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Qi P, Qi B, Gu C, Huo S, Dang X, Liu Y, Zhao B. Construction of an immune-related prognostic model and potential drugs screening for esophageal cancer based on bioinformatics analyses and network pharmacology. Immun Inflamm Dis 2024; 12:e1266. [PMID: 38804848 PMCID: PMC11131936 DOI: 10.1002/iid3.1266] [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: 04/04/2023] [Revised: 02/29/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Esophageal cancer (ESCA) is a highly invasive malignant tumor with poor prognosis. This study aimed to discover a generalized and high-sensitivity immune prognostic signature that could stratify ESCA patients and predict their overall survival, and to discover potential therapeutic drugs by the connectivity map. METHODS The key gene modules significantly related to clinical traits (survival time and state) of ESCA patients were selected by weighted gene coexpression network analysis (WCGNA), then the univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses were used to construct a 15-immune-related gene prognostic signature. RESULTS The immune-related risk model was related to clinical and pathologic factors and remained an effective independent prognostic factor. Enrichment analyses revealed that the differentially expressed genes (DEGs) of the high- and low-risk groups were associated with tumor cell proliferation and immune mechanisms. Based on the gathered data, a small molecule drug named perphenazine (PPZ) was elected. The pharmacological analysis indicates that PPZ could help in adjuvant therapy of ESCA through regulation of metabolic process and cellular proliferation, enhancement of immunologic functions, and inhibition of inflammatory reactions. Furthermore, molecular docking was performed to explore and verify the PPZ-core target interactions. CONCLUSION We succeed in structuring the immune-related prognostic model, which could be used to distinguish and predict patients' survival outcome, and screening a small molecule drug named PPZ. Prospective studies also are needed to further validate its analytical accuracy for estimating prognoses and confirm the potential use of PPZ for treating ESCA.
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Affiliation(s)
- Pengju Qi
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
- Esophageal Cancer Institute of Xinxiang Medical UniversityWeihuiHenanChina
- Life Science Research CenterThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
| | - Bo Qi
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
- Esophageal Cancer Institute of Xinxiang Medical UniversityWeihuiHenanChina
| | - Chengwei Gu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
- Esophageal Cancer Institute of Xinxiang Medical UniversityWeihuiHenanChina
| | - Shuhua Huo
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
- Esophageal Cancer Institute of Xinxiang Medical UniversityWeihuiHenanChina
| | - Xinchen Dang
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
- Esophageal Cancer Institute of Xinxiang Medical UniversityWeihuiHenanChina
| | - Yuzhen Liu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
- Esophageal Cancer Institute of Xinxiang Medical UniversityWeihuiHenanChina
- Life Science Research CenterThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
| | - Baosheng Zhao
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xinxiang Medical UniversityWeihuiHenanChina
- Esophageal Cancer Institute of Xinxiang Medical UniversityWeihuiHenanChina
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Zhou J, Zhou R, Zhu Y, Deng S, Muhuitijiang B, Li C, Shi X, Zhang L, Tan W. Investigating the impact of regulatory B cells and regulatory B cell-related genes on bladder cancer progression and immunotherapeutic sensitivity. J Exp Clin Cancer Res 2024; 43:101. [PMID: 38566204 PMCID: PMC10985985 DOI: 10.1186/s13046-024-03017-8] [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: 11/27/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Regulatory B cells (Bregs), a specialized subset of B cells that modulate immune responses and maintain immune tolerance in malignant tumors, have not been extensively investigated in the context of bladder cancer (BLCA). This study aims to elucidate the roles of Bregs and Breg-related genes in BLCA. METHODS We assessed Breg infiltration levels in 34 pairs of BLCA and corresponding paracancerous tissues using immunohistochemical staining. We conducted transwell and wound healing assays to evaluate the impact of Bregs on the malignant phenotype of SW780 and T24 cells. Breg-related genes were identified through gene sets and transcriptional analysis. The TCGA-BLCA cohort served as the training set, while the IMvigor210 and 5 GEO cohorts were used as external validation sets. We employed LASSO regression and random forest for feature selection and developed a risk signature using Cox regression. Primary validation of the risk signature was performed through immunohistochemical staining and RT-qPCR experiments using the 34 local BLCA samples. Additionally, we employed transfection assays and flow cytometry to investigate Breg expansion ability and immunosuppressive functions. RESULTS Breg levels in BLCA tissues were significantly elevated compared to paracancerous tissues (P < 0.05) and positively correlated with tumor malignancy (P < 0.05). Co-incubation of SW780 and T24 cells with Bregs resulted in enhanced invasion and migration abilities (all P < 0.05). We identified 27 Breg-related genes, including CD96, OAS1, and CSH1, which were integrated into the risk signature. This signature demonstrated robust prognostic classification across the 6 cohorts (pooled HR = 2.25, 95% CI = 1.52-3.33). Moreover, the signature exhibited positive associations with advanced tumor stage (P < 0.001) and Breg infiltration ratios (P < 0.05) in the local samples. Furthermore, the signature successfully predicted immunotherapeutic sensitivity in three cohorts (all P < 0.05). Knockdown of CSH1 in B cells increased Breg phenotype and enhanced suppressive ability against CD8 + T cells (all P < 0.05). CONCLUSIONS Bregs play a pro-tumor role in the development of BLCA. The Breg-related gene signature established in this study holds great potential as a valuable tool for evaluating prognosis and predicting immunotherapeutic response in BLCA patients.
