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Cai H, Li X, Liu Y, Ke J, Liu K, Xie Y, Xie C, Zhou D, Han M, Ji B. Decitabine-based nanoparticles for enhanced immunotherapy of hepatocellular carcinoma via DNA hypermethylation reversal. CHEMICAL ENGINEERING JOURNAL 2024; 492:152175. [DOI: 10.1016/j.cej.2024.152175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
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Yang M, Wang D, Wang X, Mei J, Gong Q. Role of Folate in Liver Diseases. Nutrients 2024; 16:1872. [PMID: 38931227 PMCID: PMC11206401 DOI: 10.3390/nu16121872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Folate is a water-soluble B vitamin involved in the synthesis of purines and pyrimidines and is one of the essential vitamins for human growth and reproduction. Folate deficiency due to low dietary intake, poor absorption of folate, and alterations in folate metabolism due to genetic defects or drug interactions significantly increases the risk of diseases such as neural tube defects, cardiovascular disease, cancer, and cognitive dysfunction. Recent studies have shown that folate deficiency can cause hyperhomocysteinemia, which increases the risk of hypertension and cardiovascular disease, and that high homocysteine levels are an independent risk factor for liver fibrosis and cirrhosis. In addition, folate deficiency results in increased secretion of pro-inflammatory factors and impaired lipid metabolism in the liver, leading to lipid accumulation in hepatocytes and fibrosis. There is substantial evidence that folate deficiency contributes to the development and progression of a variety of liver diseases, including non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), alcoholic liver disease (ALD), viral hepatitis, hepatic fibrosis, and liver cancer. Here we review key studies on the role of folate in the pathophysiology of liver diseases, summarize the current status of studies on folate in the treatment of liver diseases, and speculate that folate may be a potential therapeutic target for liver diseases.
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Affiliation(s)
- Minlan Yang
- School of Medicine, Yangtze University, Jingzhou 434020, China
| | | | | | | | - Quan Gong
- School of Medicine, Yangtze University, Jingzhou 434020, China
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Du Y, Xu Y, Guo X, Tan C, Zhu X, Liu G, Lyu X, Bei C. Methylation-regulated tumor suppressor gene PDE7B promotes HCC invasion and metastasis through the PI3K/AKT signaling pathway. BMC Cancer 2024; 24:624. [PMID: 38778317 PMCID: PMC11112795 DOI: 10.1186/s12885-024-12364-w] [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: 10/04/2023] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) has a high mortality rate, and the mechanisms underlying tumor development and progression remain unclear. However, inactivated tumor suppressor genes might play key roles. DNA methylation is a critical regulatory mechanism for inactivating tumor suppressor genes in HCC. Therefore, this study investigated methylation-related tumor suppressors in HCC to identify potential biomarkers and therapeutic targets. METHODS We assessed genome-wide DNA methylation in HCC using whole genome bisulfite sequencing (WGBS) and RNA sequencing, respectively, and identified the differential expression of methylation-related genes, and finally screened phosphodiesterase 7B (PDE7B) for the study. The correlation between PDE7B expression and clinical features was then assessed. We then analyzed the changes of PDE7B expression in HCC cells before and after DNA methyltransferase inhibitor treatment by MassArray nucleic acid mass spectrometry. Furthermore, HCC cell lines overexpressing PDE7B were constructed to investigate its effect on HCC cell function. Finally, GO and KEGG were applied for the enrichment analysis of PDE7B-related pathways, and their effects on the expression of pathway proteins and EMT-related factors in HCC cells were preliminarily explored. RESULTS HCC exhibited a genome-wide hypomethylation pattern. We screened 713 hypomethylated and 362 hypermethylated mCG regions in HCC and adjacent normal tissues. GO analysis showed that the main molecular functions of hypermethylation and hypomethylation were "DNA-binding transcriptional activator activity" and "structural component of ribosomes", respectively, whereas KEGG analysis showed that they were enriched in "bile secretion" and "Ras-associated protein-1 (Rap1) signaling pathway", respectively. PDE7B expression was significantly down-regulated in HCC tissues, and this low expression was negatively correlated with recurrence and prognosis of HCC. In addition, DNA methylation regulates PDE7B expression in HCC. On the contrary, overexpression of PDE7B inhibited tumor proliferation and metastasis in vitro. In addition, PDE7B-related genes were mainly enriched in the PI3K/ATK signaling pathway, and PDE7B overexpression inhibited the progression of PI3K/ATK signaling pathway-related proteins and EMT. CONCLUSION PDE7B expression in HCC may be regulated by promoter methylation. PDE7B can regulate the EMT process in HCC cells through the PI3K/AKT pathway, which in turn affects HCC metastasis and invasion.
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Affiliation(s)
- Yuanxiao Du
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
| | - Yuqiu Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
| | - Xuefeng Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Chao Tan
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Xiaonian Zhu
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China
| | - Guoyu Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
| | - Xiao Lyu
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China
| | - Chunhua Bei
- Department of Epidemiology and Health Statistics, School of Public Health, Guilin Medical University, Huan Cheng North 2nd Road 109, Guilin, Guangxi, 541004, China.
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, School of Public Health, Guilin Medical University, Guilin, China.
