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Qiao L, Xu Z, Chen Y, Chen W, Liang Y, Wei Y, Wang K, Yu Y, Yan W. Integrated analysis of single-cell and bulk RNA sequencing data reveals a cellular senescence-related signature in hepatocellular carcinoma. Front Cell Dev Biol 2024; 12:1407428. [PMID: 38887516 PMCID: PMC11180799 DOI: 10.3389/fcell.2024.1407428] [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: 03/26/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
The mortality of hepatocellular carcinoma (HCC) is on the rise globally, particularly in the Western world, with etiology gradually shifting from virus-related liver diseases to metabolic disorders such as non-alcoholic fatty liver disease. Early detection of HCC is challenging, and effective prognostic indicators are currently lacking, urgently necessitating reliable markers to assist in treatment planning and clinical management. Here, we introduce hepatocellular carcinoma senescence genes (HSG) to assess cellular senescence in HCC and devise a hepatocellular carcinoma senescence score (HSS) for prognostic prediction. Higher HSS levels signify poorer prognosis and increased tumor proliferation activity. Additionally, we observe alterations in the tumor immune microenvironment with higher HSS levels, such as increased infiltration of Treg, potentially providing a basis for immunotherapy. Furthermore, we identify key genes, such as PTTG1, within the senescence gene set and demonstrate their regulatory roles in HCC cells and Treg through experimentation. In summary, we establish a scoring system based on hepatocellular carcinoma senescence genes for prognostic prediction in HCC, potentially offering guidance for clinical treatment planning.
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Affiliation(s)
- Lei Qiao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Medical Key Laboratory, Nanjing, Jiangsu Province, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Zibo Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Medical Key Laboratory, Nanjing, Jiangsu Province, China
| | - Yuheng Chen
- School of Public Health, Southeast University, Nanjing, Jiangsu Province, China
| | - Wenwei Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Medical Key Laboratory, Nanjing, Jiangsu Province, China
| | - Yuan Liang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Medical Key Laboratory, Nanjing, Jiangsu Province, China
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu Province, China
| | - Yi Wei
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Medical Key Laboratory, Nanjing, Jiangsu Province, China
| | - Kang Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Medical Key Laboratory, Nanjing, Jiangsu Province, China
| | - Yue Yu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Jiangsu Provincial Medical Innovation Center, Jiangsu Provincial Medical Key Laboratory, Nanjing, Jiangsu Province, China
| | - Wei Yan
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
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Qin S, Xie B, Wang Q, Yang R, Sun J, Hu C, Liu S, Tao Y, Xiao D. New insights into immune cells in cancer immunotherapy: from epigenetic modification, metabolic modulation to cell communication. MedComm (Beijing) 2024; 5:e551. [PMID: 38783893 PMCID: PMC11112485 DOI: 10.1002/mco2.551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Cancer is one of the leading causes of death worldwide, and more effective ways of attacking cancer are being sought. Cancer immunotherapy is a new and effective therapeutic method after surgery, radiotherapy, chemotherapy, and targeted therapy. Cancer immunotherapy aims to kill tumor cells by stimulating or rebuilding the body's immune system, with specific efficiency and high safety. However, only few tumor patients respond to immunotherapy and due to the complex and variable characters of cancer immune escape, the behavior and regulatory mechanisms of immune cells need to be deeply explored from more dimensions. Epigenetic modifications, metabolic modulation, and cell-to-cell communication are key factors in immune cell adaptation and response to the complex tumor microenvironment. They collectively determine the state and function of immune cells through modulating gene expression, changing in energy and nutrient demands. In addition, immune cells engage in complex communication networks with other immune components, which are mediated by exosomes, cytokines, and chemokines, and are pivotal in shaping the tumor progression and therapeutic response. Understanding the interactions and combined effects of such multidimensions mechanisms in immune cell modulation is important for revealing the mechanisms of immunotherapy failure and developing new therapeutic targets and strategies.
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Affiliation(s)
- Sha Qin
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Bin Xie
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Qingyi Wang
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Rui Yang
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Jingyue Sun
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
| | - Chaotao Hu
- Regenerative Medicine, Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Shuang Liu
- Department of OncologyInstitute of Medical SciencesNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangsha, Hunan, China. UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of CarcinogenesisCancer Research Institute and School of Basic MedicineCentral South universityChangshaHunanChina
| | - Desheng Xiao
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic Medical ScienceXiangya School of MedicineCentral South UniversityChangshaHunanChina
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Wang Y, He J, Zhao Q, Bo J, Zhou Y, Sun H, Ding B, Ren M. Evaluating the predictive value of angiogenesis-related genes for prognosis and immunotherapy response in prostate adenocarcinoma using machine learning and experimental approaches. Front Immunol 2024; 15:1416914. [PMID: 38817605 PMCID: PMC11137278 DOI: 10.3389/fimmu.2024.1416914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024] Open
Abstract
Background Angiogenesis, the process of forming new blood vessels from pre-existing ones, plays a crucial role in the development and advancement of cancer. Although blocking angiogenesis has shown success in treating different types of solid tumors, its relevance in prostate adenocarcinoma (PRAD) has not been thoroughly investigated. Method This study utilized the WGCNA method to identify angiogenesis-related genes and assessed their diagnostic and prognostic value in patients with PRAD through cluster analysis. A diagnostic model was constructed using multiple machine learning techniques, while a prognostic model was developed employing the LASSO algorithm, underscoring the relevance of angiogenesis-related genes in PRAD. Further analysis identified MAP7D3 as the most significant prognostic gene among angiogenesis-related genes using multivariate Cox regression analysis and various machine learning algorithms. The study also investigated the correlation between MAP7D3 and immune infiltration as well as drug sensitivity in PRAD. Molecular docking analysis was conducted to assess the binding affinity of MAP7D3 to angiogenic drugs. Immunohistochemistry analysis of 60 PRAD tissue samples confirmed the expression and prognostic value of MAP7D3. Result Overall, the study identified 10 key angiogenesis-related genes through WGCNA and demonstrated their potential prognostic and immune-related implications in PRAD patients. MAP7D3 is found to be closely associated with the prognosis of PRAD and its response to immunotherapy. Through molecular docking studies, it was revealed that MAP7D3 exhibits a high binding affinity to angiogenic drugs. Furthermore, experimental data confirmed the upregulation of MAP7D3 in PRAD, correlating with a poorer prognosis. Conclusion Our study confirmed the important role of angiogenesis-related genes in PRAD and identified a new angiogenesis-related target MAP7D3.
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Affiliation(s)
| | | | | | | | | | | | - BeiChen Ding
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - MingHua Ren
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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He S, Zhao Z. Genetically engineered cell-derived nanovesicles for cancer immunotherapy. NANOSCALE 2024; 16:8317-8334. [PMID: 38592744 PMCID: PMC11075450 DOI: 10.1039/d3nr06565k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The emergence of immunotherapy has marked a new epoch in cancer treatment, presenting substantial clinical benefits. Extracellular vesicles (EVs), as natural nanocarriers, can deliver biologically active agents in cancer therapy with their inherent biocompatibility and negligible immunogenicity. However, natural EVs have limitations such as inadequate targeting capability, low loading efficacy, and unpredictable side effects. Through progress in genetic engineering, EVs have been modified for enhanced delivery of immunomodulatory agents and antigen presentation with specific cancer targeting ability, deepening the role of EVs in cancer immunotherapy. This review briefly describes typical EV sources, isolation methods, and adjustable targeting of EVs. Furthermore, this review highlights the genetic engineering strategies developed for delivering immunomodulatory agents and antigen presentation in EV-based systems. The prospects and challenges of genetically engineered EVs as cancer immunotherapy in clinical translation are also discussed.
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Affiliation(s)
- Shan He
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, USA.
| | - Zongmin Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, USA.
- Translational Oncology Program, University of Illinois Cancer Center, Chicago, IL 60612, USA
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Liu R, Liu J, Cao Q, Chu Y, Chi H, Zhang J, Fu J, Zhang T, Fan L, Liang C, Luo X, Yang X, Li B. Identification of crucial genes through WGCNA in the progression of gastric cancer. J Cancer 2024; 15:3284-3296. [PMID: 38817876 PMCID: PMC11134444 DOI: 10.7150/jca.95757] [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: 02/27/2024] [Accepted: 04/11/2024] [Indexed: 06/01/2024] Open
Abstract
Background: To explore the hub gene closely related to the progression of gastric cancer (GC), so as to provide a theoretical basis for revealing the therapeutic mechanism of GC. Methods: The gene expression profile and clinical data of GSE15459 in Gene Expression Omnibus (GEO) database were downloaded. The weighted gene co-expression network analysis (WGCNA) was used to screen the key modules related to GC progression. Survival analysis was used to assess the influence of hub genes on patients' outcomes. CIBERSORT analysis was used to predict the tissue infiltrating immune cells in patients. Immunohistochemical staining was conducted to further verify the expression of hub genes. Results: Through WGCNA, a total of 26 co-expression modules were constructed, in which salmon module and royalblue module had strong correlation with GC progression. The results of enrichment analysis showed that genes in the two modules were mainly involved in toll-like receptor signaling pathway, cholesterol metabolism and neuroactive ligand-receptor interaction. Six hub genes (C1QA, C1QB, C1QC, FCER1G, FPR3 and TYROBP) related to GC progression were screened. Survival analysis showed overall survival in the high expression group was significantly lower than that in the low expression group. CIBERSORT analysis revealed that immune characteristics difference between patients in early stage and advanced stage. Immunohistochemical results confirmed that C1QB, FCER1G, FPR3 and TYROBP were significantly associated with disease progression in GC. Conclusion: Our study identified that C1QB, FCER1G, FPR3 and TYROBP played important roles in the progression of GC, and their specific mechanisms are worth further study.
