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Wang X, Han T, Wang Y, Yang R, Yang Q, Li J. Integrative analysis of the immunological significances of guanylate binding protein family genes in microsatellite stability colorectal cancer. Heliyon 2024; 10:e37741. [PMID: 39315131 PMCID: PMC11417218 DOI: 10.1016/j.heliyon.2024.e37741] [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: 06/05/2024] [Revised: 09/07/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024] Open
Abstract
Background Microsatellite stability (MSS) colorectal cancer (CRC) has poor sensitivity to immunotherapy and its underlying mechanisms are still unclear. Guanylate binding proteins (GBPs) are a family of GTPase involving innate immune responses by providing defense against invading microbes and pathogens. However, the immunological significances of GBPs in MSS CRC remain unknown. Methods We utilized bioinformatic tools to comprehensively analysis the expression pattern, clinical relevance, prognostic value, biological function, and immunoregulation effect of distinct GBP members in MSS CRC. Results The expression of all seven GBPs in MSS samples are remarkably decreased compared to microsatellite instability-high (MSI-H) samples. Among them, GBP1/2/4/5 are obviously correlated with distant metastasis status. High expression of GBP1/4/5/6 was remarkably related to favorable overall survival (OS) and progression-free survival (PFS) in CRC patients with MSS tumor. Subsequent enrichment analysis revealed that Interferon-gamma (IFN-γ) and NOD-like receptor signaling are the most relevant functions. Besides, the expression patterns of GBPs are remarkably associated with several tumor infiltrated immune cells (e.g. regulatory T cells, CD4+ T cells, and macrophages) and diverse immunoregulatory molecules (e.g. immune checkpoint biomarkers (ICBs) and major histocompatibility complex (MHC) molecules). Moreover, high GBP1/2/4/5 expression predicted better immunotherapy responsiveness in immunotherapy cohorts. Conclusion These findings might provide novel insights for the identification of therapeutic targets and potential prognostic biomarkers of GBP family in CRC with MSS samples.
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Affiliation(s)
| | | | - Yinchun Wang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, PR China
| | - Rui Yang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, PR China
| | - Qingqiang Yang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, PR China
| | - Jianxin Li
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, PR China
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2
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Hasegawa M, Amano Y, Kihara A, Matsubara D, Fukushima N, Takahashi H, Chikamatsu K, Nishino H, Mori Y, Yoshida N, Niki T. Guanylate binding protein 5 is an immune-related biomarker of oral squamous cell carcinoma: A retrospective prognostic study with bioinformatic analysis. Cancer Med 2024; 13:e7431. [PMID: 38978333 PMCID: PMC11231040 DOI: 10.1002/cam4.7431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 06/02/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Cancer utilizes immunosuppressive mechanisms to create a tumor microenvironment favorable for its progression. The purpose of this study is to histologically characterize the immunological properties of the tumor microenvironment of oral squamous cell carcinoma (OSCC) and identify key molecules involved in the immunological microenvironment and patient prognosis. METHODS First, overlapping differentially expressed genes (DEGs) were screened from OSCC transcriptome data in public databases. Correlation analysis of DEGs with known immune-related genes identified genes involved in the immune microenvironment of OSCC. Next, stromal patterns of tumor were classified and immunohistochemical staining was performed for immune cell markers (CD3, CD4, Foxp3, CD8, CD20, CD68, and CD163), programmed death-ligand 1 (PD-L1), and guanylate binding protein 5 (GBP5) in resected specimens obtained from 110 patients with OSCC who underwent resection. Correlations between each factor and their prognostic impact were analyzed. RESULTS Among the novel OSCC-specific immune-related genes screened (including ADAMDEC1, CXCL9, CXCL13, DPT, GBP5, IDO1, and PLA2G7), GBP5 was selected as the target gene. Histopathologic analysis showed that multiple T-cell subsets and CD20-positive cells were less common in the advanced stages, whereas CD163-positive cells were more common in advanced stages. The immature type in the stromal pattern category was associated with less immune cell infiltration, lower expression of PD-L1 in immune cells, lower expression of GBP5 in the stroma, and shorter overall survival and recurrence-free survival. Expression of GBP5 in the tumor and stroma correlated with immune cell infiltration of tumors and PD-L1 expression in tumor and immune cells. Patients with low tumor GBP5 expression and high stromal expression had significantly longer overall survival and recurrence-free survival. CONCLUSIONS The stromal pattern category may reflect both invasive and immunomodulatory potentials of cancer-associated fibroblasts in OSCC. GBP5 has been suggested as a potential biomarker to predict the prognosis and therapeutic efficacy of immune checkpoint inhibitors.
