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Tsai PC, Huang CF, Yeh ML, Hsieh MH, Kuo HT, Hung CH, Tseng KC, Lai HC, Peng CY, Wang JH, Chen JJ, Lee PL, Chien RN, Yang CC, Lo GH, Kao JH, Liu CJ, Liu CH, Yan SL, Lin CY, Su WW, Chu CH, Chen CJ, Tung SY, Tai CM, Lin CW, Lo CC, Cheng PN, Chiu YC, Wang CC, Cheng JS, Tsai WL, Lin HC, Huang YH, Chen CY, Huang JF, Dai CY, Wan-Long WL, Bair MJ, Yu ML. Metformin and statins reduce hepatocellular carcinoma risk in chronic hepatitis C patients with failed antiviral therapy. Clin Mol Hepatol 2024:cmh.2024.0038. [PMID: 38637957 DOI: 10.3350/cmh.2024.0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/18/2025] [Indexed: 04/20/2024] Open
Abstract
Backgrounds and Aim Chronic hepatitis C (CHC) patients who fail antiviral therapy have a high risk of developing hepatocellular carcinoma (HCC). We investigated the effects of metformin and statins, commonly used to treat diabetes mellitus (DM) and hyperlipidemia (HLP), on HCC risk in CHC patients who failed antiviral therapy. Methods CHC patients with failed interferon-based therapy were enrolled in a large-scale multicenter cohort study in Taiwan (T-COACH). HCC occurrence 1.5 years after the end of antiviral therapy was identified by linking to the cancer registry databases from 2003 to 2019. After considering death and liver transplantation as competing risks, Gray's cumulative incidence and Cox sub-distribution hazards for HCC development were used. Results Among the 2,779 CHC patients, 480 (17.3%) developed new-onset HCC and 238 (8.6%) died after antiviral therapy. Metformin non-users with DM had a 51% higher risk of liver cancer than patients without DM, while statin users with HLP had a 50% lower risk of liver cancer than patients without HLP. The 5-year cumulative incidence of HCC was 16.5% in metformin non-users, significantly higher in metformin non-users than in patients without DM (11.3%; adjusted sub-distribution hazard ratio [aSHR]=1.51; P=0.007) and metformin users (3.1%; aSHR=1.59; P=0.022). Conversely, HLP statin users had a significantly lower HCC risk than patients without HLP (3.8% vs. 12.5%; aSHR=0.50; P<0.001). Notably, the unfavorable effect of non-metformin use on increased HCC risk was mainly observed among patients without cirrhosis but not in patients with cirrhosis. In contrast, a favorable effect of statins reduced the risk of HCC in both cirrhotic and non-cirrhotic patients. Conclusion Metformin for DM and statins for HLP have chemopreventive effects on HCC risk in CHC patients who failed antiviral therapy. These findings emphasize the importance of personalized preventive strategies for managing patients with these clinical profiles.
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Affiliation(s)
- Pei-Chien Tsai
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis Centre, Kaohsiung Medical University Hospital; Hepatitis Research Centre, School of Medicine and Centre for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Feng Huang
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis Centre, Kaohsiung Medical University Hospital; Hepatitis Research Centre, School of Medicine and Centre for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Lun Yeh
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis Centre, Kaohsiung Medical University Hospital; Hepatitis Research Centre, School of Medicine and Centre for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Meng-Hsuan Hsieh
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis Centre, Kaohsiung Medical University Hospital; Hepatitis Research Centre, School of Medicine and Centre for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Health Management Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hsing-Tao Kuo
- Division of Hepatogastroenterology, Department of Internal Medicine, Chi Mei Medical Centre, Tainan, Taiwan
| | - Chao-Hung Hung
- Division of Hepatogastroenterology, Department of Internal Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Kuo-Chih Tseng
- Department of Gastroenterology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Hsueh-Chou Lai
- Division of Hepatogastroenterology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Cheng-Yuan Peng
- Division of Hepatogastroenterology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Jing-Houng Wang
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Jyh-Jou Chen
- Division of Gastroenterology and Hepatology, Chi-Mei Medical Centre, Liouying, Tainan, Taiwan
| | - Pei-Lun Lee
- Division of Gastroenterology and Hepatology, Chi-Mei Medical Centre, Liouying, Tainan, Taiwan
| | - Rong-Nan Chien
- Division of Hepatology, Department of Gastroenterology and Hepatology, Linkou Medical Centre, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Chi-Chieh Yang
- Division of Gastroenterology, Department of Internal Medicine, Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Gin-Ho Lo
- Division of Gastroenterology and Hepatology, Department of Medicine, E-Da Hospital and School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Jia-Horng Kao
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Gastroenterology and Hepatology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Jen Liu
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Gastroenterology and Hepatology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chen-Hua Liu
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Gastroenterology and Hepatology, National Taiwan University Hospital, Taipei, Taiwan