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Affiliation(s)
- Rui Liu
- Vascular surgery Department, The Affiliated Hospital of Southwest Medical University, Lu Zhou, China
- Department of gastrointestinal surgery, Meishan People 's Hospital, Meishan, China
| | - Jie Liu
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Sichuan, China
- Academician (Expert) Workstation of Sichuan Province, Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, The Affiliated Hospital of Southwest Medical University, Sichuan, China
- Department of general surgery, Dazhou Central Hospital, Dazhou, China
| | - Qiang Cao
- School of Medicine, Macau University of Science and Technology, 999078, Macau, China
| | - Yanpeng Chu
- Department of general surgery, Dazhou Central Hospital, Dazhou, China
- Medical College, Sichuan University of Arts and Science, Dazhou, China
| | - Hao Chi
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Sichuan, China
- Academician (Expert) Workstation of Sichuan Province, Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, The Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Jun Zhang
- Department of general surgery, Dazhou Central Hospital, Dazhou, China
| | - Jiangping Fu
- Oncology department, Dazhou Central Hospital, Dazhou, China
| | - Tianchi Zhang
- Department of general surgery, Dazhou Central Hospital, Dazhou, China
| | - Linguang Fan
- Department of general surgery, Dazhou Central Hospital, Dazhou, China
| | - Chaozhong Liang
- Department of general surgery, Dazhou Central Hospital, Dazhou, China
| | - Xiufang Luo
- Geriatric department, Dazhou Central Hospital, Dazhou, China
| | - Xiaoli Yang
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Sichuan, China
- Academician (Expert) Workstation of Sichuan Province, Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, The Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Bo Li
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Sichuan, China
- Academician (Expert) Workstation of Sichuan Province, Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, The Affiliated Hospital of Southwest Medical University, Sichuan, China
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Zhao S, Zhang P, Niu S, Xie J, Liu Y, Liu Y, Zhao N, Cheng C, Lu P. Targeting nucleotide metabolic pathways in colorectal cancer by integrating scRNA-seq, spatial transcriptome, and bulk RNA-seq data. Funct Integr Genomics 2024; 24:72. [PMID: 38594466 PMCID: PMC11004054 DOI: 10.1007/s10142-024-01356-5] [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: 02/21/2024] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Colorectal cancer is a malignant tumor of the digestive system originating from abnormal cell proliferation in the colon or rectum, often leading to gastrointestinal symptoms and severe health issues. Nucleotide metabolism, which encompasses the synthesis of DNA and RNA, is a pivotal cellular biochemical process that significantly impacts both the progression and therapeutic strategies of colorectal cancer METHODS: For single-cell RNA sequencing (scRNA-seq), five functions were employed to calculate scores related to nucleotide metabolism. Cell developmental trajectory analysis and intercellular interaction analysis were utilized to explore the metabolic characteristics and communication patterns of different epithelial cells. These findings were further validated using spatial transcriptome RNA sequencing (stRNA-seq). A risk model was constructed using expression profile data from TCGA and GEO cohorts to optimize clinical decision-making. Key nucleotide metabolism-related genes (NMRGs) were functionally validated by further in vitro experiments. RESULTS In both scRNA-seq and stRNA-seq, colorectal cancer (CRC) exhibited unique cellular heterogeneity, with myeloid cells and epithelial cells in tumor samples displaying higher nucleotide metabolism scores. Analysis of intercellular communication revealed enhanced signaling pathways and ligand-receptor interactions between epithelial cells with high nucleotide metabolism and fibroblasts. Spatial transcriptome sequencing confirmed elevated nucleotide metabolism states in the core region of tumor tissue. After identifying differentially expressed NMRGs in epithelial cells, a risk prognostic model based on four genes effectively predicted overall survival and immunotherapy outcomes in patients. High-risk group patients exhibited an immunosuppressive microenvironment and relatively poorer prognosis and responses to chemotherapy and immunotherapy. Finally, based on data analysis and a series of cellular functional experiments, ACOX1 and CPT2 were identified as novel therapeutic targets for CRC. CONCLUSION In this study, a comprehensive analysis of NMRGs in CRC was conducted using a combination of single-cell sequencing, spatial transcriptome sequencing, and high-throughput data. The prognostic model constructed with NMRGs shows potential as a standalone prognostic marker for colorectal cancer patients and may significantly influence the development of personalized treatment approaches for CRC.
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Affiliation(s)
- Songyun Zhao
- Wuxi Medical Center of Nanjing Medical University, Wuxi, China
- Department of Neurosurgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Pengpeng Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Sen Niu
- Wuxi Medical Center of Nanjing Medical University, Wuxi, China
- Department of General Surgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Jiaheng Xie
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yuankun Liu
- Wuxi Medical Center of Nanjing Medical University, Wuxi, China
- Department of Neurosurgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Yuan Liu
- Wuxi Medical Center of Nanjing Medical University, Wuxi, China
- Department of General Surgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Ning Zhao
- Wuxi Medical Center of Nanjing Medical University, Wuxi, China
| | - Chao Cheng
- Wuxi Medical Center of Nanjing Medical University, Wuxi, China.
- Department of Neurosurgery, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China.
| | - Peihua Lu
- Wuxi Medical Center of Nanjing Medical University, Wuxi, China.
- Department of Clinical Research Center, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China.
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Rong D, Su Y, Jia D, Zeng Z, Yang Y, Wei D, Lu H, Cao Y. Experimentally validated oxidative stress -associated prognostic signatures describe the immune landscape and predict the drug response and prognosis of SKCM. Front Immunol 2024; 15:1387316. [PMID: 38660305 PMCID: PMC11039952 DOI: 10.3389/fimmu.2024.1387316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Background Skin Cutaneous Melanoma (SKCM) incidence is continually increasing, with chemotherapy and immunotherapy being among the most common cancer treatment modalities. This study aims to identify novel biomarkers for chemotherapy and immunotherapy response in SKCM and explore their association with oxidative stress. Methods Utilizing TCGA-SKCM RNA-seq data, we employed Weighted Gene Co-expression Network Analysis (WGCNA) and Protein-Protein Interaction (PPI) networks to identify six core genes. Gene co-expression analysis and immune-related analysis were conducted, and specific markers associated with oxidative stress were identified using Gene Set Variation Analysis (GSVA). Single-cell analysis revealed the expression patterns of Oxidative Stress-Associated Genes (OSAG) in the tumor microenvironment. TIDE analysis was employed to explore the association between immune therapy response and OSAG, while CIBERSORT was used to analyze the tumor immune microenvironment. The BEST database demonstrated the impact of the Oxidative Stress signaling pathway on chemotherapy drug resistance. Immunohistochemical staining and ROC curve evaluation were performed to assess the protein expression levels of core genes in SKCM and normal samples, with survival analysis utilized to determine their diagnostic value. Results We identified six central genes associated with SKCM metastasis, among which the expression of DSC2 and DSC3 involved in the oxidative stress pathway was closely related to immune cell infiltration. DSC2 influenced drug resistance in SKMC patients. Furthermore, downregulation of DSC2 and DSC3 expression enhanced the response of SKCM patients to immunotherapy. Conclusion This study identified two Oxidative Stress-Associated genes as novel biomarkers for SKCM. Additionally, targeting the oxidative stress pathway may serve as a new strategy in clinical practice to enhance SKCM chemotherapy and sensitivity.
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Affiliation(s)
- Dongyun Rong
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yushen Su
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Dechao Jia
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhirui Zeng
- Department of anorectal surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
- School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan Yang
- Department of Internal Medicine, The Third Affiliated Hospital of Guizhou Medical University, Duyun, Guizhou, China
| | - Dalong Wei
- Department of Burns, Plastic Surgery and Wound Repair, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Key Laboratory of Tumor Molecular Pathology of Baise, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Honguan Lu
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yu Cao
- Clinical Medical School, Guizhou Medical University, Guiyang, Guizhou, China
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Jiang H, Li B, Wu M, Wang Q, Li Y. Association of the Advanced Lung Cancer Inflammation Index (ALI) and Gustave Roussy Immune (GRIm) score with immune checkpoint inhibitor efficacy in patients with gastrointestinal and lung cancer. BMC Cancer 2024; 24:428. [PMID: 38589844 PMCID: PMC11000368 DOI: 10.1186/s12885-024-12149-1] [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: 11/29/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
OBJECTIVE This study aimed to conduct a comprehensive analysis, evaluating the prognostic significance of the baseline Advanced Lung Cancer Inflammation Index (ALI) and Gustave Roussy Immune (GRIm) Score in patients undergoing immune checkpoint inhibitor (ICI) therapy. METHODS A comprehensive search was performed across various databases, including PubMed, the Cochrane Library, EMBASE, and Google Scholar, until October 21, 2023, to compile relevant articles for analysis. The investigation encompassed diverse clinical outcomes, including overall survival (OS) and progression-free survival (PFS). RESULTS This analysis included a total of 15 articles, comprising 19 studies involving 3335 patients. Among the 19 studies, nine studies focused on NSCLC, and six studies were conducted on HCC. Pooled results revealed that patients with elevated ALI levels experienced prolonged OS (HR: 0.51, 95% CI: 0.37-0.70, p < 0.001) and extended PFS (HR: 0.61, 95% CI: 0.52-0.72, p < 0.001). Furthermore, a GRIm score > 1 was associated with reduced OS (HR: 2.07, 95% CI: 1.47-2.92, p < 0.001) and diminished PFS (HR: 1.78, 95% CI: 1.35-2.34, p < 0.001) in cancer patients receiving ICIs. Subgroup analysis indicated that ALI cutoff values of 18 exhibited enhanced predictive potential. Additionally, for HCC patients, those with HCC-GRIm score > 2 showed a substantially decreased risk of mortality compared to individuals with HCC-GRIm score ≤ 2 (HR: 2.63, 95% CI: 1.89-3.65, p < 0.001). CONCLUSION The ALI and GRIm score served as dependable prognostic indicators for patients undergoing ICI therapy in the context of cancer treatment.
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Affiliation(s)
- Hao Jiang
- Department of General Surgery, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
| | - Borui Li
- Department of Urologic Surgery, Cancer Hospital of China Medical University (Liaoning Cancer Hospital & Institute), Shenyang, China
| | - Min Wu
- Department of Oncology, The Third People's Hospital of Honghe Prefecture, Gejiu, China
| | - Qimei Wang
- Hunan Academy of Traditional Chinese Medicine, Changsha, China.
| | - Yijin Li
- Department of Colorectal and Anorectal Surgery, Hunan Hospital of Integrated Tradmonal Chinese and Western Medicine (Hunan Academy of Traditional Chinese Medicine Affiliated Hospital), Changsha, China.
