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Zhu X, Gao J, Qiu C. Integrative analysis reveals key lysosomal genes as potential therapeutic targets in Alzheimer's disease. Metab Brain Dis 2024:10.1007/s11011-024-01409-5. [PMID: 39150655 DOI: 10.1007/s11011-024-01409-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder with early autophagy deficits. Our study probed the role of lysosomal-related genes (LRGs) in AD. Using the Gene Expression Omnibus (GEO) database, we analyzed differentially expressed genes (DEGs) in AD. AD-related genes and lysosomal-related genes (LRGs) were extracted from public databases. Leveraging the UpSetR package, we identified differentially expressed LRGs (DE-LRGs). Subsequently, consensus cluster analysis was used to stratify AD patients into distinct molecular subtypes based on DE-LRGs. Immune cell patterns were studied via Single-Sample Gene Set Enrichment Analysis (ssGSEA). Molecular pathways were assessed through Gene Set Variation Analysis (GSVA), while Mendelian Randomization (MR) discerned potential gene-AD causations. To reinforce our bioinformatics findings, we conducted in vitro experiments. In total, 52 DE-LRGs were identified, with LAMP1, VAMP2, and CTSB as standout hub genes. Leveraging the 52 DE-LRGs, AD patients were categorized into three distinct molecular subtypes. Interestingly, the three aforementioned hub genes exhibited significant predictive accuracy for AD differentiation across the subtypes. The ssGSEA further illuminated correlations between LAMP1, VAMP2, and CTSB with plasma cells, fibroblasts, eosinophils, and endothelial cells. GSVA analysis underscored significant associations of LAMP1, VAMP2, and CTSB with NOTCH, TGFβ, and P53 pathways. Compellingly, MR findings indicated a potential causative relationship between LAMP1, CTSB, and AD. Augmenting our bioinformatics conclusions, in vitro tests revealed that LAMP1 potentially alleviates AD progression by amplifying autophagic processes. LAMP1 and CTSB emerge as potential AD biomarkers, paving the way for innovative therapeutic interventions.
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Affiliation(s)
- Xiangzhen Zhu
- Department of Psychiatry, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310006, Zhejiang, China
| | - Jingfang Gao
- Department of Psychiatry, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310006, Zhejiang, China
| | - Chao Qiu
- Department of Neurology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, 310006, Zhejiang, China.
- Department of Neurology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), No.54 Youdian Road, Hangzhou, 310006, Zhejiang, China.
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Zhang S, Ren L, Li W, Zhang Y, Yang Y, Yang H, Xu F, Cao W, Li X, Zhang X, Du G, Wang J. Interferon Gamma Inducible Protein 30: from biological functions to potential therapeutic target in cancers. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00979-x. [PMID: 39141317 DOI: 10.1007/s13402-024-00979-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Interferon Gamma Inducible Protein 30 (IFI30), also known as Gamma-Interferon-Inducible Lysosomal Thiol Reductase (GILT), is predominantly found in lysosomes and the cytoplasm. As the sole enzyme identified to catalyze disulfide bond reduction in the endocytic pathway, IFI30 contributes to both major histocompatibility complex (MHC) class I-restricted antigen cross-presentation and MHC class II-restricted antigen processing by decreasing the disulfide bonds of endocytosed proteins. Remarkably, emerging research has revealed that IFI30 is involved in tumorigenesis, tumor development, and the tumor immune response. Targeting IFI30 may provide new strategies for cancer therapy and improve the prognosis of patients. This review provided a comprehensive overview of the research progress on IFI30 in tumor progression, cellular redox status, autophagy, tumor immune response, and drug sensitivity, with a view to providing the theoretical basis for pharmacological intervention of IFI30 in tumor therapy, particularly in immunotherapy.
