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Wu X, Yuan C, Pan J, Zhou Y, Pan X, Kang J, Ren L, Gong L, Li Y. CXCL9, IL2RB, and SPP1, potential diagnostic biomarkers in the co-morbidity pattern of atherosclerosis and non-alcoholic steatohepatitis. Sci Rep 2024; 14:16364. [PMID: 39013959 PMCID: PMC11252365 DOI: 10.1038/s41598-024-66287-4] [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: 04/02/2024] [Accepted: 07/01/2024] [Indexed: 07/18/2024] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a hepatocyte inflammation based on hepatocellular steatosis, yet there is no effective drug treatment. Atherosclerosis (AS) is caused by lipid deposition in the endothelium, which can lead to various cardiovascular diseases. NASH and AS share common risk factors, and NASH can also elevate the risk of AS, causing a higher morbidity and mortality rate for atherosclerotic heart disease. Therefore, timely detection and diagnosis of NASH and AS are particularly important. In this study, differential gene expression analysis and weighted gene co-expression network analysis were performed on the AS (GSE100927) and NASH (GSE89632) datasets to obtain common crosstalk genes, respectively. Then, candidate Hub genes were screened using four topological algorithms and externally validated in the GSE43292 and GSE63067 datasets to obtain Hub genes. Furthermore, immune infiltration analysis and gene set variation analysis were performed on the Hub genes to explore the underlying mechanisms. The DGIbd database was used to screen candidate drugs for AS and NASH. Finally, a NASH model was constructed using free fatty acid-induced human L02 cells, an AS model was constructed using lipopolysaccharide-induced HUVECs, and a co-morbidity model was constructed using L02 cells and HUVECs to verify Hub gene expression. The result showed that a total of 113 genes common to both AS and NASH were identified as crosstalk genes, and enrichment analysis indicated that these genes were mainly involved in the regulation of immune and metabolism-related pathways. 28 candidate Hub genes were screened according to four topological algorithms, and CXCL9, IL2RB, and SPP1 were identified as Hub genes after in vitro experiments and external dataset validation. The ROC curves and SVM modeling demonstrated the good diagnostic efficacy of these three Hub genes. In addition, the Hub genes are strongly associated with immune cell infiltration, especially macrophages and γ-δ T cell infiltration. Finally, five potential therapeutic drugs were identified. has-miR-185 and hsa-miR-335 were closely related to AS and NASH. This study demonstrates that CXCL9, IL2RB, and SPP1 may serve as potential biomarkers for the diagnosis of the co-morbidity patterns of AS and NASH and as potential targets for drug therapy.
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Affiliation(s)
- Xize Wu
- Liaoning University of Traditional Chinese Medicine, No. 79 Chongshan East Road, Huanggu District, Shenyang, 110847, Liaoning, China
- Nantong Hospital of Traditional Chinese Medicine, Nantong Hospital Affiliated to Nanjing University of Chinese Medicine, Nantong, 226000, Jiangsu, China
| | - Changbin Yuan
- Liaoning University of Traditional Chinese Medicine, No. 79 Chongshan East Road, Huanggu District, Shenyang, 110847, Liaoning, China
| | - Jiaxiang Pan
- The Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, 110032, Liaoning, China
| | - Yi Zhou
- Liaoning University of Traditional Chinese Medicine, No. 79 Chongshan East Road, Huanggu District, Shenyang, 110847, Liaoning, China
| | - Xue Pan
- Liaoning University of Traditional Chinese Medicine, No. 79 Chongshan East Road, Huanggu District, Shenyang, 110847, Liaoning, China
- Dazhou Vocational College of Chinese Medicine, Dazhou, 635000, Sichuan, China
| | - Jian Kang
- Liaoning University of Traditional Chinese Medicine, No. 79 Chongshan East Road, Huanggu District, Shenyang, 110847, Liaoning, China
| | - Lihong Ren
- Nantong Hospital of Traditional Chinese Medicine, Nantong Hospital Affiliated to Nanjing University of Chinese Medicine, Nantong, 226000, Jiangsu, China.
| | - Lihong Gong
- Liaoning University of Traditional Chinese Medicine, No. 79 Chongshan East Road, Huanggu District, Shenyang, 110847, Liaoning, China.
- The Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, 110032, Liaoning, China.