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Karri RL, Bojji M, Rudraraju A, Mohammad AS, Kosuru V, Kalisipudi S. Unraveling the Molecular Complexity of Adenoid Cystic Carcinoma (ACC): A Comprehensive Exploration of Hub Genes, Protein-Protein Interaction (PPI) Networks, microRNA (miRNA) Involvement, and Drug-Gene Interactions (DGIs). Cureus 2024; 16:e54730. [PMID: 38524085 PMCID: PMC10961157 DOI: 10.7759/cureus.54730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Background Adenoid cystic carcinoma (ACC) poses clinical challenges with its unique histology and potential for perineural invasion, recurrence, and distant metastases. Recent genomic advancements have unveiled key genetic alterations in ACC, offering insights into its pathogenesis. Aim This study aims to unravel the intricate molecular landscape of ACC through a comprehensive analysis of gene expression patterns. By integrating data from multiple microarray datasets, the study explores differentially expressed genes (DEGs), their functional enrichment, protein-protein interactions (PPI), hub genes, microRNA (miRNA) involvement, transcription factors, and potential drug-gene interactions. Methods Three microarray datasets (GSE88804, GSE153002, and GSE36820) related to ACC were selected from the Gene Expression Omnibus (GEO) repository. DEGs were identified using GEO2R and further analyzed for commonalities and differences. Functional enrichment analysis, including Gene Set Enrichment Analysis (GSEA), provided insights into biological processes, cellular components, molecular functions, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with ACC. PPI networks and hub genes were identified using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) (STRING Consortium, Lausanne, Switzerland) database and Cytoscape (Cytoscape Consortium, California, United States). The study also explored miRNAs, transcription factors, and potential drug-gene interactions. Results The integrated analysis revealed 339 common upregulated and 643 downregulated DEGs in ACC. Functional and pathway enrichment analyses unveiled the involvement of these genes in critical cellular processes, signaling cascades, and pathways. The PPI network, comprising 904 nodes and 4139 edges, highlighted the complexity of interactions. Hub genes, including KIF11, BUB1, and DLGAP5, were identified, shedding light on their pivotal roles in cell cycle regulation. The study also identified miRNAs (e.g., hsa-mir-7-5p and hsa-mir-138-5p) and transcription factors (e.g., E2F1 and TP53) associated with ACC. Drug-gene interactions have identified potential therapeutic options, including amsacrine and rucaparib. Conclusions The ACC gene expression highlights a nuanced molecular landscape, identifying pivotal hub genes such as KIF11 and CDK1 as potential therapeutic targets for ACC, given their roles in cell cycle progression. The dysregulation of microRNAs and transcription factors adds complexity to ACC's molecular profile. Exploration of drug-gene interactions reveals promising therapeutic strategies, involving FDA-approved drugs such as amsacrine and rucaparib, providing avenues for personalized interventions.
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Affiliation(s)
- Roja L Karri
- Oral and Maxillofacial Pathology, GSL Dental College and Hospital, Rajahmundry, IND
| | - Manasa Bojji
- Oral and Maxillofacial Pathology, Malla Reddy Dental College for Women, Hyderabad, IND
| | | | - Abdul Sadik Mohammad
- Pediatric and Preventive Dentistry, GSL Dental College and Hospital, Rajahmundry, IND
| | - Vamseedhar Kosuru
- Pediatric and Preventive Dentistry, Narayana Dental College and Hospital, Nellore, IND
| | - Sandeep Kalisipudi
- Pediatric and Preventive Dentistry, Lenora Institute of Dental Sciences, Rajahmundry, IND
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Zhang Y, Wang JW, Su X, Li JE, Wei XF, Yang JR, Gao S, Fan YC, Wang K. F-box protein 43 promoter methylation as a novel biomarker for hepatitis B virus-associated hepatocellular carcinoma. Front Microbiol 2023; 14:1267844. [PMID: 38029156 PMCID: PMC10652413 DOI: 10.3389/fmicb.2023.1267844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) has a high prevalence and poor prognosis worldwide. Therefore, it is urgent to find effective and timely diagnostic markers. The objective of this study was to evaluate the diagnostic value of F-box protein 43 promoter methylation in peripheral blood mononuclear cells (PBMCs) for HCC. Method A total of 247 participants were included in this study, comprising individuals with 123 hepatitis B virus-associated HCC, 79 chronic hepatitis B, and 45 healthy controls. F-box protein 43 methylation and mRNA levels in PBMCs were detected by MethyLight and quantitative real-time PCR. Result F-box protein 43 promoter methylation levels were significantly lower in HCC PBMCs than the chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Relative mRNA expression levels of F-box protein 43 in HCC PBMCs were significantly higher than those in chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Receiver operating characteristic analysis of F-box protein 43 promoter methylation levels yielded an area under curve (AUC) of 0.793 with 76.42% sensitivity and 68.35% specificity when differentiating HCC from chronic hepatitis. These values for the F-box protein 43 promoter methylation level were superior to those of the alpha-fetoprotein serum (AFP) level (AUC: 0.780, sensitivity: 47.97%, and specificity: 96.20%), with increments in values for the combination of F-box protein 43 promoter methylation AFP levels (AUC: 0.888, sensitivity: 76.42%, and specificity: 86.08%). Conclusion Hypomethylation of the F-box protein 43 promoter in PBMCs is a promising biochemical marker for HBV-associated HCC.
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Affiliation(s)
- Ying Zhang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing-Wei Wang
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xing Su
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jin-E Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Xue-Fei Wei
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jie-Ru Yang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
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Zhang X, Cong P, Tian L, Zheng Y, Zhang H, Liu Q, Wu T, Zhang Q, Wu H, Huang X, Xiong L. Genomic gain/methylation modification/hsa-miR-132-3p increases RRS1 overexpression in liver hepatocellular carcinoma. Cancer Sci 2023; 114:4329-4342. [PMID: 37705317 PMCID: PMC10637089 DOI: 10.1111/cas.15933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
This study aimed to determine the upstream regulatory factors affecting ribosome biogenesis regulator 1 homolog (RRS1) expression and the development and prognosis of liver hepatocellular carcinoma (LIHC). The expression profiles of RRS1 were evaluated in pan-cancer tissues and liver tumor cell lines. The associations of RRS1 with pan-cancer survival, immune infiltrations, immune checkpoints, and drug sensitivity were identified. We explored the potential upstream regulatory mechanisms of RRS1 expression. Hsa-miR-132-3p knockdown, CCK-8 assays, transwell, and wound healing assays were performed to validate the regulatory effect of hsa-miR-132-3p on RRS1 expression and the development of LIHC. Our findings demonstrated that RRS1 was significantly elevated in 27 types of cancers. RRS1 predicts a poor outcome of LIHC, lung adenocarcinoma, head and neck cancer, and kidney papillary cell carcinoma. RRS1 expression showed a significant association with immune cell infiltrates and the expression of immune checkpoints-related genes in LIHC tissues. Increased RRS1 expression may have a negative effect on these anticancer drugs of LIHC. Low methylation of the RRS1 promoter and its genomic gain may elevate RRS1 expression and predict poor prognosis for LIHC. Increased hsa-miR-132-3p expression may elevate RRS1 expression and result in poor prognosis for LIHC. Hsa-miR-132-3p inhibition can decrease RRS1 expression and the development of liver tumor cell lines. Low methylation of the RRS1 promoter, RRS1 genomic gain, and hsa-miR-132-3p upregulation in LIHC may promote RRS1 upregulation and thus lead to the development and poor prognosis for LIHC. RRS1 is a promising therapeutic target for LIHC.