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Affiliation(s)
- Jiawei Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Ranran Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Yuanchao Zhu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Shikai Deng
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, No. 1023-1063 Shatai South Road, Baiyun District, Guangzhou, Guangdong, 510080, China
| | - Bahaerguli Muhuitijiang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Chengyao Li
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, No. 1023-1063 Shatai South Road, Baiyun District, Guangzhou, Guangdong, 510080, China
| | - Xiaojun Shi
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China
| | - Ling Zhang
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, No. 1023-1063 Shatai South Road, Baiyun District, Guangzhou, Guangdong, 510080, China.
| | - Wanlong Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510080, China.
- The First Clinical Medical College, Southern Medical University, Guangzhou, Guangdong, 510080, China.
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Tang R, Wang H, Liu J, Song L, Hou H, Liu M, Wang J, Wang J. TFRC, associated with hypoxia and immune, is a prognostic factor and potential therapeutic target for bladder cancer. Eur J Med Res 2024; 29:112. [PMID: 38336764 PMCID: PMC10854140 DOI: 10.1186/s40001-024-01688-9] [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: 12/28/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Bladder cancer is a common malignancy of the urinary system, and the survival rate and recurrence rate of patients with muscular aggressive (MIBC) bladder cancer are not ideal. Hypoxia is a pathological process in which cells acquire special characteristics to adapt to anoxic environment, which can directly affect the proliferation, invasion and immune response of bladder cancer cells. Understanding the exact effects of hypoxia and immune-related genes in BLCA is helpful for early assessment of the prognosis of BLCA. However, the prognostic model of BLCA based on hypoxia and immune-related genes has not been reported. PURPOSE Hypoxia and immune cell have important role in the prognosis of bladder cancer (BLCA). The aim of this study was to investigate whether hypoxia and immune related genes could be a novel tools to predict the overall survival and immunotherapy of BLCA patients. METHODS First, we downloaded transcriptomic data and clinical information of BLCA patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A combined hypoxia and immune signature was then constructed on the basis of the training cohort via least absolute shrinkage and selection operator (LASSO) analysis and validated in test cohort. Afterwards, Kaplan-Meier curves, univariate and multivariate Cox and subgroup analysis were employed to assess the accuracy of our signature. Immune cell infiltration, checkpoint and the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm were used to investigate the immune environment and immunotherapy of BLCA patients. Furthermore, we confirmed the role of TFRC in bladder cancer cell lines T24 and UMUC-3 through cell experiments. RESULTS A combined hypoxia and immune signature containing 8 genes were successfully established. High-risk group in both training and test cohorts had significantly poorer OS than low-risk group. Univariate and multivariate Cox analysis indicated our signature could be regarded as an independent prognostic factor. Different checkpoint was differently expressed between two groups, including CTLA4, HAVCR2, LAG3, PD-L1 and PDCD1. TIDE analysis indicated high-risk patients had poor response to immunotherapy and easier to have immune escape. The drug sensitivity analysis showed that high-risk group patients were more potentially sensitive to many drugs. Meanwhile, TFRC could inhibit the proliferation and invasion ability of T24 and UMUC-3 cells. CONCLUSION A combined hypoxia and immune-related gene could be a novel predictive model for OS and immunotherapy estimation of BLCA patients and TFRC could be used as a potential therapeutic target in the future.
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Affiliation(s)
- Runhua Tang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing, 100730, China
| | - Haoran Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing, 100730, China
| | - Jianyong Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing, 100730, China
| | - Liuqi Song
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing, 100730, China
| | - Huimin Hou
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing, 100730, China
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing, 100730, China
- Fifth School of Clinical Medicine, Peking University, Beijing, China
| | - Jianye Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing, 100730, China
| | - Jianlong Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing, 100730, China.
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Zhang S, Cai Z, Li H. AHNAKs roles in physiology and malignant tumors. Front Oncol 2023; 13:1258951. [PMID: 38033502 PMCID: PMC10682155 DOI: 10.3389/fonc.2023.1258951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The AHNAK family currently consists of two members, namely AHNAK and AHNAK2, both of which have a molecular weight exceeding 600 kDa. Homologous sequences account for approximately 90% of their composition, indicating a certain degree of similarity in terms of molecular structure and biological functions. AHNAK family members are involved in the regulation of various biological functions, such as calcium channel modulation and membrane repair. Furthermore, with advancements in biological and bioinformatics technologies, research on the relationship between the AHNAK family and tumors has rapidly increased in recent years, and its regulatory role in tumor progression has gradually been discovered. This article briefly describes the physiological functions of the AHNAK family, and reviews and analyzes the expression and molecular regulatory mechanisms of the AHNAK family in malignant tumors using Pubmed and TCGA databases. In summary, AHNAK participates in various physiological and pathological processes in the human body. In multiple types of cancers, abnormal expression of AHNAK and AHNAK2 is associated with prognosis, and they play a key regulatory role in tumor progression by activating signaling pathways such as ERK, MAPK, Wnt, and MEK, as well as promoting epithelial-mesenchymal transition.
