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Zhao G, Zhao J, Lang J, Sun G. Activation of NFE2L2 Alleviates Endoplasmic Reticulum Stress-Mediated Pyroptosis in Murine Hippocampus: A Bioinformatics Analysis and Experimental Validation. Mol Neurobiol 2024:10.1007/s12035-024-04371-6. [PMID: 39046701 DOI: 10.1007/s12035-024-04371-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024]
Abstract
Pyroptosis has been implicated in many pathologic processes, including endoplasmic reticulum stress (ERS). However, the underlying mechanisms and molecular targets of ERS affecting pyroptosis still need further exploration. We obtained gene sets associated with ERS and pyroptosis, and the common genes were regarded as crosstalk genes linking ERS and pyroptosis. Protein-protein interaction (PPI) network was constructed, and the hub genes were obtained via Cytoscape. Moreover, to validate the efficacy of the therapeutic target, neurological tests, brain water content measurements, Nissl staining, Western blot, ELISA, TUNEL analyses, and transmission electron microscopy were performed in a mouse model. A total of 13 crosstalk genes were acquired, and enrichment analysis revealed that these genes were mainly enriched in stress-associated cellular processes and pathways, including KEAP1-NFE2L2 pathway. The hub gene, NFE2L2, was identified by Cytoscape, and tert-butylhydroquinone (tBHQ) was screened as candidate drug to activate NFE2L2. Western blot and ELISA results showed that activation of NFE2L2 could attenuate the expression of ERS and pyroptosis-related proteins by promoting nuclear translocation of Nrf2 (encoded by NFE2L2). Pathological evaluation by Nissl staining and TUNEL assay reflected a similar trend. Furthermore, activation of NFE2L2 ameliorated neurological deficits and reduced brain edema. In conclusion, our bioinformatic analysis results established the theoretical foundation of NFE2L2 as a promising therapeutic target. Moreover, in the mouse model, tBHQ pretreatment further confirmed the effectiveness of this target. We hypothesized NFE2L2 may play a key role in the progression of ERS-mediated pyroptosis. These findings may inspire new ideas to treat neurological disorders.
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Affiliation(s)
- Gengshui Zhao
- Department of Neurosurgery, Harrison International Peace Hospital Affiliated to Hebei Medical University, Hengshui, China
| | - Jianfei Zhao
- Department of Neurosurgery, The People's Hospital of Shijiazhuang City, Shijiazhuang, China
| | - Jiadong Lang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Guozhu Sun
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
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Zhao G, Zhao J, Lang J, Sun G. Activation of NFE2L2 Alleviates Endoplasmic Reticulum Stress-Mediated Pyroptosis in Murine Hippocampus: A Bioinformatics Analysis and Experimental Validation. Mol Neurobiol 2024. [DOI: org/10.1007/s12035-024-04371-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024]
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Huang Z, Chen X, Wang Y, Yuan J, Li J, Hang W, Meng H. SLC7A11 inhibits ferroptosis and downregulates PD-L1 levels in lung adenocarcinoma. Front Immunol 2024; 15:1372215. [PMID: 38655266 PMCID: PMC11035808 DOI: 10.3389/fimmu.2024.1372215] [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: 01/17/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Lung adenocarcinoma (LUAD) is a prevalent form of lung cancer originating from lung glandular cells with low survival rates despite recent therapeutic advances due to its diverse and complex nature. Recent evidence suggests a link between ferroptosis and the effectiveness of anti-PD-L1 therapy, with potential synergistic effects. Methods Our study comprehensively analyzed the expression patterns of ferroptosis regulators in LUAD and their association with prognosis and PD-L1 expression. Furthermore, we identified two distinct subtypes of LUAD through consensus clustering of ferroptosis regulators, revealing significant tumor heterogeneity, divergent PD-L1 expression, and varying prognoses between the subtypes. Results Among the selected ferroptosis regulators, SLC7A11 emerged as an independent prognostic marker for LUAD patients and exhibited a negative correlation with PD-L1 expression. Subsequent investigations revealed high expression of SLC7A11 in the LUAD population. In vitro experiments demonstrated that overexpression of SLC7A11 led to reduced PD-L1 expression and inhibited ferroptosis in A549 cells, underscoring the significant role of SLC7A11 in LUAD. Additionally, pan-cancer analyses indicated an association between SLC7A11 and the expression of immune checkpoint genes across multiple cancer types with poor prognoses. Discussion From a clinical standpoint, these findings offer a foundation for identifying and optimizing potential combination strategies to enhance the therapeutic effectiveness of immune checkpoint inhibitors and improve the prognosis of patients with LUAD.