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Affiliation(s)
- Sen Zhang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Liwen Ren
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Wan Li
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Yizhi Zhang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Yihui Yang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Hong Yang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Fang Xu
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Wanxin Cao
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Xiaoxue Li
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Xu Zhang
- Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 211198, China
| | - Guanhua Du
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
| | - Jinhua Wang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
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Bi S, Han B, Fan H, Liu Y, Cui X. Mitochondria-Related Gene MAOB is a Key Biomarker of Osteoarthritis and Inhibition of Its Expression Reduces LPS-induced Chondrocyte Damage. Biochem Genet 2024; 62:2314-2331. [PMID: 37651071 DOI: 10.1007/s10528-023-10486-7] [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: 05/11/2023] [Accepted: 08/06/2023] [Indexed: 09/01/2023]
Abstract
The mitochondria are an important organelle in cells responsible for producing energy, and its abnormal function is closely related to the occurrence and development of osteoarthritis. Finding key genes associated with mitochondrial dysfunction in osteoarthritis can provide new ideas for the study of its pathogenesis. Firstly, 371 differential expressed genes (DEGs) were obtained through bioinformatics analysis of the GSE12021 and GSE55235 datasets in the GEO database, and 24 mitochondria-related DEGs (Mito-DEGs) were obtained by crossing differential genes with mitochondrial related genes. Next, KEGG and GO analysis of Mito-DEGs showed that upregulated Mito-DEGs were mainly enriched in small molecule catabolic process and tryptophan metabolism, while downregulated Mito-DEGs were mainly enriched in acetyl-CoA metabolic process and fatty acid biosynthesis. Furthermore, the key genes ME2 and MAOB were obtained through protein-protein interaction network analysis and lasso cox analysis of the 24 Mito-DEGs. In addition, the comparison results of immune cell scores showed differences between T cells CD4 memory resting, T cells regulatory (Tregs), Mast cells resting, and Mast cells activated in the OA group and the control group. More importantly, the potential regulatory mechanisms of key genes were studied through GSEA analysis and their correlation with immune infiltrating cells, immune checkpoints, m6A, and ferroptosis. Finally, in LPS-induced C28/I2 cells, silencing MAOB reduced inflammation injury and inhibited mitochondrial damage. Our research findings suggest that MAOB may hold potential as a target for the diagnosis and treatment of osteoarthritis.
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Affiliation(s)
- Shiqi Bi
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Bo Han
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Hongjuan Fan
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Yongming Liu
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
| | - Xuewen Cui
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
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Wan R, Pan L, Wang Q, Shen G, Guo R, Qin Y, Huang X, Wang R, Fan X. Decoding Gastric Cancer: Machine Learning Insights Into the Significance of COMMDs Family in Immunotherapy and Diagnosis. J Cancer 2024; 15:3580-3595. [PMID: 38817875 PMCID: PMC11134438 DOI: 10.7150/jca.94360] [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: 01/16/2024] [Accepted: 04/27/2024] [Indexed: 06/01/2024] Open
Abstract
Copper, an indispensable trace element for the human body, serves not only as a crucial auxiliary factor in redox reactions within the organism but also as a significant constituent of numerous key metabolic enzymes. The COMMD family plays a vital role in regulating copper at both the cellular and systemic levels, particularly in the realm of tumor research, an area notably deficient in gastric cancer investigations. With the advancement of precision medical techniques, individualized and precise screening and treatment have become paramount considerations in the contemporary medical landscape for gastric cancer therapy. In light of this, we meticulously scrutinized existing transcriptomic datasets for gastric cancer, validating the expression levels and prognostic value of COMMD family genes. Simultaneously, employing the ssGSEA algorithm, we devised the COMMDs score. Enrichment analysis, gene mutations, and clinical features were incorporated into the assessment of this score. Furthermore, we contextualized the COMMDs score within the framework of the immune microenvironment, evaluating the relationship between the COMMDs family and immune factors as well as immune cells. The results suggest a correlation between the COMMDs score and various immune-related features. Based on this foundation, multiple machine learning approaches indicated Logistic Regression, with a remarkable ROC of 0.972, as the optimal diagnostic model. To accentuate the translational medical value of the COMMDs family, we selected COMMD10 as a differential gene in gastric cancer for further validation. Functional experiments revealed a decline in the proliferative and migratory capabilities of gastric cancer cells upon silencing COMMD10. Additionally, through pathway intervention, we unveiled the PI3K-AKT pathway as a potential mechanism through which COMMD10 influences gastric cancer activity. In summary, our study affirms the prospective role of the COMMDs family as potential markers for the diagnosis and treatment of gastric cancer in the future.
