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Yu TY, Zhan ZJ, Lin Q, Huang ZH. Computed tomography-based radiomics predicts the fibroblast-related gene EZH2 expression level and survival of hepatocellular carcinoma. World J Clin Cases 2024; 12:5568-5582. [DOI: 10.12998/wjcc.v12.i24.5568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/21/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common subtype of liver cancer. The primary treatment strategies for HCC currently include liver transplantation and surgical resection. However, these methods often yield unsatisfactory outcomes, leading to a poor prognosis for many patients. This underscores the urgent need to identify and evaluate novel therapeutic targets that can improve the prognosis and survival rate of HCC patients.
AIM To construct a radiomics model that can accurately predict the EZH2 expression in HCC.
METHODS Gene expression, clinical parameters, HCC-related radiomics, and fibroblast-related genes were acquired from public databases. A gene model was developed, and its clinical efficacy was assessed statistically. Drug sensitivity analysis was conducted with identified hub genes. Radiomics features were extracted and machine learning algorithms were employed to generate a radiomics model related to the hub genes. A nomogram was used to illustrate the prognostic significance of the computed Radscore and the hub genes in the context of HCC patient outcomes.
RESULTS EZH2 and NRAS were independent predictors for prognosis of HCC and were utilized to construct a predictive gene model. This model demonstrated robust performance in diagnosing HCC and predicted an unfavorable prognosis. A negative correlation was observed between EZH2 expression and drug sensitivity. Elevated EZH2 expression was linked to poorer prognosis, and its diagnostic value in HCC surpassed that of the risk model. A radiomics model, developed using a logistic algorithm, also showed superior efficiency in predicting EZH2 expression. The Radscore was higher in the group with high EZH2 expression. A nomogram was constructed to visually demonstrate the significant roles of the radiomics model and EZH2 expression in predicting the overall survival of HCC patients.
CONCLUSION EZH2 plays significant roles in diagnosing HCC and therapeutic efficacy. A radiomics model, developed using a logistic algorithm, efficiently predicted EZH2 expression and exhibited strong correlation with HCC prognosis.
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Affiliation(s)
- Ting-Yu Yu
- Department of Radiology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan 364000, Fujian Province, China
| | - Ze-Juan Zhan
- Department of Radiology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan 364000, Fujian Province, China
| | - Qi Lin
- Department of Radiology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan 364000, Fujian Province, China
| | - Zhen-Huan Huang
- Department of Radiology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan 364000, Fujian Province, China
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Lou QM, Lai FF, Li JW, Mao KJ, Wan HT, He Y. Mechanisms of cuproptosis and its relevance to distinct diseases. Apoptosis 2024; 29:981-1006. [PMID: 38824478 DOI: 10.1007/s10495-024-01983-0] [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] [Accepted: 05/21/2024] [Indexed: 06/03/2024]
Abstract
Copper is a trace element required by the organism, but once the level of copper exceeds the threshold, it becomes toxic and even causes death. The underlying mechanisms of copper-induced death are inconclusive, with different studies showing different opinions on the mechanism of copper-induced death. Multiple investigations have shown that copper induces oxidative stress, endoplasmic reticulum stress, nucleolar stress, and proteasome inhibition, all of which can result in cell death. The latest research elucidates a copper-dependent death and denominates it as cuproptosis. Cuproptosis takes place through the combination of copper and lipoylated proteins of the tricarboxylic acid cycle, triggering agglomeration of lipoylated proteins and loss of iron-sulfur cluster proteins, leading to proteotoxic stress and ultimately death. Given the toxicity and necessity of copper, abnormal levels of copper lead to diseases such as neurological diseases and cancer. The development of cancer has a high demand for copper, neurological diseases involve the change of copper contents and the binding of copper to proteins. There is a close relationship between these two kinds of diseases and copper. Here, we summarize the mechanisms of copper-related death, and the association between copper and diseases, to better figure out the influence of copper in cell death and diseases, thus advancing the clinical remedy of these diseases.
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Affiliation(s)
- Qiao-Mei Lou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Fei-Fan Lai
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jing-Wei Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Kun-Jun Mao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Hai-Tong Wan
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Yu He
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
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Chinnappan R, Makhzoum T, Arai M, Hajja A, Abul Rub F, Alodhaibi I, Alfuwais M, Elahi MA, Alshehri EA, Ramachandran L, Mani NK, Abrahim S, Mir MS, Al-Kattan K, Mir TA, Yaqinuddin A. Recent Advances in Biosensor Technology for Early-Stage Detection of Hepatocellular Carcinoma-Specific Biomarkers: An Overview. Diagnostics (Basel) 2024; 14:1519. [PMID: 39061656 PMCID: PMC11276200 DOI: 10.3390/diagnostics14141519] [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: 06/06/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Hepatocellular carcinoma is currently the most common malignancy of the liver. It typically occurs due to a series of oncogenic mutations that lead to aberrant cell replication. Most commonly, hepatocellular carcinoma (HCC) occurs as a result of pre-occurring liver diseases, such as hepatitis and cirrhosis. Given its aggressive nature and poor prognosis, the early screening and diagnosis of HCC are crucial. However, due to its plethora of underlying risk factors and pathophysiologies, patient presentation often varies in the early stages, with many patients presenting with few, if any, specific symptoms in the early stages. Conventionally, screening and diagnosis are performed through radiological examination, with diagnosis confirmed by biopsy. Imaging modalities tend to be limited by their requirement of large, expensive equipment; time-consuming operation; and a lack of accurate diagnosis, whereas a biopsy's invasive nature makes it unappealing for repetitive use. Recently, biosensors have gained attention for their potential to detect numerous conditions rapidly, cheaply, accurately, and without complex equipment and training. Through their sensing platforms, they aim to detect various biomarkers, such as nucleic acids, proteins, and even whole cells extracted by a liquid biopsy. Numerous biosensors have been developed that may detect HCC in its early stages. We discuss the recent updates in biosensing technology, highlighting its competitive potential compared to conventional methodology and its prospects as a tool for screening and diagnosis.
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Affiliation(s)
- Raja Chinnappan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Tariq Makhzoum
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Momo Arai
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Amro Hajja
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Farah Abul Rub
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Ibrahim Alodhaibi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Mohammed Alfuwais
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Muhammad Affan Elahi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
| | - Eman Abdullah Alshehri
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Lohit Ramachandran
- Microfluidics, Sensors & Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; (L.R.); (N.K.M.)
| | - Naresh Kumar Mani
- Microfluidics, Sensors & Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; (L.R.); (N.K.M.)
| | - Shugufta Abrahim
- Graduate School of Science and Engineering for Education, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan;
| | - Mohammad Shabab Mir
- School of Pharmacy, Desh Bhagat University, Mandi Gobindgarh 147301, Punjab, India;
| | - Khaled Al-Kattan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
- Lung Health Centre Department, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Tanveer Ahmad Mir
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (T.M.); (M.A.); (A.H.); (F.A.R.); (I.A.); (M.A.); (M.A.E.); (K.A.-K.); (T.A.M.)