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Affiliation(s)
- Shusen Zhang
- Hebei Province Xingtai People’s Hospital Postdoctoral Workstation, Xingtai, China
- Postdoctoral Mobile Station, Hebei Medical University, Shijiazhuang, China
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, China
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhigang Cai
- Postdoctoral Mobile Station, Hebei Medical University, Shijiazhuang, China
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hui Li
- Department of surgery, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, China
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Huang P, Qian Y, Xia Y, Wang S, Xu C, Zhu X, Gao Q. Integrated analysis identifies RAC3 as an immune-related prognostic biomarker associated with chemotherapy sensitivity in endometrial cancer. J Cell Mol Med 2023; 27:2385-2397. [PMID: 37386813 PMCID: PMC10424291 DOI: 10.1111/jcmm.17824] [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: 10/17/2022] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Endometrial cancer (EC) is one of the most common gynaecological malignant tumours with a high incidence, leading to urgent demands for exploring novel carcinogenic mechanisms and developing rational therapeutic strategies. The rac family of small GTPase 3 (RAC3) functions as an oncogene in various human malignant tumours and plays an important role in tumour development. However, the critical roles of RAC3 in the progression of EC need further investigation. Based on TCGA, single-cell RNA-Seq, CCLE and clinical specimens, we revealed that the RAC3 was specifically distributed in EC tumour cells compared to normal tissues and functioned as an independent diagnostic marker with a high area under curve (AUC) score. Meanwhile, the RAC3 expression in EC tissues was also correlated with a poor prognosis. In detail, the high levels of RAC3 in EC tissues were reversely associated with CD8+ T cell infiltration and orchestrated an immunosuppressive microenvironment. Furthermore, RAC3 accelerated tumour cell proliferation and inhibited its apoptosis, without impacting cell cycle stages. Importantly, silencing RAC3 improved the sensitivity of EC cells to chemotherapeutic drugs. In this paper, we revealed that RAC3 was predominantly expressed in EC and significantly correlated with the progression of EC via inducing immunosuppression and regulating tumour cell viability, providing a novel diagnostic biomarker and a promising strategy for sensitizing chemotherapy to EC.
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Affiliation(s)
- Pu Huang
- Department of Obstetrics and Gynecologythe Second Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yiyu Qian
- Department of Obstetrics and Gynecologythe Second Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yu Xia
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Siyuan Wang
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Cheng Xu
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecologythe Second Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Qinglei Gao
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Chen L, Huang X, Xiong L, Chen W, An L, Wang H, Hong Y, Wang H. Analysis of prognostic oncogene filaggrin ( FLG) wild-type subtype and its implications for immune checkpoint blockade therapy in bladder urothelial carcinoma. Transl Androl Urol 2022; 11:1419-1432. [PMID: 36386263 PMCID: PMC9641059 DOI: 10.21037/tau-22-573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/14/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Bladder urothelial carcinoma (BLCA) is one of the most common urinary tract malignant tumors. Immune checkpoint blockade (ICB) therapy has significantly progressed the treatment of BLCA. This study aimed to investigate the role of specific genetic mutations that may serve as immune biomarkers for ICB therapy in BLCA. METHODS Mutation information and expression profiles were acquired from The Cancer Genome Atlas (TCGA) database. Integrated bioinformatics analysis was carried out to explore the subtypes with poor prognosis of BLCA. Functional enrichment analysis was also conducted. The infiltrating immune cells and the prediction of ICB response between different subtypes were explored using the immuCellAI algorithm. Cell Counting Kit-8 (CCK-8) and flow cytometry assays were conducted to explore the effect of filaggrin (FLG) knockdown in BLCA 5637 and T24 cell lines. RESULTS An overview of mutation information in BLCA patients was shown. FLG was identified to be strongly associated with the prognosis of BLCA patients and FLG wild-type was associated with poorer outcome. Prognostic FLG wild-type was divided into 2 subtypes (Sub1 and Sub2). Following an investigation of the subtypes, Sub2 of FLG wild-type was found to be associated with poorer outcome in BLCA. The differentially expressed genes (DEGs) between Sub1 and Sub2 were screened out and the DEGs were enriched in malignant tumor proliferation, DNA damage repair, and immune-related pathways. Furthermore, Sub2 of FLG wild-type was associated with infiltrated immune cells, and responded worse to ICB. Sub2 of FLG wild-type may be used as a biomarker to predict the prognosis of BLCA patients receiving ICB. The cellular experiments revealed that knockdown of FLG could suppress BLCA cell proliferation and promote apoptosis. CONCLUSIONS FLG is an oncogene that may affect the prognosis of BLCA patients through mutation. Sub2 of FLG wild-type is associated with poor prognosis and can be used to predict ICB response for BLCA treatment. This research provides a new basis and ideas for guiding the clinical application of BLCA immunotherapy.
