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Hu D, Zhang Z, Liu X, Wu Y, An Y, Wang W, Yang M, Pan Y, Qiao K, Du C, Zhao Y, Li Y, Bao J, Qin T, Pan Y, Xia Z, Zhao X, Sun K. Generalizable transcriptome-based tumor malignant level evaluation and molecular subtyping towards precision oncology. J Transl Med 2024; 22:512. [PMID: 38807223 PMCID: PMC11134716 DOI: 10.1186/s12967-024-05326-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/19/2024] [Indexed: 05/30/2024] Open
Abstract
In cancer treatment, therapeutic strategies that integrate tumor-specific characteristics (i.e., precision oncology) are widely implemented to provide clinical benefits for cancer patients. Here, through in-depth integration of tumor transcriptome and patients' prognoses across cancers, we investigated dysregulated and prognosis-associated genes and catalogued such important genes in a cancer type-dependent manner. Utilizing the expression matrices of these genes, we built models to quantitatively evaluate the malignant levels of tumors across cancers, which could add value to the clinical staging system for improved prediction of patients' survival. Furthermore, we performed a transcriptome-based molecular subtyping on hepatocellular carcinoma, which revealed three subtypes with significantly diversified clinical outcomes, mutation landscapes, immune microenvironment, and dysregulated pathways. As tumor transcriptome was commonly profiled in clinical practice with low experimental complexity and cost, this work proposed easy-to-perform approaches for practical clinical promotion towards better healthcare and precision oncology of cancer patients.
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Affiliation(s)
- Dingxue Hu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ziteng Zhang
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, China
| | - Xiaoyi Liu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Youchun Wu
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, China
| | - Yunyun An
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Wanqiu Wang
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Mengqi Yang
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Yuqi Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Kun Qiao
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518100, China
| | - Changzheng Du
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
- Beijing Tsinghua Changgung Hospital, Tsinghua University School of Medicine, Beijing, 102218, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yan Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Integrative Microecology Clinical Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, Shenzhen Hospital, Southern Medical University, Shenzhen, 510086, China
| | - Jianqiang Bao
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tao Qin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat- Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yue Pan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat- Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Zhaohua Xia
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518100, China.
| | - Xin Zhao
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, China.
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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Yu L, Huang J. Deoxyribonuclease 1-like 3 inhibits colorectal malignancy through antagonizing NEDD4-triggered CDKN1A ubiquitination. Cell Biol Int 2024; 48:325-333. [PMID: 38108119 DOI: 10.1002/cbin.12108] [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: 05/05/2023] [Revised: 10/06/2023] [Accepted: 11/28/2023] [Indexed: 12/19/2023]
Abstract
Deoxyribonuclease 1-like 3 (DNASE1L3) has been shown to play nonnegligible roles in several types of carcinomas. Nevertheless, the biological function, clinical relevance, and influence of DNASE1L3 in colorectal cancer (CRC) remain obscure. Immunohistochemistry was adopted to examine DNASE1L3 and CDKN1A expression in CRC tissue, and the clinical significance of DNASE1L3 was assessed. Cell counting kit-8, colony formation, and transwell assays were employed for assessing tumor proliferation and migration. The mechanisms underlying the impact of DNASE1L3 were explored via western blot analysis, co-immunoprecipitation, and ubiquitination assay. It was observed that DNASE1L3 was downregulated in CRC tissues and was tightly associated with patient prognosis. DNASE1L3 impaired CRC cell proliferation and migration through elevating CDKN1A via suppressing CDKN1A ubiquitination. Meanwhile, DNASE1L3 was positively related to CDKN1A. In mechanism, DNASE1L3 and CDKN1A interacted with the E3 ubiquitin ligase NEDD4. Moreover, DNASE1L3 was competitively bound to NEDD4, thus repressing NEDD4-mediated CDKN1A ubiquitination and degradation. These discoveries implied the potential mechanisms of DNASE1L3 during tumorigenesis, suggesting that DNASE1L3 may serve as a new potential therapeutic agent for CRC.
