-related gene-based prognostic index (IRGPI) combined with clinical information. Patients were separated into high- and low-risk groups based on risk score, which had significantly difference in survival status and immune infiltrations. Furthermore, we identified CXCL11 as a key factor, which positively promotes the progression of MM and correlate with macrophage M2-like polarization and tumor immune cells infiltration. Conclusion Our findings suggest the IRGPI significantly demonstrate the differential prognosis and prediction of immune cells infiltration. It provides some insights into the complex interaction between myeloma tumor cells and the TME, as well as in the development of a novel biomarker target for anti-MM therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02608-9.
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Affiliation(s)
- Huizhong Wang
- Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,State Key Laboratory of Oncology in South China, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China
| | - Ruonan Shao
- Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,State Key Laboratory of Oncology in South China, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China
| | - Wenjian Liu
- Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,State Key Laboratory of Oncology in South China, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China
| | - Shumei Peng
- Department of Pediatrics, Guangdong Women and Children Hospital, Guangzhou, 510060, China
| | - Shenrui Bai
- Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,State Key Laboratory of Oncology in South China, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China
| | - Bibo Fu
- Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,State Key Laboratory of Oncology in South China, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China
| | - Congling Zhao
- Department of Pediatrics, Guangdong Women and Children Hospital, Guangzhou, 510060, China.
| | - Yue Lu
- Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China. .,State Key Laboratory of Oncology in South China, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China. .,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, China.
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74
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Jin X, Song Y, An Z, Wu S, Cai D, Fu Y, Zhang C, Chen L, Tang W, Zheng Z, Lu H, Lian J. A Predictive Model for Prognosis and Therapeutic Response in Hepatocellular Carcinoma Based on a Panel of Three MED8-Related Immunomodulators. Front Oncol 2022; 12:868411. [PMID: 35558516 PMCID: PMC9086905 DOI: 10.3389/fonc.2022.868411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/25/2022] [Indexed: 12/24/2022] Open
Abstract
The current tumor-node-metastasis (TNM) system is limited in predicting the survival and guiding the treatment of hepatocellular carcinoma (HCC) patients since the TNM system only focuses on the anatomical factors, regardless of the intratumoral molecule heterogeneity. Besides, the landscape of intratumoral immune genes has emerged as a prognostic indicator. The mediator complex subunit 8 (MED8) is a major polymerase regulator and has been described as an oncogene in renal cell carcinoma, but its pathophysiological significance of HCC and its contribution to the prognosis of HCC remain unclear. Here, we aimed to discuss the expression profile and clinical correlation of MED8 in HCC and construct a predictive model based on MED8-related immunomodulators as a supplement to the TNM system. According to our analyses, MED8 was overexpressed in HCC tissues and increased expression of MED8 was an indicator of poor outcome in HCC. The knockdown of MED8 weakened the proliferation, colony forming, and migration of HepG2 and Huh7 cells. Subsequently, a predictive model was identified based on a panel of three MED8-related immunomodulators using The Cancer Genome Atlas (TCGA) database and further validated in International Cancer Genome Consortium (ICGC) database. The combination of the predictive model and the TNM system could improve the performance in predicting the survival of HCC patients. High-risk patients had poor overall survival in TCGA and ICGC databases, as well as in subgroup analysis with early clinicopathology classification. It was also found that high-risk patients had a higher probability of recurrence in TCGA cohort. Furthermore, low-risk score indicated a better response to immunotherapy and drug therapy. This predictive model can be served as a supplement to the TNM system and may have implications in prognosis stratification and therapeutic guidance for HCC.
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Affiliation(s)
- Xiaojun Jin
- School of Medicine, Ningbo University, Ningbo, China.,Department of Cardiovasology, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China.,Central Laboratory, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
| | - Yongfei Song
- Department of Cardiovasology, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China.,Central Laboratory, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
| | - Zhanglu An
- Graduate School, Hebei North University, Zhangjiakou, China.,Department of Pathology, Taizhou Central Hospital (Taizhou University Affiliated Hospital), Taizhou, China
| | - Shanshan Wu
- School of Medicine, Ningbo University, Ningbo, China
| | - Dihui Cai
- School of Medicine, Ningbo University, Ningbo, China
| | - Yin Fu
- School of Medicine, Ningbo University, Ningbo, China
| | | | - Lichao Chen
- School of Medicine, Ningbo University, Ningbo, China
| | - Wen Tang
- School of Medicine, Ningbo University, Ningbo, China
| | - Zequn Zheng
- School of Medicine, Ningbo University, Ningbo, China
| | - Hongsheng Lu
- Department of Pathology, Taizhou Central Hospital (Taizhou University Affiliated Hospital), Taizhou, China
| | - Jiangfang Lian
- School of Medicine, Ningbo University, Ningbo, China.,Department of Cardiovasology, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China.,Central Laboratory, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
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Yan D, Zhao Q, Du Z, Li H, Geng R, Yang W, Zhang X, Cao J, Yi N, Zhou J, Tang Z. Development and validation of an immune-related gene signature for predicting the radiosensitivity of lower-grade gliomas. Sci Rep 2022; 12:6698. [PMID: 35461367 PMCID: PMC9035187 DOI: 10.1038/s41598-022-10601-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/22/2022] [Indexed: 12/21/2022] Open
Abstract
Radiotherapy is an important treatment modality for lower-grade gliomas (LGGs) patients. This analysis was conducted to develop an immune-related radiosensitivity gene signature to predict the survival of LGGs patients who received radiotherapy. The clinical and RNA sequencing data of LGGs were obtained from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). Lasso regression analyses were used to construct a 21-gene signature to identify the LGGs patients who could benefit from radiotherapy. Based on this radiosensitivity signature, patients were classified into a radiosensitive (RS) group and a radioresistant (RR) group. According to the Kaplan–Meier analysis results of the TCGA dataset and the two CGGA validation datasets, the RS group had a higher overall survival rate than that of the RR group. This gene signature was RT-specific and an independent prognostic indicator. The nomogram model performed well in predicting 3-, and 5-year survival of LGGs patients after radiotherapy by this gene signature and other clinical factors (age, sex, grade, IDH mutations, 1p/19q codeletion). In summary, this signature is a powerful supplement to the prognostic factors of LGGs patients with radiotherapy and may provide an opportunity to incorporate individual tumor biology into clinical decision making in radiation oncology.