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Affiliation(s)
- Liang Chen
- Urology and Lithotripsy Center, Peking University People’s Hospital, Beijing, China
| | - Xiaobo Huang
- Urology and Lithotripsy Center, Peking University People’s Hospital, Beijing, China
| | - Liulin Xiong
- Urology and Lithotripsy Center, Peking University People’s Hospital, Beijing, China
| | - Weinan Chen
- Urology and Lithotripsy Center, Peking University People’s Hospital, Beijing, China
| | - Lizhe An
- Urology and Lithotripsy Center, Peking University People’s Hospital, Beijing, China
| | - Huanrui Wang
- Urology and Lithotripsy Center, Peking University People’s Hospital, Beijing, China
| | - Yang Hong
- Urology and Lithotripsy Center, Peking University People’s Hospital, Beijing, China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, China
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Gao Z, Chen C, Gu P, Chen J, Liu X, Shen J. The tumor microenvironment and prognostic role of autophagy- and immune-related genes in bladder cancer. Cancer Biomark 2022; 35:293-303. [DOI: 10.3233/cbm-220058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: Autophagy-related genes and immune-related genes contribute significantly to the initiation and prognosis of bladder cancer (BLCA). OBJECTIVE: We aimed to explore differentially expressed autophagy-related genes (DEARGs) and immune-related genes (DEIRGs) in BLCA to create a prognostic risk assessment model and gain some insights into BLCA’s molecular underpinnings. METHODS: The prognostic DEARGs and DEIRGs were evaluated for BLCA through The Cancer Genome Atlas (TCGA) database (n= 399) and GSE13507 dataset (n= 165). The BLCA risk model was constructed and verified. The immune score, stromal score, and estimate score in different risk groups were calculated by the ESTIMATE algorithm. Immune infiltration levels were assessed by a single sample gene set enrichment analysis (GSEA) algorithm. RESULTS: In the risk model, AURKA, ACTC1, MYLK, PDGFD, PDGFRA and TNC were significantly associated with the overall survival. The pathways in cancer, T cell receptor signaling pathway and B cell receptor signaling pathway were significantly gathered in the high-risk group. Moreover, the risk score was significantly correlated with infiltrating immune cells, expression of critical immune checkpoints and mismatch repair genes including MSH6, MLH1, and MSH2. CONCLUSIONS: In this study, three DEARGs (AURKA, ACTC1, MYLK) and three DEIRGs (PDGFD, PDGFRA, TNC) were demonstrated to be potential prognostic biomarkers for BLCA patients through bioinformatics methods, which might be novel therapeutic targets and prognostic markers for BLCA, in follow up studies, we will combine experiments to verify this.
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Affiliation(s)
- Zhenhua Gao
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Chronic Kidney Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Cheng Chen
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Chronic Kidney Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Peng Gu
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Chronic Kidney Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Jianheng Chen
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xiaodong Liu
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Jihong Shen
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Chronic Kidney Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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Lu L, Wang H, Fang J, Zheng J, Liu B, Xia L, Li D. Overexpression of OAS1 Is Correlated With Poor Prognosis in Pancreatic Cancer. Front Oncol 2022; 12:944194. [PMID: 35898870 PMCID: PMC9309611 DOI: 10.3389/fonc.2022.944194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Background OAS1 expression in pancreatic cancer has been confirmed by many studies. However, the prognostic value and mechanism of OAS1 in pancreatic cancer have not been analyzed. Methods The RNA-seq in pancreatic cancer were obtained by UCSC XENA and GEO database. In addition, immunohistochemical validation and analysis were performed using samples from the 900th hospital. The prognosis of OAS1 was evaluated by timeROC package, Cox regression analysis, and Kaplan-Meier survival curves. Then, the main functional and biological signaling pathways enrichment and its relationship with the abundance of immune cells were analyzed by bioinformatics. Results OAS1 was highly expressed in pancreatic cancer compared with normal pancreatic tissue. High OAS1 expression was associated with poor overall survival (p<0.05). The OAS1 was significantly correlated to TNM staging (p=0.014). The timeROC analysis showed that the AUC of OAS1 was 0.734 for 3-year OS. In addition, the expression of OAS1 was significantly correlated with the abundance of a variety of immune markers. GSEA showed that enhanced signaling pathways associated with OAS1 include Apoptosis, Notch signaling pathway, and P53 signaling pathway. Conclusions OAS1 is a valuable prognostic factor in pancreatic cancer. Moreover, it may be a potential immunotherapeutic target.
