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Li J, Han T, Wang X, Wang Y, Yang R, Yang Q. Development of a CD8+ T cell associated signature for predicting the prognosis and immunological characteristics of gastric cancer by integrating single-cell and bulk RNA-sequencing. Sci Rep 2024; 14:4524. [PMID: 38402299 PMCID: PMC10894294 DOI: 10.1038/s41598-024-54273-9] [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: 07/13/2023] [Accepted: 02/10/2024] [Indexed: 02/26/2024] Open
Abstract
The universally poor clinical outcome makes gastric cancer (GC) still a significant public health threat, the main goal of our research is to develop a prognostic signature that can forecast the outcomes and immunological characteristics of GC via integrating single-cell and bulk RNA-sequencing. The CD8+ T cell feature genes were screened out by exploring single-cell RNA-sequencing (scRNA-seq) profiles retrieved from the TISCH2 database. Then, Cox and LASSO regressions were exploited for constructing a prognostic model in TCGA cohort based on these CD8+ T cell feature genes. Survival analysis was conducted to investigate the predictive capability of the signature for the clinical outcome of GC patients in TCGA and GEO cohorts. Additionally, we further examined the correlations between the risk signature and tumor immunotherapeutic response from the perspectives of immune infiltration, tumor mutation burden (TMB), immune checkpoint biomarker (ICB) expression, tumor microenvironment (TME), microsatellite instability (MSI), TIDE, and TCIA scores. In total, 703 CD8+ T cell feature genes were identified, eight of which were selected for constructing a prognostic signature. GC patients who possess high-risk score had significantly poorer survival outcomes than those who possess low-risk score in TCGA and GEO cohorts. Immune infiltration analysis proved that the risk score was negatively connected with the infiltration abundance of CD8+ T cells. Then, our findings demonstrated that GC patients in the high-risk subgroup possess a higher proportion of MSI-L/MSS, lower immune checkpoint biomarker expression, lower TMB, higher TIDE scores and lower TCIA scores compared to those in the low-risk subgroup. What's more, immunotherapy cohort analysis confirmed that patients who possess high-risk score are not sensitive to anti-cancer immunotherapy. Our study developed a reliable prognostic signature for GC that was significantly correlated with the immune landscape and immunotherapeutic responsiveness. The risk signature may guide clinicians to adopt more accurate and personalized treatment strategies for GC patients.
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Affiliation(s)
- Jianxin Li
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, Sichuan, 646000, People's Republic of China
| | - Ting Han
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, Sichuan, 646000, People's Republic of China
| | - Xin Wang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, Sichuan, 646000, People's Republic of China
| | - Yinchun Wang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, Sichuan, 646000, People's Republic of China
| | - Rui Yang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, Sichuan, 646000, People's Republic of China
| | - Qingqiang Yang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, Sichuan, 646000, People's Republic of China.
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Li J, Yu T, Sun J, Zeng Z, Liu Z, Ma M, Zheng Z, He Y, Kang W. Comprehensive analysis of cuproptosis-related immune biomarker signature to enhance prognostic accuracy in gastric cancer. Aging (Albany NY) 2023; 15:2772-2796. [PMID: 37036489 PMCID: PMC10120894 DOI: 10.18632/aging.204646] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/24/2023] [Indexed: 04/11/2023]
Abstract
BACKGROUND Gastric cancer (GC) is a malignant tumor with high prevalence and fatality. Cuproptosis is a recently identified copper-dependent programmed cell death mechanism. Multiple studies have demonstrated the profound impact of the immune microenvironment on tumor development. Hence, we decided to excavate the potential functional roles of cuproptosis-related immune genes (CRIGs) in GC and their values as biomarkers. METHODS Cuproptosis- and immune-related genes were curated from top published studies on cell cuproptosis and cellular immunity. Transcriptome data and clinical information were obtained from TCGA, GTEx, and GEO databases. Cox and LASSO analyses were used to establish a prognostic signature for GC. Long-term prognosis, immune infiltration, immune checkpoint, and drug response were compared between signature groups. CRIG expression in GC scRNA-seq was analyzed. Immunohistochemistry was used to evaluate CRIG and cuproptosis regulator FDX1 in GC tissues. RESULTS Seven CRIGs (ANOS1, CTLA4, ITGAV, CXCR4, NRP1, FABP3, and LGR6) were selected to establish a potent signature to forecast the long-term prognosis of patients. GC patients had worse prognosis and poor responses to chemotherapeutic drugs (5-Fluorouracil and paclitaxel) in the high-risk group. scRNA-seq revealed that CTLA4, ITGAV, CXCR4, and NRP1 enrichment in specific cell types regulated the progression of GC. Moreover, NRP1, CXCR4, LGR6, CTLA4, and FDX1 were elevated in GC tissues, with a positive correlation between their expression and FDX1. CONCLUSIONS To conclude, this study first provides insights into the functions of CRIGs in GC. Furthermore, a robust cuproptosis-related immune biomarker signature was established to forecast the long-term survival of GC patients accurately.