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76
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Wang Y, Yang Y, Zhao Z, Sun H, Luo D, Huttad L, Zhang B, Han B. A new nomogram model for prognosis of hepatocellular carcinoma based on novel gene signature that regulates cross-talk between immune and tumor cells. BMC Cancer 2022; 22:379. [PMID: 35397536 PMCID: PMC8994280 DOI: 10.1186/s12885-022-09465-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/25/2022] [Indexed: 02/07/2023] Open
Abstract
Background The combined application of immune cells and specific biomarkers related to the tumor immune microenvironment has a better predictive value for the prognosis of HCC. The purpose of this study is to construct a new prognostic model based on immune-related genes that regulate cross-talk between immune and tumor cells to assess the prognosis and explore possible mechanisms. Method The immune cell abundance ratio of 424 cases in the TCGA-LIHC database is obtained through the CIBERSORT algorithm. The differential gene analysis and cox regression analysis is used to screen IRGs. In addition, the function of IRGs was preliminarily explored through the co-culture of M2 macrophages and HCC cell lines. The clinical validation, nomogram establishment and performing tumor microenvironment score were validated. Results We identified 4 immune cells and 9 hub genes related to the prognosis. Further, we identified S100A9, CD79B, TNFRSF11B as an IRGs signature, which is verified in the ICGC and GSE76427 database. Importantly, IRGs signature is closely related to the prognosis, tumor microenvironment score, clinical characteristics and immunotherapy, and nomogram combined with clinical characteristics is more conducive to clinical promotion. In addition, after co-culture with M2 macrophages, the migration capacity and cell pseudopod of MHCC97H increased significantly. And CD79B and TNFRSF11B were significantly down-regulated in MHCC97H, Huh7 and LM3, while S100A9 was up-regulated. Conclusion We constructed an IRGs signature and discussed possible mechanisms. The nomogram established based on IRGs can accurately predict the prognosis of HCC patients. These findings may provide a suitable therapeutic target for HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09465-9.
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77
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Zhong X, Yu X, Chang H. Exploration of a Novel Prognostic Nomogram and Diagnostic Biomarkers Based on the Activity Variations of Hallmark Gene Sets in Hepatocellular Carcinoma. Front Oncol 2022; 12:830362. [PMID: 35359370 PMCID: PMC8960170 DOI: 10.3389/fonc.2022.830362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
Background The initiation and progression of tumors were due to variations of gene sets rather than individual genes. This study aimed to identify novel biomarkers based on gene set variation analysis (GSVA) in hepatocellular carcinoma. Methods The activities of 50 hallmark pathways were scored in three microarray datasets with paired samples with GSVA, and differential analysis was performed with the limma R package. Unsupervised clustering was conducted to determine subtypes with the ConsensusClusterPlus R package in the TCGA-LIHC (n = 329) and LIRI-JP (n = 232) cohorts. Differentially expressed genes among subtypes were identified as initial variables. Then, we used TCGA-LIHC as the training set and LIRI-JP as the validation set. A six-gene model calculating the risk scores of patients was integrated with the least absolute shrinkage and selection operator (LASSO) and stepwise regression analyses. Kaplan–Meier (KM) and receiver operating characteristic (ROC) curves were performed to assess predictive performances. Multivariate Cox regression analyses were implemented to select independent prognostic factors, and a prognostic nomogram was integrated. Moreover, the diagnostic values of six genes were explored with the ROC curves and immunohistochemistry. Results Patients could be separated into two subtypes with different prognoses in both cohorts based on the identified differential hallmark pathways. Six prognostic genes (ASF1A, CENPA, LDHA, PSMB2, SRPRB, UCK2) were included in the risk score signature, which was demonstrated to be an independent prognostic factor. A nomogram including 540 patients was further integrated and well-calibrated. ROC analyses in the five cohorts and immunohistochemistry experiments in solid tissues indicated that CENPA and UCK2 exhibited high and robust diagnostic values. Conclusions Our study explored a promising prognostic nomogram and diagnostic biomarkers in hepatocellular carcinoma.
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Affiliation(s)
- Xiongdong Zhong
- Department of Cardiothoracic Surgery, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Xianchang Yu
- Department of Cardiothoracic Surgery, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Hao Chang
- Department of Protein Modification and Cancer Research, Hanyu Biomed Center Beijing, Beijing, China
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78
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Yang Y, Gao L, Chen J, Xiao W, Liu R, Kan H. Lamin B1 is a potential therapeutic target and prognostic biomarker for hepatocellular carcinoma. Bioengineered 2022; 13:9211-9231. [PMID: 35436411 PMCID: PMC9161935 DOI: 10.1080/21655979.2022.2057896] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 12/01/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is an aggressive malignancy. Previous studies have found that lamin B1 (LMNB1) contributes to the development of human cancers. However, the biological functions and prognostic values of LMNB1 in HCC have not been adequately elucidated. In our present research, the expression pattern of LMNB1 was analyzed. The prognostic values of LMNB1 were evaluated by Kaplan-Meier survival analysis and Cox proportional hazards regression analysis. The effects of LMNB1 on HCC progression were assessed by Cell Counting Kit-8 (CCK-8), colony formation, wound healing, Transwell and in vivo xenograft assays. The mechanisms of LMNB1 in HCC progression were elucidated by gene set enrichment analysis (GSEA) and loss-of-function assays. Besides, a nomogram for predicting overall survival (OS) was constructed. The results demonstrated that LMNB1 was overexpressed in HCC and that increased LMNB1 expression predicted a dismal prognosis. Further experiments showed that LMNB1 facilitated cell proliferation and metastasis in HCC. Functional enrichment analysis revealed that LMNB1 modulated metastasis-associated biological functions such as focal adhesion, extracellular matrix, cell junctions and cell adhesion. Mechanistically, we revealed that LMNB1 promoted HCC progression by regulating the phosphatidylinositol 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) pathways. Moreover, incorporating LMNB1, Ki67 and Barcelona Clinic Liver Cancer (BCLC) stage into a nomogram showed better predictive accuracy than the Tumor-Node-Metastasis (TNM) stage and BCLC stage. In conclusion, LMNB1 may serve as an effective therapeutic target as well as a reliable prognostic biomarker for HCC.