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Gan Q, Li Y, Li Y, Liu H, Chen D, Liu L, Peng C. Pathways and molecules for overcoming immunotolerance in metastatic gastrointestinal tumors. Front Immunol 2024; 15:1359914. [PMID: 38646539 PMCID: PMC11026648 DOI: 10.3389/fimmu.2024.1359914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Worldwide, gastrointestinal (GI) cancer is recognized as one of the leading malignancies diagnosed in both genders, with mortality largely attributed to metastatic dissemination. It has been identified that in GI cancer, a variety of signaling pathways and key molecules are modified, leading to the emergence of an immunotolerance phenotype. Such modifications are pivotal in the malignancy's evasion of immune detection. Thus, a thorough analysis of the pathways and molecules contributing to GI cancer's immunotolerance is vital for advancing our comprehension and propelling the creation of efficacious pharmacological treatments. In response to this necessity, our review illuminates a selection of groundbreaking cellular signaling pathways associated with immunotolerance in GI cancer, including the Phosphoinositide 3-kinases/Akt, Janus kinase/Signal Transducer and Activator of Transcription 3, Nuclear Factor kappa-light-chain-enhancer of activated B cells, Transforming Growth Factor-beta/Smad, Notch, Programmed Death-1/Programmed Death-Ligand 1, and Wingless and INT-1/beta-catenin-Interleukin 10. Additionally, we examine an array of pertinent molecules like Indoleamine-pyrrole 2,3-dioxygenase, Human Leukocyte Antigen G/E, Glycoprotein A Repetitions Predominant, Clever-1, Interferon regulatory factor 8/Osteopontin, T-cell immunoglobulin and mucin-domain containing-3, Carcinoembryonic antigen-related cell adhesion molecule 1, Cell division control protein 42 homolog, and caspases-1 and -12.
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Affiliation(s)
- Qixin Gan
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Yue Li
- Department of Cardiovascular Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yuejun Li
- Department of Oncology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Haifen Liu
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Daochuan Chen
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Lanxiang Liu
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
| | - Churan Peng
- 1Department of Radiology, First Affiliated Hospital of Hunan College of TCM (Hunan Province Directly Affiliated TCM Hospital), Zhuzhou, Hunan, China
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10
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Huang Q, Zhong X, Li J, Hu R, Yi J, Sun J, Xu Y, Zhou X. Exosomal ncRNAs: Multifunctional contributors to the immunosuppressive tumor microenvironment of hepatocellular carcinoma. Biomed Pharmacother 2024; 173:116409. [PMID: 38460375 DOI: 10.1016/j.biopha.2024.116409] [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: 12/05/2023] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant liver cancer characterized by aggressive progression, unfavorable prognosis, and an increasing global health burden. Therapies that precisely target immunological checkpoints and immune cells have gained significant attention as possible therapeutics in recent years. In truth, the efficacy of immunotherapy is heavily contingent upon the tumor microenvironment (TME). Recent studies have indicated that exosomes serve as a sophisticated means of communication among biomolecules, executing an essential part in the TME of immune suppression. Exosomal non-coding RNAs (ncRNAs) can induce the activation of tumor cells and immunosuppressive immune cells that suppress the immune system, such as cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), tumor-associated neutrophils (TANs), CD+8 T cells, regulatory T cells (Tregs), and regulatory B cells (Bregs). This cell-cell crosstalk triggered by exosomal ncRNAs promotes tumor proliferation and metastasis, angiogenesis, malignant phenotype transformation, and drug resistance. Hence, it is imperative to comprehend how exosomal ncRNAs regulate tumor cells or immune cells within the TME to devise more comprehensive and productive immunotherapy programs. This study discusses the features of exosomal ncRNAs in HCC and how the activation of the exosomes redefines the tumor's immunosuppressive microenvironment, hence facilitating the advancement of HCC. Furthermore, we also explored the potential of exosomal ncRNAs as a viable biological target or natural vehicle for HCC therapy.
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Affiliation(s)
- Qi Huang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Xin Zhong
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Jing Li
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Rui Hu
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Jinyu Yi
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Jialing Sun
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Youhua Xu
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China.
| | - Xiaozhou Zhou
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China.
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11
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ZHANG YANG, QIN NANNAN, WANG XIJUN, LIANG RUI, LIU QUAN, GENG RUOYI, JIANG TIANXIAO, LIU YUNFEI, LI JINWEI. Glycogen metabolism-mediated intercellular communication in the tumor microenvironment influences liver cancer prognosis. Oncol Res 2024; 32:563-576. [PMID: 38361757 PMCID: PMC10865732 DOI: 10.32604/or.2023.029697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/11/2023] [Indexed: 02/17/2024] Open
Abstract
Glycogen metabolism plays a key role in the development of hepatocellular carcinoma (HCC), but the function of glycogen metabolism genes in the tumor microenvironment (TME) is still to be elucidated. Single-cell RNA-seq data were obtained from ten HCC tumor samples totaling 64,545 cells, and 65 glycogen metabolism genes were analyzed by a nonnegative matrix factorization (NMF). The prognosis and immune response of new glycogen TME cell clusters were predicted by using HCC and immunotherapy cohorts from public databases. HCC single-cell analysis was divided into fibroblasts, NT T cells, macrophages, endothelial cells, and B cells, which were separately divided into new cell clusters by glycogen metabolism gene annotation. Pseudo-temporal trajectory analysis demonstrated the temporal differentiation trajectory of different glycogen subtype cell clusters. Cellular communication analysis revealed extensive interactions between endothelial cells with glycogen metabolizing TME cell-related subtypes and different glycogen subtype cell clusters. SCENIC analysis of transcription factors upstream of TME cell clusters with different glycogen metabolism. In addition, TME cell clusters of glycogen metabolism were found to be enriched in expression in CAF subtypes, CD8 depleted, M1, and M2 types. Bulk-seq analysis showed the prognostic significance of glycogen metabolism-mediated TME cell clusters in HCC, while a significant immune response was found in the immunotherapy cohort in patients treated with immune checkpoint blockade (ICB), especially for CAFs, T cells, and macrophages. In summary, our study reveals for the first time that glycogen metabolism mediates intercellular communication in the hepatocellular carcinoma microenvironment while elucidating the anti-tumor mechanisms and immune prognostic responses of different subtypes of cell clusters.
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Affiliation(s)
- YANG ZHANG
- Graduate School, Kunming Medical University, Kunming, 650000, China
- Department of Vascular Surgery, Fuwai Yunnan Cardiovascular Hospital, Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, 650000, China
| | - NANNAN QIN
- Department of Gynecology Oncology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545000, China
| | - XIJUN WANG
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, China
| | - RUI LIANG
- College of Bioengineering, Chongqing University, Chongqing, 400030, China
| | - QUAN LIU
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545000, China
| | - RUOYI GENG
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, 81377, Germany
| | - TIANXIAO JIANG
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, 81377, Germany
| | - YUNFEI LIU
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, 81377, Germany
| | - JINWEI LI
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610000, China
- Department of Neurosurgery, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545000, China
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12
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Dang C, Bian Q, Wang F, Wang H, Liang Z. Machine learning identifies SLC6A14 as a novel biomarker promoting the proliferation and metastasis of pancreatic cancer via Wnt/β-catenin signaling. Sci Rep 2024; 14:2116. [PMID: 38267509 PMCID: PMC10808089 DOI: 10.1038/s41598-024-52646-8] [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: 07/12/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
Pancreatic cancer (PC) has the poorest prognosis compared to other common cancers because of its aggressive nature, late detection, and resistance to systemic treatment. In this study, we aimed to identify novel biomarkers for PC patients and further explored their function in PC progression. We analyzed GSE62452 and GSE28735 datasets, identifying 35 differentially expressed genes (DEGs) between PC specimens and non-tumors. Based on 35 DEGs, we performed machine learning and identified eight diagnostic genes involved in PC progression. Then, we further screened three critical genes (CTSE, LAMC2 and SLC6A14) using three GEO datasets. A new diagnostic model was developed based on them and showed a strong predictive ability in screen PC specimens from non-tumor specimens in GEO, TCGA datasets and our cohorts. Then, clinical assays based on TCGA datasets indicated that the expression of LAMC2 and SLC6A14 was associated with advanced clinical stage and poor prognosis. The expressions of LAMC2 and SLC6A14, as well as the abundances of a variety of immune cells, exhibited a significant positive association with one another. Functionally, we confirmed that SLC6A14 was highly expressed in PC and its knockdown suppressed the proliferation, migration, invasion and EMT signal via regulating Wnt/β-catenin signaling pathway. Overall, our findings developed a novel diagnostic model for PC patients. SLC6A14 may promote PC progression via modulating Wnt/β-catenin signaling. This work offered a novel and encouraging new perspective that holds potential for further illuminating the clinicopathological relevance of PC as well as its molecular etiology.
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Affiliation(s)
- Cunshu Dang
- Department of Hepatobiliary Gastrointestinal Surgery, Tianjin Fourth Central Hospital, No.1 Zhongshan Road, Tianjin, China.
| | - Quan Bian
- Department of Plastic and Reconstructive Surgery, Tianjin Nankai Hospital, Tianjin, China
| | - Fengbiao Wang
- Department of Hepatobiliary Gastrointestinal Surgery, Tianjin Fourth Central Hospital, No.1 Zhongshan Road, Tianjin, China
| | - Han Wang
- Department of Otorhinolaryngology-Head and Neck Surgery, Tianjin Fourth Central Hospital, Tianjin, China
| | - Zhipeng Liang
- Department of Hepatobiliary Gastrointestinal Surgery, Tianjin Fourth Central Hospital, No.1 Zhongshan Road, Tianjin, China
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Aloi N, Drago G, Ruggieri S, Cibella F, Colombo P, Longo V. Extracellular Vesicles and Immunity: At the Crossroads of Cell Communication. Int J Mol Sci 2024; 25:1205. [PMID: 38256278 PMCID: PMC10816988 DOI: 10.3390/ijms25021205] [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] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Extracellular vesicles (EVs), comprising exosomes and microvesicles, are small membranous structures secreted by nearly all cell types. They have emerged as crucial mediators in intercellular communication, playing pivotal roles in diverse physiological and pathological processes, notably within the realm of immunity. These roles go beyond mere cellular interactions, as extracellular vesicles stand as versatile and dynamic components of immune regulation, impacting both innate and adaptive immunity. Their multifaceted involvement includes immune cell activation, antigen presentation, and immunomodulation, emphasising their significance in maintaining immune homeostasis and contributing to the pathogenesis of immune-related disorders. Extracellular vesicles participate in immunomodulation by delivering a wide array of bioactive molecules, including proteins, lipids, and nucleic acids, thereby influencing gene expression in target cells. This manuscript presents a comprehensive review that encompasses in vitro and in vivo studies aimed at elucidating the mechanisms through which EVs modulate human immunity. Understanding the intricate interplay between extracellular vesicles and immunity is imperative for unveiling novel therapeutic targets and diagnostic tools applicable to various immunological disorders, including autoimmune diseases, infectious diseases, and cancer. Furthermore, recognising the potential of EVs as versatile drug delivery vehicles holds significant promise for the future of immunotherapies.
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Affiliation(s)
| | | | | | | | - Paolo Colombo
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy; (N.A.); (G.D.); (S.R.); (F.C.); (V.L.)