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Affiliation(s)
- Rong Wan
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lujuan Pan
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, No.18 Zhongshan 2nd Road, Baise, Guangxi, China
- Key Laboratory of Tumor Molecular Pathology of Baise, Guangxi, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Guanliang Shen
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - RuoNan Guo
- Department of Laboratory, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Yueqiu Qin
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, No.18 Zhongshan 2nd Road, Baise, Guangxi, China
| | - Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Ruo Wang
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Fan
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
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Dong X, Wang L, Wang D, Yu M, Yang XJ, Cai H. Proteomic study on nintedanib in gastric cancer cells. PeerJ 2024; 12:e16771. [PMID: 38406279 PMCID: PMC10893871 DOI: 10.7717/peerj.16771] [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: 08/02/2023] [Accepted: 12/18/2023] [Indexed: 02/27/2024] Open
Abstract
Background Gastric cancer is a very common gastrointestinal tumor with a high mortality rate. Nintedanib has been shown to significantly reduce tumor cell proliferation and increase apoptosis in gastric cancer cells in vitro. However, its systemic action mechanism on gastric cancer cells remains unclear. A high-throughput proteomic approach should help identify the potential mechanisms and targets of nintedanib on gastric cancer cells. Methods The effects of nintedanib on the biological behavior of gastric cancer cells were evaluated. A cytotoxic proliferation assay was performed to estimate the half maximal inhibitory concentration (IC50). AGS cells were divided into control, and nintedanib-treated groups (5 µM, 48 h), and differential protein expression was investigated using tandem mass tags (TMT) proteomics. The molecular mechanisms of these differentially expressed proteins and their network interactions were then analyzed using bioinformatics, and potential nintedanib targets were identified. Results This study identified 845 differentially expressed proteins in the nintedanib-treated group (compared to the control group), comprising 526 up-regulated and 319 down-regulated proteins. Bioinformatics analysis revealed that the differentially expressed proteins were primarily enriched in biological pathways for branched-chain amino acid metabolism, steroid biosynthesis, propionate metabolism, fatty acid metabolism, lysosome, peroxisome, and ferroptosis. Key driver analysis revealed that proteins, such as enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH), isocitrate dehydrogenase 1 (IDH1), acyl-CoA oxidase 1 (ACOX1), acyl-CoA oxidase 2 (ACOX2), acyl-CoA oxidase 3 (ACOX3), and acetyl-CoA acyltransferase 1 (ACAA1) could be linked with nintedanib action. Conclusion Nintedanib inhibits the proliferation, invasion, and metastasis of gastric cancer cells. The crossover pathways and protein networks predicted by proteomics should provide more detailed molecular information enabling the use of nintedanib against gastric cancer.
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Affiliation(s)
- Xiaohua Dong
- The First School of Clinical Medicine, Lanzhou University, LanZhou, China
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province and NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, LanZhou, China
| | - Liuli Wang
- The First School of Clinical Medicine, Lanzhou University, LanZhou, China
| | - Da Wang
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
| | - Miao Yu
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province and NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, LanZhou, China
| | - Xiao jun Yang
- The First School of Clinical Medicine, Lanzhou University, LanZhou, China
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province and NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, LanZhou, China
| | - Hui Cai
- The First School of Clinical Medicine, Lanzhou University, LanZhou, China
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province and NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, LanZhou, China
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Zhang L, Deng Y, Yang J, Deng W, Li L. Neurotransmitter receptor-related gene signature as potential prognostic and therapeutic biomarkers in colorectal cancer. Front Cell Dev Biol 2023; 11:1202193. [PMID: 38099288 PMCID: PMC10720326 DOI: 10.3389/fcell.2023.1202193] [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: 04/07/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Background: Colorectal cancer is one of the most common malignant tumors worldwide. A various of neurotransmitter receptors have been found to be expressed in tumor cells, and the activation of these receptors may promote tumor growth and metastasis. This study aimed to construct a novel neurotransmitter receptor-related genes signature to predict the survival, immune microenvironment, and treatment response of colorectal cancer patients. Methods: RNA-seq and clinical data of colorectal cancer