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Affiliation(s)
- Xiaoxia Zhang
- Department of Hospital Infection Management, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Peilin Cong
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Li Tian
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Yinggang Zheng
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Hong Zhang
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Qiong Liu
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Tingmei Wu
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Qian Zhang
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Huanghui Wu
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Xinwei Huang
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Lize Xiong
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
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Zhang Z, Sun J, Jin C, Zhang L, Wu L, Tian G. Identification and validation of a fatty acid metabolism gene signature for the promotion of metastasis in liver cancer. Oncol Lett 2023; 26:457. [PMID: 37736554 PMCID: PMC10509777 DOI: 10.3892/ol.2023.14044] [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: 06/20/2023] [Accepted: 08/10/2023] [Indexed: 09/23/2023] Open
Abstract
Metastasis is a fatal status for liver cancer, and the identification of an effective prediction model and promising therapeutic target is essential. Given the known relationship between fatty acid (FA) metabolism and the liver, the present study aimed to investigate dysregulation of genes associated with FA metabolism in liver cancer. Bioinformatics analyses were performed on data from patients with hepatocellular carcinoma (HCC) obtained from The Cancer Genome Atlas database using R software packages. Online public tools such as the Human Protein Atlas, Tumor Immune Single-Cell Hub and the University of Alabama at Birmingham Cancer Data Analysis portal were also utilized. Some essential results were further verified using in vitro experiments using HepG2 liver cancer cells. A signature consisting of three genes associated with the progression and prognosis of HCC and FA metabolism was identified. When samples were scored based on the expression of these genes and divided according to the median value, the higher score group showed a worse outcome and repressive immune microenvironment than the lower score group. Downstream pathways such as hypoxia, IL6/JAK/STAT3 and epithelial-mesenchymal transition were found to be significantly activated in the higher score group. As the core factor in the signature, mitochondrial ribosomal protein L35 (MRPL35) was found to be upregulated in HCC and to have certain impacts on the dysregulation of effective immunity. Further investigations and in vitro experiments indicated that MRPL35 facilitates the migration and invasion abilities of liver cancer, and the resistance of HCC to treatment. These findings have important implications regarding the characteristics and mechanisms of metastasis in liver cancer, and provide a promising signature based on FA metabolism-related genes that may be used to predict outcomes and explored as a novel therapeutic target in liver cancer.
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Affiliation(s)
- Zhenshan Zhang
- Department of Hepatobiliary Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250033, P.R. China
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Shanghai 201321, P.R. China
| | - Jun Sun
- Department of Hepatobiliary Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250033, P.R. China
| | - Chao Jin
- Department of Ocean, Shandong University, Weihai, Shandong 264209, P.R. China
- Department of Pharmacy, Zhejiang Qianji Fang Pharmaceutical Technology Co., Ltd., Hangzhou, Zhejiang 311710, P.R. China
| | - Likun Zhang
- Department of Clinical Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161003, P.R. China
| | - Leilei Wu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Gendong Tian
- Department of Hepatobiliary Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250033, P.R. China
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Kircali MF, Turanli B. Idiopathic Pulmonary Fibrosis Molecular Substrates Revealed by Competing Endogenous RNA Regulatory Networks. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:381-392. [PMID: 37540140 DOI: 10.1089/omi.2023.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic disease of the lung with poor prognosis. Fibrosis results from remodeling of the interstitial tissue. A wide range of gene expression changes are observed, but the role of micro RNAs (miRNAs) and circular RNAs (circRNA) is still unclear. Therefore, this study aimed to establish an messenger RNA (mRNA)-miRNA-circRNA competing endogenous RNA (ceRNA) regulatory network to uncover novel molecular signatures using systems biology tools. Six datasets were used to determine differentially expressed genes (DEGs) and miRNAs (DEmiRNA). Accordingly, protein-protein, mRNA-miRNA, and miRNA-circRNA interactions were constructed. Modules were determined and further analyzed in the Drug Gene Budger platform to identify potential therapeutic compounds. We uncovered common 724 DEGs and 278 DEmiRNAs. In the protein-protein interaction network, TMPRSS4, ESR2, TP73, CLEC4E, and TP63 were identified as hub protein coding genes. The mRNA-miRNA interaction network revealed two modules composed of ADRA1A, ADRA1B, hsa-miR-484 and CDH2, TMPRSS4, and hsa-miR-543. The DEmiRNAs in the modules further analyzed to propose potential circRNA regulators in the ceRNA network. These results help deepen the understanding of the mechanisms of IPF. In addition, the molecular leads reported herein might inform future innovations in diagnostics and therapeutics research and development for IPF.