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14
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Liu Q, Yan X, Li R, Yuan Y, Wang J, Zhao Y, Fu J, Su J. Polyamine Signal through HCC Microenvironment: A Key Regulator of Mitochondrial Preservation and Turnover in TAMs. Int J Mol Sci 2024; 25:996. [PMID: 38256070 PMCID: PMC10816144 DOI: 10.3390/ijms25020996] [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: 12/06/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver cancer, and, with increasing research on the tumor immune microenvironment (TIME), the immunosuppressive micro-environment of HCC hampers further application of immunotherapy, even though immunotherapy can provide survival benefits to patients with advanced liver cancer. Current studies suggest that polyamine metabolism is not only a key metabolic pathway for the formation of immunosuppressive phenotypes in tumor-associated macrophages (TAMs), but it is also profoundly involved in mitochondrial quality control signaling and the energy metabolism regulation process, so it is particularly important to further investigate the role of polyamine metabolism in the tumor microenvironment (TME). In this review, by summarizing the current research progress of key enzymes and substrates of the polyamine metabolic pathway in regulating TAMs and T cells, we propose that polyamine biosynthesis can intervene in the process of mitochondrial energy metabolism by affecting mitochondrial autophagy, which, in turn, regulates macrophage polarization and T cell differentiation. Polyamine metabolism may be a key target for the interactive dialog between HCC cells and immune cells such as TAMs, so interfering with polyamine metabolism may become an important entry point to break intercellular communication, providing new research space for developing polyamine metabolism-based therapy for HCC.
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Affiliation(s)
| | | | | | | | | | | | | | - Jing Su
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basical Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130012, China; (Q.L.); (X.Y.); (R.L.); (Y.Y.); (J.W.); (Y.Z.); (J.F.)
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15
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He S, Su L, Hu H, Liu H, Xiong J, Gong X, Chi H, Wu Q, Yang G. Immunoregulatory functions and therapeutic potential of natural killer cell-derived extracellular vesicles in chronic diseases. Front Immunol 2024; 14:1328094. [PMID: 38239346 PMCID: PMC10795180 DOI: 10.3389/fimmu.2023.1328094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Extracellular vesicles (EVs) have been proven to play a significant immunoregulatory role in many chronic diseases, such as cancer and immune disorders. Among them, EVs derived from NK cells are an essential component of the immune cell functions. These EVs have been demonstrated to carry a variety of toxic proteins and nucleic acids derived from NK cells and play a therapeutic role in diseases like malignancies, liver fibrosis, and lung injury. However, natural NK-derived EVs (NKEVs) have certain limitations in disease treatment, such as low yield and poor targeting. Concurrently, NK cells exhibit characteristics of memory-like NK cells, which have stronger proliferative capacity, increased IFN-γ production, and enhanced cytotoxicity, making them more advantageous for disease treatment. Recent research has shifted its focus towards engineered extracellular vesicles and their potential to improve the efficiency, specificity, and safety of disease treatments. In this review, we will discuss the characteristics of NK-derived EVs and the latest advancements in disease therapy. Specifically, we will compare different cellular sources of NKEVs and explore the current status and prospects of memory-like NK cell-derived EVs and engineered NKEVs.
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Affiliation(s)
- Shuang He
- Faculty of Chinese Medicine, and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, Macao SAR, China
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Lanqian Su
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Haiyang Hu
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Haiqi Liu
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Jingwen Xiong
- Department of Sports Rehabilitation, Southwest Medical University, Luzhou, China
| | - Xiangjin Gong
- Department of Sports Rehabilitation, Southwest Medical University, Luzhou, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Qibiao Wu
- Faculty of Chinese Medicine, and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, OH, United States
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Zhou H, Zhang Y, Jin J, Shen K, Yang Y, Lao P. Prognostic evaluation of the novel blueprint of DNA methylation sites by integrating bulk RNA-sequencing and methylation modification data in endometrial cancer. J Gene Med 2024; 26:e3638. [PMID: 38011892 DOI: 10.1002/jgm.3638] [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: 08/31/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
INTRODUCTION Endometrial cancer (EC) is a prevalent malignancy affecting the female population, with an increasing incidence among younger age groups. DNA methylation, a common epigenetic modification, is well-established to play a key role in cancer progression. We suspected whether DNA methylation could be used as biomarkers for EC prognosis. METHODS In the present study, we analyzed bulk RNA-sequencing data from 544 EC patients and DNA methylation data from 430 EC patients in the TCGA-UCEC cohort. We applied weighted correlation network analysis to select a key gene set associated with panoptosis. We conducted correlation analysis between transcriptomic data of the selected key genes and DNA methylation data to identify valuable DNA methylation sites. These sites were further screened by Cox regression and least absolute shrinkage and selection operator analysis. Immune microenvironment differences between high-risk and low-risk groups were assessed using single-sample gene set enrichment analysi, xCell and MCPcounter algorithms. RESULTS Our results identified five DNA methylation sites (cg03906681, cg04549977, cg06029846, cg10043253 and cg15658376) with significant prognostic value in EC. We constructed a prognostic model using these sites, demonstrating satisfactory predictive performance. The low-risk group showed higher immune cell infiltration. Notably, methylation of site cg03906681 was negatively related to CD8 T cell infiltration, whereas cg04549977 exhibited positive correlations with immune infiltration, particularly in macrophages, activated B cells, dendritic cells and myeloid-derived suppressor cells. PD0325901_1060 was strongly correlated with risk scores, indicating a potential therapeutic response for high-risk EC patients. CONCLUSION We have developed a robust DNA methylation-based prognostic model for EC, which holds promise for improving prognosis prediction and personalized treatment approaches. These findings may contribute to better management of EC patients, particularly in identifying those at higher risk who may benefit from tailored interventions.
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Affiliation(s)
- Huanzhen Zhou
- Department of Obstetrics And Gynaecology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yingzhi Zhang
- Department of Obstetrics And Gynaecology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Jing Jin
- Department of Obstetrics And Gynaecology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Kewei Shen
- Department of Obstetrics And Gynaecology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yang Yang
- Department of Obstetrics And Gynaecology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Peiwei Lao
- Department of Obstetrics And Gynaecology, The First Affiliated Hospital of Ningbo University, Ningbo, China
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Zhang S, Jiang C, Jiang L, Chen H, Huang J, Gao X, Xia Z, Tran LJ, Zhang J, Chi H, Yang G, Tian G. Construction of a diagnostic model for hepatitis B-related hepatocellular carcinoma using machine learning and artificial neural networks and revealing the correlation by immunoassay. Tumour Virus Res 2023; 16:200271. [PMID: 37774952 PMCID: PMC10638043 DOI: 10.1016/j.tvr.2023.200271] [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: 06/03/2023] [Revised: 08/21/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
HBV infection profoundly escalates hepatocellular carcinoma (HCC) susceptibility, responsible for a majority of HCC cases. HBV-driven immune-mediated hepatocyte impairment significantly fuels HCC progression. Regrettably, inconspicuous early HCC symptoms often culminate in belated diagnoses. Nevertheless, surgically treated early-stage HCC patients relish augmented five-year survival rates. In contrast, advanced HCC exhibits feeble responses to conventional interventions like radiotherapy, chemotherapy, and surgery, leading to diminished survival rates. This investigation endeavors to unearth diagnostic hallmark genes for HBV-HCC leveraging a bioinformatics framework, thus refining early HBV-HCC detection. Candidate genes were sieved via differential analysis and Weighted Gene Co-Expression Network Analysis (WGCNA). Employing three distinct machine learning algorithms unearthed three feature genes (HHIP, CXCL14, and CDHR2). Melding these genes yielded an innovative Artificial Neural Network (ANN) diagnostic blueprint, portending to alleviate patient encumbrance and elevate life quality. Immunoassay scrutiny unveiled accentuated immune damage in HBV-HCC patients relative to solitary HCC. Through consensus clustering, HBV-HCC was stratified into two subtypes (C1 and C2), the latter potentially indicating milder immune impairment. The diagnostic model grounded in these feature genes showcased robust and transferrable prognostic potentialities, introducing a novel outlook for early HBV-HCC diagnosis. This exhaustive immunological odyssey stands poised to expedite immunotherapeutic curatives' emergence for HBV-HCC.
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Affiliation(s)
- Shengke Zhang
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Chenglu Jiang
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Lai Jiang
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Haiqing Chen
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Jinbang Huang
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Xinrui Gao
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, 81377, Germany
| | - Lisa Jia Tran
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, 81377, Germany
| | - Jing Zhang
- Division of Basic Biomedical Sciences, The University of South Dakota Sanford School of Medicine, Vermillion, 57069, USA
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China.
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, 45701, USA.
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China.
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Shi T, Li M, Yu Y. Machine learning-enhanced insights into sphingolipid-based prognostication: revealing the immunological landscape and predictive proficiency for immunomotherapy and chemotherapy responses in pancreatic carcinoma. Front Mol Biosci 2023; 10:1284623. [PMID: 38028544 PMCID: PMC10643633 DOI: 10.3389/fmolb.2023.1284623] [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: 08/28/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Background: With a poor prognosis for affected individuals, pancreatic adenocarcinoma (PAAD) is known as a complicated and diverse illness. Immunocytes have become essential elements in the development of PAAD. Notably, sphingolipid metabolism has a dual function in the development of tumors and the invasion of the immune system. Despite these implications, research on the predictive ability of sphingolipid variables for PAAD prognosis is strikingly lacking, and it is yet unclear how they can affect PAAD immunotherapy and targeted pharmacotherapy. Methods: The investigation process included SPG detection while also being pertinent to the prognosis for PAAD. Both the analytical capability of CIBERSORT and the prognostic capability of the pRRophetic R package were used to evaluate the immunological environments of the various HCC subtypes. In addition, CCK-8 experiments on PAAD cell lines were carried out to confirm the accuracy of drug sensitivity estimates. The results of these trials, which also evaluated cell survival and migratory patterns, confirmed the usefulness of sphingolipid-associated genes (SPGs). Results: As a result of this thorough investigation, 32 SPGs were identified, each of which had a measurable influence on the dynamics of overall survival. This collection of genes served as the conceptual framework for the development of a prognostic model, which was carefully assembled from 10 chosen genes. It should be noted that this grouping of patients into cohorts with high and low risk was a sign of different immune profiles and therapy responses. The increased abundance of SPGs was identified as a possible sign of inadequate responses to immune-based treatment approaches. The careful CCK-8 testing carried out on PAAD cell lines was of the highest importance for providing clear confirmation of drug sensitivity estimates. Conclusion: The significance of Sphingolipid metabolism in the complex web of PAAD development is brought home by this study. The novel risk model, built on the complexity of sphingolipid-associated genes, advances our understanding of PAAD and offers doctors a powerful tool for developing personalised treatment plans that are specifically suited to the unique characteristics of each patient.