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Affiliation(s)
- Yongyu Yang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lei Gao
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Junzhang Chen
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wang Xiao
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ruoqi Liu
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Heping Kan
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Sun K, Zhang L, Chen P, Qi D, Liu H, Bao H, Wang X, Li T. Circular RNA circ SET domain containing 2 (circSETD2) inhibits hepatocellular carcinoma cell proliferation and invasion in vivo and in vitro. Bioengineered 2022; 13:7293-7302. [PMID: 35260047 PMCID: PMC8974196 DOI: 10.1080/21655979.2022.2048577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Liver cancer is a common malignant tumor with high incidence and mortality rates. However, a reliable prognostic signature has not yet been confirmed. Circular RNAs (circRNAs) play a role in the development and prognosis of numerous malignancies as well as liver cancer. Therefore, identifying abnormally expressed circRNAs in liver cancer tissue is essential for early diagnosis and treatment. This study found that circular RNA circ SET domain containing 2 (circSETD2) is abnormally expressed in liver cancer tissues, but the role and molecular mechanismsin the occurrence and development of liver cancer are still unclear. The expression level of circSETD2 was evaluated through Quantitative Real-time Polymerase chain reaction (qRT-PCR) in cancerous liver tissues (30 cases), liver cancer cell lines and para-cancerous tissues. Knockdown and overexpression circSETD2 lentiviral vector was constructed and applied to transfect hepatoma cells. Cell Counting Kit-8 (CCK-8), colony formation assay, flow cytometry and Transwell assay were used to examine the effects of circSETD2 overexpression or knockdown on liver cancer migration, invasion, cell cycle and cell proliferation. The tumourigenicity in vivo was utilized to assess the effect of circSETD2 on the proliferation of liver cancer cells. circSETD2 expression is lower in cell lines and liver cancer tissues. circSETD2 knockdown can considerably increase liver cancer cells’ invasion, proliferation and colony formation. While In vitro and in vivo, circSETD2 overexpression shows opposite effect. Western blot showed that circSETD2 knockdown can considerably promote E-cadherin expression and inhibit Vimentin, N-cadherin, matrix metallopeptidase-9 (MMP-9) and MMP-2 expression. These findings improve our understanding of the mechanisms of liver cancer progression and will guide future development of therapeutic strategies against the disease by targeting circ-SETD2.
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Affiliation(s)
- Keyan Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Lei Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Peng Chen
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Debin Qi
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Hao Liu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Haili Bao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Xiongwei Wang
- Department of Neurosurgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tao Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai China
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80
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Qiu ZQ, Wang X, Ji XW, Jiang FJ, Han XY, Zhang WL, An YH. The clinical relevance of epithelial-mesenchymal transition and its correlations with tumorigenic immune infiltrates in hepatocellular carcinoma. Immunology 2022; 166:185-196. [PMID: 35274290 DOI: 10.1111/imm.13465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a cancer with extremely high mortality. Epithelial-mesenchymal transition (EMT) may play an important role in the occurrence, invasion, and prognosis of HCC; however, its relationship with immunity in HCC has not yet been studied. Therefore, we investigated the diagnostic and prognostic values of EMT and explored its potential connections with tumorigenic immune infiltrates in HCC. We first proposed a quantitative metric of EMT activity, the EMT score. After applying this metric to 20 datasets from the Integrative Molecular Database of Hepatocellular Carcinoma, The Cancer Genome Atlas, and the Gene Expression Omnibus, we explored the ability of the EMT score to stratify across sample types. We then applied the EMT score for survival analysis and to differentiate patients with/without vascular invasion to test its prognostic value. We also collected and calculated data on the abundance of immune cells and immune cell markers in HCC and investigated their correlations with EMT scores. Finally, we synthesized and analyzed 20 datasets and constructed an EMT-gene-immune linkage network. The results showed higher EMT scores in HCC samples than in cirrhotic and normal livers. The cases with higher EMT scores also showed poorer performance in terms of prognostic factors such as vascular invasion and overall survival time. Our research demonstrated a broad correlation between EMT and the tumor immune microenvironment, and we uncovered multiple potential linkers associated with both EMT and immunity. Studying EMT has clinical relevance and high diagnostic and prognostic value for HCC.
