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Wang M, Yan X, Dong Y, Li X, Gao B. From driver genes to gene families: A computational analysis of oncogenic mutations and ubiquitination anomalies in hepatocellular carcinoma. Comput Biol Chem 2024; 112:108119. [PMID: 38852361 DOI: 10.1016/j.compbiolchem.2024.108119] [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: 03/19/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is a widespread primary liver cancer with a high fatality rate. Despite several genes with oncogenic effects in HCC have been identified, many remain undiscovered. In this study, we conducted a comprehensive computational analysis to explore the involvement of genes within the same families as known driver genes in HCC. Specifically, we expanded the concept beyond single-gene mutations to encompass gene families sharing homologous structures, integrating various omics data to comprehensively understand gene abnormalities in cancer. Our analysis identified 74 domains with an enriched mutation burden, 404 domain mutation hotspots, and 233 dysregulated driver genes. We observed that specific low-frequency somatic mutations may contribute to HCC occurrence, potentially overlooked by single-gene algorithms. Furthermore, we systematically analyzed how abnormalities in the ubiquitinated proteasome system (UPS) impact HCC, finding that abnormal genes in E3, E2, DUB families, and Degron genes often result in HCC by affecting the stability of oncogenic or tumor suppressor proteins. In conclusion, expanding the exploration of driver genes to include gene families with homologous structures emerges as a promising strategy for uncovering additional oncogenic alterations in HCC.
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Affiliation(s)
- Meng Wang
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xinyue Yan
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Yanan Dong
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xiaoqin Li
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China.
| | - Bin Gao
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
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2
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Njei B, Al-Ajlouni YA, Ameyaw P, Njei LP, Boateng S. Role of ammonia and glutamine in the pathogenesis and progression of metabolic dysfunction-associated steatotic liver disease: A systematic review. J Gastroenterol Hepatol 2024; 39:1788-1808. [PMID: 38763916 DOI: 10.1111/jgh.16603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/10/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) affects over 30% of the global population, with a significant risk of advancing to liver cirrhosis and hepatocellular carcinoma. The roles of ammonia and glutamine in MASLD's pathogenesis are increasingly recognized, prompting this systematic review. This systematic review was conducted through a meticulous search of literature on December 21, 2023, across five major databases, focusing on studies that addressed the relationship between ammonia or glutamine and MASLD. The quality of the included studies was evaluated using CASP checklists. This study is officially registered in the PROSPERO database (CRD42023495619) and was conducted without external funding or sponsorship. Following PRISMA guidelines, 13 studies were included in this review. The studies were conducted globally, with varying sample sizes and study designs. The appraisal indicated a mainly low bias, confirming the reliability of the evidence. Glutamine's involvement in MASLD emerged as multifaceted, with its metabolic role being critical for liver function and disease progression. Variable expressions of glutamine synthetase and glutaminase enzymes highlight metabolic complexity whereas ammonia's impact through urea cycle dysfunction suggests avenues for therapeutic intervention. However, human clinical trials are lacking. This review emphasizes the necessity of glutamine and ammonia in understanding MASLD and identifies potential therapeutic targets. The current evidence, while robust, points to the need for human studies to corroborate preclinical findings. A personalized approach to treatment, informed by metabolic differences in MASLD patients, is advocated, alongside future large-scale clinical trials for a deeper exploration into these metabolic pathways.
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Affiliation(s)
- Basile Njei
- International Medicine Program, Section of Digestive Diseases, Yale University, New Haven, Connecticut, USA
| | | | - Prince Ameyaw
- Yale Affiliated Hospitals Program, Bridgeport, Connecticut, USA
| | - Lea-Pearl Njei
- University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Sarpong Boateng
- Yale Affiliated Hospitals Program, Bridgeport, Connecticut, USA
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3
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Chen Y, Liu H, Wang C, Chen W, Li L, Wu J, Wang G, Ling GS, Fu R. The histone demethylase JMJD1C regulates CPS1 expression and promotes the proliferation of paroxysmal nocturnal haemoglobinuria clones through cell metabolic reprogramming. Br J Haematol 2024; 204:2468-2479. [PMID: 38650379 DOI: 10.1111/bjh.19477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/25/2024]
Abstract
Paroxysmal nocturnal haemoglobinuria (PNH) is a disorder resulting from erythrocyte membrane deficiencies caused by PIG-A gene mutations. While current treatments alleviate symptoms, they fail to address the underlying cause of the disease-the pathogenic PNH clones. In this study, we found that the expression of carbamoyl phosphate synthetase 1 (CPS1) was downregulated in PNH clones, and the level of CPS1 was negatively correlated with the proportion of PNH clones. Using PIG-A knockout K562 (K562 KO) cells, we demonstrated that CPS1 knockdown increased cell proliferation and altered cell metabolism, suggesting that CPS1 participates in PNH clonal proliferation through metabolic reprogramming. Furthermore, we observed an increase in the expression levels of the histone demethylase JMJD1C in PNH clones, and JMJD1C expression was negatively correlated with CPS1 expression. Knocking down JMJD1C in K562 KO cells upregulated CPS1 and H3K36me3 expression, decreased cell proliferation and increased cell apoptosis. Chromatin immunoprecipitation analysis further demonstrated that H3K36me3 regulated CPS1 expression. Finally, we demonstrated that histone demethylase inhibitor JIB-04 can suppressed K562 KO cell proliferation and reduced the proportion of PNH clones in PNH mice. In conclusion, aberrant regulation of the JMJD1C-H3K36me3-CPS1 axis contributes to PNH clonal proliferation. Targeting JMJD1C with a specific inhibitor unveils a potential strategy for treating PNH patients.
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Affiliation(s)
- Yingying Chen
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Bone Marrow Failure and Malignant Hemopoietic Clone Control, Tianjin, China
- LKS Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Hui Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Bone Marrow Failure and Malignant Hemopoietic Clone Control, Tianjin, China
| | - Chaomeng Wang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Bone Marrow Failure and Malignant Hemopoietic Clone Control, Tianjin, China
| | - Weixin Chen
- LKS Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Liyan Li
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Bone Marrow Failure and Malignant Hemopoietic Clone Control, Tianjin, China
| | - Junshu Wu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Bone Marrow Failure and Malignant Hemopoietic Clone Control, Tianjin, China
| | - Guanrou Wang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Bone Marrow Failure and Malignant Hemopoietic Clone Control, Tianjin, China
| | - Guang Sheng Ling
- LKS Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
- Department of Medicine, LKS Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Bone Marrow Failure and Malignant Hemopoietic Clone Control, Tianjin, China
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Wang M, Yan X, Dong Y, Li X, Gao B. Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment. PLoS Comput Biol 2024; 20:e1012113. [PMID: 38728362 PMCID: PMC11230636 DOI: 10.1371/journal.pcbi.1012113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 07/08/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
The heterogeneity of Hepatocellular Carcinoma (HCC) poses a barrier to effective treatment. Stratifying highly heterogeneous HCC into molecular subtypes with similar features is crucial for personalized anti-tumor therapies. Although driver genes play pivotal roles in cancer progression, their potential in HCC subtyping has been largely overlooked. This study aims to utilize driver genes to construct HCC subtype models and unravel their molecular mechanisms. Utilizing a novel computational framework, we expanded the initially identified 96 driver genes to 1192 based on mutational aspects and an additional 233 considering driver dysregulation. These genes were subsequently employed as stratification markers for further analyses. A novel multi-omics subtype classification algorithm was developed, leveraging mutation and expression data of the identified stratification genes. This algorithm successfully categorized HCC into two distinct subtypes, CLASS A and CLASS B, demonstrating significant differences in survival outcomes. Integrating multi-omics and single-cell data unveiled substantial distinctions between these subtypes regarding transcriptomics, mutations, copy number variations, and epigenomics. Moreover, our prognostic model exhibited excellent predictive performance in training and external validation cohorts. Finally, a 10-gene classification model for these subtypes identified TTK as a promising therapeutic target with robust classification capabilities. This comprehensive study provides a novel perspective on HCC stratification, offering crucial insights for a deeper understanding of its pathogenesis and the development of promising treatment strategies.
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Affiliation(s)
- Meng Wang
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Xinyue Yan
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Yanan Dong
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Xiaoqin Li
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Bin Gao
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
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Luo J, Zhu WC, Chen QX, Yang CF, Huang BJ, Zhang SJ. A prognostic model based on DNA methylation-related gene expression for predicting overall survival in hepatocellular carcinoma. Front Oncol 2024; 13:1171932. [PMID: 38304027 PMCID: PMC10830715 DOI: 10.3389/fonc.2023.1171932] [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: 05/02/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) continues to increase in morbidity and mortality among all types of cancer. DNA methylation, an important epigenetic modification, is associated with cancer occurrence and progression. The objective of this study was to establish a model based on DNA methylation risk scores for identifying new potential therapeutic targets in HCC and preventing cancer progression. Methods Transcriptomic, clinical, and DNA methylation data on 374 tumor tissues and 50 adjacent normal tissues were downloaded from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma database. The gene expression profiles of the GSE54236 liver cancer dataset, which contains data on 161 liver tissue samples, were obtained from the Gene Expression Omnibus database. We analyzed the relationship between DNA methylation and gene expression levels after identifying the differentially methylated and expressed genes. Then, we developed and validated a risk score model based on the DNA methylation-driven genes. A tissue array consisting of 30 human hepatocellular carcinoma samples and adjacent normal tissues was used to assess the protein and mRNA expression levels of the marker genes by immunohistochemistry and qRT-PCR, respectively. Results Three methylation-related differential genes were identified in our study: GLS, MEX3B, and GNA14. The results revealed that their DNA methylation levels were negatively correlated with local gene expression regulation. The gene methylation levels correlated strongly with the prognosis of patients with liver cancer. This was confirmed by qRT-PCR and immunohistochemical verification of the expression of these genes or proteins in tumors and adjacent tissues. These results revealed the relationship between the level of relevant gene methylation and the prognosis of patients with liver cancer as well as the underlying cellular and biological mechanisms. This allows our gene signature to provide more accurate and appropriate predictions for clinical applications. Conclusion Through bioinformatics analysis and experimental validation, we obtained three DNA methylation marker: GLS, MEX3B, and GNA14. This helps to predict the prognosis and may be a potential therapeutic target for HCC patients.
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Affiliation(s)
- Jin Luo
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Traditional Chinese Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Wan-Cui Zhu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qiu-Xia Chen
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chang-Fu Yang
- Department of Oncology, The People’s Hospital of Gaozhou, Gaozhou, China
| | - Bi-Jun Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shi-Jun Zhang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Zhai F, Wang J, Luo X, Ye M, Jin X. Roles of NOLC1 in cancers and viral infection. J Cancer Res Clin Oncol 2023; 149:10593-10608. [PMID: 37296317 DOI: 10.1007/s00432-023-04934-5] [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: 04/15/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The nucleolus is considered the center of metabolic control and an important organelle for the biogenesis of ribosomal RNA (rRNA). Nucleolar and coiled-body phosphoprotein 1(NOLC1), which was originally identified as a nuclear localization signal-binding protein is a nucleolar protein responsible for nucleolus construction and rRNA synthesis, as well as chaperone shuttling between the nucleolus and cytoplasm. NOLC1 plays an important role in a variety of cellular life activities, including ribosome biosynthesis, DNA replication, transcription regulation, RNA processing, cell cycle regulation, apoptosis, and cell regeneration. PURPOSE In this review, we introduce the structure and function of NOLC1. Then we elaborate its upstream post-translational modification and downstream regulation. Meanwhile, we describe its role in cancer development and viral infection which provide a direction for future clinical applications. METHODS The relevant literatures from PubMed have been reviewed for this article. CONCLUSION NOLC1 plays an important role in the progression of multiple cancers and viral infection. In-depth study of NOLC1 provides a new perspective for accurate diagnosis of patients and selection of therapeutic targets.
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Affiliation(s)
- Fengguang Zhai
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China
| | - Jie Wang
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China
| | - Xia Luo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Meng Ye
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China.
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China.