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Guo Z, Liu J, Liang G, Liang H, Zhong M, Tomlinson S, He S, Ouyang G, Yuan G. Identification and validation of cuproptosis-related genes in acetaminophen-induced liver injury using bioinformatics analysis and machine learning. Front Immunol 2024; 15:1371446. [PMID: 38994365 PMCID: PMC11236684 DOI: 10.3389/fimmu.2024.1371446] [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: 01/16/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Background Acetaminophen (APAP) is commonly used as an antipyretic analgesic. However, acetaminophen overdose may contribute to liver injury and even liver failure. Acetaminophen-induced liver injury (AILI) is closely related to mitochondrial oxidative stress and dysfunction, which play critical roles in cuproptosis. Here, we explored the potential role of cuproptosis-related genes (CRGs) in AILI. Methods The gene expression profiles were obtained from the Gene Expression Omnibus database. The differential expression of CRGs was determined between the AILI and control samples. Protein protein interaction, correlation, and functional enrichment analyses were performed. Machine learning was used to identify hub genes. Immune infiltration was evaluated. The AILI mouse model was established by intraperitoneal injection of APAP solution. Quantitative real-time PCR and western blotting were used to validate hub gene expression in the AILI mouse model. The copper content in the mouse liver samples and AML12 cells were quantified using a colorimetric assay kit. Ammonium tetrathiomolybdate (ATTM), was administered to mouse models and AML12 cells in order to investigate the effects of copper chelator on AILI. Results The analysis identified 7,809 differentially expressed genes, 4,245 of which were downregulated and 3,564 of which were upregulated. Four optimal feature genes (OFGs; SDHB, PDHA1, NDUFB2, and NDUFB6) were identified through the intersection of two machine learning algorithms. Further nomogram, decision curve, and calibration curve analyses confirmed the diagnostic predictive efficacy of the four OFGs. Enrichment analysis indicated that the OFGs were involved in multiple pathways, such as IL-17 pathway and chemokine signaling pathway, that are related to AILI progression. Immune infiltration analysis revealed that macrophages were more abundant in AILI than in control samples, whereas eosinophils and endothelial cells were less abundant. Subsequently, the AILI mouse model was successfully established, and histopathological analysis using hematoxylin-eosin staining along with liver function tests revealed a significant induction of liver injury in the APAP group. Consistent with expectations, both mRNA and protein levels of the four OFGs exhibited a substantial decrease. The administration of ATTAM effectively mitigates copper elevation induced by APAP in both mouse model and AML12 cells. However, systemic administration of ATTM did not significantly alleviate AILI in the mouse model. Conclusion This study first revealed the potential role of CRGs in the pathological process of AILI and offered novel insights into its underlying pathogenesis.
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Affiliation(s)
- Zhenya Guo
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases (Guangxi Medical University), Nanning, Guangxi, China
| | - Jiaping Liu
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases (Guangxi Medical University), Nanning, Guangxi, China
| | - Guozhi Liang
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases (Guangxi Medical University), Nanning, Guangxi, China
| | - Haifeng Liang
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases (Guangxi Medical University), Nanning, Guangxi, China
| | - Mingbei Zhong
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases (Guangxi Medical University), Nanning, Guangxi, China
| | - Stephen Tomlinson
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States
| | - Songqing He
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases (Guangxi Medical University), Nanning, Guangxi, China
| | - Guoqing Ouyang
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases (Guangxi Medical University), Nanning, Guangxi, China
| | - Guandou Yuan
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases (Guangxi Medical University), Nanning, Guangxi, China
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Xin S, Su J, Li R, Cao Q, Wang H, Wei Z, Wang C, Zhang C, Zhang J, Zhang Z, Li G, Qin W. Prognostic and therapeutic model based on disulfidptosis-related genes for patients with clear cell renal cell carcinoma. Heliyon 2024; 10:e32258. [PMID: 38882384 PMCID: PMC11180324 DOI: 10.1016/j.heliyon.2024.e32258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
Disulfidptosis, a newly discovered mode of cell death caused by excessive accumulation of intracellular disulfide compounds, is closely associated with tumor development. This study focused on the relationship between disulfidptosis and clear cell renal cell carcinoma (ccRCC). Firstly, the characterizations of disulfidptosis-related genes (DRGs) in ccRCC were showed, which included number variation (CNV), single nucleotide variation (SNV), DNA methylation, mRNA expression and gene mutation. Then, the ccRCC samples were classified into three clusters through unsupervised clustering based on DRGs. Survival and pathway enrichment differences were evaluated among the three clusters. Subsequently, the differentially expressed genes (DEGs) among the three clusters were screened by univariate Cox, LASSO, and multivariate Cox analysis, and five key DEGs were obtained. Based on the five key DEGs, the ccRCC samples were reclassified into two geneclusters and the survival differences and immune cell infiltration between two geneclusters was investigated. In next step, ccRCC samples were divided into two groups according to PCA scores of five key DEGs, namely high PCA score group (HPSG) and low PCA score group (LPSG). On this basis, differences in survival prognosis, immune cell infiltration and correlation with immune checkpoint, as well as differences in sensitivity to targeted drugs were compared between HPSG and LPSG. The expression levels of four immune checkpoints were higher in HPSG than in LPSG, whereas the LPSG was more sensitive to targeted drug therapy than the HPSG. Finally, validation experiments on HDAC4 indicated that HDAC4 could increase the proliferation and colony formation ability of ccRCC cells.