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Affiliation(s)
- Zhi-Qiang Qiu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Xiang Wang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Xiang-Wen Ji
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
| | - Fen-Jun Jiang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China.,Department of Research and Development, Beijing Yihua Biological Technology Co., Ltd, Beijing, 100041, China
| | - Xin-Ye Han
- Department of Research and Development, Beijing Yihua Biological Technology Co., Ltd, Beijing, 100041, China
| | - Wei-Li Zhang
- Department of Inpatient Administration and Medical Record Management, Third Medical Center, General Hospital of Chinese PLA, Beijing, 100039, China
| | - Yi-Hua An
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China
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Tian S, Hu Y, Yang C, Yu J, Liu J, Xuan G, Liu Y, Sun K, Zhang M, Ma S, Shang Y, Zhou X, Han Y. A novel immune checkpoint-related gene signature for hepatocellular carcinoma to predict clinical outcomes and therapeutic response. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:4719-4736. [PMID: 35430837 DOI: 10.3934/mbe.2022220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Immune checkpoint genes (ICGs) have recently been proven to perform instrumental functions in the maintenance of immune homeostasis and represent a promising therapeutic strategy; however, their expression patterns and prognostic values are not fully elucidated in hepatocellular carcinoma (HCC). In this investigation, we focused on establishing and validating a prognostic gene signature to facilitate decision-making in clinical practice. Clinical information, as well as transcriptome data, was obtained from the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) database. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) Cox method were employed to build a multi-gene signature in the TCGA database, while the ICGC database was used for validation. Subsequently, utilizing the six-gene signature, we were able to categorize patients into high- and low-risk groups. In two cohorts, survival analysis findings revealed a dismal outlook for the high-risk group. The receiver operating characteristic curves were utilized to estimate the gene signature's prediction ability. Moreover, correlation analysis showed high-risk group was linked to advanced pathological stage, infiltration of immune cells and therapeutic response. In summary, this unique gene profile might serve not only as a useful prognostic indicator but also as a marker of therapy responsiveness in HCC.
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Affiliation(s)
- Siyuan Tian
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Yinan Hu
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Chunmei Yang
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Jiahao Yu
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Jingyi Liu
- Department of Radiation Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, China
| | - Guoyun Xuan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Yansheng Liu
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Keshuai Sun
- Department of Gastroenterology, The Air Force Hospital from Eastern Theater of PLA, Nanjing 210002, China
| | - Miao Zhang
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Shuoyi Ma
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Yulong Shang
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Xia Zhou
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
| | - Ying Han
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, China
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Xu Q, Miao D, Song X, Chen Z, Zeng L, Zhao L, Xu J, Lin Z, Yu F. Glycolysis-Related Gene Signature Can Predict Survival and Immune Status of Hepatocellular Carcinoma. Ann Surg Oncol 2022; 29:3963-3976. [PMID: 35266081 DOI: 10.1245/s10434-022-11502-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/07/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Concise and precise prognostic models are urgently needed due to the intricate genetic variations among hepatocellular carcinoma (HCC) cells. Disorder or change in glycolysis metabolism has been considered one of the "hallmarks" of cancer. However, the prognostic value of glycolysis-related genes in HCC remains elusive. METHODS A multigene prognostic model was constructed by least absolute shrinkage and selection operator Cox regression analysis in the The Cancer Genome Atlas (TCGA) cohort with 365 HCC patients and validated in the International Cancer Genome Consortium (ICGC) cohort with 231 HCC patients. The Kaplan-Meier methodology and time-dependent receiver operating characteristic curve were employed to confirm its predictive capability. A predictive nomogram was established based on the stepwise multivariate regression model. The differential expression of prognostic genes between HCC tissues and normal tissues was verified by quantitative real-time polymerase chain reaction (PCR) and immunohistochemistry in an independent sample cohort with 30 HCC patients. RESULTS The glycolysis-related gene signature and the nomogram model exhibited robust validity in predicting prognosis. The risk score was an independent predictor for overall survival (OS). Expression levels of immune checkpoint genes and cell cycle genes were significantly elevated in the high-risk group. The high-risk group presented high levels of immune exclusion. The risk score can distinguish the effect of immunotherapy in the IMvigor210 cohort. The prognostic gene expression showed a significant difference between HCC tissues and adjacent nontumorous tissues in the independent sample cohort. CONCLUSION The currently established glycolysis-related gene signature can accurately predict prognosis and reflect immune status, which may be a therapeutic alternative.
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Affiliation(s)
- Qian Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dan Miao
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xian Song
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhuoyan Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Liuwei Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Luying Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jun Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhuo Lin
- Laboratory Animal Centre, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Fujun Yu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
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83
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Lin Z, Xu Q, Song X, Zeng Y, Zeng L, Zhao L, Xu J, Miao D, Chen Z, Yu F. Comprehensive Analysis Identified Mutation-Gene Signature Impacts the Prognosis Through Immune Function in Hepatocellular Carcinoma. Front Oncol 2022; 12:748557. [PMID: 35311113 PMCID: PMC8931204 DOI: 10.3389/fonc.2022.748557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/04/2022] [Indexed: 12/20/2022] Open
Abstract
BackgroundHepatocellular carcinoma (HCC) is a life-threatening and refractory malignancy with poor outcome. Genetic mutations are the hallmark of cancer. Thus far, there is no comprehensive prognostic model constructed by mutation-gene transcriptome in HCC. The prognostic value of mutation-gene signature in HCC remains elusive.MethodsRNA expression profiles and the corresponding clinical information were recruited from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. The least absolute shrinkage and selection operator (LASSO) Cox regression analysis was employed to establish gene signature. Kaplan–Meier curve and time-dependent receiver operating characteristic curve were implemented to evaluate the prognostic value. The Wilcoxon test was performed to analyze the expression of immune checkpoint genes, cell cycle genes, and tumor drug resistance genes in different risk groups. Finally, quantitative real-time PCR (qRT-RCR) and immunohistochemistry (IHC) were performed to validate the mRNA and protein expression between HCC and adjacent nontumorous tissues in an independent cohort.ResultsA prognostic model consisting of five mutated genes was established by LASSO Cox regression analysis. The prognostic model classified patients into high- and low-risk groups. Compared with the low‐risk group, patients in the high‐risk group had significantly worse survival results. The prognostic model can accurately predict the overall survival of HCC patients and predict overall survival more accurately when combined with stage. Furthermore, the immune checkpoint genes, cell cycle genes, and tumor drug resistance genes were higher expressed in the high-risk group compared in the low-risk group. In addition, the expression level of prognostic signature genes was validated in an independent sample cohort, which was consistent with RNA sequencing expression in the TCGA database.ConclusionThe prediction model of HCC constructed using mutation-related genes is of great significance for clinical decision making and the personalized treatment of patients with HCC.