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Mahé M, Rios-Fuller TJ, Karolin A, Schneider RJ. Genetics of enzymatic dysfunctions in metabolic disorders and cancer. Front Oncol 2023; 13:1230934. [PMID: 37601653 PMCID: PMC10433910 DOI: 10.3389/fonc.2023.1230934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Inherited metabolic disorders arise from mutations in genes involved in the biogenesis, assembly, or activity of metabolic enzymes, leading to enzymatic deficiency and severe metabolic impairments. Metabolic enzymes are essential for the normal functioning of cells and are involved in the production of amino acids, fatty acids and nucleotides, which are essential for cell growth, division and survival. When the activity of metabolic enzymes is disrupted due to mutations or changes in expression levels, it can result in various metabolic disorders that have also been linked to cancer development. However, there remains much to learn regarding the relationship between the dysregulation of metabolic enzymes and metabolic adaptations in cancer cells. In this review, we explore how dysregulated metabolism due to the alteration or change of metabolic enzymes in cancer cells plays a crucial role in tumor development, progression, metastasis and drug resistance. In addition, these changes in metabolism provide cancer cells with a number of advantages, including increased proliferation, resistance to apoptosis and the ability to evade the immune system. The tumor microenvironment, genetic context, and different signaling pathways further influence this interplay between cancer and metabolism. This review aims to explore how the dysregulation of metabolic enzymes in specific pathways, including the urea cycle, glycogen storage, lysosome storage, fatty acid oxidation, and mitochondrial respiration, contributes to the development of metabolic disorders and cancer. Additionally, the review seeks to shed light on why these enzymes represent crucial potential therapeutic targets and biomarkers in various cancer types.
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Affiliation(s)
| | | | | | - Robert J. Schneider
- Department of Microbiology, Grossman NYU School of Medicine, New York, NY, United States
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Ong KH, Hsieh YY, Sun DP, Huang SKH, Tian YF, Chou CL, Shiue YL, Joseph K, Chang IW. Underexpression of Carbamoyl Phosphate Synthetase I as Independent Unfavorable Prognostic Factor in Intrahepatic Cholangiocarcinoma: A Potential Theranostic Biomarker. Diagnostics (Basel) 2023; 13:2296. [PMID: 37443694 DOI: 10.3390/diagnostics13132296] [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: 05/25/2023] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (IHCC) is the second most common malignant neoplasm of the liver. In spite of the increasing incidence worldwide, it is relatively rare in Western countries. IHCC is relatively common in Eastern and Southeastern Asia. Patients with IHCC are usually diagnosed at an advanced stage, therefore, the clinical outcome is dismal. Dysregulation of urea cycle metabolic enzyme expression is found in different types of cancers. Nevertheless, a comprehensive evaluation of genes related to the urea cycle (i.e., GO:0000050) has not been conducted in IHCC. By performing a comparative analysis of gene expression profiles, we specifically examined genes associated with the urea cycle (GO:0000050) in a publicly accessible transcriptomic dataset (GSE26566). Interestingly, CPS1 was identified as the second most prominently down-regulated gene in this context. Tumor tissues of 182 IHCC patients who underwent curative-intent hepatectomy were enrolled. The expression level of CPS1 protein in our IHCC cohort was assessed by immunohistochemical study. Subsequent to that, statistical analyses were carried out to examine the expression of CPS1 in relation to various clinicopathological factors, as well as to assess its impact on survival outcomes. We noticed that lower immunoreactivity of CPS1 in IHCC was associated with tumor progression (pT status) with statistical significance (p = 0.003). CPS1 underexpression was not only negatively correlated to overall survival (OS), disease-free survival (DFS), local recurrence-free survival (LRFS) and metastasis-free survival (MeFS) in univariate analysis but also an independent prognosticator to forecast poorer clinical outcome for all prognostic indices (OS, DFS, LRFS and MeFs) in patients with IHCC (all p ≤ 0.001). These results support that CPS1 may play a crucial role in IHCC oncogenesis and tumor progression and serve as a novel prognostic factor and a potential diagnostic and theranostic biomarker.
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Affiliation(s)
- Khaa Hoo Ong
- Division of Gastroenterology & General Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan
- Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Yao-Yu Hsieh
- Division of Hematology and Oncology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, Taipei 235, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Ding-Ping Sun
- Division of Gastroenterology & General Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan
| | - Steven Kuan-Hua Huang
- Division of Urology, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan
| | - Yu-Feng Tian
- Division of Colon and Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan
| | - Chia-Ling Chou
- Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
- Division of Colon and Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Keva Joseph
- St. Jude Hospital, Vieux Fort LC12 201, Saint Lucia
| | - I-Wei Chang
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Clinical Pathology, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
- Department of Pathology, Taipei Medical University Hospital, Taipei 110, Taiwan
- Department of Pathology, Shuang Ho Hospital, Taipei Medical University, Taipei 235, Taiwan
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Sgro A, Cursons J, Waryah C, Woodward EA, Foroutan M, Lyu R, Yeoh GCT, Leedman PJ, Blancafort P. Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma. Clin Epigenetics 2023; 15:73. [PMID: 37120619 PMCID: PMC10149030 DOI: 10.1186/s13148-023-01482-0] [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: 11/22/2022] [Accepted: 04/09/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Epigenetic silencing of tumor suppressor genes (TSGs) is a key feature of oncogenesis in hepatocellular carcinoma (HCC). Liver-targeted delivery of CRISPR-activation (CRISPRa) systems makes it possible to exploit chromatin plasticity, by reprogramming transcriptional dysregulation. RESULTS Using The Cancer Genome Atlas HCC data, we identify 12 putative TSGs with negative associations between promoter DNA methylation and transcript abundance, with limited genetic alterations. All HCC samples harbor at least one silenced TSG, suggesting that combining a specific panel of genomic targets could maximize efficacy, and potentially improve outcomes as a personalized treatment strategy for HCC patients. Unlike epigenetic modifying drugs lacking locus selectivity, CRISPRa systems enable potent and precise reactivation of at least 4 TSGs tailored to representative HCC lines. Concerted reactivation of HHIP, MT1M, PZP, and TTC36 in Hep3B cells inhibits multiple facets of HCC pathogenesis, such as cell viability, proliferation, and migration. CONCLUSIONS By combining multiple effector domains, we demonstrate the utility of a CRISPRa toolbox of epigenetic effectors and gRNAs for patient-specific treatment of aggressive HCC.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Joseph Cursons
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Charlene Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Eleanor A Woodward
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Momeneh Foroutan
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Melbourne, VIC, 3065, Australia
- Melbourne Integrative Genomics/School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Royal Parade, Parkville, VIC, 3010, Australia
| | - George C T Yeoh
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- School of Molecular Sciences, University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Peter J Leedman
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, Perth, WA, 6009, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia.
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
- School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia.
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10
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Foglia B, Beltrà M, Sutti S, Cannito S. Metabolic Reprogramming of HCC: A New Microenvironment for Immune Responses. Int J Mol Sci 2023; 24:ijms24087463. [PMID: 37108625 PMCID: PMC10138633 DOI: 10.3390/ijms24087463] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Hepatocellular carcinoma is the most common primary liver cancer, ranking third among the leading causes of cancer-related mortality worldwide and whose incidence varies according to geographical area and ethnicity. Metabolic rewiring was recently introduced as an emerging hallmark able to affect tumor progression by modulating cancer cell behavior and immune responses. This review focuses on the recent studies examining HCC's metabolic traits, with particular reference to the alterations of glucose, fatty acid and amino acid metabolism, the three major metabolic changes that have gained attention in the field of HCC. After delivering a panoramic picture of the peculiar immune landscape of HCC, this review will also discuss how the metabolic reprogramming of liver cancer cells can affect, directly or indirectly, the microenvironment and the function of the different immune cell populations, eventually favoring the tumor escape from immunosurveillance.
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Affiliation(s)
- Beatrice Foglia
- Unit of Experimental Medicine and Clinical Pathology, Department of Clinical and Biological Sciences, University of Torino, 10125 Torino, Italy
| | - Marc Beltrà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Salvatore Sutti
- Department of Health Sciences, Interdisciplinary Research Center for Autoimmune Diseases, University of East Piedmont, 28100 Novara, Italy
| | - Stefania Cannito
- Unit of Experimental Medicine and Clinical Pathology, Department of Clinical and Biological Sciences, University of Torino, 10125 Torino, Italy
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11
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Metabolism as a New Avenue for Hepatocellular Carcinoma Therapy. Int J Mol Sci 2023; 24:ijms24043710. [PMID: 36835122 PMCID: PMC9964410 DOI: 10.3390/ijms24043710] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Hepatocellular carcinoma is today the sixth leading cause of cancer-related death worldwide, despite the decreased incidence of chronic hepatitis infections. This is due to the increased diffusion of metabolic diseases such as the metabolic syndrome, diabetes, obesity, and nonalcoholic steatohepatitis (NASH). The current protein kinase inhibitor therapies in HCC are very aggressive and not curative. From this perspective, a shift in strategy toward metabolic therapies may represent a promising option. Here, we review current knowledge on metabolic dysregulation in HCC and therapeutic approaches targeting metabolic pathways. We also propose a multi-target metabolic approach as a possible new option in HCC pharmacology.
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12
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Unraveling the therapeutic potential of carbamoyl phosphate synthetase 1 (CPS1) in human disease. Bioorg Chem 2022; 130:106253. [DOI: 10.1016/j.bioorg.2022.106253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2022]
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13
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Duff C, Baruteau J. Modelling urea cycle disorders using iPSCs. NPJ Regen Med 2022; 7:56. [PMID: 36163209 PMCID: PMC9513077 DOI: 10.1038/s41536-022-00252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
The urea cycle is a liver-based pathway enabling disposal of nitrogen waste. Urea cycle disorders (UCDs) are inherited metabolic diseases caused by deficiency of enzymes or transporters involved in the urea cycle and have a prevalence of 1:35,000 live births. Patients present recurrent acute hyperammonaemia, which causes high rate of death and neurological sequelae. Long-term therapy relies on a protein-restricted diet and ammonia scavenger drugs. Currently, liver transplantation is the only cure. Hence, high unmet needs require the identification of effective methods to model these diseases to generate innovative therapeutics. Advances in both induced pluripotent stem cells (iPSCs) and genome editing technologies have provided an invaluable opportunity to model patient-specific phenotypes in vitro by creating patients' avatar models, to investigate the pathophysiology, uncover novel therapeutic targets and provide a platform for drug discovery. This review summarises the progress made thus far in generating 2- and 3-dimensional iPSCs models for UCDs, the challenges encountered and how iPSCs offer future avenues for innovation in developing the next-generation of therapies for UCDs.
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Affiliation(s)
- Claire Duff
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Julien Baruteau
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- National Institute of Health Research Great Ormond Street Biomedical Research Centre, London, UK.
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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Hou G, Ding D, Tian T, Dong W, Sun D, Liu G, Yang Y, Zhou W. Metabolomics-based classification reveals subtypes of hepatocellular carcinoma. Mol Carcinog 2022; 61:989-1001. [PMID: 36121331 DOI: 10.1002/mc.23455] [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: 05/12/2022] [Revised: 06/24/2022] [Accepted: 07/27/2022] [Indexed: 11/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related death, and the prognosis varies due to its high heterogeneity, systematic evaluation of HCC is mainly based on genomic and transcriptomic features, metabolomics-based classification has yet to be reported. Here we performed RNA-seq on 50 paired samples and metabolomics analysis on 72 paired samples of both normal and tumor tissues from HCC patients. Through unsupervised hierarchical cluster analysis with train and test data sets, metabolic and gene expression signatures were identified. We found that most fluxes related to glutamate are attenuated, except for the glutamate-proline pathway. Three subgroups were identified with distinct survival, clinical observations, and metabolic/gene signatures. S1 is characterized by a relatively poor prognosis, a low concentration of the degradation products of phosphatidylcholine and phosphatidylethanolamine, an enrichment of specific genes related to focal adhesion, and an upregulation of genes on chromosome 6q27. Beyond commonly downregulated metabolites, S2 tumors are largely characterized by few alterations in metabolites and genes, as well as low incidence of mutations/loss of heterozygosity, the metabolite signature of this group consists of hexoses and their phosphates, and the prognosis is the best, with a 5-year survival rate of greater than 80%. S3 is characterized by the worst survival (an approximately 20% 5-year survival rate), unsaturated fatty acid metabolites, an upregulation of specific genes involved in metastasis, and an upregulation of genes on chromosome 1q21. The metabolite-based classifications are more stable and reproducible, with each subgroup characterized by a distinct molecular signature and disease prognosis.