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Affiliation(s)
- Shiyong Xin
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Junjie Su
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Ruixin Li
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Qiong Cao
- Department of Pathology, The Third Affiliated Hospital of Henan University of Science and Technology, 471003, China
| | - Haojie Wang
- Department of Central Laboratory, Zhengzhou University, Luoyang Central Hospital, Luoyang, 471003, China
| | - Zhihao Wei
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, 471023, China
| | - Chengliang Wang
- Department of Urology, Shangcheng County People's Hospital, Xinyang, 464000, China
| | - Chengdong Zhang
- Department of Urology, Xinxiang City First People's Hospital, Xinxiang, 453000, China
| | - Jianguo Zhang
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Zheng Zhang
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Guanyu Li
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Wang Qin
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
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Wu H, Yang Z, Chang C, Wang Z, Zhang D, Guo Q, Zhao B. A novel disulfide death-related genes prognostic signature identifies the role of IPO4 in glioma progression. Cancer Cell Int 2024; 24:168. [PMID: 38734657 PMCID: PMC11088110 DOI: 10.1186/s12935-024-03358-6] [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: 11/06/2023] [Accepted: 05/06/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND "Disulfide death," a form of cellular demise, is triggered by the abnormal accumulation of intracellular disulfides under conditions of glucose deprivation. However, its role in the prognosis of glioma remains undetermined. Therefore, the main objective of this study is to establish prognostic signature based on disulfide death-related genes (DDRGs) and to provide new solutions in choosing the effective treatment of glioma. METHODS The RNA transcriptome, clinical information, and mutation data of glioma samples were sourced from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), while normal samples were obtained from the Genotype-Tissue Expression (GTEx). DDRGs were compiled from previous studies and selected through differential analysis and univariate Cox regression analysis. The molecular subtypes were determined through consensus clustering analysis. Further, LASSO analysis was employed to select characteristic genes, and subsequently, a risk model comprising seven DDRGs was constructed based on multivariable Cox analysis. Kaplan-Meier survival curves were employed to assess survival differences between high and low-risk groups. Additionally, functional analyses (GO, KEGG, GSEA) were conducted to explore the potential biological functions and signaling pathways of genes associated with the model. The study also explored immune checkpoint (ICP) genes, immune cell infiltration levels, and immune stromal scores. Finally, the effect of Importin-4(IPO4) on glioma has been further confirmed through RT-qPCR, Western blot, and cell functional experiments. RESULTS 7 genes associated with disulfide death were obtained and two subgroups of patients with different prognosis and clinical characteristics were identified. Risk signature was subsequently developed and proved to serve as an prognostic predictor. Notably, the high-risk group exhibited an immunosuppressive microenvironment characterized by a high concentration of M2 macrophages and regulatory T cells (Tregs). In contrast, the low-risk group showed lower half-maximal inhibitory concentration (IC50) values. Therefore, patients in the high-risk group may benefit more from immunotherapy, while patients in the low-risk group may benefit more from chemotherapy. In addition, in vitro experiments have shown that inhibition of the expression of IPO4 leads to a significant reduction in the proliferation, migration, and invasion of glioma cells. CONCLUSION This study identified two glioma subtypes and constructed a prognostic signature based on DDRGs. The signature has the potential to optimize the selection of patients for immune- and chemotherapy and provided a potential therapeutic target for glioma.
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Affiliation(s)
- HaoYuan Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ZhiHao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ChenXi Chang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ZhiWei Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - DeRan Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - QingGuo Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China.
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7
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Ouyang G, Li Q, Wei Y, Dai W, Deng H, Liu Y, Li J, Li M, Luo S, Li S, Liang Y, Pan G, Yang J, Gan T. Identification of PANoptosis-related subtypes, construction of a prognosis signature, and tumor microenvironment landscape of hepatocellular carcinoma using bioinformatic analysis and experimental verification. Front Immunol 2024; 15:1323199. [PMID: 38742112 PMCID: PMC11089137 DOI: 10.3389/fimmu.2024.1323199] [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: 10/17/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most lethal malignancies worldwide. PANoptosis is a recently unveiled programmed cell death pathway, Nonetheless, the precise implications of PANoptosis within the context of HCC remain incompletely elucidated. Methods We conducted a comprehensive bioinformatics analysis to evaluate both the expression and mutation patterns of PANoptosis-related genes (PRGs). We categorized HCC into two clusters and identified differentially expressed PANoptosis-related genes (DEPRGs). Next, a PANoptosis risk model was constructed using LASSO and multivariate Cox regression analyses. The relationship between PRGs, risk genes, the risk model, and the immune microenvironment was studies. In addition, drug sensitivity between high- and low-risk groups was examined. The expression profiles of these four risk genes were elucidate by qRT-PCR or immunohistochemical (IHC). Furthermore, the effect of CTSC knock down on HCC cell behavior was verified using in vitro experiments. Results We constructed a prognostic signature of four DEPRGs (CTSC, CDCA8, G6PD, and CXCL9). Receiver operating characteristic curve analyses underscored the superior prognostic capacity of this signature in assessing the outcomes of HCC patients. Subsequently, patients were stratified based on their risk scores, which revealed that the low-risk group had better prognosis than those in the high-risk group. High-risk group displayed a lower Stromal Score, Immune Score, ESTIMATE score, and higher cancer stem cell content, tumor mutation burden (TMB) values. Furthermore, a correlation was noted between the risk model and the sensitivity to 56 chemotherapeutic agents, as well as immunotherapy efficacy, in patient with. These findings provide valuable guidance for personalized clinical treatment strategies. The qRT-PCR analysis revealed that upregulated expression of CTSC, CDCA8, and G6PD, whereas downregulated expression of CXCL9 in HCC compared with adjacent tumor tissue and normal liver cell lines. The knockdown of CTSC significantly reduced both HCC cell proliferation and migration. Conclusion Our study underscores the promise of PANoptosis-based molecular clustering and prognostic signatures in predicting patient survival and discerning the intricacies of the tumor microenvironment within the context of HCC. These insights hold the potential to advance our comprehension of the therapeutic contribution of PANoptosis plays in HCC and pave the way for generating more efficacious treatment strategies.