- Liaoning Provincial Key Laboratory of TCM Geriatric Cardio-Cerebrovascular Diseases, Shenyang, 110847, Liaoning, China.
| | - Yue Li
- The Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, 110032, Liaoning, China.
- Liaoning Provincial Key Laboratory of TCM Geriatric Cardio-Cerebrovascular Diseases, Shenyang, 110847, Liaoning, China.
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Zhong Z, Xu M, Ge C, Tan J. Exploring shared molecular signatures and regulatory mechanisms in nonalcoholic steatohepatitis and inflammatory bowel disease using integrative bioinformatics analysis. Sci Rep 2024; 14:12085. [PMID: 38802459 PMCID: PMC11130338 DOI: 10.1038/s41598-024-62310-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: 02/27/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
The co-existence of inflammatory bowel disease (IBD) and non-alcoholic steatohepatitis (NASH) has raised interest in identifying shared molecular mechanisms and potential therapeutic targets. However, the relationship between these two diseases remains unclear and effective medical treatments are still lacking. Through the bioinformatics analysis in this study, 116 shared differentially expressed genes (SDEGs) were identified between IBD and NASH datasets. GO and KEGG pathway analyses revealed significant involvement of SDEGs in apoptotic processes, cell death, defense response, cytokine and chemokine activity, and signaling pathways. Furthermore, weighted gene co-expression network analysis (WGCNA) identified five shared signature genes associated specifically with IBD and NASH, they were CXCL9, GIMAP2, ADAMTS5, GRAP, and PRF1. These five genes represented potential diagnostic biomarkers for distinguishing patients with diseases from healthy individuals by using two classifier algorithms and were positively related to autophagy, ferroptosis, angiogenesis, and immune checkpoint factors in the two diseases. Additionally, single-cell analysis of IBD and NASH samples highlighted the expression of regulatory genes in various immune cell subtypes, emphasizing their significance in disease pathogenesis. Our work elucidated the shared signature genes and regulatory mechanisms of IBD and NASH, which could provide new potential therapies for patients with IBD and NASH.
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Affiliation(s)
- Zixuan Zhong
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, 400067, People's Republic of China.
- Research Center of Brain Intellectual Promotion and Development for Children Aged 0-6 Years, Chongqing University of Education, Chongqing, 400067, People's Republic of China.
| | - Minxuan Xu
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, 400067, People's Republic of China
- Research Center of Brain Intellectual Promotion and Development for Children Aged 0-6 Years, Chongqing University of Education, Chongqing, 400067, People's Republic of China
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400030, People's Republic of China
| | - Chenxu Ge
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, 400067, People's Republic of China
- Research Center of Brain Intellectual Promotion and Development for Children Aged 0-6 Years, Chongqing University of Education, Chongqing, 400067, People's Republic of China
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400030, People's Republic of China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, 400067, People's Republic of China
- Research Center of Brain Intellectual Promotion and Development for Children Aged 0-6 Years, Chongqing University of Education, Chongqing, 400067, People's Republic of China
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Herrera-Marcos LV, Martínez-Beamonte R, Arnal C, Barranquero C, Puente-Lanzarote JJ, Lou-Bonafonte JM, Gonzalo-Romeo G, Mocciaro G, Jenkins B, Surra JC, Rodríguez-Yoldi MJ, Alastrué-Vera V, Letosa J, García-Gil A, Güemes A, Koulman A, Osada J. Lipidomic signatures discriminate subtle hepatic changes in the progression of porcine nonalcoholic steatohepatitis. Am J Physiol Gastrointest Liver Physiol 2024; 326:G411-G425. [PMID: 38375587 DOI: 10.1152/ajpgi.00264.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/05/2024] [Accepted: 02/11/2024] [Indexed: 02/21/2024]
Abstract
Recently, the development of nonalcoholic steatohepatitis (NASH) in common strains of pigs has been achieved using a diet high in saturated fat, fructose, cholesterol, and cholate and deficient in choline and methionine. The aim of the present work was to characterize the hepatic and plasma lipidomic changes that accompany the progression of NASH and its reversal by switching pigs back to a chow diet. One month of this extreme steatotic diet was sufficient to induce porcine NASH. The lipidomic platform using liquid chromatography-mass spectrometry analyzed 467 lipid species. Seven hepatic phospholipids [PC(30:0), PC(32:0), PC(33:0), PC(33:1), PC(34:0), PC(34:3) and PC(36:2)] significantly discriminated the time of dietary exposure, and PC(30:0), PC(33:0), PC(33:1) and PC(34:0) showed rapid adaptation in the reversion period. Three transcripts (CS, MAT1A, and SPP1) showed significant changes associated with hepatic triglycerides and PC(33:0). Plasma lipidomics revealed that these species [FA 16:0, FA 18:0, LPC(17:1), PA(40:5), PC(37:1), TG(45:0), TG(47:2) and TG(51:0)] were able to discriminate the time of dietary exposure. Among