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MESH Headings
- Adult
- Aged
- Female
- Humans
- Male
- Middle Aged
- B7-H1 Antigen/metabolism
- B7-H1 Antigen/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/immunology
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/metabolism
- Computational Biology/methods
- Gene Expression Regulation, Neoplastic
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/immunology
- GTP-Binding Proteins/metabolism
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Mouth Neoplasms/immunology
- Mouth Neoplasms/pathology
- Mouth Neoplasms/genetics
- Mouth Neoplasms/mortality
- Mouth Neoplasms/metabolism
- Mouth Neoplasms/surgery
- Prognosis
- Retrospective Studies
- Tumor Microenvironment/immunology
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Affiliation(s)
- Masayo Hasegawa
- Department of Integrative PathologyJichi Medical UniversityShimotsukeTochigiJapan
- Department of Otolaryngology‐Head and Neck SurgeryJichi Medical University Saitama Medical CenterSaitamaJapan
| | - Yusuke Amano
- Department of Integrative PathologyJichi Medical UniversityShimotsukeTochigiJapan
| | - Atsushi Kihara
- Department of Integrative PathologyJichi Medical UniversityShimotsukeTochigiJapan
| | - Daisuke Matsubara
- Department of Integrative PathologyJichi Medical UniversityShimotsukeTochigiJapan
- Department of Pathology, Faculty of medicineUniversity of TsukubaTsukubaIbarakiJapan
| | - Noriyoshi Fukushima
- Department of Integrative PathologyJichi Medical UniversityShimotsukeTochigiJapan
| | - Hideyuki Takahashi
- Department of Otolaryngology‐Head and Neck SurgeryGunma University Graduate School of MedicineMaebashiGunmaJapan
| | - Kazuaki Chikamatsu
- Department of Otolaryngology‐Head and Neck SurgeryGunma University Graduate School of MedicineMaebashiGunmaJapan
| | - Hiroshi Nishino
- Department of Otolaryngology‐Head and Neck SurgeryJichi Medical UniversityShimotsukeTochigiJapan
| | - Yoshiyuki Mori
- Department of Dentistry, Oral and Maxillofacial SurgeryJichi Medical University Saitama Medical CenterSaitamaJapan
| | - Naohiro Yoshida
- Department of Otolaryngology‐Head and Neck SurgeryJichi Medical University Saitama Medical CenterSaitamaJapan
| | - Toshiro Niki
- Department of Integrative PathologyJichi Medical UniversityShimotsukeTochigiJapan
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3
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Chiu HW, Lin CH, Lee HH, Lu HW, Lin YHK, Lin YF, Lee HL. Guanylate binding protein 5 triggers NF-κB activation to foster radioresistance, metastatic progression and PD-L1 expression in oral squamous cell carcinoma. Clin Immunol 2024; 259:109892. [PMID: 38185269 DOI: 10.1016/j.clim.2024.109892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/09/2024]
Abstract
Radioresistance and metastasis are critical issues in managing oral squamous cell carcinoma (OSCC). Although immune checkpoint inhibitors (ICIs) has been recommended to treat OSCC, lacking useful biomarkers limited their anti-cancer effectiveness. We found that guanylate binding protein 5 (GBP5) is upregulated in primary tumors and associates with radioresistance in OSCC. GBP5 expression causally associated with cellular radioresistance and migration ability in the OSCC cell variants. GBP5 upregulation was examined to be correlated with NF-κB activation and programmed cell death-ligand 1 (PD-L1) elevation in OSCC samples. GBP5 knockdown was mitigated, but overexpression enhanced, NF-κB activity and PD-L1 expression in the OSCC cells. NF-κB inhibition by SN50 dramatically suppressed the GBP5-forested irradiation resistance, cellular migration ability and PD-L1 expression in OSCC cells. Importantly, GBP5 upregulation predicted a favorable outcome in cancer patients received ICI treatment. Our findings provide GBP5 as a useful biomarker to predict the anti-OSCC effectiveness of irradiation and ICIs.
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Affiliation(s)
- Hui-Wen Chiu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 11031, Taiwan
| | - Che-Hsuan Lin
- Department of Otolaryngology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Otolaryngology, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Hsun-Hua Lee
- Department of Neurology, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan; Department of Neurology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Neurology, Vertigo and Balance Impairment Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Hsiao-Wei Lu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Otolaryngology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Otolaryngology Head and Neck Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Yu-Hsien Kent Lin
- Department of Obstetrics and Gynaecology, North Shore Private Hospital, Sydney, NSW, Australia; Department of Gynecology, Ryde Hospital, Northern Sydney Local Health District, Sydney, Australia; Northern Clinical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Yuan-Feng Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan
| | - Hsin-Lun Lee
- Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Radiation Oncology, Taipei Medical University Hospital, Taipei 11031, Taiwan.