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Affiliation(s)
- Guojun Hou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Dongyang Ding
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Tao Tian
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Wei Dong
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Dapeng Sun
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Gang Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yuan Yang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Weiping Zhou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
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15
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Jiang Z, Wei C, Luo Y, Xiao Y, Wang L, Guo W, Yuan X. Ornithine aminotransferase and carbamoyl phosphate synthetase 1 involved in ammonia metabolism serve as novel targets for early stages of gastric cancer. J Clin Lab Anal 2022; 36:e24692. [PMID: 36098904 PMCID: PMC9551119 DOI: 10.1002/jcla.24692] [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: 07/26/2022] [Revised: 08/21/2022] [Accepted: 08/27/2022] [Indexed: 11/24/2022] Open
Abstract
Objective The sensitivity and specificity of current biomarkers for gastric cancer were insufficient. The aim of the present study was to screen novel biomarkers and determine the diagnostic values of ornithine aminotransferase (OAT) and carbamoyl phosphate synthetase 1 (CPS1) for detecting gastric cancer. Methods With stable isotope tags, we labelled an initial discovery group of four paired gastric cancer tissue samples and identified with LC‐ESI‐MS/MS. A validation group of 159 gastric cancer samples and 30 healthy controls were used to validate the candidate targets. GSEA was used to explore the pathways activated in gastric cancer. Results Four hundred and thirty one proteins were found differentially expressed in gastric cancer tissues. Of these proteins, OAT and CPS1 were found over‐expressed in gastric cancer patients, with sensitivity of 70.4% (95% CI: 63.3%–77.6%) and specificity of 80.5% (95% CI: 74.3%–86.7%) for ornithine aminotransferase, and with sensitivity of 68.6% (95% CI: 61.3%–75.8%) and specificity of 73% (95% CI: 66%–79.9%) for carbamoyl phosphate synthetase 1. The co‐expression of OAT and CPS1 in gastric cancer tissues has a sensitivity of 81% (95% CI: 73.2%–88.8%) and specificity of 89% (95% CI: 83%–95%). Furthermore, both OAT and CPS1 were overexpressed in patients with local invasion T3 and T4 stages than those in patients with T1 and T2 stages. The co‐expression of OAT and CPS1 was strongly correlated with histological grade I 68% (95% CI: 58.7%–77.3%) and TNM stage I/II 52% (95% CI: 42%–62%). The areas under ROC curves were up to 0.758 for the co‐expression of OAT and CPS1 in gastric cancer. GSEA results showed that two gene sets and 30 gene sets were activated in OAT high‐ and CPS1 high‐expression patients with gastric cancer, respectively. Conclusions The present findings indicated a tight correlation between the co‐expression of OAT and CPS1 and the histological grade, local invasion, and TNM stages of gastric cancer. Therefore, OAT and CPS1 might be predictors for gastric cancer invasion and potential targets for anticancer drug design for gastric cancer.
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Affiliation(s)
- Zhen Jiang
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Chen Wei
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Yaomin Luo
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Yang Xiao
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Li Wang
- Research Center for Integrative Medicine, Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Wubin Guo
- Department of General Surgery, the TCM Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiaoxia Yuan
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
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16
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Raggi C, Taddei ML, Rae C, Braconi C, Marra F. Metabolic reprogramming in cholangiocarcinoma. J Hepatol 2022; 77:849-864. [PMID: 35594992 DOI: 10.1016/j.jhep.2022.04.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 12/25/2022]
Abstract
Metabolic reprogramming is a hallmark of cancer and allows tumour cells to meet the increased energy demands required for rapid proliferation, invasion, and metastasis. Indeed, many tumour cells acquire distinctive metabolic and bioenergetic features that enable them to survive in resource-limited conditions, mainly by harnessing alternative nutrients. Several recent studies have explored the metabolic plasticity of cancer cells with the aim of identifying new druggable targets, while therapeutic strategies to limit the access to nutrients have been successfully applied to the treatment of some tumours. Cholangiocarcinoma (CCA), a highly heterogeneous tumour, is the second most common form of primary liver cancer. It is characterised by resistance to chemotherapy and poor prognosis, with 5-year survival rates of below 20%. Deregulation of metabolic pathways have been described during the onset and progression of CCA. Increased aerobic glycolysis and glutamine anaplerosis provide CCA cells with the ability to generate biosynthetic intermediates. Other metabolic alterations involving carbohydrates, amino acids and lipids have been shown to sustain cancer cell growth and dissemination. In this review, we discuss the complex metabolic rewiring that occurs during CCA development and leads to unique nutrient addiction. The possible role of therapeutic interventions based on metabolic changes is also thoroughly discussed.
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Affiliation(s)
- Chiara Raggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
| | - Maria Letizia Taddei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Colin Rae
- Institute of Cancer Sciences, The University of Glasgow, Glasgow, United Kingdom
| | - Chiara Braconi
- Institute of Cancer Sciences, The University of Glasgow, Glasgow, United Kingdom; Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Fabio Marra
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
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RNA splicing: a dual-edged sword for hepatocellular carcinoma. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:173. [PMID: 35972700 DOI: 10.1007/s12032-022-01726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/30/2022] [Indexed: 10/15/2022]
Abstract
RNA splicing is the fundamental process that brings diversity at the transcriptome and proteome levels. The spliceosome complex regulates minor and major processes of RNA splicing. Aberrant regulation is often associated with different diseases, including diabetes, stroke, hypertension, and cancer. In the majority of cancers, dysregulated alternative RNA splicing (ARS) events directly affect tumor progression, invasiveness, and often lead to poor survival of the patients. Alike the rest of the gastrointestinal malignancies, in hepatocellular carcinoma (HCC), which alone contributes to ~ 75% of the liver cancers, a large number of ARS events have been observed, including intron retention, exon skipping, presence of alternative 3'-splice site (3'SS), and alternative 5'-splice site (5'SS). These events are reported in spliceosome and non-spliceosome complexes genes. Molecules such as MCL1, Bcl-X, and BCL2 in different isoforms can behave as anti-apoptotic or pro-apoptotic, making the spliceosome complex a dual-edged sword. The anti-apoptotic isoforms of such molecules bring in resistance to chemotherapy or cornerstone drugs. However, in contrast, multiple malignant tumors, including HCC that target the pro-apoptotic favoring isoforms/variants favor apoptotic induction and make chemotherapy effective. Herein, we discuss different splicing events, aberrations, and antisense oligonucleotides (ASOs) in modulating RNA splicing in HCC tumorigenesis with a possible therapeutic outcome.
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18
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Development and Validation of a Novel Circadian Rhythm-Related Signature to Predict the Prognosis of the Patients with Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4263261. [PMID: 35993051 PMCID: PMC9391189 DOI: 10.1155/2022/4263261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/06/2022] [Accepted: 07/18/2022] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most important causes of cancer-related deaths and remains a major public health challenge worldwide. Considering the extensive heterogeneity of HCC, more accurate prognostic models are imperative. The circadian genes regulate the daily oscillations of key biological processes, such as nutrient metabolism in the liver. Circadian rhythm disruption has recently been recognized as an independent risk factor for cancer. In this study, The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) were compared and 248 differentially expressed genes (DEGs) of the circadian rhythm were identified. HCC was classified into two subtypes based on these DEGs. The prognostic value of each circadian rhythm-associated gene (CRG) for survival was assessed by constructing a multigene signature from TCGA cohort. A 6-gene signature was created by applying the least absolute shrinkage and selection operator (LASSO) Cox regression method, and all patients in TCGA cohort were divided into high- and low-risk groups according to their risk scores. The survival rate of patients with HCC in the low-risk group was significantly higher than that in the high-risk group (p < 0.001). The patients with HCC in the Gene Expression Omnibus (GEO) cohort were also divided into two risk subgroups using the risk score of TCGA cohort, and the overall survival time (OS) was prolonged in the low-risk group (p = 0.012). Based on the clinical characteristics, the risk score was an independent predictor of OS in the patients with HCC. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that multiple metabolic pathways, cell cycle, etc., were enhanced in the high-risk group. Using the metabolic pathway single-sample gene set enrichment analysis (ssGSEA), it was found that the metabolic pathways in the high- and low-risk groups between TCGA and GEO cohorts were altered essentially in the same way. In conclusion, the circadian genes play an important role in HCC metabolic rearrangements and can be further used to predict the prognosis the patients with HCC.
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19
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Missiaen R, Anderson NM, Kim LC, Nance B, Burrows M, Skuli N, Carens M, Riscal R, Steensels A, Li F, Simon MC. GCN2 inhibition sensitizes arginine-deprived hepatocellular carcinoma cells to senolytic treatment. Cell Metab 2022; 34:1151-1167.e7. [PMID: 35839757 PMCID: PMC9357184 DOI: 10.1016/j.cmet.2022.06.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 04/01/2022] [Accepted: 06/20/2022] [Indexed: 12/14/2022]
Abstract
Hepatocellular carcinoma (HCC) is a typically fatal malignancy exhibiting genetic heterogeneity and limited therapy responses. We demonstrate here that HCCs consistently repress urea cycle gene expression and thereby become auxotrophic for exogenous arginine. Surprisingly, arginine import is uniquely dependent on the cationic amino acid transporter SLC7A1, whose inhibition slows HCC cell growth in vitro and in vivo. Moreover, arginine deprivation engages an integrated stress response that promotes HCC cell-cycle arrest and quiescence, dependent on the general control nonderepressible 2 (GCN2) kinase. Inhibiting GCN2 in arginine-deprived HCC cells promotes a senescent phenotype instead, rendering these cells vulnerable to senolytic compounds. Preclinical models confirm that combined dietary arginine deprivation, GCN2 inhibition, and senotherapy promote HCC cell apoptosis and tumor regression. These data suggest novel strategies to treat human liver cancers through targeting SLC7A1 and/or a combination of arginine restriction, inhibition of GCN2, and senolytic agents.
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Affiliation(s)
- Rindert Missiaen
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicole M Anderson
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura C Kim
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Bailey Nance
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle Burrows
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicolas Skuli
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Madeleine Carens
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Romain Riscal
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - An Steensels
- Department of Medicine, Division of Hematology-Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA; Department of Pediatrics, Comprehensive Bone Marrow Failure Center, Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fuming Li
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
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20
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Fu Y, Liu S, Rodrigues RM, Han Y, Guo C, Zhu Z, He Y, Mackowiak B, Feng D, Gao B, Zeng S, Shen H. Activation of VIPR1 suppresses hepatocellular carcinoma progression by regulating arginine and pyrimidine metabolism. Int J Biol Sci 2022; 18:4341-4356. [PMID: 35864952 PMCID: PMC9295067 DOI: 10.7150/ijbs.71134] [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: 01/16/2022] [Accepted: 05/27/2022] [Indexed: 12/09/2022] Open
Abstract
Background and aims: Vasoactive intestinal polypeptide type-I receptor (VIPR1) overexpression has been reported in numerous types of malignancies and utilized to develop novel target therapeutics and radiolabeled VIP analogue-based tumor imaging technology, but its role in liver carcinogenesis has not been explored. In the current study, we investigated the role of the VIP/VIPR1 signaling in controlling hepatocellular carcinoma (HCC) progression. Approach and results: By analyzing clinical samples, we found the expression level of VIPR1 was downregulated in human HCC tissues, which was correlated with advanced clinical stages, tumor growth, recurrence, and poor outcomes of HCC clinically. In vitro and in vivo studies revealed that activation of VIPR1 by VIP markedly inhibited HCC growth and metastasis. Intriguingly, transcriptome sequencing analyses revealed that activation of VIPR1 by VIP regulated arginine biosynthesis. Mechanistical studies in cultured HCC cells demonstrated that VIP treatment partially restored the expression of arginine anabolic key enzyme argininosuccinate synthase (ASS1), and to some extent, inhibited de novo pyrimidine synthetic pathway by downregulating the activation of CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase). VIP treatment upregulated ASS1 and subsequently suppressed CAD phosphorylation in an mTOR/p70S6K signaling dependent manner. Clinically, we found human HCC samples were associated with downregulation of ASS1 but upregulation of CAD phosphorylation, and that VIPR1 levels positively correlated with ASS1 levels and serum levels of urea, the end product of the urea cycle and arginine metabolism in HCC. Conclusions: Loss of VIPR1 expression in HCC facilitates CAD phosphorylation and tumor progression, and restoration of VIPR1 and treatment with the VIPR1 agonist may be a promising approach for HCC treatment.