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Affiliation(s)
- Lingling Lu
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Huaxiang Wang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, China
| | - Jian Fang
- Department of Hepatobiliary Medicine, The Third Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jiaolong Zheng
- Department of Hepatobiliary Disease, The 900th Hospital of the People’s Liberation Army Joint Logistics Support Force, Fuzhou, China
| | - Bang Liu
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Lei Xia
- Department of Hepatobiliary Medicine, The Third Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Dongliang Li
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of Hepatobiliary Disease, The 900th Hospital of the People’s Liberation Army Joint Logistics Support Force, Fuzhou, China
- *Correspondence: Dongliang Li,
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Hou J, Lu Z, Dong R, Wu G, Nie H, Yang G, Tang C, Qu G, Xu Y. A Necroptosis-Related lncRNA to Develop a Signature to Predict the Outcome, Immune Landscape, and Chemotherapeutic Responses in Bladder Urothelial Carcinoma. Front Oncol 2022; 12:928204. [PMID: 35814472 PMCID: PMC9270023 DOI: 10.3389/fonc.2022.928204] [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: 04/25/2022] [Accepted: 05/18/2022] [Indexed: 12/24/2022] Open
Abstract
Objective Many studies have drawn their attention to the immunotherapy of bladder urothelial carcinoma in terms of immunologic mechanisms of human body. These include immunogenicity of the tumor cells and involvement of long non-coding RNA (lncRNA). We constructed a necroptosis-related long noncoding RNA (nrlncRNA) risk factor model to predict BLCA outcomes and calculate correlations with chemosensitivity and immune infiltration. Methods Transcriptomic data from BLCA specimens were accessed from The Cancer Genome Atlas, and nrlncRNAs were identified by performing co-expression analysis. Univariate analysis was performed to identify differentially expressed nrlncRNA pairs. We constructed least absolute contraction and selector operation regression models and drew receiver operating characteristic curves for 1-, 3-, and 5-year survival rates. Akaike information criterion (AIC) values for survival over 1 year were determined as cutoff values in high- and low-risk subgroups. We reassessed the differences between subgroups in terms of survival, clinicopathological characteristics, chemotherapy efficacy, tumor-infiltrating immune cells, and markers of immunosuppression. Results We identified a total of 260 necroptosis-related lncRNA pairs, of which we incorporated 13 into the prognostic model. Areas under the curve of 1-, 3-, and 5- year survival time were 0.763, 0.836, and 0.842, respectively. We confirmed the excellent predictive performance of the risk model. Based on AIC values, we confirmed that the high-risk group was susceptible to unfavorable outcomes. The risk scores correlated with survival were age, clinical stage, grade, and tumor node metastases. The risk model was an independent predictor and demonstrated higher predictive power. The risk model can also be utilized to determine immune cell infiltration status, expression levels of immune checkpoint genes, and the sensitivity to cisplatin, doxorubicin, and methotrexate. Conclusion We constructed a novel necroptosis-related signature that predicts BLCA outcomes and performs satisfactorily in the immune landscape and chemotherapeutic responses.
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Affiliation(s)
- Jian Hou
- Department of Urology, Zhuzhou Central Hospital, Zhuzhou, China
- Division of Urology, Department of Surgery, The University of Hongkong-ShenZhen Hospital, ShenZhen, China
| | - Zhenquan Lu
- Division of Urology, Department of Surgery, The University of Hongkong-ShenZhen Hospital, ShenZhen, China
| | - Runan Dong
- Division of Urology, Department of Surgery, The University of Hongkong-ShenZhen Hospital, ShenZhen, China
| | - Guoqing Wu
- Division of Urology, Department of Surgery, The University of Hongkong-ShenZhen Hospital, ShenZhen, China
| | - Haibo Nie
- Department of Urology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Guang Yang
- Department of Urology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Cheng Tang
- Department of Urology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Genyi Qu
- Department of Urology, Zhuzhou Central Hospital, Zhuzhou, China
- *Correspondence: Genyi Qu, ; Yong Xu,
| | - Yong Xu
- Department of Urology, Zhuzhou Central Hospital, Zhuzhou, China
- *Correspondence: Genyi Qu, ; Yong Xu,
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10
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Stroggilos R, Frantzi M, Zoidakis J, Mokou M, Moulavasilis N, Mavrogeorgis E, Melidi A, Makridakis M, Stravodimos K, Roubelakis MG, Mischak H, Vlahou A. Gene Expression Monotonicity across Bladder Cancer Stages Informs on the Molecular Pathogenesis and Identifies a Prognostic Eight-Gene Signature. Cancers (Basel) 2022; 14:cancers14102542. [PMID: 35626146 PMCID: PMC9140126 DOI: 10.3390/cancers14102542] [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: 03/29/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 01/27/2023] Open
Abstract
Despite advancements in molecular classification, tumor stage and grade still remain the most relevant prognosticators used by clinicians to decide on patient management. Here, we leverage publicly available data to characterize bladder cancer (BLCA)’s stage biology based on increased sample sizes, identify potential therapeutic targets, and extract putative biomarkers. A total of 1135 primary BLCA transcriptomes from 12 microarray studies were compiled in a meta-cohort and analyzed for monotonal alterations in pathway activities, gene expression, and co-expression patterns with increasing stage (Ta–T1–T2–T3–T4), starting from the non-malignant tumor-adjacent urothelium. The TCGA-2017 and IMvigor-210 RNA-Seq data were used to validate our findings. Wnt, MTORC1 signaling, and MYC activity were monotonically increased with increasing stage, while an opposite trend was detected for the catabolism of fatty acids, circadian clock genes, and the metabolism of heme. Co-expression network analysis highlighted stage- and cell-type-specific genes of potentially synergistic therapeutic value. An eight-gene signature, consisting of the genes AKAP7, ANLN, CBX7, CDC14B, ENO1, GTPBP4, MED19, and ZFP2, had independent prognostic value in both the discovery and validation sets. This novel eight-gene signature may increase the granularity of current risk-to-progression estimators.