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Affiliation(s)
| | | | - Yabin Yu
- Department of Hepatobiliary Surgery, The Affiliated Huaian No 1 People’s Hospital of Nanjing Medical University, Huaian, China
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Liu Y, Liu N, Zhou X, Zhao L, Wei W, Hu J, Luo Z. Constructing a prognostic model for head and neck squamous cell carcinoma based on glucose metabolism related genes. Front Endocrinol (Lausanne) 2023; 14:1245629. [PMID: 37876534 PMCID: PMC10591078 DOI: 10.3389/fendo.2023.1245629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Background Glucose metabolism (GM) plays a crucial role in cancer cell proliferation, tumor growth, and survival. However, the identification of glucose metabolism-related genes (GMRGs) for effective prediction of prognosis in head and neck squamous cell carcinoma (HNSC) is still lacking. Methods We conducted differential analysis between HNSC and Normal groups to identify differentially expressed genes (DEGs). Key module genes were obtained using weighted gene co-expression network analysis (WGCNA). Intersection analysis of DEGs, GMRGs, and key module genes identified GMRG-DEGs. Univariate and multivariate Cox regression analyses were performed to screen prognostic-associated genes. Independent prognostic analysis of clinical traits and risk scores was implemented using Cox regression. Gene set enrichment analysis (GSEA) was used to explore functional pathways and genes between high- and low-risk groups. Immune infiltration analysis compared immune cells between the two groups in HNSC samples. Drug prediction was performed using the Genomics of Drug Sensitivity in Cancer (GDSC) database. Quantitative real-time fluorescence PCR (qRT-PCR) validated the expression levels of prognosis-related genes in HNSC patients. Results We identified 4973 DEGs between HNSC and Normal samples. Key gene modules, represented by black and brown module genes, were identified. Intersection analysis revealed 76 GMRG-DEGs. Five prognosis-related genes (MTHFD2, CDKN2A, TPM2, MPZ, and DNMT1) were identified. A nomogram incorporating age, lymph node status (N), and risk score was constructed for survival prediction in HNSC patients. Immune infiltration analysis showed significant differences in five immune cell types (Macrophages M0, memory B cells, Monocytes, Macrophages M2, and Dendritic resting cells) between the high- and low-risk groups. GDSC database analysis identified 53 drugs with remarkable differences between the groups, including A.443654 and AG.014699. DNMT1 and MTHFD2 were up-regulated, while MPZ was down-regulated in HNSC. Conclusion Our study highlights the significant association of five prognosis-related genes (MTHFD2, CDKN2A, TPM2, MPZ, and DNMT1) with HNSC. These findings provide further evidence of the crucial role of GMRGs in HNSC.
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Affiliation(s)
- Yu Liu
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Nana Liu
- Department of Onclogy, People’s Hospital of Chongqing Hechuan, Chongqing, China
| | - Xue Zhou
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lingqiong Zhao
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Wei Wei
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Jie Hu
- Department of Otolaryngology Head and Neck Surgery, Chongqing General Hospital, Chongqing, China
| | - Zhibin Luo
- Department of Oncology, Chongqing General Hospital, Chongqing, China
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Zhao X, Zhang J, Liu J, Luo S, Ding R, Miao X, Wu T, Jia J, Cheng X. Molecular characterization of cancer-intrinsic immune evasion genes indicates prognosis and tumour microenvironment infiltration in osteosarcoma. Aging (Albany NY) 2023; 15:10272-10290. [PMID: 37796192 PMCID: PMC10599718 DOI: 10.18632/aging.205074] [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: 06/06/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Cancer-intrinsic immune evasion (IE) to cells is a critical factor in tumour growth and progression, yet the molecular characterization of IE genes (IEGs) in osteosarcoma remains underexplored. In this study, 85 osteosarcoma patients were comprehensively analyzed based on 182 IEGs, leading to the identification of two IE clusters linked to distinct biological processes and clinical outcomes. In addition, two IE clusters demonstrated diverse immune cell infiltration patterns, with IEGcluster A displaying increased levels compared to IEGcluster B. Moreover, an IE score was identified as an independent prognostic factor and nomogram may serve as a practical tool for the individual prognostic evaluation of patients with osteosarcoma. Finally, GBP1, a potential biomarker with high expression in osteosarcoma was identified. The findings of this study highlight the presence of two IE clusters, each associated with differing patient outcomes and immune infiltration properties. The IE score may serve to assess individual patient IE characteristics, enhance comprehension of immune features, and guide more efficacious treatment approaches.
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Affiliation(s)
- Xiaokun Zhao
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jian Zhang
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
- Institute of Orthopedics of Jiangxi, Nanchang, Jiangxi 330006, China
| | - Jiahao Liu
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Shengzhong Luo
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Rui Ding
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xinxin Miao
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
- Institute of Minimally Invasive Orthopedics, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Tianlong Wu
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
- Institute of Minimally Invasive Orthopedics, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jingyu Jia
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xigao Cheng
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
- Institute of Orthopedics of Jiangxi, Nanchang, Jiangxi 330006, China
- Institute of Minimally Invasive Orthopedics, Nanchang University, Nanchang, Jiangxi 330006, China
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Zhang P, Zhang H, Tang J, Ren Q, Zhang J, Chi H, Xiong J, Gong X, Wang W, Lin H, Li J, Huang C. The integrated single-cell analysis developed an immunogenic cell death signature to predict lung adenocarcinoma prognosis and immunotherapy. Aging (Albany NY) 2023; 15:10305-10329. [PMID: 37796202 PMCID: PMC10599752 DOI: 10.18632/aging.205077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/06/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND Research on immunogenic cell death (ICD) in lung adenocarcinoma (LUAD) has been relatively limited. This study aims to create ICD-related signatures for accurate survival prognosis prediction in LUAD patients, addressing the challenge of lacking reliable early prognostic indicators for this type of cancer. METHODS Using single-cell RNA sequencing (scRNA-seq) analysis, ICD activity in cells was calculated by AUCell algorithm, divided into high- and low-ICD groups according to median values, and key ICD regulatory genes were identified through differential analysis, and these genes were integrated into TCGA data to construct prognostic signatures using LASSO and COX regression analysis, and multi-dimensional analysis of ICD-related signatures in terms of prognosis, immunotherapy, tumor microenvironment (TME), and mutational landscape. RESULTS The constructed signature reveals a pronounced disparity in prognosis between the high- and low-risk groups of LUAD patients. The statistical discrepancies in survival times among LUAD patients from both the TCGA and GEO databases further corroborate this observation. Additionally, heightened levels of immune cell infiltration expression are evidenced in the low-risk group, suggesting a potential benefit from immunotherapeutic interventions for these patients. The expression levels of pivotal risk-associated genes in tissue samples were assessed utilizing qRT-PCR, thereby unveiling PITX3 as a plausible therapeutic target in the context of LUAD. CONCLUSIONS Our constructed ICD-related signatures provide help in predicting the prognosis and immunotherapy of LUAD patients, and to some extent guide the clinical treatment of LUAD patients.
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Affiliation(s)
- Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Haotian Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Junjie Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qianhe Ren
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jieying Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Jingwen Xiong
- Department of Sports Rehabilitation, Southwest Medical University, Luzhou, China
| | - Xiangjin Gong
- Department of Sports Rehabilitation, Southwest Medical University, Luzhou, China
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haoran Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chenjun Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Zou L, Meng L, Xu Y, Wang K, Zhang J. Revealing the diagnostic value and immune infiltration of senescence-related genes in endometriosis: a combined single-cell and machine learning analysis. Front Pharmacol 2023; 14:1259467. [PMID: 37860112 PMCID: PMC10583561 DOI: 10.3389/fphar.2023.1259467] [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: 07/16/2023] [Accepted: 09/05/2023] [Indexed: 10/21/2023] Open
Abstract
Introduction: Endometriosis is a prevalent and recurrent medical condition associated with symptoms such as pelvic discomfort, dysmenorrhea, and reproductive challenges. Furthermore, it has the potential to progress into a malignant state, significantly impacting the quality of life for affected individuals. Despite its significance, there is currently a lack of precise and non-invasive diagnostic techniques for this condition. Methods: In this study, we leveraged microarray datasets and employed a multifaceted approach. We conducted differential gene analysis, implemented weighted gene co-expression network analysis (WGCNA), and utilized machine learning algorithms, including random forest, support vector machine, and LASSO analysis, to comprehensively explore senescence-related genes (SRGs) associated with endometriosis. Discussion: Our comprehensive analysis, which also encompassed profiling of immune cell infiltration and single-cell analysis, highlights the therapeutic potential of this gene assemblage as promising targets for alleviating endometriosis. Furthermore, the integration of these biomarkers into diagnostic protocols promises to enhance diagnostic precision, offering a more effective diagnostic journey for future endometriosis patients in clinical settings. Results: Our meticulous investigation led to the identification of a cluster of genes, namely BAK1, LMNA, and FLT1, which emerged as potential discerning biomarkers for endometriosis. These biomarkers were subsequently utilized to construct an artificial neural network classifier model and were graphically represented in the form of a Nomogram.