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Affiliation(s)
- Jie Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
| | - Tian Yu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
| | - Juan Sun
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
| | - Ziyang Zeng
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
| | - Zhen Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
| | - Mingwei Ma
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
| | - Zicheng Zheng
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
| | - Yixuan He
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
| | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100730, People’s Republic of China
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KDM6B promotes gastric carcinogenesis and metastasis via upregulation of CXCR4 expression. Cell Death Dis 2022; 13:1068. [PMID: 36564369 PMCID: PMC9789124 DOI: 10.1038/s41419-022-05458-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
KDM6B (Lysine-specific demethylase 6B) is a histone lysine demethyltransferase that plays a key role in many types of cancers. However, its potential role in gastric cancer (GC) remains unclear. Here, we focused on the clinical significance and potential role of KDM6B in GC. We found that the KDM6B expression is upregulated in GC tissues and that its high expression in patients is related to poor prognosis. KDM6B ectopic expression promotes GC cells' proliferation and metastasis, while its inhibition has opposite effects in vitro and in vivo. Mechanistically, KDM6B promotes GC cells proliferation and metastasis through its enzymatic activity through the induction of H3K27me3 demethylation near the CXCR4 (C-X-C chemokine receptor type 4) promoter region, resulting in the upregulation of CXCR4 expression. Furthermore, H. pylori was found to induce KDM6B expression. In conclusion, our results suggest that KDM6B is aberrantly expressed in GC and plays a key role in gastric carcinogenesis and metastasis through CXCR4 upregulation. Our work also suggests that KDM6B may be a potential oncogenic factor and a therapeutic target for GC.
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Alsayed RKME, Khan AQ, Ahmad F, Ansari AW, Alam MA, Buddenkotte J, Steinhoff M, Uddin S, Ahmad A. Epigenetic Regulation of CXCR4 Signaling in Cancer Pathogenesis and Progression. Semin Cancer Biol 2022; 86:697-708. [PMID: 35346802 DOI: 10.1016/j.semcancer.2022.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/08/2023]
Abstract
Signaling involving chemokine receptor CXCR4 and its ligand SDF-1/CXL12 has been investigated for many years for its possible role in cancer progression and pathogenesis. Evidence emerging from clinical studies in recent years has further established diagnostic as well as prognostic importance of CXCR4 signaling. CXCR4 and SDF-1 are routinely reported to be elevated in tumors, distant metastases, which correlates with poor survival of patients. These findings have kindled interest in the mechanisms that regulate CXCR4/SDF-1 expression. Of note, there is a particular interest in the epigenetic regulation of CXCR4 signaling that may be responsible for upregulated CXCR4 in primary as well as metastatic cancers. This review first lists the clinical evidence supporting CXCR4 signaling as putative cancer diagnostic and/or prognostic biomarker, followed by a discussion on reported epigenetic mechanisms that affect CXCR4 expression. These mechanisms include regulation by non-coding RNAs, such as, microRNAs, long non-coding RNAs and circular RNAs. Additionally, we also discuss the regulation of CXCR4 expression through methylation and acetylation. Better understanding and appreciation of epigenetic regulation of CXCR4 signaling can invariably lead to identification of novel therapeutic targets as well as therapies to regulate this oncogenic signaling.
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Affiliation(s)
- Reem Khaled M E Alsayed
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Fareed Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Abdul Wahid Ansari
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Majid Ali Alam
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Jorg Buddenkotte
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Martin Steinhoff
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar; Weill Cornell Medicine-Qatar, Medical School, Doha, 24144, Qatar; Dept. of Dermatology, Weill Cornell Medicine, New York, 10065, NY, USA
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Laboratory Animal Research Center, Qatar University, Doha, 2713, Qatar
| | - Aamir Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar.
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