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Chang YF, Wang HH, Shu CW, Tsai WL, Lee CH, Chen CL, Liu PF. TMEM211 Promotes Tumor Progression and Metastasis in Colon Cancer. Curr Issues Mol Biol 2023; 45:4529-4543. [PMID: 37367036 DOI: 10.3390/cimb45060287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Colon cancer is the third most important cancer type, leading to a remarkable number of deaths, indicating the necessity of new biomarkers and therapeutic targets for colon cancer patients. Several transmembrane proteins (TMEMs) are associated with tumor progression and cancer malignancy. However, the clinical significance and biological roles of TMEM211 in cancer, especially in colon cancer, are still unknown. In this study, we found that TMEM211 was highly expressed in tumor tissues and the increased TMEM211 was associated with poor prognosis in colon cancer patients from The Cancer Genome Atlas (TCGA) database. We also showed that abilities regarding migration and invasion were reduced in TMEM211-silenced colon cancer cells (HCT116 and DLD-1). Moreover, TMEM211-silenced colon cancer cells showed decreased levels of Twist1, N-cadherin, Snail and Slug but increased levels of E-cadherin. Levels of phosphorylated ERK, AKT and RelA (NF-κB p65) were also decreased in TMEM211-silenced colon cancer cells. Our findings indicate that TMEM211 regulates epithelial-mesenchymal transition for metastasis through coactivating the ERK, AKT and NF-κB signaling pathways, which might provide a potential prognostic biomarker or therapeutic target for colon cancer patients in the future.
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Affiliation(s)
- Yung-Fu Chang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
| | - Hsing-Hsang Wang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chih-Wen Shu
- Institute of BioPharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Wei-Lun Tsai
- Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan
| | - Cheng-Hsin Lee
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chun-Lin Chen
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Pei-Feng Liu
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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5
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Tseng CC, Hung CC, Shu CW, Lee CH, Chen CF, Kuo MS, Kao YY, Chen CL, Ger LP, Liu PF. The Clinical and Biological Effects of Receptor Expression-Enhancing Protein 6 in Tongue Squamous Cell Carcinoma. Biomedicines 2023; 11:biomedicines11051270. [PMID: 37238941 DOI: 10.3390/biomedicines11051270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
There are currently no effective biomarkers for the diagnosis and treatment of tongue squamous cell carcinoma (TSCC), which causes a poor 5-year overall survival rate. Thus, it is crucial to identify more effective diagnostic/prognostic biomarkers and therapeutic targets for TSCC patients. The receptor expression-enhancing protein 6 (REEP6), a transmembrane endoplasmic reticulum resident protein, controls the expression or transport of a subset of proteins or receptors. Although it was reported that REEP6 plays a role in lung and colon cancers, its clinical impact and biological role in TSCC are still unknown. The present study aimed to identify a novel effective biomarker and therapeutic target for TSCC patients. Expression levels of REEP6 in specimens from TSCC patients were determined with immunohistochemistry. Gene knockdown was used to evaluate the effects of REEP6 in cancer malignancy (colony/tumorsphere formation, cell cycle regulation, migration, drug resistance and cancer stemness) of TSCC cells. The clinical impact of REEP6 expression and gene co-expression on prognosis were analyzed in oral cancer patients including TSCC patients from The Cancer Genome Atlas database. Tumor tissues had higher levels of REEP6 compared to normal tissues in TSCC patients. Higher REEP6 expression was related to shorter disease-free survival (DFS) in oral cancer patients with poorly differentiated tumor cells. REEP6-knocked-down TSCC cells showed diminished colony/tumorsphere formation, and they also caused G1 arrest and decreased migration, drug resistance and cancer stemness. A high co-expression of REEP6/epithelial-mesenchymal transition or cancer stemness markers also resulted in poor DFS in oral cancer patients. Thus, REEP6 is involved in the malignancy of TSCC and might serve as a potential diagnostic/prognostic biomarker and therapeutic target for TSCC patients.