them, FA 16:0, FA 18:0, LPC(17:1) and PA(40:5) changed the trend in the reversion phase. Plasma LDL-cholesterol and IL12P40 were good parameters to study the progression of NASH, but their capacity was surpassed by hepatic [PC(33:0), PC(33:1), and PC(34:0)] or plasma lipid [FA 16:0, FA 18:0, and LPC(17:1)] species. Taken together, these lipid species can be used as biomarkers of metabolic changes in the progression and regression of NASH in this model. The lipid changes suggest that the development of NASH also affects peripheral lipid metabolism.NEW & NOTEWORTHY A NASH stage was obtained in crossbred pigs. Hepatic [PC(33:0), PC(33:1) and PC(34:0)] or plasma [FA 16:0, FA 18:0 and LPC(17:1)] species were sensitive parameters to detect subtle changes in development and regression of nonalcoholic steatohepatitis (NASH). These findings may delineate the liquid biopsy to detect subtle changes in progression or in treatments. Furthermore, phospholipid changes according to the insult-inducing NASH may play an important role in accepting or rejecting fatty livers in transplantation.
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Affiliation(s)
- Luis V Herrera-Marcos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, Zaragoza, Spain
| | - Roberto Martínez-Beamonte
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, Zaragoza, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Arnal
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Barranquero
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, Zaragoza, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan J Puente-Lanzarote
- Servicio de Bioquímica Clínica, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | - José M Lou-Bonafonte
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Farmacología, Fisiología, Medicina Legal y Forense, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Gonzalo Gonzalo-Romeo
- Servicio General de Apoyo a la Investigación, División de Experimentación Animal, Universidad de Zaragoza, Zaragoza, Spain
| | - Gabriele Mocciaro
- Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Benjamin Jenkins
- Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Joaquín C Surra
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Producción Animal y Ciencia de los Alimentos, Escuela Politécnica Superior de Huesca, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Huesca, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - María J Rodríguez-Yoldi
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Farmacología, Fisiología, Medicina Legal y Forense, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Jesús Letosa
- Industrial Zootécnica Aragonesa S.L. (INZAR, S.L.), Zaragoza, Spain
| | - Agustín García-Gil
- Departamento de Cirugía, Facultad de Medicina, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
| | - Antonio Güemes
- Departamento de Cirugía, Facultad de Medicina, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
| | - Albert Koulman
- Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Jesús Osada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón-Universidad de Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, Zaragoza, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
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Liu Y, Li J, Tian S, Lan Q, Sun Z, Liu C, Dong W. Identification and validation of hub genes expressed in ulcerative colitis with metabolic dysfunction-associated steatotic liver disease. Front Immunol 2024; 15:1357632. [PMID: 38550602 PMCID: PMC10972886 DOI: 10.3389/fimmu.2024.1357632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024] Open
Abstract
Objective Ulcerative colitis (UC) and metabolic dysfunction-associated steatotic liver disease (MASLD) are closely intertwined; however, the precise molecular mechanisms governing their coexistence remain unclear. Methods We obtained UC (GSE75214) and MASLD (GSE151158) datasets from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were acquired by the 'edgeR' and 'limma' packages of R. We then performed functional enrichment analysis of common DEGs. Hub genes were selected using the cytoHubba plugin and validated using GSE87466 for UC and GSE33814 for MASLD. Immunohistochemistry was employed to validate the hub genes' expression in clinical samples. Immune infiltration and gene set enrichment analyses of the hub genes were performed. Finally, we estimated the Spearman's correlation coefficients for the clinical correlation of the core genes. Results Within a cohort of 26 differentially regulated genes in both UC and MASLD, pathways involving cytokine-mediated signaling, cell chemotaxis, and leukocyte migration were enriched. After further validation, CXCR4, THY1, CCL20, and CD2 were identified as the hub genes. Analysis of immune infiltration patterns highlighted an association between elevated pivotal gene expression and M1 macrophage activation. Immunohistochemical staining revealed widespread expression of pivotal genes in UC- and MASLD-affected tissues. Furthermore, significant correlations were observed between the increased expression of hub genes and biochemical markers, such as albumin and prothrombin time. Conclusion This bioinformatics analysis highlights CXCR4, THY1, CCL20, and CD2 as crucial genes involved in the co-occurrence of UC and MASLD, providing insights into the underlying mechanisms of these two conditions.
