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Sun L, Fan C, Xu P, Sun FH, Tang HH, Wang WD. Identification of prognostic biomarkers for hepatocellular carcinoma with vascular invasion. Am J Transl Res 2024; 16:2828-2839. [PMID: 39114683 PMCID: PMC11301501 DOI: 10.62347/sqzw3775] [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: 03/27/2024] [Accepted: 05/20/2024] [Indexed: 08/10/2024]
Abstract
OBJECTIVE Vascular invasion (VI) profoundly impacts the prognosis of hepatocellular carcinoma (HCC), yet the underlying biomarkers and mechanisms remain elusive. This study aimed to identify prognostic biomarkers for HCC patients with VI. METHODS Transcriptome data from primary HCC tissues and HCC tissues with VI were obtained through the Genome Expression Omnibus database. Differentially expressed genes (DEGs) in the two types of tissues were analyzed using functional enrichment analysis to evaluate their biological functions. We examined the correlation between DEGs and prognosis by combining HCC transcriptome data and clinical information from The Cancer Genome Atlas database. Univariate and multivariate Cox regression analyses, along with the least absolute shrinkage and selection operator (LASSO) method were utilized to develop a prognostic model. The effectiveness of the model was assessed through time-dependent receiver operating characteristic (ROC) curve, calibration diagram, and decision curve analysis. RESULTS In the GSE20017 and GSE5093 datasets, a total of 83 DEGs were identified. Gene Ontology analysis indicated that these DEGs were predominantly associated with xenobiotic stimulus, collagen-containing extracellular matrix, and oxygen binding. Additionally, Kyoto Encyclopedia of Genes and Genomes analysis revealed that the DEGs were primarily involved in immune defense and cellular signal transduction. Cox and LASSO regression further identified 7 genes (HSPA8, ABCF2, EAF1, MARCO, EPS8L3, PLA3G1B, C6), which were used to construct a predictive model in the training cohort. We used X-tile software to calculate the optimal cut-off value to stratify HCC patients into low-risk and high-risk groups. Notably, the high-risk group exhibited poorer prognosis than the low-risk group (P < 0.001). The model demonstrated area under the ROC curve (AUC) values of 0.815, 0.730, and 0.710 at 1-year, 3-year, and 5-year intervals in the training cohort, respectively. In the validation cohort, the corresponding AUC values were 0.701, 0.571, and 0.575, respectively. The C-index of the calibration curve for the training and validation cohorts were 0.716 and 0.665. Decision curve analysis revealed the model's efficacy in guiding clinical decision-making. CONCLUSIONS The study indicates that 7 genes may be potential prognostic biomarkers and treatment targets for HCC patients with VI.
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Affiliation(s)
| | - Chen Fan
- Department of Interventional Radiology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Cencer, Nanjing Medical UniversityWuxi 214000, Jiangsu, China
| | - Ping Xu
- Department of Interventional Radiology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Cencer, Nanjing Medical UniversityWuxi 214000, Jiangsu, China
| | - Fei-Hu Sun
- Department of Interventional Radiology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Cencer, Nanjing Medical UniversityWuxi 214000, Jiangsu, China
| | - Hao-Huan Tang
- Department of Interventional Radiology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Cencer, Nanjing Medical UniversityWuxi 214000, Jiangsu, China
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Kralova K, Vrtelka O, Fouskova M, Smirnova TA, Michalkova L, Hribek P, Urbanek P, Kuckova S, Setnicka V. Comprehensive spectroscopic, metabolomic, and proteomic liquid biopsy in the diagnostics of hepatocellular carcinoma. Talanta 2024; 270:125527. [PMID: 38134814 DOI: 10.1016/j.talanta.2023.125527] [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: 07/15/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
Liquid biopsy is a very topical issue in clinical diagnostics research nowadays. In this study, we explored and compared various analytical approaches to blood plasma analysis. Finally, we proposed a comprehensive procedure, which, thanks to the utilization of multiple analytical techniques, allowed the targeting of various biomolecules in blood plasma reflecting diverse biological processes underlying disease development. The potential of such an approach, combining proteomics, metabolomics, and vibrational spectroscopy along with preceding blood plasma fractionation, was demonstrated on blood plasma samples of patients suffering from hepatocellular carcinoma in cirrhotic terrain (n = 20) and control subjects with liver cirrhosis (n = 20) as well as healthy subjects (n = 20). Most of the applied methods allowed the classification of the samples with an accuracy exceeding 80.0 % and therefore have the potential to be used as a stand-alone method in clinical diagnostics. Moreover, a final panel of 48 variables obtained by a combination of the utilized analytical methods enabled the discrimination of the hepatocellular carcinoma samples from cirrhosis with 94.3 % cross-validated accuracy. Thus, this study, although limited by the cohort size, clearly demonstrated the benefit of the multimethod approach in clinical diagnosis.
