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Chillotti S, Maloberti T, Degiovanni A, Malvi D, D'Errico A, de Biase D, Vasuri F. Hepatocellular Carcinomas with Concomitant Mutations of TERT, TP53, and CTNNB1: Is There a Role for Artificial Intelligence? Crit Rev Oncog 2023; 28:31-35. [PMID: 37968991 DOI: 10.1615/critrevoncog.2023049650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
TP53, CTNNB1, and TERT-promoter mutations are the most common driver mutations in hepatocellular carcinoma (HCC). The morphological and genetical HCC heterogeneities are difficult to discriminate by the eye of the pathologist. Here, we describe two rare cases of HCC with simultaneous co-mutation of all three of genes, which represent a poorly described occurrence in the literature. In these two cases, areas with different tumor grade and different β-catenin and Glutamine Synthetase expression (performed by automated immunohistochemistry) were observed. NGS analysis was performed in these different areas, to check for potential diversity of mutation burden on the different regions, but no differences were found: all micro-areas analyzed showed the co-presence of mutations in TP53, CTNNB1, and TERT. The evidence that all mutations were found in all the different areas analyzed by NGS leads to hypothesize that the tumor is not composed of different clones harboring different mutations. All the variants are harbored by the same neoplastic clone, albeit leading to different phenotypes. Mutation prediction Artificial Intelligence models could help the morpho-genetic classification of HCC in the future, since they can find variabilities not obvious to the human eye, with increased sensitivity, specificity and reproducibility.
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Affiliation(s)
- Stefano Chillotti
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy; School of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, University of Bologna
| | - Thais Maloberti
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Italy
| | - Alessio Degiovanni
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy
| | - Deborah Malvi
- Pathology Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Antonia D'Errico
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Italy
| | - Dario de Biase
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy; Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Francesco Vasuri
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy
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Suter P, Dazert E, Kuipers J, Ng CKY, Boldanova T, Hall MN, Heim MH, Beerenwinkel N. Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS Comput Biol 2022; 18:e1009767. [PMID: 36067230 PMCID: PMC9481159 DOI: 10.1371/journal.pcbi.1009767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 09/16/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Comprehensive molecular characterization of cancer subtypes is essential for predicting clinical outcomes and searching for personalized treatments. We present bnClustOmics, a statistical model and computational tool for multi-omics unsupervised clustering, which serves a dual purpose: Clustering patient samples based on a Bayesian network mixture model and learning the networks of omics variables representing these clusters. The discovered networks encode interactions among all omics variables and provide a molecular characterization of each patient subgroup. We conducted simulation studies that demonstrated the advantages of our approach compared to other clustering methods in the case where the generative model is a mixture of Bayesian networks. We applied bnClustOmics to a hepatocellular carcinoma (HCC) dataset comprising genome (mutation and copy number), transcriptome, proteome, and phosphoproteome data. We identified three main HCC subtypes together with molecular characteristics, some of which are associated with survival even when adjusting for the clinical stage. Cluster-specific networks shed light on the links between genotypes and molecular phenotypes of samples within their respective clusters and suggest targets for personalized treatments.