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Affiliation(s)
- Lian Zou
- Chongqing Emergency Medical Center, Department of Obstetrics and Gynecology in Chongging University Central Hospital, Chongqing, China
| | - Lou Meng
- Chongqing Emergency Medical Center, Department of Obstetrics and Gynecology in Chongging University Central Hospital, Chongqing, China
| | - Yan Xu
- Chongqing Emergency Medical Center, Department of Obstetrics and Gynecology in Chongging University Central Hospital, Chongqing, China
| | - Kana Wang
- Department of Gynecology, West China Second Hospital of Sichuan University, Chengdu, China
| | - Jiawen Zhang
- Department of Gynecology, West China Second Hospital of Sichuan University, Chengdu, China
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Li Y, Cai H, Yang J, Xie X, Pei S, Wu Y, Zhang J, Song G, Zhang J, Zhang Q, Chi H, Yang G. Decoding tumor heterogeneity in uveal melanoma: basement membrane genes as novel biomarkers and therapeutic targets revealed by multi-omics approaches for cancer immunotherapy. Front Pharmacol 2023; 14:1264345. [PMID: 37822877 PMCID: PMC10562578 DOI: 10.3389/fphar.2023.1264345] [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: 07/20/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023] Open
Abstract
Background: Uveal melanoma (UVM) is a primary intraocular malignancy that poses a significant threat to patients' visual function and life. The basement membrane (BM) is critical for establishing and maintaining cell polarity, adult function, embryonic and organ morphogenesis, and many other biological processes. Some basement membrane protein genes have been proven to be prognostic biomarkers for various cancers. This research aimed to develop a novel risk assessment system based on BMRGs that would serve as a theoretical foundation for tailored and accurate treatment. Methods: We used gene expression profiles and clinical data from the TCGA-UVM cohort of 80 UVM patients as a training set. 56 UVM patients from the combined cohort of GSE84976 and GSE22138 were employed as an external validation dataset. Prognostic characteristics of basement membrane protein-related genes (BMRGs) were characterized by Lasso, stepwise multifactorial Cox. Multivariate analysis revealed BMRGs to be independent predictors of UVM. The TISCH database probes the crosstalk of BMEGs in the tumor microenvironment at the single-cell level. Finally, we investigated the function of ITGA5 in UVM using multiple experimental techniques, including CCK8, transwell, wound healing assay, and colony formation assay. Results: There are three genes in the prognostic risk model (ADAMTS10, ADAMTS14, and ITGA5). After validation, we determined that the model is quite reliable and accurately forecasts the prognosis of UVM patients. Immunotherapy is more likely to be beneficial for UVM patients in the high-risk group, whereas the survival advantage may be greater for UVM patients in the low-risk group. Knockdown of ITGA5 expression was shown to inhibit the proliferation, migration, and invasive ability of UVM cells in vitro experiments. Conclusion: The 3-BMRGs feature model we constructed has excellent predictive performance which plays a key role in the prognosis, informing the individualized treatment of UVM patients. It also provides a new perspective for assessing pre-immune efficacy.
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Affiliation(s)
- Yunyue Li
- Queen Mary College, Medical School of Nanchang University, Nanchang, China
| | - Huabao Cai
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jinyan Yang
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xixi Xie
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Shengbin Pei
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yifan Wu
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinhao Zhang
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Guobin Song
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Jieying Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qinhong Zhang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, OH, United States
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Zhang S, Jiang C, Jiang L, Chen H, Huang J, Zhang J, Wang R, Chi H, Yang G, Tian G. Uncovering the immune microenvironment and molecular subtypes of hepatitis B-related liver cirrhosis and developing stable a diagnostic differential model by machine learning and artificial neural networks. Front Mol Biosci 2023; 10:1275897. [PMID: 37808522 PMCID: PMC10556489 DOI: 10.3389/fmolb.2023.1275897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Background: Hepatitis B-related liver cirrhosis (HBV-LC) is a common clinical disease that evolves from chronic hepatitis B (CHB). The development of cirrhosis can be suppressed by pharmacological treatment. When CHB progresses to HBV-LC, the patient's quality of life decreases dramatically and drug therapy is ineffective. Liver transplantation is the most effective treatment, but the lack of donor required for transplantation, the high cost of the procedure and post-transplant rejection make this method unsuitable for most patients. Methods: The aim of this study was to find potential diagnostic biomarkers associated with HBV-LC by bioinformatics analysis and to classify HBV-LC into specific subtypes by consensus clustering. This will provide a new perspective for early diagnosis, clinical treatment and prevention of HCC in HBV-LC patients. Two study-relevant datasets, GSE114783 and GSE84044, were retrieved from the GEO database. We screened HBV-LC for feature genes using differential analysis, weighted gene co-expression network analysis (WGCNA), and three machine learning algorithms including least absolute shrinkage and selection operator (LASSO), support vector machine recursive feature elimination (SVM-RFE), and random forest (RF) for a total of five methods. After that, we constructed an artificial neural network (ANN) model. A cohort consisting of GSE123932, GSE121248 and GSE119322 was used for external validation. To better predict the risk of HBV-LC development, we also built a nomogram model. And multiple enrichment analyses of genes and samples were performed to understand the biological processes in which they were significantly enriched. And the different subtypes of HBV-LC were analyzed using the Immune infiltration approach. Results: Using the data downloaded from GEO, we developed an ANN model and nomogram based on six feature genes. And consensus clustering of HBV-LC classified them into two subtypes, C1 and C2, and it was hypothesized that patients with subtype C2 might have milder clinical symptoms by immune infiltration analysis. Conclusion: The ANN model and column line graphs constructed with six feature genes showed excellent predictive power, providing a new perspective for early diagnosis and possible treatment of HBV-LC. The delineation of HBV-LC subtypes will facilitate the development of future clinical treatment of HBV-LC.
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Affiliation(s)
- Shengke Zhang
- Department of Clinical Medicine, School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chenglu Jiang
- Department of Clinical Medicine, School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lai Jiang
- Department of Clinical Medicine, School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Haiqing Chen
- Department of Clinical Medicine, School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinbang Huang
- Department of Clinical Medicine, School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jieying Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Rui Wang
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, China
- Academician (Expert) Workstation of Sichuan Province, Luzhou, China
| | - Hao Chi
- Department of Clinical Medicine, School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, United States
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China
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Wu X, Zhou Z, Cao Q, Chen Y, Gong J, Zhang Q, Qiang Y, Lu Y, Cao G. Reprogramming of Treg cells in the inflammatory microenvironment during immunotherapy: a literature review. Front Immunol 2023; 14:1268188. [PMID: 37753092 PMCID: PMC10518452 DOI: 10.3389/fimmu.2023.1268188] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
Regulatory T cells (Treg), as members of CD4+ T cells, have garnered extensive attention in the research of tumor progression. Treg cells have the function of inhibiting the immune effector cells, preventing tissue damage, and suppressing inflammation. Under the stimulation of the tumor inflammatory microenvironment (IM), the reprogramming of Treg cells enhances their suppression of immune responses, ultimately promoting tumor immune escape or tumor progression. Reducing the number of Treg cells in the IM or lowering the activity of Treg cells while preventing their reprogramming, can help promote the body's anti-tumor immune responses. This review introduces a reprogramming mechanism of Treg cells in the IM; and discusses the regulation of Treg cells on tumor progression. The control of Treg cells and the response to Treg inflammatory reprogramming in tumor immunotherapy are analyzed and countermeasures are proposed. This work will provide a foundation for downregulating the immunosuppressive role of Treg in the inflammatory environment in future tumor immunotherapy.
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Affiliation(s)
- Xinyan Wu
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhigang Zhou
- Department of Oncology, Changde Hospital, Xiangya School of Medicine, Central South University, Changde, China
| | - Qiang Cao
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
- School of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Yuquan Chen
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China
| | - Junling Gong
- School of Public Health, Nanchang University, Qianhu, Nanchang, China
| | - Qi Zhang
- Undergraduate Department, Taishan University, Taian, China
| | - Yi Qiang
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
| | - Yanfeng Lu
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
| | - Guangzhu Cao
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
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Xu W, Zhang W, Zhao D, Wang Q, Zhang M, Li Q, Zhu W, Xu C. Unveiling the role of regulatory T cells in the tumor microenvironment of pancreatic cancer through single-cell transcriptomics and in vitro experiments. Front Immunol 2023; 14:1242909. [PMID: 37753069 PMCID: PMC10518406 DOI: 10.3389/fimmu.2023.1242909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
Background In order to investigate the impact of Treg cell infiltration on the immune response against pancreatic cancer within the tumor microenvironment (TME), and identify crucial mRNA markers associated with Treg cells in pancreatic cancer, our study aims to delve into the role of Treg cells in the anti-tumor immune response of pancreatic cancer. Methods The ordinary transcriptome data for this study was sourced from the GEO and TCGA databases. It was analyzed using single-cell sequencing analysis and machine learning. To assess the infiltration level of Treg cells in pancreatic cancer tissues, we employed the CIBERSORT method. The identification of genes most closely associated with Treg cells was accomplished through the implementation of weighted gene co-expression network analysis (WGCNA). Our analysis of single-cell sequencing data involved various quality control methods, followed by annotation and advanced analyses such as cell trajectory analysis and cell communication analysis to elucidate the role of Treg cells within the pancreatic cancer microenvironment. Additionally, we categorized the Treg cells into two subsets: Treg1 associated with favorable prognosis, and Treg2 associated with poor prognosis, based on the enrichment scores of the key genes. Employing the hdWGCNA method, we analyzed these two subsets to identify the critical signaling pathways governing their mutual transformation. Finally, we conducted PCR and immunofluorescence staining in vitro to validate the identified key genes. Results Based on the results of immune infiltration analysis, we observed significant infiltration of Treg cells in the pancreatic cancer microenvironment. Subsequently, utilizing the WGCNA and machine learning algorithms, we ultimately identified four Treg cell-related genes (TRGs), among which four genes exhibited significant correlations with the occurrence and progression of pancreatic cancer. Among them, CASP4, TOB1, and CLEC2B were associated with poorer prognosis in pancreatic cancer patients, while FYN showed a correlation with better prognosis. Notably, significant differences were found in the HIF-1 signaling pathway between Treg1 and Treg2 cells identified by the four genes. These conclusions were further validated through in vitro experiments. Conclusion Treg cells played a crucial role in the pancreatic cancer microenvironment, and their presence held a dual significance. Recognizing this characteristic was vital for understanding the limitations of Treg cell-targeted therapies. CASP4, FYN, TOB1, and CLEC2B exhibited close associations with infiltrating Treg cells in pancreatic cancer, suggesting their involvement in Treg cell functions. Further investigation was warranted to uncover the mechanisms underlying these associations. Notably, the HIF-1 signaling pathway emerged as a significant pathway contributing to the duality of Treg cells. Targeting this pathway could potentially revolutionize the existing treatment approaches for pancreatic cancer.