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Affiliation(s)
- Katerina Kralova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Ondrej Vrtelka
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Marketa Fouskova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Tatiana Anatolievna Smirnova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Lenka Michalkova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic; Department of Analytical Chemistry, Institute of Chemical Process Fundamentals of the CAS, Rozvojova 135, 165 02, Prague 6, Czech Republic
| | - Petr Hribek
- Military University Hospital Prague, Department of Medicine 1st Faculty of Medicine Charles University and Military University Hospital Prague, U Vojenske Nemocnice 1200, 169 02, Prague 6, Czech Republic; Department of Internal Medicine, Faculty of Military Health Sciences in Hradec Kralove, University of Defense, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic
| | - Petr Urbanek
- Military University Hospital Prague, Department of Medicine 1st Faculty of Medicine Charles University and Military University Hospital Prague, U Vojenske Nemocnice 1200, 169 02, Prague 6, Czech Republic
| | - Stepanka Kuckova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Vladimir Setnicka
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic.
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Porukala M, Vinod PK. Gene expression signatures of stepwise progression of Hepatocellular Carcinoma. PLoS One 2023; 18:e0296454. [PMID: 38157373 PMCID: PMC10756545 DOI: 10.1371/journal.pone.0296454] [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: 08/17/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
The molecular pathogenesis of Hepatocellular Carcinoma (HCC) is a complex process progressing from premalignant stages to cancer in a stepwise manner. Mostly, HCC is detected at advanced stages, leading to high mortality rates. Hence, characterising the molecular underpinnings of HCC from normal to cancer state through precancerous state may help in early detection and improve its prognosis and treatment. In this work, we analysed the transcriptomic profile of tumour and premalignant samples from HCC or chronic liver disease patients, who had undergone either total or partial hepatectomy. The normal samples from patients with metastatic cancer/polycystic liver disease/ cholangiocarcinoma were also included. A gene co-expression network approach was applied to identify hierarchical changes: modules, pathways, and genes related to different trajectories of HCC and patient survival. Our analysis shows that the progression from premalignant conditions to tumour is accompanied by differences in the downregulation of genes associated with HNF4A activity and the immune system and upregulation of cell cycle genes, bringing about variability in patient outcomes. However, an increase in immune and cell cycle activity is observed in premalignant samples. Interestingly, co-expression modules and genes from premalignant stages are associated with survival. THBD, a classical marker for dendritic cells, is a predictor of survival at the premalignant stage. Further, genes linked to microtubules, kinetochores, and centromere are altered in both premalignant and tumour conditions and are associated with survival. Our analysis revealed a three-way molecular axis of liver function, immune pathways, and cell cycle driving HCC pathogenesis.
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Affiliation(s)
- Manisri Porukala
- Centre for Computational Natural Sciences and Bioinformatics, IIIT, Hyderabad, India
| | - P. K. Vinod
- Centre for Computational Natural Sciences and Bioinformatics, IIIT, Hyderabad, India
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Wang Q, Lin Y, Yu W, Chen X, He Q, Ye Z. The core role of macrophages in hepatocellular carcinoma: the definition of molecular subtypes and the prognostic risk system. Front Pharmacol 2023; 14:1228052. [PMID: 37693905 PMCID: PMC10491020 DOI: 10.3389/fphar.2023.1228052] [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: 05/24/2023] [Accepted: 08/11/2023] [Indexed: 09/12/2023] Open
Abstract
Background: In patients with hepatocellular carcinoma (HCC), the tumor microenvironment (TME) is resistant to immunotherapy because of its specificity. It is meaningful to explore the role of macrophage, which is one of the most abundant immune cells in the TME, in cellular communication and its effect on the prognosis and immunotherapy of HCC. Methods: Dimensionality reduction and clustering of the single-cell RNA-seq data from the GSE149614 dataset were carried out to identify the cellular composition of HCC. CellChat was used to analyze the communication between different cells. The specifically highly expressed genes of macrophages were extracted for univariate Cox regression analysis to obtain prognostic genes for HCC cluster analysis, and the risk system of macrophage-specifically highly expressed genes was developed by random forest analysis and multivariate Cox regression analysis. Prognosis, TME infiltration, potential responses to immunotherapy, and antineoplastic drugs were compared among molecular subtypes and between risk groups. Results: We found that HCC included nine identifiable cell types, of which macrophages had the highest communication intensity with each of the other eight cell types. Of the 179 specifically highly expressed genes of macrophage, 56 were significantly correlated with the prognosis of HCC, which classified HCC into three subtypes, which were reproducible and produced different survival outcomes, TME infiltration, and immunotherapy responses among the subtypes. In the integration of four macrophage-specifically highly expressed genes for the development of a risk system, the risk score was significantly involved in higher immune cell infiltration, poor prognosis, immunotherapy response rate, and sensitivity of six drugs. Conclusion: In this study, through single-cell RNA-seq data, we identified nine cell types, among which macrophage had the highest communication intensity with the rest of the cell types. Based on specifically highly expressed genes of macrophage, we successfully divided HCC patients into three clusters with distinct prognosis, TME, and therapeutic response. Additionally, a risk system was constructed, which provided a potential reference index for the prognostic target and preclinical individualized treatment of HCC.