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Affiliation(s)
- Muhammed Fatih Kircali
- School of Medicine, Marmara University, Istanbul, Türkiye
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
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Wu H, Liu S, Wu D, Zhou H, Sui G, Wu G. Cell division cycle-associated 8 is a prognostic biomarker related to immune invasion in hepatocellular carcinoma. Cancer Med 2023; 12:10138-10155. [PMID: 36855818 PMCID: PMC10166956 DOI: 10.1002/cam4.5718] [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: 09/30/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Cell division cycle-associated 8 (CDCA8) is involved in numerous signaling networks, and it serves a crucial modulatory function in multiple malignant tumors. However, its significance in prognosis and immune infiltration in hepatocellular carcinoma (HCC) remains unclear. MATERIALS AND METHODS Herein, we examined the CDCA8 levels in tumor tissues, as well as its associated signaling pathways and correlation with immune infiltration. Additionally, we further clarified the prognostic significance of CDCA8 among HCC patients. HCC patient information was recruited from The Cancer Genome Atlas (TCGA). Using bioinformatics, the following parameters were analyzed among HCC patients: CDCA8 expression, enrichment analysis, immune infiltration, and prognosis analysis. Moreover, we employed in vitro investigations, such as, qRT-PCR, immunohistochemistry (IHC), and cell functional experiments to validate our results. RESULTS Elevated CDCA8 expression in HCC patients was markedly associated with T stage, pathological status (PS), tumor status (TS), histologic grade (HG), and AFP. Elevated CDCA8 expression HCC patients exhibited reduced overall survival (OS) (p < 0.001), disease-specific survival (DSS) (p < 0.001), and progress free interval (PFI) H(p < 0.001). According to the ROC analysis, the area under the curve (AUC) was 0.997. Multivariate analysis revealed that CDCA8 was a stand-alone prognostic indicator of patient OS (p = 0.009) and DSS (p = 0.006). A nomogram was then generated based on the multivariate analysis, and the C-indexes and calibration chart revealed excellent predictive performance in determining HCC patient outcome. Based on the GSEA analysis, CDCA8 modulated the P53, Notch, PPAR, E2F networks. We observed a direct link between CDCA8 levels and Th2 and T helper cells, and a negative link between CDCA8 levels and dendritic cells (DC), neutrophils, cytotoxic cells, and CD8 T cells. Furthermore, CDCA8 deficiency inhibited liver cancer cell proliferation and invasion. CONCLUSION In conclusion, these findings indicate that CDCA8 is a new molecular bioindicator of HCC patient prognosis, and it is an excellent candidate for therapeutic target against HCC.
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Affiliation(s)
- Haomin Wu
- Department of General Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Shiqi Liu
- Department of General Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Di Wu
- Department of General Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Haonan Zhou
- Department of General Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Guoxin Sui
- Department of General Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Gang Wu
- Department of General Surgery, The First Hospital of China Medical University, Shenyang, China
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Dong H, Sun M, Li H, Yue Y. CXCR3 predicts the prognosis of endometrial adenocarcinoma. BMC Med Genomics 2023; 16:20. [PMID: 36750966 PMCID: PMC9903462 DOI: 10.1186/s12920-023-01451-9] [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: 05/13/2022] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
OBJECTIVES Currently, endometrial adenocarcinoma lacks an effective prognostic indicator. This study was to develop and validate a gene biomarker and a nomogram to predict the survival of endometrial adenocarcinoma, explore potential mechanisms and select sensitive drugs. METHODS 425 endometrial adenocarcinoma cases with RNA sequencing data from TCGA were used to identify the most immune-related module by WGCNA. As an external test set, 103 cases from GSE17025 were used. Immune-related genes were downloaded from Innate DB. The three sets of data were used to identify the prognostic genes. Based on 397 cases with complete clinical data from TCGA, randomly divided into the training set (n = 199) and test set (n = 198), we identified CXCR3 as the prognostic gene biomarker. Age, grade, FIGO stage, and risk were used to develop and validate a predictive nomogram. AUC, C-index, calibration curve and K-M estimate evaluated the model's predictive performance. KEGG enrichment analysis, immune functions, TMB, the effectiveness of immunotherapy, and drug sensitivity between the high-risk and low-risk groups. RESULTS CXCR3 was identified as a prognostic biomarker. We calculated the risk score and divided the cases into the high-risk and low-risk groups by the median value of the risk score. The OS of the high-risk group was better than the low-risk group. The risk was the prognostic indicator independent of age, grade, and FIGO stage. We constructed the nomogram including age, grade, FIGO stage, and risk to predict the prognosis of endometrial adenocarcinoma. The top five KEGG pathways enriched by the DEGs between the high- and low-risk groups were viral protein interaction with cytokine and cytokine receptors, cytokine-cytokine receptor interaction, chemokine signaling pathway, natural killer cell-mediated cytotoxicity, and cell adhesion molecules. We analyzed the difference in immune cells and found that CD8+ T cells, activated CD4+ T cells, T helper cells, monocytes, and M1 macrophages were infiltrated more in the low-risk group. However, M0 macrophages and activated dendritic cells were more in the high-risk group. The immune function including APC coinhibition, APC costimulation, CCR, checkpoint, cytolytic activity, HLA, inflammation-promoting, MHC-I, parainflammation, T cell coinhibition, T cell costimulation, type I-IFN-response, and type II-IFN-response were better in the low-risk group. TMB and TIDE scores were both better in the low-risk group. By 'the pRRophetic' package, we found 56 sensitive drugs for different risk groups. CONCLUSION We identified CXCR3 as the prognostic biomarker. We also developed and validated a predictive nomogram model combining CXCR3, age, histological grade, and FIGO stage for endometrial adenocarcinoma, which could help explore the precise treatment.
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Affiliation(s)
- He Dong
- grid.430605.40000 0004 1758 4110Department of Gynecologic Oncology, The First Hospital of Jilin University, Changchun, China
| | - Mengzi Sun
- grid.64924.3d0000 0004 1760 5735Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, China
| | - Hua Li
- grid.430605.40000 0004 1758 4110Department of Abdominal Ultrasound, The First Hospital of Jilin University, Changchun, China
| | - Ying Yue
- Department of Gynecologic Oncology, The First Hospital of Jilin University, Changchun, China.