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Affiliation(s)
- Yaojie Fu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shanshan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Robim M Rodrigues
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Cao Guo
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhanwei Zhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yong He
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bryan Mackowiak
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dechun Feng
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
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21
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Parker AL, Toulabi L, Oike T, Kanke Y, Patel D, Tada T, Taylor S, Beck JA, Bowman E, Reyzer ML, Butcher D, Kuhn S, Pauly GT, Krausz KW, Gonzalez FJ, Hussain SP, Ambs S, Ryan BM, Wang XW, Harris CC. Creatine riboside is a cancer cell-derived metabolite associated with arginine auxotrophy. J Clin Invest 2022; 132:157410. [PMID: 35838048 PMCID: PMC9282934 DOI: 10.1172/jci157410] [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: 12/08/2021] [Accepted: 05/25/2022] [Indexed: 12/17/2022] Open
Abstract
The metabolic dependencies of cancer cells have substantial potential to be exploited to improve the diagnosis and treatment of cancer. Creatine riboside (CR) is identified as a urinary metabolite associated with risk and prognosis in lung and liver cancer. However, the source of high CR levels in patients with cancer as well as their implications for the treatment of these aggressive cancers remain unclear. By integrating multiomics data on lung and liver cancer, we have shown that CR is a cancer cell–derived metabolite. Global metabolomics and gene expression analysis of human tumors and matched liquid biopsies, together with functional studies, revealed that dysregulation of the mitochondrial urea cycle and a nucleotide imbalance were associated with high CR levels and indicators of a poor prognosis. This metabolic phenotype was associated with reduced immune infiltration and supported rapid cancer cell proliferation that drove aggressive tumor growth. CRhi cancer cells were auxotrophic for arginine, revealing a metabolic vulnerability that may be exploited therapeutically. This highlights the potential of CR not only as a poor-prognosis biomarker but also as a companion biomarker to inform the administration of arginine-targeted therapies in precision medicine strategies to improve survival for patients with cancer.
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Affiliation(s)
- Amelia L Parker
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Leila Toulabi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Takahiro Oike
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Yasuyuki Kanke
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Daxeshkumar Patel
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Takeshi Tada
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Sheryse Taylor
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Jessica A Beck
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Elise Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Michelle L Reyzer
- National Research Resource for Imaging Mass Spectrometry, Vanderbilt University, Nashville, Tennessee, USA
| | - Donna Butcher
- Pathology and Histotechnology Laboratory, Frederick National Laboratory, Frederick, Maryland, USA
| | - Skyler Kuhn
- Center for Cancer Research Collaborative Bioinformatics Resource
| | | | | | | | - S Perwez Hussain
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA.,Liver Cancer Program, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
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22
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Zhou L, Wang QL, Mao LH, Chen SY, Yang ZH, Liu X, Gao YH, Li XQ, Zhou ZH, He S. Hepatocyte-Specific Knock-Out of Nfib Aggravates Hepatocellular Tumorigenesis via Enhancing Urea Cycle. Front Mol Biosci 2022; 9:875324. [PMID: 35655758 PMCID: PMC9152321 DOI: 10.3389/fmolb.2022.875324] [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: 02/14/2022] [Accepted: 03/28/2022] [Indexed: 12/23/2022] Open
Abstract
Nuclear Factor I B (NFIB) has been reported to promote tumor growth, metastasis, and liver regeneration, but its mechanism in liver cancer is not fully elucidated. The present study aims to reveal the role of NFIB in hepatocellular carcinogenesis. In our study, we constructed hepatocyte-specific NFIB gene knockout mice with CRISPR/Cas9 technology (Nfib-/-; Alb-cre), and induced liver cancer mouse model by intraperitoneal injection of DEN/CCl4. First, we found that Nfib-/- mice developed more tumor nodules and had heavier livers than wild-type mice. H&E staining indicated that the liver histological severity of Nfib-/- group was more serious than that of WT group. Then we found that the differentially expressed genes in the tumor tissue between Nfib-/- mice and wild type mice were enriched in urea cycle. Furthermore, ASS1 and CPS1, the core enzymes of the urea cycle, were significantly upregulated in Nfib-/- tumors. Subsequently, we validated that the expression of ASS1 and CPS1 increased after knockdown of NFIB by lentivirus in normal hepatocytes and also promoted cell proliferation in vitro. In addition, ChIP assay confirmed that NFIB can bind with promoter region of both ASS1 and CPS1 gene. Our study reveals for the first time that hepatocyte-specific knock-out of Nfib aggravates hepatocellular tumor development by enhancing the urea cycle.
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Affiliation(s)
- Li Zhou
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing-Liang Wang
- Department of Pathology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin-Hong Mao
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Gastroenterology, Chengdu Second People's Hospital, Sichuan, China
| | - Si-Yuan Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zi-Han Yang
- Department of Biomedical Science, City University of Hong Kong, Hong Kong, China
| | - Xue Liu
- Department of Pathology, College of Basic Medicine, Jining Medical University, Jining, China
| | - Yu-Hua Gao
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, China
| | - Xiao-Qin Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Hang Zhou
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Song He
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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23
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Rojas Á, García-Lozano MR, Gil-Gómez A, Romero-Gómez M, Ampuero J. Glutaminolysis-ammonia-urea Cycle Axis, Non-alcoholic Fatty Liver Disease Progression and Development of Novel Therapies. J Clin Transl Hepatol 2022; 10:356-362. [PMID: 35528989 PMCID: PMC9039703 DOI: 10.14218/jcth.2021.00247] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/29/2021] [Accepted: 10/14/2021] [Indexed: 12/04/2022] Open
Abstract
The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing worldwide, reflecting the current epidemics of obesity, insulin resistance, type 2 diabetes mellitus, and metabolic syndrome. NAFLD is characterized by the accumulation of fat in the liver, and is known to be a cause of cirrhosis. Although many pathways have been proposed, the cause of NAFLD-linked fibrosis progression is still unclear, which posed challenges for the development of new therapies to prevent NASH-related cirrhosis and hepatocellular carcinoma. Cirrhosis is associated with activation of hepatic stellate cells (HSC) and accumulation of excess extracellular matrix proteins, and inhibiting the activation of HSCs would be expected to slow the progression of NAFLD-cirrhosis. Multiple molecular signals and pathways such as oxidative stress and glutaminolysis have been reported to promote HSC activation. Both mechanisms are plausible antifibrotic targets in NASH, as the activation of HSCs the proliferation of myofibroblasts depend on those processes. This review summarizes the role of the glutaminolysis-ammonia-urea cycle axis in the context of NAFLD progression, and shows how the axis could be a novel therapeutic target.
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Affiliation(s)
- Ángela Rojas
- Department of Unit of Digestive Diseases, Virgen del Rocío University Hospital, Seville, Spain
- SeLiver group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital/CSIC/ University of Seville, Seville, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - María Rosario García-Lozano
- Department of Unit of Digestive Diseases, Virgen del Rocío University Hospital, Seville, Spain
- SeLiver group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital/CSIC/ University of Seville, Seville, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071, Seville, Spain
| | - Antonio Gil-Gómez
- Department of Unit of Digestive Diseases, Virgen del Rocío University Hospital, Seville, Spain
- SeLiver group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital/CSIC/ University of Seville, Seville, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Manuel Romero-Gómez
- Department of Unit of Digestive Diseases, Virgen del Rocío University Hospital, Seville, Spain
- SeLiver group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital/CSIC/ University of Seville, Seville, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Javier Ampuero
- Department of Unit of Digestive Diseases, Virgen del Rocío University Hospital, Seville, Spain
- SeLiver group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital/CSIC/ University of Seville, Seville, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
- Correspondence to: Javier Ampuero, Digestive Disease Department and CIBERehd, Virgen del Rocio University Hospital, Avenida Manuel Siurot s/n, Sevilla 41013, Spain. ORCID: https://orcid.org/0000-0002-8332-2122. Tel: +34-955-015761, Fax: +34-955-015899, E-mail:
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24
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Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma. Signal Transduct Target Ther 2022; 7:53. [PMID: 35210398 PMCID: PMC8873499 DOI: 10.1038/s41392-022-00873-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/23/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
This study investigates aberrant DNA methylations as potential diagnosis and prognosis markers for esophageal squamous-cell carcinoma (ESCC), which if diagnosed at advanced stages has <30% five-year survival rate. Comparing genome-wide methylation sites of 91 ESCC and matched adjacent normal tissues, we identified 35,577 differentially methylated CpG sites (DMCs) and characterized their distribution patterns. Integrating whole-genome DNA and RNA-sequencing data of the same samples, we found multiple dysregulated transcription factors and ESCC-specific genomic correlates of identified DMCs. Using featured DMCs, we developed a 12-marker diagnostic panel with high accuracy in our dataset and the TCGA ESCC dataset, and a 4-marker prognostic panel distinguishing high-risk patients. In-vitro experiments validated the functions of 4 marker host genes. Together these results provide additional evidence for the important roles of aberrant DNA methylations in ESCC development and progression. Our DMC-based diagnostic and prognostic panels have potential values for clinical care of ESCC, laying foundations for developing targeted methylation assays for future non-invasive cancer detection methods.
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25
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Yang Z, Stemmer PM, Petriello MC. Proteomics-Based Identification of Interaction Partners of the Xenobiotic Detoxification Enzyme FMO3 Reveals Involvement in Urea Cycle. TOXICS 2022; 10:60. [PMID: 35202247 PMCID: PMC8877285 DOI: 10.3390/toxics10020060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023]
Abstract
The hepatic xenobiotic metabolizing enzyme flavin-containing monooxygenase 3 (FMO3) has been implicated in the development of cardiometabolic disease primarily due to its enzymatic product trimethylamine-N oxide (TMAO), which has recently been shown to be associated with multiple chronic diseases, including kidney and coronary artery diseases. Although TMAO may have causative roles as a pro-inflammatory mediator, the possibility for roles in metabolic disease for FMO3, irrespective of TMAO formation, does exist. We hypothesized that FMO3 may interact with other proteins known to be involved in cardiometabolic diseases and that modulating the expression of FMO3 may impact on these interaction partners. Here, we combine a co-immunoprecipitation strategy coupled to unbiased proteomic workflow to report a novel protein:protein interaction network for FMO3. We identified 51 FMO3 protein interaction partners, and through gene ontology analysis, have identified urea cycle as an enriched pathway. Using mice deficient in FMO3 on two separate backgrounds, we validated and further investigated expressional and functional associations between FMO3 and the identified urea cycle genes. FMO3-deficient mice showed hepatic overexpression of carbamoylphosphate synthetase (CPS1), the rate-limiting gene of urea cycle, and increased hepatic urea levels, especially in mice of FVB (Friend leukemia virus B strain) background. Finally, overexpression of FMO3 in murine AML12 hepatocytes led to downregulation of CPS1. Although there is past literature linking TMAO to urea cycle, this is the first published work showing that FMO3 and CPS1 may directly interact, implicating a role for FMO3 in chronic kidney disease irrespective of TMAO formation.
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Affiliation(s)
- Zhao Yang
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
- Department of Pharmaceutical Sciences, College of Pharmacy, Wayne State University, Detroit, MI 48202, USA
| | - Michael C. Petriello
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, MI 48202, USA
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26
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Zhang M, Wang S, Sun L, Gan L, Lin Y, Shao J, Jiang H, Li M. Ammonia induces changes in carbamoyl phosphate synthetase I and its regulation of glutamine synthesis and urea cycle in yellow catfish Pelteobagrus fulvidraco. FISH & SHELLFISH IMMUNOLOGY 2022; 120:242-251. [PMID: 34856372 DOI: 10.1016/j.fsi.2021.11.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Fishes can adapt to certain levels of environmental ammonia in water, but the strategies utilized to defend against ammonia toxicity are not exactly the same. The carbamyl phosphate synthase I (CPS I) plays an important role in the regulation of glutamine synthesis and urea cycle, which are the most common strategies for ammonia detoxification. In this study, CPS I was cloned from the yellow catfish. The full-length cDNAs of the CPS I was 5 034 bp, with open reading frames of 4 461 bp. Primary amino acid sequence alignment of CPS I revealed conserved similarity between the functional domains of the yellow catfish CPS I protein with CPS I proteins of other animals. The mRNA expression of CPS I was significantly up-regulated in liver and kidney tissues after acute ammonia stress. The CPS I RNA interference (RNAi) down-regulated the mRNA expressions of CPS I and ornithine transcarbamylase (OTC), but up-regulated glutamine synthetase (GS) and glutamate dehydrogenase (GDH) expressions in primary culture of liver cell after acute ammonia stress. Similarly, the activity of enzymes related to urea cycle decreased significantly, while the activity of enzymes related to glutamine synthesis increased significantly. The results of RNAi in vitro suggested that when the urea cycle is disturbed, the glutamine synthesis will be activated to cope with ammonia toxicity.