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Affiliation(s)
- Qiaona Wang
- Department of Breast Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yunshou Lin
- Department of Hernia and Hepatobiliary Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Wenguan Yu
- Department of Hernia and Hepatobiliary Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Xiaogang Chen
- Department of Hernia and Hepatobiliary Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Qingqing He
- Department of Breast Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Zhiyu Ye
- Department of Hernia and Hepatobiliary Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
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Walakira A, Skubic C, Nadižar N, Rozman D, Režen T, Mraz M, Moškon M. Integrative computational modeling to unravel novel potential biomarkers in hepatocellular carcinoma. Comput Biol Med 2023; 159:106957. [PMID: 37116239 DOI: 10.1016/j.compbiomed.2023.106957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/17/2023] [Accepted: 04/16/2023] [Indexed: 04/30/2023]
Abstract
Hepatocellular carcinoma (HCC) is a major health problem around the world. The management of this disease is complicated by the lack of noninvasive diagnostic tools and the few treatment options available. Better clinical outcomes can be achieved if HCC is detected early, but unfortunately, clinical signs appear when the disease is in its late stages. We aim to identify novel genes that can be targeted for the diagnosis and therapy of HCC. We performed a meta-analysis of transcriptomics data to identify differentially expressed genes and applied network analysis to identify hub genes. Fatty acid metabolism, complement and coagulation cascade, chemical carcinogenesis and retinol metabolism were identified as key pathways in HCC. Furthermore, we integrated transcriptomics data into a reference human genome-scale metabolic model to identify key reactions and subsystems relevant in HCC. We conclude that fatty acid activation, purine metabolism, vitamin D, and E metabolism are key processes in the development of HCC and therefore need to be further explored for the development of new therapies. We provide the first evidence that GABRP, HBG1 and DAK (TKFC) genes are important in HCC in humans and warrant further studies.
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Affiliation(s)
- Andrew Walakira
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Cene Skubic
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nejc Nadižar
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Mraz
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Moškon
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
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Zhang G, Zhang K, Zhao Y, Yang Q, Lv X. A novel stemness-hypoxia-related signature for prognostic stratification and immunotherapy response in hepatocellular carcinoma. BMC Cancer 2022; 22:1103. [DOI: 10.1186/s12885-022-10195-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The specific differentiation potential, unlimited proliferation, and self-renewal capacity of cancer stem cells (CSCs) are closely related to the occurrence, recurrence, and drug resistance of hepatocellular carcinoma (HCC), as well as hypoxia. Therefore, an in-depth analysis of the relationship between HCC stemness, oxygenation status, and the effectiveness of immunotherapy is necessary to improve the poor prognosis of HCC patients.
Methods
The weighted gene co-expression network analysis (WGCNA) was utilized to find hypoxia-related genes, and the stemness index (mRNAsi) was evaluated using the one-class logistic regression (OCLR) technique. Based on stemness-hypoxia-related genes (SHRGs), population subgroup categorization using NMF cluster analysis was carried out. The relationship between SHRGs and survival outcomes was determined using univariate Cox regression. The LASSO-Cox regression strategy was performed to investigate the quality and establish the classifier associated with prognosis. The main effect of risk scores on the tumor microenvironment (TME) and its response to immune checkpoint drugs was also examined. Finally, qRT-PCR was performed to explore the expression and prognostic value of the signature in clinical samples.