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Affiliation(s)
- Zhenyao Huang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Xia Chen
- Department of Respiratory Medicine, Xuyi People’s Hospital, Huai’an, Jiangsu, China
| | - Yun Wang
- Department of Dermatology, the Affiliated Huai'an Hospital of Xuzhou Medical University, the Second People's Hospital of Huai’an, Huai’an, China
| | - Jiali Yuan
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Jing Li
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Wenlu Hang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Hao Meng
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
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Wei H, Yang J, Chen X, Liu M, Zhang H, Sun W, Wang Y, Zhou Y. BAIAP2L2 is a novel prognostic biomarker related to migration and invasion of HCC and associated with cuprotosis. Sci Rep 2023; 13:8692. [PMID: 37248248 DOI: 10.1038/s41598-023-35420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, and its pathophysiological mechanisms remain unknown. IRSp53 family members, such as BAIAP2L1, participate in the progression of multiple tumors. However, the role of BAIAP2L2 in HCC remains unclear. This study comprehensively analyzed the potential role of BAIAP2L2 in HCC using bioinformatic techniques. The expression of BAIAP2L2 in HCC was analyzed using The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), International Cancer Genome Consortium (ICGC), and Human Protein Atlas (HPA) databases and in vitro experiments. In addition, the prognostic value of BAIAP2L2 in HCC was analyzed using the TCGA database. TCGA and GEO database were used to analyze the role of BAIAP2L2 in immune features. We also explored the function of BAIAP2L2 in methylation and cuprotosis. The CellMiner database was used to analyze the relationship between BAIAP2L2 expression and drug sensitivity. Our study revealed that BAIAP2L2 is overexpressed in HCC and promotes the migration and invasion of HCC cells. BAIAP2L2 may affect the prognosis of HCC by regulating immunity, methylation, and cuprotosis. BAIAP2L2 is a novel HCC prognostic gene involved in immune infiltration associated with cuprotosis and may be a potential prognosis and therapeutic target for HCC.
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Affiliation(s)
- Hui Wei
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Jing Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Xia Chen
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Mengxiao Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Weiming Sun
- Department of Endocrinology, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Yuping Wang
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China.
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
| | - Yongning Zhou
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China.
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
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Chen MM, Guo W, Chen SM, Guo XZ, Xu L, Ma XY, Wang YX, Xie C, Meng LH. Xanthine dehydrogenase rewires metabolism and the survival of nutrient deprived lung adenocarcinoma cells by facilitating UPR and autophagic degradation. Int J Biol Sci 2023; 19:772-788. [PMID: 36778128 PMCID: PMC9909990 DOI: 10.7150/ijbs.78948] [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: 09/15/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Xanthine dehydrogenase (XDH) is the rate-limiting enzyme in purine catabolism by converting hypoxanthine to xanthine and xanthine to uric acid. The altered expression and activity of XDH are associated with the development and prognosis of multiple types of cancer, while its role in lung adenocarcinoma (LUAD) remains unknown. Herein, we demonstrated that XDH was highly expressed in LUAD and was significantly correlated with poor prognosis. Though inhibition of XDH displayed moderate effect on the viability of LUAD cells cultured in the complete medium, it significantly attenuated the survival of starved cells. Similar results were obtained in XDH-knockout cells. Nucleosides supplementation rescued the survival of starved LUAD cells upon XDH inhibition, while inhibition of purine nucleoside phosphorylase abrogated the process, indicating that nucleoside degradation is required for the XDH-mediated survival of LUAD cells. Accordingly, metabolic flux revealed that ribose derived from nucleoside fueled key carbon metabolic pathways to sustain the survival of starved LUAD cells. Mechanistically, down-regulation of XDH suppressed unfolded protein response (UPR) and autophagic flux in starved LUAD cells. Inhibition of XDH decreased the level of amino acids produced by autophagic degradation, which was accompanied with down-regulation of mTORC1 signaling. Supplementation of amino acids including glutamine or glutamate rescued the survival of starved LUAD cells upon knockout or inhibition of XDH. Finally, XDH inhibitors potentiated the anti-cancer activity of 2-deoxy-D-glucose that induced UPR and/or autophagy in vitro and in vivo. In summary, XDH plays a crucial role in the survival of starved LUAD cells and targeting XDH may improve the efficacy of drugs that induce UPR and autophagy in the therapy of LUAD.