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Affiliation(s)
- Guoqing Ouyang
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
- Guangxi Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
- Liuzhou Hepatobiliary and Pancreatic Diseases Precision Diagnosis Research Center of Engineering Technology, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Qiuyun Li
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
- Liuzhou Hepatobiliary and Pancreatic Diseases Precision Diagnosis Research Center of Engineering Technology, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Yangnian Wei
- Department of Hepatobiliary Surgery, Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Wenbin Dai
- Department of Pathology, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Haojian Deng
- Department of Emergency Medical, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Youli Liu
- Department of Pathology, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Jiaguang Li
- Department of Pathology, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Mingjuan Li
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Shunwen Luo
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Shuang Li
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Yunying Liang
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Guandong Pan
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
- Liuzhou Hepatobiliary and Pancreatic Diseases Precision Diagnosis Research Center of Engineering Technology, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Jianqing Yang
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
- Liuzhou Hepatobiliary and Pancreatic Diseases Precision Diagnosis Research Center of Engineering Technology, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Tao Gan
- Department of General Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
- Department of Emergency Medical, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
- Key Specialty Department of Emergency Medicine in Guangxi, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
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Wang M, Xu X, Li J, Gao Z, Ding Y, Chen X, Xiang Q, Shen L. Integrated bioinformatics and experiment revealed that cuproptosis is the potential common pathogenesis of three kinds of primary cardiomyopathy. Aging (Albany NY) 2023; 15:14210-14241. [PMID: 38085668 PMCID: PMC10756114 DOI: 10.18632/aging.205298] [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: 06/22/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023]
Abstract
Cuproptosis is a recently reported new mode of programmed cell death which might be a potential co-pathogenesis of three kinds of primary cardiomyopathy. However, no investigation has reported a clear relevance between primary cardiomyopathy and cuproptosis. In this study, the differential cuproptosis-related genes (CRGs) shared by three kinds of primary cardiomyopathy were identified in training sets. As a result, four CRGs shared by three kinds of primary cardiomyopathy were acquired and they were mainly related to biological processes such as cell death and immuno-inflammatory response through differential analysis, correlation analysis, GSEA, GSVA and immune cell infiltration analysis. Then, three key CRGs (K-CRGs) with high diagnostic value were identified by LASSO regression. The results of nomogram, machine learning, ROC analysis, calibration curve and decision curve indicated that the K-CRGs exhibited outstanding performance in the diagnosis of three kinds of primary cardiomyopathy. After that, in each disease, two molecular subtypes clusters were distinguished. There were many differences between different clusters in the biological processes associated with cell death and immunoinflammation and K-CRGs had excellent molecular subtype identification efficacy. Eventually, results from validation datasets and in vitro experiments verified the role of K-CRGs in diagnosis of primary cardiomyopathy, identification of primary cardiomyopathic molecular subtypes and pathogenesis of cuproptosis. In conclusion, this study found that cuproptosis might be the potential common pathogenesis of three kinds of primary cardiomyopathy and K-CRGs might be promising biomarkers for the diagnosis and molecular subtypes identification of primary cardiomyopathy.
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Affiliation(s)
- Mengxi Wang
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaozhuo Xu
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jianghong Li
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ziwei Gao
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuhan Ding
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaohu Chen
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Qian Xiang
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Le Shen
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
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Wang M, Zheng L, Ma S, Lin R, Li J, Yang S. Cuproptosis: emerging biomarkers and potential therapeutics in cancers. Front Oncol 2023; 13:1288504. [PMID: 38023234 PMCID: PMC10662309 DOI: 10.3389/fonc.2023.1288504] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The sustenance of human life activities depends on copper, which also serves as a crucial factor for vital enzymes. Under typical circumstances, active homeostatic mechanisms keep the intracellular copper ion concentration low. Excess copper ions cause excessive cellular respiration, which causes cytotoxicity and cell death as levels steadily rise above a threshold. It is a novel cell death that depends on mitochondrial respiration, copper ions, and regulation. Cuproptosis is now understood to play a role in several pathogenic processes, including inflammation, oxidative stress, and apoptosis. Copper death is a type of regulatory cell death(RCD).Numerous diseases are correlated with the development of copper homeostasis imbalances. One of the most popular areas of study in the field of cancer is cuproptosis. It has been discovered that cancer angiogenesis, proliferation, growth, and metastasis are all correlated with accumulation of copper ions. Copper ion concentrations can serve as a crucial marker for cancer development. In order to serve as a reference for clinical research on the product, diagnosis, and treatment of cancer, this paper covers the function of copper ion homeostasis imbalance in malignant cancers and related molecular pathways.
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Affiliation(s)
- Min Wang
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Lianwen Zheng
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Shuai Ma
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Ruixin Lin
- Department of Hepato-Biliary-Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Jiahui Li
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Shuli Yang
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
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Zhong A, Wang F, Zhou Y, Ding N, Yang G, Chai X. Molecular Subtypes and Machine Learning-Based Predictive Models for Intracranial Aneurysm Rupture. World Neurosurg 2023; 179:e166-e186. [PMID: 37597661 DOI: 10.1016/j.wneu.2023.08.043] [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: 04/26/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND The determination of biological mechanisms and biomarkers related to intracranial aneurysm (IA) rupture is of utmost significance for the development of effective preventive and therapeutic strategies in the clinical field. METHODS GSE122897 and GSE13353 datasets were downloaded from Gene Expression Omnibus. Data extracted from GSE122897 were used for analyzing differential gene expression, and consensus clustering was performed to identify stable molecular subtypes. Clinical characteristics were compared between subgroups, and fast gene set enrichment analysis and weighted gene coexpression network analysis were performed. Hub genes were identified via least absolute shrinkage and selection operator analysis. Predictive models were constructed based on hub genes using the Light Gradient Boosting Machine, eXtreme Gradient Boosting, and logistic regression algorithm. Immune cell infiltration in IA samples was analyzed using Microenvironment Cell Population counter, CIBERSORT, and xCell algorithm. The correlation between hub genes and immune cells was analyzed. The predictive model and immune cell infiltration were validated using data from the GSE13353 dataset. RESULTS A total of 43 IA samples were classified into 2 subgroups based on gene expression profiles. Subgroup I had a higher risk of rupture, while 70% of subgroup II remained unruptured. In subgroup I, specific genes were associated with inflammation and immunity, and weighted gene coexpression network analysis revealed that the black module genes were linked to IA rupture. We identified 4 hub genes (spermine synthase, macrophage receptor with collagenous structure, zymogen granule protein 16B, and LIM and calponin-homology domains 1), which constructed predictive models with good diagnostic performance in differentiating between ruptured and unruptured IA samples. Monocytic lineage was found to be a significant factor in IA rupture, and the 4 hub genes were linked to monocytic lineage (P < 0.05). CONCLUSIONS We reveal a new molecular subtype that can reflect the actual pathological state of IA rupture, and our predictive models constructed by machine learning algorithms can efficiently predict IA rupture.