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11
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Yu F, Huang X, Zhou D, Zhao Z, Wu F, Qian B, Wang Q, Chen J, Liang Q, Jiang Y, Ding Q, He Q, Tang J, Wang X, Liu W, Chen C. Genetic, DNA methylation, and immune profile discrepancies between early-stage single primary lung cancer and synchronous multiple primary lung cancer. Clin Epigenetics 2023; 15:4. [PMID: 36611170 PMCID: PMC9824942 DOI: 10.1186/s13148-023-01422-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND To explore the possible carcinogenesis and help better diagnose and treat patients with synchronous multiple primary lung cancers (sMPLC), we systematically investigated the genetic and DNA methylation profiles of early-stage sMPLC and single primary lung cancer (SPLC) and explored the immune profiles in the tumor microenvironment. METHODS Hundred and ninety-one patients with 191 nodules in the SPLC group and 132 patients with 295 nodules in the sMPLC group were enrolled. All the samples were subjected to wide panel-genomic sequencing. Genome-wide DNA methylation was assessed using the Infinium Human Methylation 850 K BeadChip. RNA-seq and CIBERSORT analyses were performed to identify the immune characteristics in these two groups. RESULTS Lesions from sMPLC patients had lower TMB levels than that from SPLC patients. sMPLC had a similar genetic mutational landscape with SPLC, despite some subgroup genetic discrepancies. Distinct DNA methylation patterns were identified between the two groups. The differentially methylated genes were related to immune response pathways. RNA-seq analyses revealed more immune-related DEGs in sMPLC. Accordingly, more immune-related biological processes and pathways were identified in sMPLC. Aberrant DNA methylation was associated with the abnormal expression of immune-related genes. CIBERSORT analysis revealed the infiltration of immune cells was different between the two groups. CONCLUSION Our study for the first time demonstrated genetic, epigenetic, and immune profile discrepancies between sMPLC and SPLC. Relative to the similar genetic mutational landscape, the DNA methylation patterns and related immune profiles were significantly different between sMPLC and SPLC, indicating their essential roles in the initiation and development of sMPLC.
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Affiliation(s)
- Fenglei Yu
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Xiaojie Huang
- grid.452708.c0000 0004 1803 0208Department of Cardiovascular Surgery, Second Xiangya Hospital of Central South University, Changsha, Hunan People’s Republic of China
| | - Danting Zhou
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Zhenyu Zhao
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Fang Wu
- grid.452708.c0000 0004 1803 0208Department of Oncology, Second Xiangya Hospital of Central South University, Changsha, Hunan People’s Republic of China
| | - Banglun Qian
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Qiang Wang
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Juan Chen
- grid.452708.c0000 0004 1803 0208Department of Radiology, Second Xiangya Hospital of Central South University, Changsha, Hunan People’s Republic of China
| | - Qingchun Liang
- grid.452708.c0000 0004 1803 0208Department of Pathology, Second Xiangya Hospital of Central South University, Changsha, Hunan People’s Republic of China
| | - Yi Jiang
- grid.452708.c0000 0004 1803 0208Department of Pathology, Second Xiangya Hospital of Central South University, Changsha, Hunan People’s Republic of China
| | - Qi Ding
- grid.512993.5Geneplus-Beijing Institute, Beijing, People’s Republic of China
| | - Qiongzhi He
- grid.512993.5Geneplus-Beijing Institute, Beijing, People’s Republic of China
| | - Jingqun Tang
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Xiang Wang
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Wenliang Liu
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Chen Chen
- grid.452708.c0000 0004 1803 0208Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan People’s Republic of China ,grid.452708.c0000 0004 1803 0208Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
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12
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Zhang J, Xiao J, Wang Y, Zheng X, Cui J, Wang C. A universal co-expression gene network and prognostic model for hepatic-biliary-pancreatic cancers identified by integrative analyses. FEBS Open Bio 2022; 12:2006-2024. [PMID: 36054420 PMCID: PMC9623511 DOI: 10.1002/2211-5463.13478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/12/2022] [Accepted: 08/25/2022] [Indexed: 01/25/2023] Open
Abstract
Hepatic, biliary and pancreatic cancers are a diverse set of malignancies with poor prognoses. It is possible that common molecular mechanisms are involved in the carcinogenesis of these cancers. Here, we identified LINC01537 and seven protein-coding genes by integrative analysis of transcriptomes of mRNAs, microRNAs and long non-coding RNAs from cholangiocarcinoma, hepatocellular carcinoma and pancreatic adenocarcinoma cohorts in TCGA. A predictive model constructed from seven biomarkers was established to successfully predict the survival rate of patients, which was then further verified in external cohorts. Additionally, patients with high-risk scores in our model were prone to epithelial-mesenchymal transition. Finally, activation of the biomarker PDE2A significantly attenuated migration and epithelial-mesenchymal transition in the HepG2 liver cancer cell line.
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Affiliation(s)
- Jing Zhang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Juan Xiao
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and RepairAffiliated Hospital of Guilin Medical UniversityChina
| | - Yixuan Wang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Xiao Zheng
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Jiajun Cui
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Chaochen Wang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
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13
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Integrative analysis of the roles of lncRNAs and mRNAs in ischaemic preconditioning to alleviate liver ischaemia-reperfusion injury in mice. Biochem Biophys Res Commun 2022; 627:30-38. [PMID: 36007332 DOI: 10.1016/j.bbrc.2022.08.041] [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: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022]
Abstract
The objective of our study was to elucidate the possible underlying mechanism for the protective effect of ischaemic preconditioning (IPC) against ischaemia-reperfusion (I/R) injury and to provide new research perspectives of long non-coding RNAs (lncRNAs). In this study, serum and liver tissue samples were collected to measure indexes of liver injury from a mouse liver model in sham, I/R injury and I/R + IPC groups. Furthermore, liver samples from 5 randomly selected mice per group were extracted and subjected to the microarray and subsequent bioinformatics analysis. IPC ameliorated liver damage by lowered liver transaminase levels and pro-inflammatory cytokines. A total of 167 lncRNAs and 108 messenger RNAs (mRNAs) were significantly differentially expressed genes (DEGs) between the I/R + IPC and I/R groups. Gene Ontology (GO) analysis revealed that these genes were mainly related to unfolded proteins, responses to topologically incorrect proteins, responses to temperature stimuli, protein folding and protein refolding. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the DEGs were enriched in the following pathways: protein processing in the endoplasmic reticulum; antigen processing and presentation; and fructose and mannose metabolism. Additionally, the 7 selected DEGs (Hspa1ab, Chka, Clec2h, Mvd, Adra1a, AK085737 and AK088966) were validated in modules of the lncRNA-mRNA weighted coexpression network, which agreed with the qRT-PCR and chip data. And the identified differentially expressed lncRNAs and mRNAs may provide new clues to understand the pivotal pathophysiological mechanism by which IPC alleviates I/R-caused liver damage.