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Affiliation(s)
- Zhuo Lin
- Laboratory Animal Centre, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qian Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xian Song
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuan Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liuwei Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Luying Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jun Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan Miao
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhuoyan Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Fujun Yu, ; Zhuoyan Chen,
| | - Fujun Yu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Fujun Yu, ; Zhuoyan Chen,
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Wang Y, Ge F, Sharma A, Rudan O, Setiawan MF, Gonzalez-Carmona MA, Kornek MT, Strassburg CP, Schmid M, Schmidt-Wolf IGH. Immunoautophagy-Related Long Noncoding RNA (IAR-lncRNA) Signature Predicts Survival in Hepatocellular Carcinoma. BIOLOGY 2021; 10:1301. [PMID: 34943216 PMCID: PMC8698564 DOI: 10.3390/biology10121301] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND The dysregulation of autophagy and immunological processes has been linked to various pathophysiological conditions, including cancer. Most notably, their particular involvement in hepatocellular carcinoma (HCC) is becoming increasingly evident. This has led to the possibility of developing a prognostic signature based on immuno-autophagy-related (IAR) genes. Given that long non-coding RNAs (lncRNAs) also play a special role in HCC, a combined signature utilizing IAR genes and HCC-associated long noncoding RNAs (as IARlncRNA) may potentially help in the clinical scenario. METHOD We used Pearson correlation analysis, Kaplan-Meier survival curves, univariate and multivariate Cox regression, and ROC curves to generate and validate a prognostic immuno-autophagy-related long non-coding RNA (IARlncRNA) signature. The Chi-squared test was utilized to investigate the correlation between the obtained signature and the clinical characteristics. CIBERSORT algorithms and the Wilcoxon rank sum test were applied to investigate the correlation between signature and infiltrating immune cells. GO and KEGG analyses were performed to derived signature-dependent pathways. RESULTS Herein, we build an IAR-lncRNA signature (as first in the literature) and demonstrate its prognostic ability in hepatocellular carcinoma. Primarily, we identified three IARlncRNAs (MIR210HG, AC099850.3 and CYTOR) as unfavorable prognostic determinants. The obtained signature predicted the high-risk HCC group with shorter overall survival, and was further associated with clinical characteristics such as tumor grade (t = 10.918, p = 0.001). Additionally, several infiltrating immune cells showed varied fractions between the low-risk group and the high-risk HCC groups in association with the obtained signature. In addition, pathways analysis described by the signature clearly distinguishes both risk groups in HCC. CONCLUSIONS The immuno-autophagy-related long non-coding RNA (IARlncRNA) signature we established exhibits a prognostic ability in hepatocellular carcinoma. To our knowledge, this is the first attempt in the literature to combine three determinants (immune, autophagy and LnRNAs), thus requiring molecular validation of this obtained signature in clinical samples.
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Affiliation(s)
- Yulu Wang
- Center for Integrated Oncology (CIO), Department of Integrated Oncology, University Hospital of Bonn, 53127 Bonn, Germany; (Y.W.); (F.G.); (A.S.); (O.R.); (M.F.S.)
| | - Fangfang Ge
- Center for Integrated Oncology (CIO), Department of Integrated Oncology, University Hospital of Bonn, 53127 Bonn, Germany; (Y.W.); (F.G.); (A.S.); (O.R.); (M.F.S.)
| | - Amit Sharma
- Center for Integrated Oncology (CIO), Department of Integrated Oncology, University Hospital of Bonn, 53127 Bonn, Germany; (Y.W.); (F.G.); (A.S.); (O.R.); (M.F.S.)
- Department of Neurosurgery, University Hospital of Bonn, 53127 Bonn, Germany
| | - Oliver Rudan
- Center for Integrated Oncology (CIO), Department of Integrated Oncology, University Hospital of Bonn, 53127 Bonn, Germany; (Y.W.); (F.G.); (A.S.); (O.R.); (M.F.S.)
| | - Maria F. Setiawan
- Center for Integrated Oncology (CIO), Department of Integrated Oncology, University Hospital of Bonn, 53127 Bonn, Germany; (Y.W.); (F.G.); (A.S.); (O.R.); (M.F.S.)
| | - Maria A. Gonzalez-Carmona
- Department of Internal Medicine I, University Hospital of Bonn, 53127 Bonn, Germany; (M.A.G.-C.); (M.T.K.); (C.P.S.)
| | - Miroslaw T. Kornek
- Department of Internal Medicine I, University Hospital of Bonn, 53127 Bonn, Germany; (M.A.G.-C.); (M.T.K.); (C.P.S.)
| | - Christian P. Strassburg
- Department of Internal Medicine I, University Hospital of Bonn, 53127 Bonn, Germany; (M.A.G.-C.); (M.T.K.); (C.P.S.)
| | - Matthias Schmid
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital of Bonn, 53127 Bonn, Germany;
| | - Ingo G. H. Schmidt-Wolf
- Center for Integrated Oncology (CIO), Department of Integrated Oncology, University Hospital of Bonn, 53127 Bonn, Germany; (Y.W.); (F.G.); (A.S.); (O.R.); (M.F.S.)