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Affiliation(s)
- Man-Man Chen
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Guo
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Meng Chen
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Xiao-Zhen Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Lan Xu
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Xiao-Yu Ma
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu-Xiang Wang
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Cen Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling-Hua Meng
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Missner AA, Johns JD, Gu S, Hoa M. Repurposable Drugs That Interact with Steroid Responsive Gene Targets for Inner Ear Disease. Biomolecules 2022; 12:1641. [PMID: 36358991 PMCID: PMC9687275 DOI: 10.3390/biom12111641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/25/2022] [Accepted: 11/02/2022] [Indexed: 10/28/2023] Open
Abstract
Corticosteroids, oral or transtympanic, remain the mainstay for inner ear diseases characterized by hearing fluctuation or sudden changes in hearing, including sudden sensorineural hearing loss (SSNHL), Meniere's disease (MD), and autoimmune inner ear disease (AIED). Despite their use across these diseases, the rate of complete recovery remains low, and results across the literature demonstrates significant heterogeneity with respect to the effect of corticosteroids, suggesting a need to identify more efficacious treatment options. Previously, our group has cross-referenced steroid-responsive genes in the cochlea with published single-cell and single-nucleus transcriptome datasets to demonstrate that steroid-responsive differentially regulated genes are expressed in spiral ganglion neurons (SGN) and stria vascularis (SV) cell types. These differentially regulated genes represent potential druggable gene targets. We utilized multiple gene target databases (DrugBank, Pharos, and LINCS) to identify orally administered, FDA approved medications that potentially target these genes. We identified 42 candidate drugs that have been shown to interact with these genes, with an emphasis on safety profile, and tolerability. This study utilizes multiple databases to identify drugs that can target a number of druggable genes in otologic disorders that are commonly treated with steroids, providing a basis for establishing novel repurposing treatment trials.
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Affiliation(s)
| | - James Dixon Johns
- Department of Otolaryngology-Head and Neck Surgery, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Shoujun Gu
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Hoa
- Department of Otolaryngology-Head and Neck Surgery, Georgetown University Medical Center, Washington, DC 20007, USA
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Han X, Long W, Liu Y, Xu J. Prognostic value and immunological role of BAIAP2L2 in liver hepatocellular carcinoma: A pan-cancer analysis. Front Surg 2022; 9:985034. [PMID: 36338652 PMCID: PMC9634486 DOI: 10.3389/fsurg.2022.985034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/28/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND In recent years, the role of BAI1-associated protein 2-like 2 (BAIAP2L2) in the prognosis and immune microenvironment of various cancers has attracted increasing attention. However, its clinical value and immune infiltration in liver hepatocellular carcinoma (LIHC) remain unclear. OBJECTIVE To investigate the prognostic value of BAIAP2L2 and its correlation with immune infiltration in LIHC, we conducted corresponding data mining. METHODS In this study, The Cancer Genome Atlas, GTEx, StarBase, UALCAN, TIMER, GEPIA, Human Protein Atlas, Kaplan-Meier Plotter, cBioPortal, LinkedOmics, STRING and BioGPS databases were used to analyze BAIAP2L2 in cancers. Logistic regression and Cox regression were performed to analyze the correlation between clinical features and BAIAP2L2 expression in LIHC. In addition, the diagnostic and prognostic values of BAIAP2L2 in LIHC were determined by receiver operating characteristic (ROC) curves and nomograms. Single-sample gene set enrichment analysis (ssGSEA), BioGPS and TIMER were used to analyze the correlation between BAIAP2L2 and immune infiltration. More importantly, quantitative real-time polymerase chain reaction was used to verify BAIAP2L2 expression in a liver cancer cell line and a normal cell line. Visualization of data was mostly achieved using R language, version 3.6.3. RESULTS High BAIAP2L2 levels indicated poor overall survival (OS) and disease-free survival (DFS) of patients with LIHC. Abnormally increased expression of BAIAP2L2 in LIHC may be the result of both genetic alterations and lower DNA methylation levels. Furthermore, Cox regression analysis showed that high BAIAP2L2 expression was an independent risk factor for OS and DFS in patients with liver cancer. ROC curves and nomograms also confirmed the diagnostic and prognostic values of BAIAP2L2 in LIHC. Additionally, a PPI network of BAIAP2L2 was established and results implyed that BAIAP2L2 interacts with MTSS1, AMPH, FCHO1, SYT9, PDK2, MTSS1L, PM20D1, CHST4 and PALM3. ssGSEA showed that BAIAP2L2 was associated with T cells and natural killer cells. Simultaneously, the TIMER database showed that the expression of BAIAP2L2 in LIHC was positively correlated with tumor infiltrating cells, including B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells. CONCLUSIONS Through pan-cancer analysis, prognostic and immunological value of BAIAP2L2 in LIHC was identified. This is the first report on the potential of BAIAP2L2 as a prognostic biomarker and its correlation with immune infiltration in LIHC.