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14
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Liu HH, Wang J, Zhang Y, Fan YC, Wang K. Prognostic potential of the small GTPase Ran and its methylation in hepatocellular carcinoma. Hepatobiliary Pancreat Dis Int 2022; 21:248-256. [PMID: 35367146 DOI: 10.1016/j.hbpd.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/03/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common malignant tumor with high mortality. The prognostic significance of Ran, a member of Ras superfamily, remains unclear in HCC patients. METHODS Based on The Cancer Genome Atlas (TCGA) database and Tumor Immune Estimation Resource (TIMER), we analyzed the correlations among Ran expression, promoter methylation and immune cell infiltration. We also investigated the Ran expression levels in HCC tissues and normal tissues by using quantitative real-time PCR. RESULTS Ran mRNA expression was significantly increased in HCC tissues compared with the normal tissues (P < 0.001). Time-dependent receiver operating characteristic (ROC) curves showed that Ran expression had predictive value of the 1-, 3- and 5-year overall survival for HCC patients, and the areas under the curves (AUC) were 0.747, 0.634 and 0.704, respectively. Cox regression analysis showed that Ran expression was an independent prognostic factor for HCC patients (HR = 1.492, 95% CI: 1.129-1.971, P = 0.005). We also found a negative relationship between Ran mRNA expression and its promoter methylation (r = -0.36, P < 0.001). High Ran expression and promoter hypomethylation predicted worse overall survival and progression-free survival (P < 0.05) and were involved in the progression of HCC. Ran expression exhibited significant correlations with immune infiltrates and prognostic immune-related genes. CONCLUSIONS The present study provides further insight into the prognosis of HCC, and Ran could serve as a biomarker for predicting the survival of HCC patients.
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Affiliation(s)
- Hui-Hui Liu
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250000, China
| | - Ju Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250000, China
| | - Ying Zhang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250000, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250000, China; Shenzhen Research Institute of Shandong University, Shenzhen 518000, China; Institute of Hepatology, Shandong University, Jinan 250000, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250000, China; Shenzhen Research Institute of Shandong University, Shenzhen 518000, China; Institute of Hepatology, Shandong University, Jinan 250000, China.
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15
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Lelou E, Corlu A, Nesseler N, Rauch C, Mallédant Y, Seguin P, Aninat C. The Role of Catecholamines in Pathophysiological Liver Processes. Cells 2022; 11:cells11061021. [PMID: 35326472 PMCID: PMC8947265 DOI: 10.3390/cells11061021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 02/06/2023] Open
Abstract
Over the last few years, the number of research publications about the role of catecholamines (epinephrine, norepinephrine, and dopamine) in the development of liver diseases such as liver fibrosis, fatty liver diseases, or liver cancers is constantly increasing. However, the mechanisms involved in these effects are not well understood. In this review, we first recapitulate the way the liver is in contact with catecholamines and consider liver implications in their metabolism. A focus on the expression of the adrenergic and dopaminergic receptors by the liver cells is also discussed. Involvement of catecholamines in physiological (glucose metabolism, lipids metabolism, and liver regeneration) and pathophysiological (impact on drug-metabolizing enzymes expression, liver dysfunction during sepsis, fibrosis development, or liver fatty diseases and liver cancers) processes are then discussed. This review highlights the importance of understanding the mechanisms through which catecholamines influence liver functions in order to draw benefit from the adrenergic and dopaminergic antagonists currently marketed. Indeed, as these molecules are well-known drugs, their use as therapies or adjuvant treatments in several liver diseases could be facilitated.
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Affiliation(s)
- Elise Lelou
- INSERM, Université Rennes, INRAE, Institut NuMeCan, Nutrition, Metabolisms and Cancer, F-35000 Rennes, France; (E.L.); (A.C.); (N.N.); (C.R.); (Y.M.); (P.S.)
| | - Anne Corlu
- INSERM, Université Rennes, INRAE, Institut NuMeCan, Nutrition, Metabolisms and Cancer, F-35000 Rennes, France; (E.L.); (A.C.); (N.N.); (C.R.); (Y.M.); (P.S.)
| | - Nicolas Nesseler
- INSERM, Université Rennes, INRAE, Institut NuMeCan, Nutrition, Metabolisms and Cancer, F-35000 Rennes, France; (E.L.); (A.C.); (N.N.); (C.R.); (Y.M.); (P.S.)
- CHU Rennes, Department of Anesthesia and Critical Care, F-35000 Rennes, France
| | - Claudine Rauch
- INSERM, Université Rennes, INRAE, Institut NuMeCan, Nutrition, Metabolisms and Cancer, F-35000 Rennes, France; (E.L.); (A.C.); (N.N.); (C.R.); (Y.M.); (P.S.)
| | - Yannick Mallédant
- INSERM, Université Rennes, INRAE, Institut NuMeCan, Nutrition, Metabolisms and Cancer, F-35000 Rennes, France; (E.L.); (A.C.); (N.N.); (C.R.); (Y.M.); (P.S.)
- CHU Rennes, Department of Anesthesia and Critical Care, F-35000 Rennes, France
| | - Philippe Seguin
- INSERM, Université Rennes, INRAE, Institut NuMeCan, Nutrition, Metabolisms and Cancer, F-35000 Rennes, France; (E.L.); (A.C.); (N.N.); (C.R.); (Y.M.); (P.S.)
- CHU Rennes, Department of Anesthesia and Critical Care, F-35000 Rennes, France
| | - Caroline Aninat
- INSERM, Université Rennes, INRAE, Institut NuMeCan, Nutrition, Metabolisms and Cancer, F-35000 Rennes, France; (E.L.); (A.C.); (N.N.); (C.R.); (Y.M.); (P.S.)