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Affiliation(s)
- Lifei Yu
- Department of Gastroenterology, Changzhou No. 2 People's Hospital, The Affiliated Hospital of Nanjing Medical University, Changzhou, China
| | - Jin Huang
- Department of Gastroenterology, Changzhou No. 2 People's Hospital, The Affiliated Hospital of Nanjing Medical University, Changzhou, China
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Xiao B, Ge Y, Zhao R, Zhang Y, Guo Y, Zhang S, Li B, Qiu P, Chao Z, Zuo S. NAP1L5 facilitates pancreatic ductal adenocarcinoma progression via TRIM29-mediated ubiquitination of PHLPP1. Biochem Pharmacol 2023; 217:115811. [PMID: 37717692 DOI: 10.1016/j.bcp.2023.115811] [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: 07/12/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is considered one of the most aggressive solid tumours in humans. Despite its high mortality rate, effective targeted therapeutic strategies remain limited due to incomplete understanding of the underlying biological mechanisms. The NAP1L gene family has been implicated in the development and progression of various human tumours. However, the specific function and role of NAP1L5 (nucleosome assembly protein-like 5) in PDAC have not been fully elucidated. Therefore, in this study, we aimed to investigate the role of NAP1L5 in PDAC and explore the regulatory relationship between NAP1L5 and its potential downstream molecule PHLPP1 (PH domain Leucine-rich repeat Protein Phosphatase 1) in PDAC. Our study revealed that NAP1L5 is notably upregulated in PDAC. Moreover, both in vivo and in vitro experiments demonstrated that knockdown of NAP1L5 suppressed the proliferation of PDAC cells. Mechanistically, NAP1L5 was found to promote PDAC progression by activating the AKT/mTOR signalling pathway in a PHLPP1-dependent manner. Specifically, NAP1L5 binds to PHLPP1 and facilitates the ubiquitination-mediated degradation of PHLPP1, ultimately resulting in reduced PHLPP1 expression. Notably, TRIM29, recruited by NAP1L5, was found to be involved in facilitating K48-linked ubiquitination of PHLPP1. Our findings indicate that NAP1L5 overexpression promotes the proliferation of PDAC cells by inhibiting PHLPP1 expression. These novel insights suggest that NAP1L5 may serve as a potential therapeutic target for PDAC.
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Affiliation(s)
- Benli Xiao
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China; Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yuzhen Ge
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Rui Zhao
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yewei Zhang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yi Guo
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Shilong Zhang
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Bo Li
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Peng Qiu
- Department of Biliary and Pancreatic Surgery, Cancer Research Center Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Chao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shi Zuo
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China; Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, China; Precision Medicine Research Institute of Guizhou, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.
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Zhang Y, Yang J, Xie S, Chen H, Zhong J, Lin X, Yu Z, Xia J. A novel prognostic signature based on immunogenic cell death score predicts outcomes and response to transcatheter arterial chemoembolization and immunotherapy in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:11411-11429. [PMID: 37382674 DOI: 10.1007/s00432-023-05017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
PURPOSE The phenomenon of immunogenic cell death (ICD) is intricately linked to numerous antitumor treatments and exerts a profound regulatory function in the tumor immune microenvironment (TIME). We aimed to establish a prognostic signature from the ICD-related biomarkers to differentiate the TIME in hepatocellular carcinoma and predict diverse outcomes for patients with liver cancer. METHODS ICD score-related genes (ICDSGs) were identified using the weighted gene co-expression network analysis (WGCNA). The ICD score-related signature (ICDSsig) was established by applying LASSO and Cox regression. Model precision was verified using the external datasets. We used independent prognostic variables in clinicopathologic factors to develop a nomogram. Further, clinical characteristics, immune and molecular landscapes, the responses of transcatheter arterial chemoembolization (TACE) and immunotherapy, and chemotherapy sensitivity were analyzed for high- and low-risk patients. RESULTS ICD score-calculated using the single-sample gene set enrichment analysis (ssGSEA)-displayed strong associations with the TIME in HCC. We identified 34 ICDSGs after integrating the TCGA and GSE104580 datasets. Then, three novel ICDSGs (DNASE1L3, KLRB1, and LILRB1) were screened out to construct the ICDSsig; the prognostic signature performed well in the external databases. The high-risk patients had worse outcomes owing to their advanced pathological state, non-response of TACE, and immune-cold phenotype in the immune landscapes. The immune checkpoint genes, N6-methyladenosine-relevant genes, and microsatellite instability score were increased in the high-risk subgroup, thereby indicating a favorable sensitivity to immunotherapy. Common chemotherapy drugs were more effective in high-risk patients due to low half-maximal inhibitory concentration values. CONCLUSION The ICDSsig can potentially predict outcomes and therapeutic responses for patients with liver cancer and may assist clinicians in designing individualized treatment strategies.
