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Wang Z, Chen X, Zhang J, Chen X, Peng J, Huang W. Based on disulfidptosis-related glycolytic genes to construct a signature for predicting prognosis and immune infiltration analysis of hepatocellular carcinoma. Front Immunol 2023; 14:1204338. [PMID: 37680641 PMCID: PMC10482091 DOI: 10.3389/fimmu.2023.1204338] [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: 04/12/2023] [Accepted: 08/04/2023] [Indexed: 09/09/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) comprises several distinct molecular subtypes with varying prognostic implications. However, a comprehensive analysis of a prognostic signature for HCC based on molecular subtypes related to disulfidptosis and glycolysis, as well as associated metabolomics and the immune microenvironment, is yet to be fully explored. Methods Based on the differences in the expression of disulfide-related glycolytic genes (DRGGs), patients with HCC were divided into different subtypes by consensus clustering. Establish and verify a risk prognosis signature. Finally, the expression level of the key gene SLCO1B1 in the signature was evaluated using immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR) in HCC. The association between this gene and immune cells was explored using multiplex immunofluorescence. The biological functions of the cell counting kit-8, wound healing, and colony formation assays were studied. Results Different subtypes of patients have specific clinicopathological features, prognosis and immune microenvironment. We identified seven valuable genes and constructed a risk-prognosis signature. Analysis of the risk score revealed that compared to the high-risk group, the low-risk group had a better prognosis, higher immune scores, and more abundant immune-related pathways, consistent with the tumor subtypes. Furthermore, IHC and qRT-PCR analyses showed decreased expression of SLCO1B1 in HCC tissues. Functional experiments revealed that SLCO1B1 overexpression inhibited the proliferation, migration, and invasion of HCC cells. Conclusion We developed a prognostic signature that can assist clinicians in predicting the overall survival of patients with HCC and provides a reference value for targeted therapy.
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Affiliation(s)
- Zhijian Wang
- Department of General Practice, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuenuo Chen
- Department of Infectious Disease, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jia Zhang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuanxin Chen
- Department of Infectious Disease, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiayi Peng
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wenxiang Huang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Yuan D, Chu J, Lin H, Zhu G, Qian J, Yu Y, Yao T, Ping F, Chen F, Liu X. Mechanism of homocysteine-mediated endothelial injury and its consequences for atherosclerosis. Front Cardiovasc Med 2023; 9:1109445. [PMID: 36727029 PMCID: PMC9884709 DOI: 10.3389/fcvm.2022.1109445] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Homocysteine (Hcy) is an intermediate amino acid formed during the conversion from methionine to cysteine. When the fasting plasma Hcy level is higher than 15 μmol/L, it is considered as hyperhomocysteinemia (HHcy). The vascular endothelium is an important barrier to vascular homeostasis, and its impairment is the initiation of atherosclerosis (AS). HHcy is an important risk factor for AS, which can promote the development of AS and the occurrence of cardiovascular events, and Hcy damage to the endothelium is considered to play a very important role. However, the mechanism by which Hcy damages the endothelium is still not fully understood. This review summarizes the mechanism of Hcy-induced endothelial injury and the treatment methods to alleviate the Hcy induced endothelial dysfunction, in order to provide new thoughts for the diagnosis and treatment of Hcy-induced endothelial injury and subsequent AS-related diseases.
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Liu B, Wang S, Xu M, Ma Y, Sun R, Ding H, Li L. The double-edged role of hydrogen sulfide in the pathomechanism of multiple liver diseases. Front Pharmacol 2022; 13:899859. [PMID: 36588686 PMCID: PMC9800830 DOI: 10.3389/fphar.2022.899859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
In mammalian systems, hydrogen sulfide (H2S)-one of the three known gaseous signaling molecules in mammals-has been found to have a variety of physiological functions. Existing studies have demonstrated that endogenous H2S is produced through enzymatic and non-enzymatic pathways. The liver is the body's largest solid organ and is essential for H2S synthesis and elimination. Mounting evidence suggests H2S has essential roles in various aspects of liver physiological processes and pathological conditions, such as hepatic lipid metabolism, liver fibrosis, liver ischemia‒reperfusion injury, hepatocellular carcinoma, hepatotoxicity, and acute liver failure. In this review, we discuss the functions and underlying molecular mechanisms of H2S in multiple liver pathophysiological conditions.