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Affiliation(s)
- Rafael Stroggilos
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Maria Frantzi
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany; (M.F.); (M.M.); (H.M.)
| | - Jerome Zoidakis
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Marika Mokou
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany; (M.F.); (M.M.); (H.M.)
| | - Napoleon Moulavasilis
- 1st Department of Urology, Laiko Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.M.); (K.S.)
| | - Emmanouil Mavrogeorgis
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Anna Melidi
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Manousos Makridakis
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Konstantinos Stravodimos
- 1st Department of Urology, Laiko Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.M.); (K.S.)
| | - Maria G. Roubelakis
- Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
- Cell and Gene Therapy Laboratory, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany; (M.F.); (M.M.); (H.M.)
| | - Antonia Vlahou
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
- Correspondence: ; Tel.: +30-210-659-7506; Fax: +30-210-659-7545
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11
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Yao Y, Kong X, Liu R, Xu F, Liu G, Sun C. Development of a Novel Immune-Related Gene Prognostic Index for Breast Cancer. Front Immunol 2022; 13:845093. [PMID: 35558081 PMCID: PMC9086776 DOI: 10.3389/fimmu.2022.845093] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/28/2022] [Indexed: 01/05/2023] Open
Abstract
Objective To construct an immune-related gene prognostic index (IRGPI) for breast cancer (BC) and investigate its prognostic specificity and the molecular and immune characteristics. Methods BC hub genes were identified from The Cancer Genome Atlas and immune-related databases using weighted gene co-expression network analysis (WGCNA). IRGPI was constructed using univariate, LASSO, and multivariate regression analyses, and was validated with GSE58812 and GSE97342 in the Gene Expression Omnibus database (GEO). At the same time, we evaluated the predictive ability of IRGPI for different BC subtypes. Subsequently, the molecular and immune characteristics, clinical relevance, and benefits of immune checkpoint inhibitor treatment were analyzed for different IRGPI subgroups. Results IRGPI consisted of six genes: SOCS3, TCF7L2, TSLP NPR3, ANO6, and HMGB3. The IRGPI 1-, 5-, and 10-years area under curve (AUC) values were 0.635, 0.752, and 0.753, respectively, indicating that IRGPI has good potential in predicting the long-term survival of BC patients, consistent with the results in the GEO cohort. IRGPI showed good predictive power in four different breast cancer subtypes: ER positive, PR positive, HER2 positive and triple-negative (P<0.01). Compared with the low-IRGPI group, the high-IRGPI group had a worse prognosis and a lower degree of immune infiltrating cells (p < 0.05). IRGPI showed specificity in distinguishing age, TNM stage, ER, and HER2 statuses, and our study found that the high-IRGPI group had low tumor immune dysfunction and exclusion (TIDE), microsatellite instability (MSI), and T cell dysfunction scores (p < 0.05). In addition, compared with the TIDE and TIS models, showed that the AUCs of IRGPI were better during the 5-year follow-up. Conclusion IRGPI can be used as an independent prognostic indicator of breast cancer, providing a method for monitoring the long-term treatment of BC.
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Affiliation(s)
- Yan Yao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xinru Kong
- Innovative Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Fei Xu
- Department of Geriatric Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Gongxi Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Changgang Sun
- Innovative Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China.,Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,College of Traditional Chinese Medicine, Weifang Medical University, Weifang, China
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12
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Wang C, Chen S, Li S, Mi H. A Prognostic Model for Predicting Tumor Mutation Burden and Tumor-Infiltrating Immune Cells in Bladder Urothelial Carcinoma. Front Genet 2022; 13:708003. [PMID: 35251120 PMCID: PMC8896886 DOI: 10.3389/fgene.2022.708003] [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: 05/11/2021] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
Tremendous progress has been made in development of immunotherapeutic approaches for treatment of bladder urothelial carcinoma (BLCA). However, efficacy and safety of these approaches remain unsatisfactory, necessitating further investigations for identification of indicators for predicting prognosis and efficacy. In this study, we downloaded transcriptomic and clinical data of BLCA patients from The Cancer Genome Atlas (TCGA) database, and identified differentially expressed genes (DEGs) between tumor and normal tissues. We incorporated these DEGs in an intersection analysis with immune-related genes (IRGs) obtained from the Immunology Database and Analysis Portal (ImmPort) database, and identified immune-related DEGs. These genes were subjected to Cox and least absolute shrinkage and selection operator (LASSO) regression analyses, then a prognostic model containing AHNAK, OAS1, NGF, PPY and SCG2 genes was constructed, for prediction of prognosis of BLCA and efficacy of immunotherapy. Finally, we explored the relationship between the prognostic model and tumor mutational burden (TMB), abundance of tumor-infiltrating immune cells (TICs) and immunotherapeutic targets, and found that patients with higher risk score (RS) had poorer prognosis and significantly lower levels of TMB. Patients in the low-RS group exhibited higher numbers of lymphoid cells, whereas those in the high-RS group exhibited higher proportions of myeloid cells. However, patients with high-RS tended to respond better to immunotherapy relative to those in the low-RS group. The constructed prognostic model provides a new tool for predicting prognosis of BLCA patients and efficacy of immunotherapy, offering a feasible option for management of the disease.