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Affiliation(s)
- Yunjie Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Wenzhou Medical University, Wenzhou, 325000, China
| | - Junhui Yang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Wenzhou Medical University, Wenzhou, 325000, China
| | - Shicheng Xie
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Wenzhou Medical University, Wenzhou, 325000, China
| | - Hanbin Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Wenzhou Medical University, Wenzhou, 325000, China
| | - Jinwei Zhong
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Wenzhou Medical University, Wenzhou, 325000, China
| | - Xiaoben Lin
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhijie Yu
- Wenzhou Key Laboratory of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Jinglin Xia
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
- National Medical Center & National Clinical Research Center for Interventional Medicine. Liver Cancer Institute, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
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Ma Q, Lu Q, Lei X, Zhao J, Sun W, Wang J, Zhu Q, Huang D. UCHL3 promotes hepatocellular carcinoma cell migration by de-ubiquitinating and stabilizing Vimentin. Front Oncol 2023; 13:1088475. [PMID: 36969045 PMCID: PMC10036040 DOI: 10.3389/fonc.2023.1088475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
BackgroundHepatocellular carcinoma (HCC) is a common malignant tumor associated with a poor prognosis. Ubiquitin carboxyl-terminal hydrolase L3 (UCHL3) has been reported to promote diverse tumors, but little is known about its role in HCC.MethodsExpression levels of UCHL3 in Huh7 and Hep3B cells were measured by qRT-PCR. UCHL3, Vimentin protein levels, and ubiquitination levels were determined by Western blot assay. co-immunoprecipitation, Immunofluorescence, and IHC were used to detect the interaction and expression association between UCHL3 and Vimentin in the cells. Wound healing and Transwell assays were used to measure cell migration. Spheroid formation assay were used to assess stem-like properties.ResultsUCHL3 expression was found to be significantly elevated in HCC and associated with poor prognosis. UCHL3 promoted migration and stem-like properties of HCC cells. Vimentin was identified as a potential de-ubiquitination substrate of UCHL3 and UCHL3 interacted with and promoted the de-ubiquitination of Vimentin, enhancing its stability. Moreover, the suppression of UCHL3 by siRNA or the inhibition by TCID upregulated ubiquitinated Vimentin. Vimentin attenuated the suppression of cell migration caused by knockdown of UCHL3.ConclusionUCHL3 was highly expressed in HCC and functioned as an oncogene. Vimentin is a novel substrate of UCHL3 and its stabilization and de-ubiquitination enhanced HCC cell migration.
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Affiliation(s)
- Qiancheng Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xiangxiang Lei
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Jie Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Wen Sun
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jun Wang
- Department of Emergency and Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Qing Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- *Correspondence: Qing Zhu, ; Dongsheng Huang,
| | - Dongsheng Huang
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Qing Zhu, ; Dongsheng Huang,
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Bai Q, He X, Hu T. Pan‑cancer analysis of the deoxyribonuclease gene family. Mol Clin Oncol 2023; 18:19. [PMID: 36798465 PMCID: PMC9926046 DOI: 10.3892/mco.2023.2615] [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: 07/27/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Deoxyribonuclease (DNase) is an enzyme that catalyzes the cleavage of phosphodiester bonds in the main chain of DNA to degrade DNA. DNase serves a vital role in several immune-related diseases. The present study linked the expression of DNase with overall survival (OS), performed pan-cancer co-expression analysis, and assessed the association between DNase and immune infiltration subtypes, tumor microenvironment and drug sensitivity through pan-cancer studies. Furthermore, gene expression data and clinical data were downloaded from The Cancer Genome Atlas. Next, through a series of bioinformatics analyses, DNase expression and survival, immune subtypes, tumor microenvironment and drug sensitivity in 33 tumor types were systematically studied. The expression of the DNase gene family was shown to have an apparent intratumoral heterogeneity. The expression of DNase 2, lysosomal (DNASE2) was the highest in tumors, whereas that of DNASE2 β was the lowest. DNase 1-like 3 (DNASE1L3) was mainly downregulated in tumors, whereas the rest of the DNases were mainly upregulated in tumors. The expression of DNase family members was also found to be associated with the OS rate of patients. DNase family genes may serve an essential role in the tumor microenvironment. DNase family gene expression was related to the content of cytotoxic cells, Immunescore, Stromalscore, Estimatescore and Tumorpurity. The present study also revealed that the DNase genes may be involved in the drug resistance of cancer cells. Finally, the correlation between DNase, and clinical stage and tumor microenvironment in hepatocellular carcinoma (HCC) was studied. In addition, the difference in DNASE1L3 expression between HCC and adjacent normal tissues, and the relationship between DNASE1L3 expression and clinical stage was verified by analyzing three groups in a Gene Expression Omnibus dataset and by performing immunohistochemistry. In conclusion, the present study assessed DNase gene expression, analyzed its relationship with patient OS, performed pan-cancer co-expression analysis, and assessed the association between DNase and immune infiltration subtypes, tumor microenvironment and drug sensitivity. The present study also confirmed the value of further laboratory research on DNases and their prospects in clinical cancer treatment.
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Affiliation(s)
- Qingquan Bai
- Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, D-13353 Berlin, Germany,Cancer Research Center, School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China,Correspondence to: Dr Qingquan Bai, Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Xiao He
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, P.R. China
| | - Tianhui Hu
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China,Correspondence to: Dr Qingquan Bai, Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, Augustenburger Platz 1, D-13353 Berlin, Germany
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