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Affiliation(s)
- Bihan Liu
- Department of Hepatology and Gastroenterology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shanshan Wang
- Department of Hepatology and Gastroenterology, Beijing Youan Hospital, Capital Medical University, Beijing, China,Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Ming Xu
- Brainnetome Center and National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China,School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Ma
- Department of Hepatology and Gastroenterology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Rui Sun
- Department of Hepatology and Gastroenterology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Huiguo Ding
- Department of Hepatology and Gastroenterology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Lei Li
- Department of Hepatology and Gastroenterology, Beijing Youan Hospital, Capital Medical University, Beijing, China,*Correspondence: Lei Li,
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Mei M, Liu D, Tang X, You Y, Peng B, He X, Huang J. Vitamin B6 Metabolic Pathway is Involved in the Pathogenesis of Liver Diseases via Multi-Omics Analysis. J Hepatocell Carcinoma 2022; 9:729-750. [PMID: 35979344 PMCID: PMC9377404 DOI: 10.2147/jhc.s370255] [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: 04/20/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To clarify the underlying regulatory mechanisms of progression from liver cirrhosis to hepatocellular carcinoma (HCC), we analyzed the microbiomics, metabolomics, and proteomics in plasma and tissues from patients with HCC or decompensated liver cirrhosis (DC). Patients and Methods Tissues and plasma from 44 HCC patients and 28 patients with DC were collected for metabolomic analysis. 16S rRNA sequencing was performed in nine HCC tissues (HCCT), four distal noncancerous tissues (HCCN), and 11 DC tissues (DCT). Five HCC tissues had liver cirrhosis (HCCT-LC). Five hepatocellular carcinoma tissues without liver cirrhosis (HCCT-NLC) and five DCT were selected for proteomic sequencing. After combining proteomic and metabolomic analysis, we constructed a mouse model of chronic liver injury using carbon tetrachloride (CCl4) and treated them with vitamin B6 (VB6). Results 16s rRNA sequence results showed that HCC tissues had higher alpha diversity. The highest LDA scores were detected for Elizabethkingia in HCCT, Subsaxibacter in DCT, and Stenotrophomon in HCCN. Metabolomics results demonstrated some metabolites, including capric acid, L-threonate, choline, alpha-D-Glucose, D-ribose, betaine, 2E-eicosenoic acid, linoleic acid, L-palmitoylcarnitine, taurodeoxycholic acid, L-pyroglutamic acid, androsterone sulfate, and phthalic acid mono-2-ethylhexyl ester (MEHP), had better diagnostic efficacy than AFP (AUC: 0.852; 95% CI: 0.749, 0.954). In a combined analysis of metabolomics and proteomics, we found that HCCT-LC had more obvious disorders of VB6 metabolism and pentose and glucuronate interconversions than DCT, and kynurenine metabolism disorder was more significant in HCCT-LC than in HCCT-NLC. In the CCl4-induced chronic liver injury model, after VB6 supplementation, inflammatory cell infiltration, hepatocyte edema, and degeneration were significantly improved. Conclusion We found significant differences in the flora distribution between HCCT and DC; MEHP was a new diagnostic biomarker of HCC, and VB6 ameliorated the inflammatory cell infiltration, hepatocyte edema, and degeneration in chronic liver injury.
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Affiliation(s)
- Meihua Mei
- Organ Transplant Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial Key Laboratory of Organ Donation & Transplant Immunology, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial International Cooperation Base of Science & Technology (Organ Transplantation), Guangzhou, 510080, People's Republic of China.,Department of Laboratory Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Danping Liu
- Organ Transplant Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial Key Laboratory of Organ Donation & Transplant Immunology, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial International Cooperation Base of Science & Technology (Organ Transplantation), Guangzhou, 510080, People's Republic of China.,Department of Laboratory Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Xiuxin Tang
- Organ Transplant Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial Key Laboratory of Organ Donation & Transplant Immunology, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial International Cooperation Base of Science & Technology (Organ Transplantation), Guangzhou, 510080, People's Republic of China.,Department of Laboratory Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Ying You
- Organ Transplant Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial Key Laboratory of Organ Donation & Transplant Immunology, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial International Cooperation Base of Science & Technology (Organ Transplantation), Guangzhou, 510080, People's Republic of China.,Department of Laboratory Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Baogang Peng
- Hepatobiliary Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Xiaoshun He
- Organ Transplant Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial Key Laboratory of Organ Donation & Transplant Immunology, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial International Cooperation Base of Science & Technology (Organ Transplantation), Guangzhou, 510080, People's Republic of China
| | - Junqi Huang