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Affiliation(s)
- Polina Suter
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eva Dazert
- Biozentrum, University of Basel, Basel, Switzerland
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Charlotte K. Y. Ng
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Tuyana Boldanova
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Markus H. Heim
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, Clarunis, University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
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Qu J, Lu W, Chen M, Gao W, Zhang C, Guo B, Yang J. Combined effect of recombinant human adenovirus p53 and curcumin in the treatment of liver cancer. Exp Ther Med 2020; 20:18. [PMID: 32934683 PMCID: PMC7471865 DOI: 10.3892/etm.2020.9145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 01/17/2020] [Indexed: 01/27/2023] Open
Abstract
The development of an effective therapeutic intervention for liver cancer is a worldwide challenge that remains to be adequately addressed. Of note, TP53, which encodes the p53 protein, is an important tumor suppressor gene, 61% of TP53 is functionally inactivated in liver cancer. Recombinant human adenovirus p53 (rAd-p53) is the first commercial product that has been used for gene therapy. In the present study, the combined mechanistic effects of rAd-p53 and curcumin, a naturally occurring compound with previously reported anti-inflammatory, antioxidant and anti-cancer properties, were assessed in liver cancer cells, using HepG2 cells as the model cell line. The administration of either curcumin or rAd-p53 promoted apoptosis, suppressed epithelial-mesenchymal transition (EMT) and blocked G2/M phase progression in HepG2 cells, which were potentiated further when both agents were applied together. Combined rAd-p53 and curcumin treatment resulted in higher p53 (P<0.01) and p21 (P<0.01) expression compared with rAd-p53 or curcumin were added alone, suggesting an additive effect on TP53 expression. Additionally, curcumin and rAd-p53 were demonstrated to regulate the activation of mitogen-activated protein kinases (MAPKs) ERK1/2, p38 MAPK and JNK. These results indicated that the combination of rAd-p53 with curcumin synergistically potentiates apoptosis and inhibit EMT compared with either rAd-p53 or curcumin treatment alone via the regulation of TP53 regulation. Mechanistically, this effect on TP53 expression may involve the ERK1/2, p38 MAPK and JNK signaling pathways. The current study provides new insights that can potentially advance the development of therapeutic strategies for liver cancer treatment.
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Affiliation(s)
- Juan Qu
- Department of Gastroenterology, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Wei Lu
- Department of Gastroenterology, Tianjin Cancer Hospital, Tianjin 300060, P.R. China
| | - Ming Chen
- Department of Hepatopathy and Hepatic Oncology, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Wei Gao
- Department of Hepatopathy and Hepatic Oncology, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Cong Zhang
- Department of Hepatopathy and Hepatic Oncology, Tianjin Nankai Hospital, Tianjin 300100, P.R. China
| | - Bin Guo
- College of Acu-moxibustion and Massage, Hunan University of Chinese Medicine, Changsha, Hunan 410208, P.R. China
| | - Jizhi Yang
- Department of Traditional Chinese Medicine, Chentangzhuang Street Health Service Center, Tianjin 300222, P.R. China
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Friemel J, Frick L, Unger K, Egger M, Parrotta R, Böge YT, Adili A, Karin M, Luedde T, Heikenwalder M, Weber A. Characterization of HCC Mouse Models: Towards an Etiology-Oriented Subtyping Approach. Mol Cancer Res 2019; 17:1493-1502. [PMID: 30967480 DOI: 10.1158/1541-7786.mcr-18-1045] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/18/2019] [Accepted: 04/03/2019] [Indexed: 11/16/2022]
Abstract
Murine liver tumors often fail to recapitulate the complexity of human hepatocellular carcinoma (HCC), which might explain the difficulty to translate preclinical mouse studies into clinical science. The aim of this study was to evaluate a subtyping approach for murine liver cancer models with regard to etiology-defined categories of human HCC, comparing genomic changes, histomorphology, and IHC profiles. Sequencing and analysis of gene copy-number changes [by comparative genomic hybridization (CGH)] in comparison with etiology-dependent subsets of HCC patients of The Cancer Genome Atlas (TCGA) database were conducted using specimens (75 tumors) of five different HCC mouse models: diethylnitrosamine (DEN) treated wild-type C57BL/6 mice, c-Myc and AlbLTαβ transgenic mice as well as TAK1LPC-KO and Mcl-1Δhep mice. Digital microscopy was used for the assessment of morphology and IHC of liver cell markers (A6-CK7/19, glutamine synthetase) in mouse and n = 61 human liver tumors. Tumor CGH profiles of DEN-treated mice and c-Myc transgenic mice matched alcohol-induced HCC, including morphologic findings (abundant inclusion bodies, fatty change) in the DEN model. Tumors from AlbLTαβ transgenic mice and TAK1LPC-KO models revealed the highest overlap with NASH-HCC CGH profiles. Concordant morphology (steatosis, lymphocyte infiltration, intratumor heterogeneity) was found in AlbLTαβ murine livers. CGH profiles from the Mcl-1Δhep model displayed similarities with hepatitis-induced HCC and characteristic human-like phenotypes (fatty change, intertumor and intratumor heterogeneity). IMPLICATIONS: Our findings demonstrate that stratifying preclinical mouse models along etiology-oriented genotypes and human-like phenotypes is feasible. This closer resemblance of preclinical models is expected to better recapitulate HCC subgroups and thus increase their informative value.
