1
|
Deng B, Liu Y, Chen Y, He P, Ma J, Tan Z, Zhang J, Dong W. Exploring the butyrate metabolism-related shared genes in metabolic associated steatohepatitis and ulcerative colitis. Sci Rep 2024; 14:15949. [PMID: 38987612 PMCID: PMC11237055 DOI: 10.1038/s41598-024-66574-0] [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: 03/20/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024] Open
Abstract
Metabolic-associated steatohepatitis (MASH) and ulcerative colitis (UC) exhibit a complex interconnection with immune dysfunction, dysbiosis of the gut microbiota, and activation of inflammatory pathways. This study aims to identify and validate critical butyrate metabolism-related shared genes between both UC and MASH. Clinical information and gene expression profiles were sourced from the Gene Expression Omnibus (GEO) database. Shared butyrate metabolism-related differentially expressed genes (sBM-DEGs) between UC and MASH were identified via various bioinformatics methods. Functional enrichment analysis was performed, and UC patients were categorized into subtypes using the consensus clustering algorithm based on sBM-DEGs. Key genes within sBM-DEGs were screened through Random Forest, Support Vector Machines-Recursive Feature Elimination, and Light Gradient Boosting. The diagnostic efficacy of these genes was evaluated using receiver operating characteristic (ROC) analysis on independent datasets. Additionally, the expression levels of characteristic genes were validated across multiple independent datasets and human specimens. Forty-nine shared DEGs between UC and MASH were identified, with enrichment analysis highlighting significant involvement in immune, inflammatory, and metabolic pathways. The intersection of butyrate metabolism-related genes with these DEGs produced 10 sBM-DEGs. These genes facilitated the identification of molecular subtypes of UC patients using an unsupervised clustering approach. ANXA5, CD44, and SLC16A1 were pinpointed as hub genes through machine learning algorithms and feature importance rankings. ROC analysis confirmed their diagnostic efficacy in UC and MASH across various datasets. Additionally, the expression levels of these three hub genes showed significant correlations with immune cells. These findings were validated across independent datasets and human specimens, corroborating the bioinformatics analysis results. Integrated bioinformatics identified three significant biomarkers, ANXA5, CD44, and SLC16A1, as DEGs linked to butyrate metabolism. These findings offer new insights into the role of butyrate metabolism in the pathogenesis of UC and MASH, suggesting its potential as a valuable diagnostic biomarker.
Collapse
Affiliation(s)
- Beiying Deng
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No 99 Zhangzhidong Road, Wuhan, 430060, Hubei Province, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yinghui Liu
- Department of Geriatric, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ying Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No 99 Zhangzhidong Road, Wuhan, 430060, Hubei Province, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Pengzhan He
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No 99 Zhangzhidong Road, Wuhan, 430060, Hubei Province, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingjing Ma
- Department of Geriatric, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zongbiao Tan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No 99 Zhangzhidong Road, Wuhan, 430060, Hubei Province, China
| | - Jixiang Zhang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No 99 Zhangzhidong Road, Wuhan, 430060, Hubei Province, China
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, No 99 Zhangzhidong Road, Wuhan, 430060, Hubei Province, China.
| |
Collapse
|
2
|
Wang L, Niu X. Immunoregulatory Roles of Osteopontin in Diseases. Nutrients 2024; 16:312. [PMID: 38276550 PMCID: PMC10819284 DOI: 10.3390/nu16020312] [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: 11/17/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Osteopontin (OPN) is a multifunctional protein that plays a pivotal role in the immune system. It is involved in various biological processes, including cell adhesion, migration and survival. The study of the immunomodulatory effects of OPN is of paramount importance due to its potential therapeutic applications. A comprehensive understanding of how OPN regulates the immune response could pave the way for the development of novel treatments for a multitude of diseases, including autoimmune disorders, infectious diseases and cancer. Therefore, in the following paper, we provide a systematic overview of OPN and its immunoregulatory roles in various diseases, laying the foundation for the development of OPN-based therapies in the future.