| | - Sheng-Lei Yan
- Division of Gastroenterology, Department of Internal Medicine, Chang Bing Show-Chwan Memorial Hospital, Changhua, Taiwan
| | - Chun-Yen Lin
- Division of Hepatology, Department of Gastroenterology and Hepatology, Linkou Medical Centre, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Wei-Wen Su
- Division of Gastroenterology, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Cheng-Hsin Chu
- Division of Gastroenterology, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chih-Jen Chen
- Division of Gastroenterology, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shui-Yi Tung
- Division of Hepatogastroenterology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chi-Ming Tai
- Division of Gastroenterology and Hepatology, Department of Medicine, E-Da Hospital and School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Chih-Wen Lin
- Division of Gastroenterology and Hepatology, Department of Medicine, E-Da Hospital and School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Ching-Chu Lo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Martin De Porres Hospital-Daya, Chiayi, Taiwan
| | - Pin-Nan Cheng
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Cheng Chiu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Chi Wang
- Division of Gastroenterology, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and School of Medicine, Tzu Chi University, New Taipei, Taiwan
| | - Jin-Shiung Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wei-Lun Tsai
- Division of Gastroenterology and Hepatology, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Han-Chieh Lin
- Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Hsiang Huang
- Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chi-Yi Chen
- Department of Internal Medicine, Chiayi Christian Hospital, Chiayi, Taiwan
| | - Jee-Fu Huang
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis Centre, Kaohsiung Medical University Hospital; Hepatitis Research Centre, School of Medicine and Centre for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Yen Dai
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis Centre, Kaohsiung Medical University Hospital; Hepatitis Research Centre, School of Medicine and Centre for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wan-Long Wan-Long
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis Centre, Kaohsiung Medical University Hospital; Hepatitis Research Centre, School of Medicine and Centre for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Jong Bair
- Division of Gastroenterology, Department of Internal Medicine, Taitung Mackay Memorial Hospital, Taitung; Mackay Medical College, Taipei, Taiwan
| | - Ming-Lung Yu
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis Centre, Kaohsiung Medical University Hospital; Hepatitis Research Centre, School of Medicine and Centre for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- School of Medicine and Doctoral Program of Clinical and Experimental Medicine, College of Medicine and Centre of Excellence for Metabolic Associated Fatty Liver Disease, National Sun Yat-sen University, Kaohsiung, Taiwan
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2
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Qiu G, Chen J, Liao W, Liu Y, Wen Z, Zhao Y. Gadoxetic acid-enhanced MRI combined with T1 mapping and clinical factors to predict Ki-67 expression of hepatocellular carcinoma. Front Oncol 2023; 13:1134646. [PMID: 37456233 PMCID: PMC10348748 DOI: 10.3389/fonc.2023.1134646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Objectives To explore the predictive value of gadoxetic acid-enhanced magnetic resonance imaging (MRI) combined with T1 mapping and clinical factors for Ki-67 expression in hepatocellular carcinoma (HCC). Methods A retrospective study was conducted on 185 patients with pathologically confirmed solitary HCC from two institutions. All patients underwent preoperative T1 mapping on gadoxetic acid-enhanced MRI. Patients from institution I (n = 124) and institution II (n = 61) were respectively assigned to the training and validation sets. Univariable and multivariable analyses were performed to assess the correlation of clinico-radiological factors with Ki-67 labeling index (LI). Based on the significant factors, a predictive nomogram was developed and validated for Ki-67 LI. The performance of the nomogram was evaluated on the basis of its calibration, discrimination, and clinical utility. Results Multivariable analysis showed that alpha-fetoprotein (AFP) levels > 20ng/mL, neutrophils to lymphocyte ratio > 2.25, non-smooth margin, tumor-to-liver signal intensity ratio in the hepatobiliary phase ≤ 0.6, and post-contrast T1 relaxation time > 705 msec were the independent predictors of Ki-67 LI. The nomogram based on these variables showed the best predictive performance with area under the receiver operator characteristic curve (AUROC) 0.899, area under the precision-recall curve (AUPRC) 0.946 and F1 score of 0.912; the respective values were 0.823, 0.879 and 0.857 in the validation set. The Kaplan-Meier curves illustrated that the cumulative recurrence probability at 2 years was significantly higher in patients with high Ki-67 LI than in those with low Ki-67 LI (39.6% [53/134] vs. 19.6% [10/51], p = 0.011). Conclusions Gadoxetic acid-enhanced MRI combined with T1 mapping and several clinical factors can preoperatively predict Ki-67 LI with high accuracy, and thus enable risk stratification and personalized treatment of HCC patients.