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Affiliation(s)
- Aifang Zhong
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Trauma Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Feichi Wang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Trauma Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Zhou
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Trauma Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ning Ding
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Trauma Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guifang Yang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Trauma Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangping Chai
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Trauma Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Ouyang G, Wu Z, Liu Z, Pan G, Wang Y, Liu J, Guo J, Liu T, Huang G, Zeng Y, Wei Z, He S, Yuan G. Identification and validation of potential diagnostic signature and immune cell infiltration for NAFLD based on cuproptosis-related genes by bioinformatics analysis and machine learning. Front Immunol 2023; 14:1251750. [PMID: 37822923 PMCID: PMC10562635 DOI: 10.3389/fimmu.2023.1251750] [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: 07/02/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Background and aims Cuproptosis has been identified as a key player in the development of several diseases. In this study, we investigate the potential role of cuproptosis-related genes in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Method The gene expression profiles of NAFLD were obtained from the Gene Expression Omnibus database. Differential expression of cuproptosis-related genes (CRGs) were determined between NAFLD and normal tissues. Protein-protein interaction, correlation, and function enrichment analyses were performed. Machine learning was used to identify hub genes. Immune infiltration was analyzed in both NAFLD patients and controls. Quantitative real-time PCR was employed to validate the expression of hub genes. Results Four datasets containing 115 NAFLD and 106 control samples were included for bioinformatics analysis. Three hub CRGs (NFE2L2, DLD, and POLD1) were identified through the intersection of three machine learning algorithms. The receiver operating characteristic curve was plotted based on these three marker genes, and the area under the curve (AUC) value was 0.704. In the external GSE135251 dataset, the AUC value of the three key genes was as high as 0.970. Further nomogram, decision curve, calibration curve analyses also confirmed the diagnostic predictive efficacy. Gene set enrichment analysis and gene set variation analysis showed these three marker genes involved in multiple pathways that are related to the progression of NAFLD. CIBERSORT and single-sample gene set enrichment analysis indicated that their expression levels in macrophages, mast cells, NK cells, Treg cells, resting dendritic cells, and tumor-infiltrating lymphocytes were higher in NAFLD compared with control liver samples. The ceRNA network demonstrated a complex regulatory relationship between the three hub genes. The mRNA level of these hub genes were further confirmed in a mouse NAFLD liver samples. Conclusion Our study comprehensively demonstrated the relationship between NAFLD and cuproptosis, developed a promising diagnostic model, and provided potential targets for NAFLD treatment and new insights for exploring the mechanism for NAFLD.
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Affiliation(s)
- Guoqing Ouyang
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
- Liuzhou Key Laboratory of Liver Cancer Research, Liuzhou People’s Hospital, Liuzhou, Guangxi, China
| | - Zhan Wu
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Zhipeng Liu
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Guandong Pan
- Liuzhou Key Laboratory of Liver Cancer Research, Liuzhou People’s Hospital, Liuzhou, Guangxi, China
- Liuzhou Hepatobiliary and Pancreatic Diseases Precision Diagnosis Research Center of Engineering Technology, Liuzhou People’s Hospital by Liuzhou Science and Technology Bureau, Liuzhou, Guangxi, China
| | - Yong Wang
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Jing Liu
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Jixu Guo
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Tao Liu
- Department of General Surgery, Luzhai People’s Hospital, Liuzhou, Guangxi, China
| | - Guozhen Huang
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Yonglian Zeng
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Zaiwa Wei
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Songqing He
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Guandou Yuan
- Division of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, Guangxi, China
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Wang H, Yang Z, He X, Guo F, Sun H, Xu S, Xu C, Wang Z, Wen H, Teng Z, Wang Y, Han Z. Cuproptosis related gene PDHB is identified as a biomarker inversely associated with the progression of clear cell renal cell carcinoma. BMC Cancer 2023; 23:804. [PMID: 37641032 PMCID: PMC10464351 DOI: 10.1186/s12885-023-11324-0] [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: 01/11/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Cuproptosis is a newly discovered programmed cell death dependent on mitochondrial respiratory disorder induced by copper overload. Pyruvate dehydrogenase E1 subunit beta (PDHB) is one of the cuproptosis genesand is a nuclear-encoded pyruvate dehydrogenase, which catalyzes the conversion of pyruvate to acetyl coenzyme A. However, the mechanism of PDHB in clear cell renal cell carcinoma (ccRCC) remains unclear. METHODS We used data from TCGA and GEO to assess the expression of PDHB in normal and tumor tissues. We further analyzed the relationship between PDHB and somatic mutations and immune infiltration. Finally, we preliminarily explored the impact of PDHB on ccRCC. RESULTS The expression level of PDHB was lower in tumor tissue compared with normal tissue. Meanwhile, the expression level of PDHB was also lower in high-grade tumors than low-grade tumors. PDHB is positively correlated with prognosis in ccRCC. Furthermore, PDHB may be associated with decreased risk of VHL, PBRM1 and KDM5C mutations. In 786-O cells, copper chloride could promote the expression of cuproptosis genes (DLAT, PDHB and FDX1) and inhibit cell growth. Last but not least, we found that PDHB could inhibit the proliferation and migration of ccRCC cells. CONCLUSION Our results demonstrated that PDHB could inhibit the proliferation, migration and invasion in ccRCC cells, which might be a prognostic predictor of ccRCC. Targeting this molecular might provide a new therapeutic strategy for patients with advanced ccRCC.
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Affiliation(s)
- Hu Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Xingyu He
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Fengran Guo
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Hao Sun
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Sen Xu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Chao Xu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Zhu Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Hongzhuang Wen
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Zhihai Teng
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China
| | - Yaxuan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China.
| | - Zhenwei Han
- Department of Urology, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, 050000, China.
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Wang M, Cheng L, Gao Z, Li J, Ding Y, Shi R, Xiang Q, Chen X. Investigation of the shared molecular mechanisms and hub genes between myocardial infarction and depression. Front Cardiovasc Med 2023; 10:1203168. [PMID: 37547246 PMCID: PMC10401437 DOI: 10.3389/fcvm.2023.1203168] [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: 04/17/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
Background The pathogenesis of myocardial infarction complicating depression is still not fully understood. Bioinformatics is an effective method to study the shared pathogenesis of multiple diseases and has important application value in myocardial infarction complicating depression. Methods The differentially expressed genes (DEGs) between control group and myocardial infarction group (M-DEGs), control group and depression group (D-DEGs) were identified in the training set. M-DEGs and D-DEGs were intersected to obtain DEGs shared by the two diseases (S-DEGs). The GO, KEGG, GSEA and correlation analysis were conducted to analyze the function of DEGs. The biological function differences of myocardial infarction and depression were analyzed by GSVA and immune cell infiltration analysis. Four machine learning methods, nomogram, ROC analysis, calibration curve and decision curve were conducted to identify hub S-DEGs and predict depression risk. The unsupervised cluster analysis was constructed to identify myocardial infarction molecular subtype clusters based on hub S-DEGs. Finally, the value of these genes was verified in the validation set, and blood samples were collected for RT-qPCR experiments to further verify the changes in expression levels of these genes in myocardial infarction and depression. Results A total of 803 M-DEGs, 214 D-DEGs, 13 S-DEGs and 6 hub S-DEGs (CD24, CSTA, EXTL3, RPS7, SLC25A5 and ZMAT3) were obtained in the training set and they were all involved in immune inflammatory response. The GSVA and immune cell infiltration analysis results also suggested that immune inflammation may be the shared pathogenesis of myocardial infarction and depression. The diagnostic models based on 6 hub S-DEGs found that these genes showed satisfactory combined diagnostic performance for depression. Then, two molecular subtypes clusters of myocardial infarction were identified, many differences in immune inflammation related-biological functions were found between them, and the hub S-DEGs had satisfactory molecular subtypes identification performance. Finally, the analysis results of the validation set further confirmed the value of these hub genes, and the RT-qPCR results of blood samples further confirmed the expression levels of these hub genes in myocardial infarction and depression. Conclusion Immune inflammation may be the shared pathogenesis of myocardial infarction and depression. Meanwhile, hub S-DEGs may be potential biomarkers for the diagnosis and molecular subtype identification of myocardial infarction and depression.