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Identification of an Immune-Related Biomarker Model Based on the CircRNA-Associated Regulatory Network for Esophageal Carcinoma. JOURNAL OF ONCOLOGY 2021; 2021:1334571. [PMID: 34840568 PMCID: PMC8612787 DOI: 10.1155/2021/1334571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022]
Abstract
Esophageal carcinoma (ESCA) is one of the most frequent types of malignant tumor that has a dismal prognosis. This research applied datasets aimed from the GEO and TCGA to create a prognostic signature for forecasting the clinical outcome of ESCA patients on the basis of a circRNA-associated regulatory network. Methods. A regulatory network associated with ESCA was established based on transcriptome data of circRNAs, miRNAs, and mRNAs. Functional annotations were implemented to further explore the mechanism of ESCA. Cox relative regression method was applied to create a risk signature. Besides, the immune microenvironment of the signature was investigated by utilizing the CIBERSORT algorithm. Results. Based on 27 DEcircRNAs, 65 DEmiRNAs, and 780 DEmRNAs, the circRNA-miRNA-mRNA network was finally set up. Functional enrichment unearthed that the regulatory network might participate in phosphorylation negative regulation, MAPK pathway, and PI3K/AKT pathway. This study established a risk scoring signature based on the seven immune-related genes (IRGs) (MARP14, RASGR1, PTK2, HMGB1, DKK1, RARB, and IGF1R), which was validated for its reliability. A stable and accurate nomogram combining immune-related risk scores with clinical features was constructed. Furthermore, we observed that the risk model was also related to the immunocyte infiltration. Conclusion. Our study successfully created a circRNA-associated regulatory network and further developed an immune-related model to forecast the clinical outcome of ESCA patients as well as to assess their immune status.
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86
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Fu XW, Song CQ. Identification and Validation of Pyroptosis-Related Gene Signature to Predict Prognosis and Reveal Immune Infiltration in Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:748039. [PMID: 34820376 PMCID: PMC8606409 DOI: 10.3389/fcell.2021.748039] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 12/26/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is characterized by a poor prognosis and accounts for the fourth common cause of cancer-related deaths. Recently, pyroptosis has been revealed to be involved in the progression of multiple cancers. However, the role of pyroptosis in the HCC prognosis remains elusive. Methods: The clinical information and RNA-seq data of the HCC patients were collected from the TCGA-LIHC datasets, and the differential pyroptosis-related genes (PRG) were firstly explored. The univariate Cox regression and consensus clustering were applied to recognize the HCC subtypes. The prognostic PRGs were then submitted to the LASSO regression analysis to build a prognostic model in the TCGA training cohort. We further evaluated the predictive model in the TCGA test cohort and ICGC validation cohort (LIRI-JP). The accuracy of prediction was validated using the Kaplan—Meier (K-M) and receiver operating characteristic (ROC) analyses. The single-sample gene set enrichment analysis (ssGSEA) was used to determine the differential immune cell infiltrations and related pathways. Finally, the expression of the prognostic genes was validated by qRT-PCR in vivo and in vitro. Results: We identified a total of 26 differential PRGs, among which three PRGs comprising GSDME, GPX4, and SCAF11 were subsequently chosen for constructing a prognostic model. This model significantly distinguished the HCC patients with different survival years in the TCGA training, test, and ICGC validation cohorts. The risk score of this model was confirmed as an independent prognostic factor. A nomogram was generated indicating the survival years for each HCC patient. The ssGSEA demonstrated several tumor-infiltrating immune cells to be remarkably associated with the risk scores. The qRT-PCR results also showed the apparent dysregulation of PRGs in HCC. Finally, the drug sensitivity was analyzed, indicating that Lenvatinib might impact the progression of HCC via targeting GSDME, which was also validated in human Huh7 cells. Conclusion: The PRG signature comprised of GSDME, GPX4, and SCAF11 can serve as an independent prognostic factor for HCC patients, which would provide further evidence for more clinical and functional studies.
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Affiliation(s)
- Xiao-Wei Fu
- Fudan University, Shanghai, China.,Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Laboratory of Gene Therapeutic Biology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chun-Qing Song
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Laboratory of Gene Therapeutic Biology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
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87
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Construction and Validation of an Immune-Related Gene Prognostic Index for Esophageal Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:7430315. [PMID: 34722771 PMCID: PMC8553461 DOI: 10.1155/2021/7430315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/20/2021] [Indexed: 12/02/2022]
Abstract
Immune checkpoint inhibitor (ICI) therapy may benefit patients with advanced esophageal squamous cell carcinoma (ESCC); however, novel biomarkers are needed to help predict the response of patients to treatment. Differentially expressed immune-related genes within The Cancer Genome Atlas ESCC dataset were selected using the weighted gene coexpression network and lasso Cox regression analyses. Based on these data, an immune-related gene prognostic index (IRGPI) was constructed. The molecular characteristics of the different IRGPI subgroups were assessed using mutation information and gene set enrichment analysis. Differences in immune cell infiltration and the response to ICI therapy and other drugs were also analyzed. Additionally, tumor and adjacent control tissues were collected from six patients with ESCC and the expression of these genes was verified using real-time quantitative polymerase chain reaction. IRGPI was designed based on CLDN1, HCAR3, FNBP1L, and BRCA2, the expression of which was confirmed in ESCC samples. The prognosis of patients in the high-IRGPI group was poor, as verified using publicly available expression data. KMT2D mutations were more common in the high-IRGPI group. Enrichment analysis revealed an active immune response, and immune infiltration assessment showed that the high-IRGPI group had an increased infiltration degree of CD8 T cells, which contributed to the improved response to ICI treatment. Collectively, these data demonstrate that IRGPI is a robust biomarker for predicting the prognosis and response to therapy of patients with ESCC.