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Affiliation(s)
- Chung-Chih Tseng
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Department of Dentistry, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung 81342, Taiwan
| | - Chung-Ching Hung
- Department of Otolaryngology, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung 81342, Taiwan
| | - Chih-Wen Shu
- Institute of BioPharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Cheng-Hsin Lee
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chun-Feng Chen
- Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan
| | - Mei-Shu Kuo
- Department of Biotechnology, Chia Nan University, Tainan 71710, Taiwan
| | - Yu-Ying Kao
- Department of Biotechnology, Chia Nan University, Tainan 71710, Taiwan
| | - Chun-Lin Chen
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan
| | - Pei-Feng Liu
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
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6
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Li X, Song D, Su S, He X, Cao F, Yang C, Li K, Huang S, Li C, Wang C, Zhang A, Pang P, Zheng Y. Critical role of guanylate binding protein 5 in tumor immune microenvironment and predictive value of immunotherapy response. Front Genet 2022; 13:984615. [PMID: 36246628 PMCID: PMC9561824 DOI: 10.3389/fgene.2022.984615] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The guanylate-binding proteins (GBPs) are the latest potential targets of immunotherapy. However, the role of GBP5 in pan-cancer, including colorectal cancer (CRC), remains unclear. This study aims to explore the effect of GBP5 on immunity in pan-cancer. Methods: Based on the RNA sequencing data of 33 cancers obtained from The Cancer Genome Atlas, we analyzed the clinical significance of GBPs and focused on the correlation between GBP5 and tumor microenvironment (TME). Immunotherapy cohort IMvigor210 was used to explore the relationship between treatment response and GBPs. Then, we further analyzed the expression of GBP5 in immune cells using single-cell transcriptome cohort GSE146771 and GSE132465 from the Gene Expression Omnibus database. Finally, a prognostic model based on GBP5 expression was established and validated. Results: We found that the expression of GBP3/4/5 is higher in colorectal cancer than in normal tissues, and GBP5 is a better predictor of good treatment response to immune checkpoint blockade than other GBPs. In most other cancers, GBP5 is also elevated in tumors compared with normal tissues and is associated with a better prognosis. As for TME, GBP5 is generally positively correlated with immune score, the level of tumor-infiltrating immune cells and immune-related genes. Single-cell analysis showed that GBP5 was mainly expressed in myeloid cells and T cells. The GBP5-related prognostic model we constructed in CRC can predict the survival of patients and propose some genes for subsequent research. Conclusion: This study revealed a strong correlation between GBP5 and immunity in generalized cancer and provided evidence that CRC may be a suitable cancer type for anti-GBP5 therapy.
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Affiliation(s)
- Xiang Li
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Dan Song
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Song Su
- The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaobo He
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fengyu Cao
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chao Yang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Kai Li
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shuoyang Huang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Changhua Li
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chenhong Wang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Aikang Zhang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Pengcheng Pang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yongbin Zheng
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Yongbin Zheng,
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7
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Fu J, Qin W, Tong Q, Li Z, Shao Y, Liu Z, Liu C, Wang Z, Xu X. A novel DNA methylation-driver gene signature for long-term survival prediction of hepatitis-positive hepatocellular carcinoma patients. Cancer Med 2022; 11:4721-4735. [PMID: 35637633 PMCID: PMC9741990 DOI: 10.1002/cam4.4838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Abnormal DNA methylation is one of the most general epigenetic modifications in hepatocellular carcinoma (HCC). Recent research showed that DNA methylation was a prognostic indicator of all-cause HCC and nonviral HCC. However, whether DNA methylation-driver genes could be used for predicting survival, the probability of hepatitis-positive HCC remains unclear. METHODS In this study, DNA methylation-driver genes (MDGs) were screened by a joint analysis of methylome and transcriptome data of 142 hepatitis-positive HCC patients. Subsequently, a prognostic risk score and nomogram were constructed. Finally, correlation analyses between the risk score and signaling pathways and immunity were conducted by GSVA and CIBERSORT. RESULTS Through random forest screening and Cox progression analysis, 10 prognostic methylation-driver genes (AC008271.1, C11orf53, CASP8, F2RL2, GBP5, LUCAT1, RP11-114B7.6, RP11-149I23.3, RP11-383 J24.1, and SLC35G2) were screened out. As a result, a prognostic risk score signature was constructed. The independent value of the risk score for prognosis prediction were addressed in the TCGA-HCC and the China-HCC cohorts. Next, clinicopathological features were analyzed and HBV status and histological grade were screened to construct a nomogram together with the risk score. The prognostic efficiency of the nomogram was validated by the calibration curves and the concordance index (C index: 0.829, 95% confidence interval: 0.794-0.864), while its clinical application ability was confirmed by decision curve analysis (DCA). At last, the relationship between the risk score and signaling pathways, as well as the correlations between immune cells were elucidated preliminary. CONCLUSIONS Taken together, our study explored a novel DNA methylation-driver gene risk score signature and an efficient nomogram for long-term survival prediction of hepatitis-positive HCC patients.
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Affiliation(s)
- Jie Fu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Wei Qin
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Qing Tong
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhenghao Li
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Yaoli Shao
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiqiang Liu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Chun Liu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zicheng Wang
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xundi Xu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of General SurgerySouth China Hospital of Shenzhen UniversityShenzhenChina
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