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Affiliation(s)
- Mengxi Wang
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liying Cheng
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ziwei Gao
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianghong Li
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuhan Ding
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ruijie Shi
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qian Xiang
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaohu Chen
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Department of Cardiology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
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Shi Y, Qiu P, Zhao K, Li X, Feng Y, Deng Z, Wang J. Identifying a novel cuproptosis-related necroptosis gene subtype-related signature for predicting the prognosis, tumor microenvironment, and immunotherapy of hepatocellular carcinoma. Front Mol Biosci 2023; 10:1165243. [PMID: 37287752 PMCID: PMC10242026 DOI: 10.3389/fmolb.2023.1165243] [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: 02/13/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023] Open
Abstract
Background: Cuproptosis and necroptosis represent two distinct programmed cell death modalities implicated in neoplastic progression; however, the role of combining cuproptosis and necroptosis in hepatocellular carcinoma (HCC) remains to be elucidated. Methods: A total of 29 cuproptosis-related necroptosis genes (CRNGs) were identified, followed by an extensive analysis of their mutational characteristics, expression patterns, prognostic implications, and associations with the tumor microenvironment (TME). Subsequently, a CRNG subtype-related signature was developed, and its value of prognostic prediction, TME, and therapeutic responses in HCC were thoroughly investigated. Last, quantitative real-time PCR and Western blotting were employed for investigating the signature gene expression in 15 paired clinical tissue samples. Results: Two distinct CRNG subtypes were discerned, demonstrating associations between CRNG expression patterns, clinicopathological attributes, prognosis, and the TME. A CRNG subtype-related prognostic signature, subjected to external validation, was constructed, serving as an independent prognostic factor for HCC patients, indicating poor prognosis for high-risk individuals. Concurrently, the signature's correlations with an immune-suppressive TME, mutational features, stemness properties, immune checkpoint genes, chemoresistance-associated genes, and drug sensitivity were observed, signifying its utility in predicting treatment responses. Subsequently, highly accurate and clinically convenient nomograms were developed, and the signature genes were validated via quantitative real-time PCR and Western blotting, further substantiating the stability and dependability of the CRNG subtype-related prognostic signature. Conclusion: Overall, this investigation presented an extensive panorama of CRNGs and developed the CRNG subtype-related prognostic signature, which holds potential for implementation in personalized treatment strategies and prognostic forecasting for HCC patients.
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Affiliation(s)
- Yuanxin Shi
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Qiu
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Zhao
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangyu Li
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yunxiang Feng
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhengdong Deng
- Department of Pediatric Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianming Wang
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Affiliated Tianyou Hospital, Wuhan University of Science and Technology, Wuhan, China
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15
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Ren Z, Zhang J, Zheng D, Luo Y, Song Z, Chen F, Li A, Liu X. Identification of Prognosis-Related Oxidative Stress Model with Immunosuppression in HCC. Biomedicines 2023; 11:biomedicines11030695. [PMID: 36979675 PMCID: PMC10045103 DOI: 10.3390/biomedicines11030695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/10/2023] [Accepted: 02/19/2023] [Indexed: 03/03/2023] Open
Abstract
For hepatocellular carcinoma (HCC) patients, we attempted to establish a new oxidative stress (OS)-related prognostic model for predicting prognosis, exploring immune microenvironment, and predicting the immunotherapy response. Significantly differently expressed oxidative stress-related genes (DEOSGs) between normal and HCC samples from the Cancer Genome Atlas (TCGA) were screened, and then based on weighted gene coexpression network analysis (WGCNA), HCC-related hub genes were discovered. Based on the least absolute shrinkage and selection operator (LASSO) and cox regression analysis, a prognostic model was developed. We validated the prognostic model’s predictive power using an external validation cohort: the International Cancer Genome Consortium (ICGC).Then a nomogram was determined. Furthermore, we also examined the relationship of the risk model and clinical characteristics as well as immune microenvironment. 434 DEOSGs, comprising 62 downregulated and 372 upregulated genes (p < 0.05 and |log2FC| ≥ 1), and 257 HCC-related hub genes were recognized in HCC. Afterward, we built a five-DEOSG (LOX, CYP2C9, EIF2B4, EZH2, and SRXN1) prognostic risk model. Using the nomogram, the risk model was shown to have good prognostic value. Compared to the low risk group, HCC patients with high risk had poorer outcomes, worse pathological grades, and advanced tumor stages (p < 0.05). There were significant increases in LOX, EIF2B4, EZH2, and SRXN1 expression in HCC samples, while CYP2C9 expression was decreased. Finally, Real-time PCR (RT-qPCR) confirmed the mRNA expressions of five genes (CYP2C9, EIF2B4, EZH2, SRXN1, LOX) in HCC cell lines. Our study constructed a prognostic OS-related model with strong predictive power and potential as an immunosuppressive biomarker for HCC leading to improving prediction and providing new insights for HCC immunotherapy.
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Affiliation(s)
- Zhixuan Ren
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Jiakang Zhang
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Dayong Zheng
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Yue Luo
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Zhenghui Song
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Fengsheng Chen
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
| | - Aimin Li
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
- Correspondence: (A.L.); (X.L.)
| | - Xinhui Liu
- Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Cancer Center, Southern Medical University, Guangzhou 510315, China
- Correspondence: (A.L.); (X.L.)