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Affiliation(s)
- Muzi Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China; College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Shidong Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Liying Sun
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Lei Gan
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Yanhong Lin
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jian Shao
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Haibo Jiang
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Ming Li
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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27
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Ridder DA, Weinmann A, Schindeldecker M, Urbansky LL, Berndt K, Gerber TS, Lang H, Lotz J, Lackner KJ, Roth W, Straub BK. Comprehensive clinicopathologic study of alpha fetoprotein-expression in a large cohort of patients with hepatocellular carcinoma. Int J Cancer 2021; 150:1053-1066. [PMID: 34894400 DOI: 10.1002/ijc.33898] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022]
Abstract
Alpha fetoprotein (AFP) is the most widely used diagnostic and prognostic serum biomarker for hepatocellular carcinoma (HCC). Despite its wide clinical use, a systematic clinicopathologic study comparing AFP expression in HCC in situ with serum AFP concentrations has not yet been conducted. To analyze AFP expression in a large cohort of patients by immunohistochemistry, we employed a comprehensive tissue microarray with 871 different HCCs of overall 561 patients. AFP immunoreactivity was detected in only about 20% of HCC core biopsies, whereas 48.9% of the patients displayed increased serum values (>12 ng/mL). Immunostaining of whole tumor slides revealed that lack of detectable immunoreactivity in core biopsies in a subgroup of patients with elevated AFP serum concentrations is due to heterogeneous intratumoral AFP expression. Serum AFP concentrations and AFP expression in situ were moderately correlated (Spearman's rank correlation coefficient .53, P = 1.2e - 13). High AFP expression detected in serum (>227.3 ng/mL) or in situ predicted unfavorable prognosis and was associated with vascular invasion, higher tumor grade and macrotrabecular-massive tumor subtype. Multivariate and ROC curve analysis demonstrated that high AFP concentrations in serum is an independent prognostic parameter and represents the more robust prognostic predictor in comparison to AFP immunostaining of core biopsies. The previously published vessels encapsulating tumor clusters (VETC) pattern turned out as an additional, statistically independent prognostic parameter. AFP-positivity was associated with increased tumor cell apoptosis, but not with increased vascular densities. Additionally, AFP-positive tumors displayed increased proliferation rates, urea cycle dysregulation and signs of genomic instability, which may constitute the basis for their increased aggressiveness.
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Affiliation(s)
- Dirk Andreas Ridder
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Arndt Weinmann
- Department of Internal Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Mario Schindeldecker
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany.,Tissue Biobank, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Lana Louisa Urbansky
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Kristina Berndt
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Tiemo Sven Gerber
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplant Surgery, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Johannes Lotz
- Institute for Laboratory Medicine and Clinical Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Karl J Lackner
- Institute for Laboratory Medicine and Clinical Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Beate Katharina Straub
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
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28
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Hernández-Oliveras A, Izquierdo-Torres E, Hernández-Martínez G, Zarain-Herzberg Á, Santiago-García J. Transcriptional and epigenetic landscape of Ca 2+-signaling genes in hepatocellular carcinoma. J Cell Commun Signal 2021; 15:433-445. [PMID: 33398721 PMCID: PMC8222487 DOI: 10.1007/s12079-020-00597-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Calcium (Ca2+) signaling has a major role in regulating a wide range of cellular mechanisms, including gene expression, proliferation, metabolism, cell death, muscle contraction, among others. Recent evidence suggests that ~ 1600 genes are related to the Ca2+ signaling. Some of these genes' expression is altered in several pathological conditions, including different cancer types, and epigenetic mechanisms are involved. However, their expression and regulation in hepatocellular carcinoma (HCC) and the liver are barely known. Here, we aimed to explore the expression of genes involved in the Ca2+-signaling in HCC, liver regeneration, and hepatocyte differentiation, and whether their expression is regulated by epigenetic mechanisms such as DNA methylation and histone posttranslational modifications (HPM). Results show that several Ca2+-signaling genes' expression is altered in HCC samples; among these, a subset of twenty-two correlate with patients' survival. DNA methylation correlates with eight of these genes' expression, and Guadecitabine, a hypomethylating agent, regulates the expression of seven down-regulated and three up-regulated genes in HepG2 cells. The down-regulated genes displayed a marked decrease of euchromatin histone marks, whereas up-regulated genes displayed gain in these marks. Additionally, the expression of these genes is modulated during liver regeneration and showed similar profiles between in vitro differentiated hepatocytes and liver-derived hepatocytes. In conclusion, some components of the Ca2+-signaling are altered in HCC and displayed a correlation with patients' survival. DNA methylation and HMP are an attractive target for future investigations to regulate their expression. Ca2+-signaling could be an important regulator of cell proliferation and differentiation in the liver.
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Affiliation(s)
- Andrés Hernández-Oliveras
- Instituto de Investigaciones Biológicas, Universidad Veracruzana, Luis Castelazo Ayala S/N, Xalapa, Veracruz, 91190 Mexico
| | - Eduardo Izquierdo-Torres
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510 Mexico
| | - Guadalupe Hernández-Martínez
- Instituto de Investigaciones Biológicas, Universidad Veracruzana, Luis Castelazo Ayala S/N, Xalapa, Veracruz, 91190 Mexico
| | - Ángel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510 Mexico
| | - Juan Santiago-García
- Instituto de Investigaciones Biológicas, Universidad Veracruzana, Luis Castelazo Ayala S/N, Xalapa, Veracruz, 91190 Mexico
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29
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Lu L, Zhang J, Fan W, Li Y, Wang J, Li TWH, Barbier-Torres L, Mato JM, Liu T, Seki E, Matsuda M, Tomasi ML, Bhowmick NA, Yang H, Lu SC. Deregulated 14-3-3ζ and methionine adenosyltransferase α1 interplay promotes liver cancer tumorigenesis in mice and humans. Oncogene 2021; 40:5866-5879. [PMID: 34349244 PMCID: PMC9611740 DOI: 10.1038/s41388-021-01980-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
Methionine adenosyltransferase 1A (MAT1A) is a tumor suppressor downregulated in hepatocellular carcinoma and cholangiocarcinoma, two of the fastest rising cancers worldwide. We compared MATα1 (protein encoded by MAT1A) interactome in normal versus cancerous livers by mass spectrometry to reveal interactions with 14-3-3ζ. The MATα1/14-3-3ζ complex was critical for the expression of 14-3-3ζ. Similarly, the knockdown and small molecule inhibitor for 14-3-3ζ (BV02), and ChIP analysis demonstrated the role of 14-3-3ζ in suppressing MAT1A expression. Interaction between MATα1 and 14-3-3ζ occurs directly and is enhanced by AKT2 phosphorylation of MATα1. Blocking their interaction enabled nuclear MATα1 translocation and inhibited tumorigenesis. In contrast, overexpressing 14-3-3ζ lowered nuclear MATα1 levels and promoted tumor progression. However, tumor-promoting effects of 14-3-3ζ were eliminated when liver cancer cells expressed mutant MATα1 unable to interact with 14-3-3ζ. Taken together, the reciprocal negative regulation that MATα1 and 14-3-3ζ exert is a key mechanism in liver tumorigenesis.
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Affiliation(s)
- Liqing Lu
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Key Laboratory of Cancer proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Zhang
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Fan
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yuan Li
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiaohong Wang
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tony W H Li
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lucia Barbier-Torres
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - José M Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology, Park of Bizkaia, Derio, Bizkaia, Spain
| | - Ting Liu
- Key Laboratory of Cancer proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ekihiro Seki
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michitaka Matsuda
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Maria Lauda Tomasi
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Neil A Bhowmick
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Biology Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Heping Yang
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Shelly C Lu
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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30
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Wang KX, Chen YP, Lu AP, Du GH, Qin XM, Guan DG, Gao L. A metabolic data-driven systems pharmacology strategy for decoding and validating the mechanism of Compound Kushen Injection against HCC. JOURNAL OF ETHNOPHARMACOLOGY 2021; 274:114043. [PMID: 33753143 DOI: 10.1016/j.jep.2021.114043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/11/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Compound Kushen Injection (CKI) is a widely used TCM formula for treatment of carcinomatous pain and tumors of digestive system including hepatocellular carcinoma (HCC). However, the potential mechanisms of CKI for treatment of HCC have not been systematically and deeply studied. AIM OF STUDY A metabolic data-driven systems pharmacology approach was utilized to investigate the potential mechanisms of CKI for treatment of HCC. MATERIALS AND METHODS Based on phenotypic data generated by metabolomics and genotypic data of drug targets, a propagation model based on Dijkstra program was proposed to decode the effective network of key genotype-phenotype of CKI in treating HCC. The pivotal pathway was predicted by target propagation mode of our proposed model, and was validated in SMMC-7721 cells and diethylnitrosamine-induced rats. RESULTS Metabolomics results indicated that 12 differential metabolites, and 5 metabolic pathways might be involved in the anti-HCC effect of CKI. A total of 86 metabolic related genes that affected by CKI were obtained. The results calculated by propagation model showed that 6475 shortest distance chains might be involved in the anti-HCC effect of CKI. According to the results of propagation mode, EGFR was identified as the core target of CKI for the anti-HCC effect. Finally, EGFR and its related pathway EGFR-STAT3 signaling pathway were validated in vivo and in vitro. CONCLUSION The proposed method provides a methodological reference for explaining the underlying mechanism of TCM in treating HCC.
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Affiliation(s)
- Ke-Xin Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.
| | - Yu-Peng Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Ai-Ping Lu
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, China.
| | - Guan-Hua Du
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China; Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Xue-Mei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.
| | - Dao-Gang Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China; Guangdong Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China.
| | - Li Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.
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31
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Blockade of AMPK-Mediated cAMP-PKA-CREB/ATF1 Signaling Synergizes with Aspirin to Inhibit Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13071738. [PMID: 33917483 PMCID: PMC8038809 DOI: 10.3390/cancers13071738] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Epidemiological and experimental studies have demonstrated that aspirin (acetylsalicylic acid) may prevent the incidence of some types of human cancer, including colorectal cancer and hepatocellular carcinoma (HCC). In addition, preclinical studies indicate that aspirin in combination with other treatments may achieve a more significant anti-cancer effect for established tumors. This study aims to improve the anti-cancer effect of aspirin by targeting signaling pathways related to aspirin and its targets. We find that aspirin may induce cAMP–PKA–CREB/ATF1 signaling in HCC via AMPK and its downstream target carbamoyl-phosphate synthase 1 (CPS1). Blockade of PKA–CREB/ATF1 signaling by the natural agent berbamine could sensitize HCC to aspirin. This research indicates that the combination of two inexpensive drugs, aspirin and berbamine, holds promise in preventing and treating HCC. Abstract Aspirin can prevent or inhibit inflammation-related cancers, such as colorectal cancer and hepatocellular carcinoma (HCC). However, the effectiveness of chemotherapy may be compromised by activating oncogenic pathways in cancer cells. Elucidation of such chemoresistance mechanisms is crucial to developing novel strategies to maximize the anti-cancer effects of aspirin. Here, we report that aspirin markedly induces CREB/ATF1 phosphorylation in HCC cells, which compromises aspirin’s anti-HCC effect. Inhibition of AMP-activated protein kinase (AMPK) abrogates the induction of CREB/ATF1 phosphorylation by aspirin. Mechanistically, activation of AMPK by aspirin results in decreased expression of the urea cycle enzyme carbamoyl-phosphate synthase 1 (CPS1) in HCC cells and xenografts. Treatment with aspirin or CPS1 knockdown stimulates soluble adenylyl cyclase expression, thereby increasing cyclic AMP (cAMP) synthesis and stimulating PKA–CREB/ATF1 signaling. Importantly, abrogation of aspirin-induced CREB/ATF1 phosphorylation could sensitize HCC to aspirin. The bis-benzylisoquinoline alkaloid berbamine suppresses the expression of cancerous inhibitor of protein phosphatase 2A (CIP2A), leading to protein phosphatase 2A-mediated downregulation of CREB/ATF1 phosphorylation. The combination of berbamine and aspirin significantly inhibits HCC in vitro and in vivo. These data demonstrate that the regulation of cAMP-PKA-CREB/ATF1 signaling represents a noncanonical function of CPS1. Targeting the PKA–CREB/ATF1 axis may be a strategy to improve the therapeutic effects of aspirin on HCC.