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88
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Qin P, Zhang M, Liu X, Dong Z. Immunogenomic Landscape Analysis of Prognostic Immune-Related Genes in Hepatocellular Carcinoma. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:3761858. [PMID: 34745496 PMCID: PMC8570866 DOI: 10.1155/2021/3761858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/16/2021] [Indexed: 12/30/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death. HBV infection is an important risk factor for the tumorigenesis of HCC, given that the inflammatory environment is closely related to morbidity and prognosis. Consequently, it is of urgent importance to explore the immunogenomic landscape to supplement the prognosis of HCC. The expression profiles of immune-related genes (IRGs) were integrated with 377 HCC patients to generate differentially expressed IRGs based on the Cancer Genome Atlas (TCGA) dataset. These IRGs were evaluated and assessed in terms of their diagnostic and prognostic values. A total of 32 differentially expressed immune-related genes resulted as significantly correlated with the overall survival of HCC patients. The Gene Ontology functional enrichment analysis revealed that these genes were actively involved in cytokine-cytokine receptor interaction. A prognostic signature based on IRGs (HSPA4, PSME3, PSMD14, FABP6, ISG20L2, TRAF3, NDRG1, NRAS, CSPG5, and IL17D) stratified patients into high-risk versus low-risk groups in terms of overall survival and remained as an independent prognostic factor in multivariate analyses after adjusting for clinical and pathologic factors. Several IRGs (HSPA4, PSME3, PSMD14, FABP6, ISG20L2, TRAF3, NDRG1, NRAS, CSPG5, and IL17D) of clinical significance were screened in the present study, revealing that the proposed clinical-immune signature is a promising risk score for predicting the prognosis of HCC.
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Affiliation(s)
- Peng Qin
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Mengyu Zhang
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Xue Liu
- Department of Immunotherapy, Affiliated Cancer Hospital, Zhengzhou University, Zhengzhou 450003, China
| | - Ziming Dong
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
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Nie Y, Li J, Wu W, Guo D, Lei X, Zhang T, Wang Y, Mao Z, Zhang X, Song W. A Novel Nine-lncRNA Risk Signature Correlates With Immunotherapy in Hepatocellular Carcinoma. Front Oncol 2021; 11:706915. [PMID: 34604045 PMCID: PMC8479152 DOI: 10.3389/fonc.2021.706915] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/24/2021] [Indexed: 12/18/2022] Open
Abstract
Background Hepatocellular carcinoma is one of the most common malignant tumors with a very high mortality rate. The emergence of immunotherapy has brought hope for the cure of hepatocellular carcinoma. Only a small number of patients respond to immune checkpoint inhibitors, and ferroptosis and tertiary lymphoid structure contribute to the increased response rate of immune checkpoint inhibitors; thus, we first need to identify those who are sensitive to immunotherapy and then develop different methods to improve sensitivity for different groups. Methods The sequencing data of hepatocellular carcinoma from The Cancer Genome Atlas and Gene Expression Omnibus was downloaded to identify the immune-related long non-coding RNAs (lncRNAs). LncRNAs related to survival data were screened out, and a risk signature was established using Cox proportional hazard regression model. R software was used to calculate the riskScore of each patient, and the patients were divided into high- and low-risk groups. The prognostic value of riskScore and its application in clinical chemotherapeutic drugs were confirmed. The relationship between riskScore and immune checkpoint genes, ferroptosis genes, and genes related to tertiary lymphoid structure formation was analyzed by Spearman method. TIMER, CIBERSORT, ssGSEA, and ImmuCellAI were used to evaluate the relative number of lymphocytes in tumor. The Wilcoxon signed-rank test confirmed differences in immunophenoscore between the high- and low-risk groups. Results Data analysis revealed that our signature could well predict the 1-, 2-, 3-, and 5-year survival rates of hepatocellular carcinoma and to predict susceptible populations with Sorafenib. The risk signature were significantly correlated with immune checkpoint genes, ferroptosis genes, and tertiary lymphoid structure-forming genes, and predicted tumor-infiltrating lymphocyte status. There was a significant difference in IPS scores between the low-risk group and the high-risk group, while the low-risk group had higher scores. Conclusion The riskScore obtained from an immune-related lncRNA signature could successfully predict the survival time and reflect the efficacy of immune checkpoint inhibitors. More importantly, it is possible to select different treatments for different hepatocellular carcinoma patients that increase the response rate of immune checkpoint inhibitors and will help improve the individualized treatment of hepatocellular carcinoma.
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Affiliation(s)
- Ye Nie
- Xi'an Medical University, Xi'an, China.,Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Jianhui Li
- Xi'an Medical University, Xi'an, China.,Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Wenlong Wu
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Dongnan Guo
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xinjun Lei
- Xi'an Medical University, Xi'an, China.,Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Tianchen Zhang
- Xi'an Medical University, Xi'an, China.,Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yanfang Wang
- Xi'an Medical University, Xi'an, China.,Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Zhenzhen Mao
- Xi'an Medical University, Xi'an, China.,Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Xuan Zhang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Wenjie Song
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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Montella L, Sarno F, Ambrosino A, Facchini S, D’Antò M, Laterza MM, Fasano M, Quarata E, Ranucci RAN, Altucci L, Berretta M, Facchini G. The Role of Immunotherapy in a Tolerogenic Environment: Current and Future Perspectives for Hepatocellular Carcinoma. Cells 2021; 10:1909. [PMID: 34440678 PMCID: PMC8393830 DOI: 10.3390/cells10081909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
In contrast to several tumors whose prognoses are radically affected by novel immunotherapeutic approaches and/or targeted therapies, the outcomes of advanced hepatocellular carcinoma (HCC) remain poor. The underlying cirrhosis that is frequently associated with it complicates medical treatment and often determines survival. The landscape of HCC treatment had included sorafenib as the only drug available for ten years, until 2018, when lenvatinib was approved for treatment. The second-line systemic treatments available for hepatocellular carcinoma include regorafenib, cabozantinib, ramucirumab, and, more recently, immune checkpoint inhibitors. However, the median survival remains below 15 months. The results obtained in clinics should be interpreted whilst considering the peculiar role of the liver as an immune organ. A healthy liver microenvironment ordinarily experiences stimulation by gut-derived antigens. This setup elucidates the response to chronic inflammation and the altered balance between tolerance and immune response in HCC development. This paper provides an overview of the mechanisms involved in HCC pathogenesis, with a special focus on the immune implications, along with current and future clinical perspectives.