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Affiliation(s)
- Wei Xu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Wenjia Zhang
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- Department of Respiratory Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dongxu Zhao
- Department of Interventional Radiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Man Zhang
- Department of Emergency Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- The Laboratory of Emergency Medicine, School of the Secondary Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Qiang Li
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Wenxin Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Gastroenterology, Kunshan Third People’s Hospital, Suzhou, Jiangsu, China
| | - Chunfang Xu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Tang S, Wu Z, Chen L, She L, Zuo W, Luo W, Zhang Y, Liang S, Liu G, He B, He J, Zhang N. Multi-omics analysis reveals the association between elevated KIF18B expression and unfavorable prognosis, immune evasion, and regulatory T cell activation in nasopharyngeal carcinoma. Front Immunol 2023; 14:1258344. [PMID: 37744335 PMCID: PMC10514916 DOI: 10.3389/fimmu.2023.1258344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Background Nasopharyngeal carcinoma (NPC) is prevalent in Southern China. The expression profile and functions of kinesin family member 18B (KIF18B) remain unclear in NPC. Methods Bulk and single-cell transcriptome data for NPC were downloaded. KIF18B expression differences in NPC and normal tissues and its prognostic value were validated by immunohistochemistry and Cox model. We performed multi-faceted functional enrichment analysis on KIF18B. Immune infiltration was analyzed comprehensively by the CIBERSORT, EPIC, and quanTIseq algorithms and the BisqueRNA package and confirmed by immunofluorescence assay. The intercellular communication were investigated by the CellChat package. We explored the dynamics of KIF18B expression by pseudotime trajectory. M6A modification analysis rely on SRAMP platform. The treatment response were evaluated by Tumor Immune Dysfunction and Exclusion (TIDE) score, immunophenoscore and IC50 value. Results KIF18B overexpression in NPC led to unfavorable prognosis, and significantly associated with advanced T, N, and stage classifications. Functional analysis demonstrated that KIF18B was involved in immune suppression, epithelial-mesenchymal transition (EMT), N6-methyladenosine (m6A) modification and therapeutic responses. The deconvolution algorithm indicated that activated regulatory T cells (Tregs) had the strongest positive correlation with KIF18B among immune cells (R = 0.631). Validated by immunofluorescence assay, the high KIF18B expression group displayed a notable rise in Tregs infiltration, accompanied by a substantial decrease in the infiltration of CD8+ T cells and macrophages. In the intercellular communication network, malignant cells with high KIF18B expression implicated in more interactions, and activated and recruited Tregs by modulating cytokines, chemokines, and immune checkpoints. KIF18B was upregulated in more advanced malignant cells and influenced EMT by regulating ITGA6, VIM, and ZEB1/2. KIF18B expression was positively related to m6A "writer" and "reader" genes, and negatively related to "eraser" genes. The KIF18B high expression group exhibited a higher TIDE score and elevated IC50 values for the commonly used chemotherapy drugs, gemcitabine, oxaliplatin, and 5-fluorouracil. Conclusion KIF18B is a significant prognostic marker in NPC, and may modulate immune evasion and EMT. M6A modification may account for the aberrant overexpression of KIF18B in NPC. Furthermore, KIF18B may predict response to immunotherapy and chemotherapy.
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Affiliation(s)
- Siqi Tang
- Department of Radiation Oncology, First People’s Hospital of Foshan, Foshan, China
| | - Zhenyu Wu
- Department of Urology, First People’s Hospital of Foshan, Foshan, China
| | - Lusi Chen
- Department of Radiation Oncology, First People’s Hospital of Foshan, Foshan, China
| | - Longjiang She
- Department of Radiation Oncology, First People’s Hospital of Foshan, Foshan, China
| | - Weihan Zuo
- Department of Radiation Oncology, First People’s Hospital of Foshan, Foshan, China
| | - Weijun Luo
- Department of Radiation Oncology, First People’s Hospital of Foshan, Foshan, China
| | - Yang Zhang
- Department of Radiation Oncology, First People’s Hospital of Foshan, Foshan, China
| | - Shaoqiang Liang
- Department of Comprehensive (Head and Neck) Oncology and Hospice Ward, First People’s Hospital of Foshan, Foshan, China
| | - Guichao Liu
- Department of Radiation Oncology, First People’s Hospital of Foshan, Foshan, China
| | - Biyi He
- Department of Rhinology, First People’s Hospital of Foshan, Foshan, China
| | - Jinfeng He
- Department of Rhinology, First People’s Hospital of Foshan, Foshan, China
| | - Ning Zhang
- Department of Radiation Oncology, First People’s Hospital of Foshan, Foshan, China
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Zhao S, Wang Q, Ni K, Zhang P, Liu Y, Xie J, Ji W, Cheng C, Zhou Q. Combining single-cell sequencing and spatial transcriptome sequencing to identify exosome-related features of glioblastoma and constructing a prognostic model to identify BARD1 as a potential therapeutic target for GBM patients. Front Immunol 2023; 14:1263329. [PMID: 37727789 PMCID: PMC10505933 DOI: 10.3389/fimmu.2023.1263329] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/17/2023] [Indexed: 09/21/2023] Open
Abstract
Background Glioblastoma (GBM) is a malignant primary brain tumor. This study focused on exploring the exosome-related features of glioblastoma to better understand its cellular composition and molecular characteristics. Methods Single-cell RNA sequencing (scRNA-seq) and spatial transcriptome RNA sequencing (stRNA-seq) were used to analyze the heterogeneity of glioblastomas. After data integration, cell clustering, and annotation, five algorithms were used to calculate scores for exosome-related genes(ERGs). Cell trajectory analysis and intercellular communication analysis were performed to explore exosome-related communication patterns. Spatial transcriptome sequencing data were analyzed to validate the findings. To further utilize exosome-related features to aid in clinical decision-making, a prognostic model was constructed using GBM's bulk RNA-seq. Results Different cell subpopulations were observed in GBM, with Monocytes/macrophages and malignant cells in tumor samples showing higher exosome-related scores. After identifying differentially expressed ERGs in malignant cells, pseudotime analysis revealed the cellular status of malignant cells during development. Intercellular communication analysis highlighted signaling pathways and ligand-receptor interactions. Spatial transcriptome sequencing confirmed the high expression of exosome-related gene features in the tumor core region. A prognostic model based on six ERGs was shown to be predictive of overall survival and immunotherapy outcome in GBM patients. Finally, based on the results of scRNA-seq and prognostic modeling as well as a series of cell function experiments, BARD1 was identified as a novel target for the treatment of GBM. Conclusion This study provides a comprehensive understanding of the exosome-related features of GBM in both scRNA-seq and stRNA-seq, with malignant cells with higher exosome-related scores exhibiting stronger communication with Monocytes/macrophages. In terms of spatial data, highly scored malignant cells were also concentrated in the tumor core region. In bulk RNA-seq, patients with a high exosome-related index exhibited an immunosuppressive microenvironment, which was accompanied by a worse prognosis as well as immunotherapy outcomes. Prognostic models constructed using ERGs are expected to be independent prognostic indicators for GBM patients, with potential implications for personalized treatment strategies for GBM. Knockdown of BARD1 in GBM cell lines reduces the invasive and value-added capacity of tumor cells, and thus BARD1-positively expressing malignant cells are a risk factor for GBM patients.
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Affiliation(s)
- Songyun Zhao
- Department of Neurosurgery, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Kaixiang Ni
- Department of Neurosurgery, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Pengpeng Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yuan Liu
- Department of General Surgery, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Jiaheng Xie
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Ji
- Department of Neurosurgery, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Chao Cheng
- Department of Neurosurgery, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Qiang Zhou
- Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
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Zhang P, Zhang X, Cui Y, Gong Z, Wang W, Lin S. Revealing the role of regulatory T cells in the tumor microenvironment of lung adenocarcinoma: a novel prognostic and immunotherapeutic signature. Front Immunol 2023; 14:1244144. [PMID: 37671160 PMCID: PMC10476870 DOI: 10.3389/fimmu.2023.1244144] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
Background Regulatory T cells (Tregs), are a key class of cell types in the immune system. In the tumor microenvironment (TME), the presence of Tregs has important implications for immune response and tumor development. Relatively little is known about the role of Tregs in lung adenocarcinoma (LUAD). Methods Tregs were identified using but single-cell RNA sequencing (scRNA-seq) analysis and interactions between Tregs and other cells in the TME were investigated. Next, we used multiple bulk RNA-seq datasets to construct risk models based on marker genes of Tregs and explored differences in prognosis, mutational landscape, immune cell infiltration and immunotherapy between high- and low-risk groups, and finally, qRT-PCR and cell function experiments were performed to validate the model genes. Results The cellchat analysis showed that MIF-(CD74+CXCR4) pairs play a key role in the interaction of Tregs with other cell subpopulations, and the Tregs-associated signatures (TRAS) could well classify multiple LUAD cohorts into high- and low-risk groups. Immunotherapy may offer greater potential benefits to the low-risk group, as indicated by their superior survival, increased infiltration of immune cells, and heightened expression of immune checkpoints. Finally, the experiment verified that the model genes LTB and PTTG1 were relatively highly expressed in cancer tissues, while PTPRC was relatively highly expressed in paracancerous tissues. Colony Formation assay confirmed that knockdown of PTTG1 reduced the proliferation ability of LUAD cells. Conclusion TRAS were constructed using scRNA-seq and bulk RNA-seq to distinguish patient risk subgroups, which may provide assistance in the clinical management of LUAD patients.
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Affiliation(s)
- Pengpeng Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xiao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanan Cui
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zetian Gong
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shengrong Lin
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai, China
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Han X, Yan Z, Fan K, Guan X, Hu B, Li X, Ou Y, Cui B, An L, Zhang Y, Gong J. The combined signatures of telomere and immune cell landscape provide a prognostic and therapeutic biomarker in glioma. Front Immunol 2023; 14:1220100. [PMID: 37662954 PMCID: PMC10470026 DOI: 10.3389/fimmu.2023.1220100] [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: 05/10/2023] [Accepted: 07/20/2023] [Indexed: 09/05/2023] Open
Abstract
Background Gliomas, the most prevalent primary malignant tumors of the central nervous system in adults, exhibit slow growth in lower-grade gliomas (LGG). However, the majority of LGG cases progress to high-grade gliomas, posing challenges for prognostication. The tumor microenvironment (TME), characterized by telomere-related genes and immune cell infiltration, strongly influences glioma growth and therapeutic response. Therefore, our objective was to develop a Telomere-TME (TM-TME) classifier that integrates telomere-related genes and immune cell landscape to assess prognosis and therapeutic response in glioma. Methods This study encompassed LGG patients from the TCGA and CCGA databases. TM score and TME score were derived from the expression signatures of telomere-related genes and the presence of immune cells in LGG, respectively. The TM-TME classifier was established by combining TM and TME scores to effectively predict prognosis. Subsequently, we conducted Kaplan-Meier survival estimation, univariate Cox regression analysis, and receiver operating characteristic curves to validate the prognostic prediction capacity of the TM-TME classifier across multiple cohorts. Gene Ontology (GO) analysis, biological processes, and proteomaps were performed to annotate the functional aspects of each subgroup and visualize the cellular signaling pathways. Results The TM_low+TME_high subgroup exhibited superior prognosis and therapeutic response compared to other subgroups (P<0.001). This finding could be attributed to distinct tumor somatic mutations and cancer cellular signaling pathways. GO analysis indicated that the TM_low+TME_high subgroup is associated with the neuronal system and modulation of chemical synaptic transmission. Conversely, the TM_high+TME_low subgroup showed a strong association with cell cycle and DNA metabolic processes. Furthermore, the classifier significantly differentiated overall survival in the TCGA LGG cohort and served as an independent prognostic factor for LGG patients in both the TCGA cohort (P<0.001) and the CGGA cohort (P<0.001). Conclusion Overall, our findings underscore the significance of the TM-TME classifier in predicting prognosis and immune therapeutic response in glioma, shedding light on the complex immune landscape within each subgroup. Additionally, our results suggest the potential of integrating risk stratification with precision therapy for LGG.