Results
After identifying tumor stemness- and hypoxia-related genes through a series of bioinformatics analyses, we constructed a prognostic stratification model based on these SHRGs, which can be effectively applied to the prognostic classification of HCC patients and the prediction of immune checkpoint inhibitors (ICIs) efficacy. Independent validation of the model in the ICGC cohort yielded good results. In addition, we also constructed hypoxic cell models in Herp3B and Huh7 cells to verify the expression of genes in the prognostic model and found that C7, CLEC1B, and CXCL6 were not only related to the tumor stemness but also related to hypoxia. Finally, we found that the constructed signature had a good prognostic value in the clinical sample.
Conclusions
We constructed and validated a stemness-hypoxia-related prognostic signature that can be used to predict the efficacy of ICIs therapy. We also verified that C7, CLEC1B, and CXCL6 are indeed associated with stemness and hypoxia through a hypoxic cell model, which may provide new ideas for individualized immunotherapy.
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Xiao Z, Yeung CLS, Yam JWP, Mao X. An update on the role of complement in hepatocellular carcinoma. Front Immunol 2022; 13:1007382. [PMID: 36341431 PMCID: PMC9629811 DOI: 10.3389/fimmu.2022.1007382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
As a main producer of complement, the environment in the liver is greatly affected by the complement system. Although the complement system is considered to have the ability of nonself discrimination, remarkable studies have revealed the tight association between improper complement activation in tumour initiation and progression. As complement activation predominantly occurs within the liver, the protumourigenic role of the complement system may contribute to the development of hepatocellular carcinoma (HCC). Improvement in the understanding of the molecular targets involved in complement-mediated tumour development, metastasis, and tumour-promoting inflammation in HCC would certainly aid in the development of better treatments. This minireview is focused on recent findings of the protumourigenic role of the complement system in HCC.
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Affiliation(s)
- Zhijie Xiao
- Scientific Research Centre, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Charlie Lot Sum Yeung
- Department of Pathology, School of Clinical Medicine, Faculty of Medicine, the University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Judy Wai Ping Yam
- Department of Pathology, School of Clinical Medicine, Faculty of Medicine, the University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Xiaowen Mao
- Department of Pathology, School of Clinical Medicine, Faculty of Medicine, the University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Xiaowen Mao,
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Qian X, Yang Z, Gao L, Liu Y, Yan J. The role of complement in the clinical course of hepatocellular carcinoma. Immun Inflamm Dis 2022; 10:e569. [PMID: 34813686 PMCID: PMC8926509 DOI: 10.1002/iid3.569] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 01/10/2023] Open
Abstract
Background The complement system, an innate immune system, may either play an antitumor role, or promote tumorigenesis and cancer progression in different kinds of cancer. The function of complement in hepatocellular carcinoma (HCC) is unclear. Methods The gene expressions of the complement system were based on data obtained from TCGA and GEO. We explored gene expressions, mutation, enrichment analysis, clinicopathology, patients' outcome, and immune infiltration via Gepia2, cBioPortal, Metascape, UALCAN, Kaplan–Meier Plotter, and TIMER 2. Results Five complement genes, including C1R, C6, C7, CFP, and CFHR3, were not only found to be significantly downregulated in HCC samples compared with normal liver samples, but also found to be significantly associated with overall survival, disease‐free survival, and progress‐free survival in HCC patients. In addition, lower mRNA expression of C1R, C6, C7, and CFHR3 were found correlated with advanced cancer stages and higher tumor grades in HCC patients. Also, the expression levels of CFP were correlated with many sets of immune markers of tumor immune cells, such as those of CD8+ T cells, CD4+ T cells, B cells, M2 macrophages, neutrophils, DCs, Th1 cells, Th2 cells, and T cell exhaustion in HCC. Based on that, we developed a prognostic model for HCC patients—Riskscore = (−0.0053)*C6+(−0.0498)*C7+(−0.1045)*CFHR3. Conclusion C1R, C6, C7, CFP, and CFHR3 could be prognostic biomarkers for patients with HCC.
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Affiliation(s)
- Xinye Qian
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, China
| | - Zhoujing Yang
- Department of Anesthesiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lu Gao
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, China
| | - Yipiao Liu
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, China
| | - Jun Yan
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, China
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