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Affiliation(s)
- Juliane Friemel
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Lukas Frick
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland.,Swiss Hepato-Pancreato-Biliary Center, Department of Digestive and Transplant Surgery, University Hospital of Zurich, Zurich, Switzerland
| | - Kristian Unger
- Helmholtz Zentrum München Research Center for Environmental Health (GmbH), Research Unit Radiation Cytogenetics
| | - Michele Egger
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Rossella Parrotta
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Yannick T Böge
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Arlind Adili
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Michael Karin
- Department of Pathology, University of California, San Diego, California
| | - Tom Luedde
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Mathias Heikenwalder
- Division Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany.
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland.
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Decreased long intergenic noncoding RNA P7 predicts unfavorable prognosis and promotes tumor proliferation via the modulation of the STAT1-MAPK pathway in hepatocellular carcinoma. Oncotarget 2017; 9:36057-36066. [PMID: 30546827 PMCID: PMC6281420 DOI: 10.18632/oncotarget.23282] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/08/2017] [Indexed: 01/02/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common neoplasm and is a leading cause of cancer-related death. Despite advances in the diagnosis and management of HCC, its prognosis remain unfavorable. Accumulating evidence has shown that long intergenic noncoding RNAs (lincRNAs) play central roles in the development of HCC. In this study, we identified a long intergenic noncoding RNA referred to as lincRNA P7 in HCC and explored its clinical significance and biological functions in HCC. The expression level of lincRNA P7 was significantly aberrantly deceased in HCC cancer tissues and cells lines. Gain- and loss-of-function experiments revealed that overexpression of lincRNA P7 significantly inhibited the proliferation of HCC-derived cancer cells, whereas lincRNA P7 knockdown promoted cell growth. Mechanistically, lincRNA P7 blocked Erk1/2 signaling and repressed activation of the STAT1 pathway. In nude mouse models, we show that overexpression of lincRNA P7 effectively repressed HCC xenograft tumor growth in vivo. Moreover, a clinical investigation demonstrated that down-regulated lincRNA P7 expression correlated with liver cirrhosis, Hepatitis B virus (HBV) infection, clinical stage of the tumor and recurrence. A Kaplan-Meier survival analysis showed that the expression of lincRNA P7 was significantly related to overall survival (P = 0.003) and recurrence-free survival (P = 0.031). Collectively, our findings suggested that the down-regulation of lincRNA P7 predicts poor clinical outcomes for HCC patients and might be a powerful candidate prognostic biomarker and target in HCC.