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Fang X, Wu X, Xiang E, Luo F, Li Q, Ma Q, Yuan F, Chen P. Expression profiling of CPS1 in Correa's cascade and its association with gastric cancer prognosis. Oncol Lett 2021; 21:441. [PMID: 33868479 PMCID: PMC8045184 DOI: 10.3892/ol.2021.12702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
Carbamoyl phosphate synthetase 1 (CPS1), which is the antigen for the hepatocyte paraffin 1 antibody, exhibits focal immunoreactivity in adenocarcinoma from the gastrointestinal tract, but its expression profiles and roles in gastric cancer (GC) remain largely unknown. The present study aimed to determine the expression pattern and prognostic value of CPS1 in Correa's cascade using tissues from 32 patients with chronic atrophic gastritis with intestinal metaplasia (IM), 62 patients with low- or high-grade intraepithelial neoplasia (IN) and 401 patients with GC. The expression of CPS1 was diffuse and strongly positive in 32 cases (100%) of IM of the glandular epithelium, and gradually downregulated in Correa's cascade, with a strongly positive ratio of 21 (70%) in low-grade IN and 4 (12.5%) in high-grade IN. The levels of CPS1 expression were significantly higher in diffuse-type GC, with 37 (26%) cases strongly positive for CPS1, compared with 14 (8%) in intestinal-type and 11 (13%) cases in mixed-type GC. In intestinal-type GC, CPS1 expression was completely lost in 107 (62%) of cases, which was associated with an advanced Tumor-Node-Metastasis stage (P=0.031) and depth of invasion (P=0.037). Kaplan-Meier analysis suggested that low CPS1 expression levels were independently associated with a short overall survival (OS) time in the three types of GC (P<0.001 in intestinal-type, P=0.003 in diffuse-type and P=0.018 in mixed-type GC). Furthermore, low levels of CPS1 mRNA and high methylation levels in the CPS1 promoter were associated with a short OS time in patients with GC. These results suggested that the expression of CPS1 was progressively downregulated in Correa's cascade, and that CPS1 may serve as a prognostic marker for patients with GC, regardless of tumor type.
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Affiliation(s)
- Xuqian Fang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Xiaoqiong Wu
- Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Enfei Xiang
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Fangxiu Luo
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Qinqin Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Qianchen Ma
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Fei Yuan
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Peizhan Chen
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
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Zhang T, Hu L, Tang JF, Xu H, Tian K, Wu MN, Huang SY, Du YM, Zhou P, Lu RJ, He S, Xu JM, Si JJ, Li J, Chen DL, Ran JH. Metformin Inhibits the Urea Cycle and Reduces Putrescine Generation in Colorectal Cancer Cell Lines. Molecules 2021; 26:molecules26071990. [PMID: 33915902 PMCID: PMC8038129 DOI: 10.3390/molecules26071990] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 12/20/2022] Open
Abstract
The urea cycle (UC) removes the excess nitrogen and ammonia generated by nitrogen-containing compound composites or protein breakdown in the human body. Research has shown that changes in UC enzymes are not only related to tumorigenesis and tumor development but also associated with poor survival in hepatocellular, breast, and colorectal cancers (CRC), etc. Cytoplasmic ornithine, the intermediate product of the urea cycle, is a specific substrate for ornithine decarboxylase (ODC, also known as ODC1) for the production of putrescine and is required for tumor growth. Polyamines (spermidine, spermine, and their precursor putrescine) play central roles in more than half of the steps of colorectal tumorigenesis. Given the close connection between polyamines and cancer, the regulation of polyamine metabolic pathways has attracted attention regarding the mechanisms of action of chemical drugs used to prevent CRC, as the drug most widely used for treating type 2 diabetes (T2D), metformin (Met) exhibits antitumor activity against a variety of cancer cells, with a vaguely defined mechanism. In addition, the influence of metformin on the UC and putrescine generation in colorectal cancer has remained unclear. In our study, we investigated the effect of metformin on the UC and putrescine generation of CRC in vivo and in vitro and elucidated the underlying mechanisms. In nude mice bearing HCT116 tumor xenografts, the administration of metformin inhibited tumor growth without affecting body weight. In addition, metformin treatment increased the expression of monophosphate (AMP)-activated protein kinase (AMPK) and p53 in both HCT116 xenografts and colorectal cancer cell lines and decreased the expression of the urea cycle enzymes, including carbamoyl phosphate synthase 1 (CPS1), arginase 1 (ARG1), ornithine trans-carbamylase (OTC), and ODC. The putrescine levels in both HCT116 xenografts and HCT116 cells decreased after metformin treatment. These results demonstrate that metformin inhibited CRC cell proliferation via activating AMPK/p53 and that there was an association between metformin, urea cycle inhibition and a reduction in putrescine generation.
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Affiliation(s)
- Tao Zhang
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
- Chongqing Three Gorges Medical College, Chongqing Engineering Research Center of Antitumor Natural Drugs, Chongqing 404120, China
| | - Ling Hu
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Jia-Feng Tang
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
- Chongqing Three Gorges Medical College, Chongqing Engineering Research Center of Antitumor Natural Drugs, Chongqing 404120, China
| | - Hang Xu
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Kuan Tian
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
| | - Meng-Na Wu
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Shi-Ying Huang
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Yu-Mei Du
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Peng Zhou
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Rui-Jin Lu
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Shuang He
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Jia-Mei Xu
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
| | - Jian-Jun Si
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
| | - Jing Li
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
| | - Di-Long Chen
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
- Chongqing Three Gorges Medical College, Chongqing Engineering Research Center of Antitumor Natural Drugs, Chongqing 404120, China
| | - Jian-Hua Ran
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; (T.Z.); (L.H.); (H.X.); (K.T.); (M.-N.W.); (J.-M.X.); (J.-J.S.)
- Lab of Stem Cell and Tissue Engineering, Department of Histology and Embryology, Chongqing Medical University, Chongqing 400016, China; (J.-F.T.); (S.-Y.H.); (Y.-M.D.); (P.Z.); (R.-J.L.); (S.H.); (J.L.); (D.-L.C.)
- Correspondence: ; Tel.: +86-150-8681-4824
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Wang W, Li Q, Huang G, Lin BY, Lin D, Ma Y, Zhang Z, Chen T, Zhou J. Tandem Mass Tag-Based Proteomic Analysis of Potential Biomarkers for Hepatocellular Carcinoma Differentiation. Onco Targets Ther 2021; 14:1007-1020. [PMID: 33603407 PMCID: PMC7886252 DOI: 10.2147/ott.s273823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/28/2021] [Indexed: 01/27/2023] Open
Abstract
Purpose The poor prognosis of hepatocellular carcinoma (HCC) urgent us to discover early and effective biomarkers. In this study, we applied tandem mass tag (TMT)-based proteomic analysis to discover potential protein markers for HCC identification and differentiation. Patients and Methods Fifteen patients, well-differentiated (G1, N = 5), moderate-differentiated (G2, N = 5), and poorly differentiated (G3, N = 5), with 30 matched pair tissues (both tumor and adjacent non-tumor tissues derived from the same patient) were enrolled. All samples were subjected to TMT labeling and LC−MS/MS analysis. The identified proteins were subsequently assigned to GO and KEGG for predicting function. The identified protein candidates were validated using immunohistochemistry (IHC). Results A total of 1010 proteins were identified. Of these, 154 differentially expressed proteins (DEPs), 100 up-regulated and 54 down-regulated, were found between tumor and adjacent non-tumor tissues; 12 DEPs, 9 up-regulated and 3 down-regulated, were found between G1 and G3 tissues; 8 DEPs, 5 up-regulated and 3 down-regulated, were found between G1 and G2 tissues; 11 DEPs, 8 up-regulated and 3 down-regulated, were found between G2 and G3 tissues. Among them, ASS1 and CPS1 were significantly up-regulated while UROD and HBB were significantly down-regulated in G3 compared with G1 and G2 tumors. Three proteins, CYB5A, FKBP11 and YBX1, were significantly up-regulated in G1 compared with both G2 and G3 tumors. The 7 biomarker candidates were further verified by IHC. Conclusion A variety of DEPs related to the histological differentiation of HCC were identified, among which ASS1, CPS1, URPD and HBB proteins were potential biomarkers for distinguishing poorly differentiated HCC, while CYB5A, FKBP11 and YBX1 were potential biomarkers for distinguishing well-differentiated HCC. Our findings may further provide a new insight facilitating the diagnosis and prognosis of HCC.
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Affiliation(s)
- Wei Wang
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Qiang Li
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510000, People's Republic of China
| | - Ge Huang
- Intensive Care Unit, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Bing-Yao Lin
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Dongzi Lin
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Yan Ma
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Zhao Zhang
- Research and Development Centre, South China Institute of Biomedicine, Guangdonglongsee Biomedical Co., Ltd, Guangzhou, 510000, People's Republic of China
| | - Tao Chen
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Jie Zhou
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
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Key Enzymes in Pyrimidine Synthesis, CAD and CPS1, Predict Prognosis in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13040744. [PMID: 33670206 PMCID: PMC7916936 DOI: 10.3390/cancers13040744] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Patients with hepatocellular carcinoma (HCC) have a highly variable clinical course. Therefore, there is an urgent need to identify new prognostic markers to determine prognosis and select specific therapies. Recently, it has been demonstrated that dysregulation of the urea cycle (UC) is a common phenomenon in multiple types of cancer. Upon UC dysregulation, nitrogen is diverted toward the multifunctional enzyme carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD), and increases pyrimidine synthesis. In this study, we investigated the role of CAD and carbamoyl-phosphate synthetase 1 (CPS1), a rate-limiting enzyme of the UC highly expressed in hepatocytes, in HCC. We created a tissue microarray to analyze expression of both enzymes by immunohistochemistry in a large and well-characterized overall cohort of 871 HCCs of 561 patients that underwent surgery. CAD was induced in recurrent HCCs, and high expression predicted shorter overall survival. CPS1 was downregulated in HCC and further reduced in recurrent tumors and distant metastases. Additionally, low CPS1 was associated with short overall survival. A combined score of both enzymes was an independent prognostic marker in a multivariate Cox regression model (HR = 1.37, 95% confidence interval 1.06-1.75, p = 0.014). Inhibition of pyrimidine synthesis may represent a novel therapeutic strategy for HCC.
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Liu Z, Liu L, Lu T, Wang L, Li Z, Jiao D, Han X. Hypoxia Molecular Characterization in Hepatocellular Carcinoma Identifies One Risk Signature and Two Nomograms for Clinical Management. JOURNAL OF ONCOLOGY 2021; 2021:6664386. [PMID: 33552157 PMCID: PMC7846409 DOI: 10.1155/2021/6664386] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 12/24/2022]
Abstract
Hypoxia is a universal feature in the tumor microenvironment (TME). Nonetheless, the heterogeneous hypoxia patterns of TME have still not been elucidated in hepatocellular carcinoma (HCC). Using consensus clustering algorithm and public datasets, we identified heterogeneous hypoxia subtypes. We also revealed the specific biological and clinical characteristics via bioinformatic methods. The principal component analysis algorithm was employed to develop a hypoxia-associated risk score (HARS). We identified the two hypoxia subtypes: low hypoxia pattern (C1) and high hypoxia pattern (C2). C1 was less sensitive to immunotherapy compared to C2, consistent with the lack of immune cells and immune checkpoints (ICPs) in C1, whereas C2 was the opposite. C2 displayed worse prognosis and higher sensitivity to obatoclax relative to C1, while C1 was more sensitive to sorafenib. The two subtypes also demonstrated subtype-specific genomic variations including mutation, copy number alteration, and methylation. Moreover, we developed and validated a risk signature: HARS, which had excellent performance for predicting prognosis and immunotherapy. We revealed two hypoxia subtypes with distinct biological and clinical characteristics in HCC, which enhanced the understanding of hypoxia pattern. The risk signature was a promising biomarker for predicting prognosis and immunotherapy.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou 450052, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Taoyuan Lu
- Department of Cerebrovascular Disease, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhaonan Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou 450052, China
| | - Dechao Jiao
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou 450052, China
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Lo LH, Lam CY, To JC, Chiu CH, Keng VW. Sleeping Beauty insertional mutagenesis screen identifies the pro-metastatic roles of CNPY2 and ACTN2 in hepatocellular carcinoma tumor progression. Biochem Biophys Res Commun 2021; 541:70-77. [PMID: 33482578 DOI: 10.1016/j.bbrc.2021.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 12/12/2022]
Abstract
A forward genetic Sleeping Beauty (SB) insertional mutagenesis screen, followed by high-throughput transcriptome sequencing, was used to identify driver genes responsible for hepatocellular carcinoma (HCC)-associated metastasis. Using RNA-sequencing (RNA-seq) to identify transposon-endogenous transcriptome fusion genes, the phylogenetic lineage between the parental liver tumor and secondary metastasis can be determined to provide mechanistic insight to genetic changes involved in the metastatic evolution process. In the current study, two novel candidate genes were identified to be potentially involved in HCC-associated metastatic progression, canopy FGF signaling regulator 2 (Cnpy2) and actinin alpha 2 (Actn2). Transposon-Cnpy2 fusion transcripts were identified in both primary liver tumors and lung metastases. Its significant association with clinicopathological characteristics and correlated gene enrichment in metastasis-related mechanisms suggest its potential role in modulating local invasion and angiogenesis. Other known driver genes for human HCC that can also promote metastatic progression include epidermal growth factor receptor (Egfr) and RNA imprinted and accumulated in nucleus (Rian). Metabolic pathway related gene carbamoyl phosphate synthetase (Cps1) was identified to play an important role in early HCC development, while cell junction-related pathway gene Rac family small GTPase 1 (Rac1) was identified to take part in both HCC and pro-metastatic progression. Importantly, actinin alpha 2 (Actn2) was identified exclusively in the secondary metastasis site and its role in HCC-related metastatic process was elucidated using in vitro approaches. ACTN2-overexpression in human liver cancer cells displayed enhanced cellular motility and invasion abilities, indicating its possible function in later stage of metastasis, such as extravasation and lung colonization.