Collapse
Affiliation(s)
- Lebei Wang
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaoyin Niu
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
| |
Collapse
|
3
|
Liao Y, Wu C, Li Y, Wen J, Zhao D. MIF is a critical regulator of mononuclear phagocytic infiltration in hepatocellular carcinoma. iScience 2023; 26:107273. [PMID: 37520719 PMCID: PMC10371853 DOI: 10.1016/j.isci.2023.107273] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/03/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Immunotherapy targeting tumor-associated macrophages (TAMs) is a promising approach to treating cancer. However, the limited drug targets and ambiguous mechanisms impede the development of clinical immunotherapy strategies. To elucidate the underlying processes involved in mononuclear phagocyte (MNP) infiltration and phenotypic changes in hepatocellular carcinoma (HCC), we integrated single-cell RNA-sequencing data from 100,030 cells derived from patients with HCC and healthy individuals and compared the phenotypes and origins of the MNPs in the tumor core, tumor periphery, adjacent normal tissue, and healthy liver samples. Using machine learning and multi-omics analyses, we identified 445 infiltration-associated genes and potential drug targets affecting this process. Through in vitro experiments, we found that the expression of macrophage migration inhibitory factor (MIF) is the upstream regulator of secreted phosphoprotein 1 (SPP1) and promote migration in TAMs. Our findings also indicate that MIF promotes tumor metastasis and invasion and is a promising potential target for treating HCC.
Collapse
Affiliation(s)
- Yunxi Liao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Chenyang Wu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Jinhua Wen
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| |
Collapse
|
4
|
Wang W, Liu X, Wei P, Ye F, Chen Y, Shi L, Zhang X, Li J, Lin S, Yang X. SPP1 and CXCL9 Promote Non-alcoholic Steatohepatitis Progression Based on Bioinformatics Analysis and Experimental Studies. Front Med (Lausanne) 2022; 9:862278. [PMID: 35514751 PMCID: PMC9063562 DOI: 10.3389/fmed.2022.862278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Background and Aims Non-alcoholic fatty liver disease (NAFLD) is a major chronic liver disease worldwide, and non-alcoholic steatohepatitis (NASH) is one of its pathological subtypes. The pathogenesis of NASH has not yet been fully elucidated. The purpose of this study was to identify the hub genes and pathways involved in NASH using bioinformatics methods. The hub genes were confirmed in human and animal models. Materials and Methods Three Gene Expression Omnibus (GEO) datasets (GSE48452, GSE58979, and GSE151158) of NASH patients and healthy controls were included in the study. We used GEO2R to identify differentially expressed genes (DEGs) between NASH patients and healthy controls. Functional enrichment analyses were then performed to explore the potential functions and pathways of the DEGs. In all DEGs, only two genes were highly expressed in NASH patients throughout the three datasets; these two genes, SPP1 and CXCL9, were further studied. Serum and liver tissues from NASH patients and healthy controls were collected. Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels were measured in NASH patients and healthy controls. Liver tissues were stained with hematoxylin and eosin. Immunohistochemical staining was used to evaluate the expression levels of the two genes in liver tissues. Male C57BL/6J mice were fed a methionine choline-deficient (MCD) diet for 8 weeks, after which serum ALT and AST levels were measured and liver tissues were stained. Results SPP1 and CXCL9 were the hub genes detected in the three datasets. “Lipid metabolism,” “inflammatory response,” and “lymphocyte activation” were the most significant biological functions in GSE48452, GSE58979, and GSE151158, respectively. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the toll-like receptor signaling pathway was significantly enriched in NASH patients. Serum ALT and AST levels were significantly increased in NASH patients compared to healthy controls. Liver tissues had more serious steatosis, hepatocyte ballooning degeneration, and lobular inflammatory infiltration, and the expression of SPP1 and CXCL9 in liver cells was significantly upregulated in NASH patients compared to healthy controls. MCD diet mice were consistent with NASH patients. Conclusion SPP1 and CXCL9 may play important roles in NASH pathogenesis and could be potential therapeutic targets and biomarkers of NASH in the future. Further experimental studies are needed to confirm our results.
Collapse
Affiliation(s)
- Wen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaojing Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Peiyao Wei
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Feng Ye
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yunru Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lei Shi
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xi Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jianzhou Li
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shumei Lin
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Shumei Lin
| | - Xueliang Yang
- Department of Nutrition, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- *Correspondence: Xueliang Yang
| |
Collapse
|