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Affiliation(s)
- Yupei Liu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiao Li
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shan Tian
- Department of Infection, Union Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Qingzhi Lan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhiyi Sun
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Chuan Liu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
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Dai L, Yuan W, Jiang R, Zhan Z, Zhang L, Xu X, Qian Y, Yang W, Zhang Z. Machine learning-based integration identifies the ferroptosis hub genes in nonalcoholic steatohepatitis. Lipids Health Dis 2024; 23:23. [PMID: 38263097 PMCID: PMC10804801 DOI: 10.1186/s12944-023-01988-9] [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: 09/20/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Ferroptosis, is characterized by lipid peroxidation of fatty acids in the presence of iron ions, which leads to cell apoptosis. This leads to the disruption of metabolic pathways, ultimately resulting in liver dysfunction. Although ferroptosis is linked to nonalcoholic steatohepatitis (NASH), understanding the key ferroptosis-related genes (FRGs) involved in NASH remains incomplete. NASH may be targeted therapeutically by identifying the genes responsible for ferroptosis. METHODS To identify ferroptosis-related genes and develop a ferroptosis-related signature (FeRS), 113 machine-learning algorithm combinations were used. RESULTS The FeRS constructed using the Generalized Linear Model Boosting algorithm and Gradient Boosting Machine algorithms exhibited the best prediction performance for NASH. Eight FRGs, with ZFP36 identified by the algorithms as the most crucial, were incorporated into in FeRS. ZFP36 is significantly enriched in various immune cell types and exhibits significant positive correlations with most immune signatures. CONCLUSION ZFP36 is a key FRG involved in NASH pathogenesis.
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Affiliation(s)
- Longfei Dai
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China
| | - Wenkang Yuan
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China
| | - Renao Jiang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China
| | - Zhicheng Zhan
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China
| | - Liangliang Zhang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China
| | - Xinjian Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China
| | - Yuyang Qian
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China
| | - Wenqi Yang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China
| | - Zhen Zhang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui Province, China.
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Chang CW, Chen YS, Huang CH, Lin CH, Ng WV, Chu LJ, Trépo E, Zucman-Rossi J, Siao K, Maher JJ, Chiew MY, Chou CH, Huang HD, Teo WH, Lee IS, Lo JF, Wang XW. A genetic basis of mitochondrial DNAJA3 in nonalcoholic steatohepatitis-related hepatocellular carcinoma. Hepatology 2023:01515467-990000000-00615. [PMID: 37870291 PMCID: PMC11035488 DOI: 10.1097/hep.0000000000000637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/08/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND AND AIMS NAFLD is the most common form of liver disease worldwide, but only a subset of individuals with NAFLD may progress to NASH. While NASH is an important etiology of HCC, the underlying mechanisms responsible for the conversion of NAFLD to NASH and then to HCC are poorly understood. We aimed to identify genetic risk genes that drive NASH and NASH-related HCC. APPROACH AND RESULTS We searched genetic alleles among the 24 most significant alleles associated with body fat distribution from a genome-wide association study of 344,369 individuals and validated the top allele in 3 independent cohorts of American and European patients (N=1380) with NAFLD/NASH/HCC. We identified an rs3747579-TT variant significantly associated with NASH-related HCC and demonstrated that rs3747579 is expression quantitative trait loci of a mitochondrial DnaJ Heat Shock Protein Family (Hsp40) Member A3 ( DNAJA3 ). We also found that rs3747579-TT and a previously identified PNPLA3 as a functional variant of NAFLD to have significant additional interactions with NASH/HCC risk. Patients with HCC with rs3747579-TT had a reduced expression of DNAJA3 and had an unfavorable prognosis. Furthermore, mice with hepatocyte-specific Dnaja3 depletion developed NASH-dependent HCC either spontaneously under a normal diet or enhanced by diethylnitrosamine. Dnaja3 -deficient mice developed NASH/HCC characterized by significant mitochondrial dysfunction, which was accompanied by excessive lipid accumulation and inflammatory responses. The molecular features of NASH/HCC in the Dnaja3 -deficient mice were closely associated with human NASH/HCC. CONCLUSIONS We uncovered a genetic basis of DNAJA3 as a key player of NASH-related HCC.