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Affiliation(s)
- Xiudan Han
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, China,Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, China
| | - Wei Long
- Department of Rheumatology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ying Liu
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, China,Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, China
| | - Jixiong Xu
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanchang University, Nanchang, China,Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, China,Jiangxi Branch of National Clinical Research Center for Metabolic Disease, Nanchang, China,Correspondence: Jixiong Xu
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8
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Chen MM, Meng LH. The double faced role of xanthine oxidoreductase in cancer. Acta Pharmacol Sin 2022; 43:1623-1632. [PMID: 34811515 PMCID: PMC9253144 DOI: 10.1038/s41401-021-00800-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/19/2021] [Indexed: 01/02/2023] Open
Abstract
Xanthine oxidoreductase (XOR) is a critical, rate-limiting enzyme that controls the last two steps of purine catabolism by converting hypoxanthine to xanthine and xanthine to uric acid. It also produces reactive oxygen species (ROS) during the catalytic process. The enzyme is generally recognized as a drug target for the therapy of gout and hyperuricemia. The catalytic products uric acid and ROS act as antioxidants or oxidants, respectively, and are involved in pro/anti-inflammatory actions, which are associated with various disease manifestations, including metabolic syndrome, ischemia reperfusion injury, cardiovascular disorders, and cancer. Recently, extensive efforts have been devoted to understanding the paradoxical roles of XOR in tumor promotion. Here, we summarize the expression of XOR in different types of cancer and decipher the dual roles of XOR in cancer by its enzymatic or nonenzymatic activity to provide an updated understanding of the mechanistic function of XOR in cancer. We also discuss the potential to modulate XOR in cancer therapy.
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Affiliation(s)
- Man-man Chen
- grid.9227.e0000000119573309Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ling-hua Meng
- grid.9227.e0000000119573309Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
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Wang G, Hu W, Chen Y, Wan Y, Li Q. Integrated mPD-L1 and metabolic analysis identifies new prognostic subgroups in lung cancers with wild-type EGFR. Clin Transl Med 2021; 11:e612. [PMID: 34923764 PMCID: PMC8684767 DOI: 10.1002/ctm2.612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Affiliation(s)
- Guosheng Wang
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.,The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, New York, USA
| | - Weilei Hu
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Yundi Chen
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, New York, USA
| | - Yuan Wan
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, New York, USA
| | - Qiang Li
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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Deep Radiotranscriptomics of Non-Small Cell Lung Carcinoma for Assessing Molecular and Histology Subtypes with a Data-Driven Analysis. Diagnostics (Basel) 2021; 11:diagnostics11122383. [PMID: 34943617 PMCID: PMC8700168 DOI: 10.3390/diagnostics11122383] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022] Open
Abstract
Radiogenomic and radiotranscriptomic studies have the potential to pave the way for a holistic decision support system built on genomics, transcriptomics, radiomics, deep features and clinical parameters to assess treatment evaluation and care planning. The integration of invasive and routine imaging data into a common feature space has the potential to yield robust models for inferring the drivers of underlying biological mechanisms. In this non-small cell lung carcinoma study, a multi-omics representation comprised deep features and transcriptomics was evaluated to further explore the synergetic and complementary properties of these diverse multi-view data sources by utilizing data-driven machine learning models. The proposed deep radiotranscriptomic analysis is a feature-based fusion that significantly enhances sensitivity by up to 0.174 and AUC by up to 0.22, compared to the baseline single source models, across all experiments on the unseen testing set. Additionally, a radiomics-based fusion was also explored as an alternative methodology yielding radiomic signatures that are comparable to several previous publications in the field of radiogenomics. Furthermore, the machine learning multi-omics analysis based on deep features and transcriptomics achieved an AUC performance of up to 0.831 ± 0.09/0.925 ± 0.04 for the examined molecular and histology subtypes analysis, respectively. The clinical impact of such high-performing models can add prognostic value and lead to optimal treatment assessment by targeting specific oncogenes, namely the response of tyrosine kinase inhibitors of EGFR mutated or predicting the chemotherapy resistance of KRAS mutated tumors.