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Huang A, Zhao X, Yang XR, Li FQ, Zhou XL, Wu K, Zhang X, Sun QM, Cao Y, Zhu HM, Wang XD, Yang HM, Wang J, Tang ZY, Hou Y, Fan J, Zhou J. Circumventing intratumoral heterogeneity to identify potential therapeutic targets in hepatocellular carcinoma. J Hepatol 2017; 67:293-301. [PMID: 28323123 DOI: 10.1016/j.jhep.2017.03.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/07/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Identifying target genetic mutations in hepatocellular carcinoma (HCC) for therapy is made challenging by intratumoral heterogeneity. Circulating cell-free DNAs (cfDNA) may contain a more complete mutational spectrum compared to a single tumor sample. This study aimed to identify the most efficient strategy to identify all the mutations within heterogeneous HCCs. METHODS Whole exome sequencing (WES) and targeted deep sequencing (TDS) were carried out in 32 multi-regional tumor samples from five patients. Matched preoperative cfDNAs were sequenced accordingly. Intratumoral heterogeneity was measured using the average percentage of non-ubiquitous mutations (present in parts of tumor regions). Profiling efficiencies of single tumor specimen and cfDNA were compared. The strategy with the highest performance was used to screen for actionable mutations. RESULTS Variable levels of heterogeneity with branched and parallel evolution patterns were observed. The heterogeneity decreased at higher sequencing depth of TDS compared to measurements by WES (28.1% vs. 34.9%, p<0.01) but remained unchanged when additional samples were analyzed. TDS of single tumor specimen identified an average of 70% of the total mutations from multi-regional tissues. Although genome profiling efficiency of cfDNA increased with sequencing depth, an average of 47.2% total mutations were identified using TDS, suggesting that tissue samples outperformed it. TDS of single tumor specimen in 66 patients and cfDNAs in four unresectable HCCs showed that 38.6% (26/66 and 1/4) of patients carried mutations that were potential therapeutic targets. CONCLUSIONS TDS of single tumor specimen could identify actionable mutations targets for therapy in HCC. cfDNA may serve as secondary alternative in profiling HCC genome. LAY SUMMARY Targeted deep sequencing of single tumor specimen is a more efficient method to identify mutations in hepatocellular carcinoma made from mixed subtypes compared to circulating cell-free DNA in blood. cfDNA may serve as secondary alternative in profiling HCC genome. Identifying mutations may help clinicians choose targeted therapy for better individual treatments.
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Affiliation(s)
- Ao Huang
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Xin Zhao
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin-Rong Yang
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Fu-Qiang Li
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin-Lan Zhou
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Zhang
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Qi-Man Sun
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Ya Cao
- Cancer Research Institute, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha 410078, China
| | - Hong-Mei Zhu
- BGI-Shenzhen, Shenzhen 518083, China; BGI-Tianjin, Tianjin 300308, China
| | - Xiang-Dong Wang
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
| | - Huan-Ming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Zhao-You Tang
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
| | - Jia Fan
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
| | - Jian Zhou
- Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
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Xiao C, Wang C, Cheng S, Lai C, Zhang P, Wang Z, Zhang T, Zhang S, Liu R. The significance of low levels of LINC RP1130-1 expression in human hepatocellular carcinoma. Biosci Trends 2016; 10:378-385. [PMID: 27773892 DOI: 10.5582/bst.2016.01123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most common neoplasms. Little progress has been made in the diagnosis and treatment of HCC and its prognosis remains poor. Studies have increasingly found that long non-coding RNA (lncRNA) is involved in the regulation of the occurrence and development of HCC. To investigate the diagnostic and prognostic value of lncRNA in HCC, the current study examined 25 lncRNAs with differing levels of expression (according to the fold change) in microarray databases. Expression of LINC RP1130-1 was found to be markedly down-regulated in 51 HCC tissues compared to matching adjacent non-tumor liver tissues. The pattern of expression and clinical significance of LINC RP1130-1 were examined in HCC. The area under the receiver operating characteristic (ROC) curve was 0.74 for LINC RP1130-1. The expression of LINC RP1130-1 was associated with clinical stage, the number of tumors, portal vein tumor thrombus (PVTT), and microvascular invasion (MVI). More importantly, patients with a low level of LINC RP1130-1 expression had a shorter recurrence-free survival (RFS) (n = 51, p < 0.05) than those with a high level of LINC RP1130-1 expression. Taken together, these findings indicate that a low level of LINC RP1130-1 expression in patients with HCC may be a powerful tumor biomarker, with potential clinical use in diagnosing and predicting the prognosis for patients with HCC.
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Affiliation(s)
- Chaohui Xiao
- Departments of Surgical Oncology, Chinese People's Liberation Army (PLA) General Hospital
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