- Organ Transplant Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial Key Laboratory of Organ Donation & Transplant Immunology, Guangzhou, 510080, People's Republic of China.,Guangdong Provincial International Cooperation Base of Science & Technology (Organ Transplantation), Guangzhou, 510080, People's Republic of China.,Department of Laboratory Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
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Sun Y, Yang J, Cai H, Liu J, Liu Y, Luo J, Zhou H. Differential OAT methylation correlates with cell infiltration in tumor microenvironment and overall survival post-radiotherapy in oral squamous cell carcinoma patient. J Oral Pathol Med 2022; 51:611-619. [PMID: 35708285 DOI: 10.1111/jop.13328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Given that DNA methylation and tumor microenvironment (TME) are susceptible to radiotherapy, we aimed to figure out specific differential DNA methylation to reflect oral squamous cell carcinoma (OSCC) prognosis and associated effect on TME changes post-radiotherapy, performing as an efficient biomarker. MATERIALS AND METHODS Differentially methylation analysis was performed using data from TCGA. Curves of Kaplan Meier (K-M) survival, cumulative hazard and events, Cox proportional hazards and Linear regression model were conducted to screen and validate differential methylation genes, while multiple regression equation to analyze if ornithine aminotransferase (OAT) methylation correlates with radiotherapy. For correlation between OAT methylation and immune infiltrates, CIBERSORT and ESTIMATE algorithms were performed, following GSEA and ssGSEA analysis to evaluate biological process. RESULTS Compared to normal tissues, only OAT in OSCC was differential significantly by K-M analysis (p = 0.0364). OAT hypermethylation was associated with increased overall survival (HR: 0.65, p = 0.0358). Radiotherapy correlated with OAT methylation (β = -0.01, p = 0.0061); most patients with OAT hypermethylation were radiation-sensitive. Hypomethylated OAT correlated with higher cell infiltrations in TME. Neuroactive ligand-receptor interaction was most significantly related to OAT methylation (p = 9.2e-10). Sulfur metabolism was the most significantly in OAT hypermethylation group (p = 0.0041) and RIG-I-like receptor in OAT hypomethylation group (p = 0.0094). CONCLUSION OAT methylation can serve as a predictor of OSCC prognosis post-radiotherapy with potential mechanism by changing cell infiltrations in TME, but further experimental study deserves to carry out confirming the role and mechanism of OAT methylation in OSCC. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yu Sun
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jin Yang
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - He Cai
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Junjiang Liu
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yangfan Liu
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jingjing Luo
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Hwangbo S, Lee S, Lee S, Hwang H, Kim I, Park T. Kernel-based hierarchical structural component models for pathway analysis. Bioinformatics 2022; 38:3078-3086. [PMID: 35460238 DOI: 10.1093/bioinformatics/btac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/08/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Pathway analyses have led to more insight into the underlying biological functions related to the phenotype of interest in various types of omics data. Pathway-based statistical approaches have been actively developed, but most of them do not consider correlations among pathways. Because it is well known that there are quite a few biomarkers that overlap between pathways, these approaches may provide misleading results. In addition, most pathway-based approaches tend to assume that biomarkers within a pathway have linear associations with the phenotype of interest, even though the relationships are more complex. RESULTS To model complex effects including nonlinear effects, we propose a new approach, Hierarchical structural CoMponent analysis using Kernel (HisCoM-Kernel). The proposed method models nonlinear associations between biomarkers and phenotype by extending the kernel machine regression and analyzes entire pathways simultaneously by using the biomarker-pathway hierarchical structure. HisCoM-Kernel is a flexible model that can be applied to various omics data. It was successfully applied to three omics datasets generated by different technologies. Our simulation studies showed that HisCoM-Kernel provided higher statistical power than other existing pathway-based methods in all datasets. The application of HisCoM-Kernel to three types of omics dataset showed its superior performance compared to existing methods in identifying more biologically meaningful pathways, including those reported in previous studies. AVAILABILITY AND IMPLEMENTATION Freely available at http://statgen.snu.ac.kr/software/HisCom-Kernel/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Suhyun Hwangbo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Korea.,Department of Genomic Medicine, Seoul National University Hospital, Seoul, 03080, Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, 03080, Korea
| | - Seungyeoun Lee
- Department of Mathematics and Statistics, Sejong University, Sejong, 05006, Korea
| | - Heungsun Hwang
- Department of Psychology, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Inyoung Kim
- Department of Statistics, Virginia Tech, Blacksburg, Virginia, 24060, U.S.A
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Korea.,Department of Statistics, Seoul National University, Seoul, 151-747, Korea
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