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Affiliation(s)
- Ganbin Qiu
- Imaging Department of Zhaoqing Medical College, Zhaoqing, China
- Department of Radiology, The First People’s Hospital of Zhaoqing, Zhaoqing, China
| | - Jincan Chen
- Department of Radiology, The First People’s Hospital of Zhaoqing, Zhaoqing, China
| | - Weixiong Liao
- Imaging Department of Zhaoqing Medical College, Zhaoqing, China
| | - Yonghui Liu
- Department of Radiology, The First People’s Hospital of Zhaoqing, Zhaoqing, China
| | - Zhongyan Wen
- Department of Radiology, The First People’s Hospital of Zhaoqing, Zhaoqing, China
| | - Yue Zhao
- Department of Radiology, Central People’s Hospital of Zhanjiang, Zhanjiang, China
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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3
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Fernández-Palanca P, Payo-Serafín T, Méndez-Blanco C, San-Miguel B, Tuñón MJ, González-Gallego J, Mauriz JL. Neuropilins as potential biomarkers in hepatocellular carcinoma: a systematic review of basic and clinical implications. Clin Mol Hepatol 2023; 29:293-319. [PMID: 36726054 PMCID: PMC10121286 DOI: 10.3350/cmh.2022.0425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/31/2023] [Indexed: 02/03/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common and deadly cancers worldwide and is characterized by complex molecular carcinogenesis. Neuropilins (NRPs) NRP1 and NRP2 are the receptors of multiple proteins involved in key signaling pathways associated with tumor progression. We aimed to systematically review all the available findings on their role in HCC. We searched the Scopus, Web of Science (WOS), PubMed, Cochrane and Embase databases for articles evaluating NRPs in preclinical or clinical HCC models. This study was registered in PROSPERO (CRD42022349774) and include 49 studies. Multiple cellular and molecular processes have been associated with one or both NRPs, indicating that they are potential diagnostic and prognostic biomarkers in HCC patients. Mainly NRP1 has been shown to promote tumor cell survival and progression by modulating several signaling pathways. NRPs mainly regulate angiogenesis, invasion and migration and have shown to induce invasion and metastasis. They also regulate the immune response and tumor microenvironment, showing a crucial interplay with the hypoxia response and microRNAs in HCC. Altogether, NRP1 and NRP2 are potential biomarkers and therapeutic targets, providing novel insight into the clinical landscape of HCC patients.
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Affiliation(s)
- Paula Fernández-Palanca
- Institute of Biomedicine (IBIOMED), University of León, Campus de Vegazana s/n, 24071, León, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
| | - Tania Payo-Serafín
- Institute of Biomedicine (IBIOMED), University of León, Campus de Vegazana s/n, 24071, León, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
| | - Carolina Méndez-Blanco
- Institute of Biomedicine (IBIOMED), University of León, Campus de Vegazana s/n, 24071, León, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
| | - Beatriz San-Miguel
- Institute of Biomedicine (IBIOMED), University of León, Campus de Vegazana s/n, 24071, León, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
| | - María J Tuñón
- Institute of Biomedicine (IBIOMED), University of León, Campus de Vegazana s/n, 24071, León, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
| | - Javier González-Gallego
- Institute of Biomedicine (IBIOMED), University of León, Campus de Vegazana s/n, 24071, León, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
| | - José L Mauriz
- Institute of Biomedicine (IBIOMED), University of León, Campus de Vegazana s/n, 24071, León, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029, Madrid, Spain
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4
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Liu Y, Zhang X, Chen S, Wang J, Yu S, Li Y, Xu M, Aboubacar H, Li J, Shan T, Wang J, Cao G. Gut-derived lipopolysaccharide promotes alcoholic hepatosteatosis and subsequent hepatocellular carcinoma by stimulating neutrophil extracellular traps through TLR4. Clin Mol Hepatol 2022; 28:522-539. [PMID: 35508957 PMCID: PMC9293619 DOI: 10.3350/cmh.2022.0039] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 05/01/2022] [Indexed: 11/23/2022] Open
Abstract