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Zhu L, Guo W. Combined DNA Methylation and Transcriptomic Assessments to Determine a Prognostic Model for PD-1-Negative Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:708819. [PMID: 34458266 PMCID: PMC8385720 DOI: 10.3389/fcell.2021.708819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) has the highest incidence and mortality of any malignancy in the world. Immunotherapy has been a major breakthrough for HCC treatment, but immune checkpoint inhibitors (ICIs) are effective in only a small percentage of HCC patients. In the present study, we screened programmed cell death protein 1 (PD-1) -negative HCC samples, which are frequently resistant to ICIs, and identified their methylation and transcription characteristics through the assessment of differential gene methylation and gene expression. We also screened for potential targeted therapeutic drugs using the DrugBank database. Finally, we used a LASSO (least absolute shrinkage and selection operator) regression analysis to construct a prognostic model based on three differentially methylated and expressed genes (DMEGs). The results showed that ESTIMATE (Estimation of Stromal and Immune Cells in Malignant Tumors using Expression Data) scores for the tumor samples were significantly lower compared to normal sample ESTIMATE scores. In addition, we identified 31 DMEGs that were able to distinguish PD-1-negative samples from normal samples. A functional enrichment analysis showed that these genes were involved in a variety of tumor-related pathways and immune-related pathways, and the DrugBank screening identified potential therapeutic drugs. Finally, the prognostic model based on three DMEGs (UBD, CD5L, and CD213A2) demonstrated good predictive power for HCC prognosis and was verified using an independent cohort. The present study demonstrated the methylation characteristics of PD-1-negative HCC samples, identified several potential therapeutic drugs, and proposed a prognostic model based on UBD, CD5L, and CD213A2 methylation expression. In conclusion, this work provides an in-depth understanding of methylation in HCC samples that are not sensitive to ICIs.
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Affiliation(s)
- Lixu Zhu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
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Avery-Kiejda KA. Switching off Cancer: Is There a Role for Epigenetics? Cancers (Basel) 2021; 13:cancers13061272. [PMID: 33809396 PMCID: PMC7998574 DOI: 10.3390/cancers13061272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Affiliation(s)
- Kelly A. Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia;
- Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
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Song Y, Zhuang G, Li J, Zhang M. BAIAP2L2 facilitates the malignancy of prostate cancer (PCa) via VEGF and apoptosis signaling pathways. Genes Genomics 2021; 43:421-432. [PMID: 33646530 DOI: 10.1007/s13258-021-01061-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Prostate cancer (PCa) is the second most common type of male cancer in western. Despite key roles of brain-specific angiogenesis inhibitor 1-associated protein like 2 (BAIAP2L2) in several cancers, the function of BAIAP2L2 in PCa is never reported. OBJECTIVE We aimed to investigate the role of BAIAP2L2 in the progression of PCa and decipher the underlying mechanisms. METHODS RNA sequencing data from TCGA database were used to evaluate the expression of BAIAP2L2 in PCa. Survival analysis and Cox regression model analysis were conducted to evaluate the prognostic value of BAIAP2L2. BAIAP2L2-associated pathways were preliminary analyzed by Gene Set Enrichment Analysis (GSEA) method and confirmed by western blot assays. Cell proliferation and transwell assays were performed to determine biological behaviors in BAIAP2L2 knocked-down or overexpressed PCa cell lines including LNCaP and PC-3 cells. RESULTS In our study, BAIAP2L2 was significantly up-regulated in PCa tissues and cell lines and independently associated with the poor prognosis of PCa patients. Knockdown of BAIAP2L2 notably repressed proliferation, migration and invasion of PCa cells. And overexpression of BAIAP2L2 obtained the contrary results. Mechanically, GSEA method and western blot results of key molecules in signaling pathways implicated that the depletion of BAIAP2L2 inactivated the vascular endothelial growth factors (VEGFs) and induced apoptosis signaling pathways in PCa cells. CONCLUSIONS Overall, these findings revealed that BAIAP2L2 may support tumorigenesis and malignant development of prostate cancer cells via VEGF and apoptosis signaling pathways, and it could be considered as a promising biomarker and independent prognostic predictor of prostate cancer.
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Affiliation(s)
- Yuanzi Song
- Department of Urology, Zibo First Hospital, Emeishan East Road, Zibo, China
| | - Guishan Zhuang
- Department of Urology, Weifang People's Hospital, 151 Guangwen Street, Kuiwen District, Weifang, 261041, Shandong, China
| | - Jiazhen Li
- Intravenous Medication Center of Binzhou People's Hospital, Binzhou, Shandong, China
| | - Mingqing Zhang
- Department of Urology, Weifang People's Hospital, 151 Guangwen Street, Kuiwen District, Weifang, 261041, Shandong, China.
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