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Affiliation(s)
- Liliana Montella
- ASL NA2 NORD, Oncology Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy; (M.M.L.); (E.Q.)
| | - Federica Sarno
- Precision Medicine Department, “Luigi Vanvitelli” University of Campania, 80138 Naples, Italy; (F.S.); (L.A.)
| | - Annamaria Ambrosino
- ASL NA2 NORD, Internal Medicine Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy; (A.A.); (M.D.); (R.A.N.R.)
| | - Sergio Facchini
- Department of Precision Medicine, Division of Medical Oncology, “Luigi Vanvitelli” University of Campania, 80131 Naples, Italy; (S.F.); (M.F.)
| | - Maria D’Antò
- ASL NA2 NORD, Internal Medicine Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy; (A.A.); (M.D.); (R.A.N.R.)
| | - Maria Maddalena Laterza
- ASL NA2 NORD, Oncology Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy; (M.M.L.); (E.Q.)
| | - Morena Fasano
- Department of Precision Medicine, Division of Medical Oncology, “Luigi Vanvitelli” University of Campania, 80131 Naples, Italy; (S.F.); (M.F.)
| | - Ermelinda Quarata
- ASL NA2 NORD, Oncology Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy; (M.M.L.); (E.Q.)
| | - Raffaele Angelo Nicola Ranucci
- ASL NA2 NORD, Internal Medicine Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy; (A.A.); (M.D.); (R.A.N.R.)
| | - Lucia Altucci
- Precision Medicine Department, “Luigi Vanvitelli” University of Campania, 80138 Naples, Italy; (F.S.); (L.A.)
| | - Massimiliano Berretta
- Department of Clinical and Experimental Medicine, University of Messina, 98121 Messina, Italy;
| | - Gaetano Facchini
- ASL NA2 NORD, Oncology Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy; (M.M.L.); (E.Q.)
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91
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Zhao E, Chen S, Dang Y. A novel signature based on pairwise PD-1/PD-L1 signaling pathway genes for predicting the overall survival in patients with hepatocellular carcinoma. Clin Transl Med 2021; 11:e431. [PMID: 34047473 PMCID: PMC8140183 DOI: 10.1002/ctm2.431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/27/2021] [Accepted: 05/09/2021] [Indexed: 01/18/2023] Open
Affiliation(s)
- Enfa Zhao
- Department of Structural Heart Disease, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shimin Chen
- Department of Gastroenterology, Traditional Chinese Medical Hospital of Taihe Country, Taihe, China
| | - Ying Dang
- Department of Ultrasound Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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92
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Lin Z, Xu Q, Miao D, Yu F. An Inflammatory Response-Related Gene Signature Can Impact the Immune Status and Predict the Prognosis of Hepatocellular Carcinoma. Front Oncol 2021; 11:644416. [PMID: 33828988 PMCID: PMC8019928 DOI: 10.3389/fonc.2021.644416] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, which makes the prognostic prediction challenging. As part of the active cross-talk between the tumor and the host, inflammatory response in the tumor or its microenvironment could affect prognosis. However, the prognostic value of inflammatory response-related genes in HCC remains to be further elucidated. Methods In this study, the mRNA expression profiles and corresponding clinical data of HCC patients were downloaded from the public database. The least absolute shrinkage and selection operator Cox analysis was utilized to construct a multigene prognostic signature in the TCGA cohort. HCC patients from the ICGC cohort were used for validation. Kaplan Meier analysis was used to compare the overall survival (OS) between high- and low-risk groups. Univariate and multivariate Cox analyses were applied to determine the independent predictors for OS. Single-sample gene set enrichment analysis was utilized to calculate the immune cell infiltration score and immune related pathway activity. Gene set enrichment analysis was implemented to conduct GO terms and KEGG pathways. The qRT-PCR and immunohistochemistry were utilized to perform the mRNA and protein expression of prognostic genes between HCC tissues and normal liver tissues respectively. Results An inflammatory response-related gene signature model was constructed by LASSO Cox regression analysis. Compared with the low-risk group, patients in the high-risk group showed significantly reduced OS. Receiver operating characteristic curve analysis confirmed the predictive capacity of the prognostic gene signature. Multivariate Cox analysis revealed that the risk score was an independent predictor for OS. Functional analysis indicated that immune status was definitely different between two risk groups, and cancer-related pathways were enriched in high-risk group. The risk score was significantly correlated with tumor grade, tumor stage and immune infiltrate types. The expression levels of prognostic genes were significantly correlated with sensitivity of cancer cells to anti-tumor drugs. Furthermore, the expression of prognostic genes showed significant difference between HCC tissues and adjacent non-tumorous tissues in the separate sample cohort. Conclusion A novel signature constructed with eight inflammatory response-related genes can be used for prognostic prediction and impact the immune status in HCC. Moreover, inhibition of these genes may be a therapeutic alternative.
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Affiliation(s)
- Zhuo Lin
- Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Accurate Diagnosis and Treatment of Chronic Liver Diseases, Key Laboratory of Zhejiang Province, Wenzhou, China
| | - Qian Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan Miao
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fujun Yu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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