Background/Aims Binge drinking leads to many disorders, including alcoholic hepatosteatosis, which is characterized by intrahepatic neutrophil infiltration and increases the risk of hepatocellular carcinoma (HCC). Molecular mechanisms may involve the migration of bacterial metabolites from the gut to the liver and the activation of neutrophil extracellular traps (NETs). Methods Serum samples from both binge drinking and alcohol-avoiding patients were analyzed. Mouse models of chronic plus binge alcohol-induced hepatosteatosis and HCC models were used. Results A marker of NETs formation, lipopolysaccharide (LPS), was significantly higher in alcoholic hepatosteatosis and HCC patients and mice than in controls. Intrahepatic inflammation markers and HCC-related cytokines were decreased in mice with reduced NET formation due to neutrophil elastase (NE) deletion, and liver-related symptoms of alcohol were also alleviated in NE knockout mice. Removal of intestinal bacteria with antibiotics led to decreases in markers of NETs formation and inflammatory cytokines upon chronic alcohol consumption, and development of alcoholic hepatosteatosis and HCC was also attenuated. These functions were restored upon supplementation with the bacterial product LPS. When mice lacking toll-like receptor 4 (TLR4) received chronic alcohol feeding, intrahepatic markers of NETs formation decreased, and hepatosteatosis and HCC were alleviated. Conclusions Formation of NETs following LPS stimulation of TLR4 upon chronic alcohol use leads to increased alcoholic steatosis and subsequent HCC.
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Affiliation(s)
- Yang Liu
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Xin Zhang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Shuo Chen
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Jiazhong Wang
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Shuo Yu
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China.,Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Yiming Li
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Meng Xu
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Harouna Aboubacar
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Junhui Li
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Tao Shan
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Jixin Wang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
| | - Gang Cao
- Department of General Surgery, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, China
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Karakülah G, Yandim C. Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival. Turk J Biol 2021; 45:599-612. [PMID: 34803457 PMCID: PMC8574195 DOI: 10.3906/biy-2104-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/19/2021] [Indexed: 11/05/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Research on HCC so far primarily focused on genes and provided limited information on genomic repeats, which constitute more than half of the human genome and contribute to genomic stability. In line with this, repeat dysregulation was significantly shown to be pathological in various cancers and other diseases. In this study, we aimed to determine the full repeat expression profile of HCC for the first time. We utilised two independent RNA-seq datasets obtained from primary HCC tumours with matched normal tissues of 20 and 17 HCC patients, respectively. We quantified repeat expressions and analysed their differential expression. We also identified repeats that are cooperatively expressed with genes by constructing a gene coexpression network. Our results indicated that HCC tumours in both datasets harbour 24 differentially expressed repeats and even more elements were coexpressed with genes involved in various metabolic pathways. We discovered that two L1 elements (L1M3b, L1M3de) were downregulated and a handful of HERV subfamily repeats (HERV-Fc1-int, HERV3-int, HERVE_a-int, HERVK11D-int, HERVK14C-int, HERVL18-int) were upregulated with the exception of HERV1_LTRc, which was downregulated. Various LTR elements (LTR32, LTR9, LTR4, LTR52-int, LTR70) and MER elements (MER11C, MER11D, MER57C1, MER9a1, MER74C) were implicated along with few other subtypes including Charlie12, MLT2A2, Tigger15a, Tigger 17b. The only satellite repeat differentially expressed in both datasets was GSATII, whose expression was upregulated in 33 (>90%) out of 37 patients. Notably, GSATII expression correlated with HCC survival genes. Elements discovered here promise future studies to be considered for biomarker and HCC therapy research. The coexpression pattern of the GSATII satellite with HCC survival genes and the fact that it has been upregulated in the vast majority of patients make this repeat particularly stand out for HCC.
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Affiliation(s)
- Gökhan Karakülah
- İzmir Biomedicine and Genome Center (İBG), İzmir Turkey.,İzmir International Biomedicine and Genome Institute (İBG-İzmir), Dokuz Eylül University, İzmir Turkey
| | - Cihangir Yandim
- İzmir Biomedicine and Genome Center (İBG), İzmir Turkey.,Department of Genetics and Bioengineering, Faculty of Engineering, İzmir University of Economics, İzmir Turkey
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