- Correspondence: ; Tel.: +33-2-23-23-48-68
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Liu F, Liang J, Long P, Zhu L, Hou W, Wu X, Luo C. ZCCHC17 Served as a Predictive Biomarker for Prognosis and Immunotherapy in Hepatocellular Carcinoma. Front Oncol 2022; 11:799566. [PMID: 35071004 PMCID: PMC8770814 DOI: 10.3389/fonc.2021.799566] [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: 10/21/2021] [Accepted: 12/13/2021] [Indexed: 12/01/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the common malignant tumors. The prognosis and five-year survival rate of HCC are not promising due to tumor recurrence and metastasis. Exploring markers that contribute to the early diagnosis of HCC, markers for prognostic evaluation of HCC patients, and effective targets for treating HCC patients are in the spotlight of HCC therapy. Zinc Finger CCHC-Type Containing 17 (ZCCHC17) encodes the RNA binding protein ZCCHC17, but its role in HCC is still unclear. Here, 90 paraffin-embedded specimens combined with bioinformatics were used to comprehensively clarify the value of ZCCHC17 in the diagnosis and prognosis of HCC and its potential functions. Paraffin-embedded specimens were used to assess ZCCHC17 protein expression and its correlation with prognosis in 90 HCC patients. the public data sets of HCC patients from TCGA, ICG, and GEO databases were also used for further analysis. It was found that protein and mRNA levels of ZCCHC17 in HCC tissues were significantly higher than those in normal tissues. The abnormally high expression may be related to the abnormal DNA methylation of ZCCHC17 in tumor tissues. The high expression of ZCCHC17 is related to AFP, histologic grade, tumor status, vascular invasion, and pathological stage. Multi-data set analysis showed that patients with high ZCCHC17 expression had a worse prognosis, and multivariate cox regression analysis showed an independent prognostic significance of ZCCHC17. The results of functional analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA), indicate that ZCCHC17 is mainly involved in immune regulation. Subsequently, further single-sample gene set enrichment analysis (ssGSEA) showed that the expression of ZCCHC17 was related to the infiltration of immune cells. Importantly, we also analyzed the relationship between ZCCHC17 and immune checkpoint genes, tumor mutation burden (TMB), microsatellite instability (MSI) and TP53 status in HCC patients and evaluated the role of ZCCHC17 in cancer immunotherapy. In summary, ZCCHC17 is a novel marker for the diagnosis and prognostic evaluation of HCC. Concurrently, it regulates immune cells in the tumor microenvironment (TME) of HCC patients, which has a specific reference value for the immunotherapy of HCC.
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Affiliation(s)
- Fahui Liu
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jiadong Liang
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Puze Long
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Lilan Zhu
- Undergraduate Clinical Medicine, Youjiang Medical University for Nationalities, Baise, China
| | - Wanyun Hou
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xueming Wu
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Chunying Luo
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.,Department of Cell Biology, Medical College of Guangxi University, Nanning, China
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Femminò S, D’Ascenzo F, Ravera F, Comità S, Angelini F, Caccioppo A, Franchin L, Grosso A, Thairi C, Venturelli E, Cavallari C, Penna C, De Ferrari GM, Camussi G, Pagliaro P, Brizzi MF. Percutaneous Coronary Intervention (PCI) Reprograms Circulating Extracellular Vesicles from ACS Patients Impairing Their Cardio-Protective Properties. Int J Mol Sci 2021; 22:ijms221910270. [PMID: 34638611 PMCID: PMC8508604 DOI: 10.3390/ijms221910270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) are promising therapeutic tools in the treatment of cardiovascular disorders. We have recently shown that EVs from patients with Acute Coronary Syndrome (ACS) undergoing sham pre-conditioning, before percutaneous coronary intervention (PCI) were cardio-protective, while EVs from patients experiencing remote ischemic pre-conditioning (RIPC) failed to induce protection against ischemia/reperfusion Injury (IRI). No data on EVs from ACS patients recovered after PCI are currently available. Therefore, we herein investigated the cardio-protective properties of EVs, collected after PCI from the same patients. EVs recovered from 30 patients randomly assigned (1:1) to RIPC (EV-RIPC) or sham procedures (EV-naive) (NCT02195726) were characterized by TEM, FACS and Western blot analysis and evaluated for their mRNA content. The impact of EVs on hypoxia/reoxygenation damage and IRI, as well as the cardio-protective signaling pathways, were investigated in vitro (HMEC-1 + H9c2 co-culture) and ex vivo (isolated rat heart). Both EV-naive and EV-RIPC failed to drive cardio-protection both in vitro and ex vivo. Consistently, EV treatment failed to activate the canonical cardio-protective pathways. Specifically, PCI reduced the EV-naive Dusp6 mRNA content, found to be crucial for their cardio-protective action, and upregulated some stress- and cell-cycle-related genes in EV-RIPC. We provide the first evidence that in ACS patients, PCI reprograms the EV cargo, impairing EV-naive cardio-protective properties without improving EV-RIPC functional capability.
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Affiliation(s)
- Saveria Femminò
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (S.F.); (F.R.); (A.C.); (A.G.); (E.V.); (G.C.)
| | - Fabrizio D’Ascenzo
- Department of Medical Sciences, Division of Cardiology, University of Turin, 10126 Turin, Italy; (F.D.); (F.A.); (L.F.); (G.M.D.F.)
| | - Francesco Ravera
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (S.F.); (F.R.); (A.C.); (A.G.); (E.V.); (G.C.)
| | - Stefano Comità
- Department of Clinical and Biological Sciences, University of Turin, 10143 Orbassano, Italy; (S.C.); (C.T.); (C.P.); (P.P.)
| | - Filippo Angelini
- Department of Medical Sciences, Division of Cardiology, University of Turin, 10126 Turin, Italy; (F.D.); (F.A.); (L.F.); (G.M.D.F.)
| | - Andrea Caccioppo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (S.F.); (F.R.); (A.C.); (A.G.); (E.V.); (G.C.)
| | - Luca Franchin
- Department of Medical Sciences, Division of Cardiology, University of Turin, 10126 Turin, Italy; (F.D.); (F.A.); (L.F.); (G.M.D.F.)
| | - Alberto Grosso
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (S.F.); (F.R.); (A.C.); (A.G.); (E.V.); (G.C.)
| | - Cecilia Thairi
- Department of Clinical and Biological Sciences, University of Turin, 10143 Orbassano, Italy; (S.C.); (C.T.); (C.P.); (P.P.)
| | - Emilio Venturelli
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (S.F.); (F.R.); (A.C.); (A.G.); (E.V.); (G.C.)
| | | | - Claudia Penna
- Department of Clinical and Biological Sciences, University of Turin, 10143 Orbassano, Italy; (S.C.); (C.T.); (C.P.); (P.P.)
| | - Gaetano Maria De Ferrari
- Department of Medical Sciences, Division of Cardiology, University of Turin, 10126 Turin, Italy; (F.D.); (F.A.); (L.F.); (G.M.D.F.)
| | - Giovanni Camussi
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (S.F.); (F.R.); (A.C.); (A.G.); (E.V.); (G.C.)
| | - Pasquale Pagliaro
- Department of Clinical and Biological Sciences, University of Turin, 10143 Orbassano, Italy; (S.C.); (C.T.); (C.P.); (P.P.)
| | - Maria Felice Brizzi
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (S.F.); (F.R.); (A.C.); (A.G.); (E.V.); (G.C.)