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Affiliation(s)
- Chengbang Wang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning, China
- Guangxi Key Laboratory of Colleges and Universities, Nanning, China
| | - Shaohua Chen
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Nanning, China
- Guangxi Key Laboratory of Colleges and Universities, Nanning, China
| | - Songheng Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hua Mi
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- *Correspondence: Hua Mi,
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13
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Chen J, Lv B, Zhan Y, Zhu K, Zhang R, Chen B, Jin Y, Li Y, Zheng J, Lin C. Comprehensive Exploration of Tumor Microenvironment Modulation Based on the ESTIMATE Algorithm in Bladder Urothelial Carcinoma Microenvironment. Front Oncol 2022; 12:724261. [PMID: 35237505 PMCID: PMC8882770 DOI: 10.3389/fonc.2022.724261] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/24/2022] [Indexed: 01/11/2023] Open
Abstract
Recently, the tumor microenvironment (TME) has been reported to be closely related to the tumor initiation, progression, and prognosis. Bladder urothelial carcinoma (BLCA), one of the most common subtypes of bladder cancer worldwide, has been associated with increased morbidity and mortality in the past decade. However, whether the TME status of BLCA contributes to the prediction of BLCA prognosis still remains uncertain. In this study, the ESTIMATE algorithms were used to estimate the division of immune and stromal components in 406 BLCA samples downloaded from The Cancer Genome Atlas database (TCGA). Based on the comparison between ESTIMATE scores, the differentially expressed genes (DEGs) were selected. Using the univariate Cox regression analysis, prognosis-related DEGs were further identified (p < 0.05). The LASSO regression analysis was then used to screen 11 genes that were highly related to the TME of BLCA to generate a novel prognostic gene signature. The following survival analyses showed that this signature could effectively predict the prognosis of BLCA. The clinical value of this signature was further verified in an external cohort obtained from the First Affiliated Hospital of Wenzhou Medical University (n = 120). Based on the stage-correlation analysis and differential expression analysis, IGF1 and MMP9 were identified as the hub genes in the signature. Additionally, using CIBERSORT algorithms, we found that both IGF1 and MMP9 were significantly associated with immune infiltration. Collectively, a novel TME-related prognostic signature contributes to accurately predict the prognosis of BLCA.
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Affiliation(s)
- Ji Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Boyu Lv
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yating Zhan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kai Zhu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongrong Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bo Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yan Jin
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yeping Li
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Changyong Lin, ; Yeping Li,
| | - Jianjian Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Changyong Lin
- Department of General Surgery, Wenzhou Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Wenzhou, China
- *Correspondence: Changyong Lin, ; Yeping Li,
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14
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Kang Z, Li W, Yu YH, Che M, Yang ML, Len JJ, Wu YR, Yang JF. Identification of Immune-Related Genes Associated With Bladder Cancer Based on Immunological Characteristics and Their Correlation With the Prognosis. Front Genet 2021; 12:763590. [PMID: 34899848 PMCID: PMC8664377 DOI: 10.3389/fgene.2021.763590] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/08/2021] [Indexed: 01/21/2023] Open
Abstract
Background:To identify the immune-related genes of bladder cancer (BLCA) based on immunological characteristics and explore their correlation with the prognosis. Methods:We downloaded the gene and clinical data of BLCA from the Cancer Genome Atlas (TCGA) as the training group, and obtained immune-related genes from the Immport database. We downloaded GSE31684 and GSE39281 from the Gene Expression Omnibus (GEO) as the external validation group. R (version 4.0.5) and Perl were used to analyze all data. Result:Univariate Cox regression analysis and Lasso regression analysis revealed that 9 prognosis-related immunity genes (PIMGs) of differentially expressed immune genes (DEIGs) were significantly associated with the survival of BLCA patients (p < 0.01), of which 5 genes, including NPR2, PDGFRA, VIM, RBP1, RBP1 and TNC, increased the risk of the prognosis, while the rest, including CD3D, GNLY, LCK, and ZAP70, decreased the risk of the prognosis. Then, we used these genes to establish a prognostic model. We drew receiver operator characteristic (ROC) curves in the training group, and estimated the area under the curve (AUC) of 1-, 3- and 5-year survival for this model, which were 0.688, 0.719, and 0.706, respectively. The accuracy of the prognostic model was verified by the calibration chart. Combining clinical factors, we established a nomogram. The ROC curve in the external validation group showed that the nomogram had a good predictive ability for the survival rate, with a high accuracy, and the AUC values of 1-, 3-, and 5-year survival were 0.744, 0.770, and 0.782, respectively. The calibration chart indicated that the nomogram performed similarly with the ideal model. Conclusion:We had identified nine genes, including PDGFRA, VIM, RBP1, RBP1, TNC, CD3D, GNLY, LCK, and ZAP70, which played important roles in the occurrence and development of BLCA. The prognostic model based on these genes had good accuracy in predicting the OS of patients and might be promising candidates of therapeutic targets. This study may provide a new insight for the diagnosis, treatment and prognosis of BLCA from the perspective of immunology. However, further experimental studies are necessary to reveal the underlying mechanisms by which these genes mediate the progression of BLCA.