from The Cancer Genome Atlas database and Gene Expression Omnibus were downloaded. Neurotransmitter receptor-related gene were collected from publicly available data sources. The Weighted Gene Coexpression Network Analysis (WGCNA), Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression, Support Vector Machine-Recursive Feature Elimination (SVM-RFE), and Random Forest (RF) algorithms were employed to construct the Neurotransmitter receptor-related gene prognostic signature. Further analyses, functional enrichment, CIBERSORTx, The Tumor Immune Single Cell Center (TISCH), survival analysis, and CellMiner, were performed to analyze immune status and treatment responses. Quantitative real-time polymerase chain reaction (qRT-PCR) assays were carried out to confirm the expression levels of prognostic genes. Results: By combining machine learning algorithm and WGCNA, we identified CHRNA3, GABRD, GRIK3, and GRIK5 as Neurotransmitter receptor-related prognostic genes signature. Functional enrichment analyses showed that these genes were enriched with cellular metabolic-related pathways, such as organic acid, inorganic acid, and lipid metabolism. CIBERSORTx and Single cell analysis showed that the high expression of genes were positively correlated with immunosuppressive cells infiltration, and the genes were mainly expressed in cancer-associated fibroblasts and endothelial cells. A nomogram was further built to predict overall survival (OS). The expression of CHRNA3, GABRD, GRIK3, and GRIK5 in cancer cells significantly impacted their response to chemotherapy. Conclusion: A neurotransmitter receptor-related prognostic gene signature was developed and validated in the current study, giving novel sights of neurotransmitter in predicting the prognostic and improving the treatment of CRC.
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Affiliation(s)
- Linjie Zhang
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yizhang Deng
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jingbang Yang
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wuguo Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Liren Li
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 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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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: 6] [Impact Index Per Article: 6.0] [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 K, Liu Y, Luo H, Wang T. Efferocytosis signatures as prognostic markers for revealing immune landscape and predicting immunotherapy response in hepatocellular carcinoma. Front Pharmacol 2023; 14:1218244. [PMID: 37383726 PMCID: PMC10294713 DOI: 10.3389/fphar.2023.1218244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a highly lethal liver cancer with late diagnosis; therefore, the identification of new early biomarkers could help reduce mortality. Efferocytosis, a process in which one cell engulfs another cell, including macrophages, dendritic cells, NK cells, etc., plays a complex role in tumorigenesis, sometimes promoting and sometimes inhibiting tumor development. However, the role of efferocytosis-related genes (ERGs) in HCC progression has been poorly studied, and their regulatory effects in HCC immunotherapy and drug targeting have not been reported. Methods: We downloaded efferocytosis-related genes from the Genecards database and screened for ERGs that showed significant expression changes between HCC and normal tissues and were associated with HCC prognosis. Machine learning algorithms were used to study prognostic gene features. CIBERSORT and pRRophetic R packages were used to evaluate the immune environment of HCC subtypes and predict treatment response. CCK-8 experiments conducted on HCC cells were used to assess the reliability of drug sensitivity prediction. Results: We constructed a prognostic prediction model composed of six genes, and the ROC curve showed good predictive accuracy of the risk model. In addition, two ERG-related subgroups in HCC showed significant differences in tumor immune landscape, immune response, and prognostic stratification. The CCK-8 experiment conducted on HCC cells confirmed the reliability of drug sensitivity prediction. Conclusion: Our study emphasizes the importance of efferocytosis in HCC progression. The risk model based on efferocytosis-related genes developed in our study provides a novel precision medicine approach for HCC patients, allowing clinicians to customize treatment plans based on unique patient characteristics. The results of our investigation carry noteworthy implications for the development of individualized treatment approaches involving immunotherapy and chemotherapy, thereby potentially facilitating the realization of personalized and more efficacious therapeutic interventions for HCC.
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Affiliation(s)
- Ke Xu
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Yu Liu
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Huiyan Luo
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Tengfei Wang
- Department of Equipment, Bishan Hospital of Chongqing, Chongqing, China
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