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Affiliation(s)
- Lilian H Lo
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Coco Y Lam
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Jeffrey C To
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Cynthia H Chiu
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Vincent W Keng
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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A novel immune classification reveals distinct immune escape mechanism and genomic alterations: implications for immunotherapy in hepatocellular carcinoma. J Transl Med 2021; 19:5. [PMID: 33407585 PMCID: PMC7789239 DOI: 10.1186/s12967-020-02697-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022] Open
Abstract
Background The tumor immunological microenvironment (TIME) has a prominent impact on prognosis and immunotherapy. However, the heterogeneous TIME and the mechanisms by which TIME affects immunotherapy have not been elucidated in hepatocellular carcinoma (HCC). Methods A total of 2195 eligible HCC patients from TCGA and GEO database were collected. We comprehensively explored the different heterogeneous TIME phenotypes and its clinical significance. The potential immune escape mechanisms and what genomic alterations may drive the formation of different phenotypes were further investigated. Results We identified three phenotypes in HCC: TIME-1, the “immune-deficiency” phenotype, with immune cell depletion and proliferation; TIME-2, the “immune-suppressed” phenotype, with enrichment of immunosuppressive cells; TIME-3, the “immune-activated phenotype”, with abundant leukocytes infiltration and immune activation. The prognosis and sensitivity to both sorafenib and immunotherapy differed among the three phenotypes. We also underlined the potential immune escape mechanisms: lack of leukocytes and defective tumor antigen presentation capacity in TIME-1, increased immunosuppressive cells in TIME-2, and rich in immunoinhibitory molecules in TIME-3. The different phenotypes also demonstrated specific genomic events: TIME-1 characterized by TP53, CDKN2A, CTNNB1, AXIN1 and FOXD4 alterations; TIME-2 characterized by significant alteration patterns in the PI3K pathway; TIME-3 characterized by ARID1A mutation. Besides, the TIME index (TI) was proposed to quantify TIME infiltration pattern, and it was a superior prognostic and immunotherapy predictor. A pipeline was developed to classify single patient into one of these three subtypes and calculated the TI. Conclusions We identified three TIME phenotypes with different clinical outcomes, immune escape mechanisms and genomic alterations in HCC, which could present strategies for improving the efficacy of immunotherapy. TI as a novel prognostic and immunotherapeutic signature that could guide personalized immunotherapy and clinical management of HCC.
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Tenen DG, Chai L, Tan JL. Metabolic alterations and vulnerabilities in hepatocellular carcinoma. Gastroenterol Rep (Oxf) 2021; 9:1-13. [PMID: 33747521 PMCID: PMC7962738 DOI: 10.1093/gastro/goaa066] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/06/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Liver cancer is a serious disease. It is ranked as the cancer with the second highest number of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC), which arises from transformed hepatocytes, is the major subtype of liver cancer. It accounts for 85% of total liver-cancer cases. An important aspect of HCC that has been actively studied is its metabolism. With the liver as the primary site of numerous metabolic processes in the body, it has been shown that the metabolism of HCC cells is highly dysregulated compared to that of normal hepatocytes. It is therefore crucial to understand the metabolic alterations caused by HCC and the underlying mechanisms for these alterations. This deeper understanding will allow diagnostic and therapeutic advancements in the treatment of HCC. In this review, we will summarize the current literature in HCC metabolic alterations, induced vulnerabilities, and potential therapeutic interventions.
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Affiliation(s)
- Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Li Chai
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Justin L Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
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Fernández-Barrena MG, Arechederra M, Colyn L, Berasain C, Avila MA. Epigenetics in hepatocellular carcinoma development and therapy: The tip of the iceberg. JHEP Rep 2020; 2:100167. [PMID: 33134907 PMCID: PMC7585149 DOI: 10.1016/j.jhepr.2020.100167] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a deadly tumour whose causative agents are generally well known, but whose pathogenesis remains poorly understood. Nevertheless, key genetic alterations are emerging from a heterogeneous molecular landscape, providing information on the tumorigenic process from initiation to progression. Among these molecular alterations, those that affect epigenetic processes are increasingly recognised as contributing to carcinogenesis from preneoplastic stages. The epigenetic machinery regulates gene expression through intertwined and partially characterised circuits involving chromatin remodelers, covalent DNA and histone modifications, and dedicated proteins reading these modifications. In this review, we summarise recent findings on HCC epigenetics, focusing mainly on changes in DNA and histone modifications and their carcinogenic implications. We also discuss the potential drugs that target epigenetic mechanisms for HCC treatment, either alone or in combination with current therapies, including immunotherapies.
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Key Words
- 5acC, 5-acetylcytosine
- 5fC, 5-formylcytosine
- 5hmC, 5-hydoxymethyl cytosine
- 5mC, 5-methylcytosine
- Acetyl-CoA, acetyl coenzyme A
- BER, base excision repair
- BRD, bromodomain
- CDA, cytidine deaminase
- CGI, CpG island
- CIMP, CGI methylator phenotype
- CTLA-4, cytotoxic T-lymphocyte-associated protein 4
- DNMT, DNA methyltransferase
- DNMTi, DNMT inhibitor
- Epigenetics
- FAD, flavin adenine dinucleotide
- HAT, histone acetyltransferases
- HCC, hepatocellular carcinoma
- HDAC, histone deacetylase
- HDACi, HDAC inhibitor
- HDM, histone demethylase
- HMT, histone methyltransferase
- Hepatocellular carcinoma
- KMT, lysine methyltransferase
- LSD/KDM, lysine specific demethylases
- NAFLD, non-alcoholic fatty liver disease
- NK, natural killer
- NPC, nasopharyngeal carcinoma
- PD-L1, programmed cell death ligand-1
- PD1, programmed cell death protein 1
- PHD, plant homeodomain
- PTM, post-translational modification
- SAM, S-adenosyl-L-methionine
- TDG, thymidine-DNA-glycosylase
- TERT, telomerase reverse transcriptase
- TET, ten-eleven translocation
- TME, tumour microenvironment
- TSG, tumour suppressor gene
- Therapy
- UHRF1, ubiquitin like with PHD and ring finger domains 1
- VEGF, vascular endothelial growth factor
- ncRNAs, non-coding RNAs
- α-KG, α-ketoglutarate
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Affiliation(s)
- Maite G. Fernández-Barrena
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - María Arechederra
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Leticia Colyn
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Matias A. Avila
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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Nitzahn M, Lipshutz GS. CPS1: Looking at an ancient enzyme in a modern light. Mol Genet Metab 2020; 131:289-298. [PMID: 33317798 PMCID: PMC7738762 DOI: 10.1016/j.ymgme.2020.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023]
Abstract
The mammalian urea cycle (UC) is responsible for siphoning catabolic waste nitrogen into urea for excretion. Disruptions of the functions of any of the enzymes or transporters lead to elevated ammonia and neurological injury. Carbamoyl phosphate synthetase 1 (CPS1) is the first and rate-limiting UC enzyme responsible for the direct incorporation of ammonia into UC intermediates. Symptoms in CPS1 deficiency are typically the most severe of all UC disorders, and current clinical management is insufficient to prevent the associated morbidities and high mortality. With recent advances in basic and translational studies of CPS1, appreciation for this enzyme's essential role in the UC has been broadened to include systemic metabolic regulation during homeostasis and disease. Here, we review recent advances in CPS1 biology and contextualize them around the role of CPS1 in health and disease.
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Affiliation(s)
- Matthew Nitzahn
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Gerald S Lipshutz
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
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Berndt N, Eckstein J, Heucke N, Wuensch T, Gajowski R, Stockmann M, Meierhofer D, Holzhütter HG. Metabolic heterogeneity of human hepatocellular carcinoma: implications for personalized pharmacological treatment. FEBS J 2020; 288:2332-2346. [PMID: 33030799 DOI: 10.1111/febs.15587] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/01/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
Metabolic reprogramming is a characteristic feature of cancer cells, but there is no unique metabolic program for all tumors. Genetic and gene expression studies have revealed heterogeneous inter- and intratumor patterns of metabolic enzymes and membrane transporters. The functional implications of this heterogeneity remain often elusive. Here, we applied a systems biology approach to gain a comprehensive and quantitative picture of metabolic changes in individual hepatocellular carcinoma (HCC). We used protein intensity profiles determined by mass spectrometry in samples of 10 human HCCs and the adjacent noncancerous tissue to calibrate Hepatokin1, a complex mathematical model of liver metabolism. We computed the 24-h profile of 18 metabolic functions related to carbohydrate, lipid, and nitrogen metabolism. There was a general tendency among the tumors toward downregulated glucose uptake and glucose release albeit with large intertumor variability. This finding calls into question that the Warburg effect dictates the metabolic phenotype of HCC. All tumors comprised elevated β-oxidation rates. Urea synthesis was found to be consistently downregulated but without compromising the tumor's capacity for ammonia detoxification owing to increased glutamine synthesis. The largest intertumor heterogeneity was found for the uptake and release of lactate and the size of the cellular glycogen content. In line with the observed metabolic heterogeneity, the individual HCCs differed largely in their vulnerability against pharmacological treatment with metformin. Taken together, our approach provided a comprehensive and quantitative characterization of HCC metabolism that may pave the way for a computational a priori assessment of pharmacological therapies targeting metabolic processes of HCC.
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Affiliation(s)
- Nikolaus Berndt
- Institute for Imaging Science and Computational Modelling in Cardiovascular Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Johannes Eckstein
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Niklas Heucke
- Department of Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Tilo Wuensch
- Department of Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Robert Gajowski
- Mass Spectroscopy Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Germany
| | - Martin Stockmann
- Department of Surgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - David Meierhofer
- Mass Spectroscopy Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hermann-Georg Holzhütter
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
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Ben Kridis-Rejeb W, Ben Ayed-Guerfali D, Ammous-Boukhris N, Ayadi W, Kifagi C, Charfi S, Saguem I, Sellami-Boudawara T, Daoud J, Khanfir A, Mokdad-Gargouri R. Identification of novel candidate genes by exome sequencing in Tunisian familial male breast cancer patients. Mol Biol Rep 2020; 47:6507-6516. [PMID: 32901360 DOI: 10.1007/s11033-020-05703-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/01/2020] [Indexed: 12/11/2022]
Abstract
Male Breast Cancer (MBC) is a rare and aggressive disease that is associated with genetic factors. Mutations in BRCA1 and BRCA2 account for 10% of all MBC cases suggesting that other genetic factors are involved. The aim of the present study is to screen whole BRCA1 and BRCA2 exons using the Ampliseq BRCA panel in Tunisian MBC patients with family history. Furthermore, we performed exome sequencing using the TruSight One sequencing panel on an early onset BRCA negative patient. We showed that among the 6 MBC patients, only one (MBC-F1) harbored a novel frameshift mutation in exon 2 of the BRCA2 gene (c.17-20delAAGA, p.Lys6Xfs) resulting in a short BRCA2 protein of only 6 amino-acids. We selected 9 rare variants after applying several filter steps on the exome sequencing data. Among these variants, and based on their role in breast carcinogenesis, we retained 6 candidate genes (MSH5, DCC, ERBB3, NOTCH3, DIAPH1, and DNAH11). Further studies are needed to confirm the association of the selected genes with family MBC.