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Liu Y, Jiang Z, Zhou X, Li Y, Liu P, Chen Y, Tan J, Cai C, Han Y, Zeng S, Shen H, Feng Z. A Multi-Omics Analysis of NASH-Related Prognostic Biomarkers Associated with Drug Sensitivity and Immune Infiltration in Hepatocellular Carcinoma. J Clin Med 2023; 12:jcm12041286. [PMID: 36835825 PMCID: PMC9963320 DOI: 10.3390/jcm12041286] [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: 12/19/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Background: Nonalcoholic steatohepatitis (NASH)-driven hepatocellular carcinoma (HCC) is becoming a major health-related problem. The exploration of NASH-related prognostic biomarkers and therapeutic targets is necessary. Methods: Data were downloaded from the GEO database. The "glmnet" package was used to identify differentially expressed genes (DEGs). The prognostic model was constructed by the univariate Cox and LASSO regression analyses. Validation of the expression and prognosis by immunohistochemistry (IHC) in vitro. Drug sensitivity and immune cell infiltration were analyzed by CTR-DB and ImmuCellAI. Results: We constructed a prognostic model that identified the NASH-related gene set (DLAT, IDH3B, and MAP3K4), which was validated in a real-world cohort. Next, seven prognostic transcription factors (TFs) were identified. The prognostic ceRNA network included three mRNAs, four miRNAs, and seven lncRNAs. Finally, we found that the gene set was associated with drug response which was validated in six clinical trial cohorts. Moreover, the expression level of the gene set was inversely correlated with CD8 T cell infiltration in HCC. Conclusions: We established a NASH-related prognostic model. Upstream transcriptome analysis and the ceRNA network provided clues for mechanism exploration. The mutant profile, drug sensitivity, and immune infiltration analysis further guided precise diagnosis and treatment strategies.
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Affiliation(s)
- Yongting Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhaohui Jiang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xin Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yin Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ping Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yihong Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (H.S.); (Z.F.)
| | - Ziyang Feng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (H.S.); (Z.F.)
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17
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Zheng KW, Zhang CH, Wu W, Zhu Z, Gong JP, Li CM. FNBP4 is a Potential Biomarker Associated with Cuproptosis and Promotes Tumor Progression in Hepatocellular Carcinoma. Int J Gen Med 2023; 16:467-480. [PMID: 36760683 PMCID: PMC9907010 DOI: 10.2147/ijgm.s395881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignant tumors that lacks an efficient therapeutic approach because of its elusive molecular mechanisms. This study aimed to investigate the biological function and potential mechanism of formin-binding protein 4 (FNBP4) in HCC. Methods FNBP4 expression in tissues and cells were detected by quantitative real-time PCR (qRT‒PCR), Western blot, and immunohistochemistry (IHC). The Kaplan-Meier method was used to explore the correlation between the FNBP4 expression and clinical survival. MTT, EdU incorporation, colony formation, and Transwell assays were performed to evaluate the function of FNBP4 in cell proliferation and migration in vitro. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to explore the potential mechanism of FNBP4. The prognostic risk signature and nomogram were constructed to demonstrate the prognostic value of FNBP4. Results We found that FNBP4 was upregulated in patients with HCC and associated with poor overall survival (OS). Furthermore, knockdown of FNBP4 inhibited the proliferation and migration in HCC cells. Then, we performed a KEGG pathway analysis of the coexpressed genes associated with FNBP4 and found that FNBP4 may be associated with tumor-related signaling pathways and cuproptosis. We verified that FNBP4 could cause cell cycle progression and inactivation of the hippo signaling pathway. A prognostic risk signature containing three FNBP4-related differentially expressed cuproptosis regulators (DECRs) was established and can be used as an independent risk factor to evaluate the prognosis of patients with HCC. In addition, a nomogram including a risk score and clinicopathological factors was used to predict patient survival probabilities. Conclusion FNBP4, as a potential biomarker associated with cuproptosis, promotes HCC cell proliferation and metastasis. We provide a new potential strategy for HCC treatment by targeting FNBP4.
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Affiliation(s)
- Kai-Wen Zheng
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China,Department of Hepatobiliary Surgery, the People’s Hospital of Rongchang District, Chongqing, People’s Republic of China
| | - Chao-Hua Zhang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Wu Wu
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Zhu Zhu
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Jian-Ping Gong
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Chun-Ming Li
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China,Correspondence: Chun-Ming Li, Email
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18
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The Upregulation of GSTO2 is Associated with Colon Cancer Progression and a Poor Prognosis. JOURNAL OF ONCOLOGY 2023; 2023:4931650. [PMID: 36688005 PMCID: PMC9848813 DOI: 10.1155/2023/4931650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/13/2023]
Abstract
Colorectal cancer is the second-leading cause of cancer-related mortality in the United States. Glutathione S-transferase can affect the development of cancer. Glutathione S-transferase omega 2, a member of the GST family, plays an important role in many tumors. However, the role of Glutathione S-transferase omega 2 in the development of colon cancer remains unclear. Herein, our study aimed to investigate the exact role of Glutathione S-transferase omega 2 in colon cancer. We used RNA sequencing data from The Cancer Genome Atlas and the Genotype-Tissue Expression database to analyze Glutathione S-transferase omega 2 expressions. Then, we explore the protein information of Glutathione S-transferase omega 2 in the Human Protein Atlas, GeneCards, and String database. In addition, western blot and immunohistochemistry were performed to evaluate the protein levels of Glutathione S-transferase omega 2 in colon cancer tissues. We acquire data from the Gene Expression Omnibus and The Cancer Genome Atlas databases. Also, we performed relevant prognostic analyses of these data. In addition, we performed a statistical analysis of the clinical data from The Cancer Genome Atlas database and the expression level of Glutathione S-transferase omega 2. Then, we performed Cox regression analysis and found independent risk factors for prognosis in patients with colon cancer. The Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analyses were used to explore the potential biological functions of Glutathione S-transferase omega 2. The infiltration of colon cancer-immune cells was evaluated by the CIBERSORT method. RNA silencing was performed using siRNA constructs in HCT-116 and HT-29 cell lines. Cell Counting Kit-8 and EdU assays were performed to determine cell proliferation. Transwell experiments and scratch tests were used to determine cell migration. As for the mRNA and protein expression levels of cells, we used quantitative real-time PCR and western blot to detect them. Our research shows that Glutathione S-transferase omega 2 is overexpressed in colon cancer patients, and this overexpression is associated with a poor prognosis. The high expression of Glutathione S-transferase omega 2 is significantly correlated stage with stage, M, and N classification progression in colon cancer by statistical analysis. Univariate and multivariate Cox regression analyses showed that Glutathione S-transferase omega 2 was an independent risk factor for poor prognosis in colon cancer. In addition, we also found that Glutathione S-transferase omega 2 expression levels can affect the immune microenvironment of colon cancer cells. Gene silencing of Glutathione S-transferase omega 2 in HT-29 and HCT-116 cells significantly inhibited tumor growth and migration. In summary, we found that Glutathione S-transferase omega 2 can be used as a molecular indicator of colon cancer prognosis. In vitro, gene silencing of Glutathione S-transferase omega 2 inhibited colon cancer cells' growth and migration.