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Affiliation(s)
- Xu Han
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zihan Yan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kaiyu Fan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xueyi Guan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bohan Hu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiang Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yunwei Ou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bing Cui
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Lingxuan An
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Yaohua Zhang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Jian Gong
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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Papadakos SP, Machairas N, Stergiou IE, Arvanitakis K, Germanidis G, Frampton AE, Theocharis S. Unveiling the Yin-Yang Balance of M1 and M2 Macrophages in Hepatocellular Carcinoma: Role of Exosomes in Tumor Microenvironment and Immune Modulation. Cells 2023; 12:2036. [PMID: 37626849 PMCID: PMC10453902 DOI: 10.3390/cells12162036] [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: 06/29/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a primary liver cancer with a high mortality rate and limited treatment options. Recent research has brought attention to the significant importance of intercellular communication in the progression of HCC, wherein exosomes have been identified as critical agents facilitating cell-to-cell signaling. In this article, we investigate the impact of macrophages as both sources and targets of exosomes in HCC, shedding light on the intricate interplay between exosome-mediated communication and macrophage involvement in HCC pathogenesis. It investigates how exosomes derived from HCC cells and other cell types within the tumor microenvironment (TME) can influence macrophage behavior, polarization, and recruitment. Furthermore, the section explores the reciprocal interactions between macrophage-derived exosomes and HCC cells, stromal cells, and other immune cells, elucidating their role in tumor growth, angiogenesis, metastasis, and immune evasion. The findings presented here contribute to a better understanding of the role of macrophage-derived exosomes in HCC progression and offer new avenues for targeted interventions and improved patient outcomes.
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Affiliation(s)
- Stavros P. Papadakos
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 10679 Athens, Greece;
| | - Nikolaos Machairas
- Second Department of Propaedeutic Surgery, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece;
| | - Ioanna E. Stergiou
- Pathophysiology Department, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Konstantinos Arvanitakis
- Division of Gastroenterology and Hepatology, First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, St. Kiriakidi 1, 54636 Thessaloniki, Greece; (K.A.); (G.G.)
- Basic and Translational Research Unit (BTRU), Special Unit for Biomedical Research and Education (BRESU), Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Georgios Germanidis
- Division of Gastroenterology and Hepatology, First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, St. Kiriakidi 1, 54636 Thessaloniki, Greece; (K.A.); (G.G.)
- Basic and Translational Research Unit (BTRU), Special Unit for Biomedical Research and Education (BRESU), Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Adam Enver Frampton
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
- Oncology Section, Surrey Cancer Research Institute, Department of Clinical and Experimental Medicine, FHMS, University of Surrey, The Leggett Building, Daphne Jackson Road, Guildford GU2 7WG, UK
- HPB Surgical Unit, Royal Surrey NHS Foundation Trust, Guildford GU2 7XX, UK
| | - Stamatios Theocharis
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 10679 Athens, Greece;
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Xu W, Jiang T, Shen K, Zhao D, Zhang M, Zhu W, Liu Y, Xu C. GADD45B regulates the carcinogenesis process of chronic atrophic gastritis and the metabolic pathways of gastric cancer. Front Endocrinol (Lausanne) 2023; 14:1224832. [PMID: 37608794 PMCID: PMC10441793 DOI: 10.3389/fendo.2023.1224832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 08/24/2023] Open
Abstract
Background Gastric cancer continues to be a significant global healthcare challenge, and its burden remains substantial. The development of gastric cancer (GC) is closely linked to chronic atrophic gastritis (CAG), yet there is a scarcity of research exploring the underlying mechanisms of CAG-induced carcinogenesis. Methods In this study, we conducted a comprehensive investigation into the oncogenes involved in CAG using both bulk transcriptome and single-cell transcriptome data. Our approach employed hdWGCNA to identify pathogenic genes specific to CAG, with non-atrophic gastritis (NAG) serving as the control group. Additionally, we compared CAG with GC, using normal gastric tissue as the control group in the single-cell transcriptome analysis. By intersecting the identified pathogenic genes, we pinpointed key network molecules through protein interaction network analysis. To further refine the gene selection, we applied LASSO, SVM-RFE, and RF techniques, which resulted in a set of cancer-related genes (CRGs) associated with CAG. To identify CRGs potentially linked to gastric cancer progression, we performed a univariate COX regression analysis on the gene set. Subsequently, we explored the relationship between CRGs and immune infiltration, drug sensitivity, and clinical characteristics in gastric cancer patients. We employed GSVA to investigate how CRGs regulated signaling pathways in gastric cancer cells, while an analysis of cell communication shed light on the impact of CRGs on signal transmission within the gastric cancer tumor microenvironment. Lastly, we analyzed changes in metabolic pathways throughout the progression of gastric cancer. Results Using hdWGCNA, we have identified a total of 143 pathogenic genes that were shared by CAG and GC. To further investigate the underlying mechanisms, we conducted protein interaction network analysis and employed machine learning screening techniques. As a result, we have identified 15 oncogenes that are specifically associated with chronic atrophic gastritis. By performing ROC reanalysis and prognostic analysis, we have determined that GADD45B is the most significant gene involved in the carcinogenesis of CAG. Immunohistochemical staining and differential analysis have revealed that GADD45B expression was low in GC tissues while high in normal gastric tissues. Moreover, based on prognostic analysis, high expression of GADD45B has been correlated with poor prognosis in GC patients. Additionally, an analysis of immune infiltration has shown a relationship between GADD45B and the infiltration of various immune cells. By correlating GADD45B with clinical characteristics, we have found that it primarily affects the depth of invasion in GC. Through cell communication analysis, we have discovered that the CD99 signaling pathway network and the CDH signaling pathway network are the main communication pathways that significantly alter the microenvironment of gastric tissue during the development of chronic atrophic gastritis. Specifically, GADD45B-low GC cells were predominantly involved in the network communication of the CDH signaling pathway, while GADD45B-high GC cells played a crucial role in both signaling pathways. Furthermore, we have identified several metabolic pathways, including D-Glutamine and D-glutamate metabolism and N-Glycan biosynthesis, among others, that played important roles in the occurrence and progression of GC, in addition to the six other metabolic pathways. In summary, our study highlighted the discovery of 143 pathogenic genes shared by CAG and GC, with a specific focus on 15 oncogenes associated with CAG. We have identified GADD45B as the most important gene in the carcinogenesis of CAG, which exhibited differential expression in GC tissues compared to normal gastric tissues. Moreover, GADD45B expression was correlated with patient prognosis and is associated with immune cell infiltration. Our findings also emphasized the impact of the CD99 and CDH signaling pathway networks on the microenvironment of gastric tissue during the development of CAG. Additionally, we have identified key metabolic pathways involved in GC progression. Conclusion GADD45B, an oncogene implicated in chronic atrophic gastritis, played a critical role in GC development. Decreased expression of GADD45B was associated with the onset of GC. Moreover, GADD45B expression levels were closely tied to poor prognosis in GC patients, influencing the infiltration patterns of various cells within the tumor microenvironment, as well as impacting the metabolic pathways involved in GC progression.
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Affiliation(s)
- Wei Xu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tianxiao Jiang
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kanger Shen
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dongxu Zhao
- Department of Interventional Radiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Man Zhang
- Department of Emergency Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Wenxin Zhu
- Department of Gastroenterology, Kunshan Third People’s Hospital, Suzhou, Jiangsu, China
| | - Yunfei Liu
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Chunfang Xu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Liu T, Li C, Zhang J, Hu H, Li C. Unveiling efferocytosis-related signatures through the integration of single-cell analysis and machine learning: a predictive framework for prognosis and immunotherapy response in hepatocellular carcinoma. Front Immunol 2023; 14:1237350. [PMID: 37575252 PMCID: PMC10414188 DOI: 10.3389/fimmu.2023.1237350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 08/15/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) represents a prominent gastrointestinal malignancy with a grim clinical outlook. In this regard, the discovery of novel early biomarkers holds substantial promise for ameliorating HCC-associated mortality. Efferocytosis, a vital immunological process, assumes a central position in the elimination of apoptotic cells. However, comprehensive investigations exploring the role of efferocytosis-related genes (EFRGs) in HCC are sparse, and their regulatory influence on HCC immunotherapy and targeted drug interventions remain poorly understood. Methods RNA sequencing data and clinical characteristics of HCC patients were acquired from the TCGA database. To identify prognostically significant genes in HCC, we performed the limma package and conducted univariate Cox regression analysis. Subsequently, machine learning algorithms were employed to identify hub genes. To assess the immunological landscape of different HCC subtypes, we employed the CIBERSORT algorithm. Furthermore, single-cell RNA sequencing (scRNA-seq) was utilized to investigate the expression levels of ERFGs in immune cells and to explore intercellular communication within HCC tissues. The migratory capacity of HCC cells was evaluated using CCK-8 assays, while drug sensitivity prediction reliability was determined through wound-healing assays. Results We have successfully identified a set of nine genes, termed EFRGs, that hold significant potential for the establishment of a hepatocellular carcinoma-specific prognostic model. Furthermore, leveraging the individual risk scores derived from this model, we were able to stratify patients into two distinct risk groups, unveiling notable disparities in terms of immune infiltration patterns and response to immunotherapy. Notably, the model's capacity to accurately predict drug responses was substantiated through comprehensive experimental investigations, encompassing wound-healing assay, and CCK8 experiments conducted on the HepG2 and Huh7 cell lines. Conclusions We constructed an EFRGs model that serves as valuable tools for prognostic assessment and decision-making support in the context of immunotherapy and chemotherapy.
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Affiliation(s)
- Tao Liu
- Colorectal and Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Chao Li
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians University, Munich, Germany
| | - Jiantao Zhang
- Colorectal and Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Han Hu
- Colorectal and Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Chenyao Li
- Colorectal and Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
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