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Affiliation(s)
- Zhen Kang
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China.,Department of Urology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Wei Li
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China.,Department of Urology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Yan-Hong Yu
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China.,Department of Urology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Meng Che
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China
| | - Mao-Lin Yang
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China.,Department of Urology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Jin-Jun Len
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China.,Department of Urology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Yue-Rong Wu
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China
| | - Jun-Feng Yang
- The Affiliated Hospital, Kunming University of Science and Technology, Kunming, China.,Department of Urology, The First People's Hospital of Yunnan Province, Kunming, China
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15
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Cai H, Chen H, Huang Q, Zhu JM, Ke ZB, Lin YZ, Zheng QS, Wei Y, Xu N, Xue XY. Ubiquitination-Related Molecular Subtypes and a Novel Prognostic Index for Bladder Cancer Patients. Pathol Oncol Res 2021; 27:1609941. [PMID: 34776794 PMCID: PMC8585742 DOI: 10.3389/pore.2021.1609941] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/11/2021] [Indexed: 11/14/2022]
Abstract
Objective: To develop and validate ubiquitination-related molecular subtypes and a novel prognostic index using ubiquitination-related genes (URGs) for patients with bladder cancer (BCa). Materials and Methods: We downloaded the clinical data and transcriptome data of BCa from TCGA and GEO database. Consensus clustering analysis was conducted to identify ubiquitination-related molecular subtypes for BCa. Besides, we performed univariate and multivariate Cox regression analysis to develop a novel prognostic URGs-related index for BCa. We conducted internal and external verification in TCGA cohort and GEO cohort, respectively. Furthermore, the associations of ubiquitination-related molecular subtypes and prognostic index with tumor immune environment were also investigated. Results: A total of four ubiquitination-related molecular subtypes of BCa were finally identified. These four molecular subtypes had significantly different clinical characteristics, prognosis, PD-L1 expression level and tumor microenvironment. Besides, we developed a novel prognostic index using six URGs (including HLA-A, TMEM129, UBE2D1, UBE2N, UBE2T and USP5). The difference in OS between high and low-risk group was statistically significant in training cohort, testing cohort, and validating cohort. The area under ROC curve (AUC) for OS prediction was 0.736, 0.723, and 0.683 in training cohort, testing cohort, and validating cohort, respectively. Multivariate survival analysis showed that this index was an independent predictor for OS. This prognostic index was especially suitable for subtype 1 and 3, older, male, high grade, AJCC stage III-IV, stage N0, stage T3-4 BCa patients. Conclusions: This study identified a total of four ubiquitination-related molecular subtypes with significantly different tumor microenvironment, prognosis, clinical characteristics and PD-L1 expression level. Besides, a novel ubiquitination-related prognostic index for BCa patients was developed and successfully verified, which performed well in predicting prognosis of BCa.
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Affiliation(s)
- Hai Cai
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Hang Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qi Huang
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jun-Ming Zhu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhi-Bin Ke
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yun-Zhi Lin
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qing-Shui Zheng
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yong Wei
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ning Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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16
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Peng L, Du C, Meng C, Li J, You C, Li X, Zhao P, Cao D, Li Y. Controlling Nutritional Status Score Before Receiving Treatment as a Prognostic Indicator for Patients With Urothelial Cancer: An Exploration Evaluation Methods. Front Oncol 2021; 11:702908. [PMID: 34722249 PMCID: PMC8548688 DOI: 10.3389/fonc.2021.702908] [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: 04/30/2021] [Accepted: 09/13/2021] [Indexed: 02/05/2023] Open
Abstract
Introduction This meta-analysis aims to assess whether the Controlling nutritional status (CONUT) score before treatment can be an independent predictor of the prognosis of patients with urothelial cancer (UC). Methods The system searches Web of Science, PubMed, MEDLINE, China National Knowledge Infrastructure (CNKI), and Cochrane Library, and the search time is up to April 2021. Use STATA 16.0 and Engauge Digitizer 4.1 software for data processing and statistical analysis. Results A total of 8 studies were included in this meta-analysis. The meta-analysis results show that compared with the low CONUT group, the high CONUT group has worse over survival (OS) [HR=1.58, 95%CI (1.34, 1.86), P=0.001], cancer-specific survival (CSS) [HR=2.03, 95%CI (1.25-3.29), P=0.04] and recurrence-free survival (RFS) [HR=1.97, 95%CI (1.15, 3.40), P=0.014]; for progression-free survival (PFS), or disease-free survival (DFS), the difference between the two groups was not statistically significant [HR=2.30, 95%CI (0.72, 7.32), P=0.158]. According to different carcinoma types, cut-off value, and region, subgroup analysis of OS was performed, and similar results were obtained. Conclusions Based on current evidence, this meta-analysis proves that the CONUT score of UC patients before treatment is an independent prognostic predictor. It performs well on OS, CSS, and RFS, but the conclusions on DFS/PFS need to be treated with caution. Systematic Review Registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021251890, identifier CRD42021251890.
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Affiliation(s)
- Lei Peng
- Department of Urology, Nanchong Central Hospital, The Second Clinical College, North Sichuan Medical College (University), Nanchong, China
| | - Chunxiao Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chunyang Meng
- Department of Urology, Nanchong Central Hospital, The Second Clinical College, North Sichuan Medical College (University), Nanchong, China
| | - Jinze Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Chengyu You
- Department of Urology, Nanchong Central Hospital, The Second Clinical College, North Sichuan Medical College (University), Nanchong, China
| | - Xianhui Li
- Department of Urology, Nanchong Central Hospital, The Second Clinical College, North Sichuan Medical College (University), Nanchong, China
| | - Pan Zhao
- Department of Urology, Nanchong Central Hospital, The Second Clinical College, North Sichuan Medical College (University), Nanchong, China
| | - Dehong Cao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yunxiang Li
- Department of Urology, Nanchong Central Hospital, The Second Clinical College, North Sichuan Medical College (University), Nanchong, China
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