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19
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Ma YL, Yang YF, Wang HC, Yang CC, Yan LJ, Ding ZN, Tian BW, Liu H, Xue JS, Han CL, Tan SY, Hong JG, Yan YC, Mao XC, Wang DX, Li T. A novel prognostic scoring model based on copper homeostasis and cuproptosis which indicates changes in tumor microenvironment and affects treatment response. Front Pharmacol 2023; 14:1101749. [PMID: 36909185 PMCID: PMC9998499 DOI: 10.3389/fphar.2023.1101749] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/13/2023] [Indexed: 03/14/2023] Open
Abstract
Background: Intracellular copper homeostasis requires a complex system. It has shown considerable prospects for intervening in the tumor microenvironment (TME) by regulating copper homeostasis and provoking cuproptosis. Their relationship with hepatocellular carcinoma (HCC) remains elusive. Methods: In TCGA and ICGC datasets, LASSO and multivariate Cox regression were applied to obtain the signature on the basis of genes associated with copper homeostasis and cuproptosis. Bioinformatic tools were utilized to reveal if the signature was correlated with HCC characteristics. Single-cell RNA sequencing data analysis identified differences in tumor and T cells' pathway activity and intercellular communication of immune-related cells. Real-time qPCR analysis was conducted to measure the genes' expression in HCC and adjacent normal tissue from 21 patients. CCK8 assay, scratch assay, transwell, and colony formation were conducted to reveal the effect of genes on in vitro cell proliferation, invasion, migration, and colony formation. Results: We constructed a five-gene scoring system in relation to copper homeostasis and cuproptosis. The high-risk score indicated poor clinical prognosis, enhanced tumor malignancy, and immune-suppressive tumor microenvironment. The T cell activity was markedly reduced in high-risk single-cell samples. The high-risk HCC patients had a better expectation of ICB response and reactivity to anti-PD-1 therapy. A total of 156 drugs were identified as potential signature-related drugs for HCC treatment, and most were sensitive to high-risk patients. Novel ligand-receptor pairs such as FASLG, CCL, CD40, IL2, and IFN-Ⅱ signaling pathways were revealed as cellular communication bridges, which may cause differences in TME and immune function. All crucial genes were differentially expressed between HCC and paired adjacent normal tissue. Model-constructed genes affected the phosphorylation of mTOR and AKT in both Huh7 and Hep3B cells. Knockdown of ZCRB1 impaired the proliferation, invasion, migration, and colony formation in HCC cell lines. Conclusion: We obtained a prognostic scoring system to forecast the TME changes and assist in choosing therapy strategies for HCC patients. In this study, we combined copper homeostasis and cuproptosis to show the overall potential risk of copper-related biological processes in HCC for the first time.
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Affiliation(s)
- Yun-Long Ma
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Ya-Fei Yang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Han-Chao Wang
- Institute for Financial Studies, Shandong University, Jinan, China
| | - Chun-Cheng Yang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Lun-Jie Yan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Zi-Niu Ding
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Bao-Wen Tian
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Hui Liu
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Jun-Shuai Xue
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Cheng-Long Han
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Si-Yu Tan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Jian-Guo Hong
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Yu-Chuan Yan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Xin-Cheng Mao
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Dong-Xu Wang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China.,Department of hepatobiliary surgery, The Second Hospital of Shandong University, Jinan, China
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20
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Chuanbing Z, Zhengle Z, Ruili D, Kongfan Z, Jing T. Genes Modulating Butyrate Metabolism for Assessing Clinical Prognosis and Responses to Systematic Therapies in Hepatocellular Carcinoma. Biomolecules 2022; 13:52. [PMID: 36671437 PMCID: PMC9856074 DOI: 10.3390/biom13010052] [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: 11/22/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
Butyrate, one of the major products of the gut microbiota, has played notable roles in diverse therapies for multiple tumors. Our study aimed to determine the roles of genes that modulate butyrate metabolism (BM) in predicting the clinical prognosis and responses to systemic therapies in hepatocellular carcinoma (HCC). The genes modulating BM were available from the GeneCard database, and gene expression and clinical information were obtained from TCGA-LIHC, GEO, ICGC-JP, and CCLE databases. Candidate genes from these genes that regulate BM were then identified by univariate Cox analysis. According to candidate genes, the patients in TCGA were grouped into distinct subtypes. Moreover, BM- related gene signature (BMGs) was created via the LASSO Cox algorithm. The roles of BMGs in identifying high-risk patients of HCC, assessing the prognoses, and predicting systematic therapies were determined in various datasets. The statistical analyses were fulfilled with R 4.1.3, GraphPad Prism 8.0 and Perl 5.30.0.1 software. In the TCGA cohort, most butyrate-related genes were over-expressed in the B cluster, and patients in the B cluster showed worse prognoses. BMGs constructed by LASSO were composed of eight genes. BMGs exhibited a strong performance in evaluating the prognoses of HCC patients in various datasets, which may be superior to 33 published biomarkers. Furthermore, BMGs may contribute to the early surveillance of HCC, and BMGs could play active roles in assessing the effectiveness of immunotherapy, TACE, ablation therapy, and chemotherapeutic drugs for HCC. BMGs may be served as novel promising biomarkers for early identifying high-risk groups of HCC, as well as assessing prognoses, drug sensitivity, and the responses to immunotherapy, TACE, and ablation therapy in patients with HCC.
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Affiliation(s)
- Zhao Chuanbing
- Department of Pancreatic Surgery, Renmin Hospital of Wuhan University, Wuhan 430061, China
| | - Zhang Zhengle
- Department of Pancreatic Surgery, Renmin Hospital of Wuhan University, Wuhan 430061, China
| | - Ding Ruili
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430061, China
| | - Zhu Kongfan
- Department of Pancreatic Surgery, Renmin Hospital of Wuhan University, Wuhan 430061, China
| | - Tao Jing
- Department of Pancreatic Surgery, Renmin Hospital of Wuhan University, Wuhan 430061, China
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