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Affiliation(s)
- Ching-Wen Chang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Graduate Institute of Metabolism and Obesity Sciences, Taipei Medical University, Taipei 110301, Taiwan
| | - Yu-Syuan Chen
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chen-Hua Huang
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Wailap Victor Ng
- Department of Biotechnology and Lab Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Biochemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Lichieh Julie Chu
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Otolaryngology - Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Eric Trépo
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Paris, France; Department of Gastroenterology, Hepatopancreatology and Digestive Oncology, CUB Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Paris, France; Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Kevin Siao
- Liver Center and Department of Medicine, University of California, San Francisco, CA 94143
| | - Jacquelyn J. Maher
- Liver Center and Department of Medicine, University of California, San Francisco, CA 94143
| | - Men Yee Chiew
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu City 300093, Taiwan
| | - Chih-Hung Chou
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu City 300093, Taiwan
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu City 300093, Taiwan
| | - Hsien-Da Huang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu City 300093, Taiwan
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172
| | - Wan-Huai Teo
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - I-Shan Lee
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Jeng-Fan Lo
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Dentistry, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
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Zeng W, Xu X, Xu F, Zhu F, Li Y, Ma J. Exploring Key Genes with Diagnostic Value for Nonalcoholic Steatohepatitis Based on Bioinformatics Analysis. ACS OMEGA 2023; 8:20959-20967. [PMID: 37323410 PMCID: PMC10268261 DOI: 10.1021/acsomega.3c01709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/27/2023] [Indexed: 06/17/2023]
Abstract
We aimed to screen specific genes in liver tissue samples of patients with nonalcoholic steatohepatitis (NASH) with clinical diagnostic value based on bioinformatics analysis. The datasets of liver tissue samples from healthy individuals and NASH patients were retrieved for consistency cluster analysis to obtain the NASH sample typing, followed by verification of the diagnostic value of sample genotyping-specific genes. All samples were subjected to logistic regression analysis, followed by the establishment of the risk model, and then, the diagnostic value was determined by receiver operating characteristic curve analysis. NASH samples could be divided into cluster 1, cluster 2, and cluster 3, which could predict the nonalcoholic fatty liver disease activity score of patients. A total of 162 sample genotyping-specific genes were extracted from patient clinical parameters, and the top 20 core genes in the protein interaction network were obtained for logistic regression analysis. Five sample genotyping-specific genes (WD repeat and HMG-box DNA-binding protein 1 [WDHD1], GINS complex subunit 2 [GINS2], replication factor C subunit 3 (RFC3), secreted phosphoprotein 1 [SPP1], and spleen tyrosine kinase [SYK]) were extracted to construct the risk models with high diagnostic value in NASH. Compared with the low-risk group, the high-risk group of the model showed increased lipoproduction and decreased lipolysis and lipid β oxidation. The risk models based on WDHD1, GINS2, RFC3, SPP1, and SYK have high diagnostic value in NASH, and this risk model is closely related to lipid metabolism pathways.
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Affiliation(s)
- Wenchun Zeng
- Department
of Gastroenterology, The First People’s
Hospital of Yongkang, Affiliated to Hangzhou Medical College, Jinhua 321300, P. R. China
| | - Xiangwei Xu
- Department
of Pharmacy, The First People’s Hospital
of Yongkang, Affiliated to Hangzhou Medical College, Jinhua 321300, P. R. China
| | - Fang Xu
- Department
of Gastroenterology, The First People’s
Hospital of Yongkang, Affiliated to Hangzhou Medical College, Jinhua 321300, P. R. China
| | - Fang Zhu
- Department
of Gastroenterology, The First People’s
Hospital of Yongkang, Affiliated to Hangzhou Medical College, Jinhua 321300, P. R. China
| | - Yuecui Li
- Department
of Infectious Liver Disease, The First People’s
Hospital of Yongkang, Affiliated to Hangzhou Medical College, Jinhua 321300, P. R. China
| | - Ji Ma
- Department
of Gastroenterology, The First People’s
Hospital of Yongkang, Affiliated to Hangzhou Medical College, Jinhua 321300, P. R. China
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