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Affiliation(s)
| | - Dorra Ben Ayed-Guerfali
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Wajdi Ayadi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia
| | - Chamseddine Kifagi
- Division of Immunology & Vaccinology, DTU Nanotech, Department of Micro-and Nanotechnology, Kemitorvet, Buildings 202 and 204, Lyngby Campus, 2800, Kgs. Lyngby, Denmark
| | - Slim Charfi
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Ines Saguem
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Tahia Sellami-Boudawara
- Department of Anatomo-Pathology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Jamel Daoud
- Department of Radiotherapy, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Afef Khanfir
- Department of Oncology, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, 3038, Sfax, Tunisia.
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Multifaceted Aspects of Metabolic Plasticity in Human Cholangiocarcinoma: An Overview of Current Perspectives. Cells 2020; 9:cells9030596. [PMID: 32138158 PMCID: PMC7140515 DOI: 10.3390/cells9030596] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a deadly tumor without an effective therapy. Unique metabolic and bioenergetics features are important hallmarks of tumor cells. Metabolic plasticity allows cancer cells to survive in poor nutrient environments and maximize cell growth by sustaining survival, proliferation, and metastasis. In recent years, an increasing number of studies have shown that specific signaling networks contribute to malignant tumor onset by reprogramming metabolic traits. Several evidences demonstrate that numerous metabolic mediators represent key-players of CCA progression by regulating many signaling pathways. Besides the well-known Warburg effect, several other different pathways involving carbohydrates, proteins, lipids, and nucleic acids metabolism are altered in CCA. The goal of this review is to highlight the main metabolic processes involved in the cholangio-carcinogeneis that might be considered as potential novel druggable candidates for this disease.
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45
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Dumenci OE, U AM, Khan SA, Holmes E, Taylor-Robinson SD. Exploring Metabolic Consequences of CPS1 and CAD Dysregulation in Hepatocellular Carcinoma by Network Reconstruction. J Hepatocell Carcinoma 2020; 7:1-9. [PMID: 32021853 PMCID: PMC6955626 DOI: 10.2147/jhc.s239039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) is the fourth commonest cause of cancer-related mortality; it is associated with various genetic alterations, some involved in metabolic reprogramming. This study aimed to explore the potential metabolic impact of Carbamoyl Phosphate Synthase I (CPS1) and carbamoyl phosphate synthetase/aspartate transcarbamoylase/dihydroorotase (CAD) dysregulation through the reconstruction of a network that integrates information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, Human Metabolome Database (HMDB) and Human Protein Atlas (HPA). Methods and results Existing literature was used to determine the roles of CPS1 and CAD in HCC. CPS1 downregulation is thought to play a role in hepatocarcinogenesis through an increased glutamine availability for de novo pyrimidine biosynthesis, which CAD catalyzes the first three steps for. KEGG, HMDB and HPA were used to reconstruct a network of relevant pathways, demonstrating the relationships between genes and metabolites using the MetaboSignal package in R. The network was filtered to exclude any duplicates, and those greater than three steps away from CPS1 or CAD. Consequently, a network of 18 metabolites, 28 metabolic genes and 1 signaling gene was obtained, which indicated expression profiles and prognostic information of each gene in the network. Conclusion Information from different databases was collated to form an informative network that integrated different “-omics” approaches, demonstrating the relationships between genetic and metabolic components of urea cycle and the de novo pyrimidine biosynthesis pathway. This study paves the way for further research by acting as a template to investigate the relationships between genes and metabolites, explore their potential roles in various diseases and aid the development of new screening and treatment methods through network reconstruction.
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46
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Satriano L, Lewinska M, Rodrigues PM, Banales JM, Andersen JB. Metabolic rearrangements in primary liver cancers: cause and consequences. Nat Rev Gastroenterol Hepatol 2019; 16:748-766. [PMID: 31666728 DOI: 10.1038/s41575-019-0217-8] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/19/2019] [Indexed: 02/07/2023]
Abstract
Primary liver cancer (PLC) is the fourth most frequent cause of cancer-related death. The high mortality rates arise from late diagnosis and the limited accuracy of diagnostic and prognostic biomarkers. The liver is a major regulator, orchestrating the clearance of toxins, balancing glucose, lipid and amino acid uptake, managing whole-body metabolism and maintaining metabolic homeostasis. Tumour onset and progression is frequently accompanied by rearrangements of metabolic pathways, leading to dysregulation of metabolism. The limitation of current therapies targeting PLCs, such as hepatocellular carcinoma and cholangiocarcinoma, points towards the importance of deciphering this metabolic complexity. In this Review, we discuss the role of metabolic liver disruptions and the implications of these processes in PLCs, emphasizing their clinical relevance and value in early diagnosis and prognosis and as putative therapeutic targets. We also describe system biology approaches able to reconstruct the metabolic complexity of liver diseases. We also discuss whether metabolic rearrangements are a cause or consequence of PLCs, emphasizing the opportunity to clinically exploit the rewired metabolism. In line with this idea, we discuss circulating metabolites as promising biomarkers for PLCs.
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Affiliation(s)
- Letizia Satriano
- Biotech Research and Innovation Centre (BRIC) Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Monika Lewinska
- Biotech Research and Innovation Centre (BRIC) Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pedro M Rodrigues
- Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Jesus M Banales
- Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC) Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Jin T, Wang C, Tian Y, Dai C, Zhu Y, Xu F. Mitochondrial metabolic reprogramming: An important player in liver cancer progression. Cancer Lett 2019; 470:197-203. [PMID: 31783085 DOI: 10.1016/j.canlet.2019.11.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022]
Abstract
Mitochondria are known as essential biosynthetic, bioenergetic and signaling organelles, and play a critical role in cell differentiation, proliferation, and death. Nowadays, cancer is emergingly considered as a mitochondrial metabolic disease. Mitochondria also play an essential role in liver carcinogenesis. Liver cells are highly regenerative and require high energy. For that reason, a large number of mitochondria are present and functional in liver cells. Abnormalities in mitochondrial metabolism in human liver are known to be one of the carcinogenic factors. Interestingly, immune checkpoints regulate mitochondrial metabolic energetics of the tumor, the tumor microenvironment, as well as the tumor-specific immune response. This regulation forms a positive loop between the metabolic reprogramming of both cancer cells and immune cells. In this review, we discuss the evidence and mechanisms that mitochondria interplay with immune checkpoints to influence different steps of oncogenesis, as well as the potential of mitochondria as therapeutic targets for liver cancer therapy.
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Affiliation(s)
- Tianqiang Jin
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Chao Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Surgery, Northeast International Hospital, Shenyang, 110623, China
| | - Yu Tian
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Chaoliu Dai
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yuwen Zhu
- Department of Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Feng Xu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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Khoja S, Nitzahn M, Truong B, Lambert J, Willis B, Allegri G, Rüfenacht V, Häberle J, Lipshutz GS. A constitutive knockout of murine carbamoyl phosphate synthetase 1 results in death with marked hyperglutaminemia and hyperammonemia. J Inherit Metab Dis 2019; 42:1044-1053. [PMID: 30835861 PMCID: PMC6728231 DOI: 10.1002/jimd.12048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/31/2018] [Indexed: 12/25/2022]
Abstract
The enzyme carbamoyl phosphate synthetase 1 (CPS1; EC 6.3.4.16) forms carbamoyl phosphate from bicarbonate, ammonia, and adenosine triphosphate (ATP) and is activated allosterically by N-acetylglutamate. The neonatal presentation of bi-allelic mutations of CPS1 results in hyperammonemia with reduced citrulline and is reported as the most challenging nitrogen metabolism disorder to treat. As therapeutic interventions are limited, patients often develop neurological injury or die from hyperammonemia. Survivors remain vulnerable to nitrogen overload, being at risk for repetitive neurological injury. With transgenic technology, our lab developed a constitutive Cps1 mutant mouse and reports its characterization herein. Within 24 hours of birth, all Cps1 -/- mice developed hyperammonemia and expired. No CPS1 protein by Western blot or immunostaining was detected in livers nor was Cps1 mRNA present. CPS1 enzymatic activity was markedly decreased in knockout livers and reduced in Cps1+/- mice. Plasma analysis found markedly reduced citrulline and arginine and markedly increased glutamine and alanine, both intermolecular carriers of nitrogen, along with elevated ammonia, taurine, and lysine. Derangements in multiple other amino acids were also detected. While hepatic amino acids also demonstrated markedly reduced citrulline, arginine, while decreased, was not statistically significant; alanine and lysine were markedly increased while glutamine was trending towards significance. In conclusion we have determined that this constitutive neonatal mouse model of CPS1 deficiency replicates the neonatal human phenotype and demonstrates the key biochemical features of the disorder. These mice will be integral for addressing the challenges of developing new therapeutic approaches for this, at present, poorly treated disorder.
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Affiliation(s)
- Suhail Khoja
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Matthew Nitzahn
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Brian Truong
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Jenna Lambert
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Brandon Willis
- Mouse Biology Program, University of California, Davis, California
| | - Gabriella Allegri
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Véronique Rüfenacht
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Gerald S Lipshutz
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, California
- Intellectual and Developmental Disabilities Research Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, California
- Semel Institute for Neuroscience, David Geffen School of Medicine at UCLA, Los Angeles, California
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49
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Wu G, Yan Y, Zhou Y, Wang X, Wei J, Chen X, Lin W, Ou C, Zhou J, Xu Z. Expression and clinical significance of CPS1 in glioblastoma multiforme. Curr Res Transl Med 2019; 67:123-128. [PMID: 31492588 DOI: 10.1016/j.retram.2019.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 02/08/2023]
Abstract
Carbamoyl phosphate synthetase-1 (CPS1), the first rate-limiting mitochondrial enzyme in the urea cycle, regulates proliferation and differentiation during tumor progression. However, the detailed function of CPS1 in glioblastoma Multiforme (GBM) is still unclear. Here, we highlight mechanisms for CPS1 upregulation and the effects of upregulated CPS1 on GBM tumorigenesis. The transcriptome data from several public databases, such as Oncomine and GEPIA, revealed that CPS1 transcriptional level was significantly upregulated in GBM tissues and cells. Moreover, CPS1 was hypomethylated in GBM tissues. The Wanderer database, linked to the Cancer Genome Atlas (TCGA), showed the association between CPS1 expression or its methylation values and the clinicopathological parameters in GBM patients. Our work fully demonstrated that CPS1 expression was upregulated in GBM and this gene could be used as a potential diagnostic and prognosis indicator for GBM.
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Affiliation(s)
- Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jie Wei
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wei Lin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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Li J, Halfter K, Zhang M, Saad C, Xu K, Bauer B, Huang Y, Shi L, Mansmann UR. Computational analysis of receptor tyrosine kinase inhibitors and cancer metabolism: implications for treatment and discovery of potential therapeutic signatures. BMC Cancer 2019; 19:600. [PMID: 31208363 PMCID: PMC6580552 DOI: 10.1186/s12885-019-5804-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/06/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Receptor tyrosine kinase (RTK) inhibitors are frequently used to treat cancers and the results have been mixed, some of these small molecule drugs are highly successful while others show a more modest response. A high number of studies have been conducted to investigate the signaling mechanisms and corresponding therapeutic influence of RTK inhibitors in order to explore the therapeutic potential of RTK inhibitors. However, most of these studies neglected the potential metabolic impact of RTK inhibitors, which could be highly associated with drug efficacy and adverse effects during treatment. METHODS In order to fill these knowledge gaps and improve the therapeutic utilization of RTK inhibitors a large-scale computational simulation/analysis over multiple types of cancers with the treatment responses of RTK inhibitors was performed. The pharmacological data of all eight RTK inhibitor and gene expression profiles of 479 cell lines from The Cancer Cell Line Encyclopedia were used. RESULTS The potential metabolic impact of RTK inhibitors on different types of cancers were analyzed resulting in cancer-specific (breast, liver, pancreas, central nervous system) metabolic signatures. Many of these are in line with results from different independent studies, thereby providing indirect verification of the obtained results. CONCLUSIONS Our study demonstrates the potential of using a computational approach on signature-based-analysis over multiple cancer types. The results reveal the strength of multiple-cancer analysis over conventional signature-based analysis on a single cancer type.
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Affiliation(s)
- Jian Li
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University München, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kathrin Halfter
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University München, Munich, Germany
| | - Mengying Zhang
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University München, Munich, Germany
| | - Christian Saad
- Department of Computational Science, University of Augsburg, Augsburg, Germany
| | - Kai Xu
- Department of Orthopaedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Bernhard Bauer
- Department of Computational Science, University of Augsburg, Augsburg, Germany
| | - Yijiang Huang
- Department of Orthopaedics, Physical Medicine and Rehabilitation, University Hospital, LMU, Munich, Germany
| | - Lei Shi
- Institute of Photomedicine, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Ulrich R. Mansmann
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University München, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
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