- Correspondence: ; Tel.: +39-011-670-6653
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Sun R, Li S, Zhao K, Diao M, Li L. Identification of Ten Core Hub Genes as Potential Biomarkers and Treatment Target for Hepatoblastoma. Front Oncol 2021; 11:591507. [PMID: 33868991 PMCID: PMC8047669 DOI: 10.3389/fonc.2021.591507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
Background This study aimed to systematically investigate gene signatures for hepatoblastoma (HB) and identify potential biomarkers for its diagnosis and treatment. Materials and Methods GSE131329 and GSE81928 were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between hepatoblastoma and normal samples were identified using the Limma package in R. Then, the similarity of network traits between two sets of genes was analyzed by weighted gene correlation network analysis (WGCNA). Cytoscape was used to visualize and select hub genes. PPI network of hub genes was construed by Cytoscape. GO enrichment and KEGG pathway analyses of hub genes were carried out using ClueGO. The random forest classifier was constructed based on the hub genes using the GSE131329 dataset as the training set, and its reliability was validated using the GSE81928 dataset. The resulting core hub genes were combined with the InnateDB database to identify the innate core genes. Results A total of 4244 DEGs in HB were identified. WGCNA identified four modules that were significantly correlated with the disease status. A total of 114 hub genes were obtained within the top 20 genes of each node rank. 6982 relation pairs and 3700 nodes were contained in the PPI network of 114 hub genes. GO enrichment and KEGG pathway analyses of hub genes were focused on MAPK, cell cycle, p53, and other crucial pathways involved in HB. A random forest classifier was constructed using the 114 hub genes as feature genes, resulting in a 95.5% true positive rate when classifying HB and normal samples. A total of 35 core hub genes were obtained through the mean decrease in accuracy and mean decrease Gini of the random forest model. The classification efficiency of the random forest model was 81.4%. Finally, CDK1, TOP2A, ADRA1A, FANCI, XRCC1, TPX2, CCNB2, CDK4, GLYATL1, and CFHR3 were identified by cross-comparison with the InnateDB database. Conclusion Our study established a random forest classifier that identified 10 core genes in HB. These findings may be beneficial for the diagnosis, prediction, and targeted therapy of HB.
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Affiliation(s)
- Rui Sun
- Department of Pediatric Surgery, Capital Institute of Pediatrics, Beijing, China.,Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Simin Li
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Ke Zhao
- Department of Ophthalmology, Ningbo Hangzhou Bay Hospital, Ningbo, China
| | - Mei Diao
- Department of Pediatric Surgery, Capital Institute of Pediatrics, Beijing, China
| | - Long Li
- Department of Pediatric Surgery, Capital Institute of Pediatrics, Beijing, China
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Chen LM, Xiang L, Sun WJ, Zhai YJ, Gao S, Fan YC, Wang K. Diagnostic Value of the Hypomethylation of the WISP1 Promoter in Patients with Hepatocellular Carcinoma Associated with Hepatitis B Virus. TOHOKU J EXP MED 2020; 252:297-307. [PMID: 33239483 DOI: 10.1620/tjem.252.297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Wnt1-inducible signaling pathway protein 1 (WISP1) regulates cell proliferation, differentiation, adhesion, migration and survival. Abnormal WISP1 expression is associated with the carcinogenesis of hepatocellular carcinoma (HCC). Aberrant DNA methylation is one of the major epigenetic alterations in HCC. However, the methylation status of the WISP1 promoter is still unclear. We therefore aimed to determine the methylation status of the WISP1 promoter and evaluate its clinical value in HCC. The study enrolled 251 participants, including 123 participants with HCC, 90 participants with chronic hepatitis B (CHB) and 38 healthy controls (HCs). WISP1 methylation status, mRNA levels and plasma soluble WISP1 were detected by methylation-specific polymerase chain reaction (MSP), quantitative real-time PCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA), respectively. We found that the methylation frequency of WISP1 in patients with HCC was significantly lower than that in patients with CHB and HCs, while the relative expression levels of WISP1 mRNA were markedly higher in patients with HCC than in patients with CHB and HCs. Furthermore, the plasma soluble WISP1 in patients with HCC was obviously lower than in that in patients with CHB and HCs. Alpha-fetoprotein (AFP) is a widely recognized biomarker to diagnose HCC which lacks enough sensitivity and specificity. WISP1 promoter methylation status combined with AFP significantly improved the diagnostic ability in discriminating HCC from CHB compared with AFP or WISP1 methylation status alone. In conclusion, hypomethylation of the WISP1 gene promoter may serve as a noninvasive biomarker for detecting HBV-associated HCC.
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Affiliation(s)
- La-Mei Chen
- Department of Hepatology, Qilu Hospital of Shandong University
| | - Lin Xiang
- Department of Hepatology, Qilu Hospital of Shandong University
| | - Wei-Juan Sun
- Department of Hepatology, Qilu Hospital of Shandong University
| | - Yu-Jia Zhai
- Department of Hepatology, Qilu Hospital of Shandong University
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University.,Institute of Hepatology, Shandong University
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University.,Institute of Hepatology, Shandong University.,Shenzhen Research Institute of Shandong University
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University.,Institute of Hepatology, Shandong University.,Shenzhen Research Institute of Shandong University
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