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Ding J, Yang YY, Li PT, Ma Y, Zhang L, Zhou Y, Jin C, Li HY, Zhu YF, Liu XP, Liu ZJ, Jia HL, Liu PG, Wu J. TGF-β1/SMAD3-driven GLI2 isoform expression contributes to aggressive phenotypes of hepatocellular carcinoma. Cancer Lett 2024; 588:216768. [PMID: 38453045 DOI: 10.1016/j.canlet.2024.216768] [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: 11/27/2023] [Revised: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024]
Abstract
Hedgehog signaling is activated in response to liver injury, and modulates organogenesis. However, the role of non-canonical hedgehog activation via TGF-β1/SMAD3 in hepatic carcinogenesis is poorly understood. TGF-β1/SMAD3-mediated non-canonical activation was found in approximately half of GLI2-positive hepatocellular carcinoma (HCC), and two new GLI2 isoforms with transactivating activity were identified. Phospho-SMAD3 interacted with active GLI2 isoforms to transactivate downstream genes in modulation of stemness, epithelial-mesenchymal transition, chemo-resistance and metastasis in poorly-differentiated hepatoma cells. Non-canonical activation of hedgehog signaling was confirmed in a transgenic HBV-associated HCC mouse model. Inhibition of TGF-β/SMAD3 signaling reduced lung metastasis in a mouse in situ hepatic xenograft model. In another cohort of 55 HCC patients, subjects with high GLI2 expression had a shorter disease-free survival than those with low expression. Moreover, co-positivity of GLI2 with SMAD3 was observed in 87.5% of relapsed HCC patients with high GLI2 expression, indicating an increased risk of post-resection recurrence of HCC. The findings underscore that suppressing the non-canonical hedgehog signaling pathway may confer a potential strategy in the treatment of HCC.
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Affiliation(s)
- Jia Ding
- Department of Gastroenterology, Shanghai Jing'an District Central Hospital, Fudan University, Shanghai, 200040, China.
| | - Yong-Yu Yang
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Peng-Tao Li
- Department of Hepatobiliary & Pancreatic Surgery, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361004, China
| | - Yue Ma
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Li Zhang
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Yuan Zhou
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Cheng Jin
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Hui-Yan Li
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Yuan-Fei Zhu
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Xiu-Ping Liu
- Department of Pathology and Laboratory Medicine, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Zheng-Jin Liu
- Department of Pathology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361004, China
| | - Hu-Liang Jia
- Department of General Surgery, Huashan Hospital of Fudan University, Shanghai, 200041, China
| | - Ping-Guo Liu
- Department of Hepatobiliary & Pancreatic Surgery, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361004, China.
| | - Jian Wu
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China; Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, 200032, China; Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, 200032, China.
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2
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Qi L, Chen S, Liao Z, Fan M, Zhang J, Gao Y, Shen J, Sun Y, Wang Q. Comprehensive characterization of Fidgetin on tumor immune microenvironment evaluation and immunotherapy in human hepatocellular carcinoma. Aging (Albany NY) 2024; 16:4445-4468. [PMID: 38421251 PMCID: PMC10968695 DOI: 10.18632/aging.205598] [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: 10/18/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
Most cancers have a downregulation of Fidgetin (FIGN), which has been linked to tumor growth. However, there aren't many papers that mention FIGN's connection to hepatocellular carcinoma (HCC). Here, FIGN expression in HCC tissues was markedly reduced as compared to nearby normal liver tissues. According to univariate and multivariate Cox regression, it served as an independent predictor of survival outcomes. Patients with high levels of FIGN expression had a worse outcome. FIGN was shown to be engaged in immune-related pathways and to have a positive correlation with immunological score and immune cells according to KEGG pathway analysis. In HCC patients, FIGN was substantially linked with immunological checkpoints and the hot tumor state. Additionally, immunotherapy and chemotherapy showed a significant therapeutic response in HCC patients with low FIGN expression. This research revealed that FIGN expression was tightly related to hepatoma immunity and might be employed as a biomarker to predict patient prognosis and guide medication.
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Affiliation(s)
- Longju Qi
- Laboratory Animal Center, Medical School, Nantong University, Nantong, China
- Affiliated Nantong Hospital 3 of Nantong University, Nantong University, Nantong, China
| | - Shiyuan Chen
- Laboratory Animal Center, Medical School, Nantong University, Nantong, China
| | - Zehua Liao
- Laboratory Animal Center, Medical School, Nantong University, Nantong, China
| | - Mengjie Fan
- Laboratory Animal Center, Medical School, Nantong University, Nantong, China
| | - Jiayi Zhang
- Laboratory Animal Center, Medical School, Nantong University, Nantong, China
| | - Yuan Gao
- Laboratory Animal Center, Medical School, Nantong University, Nantong, China
| | - Jiabao Shen
- Laboratory Animal Center, Medical School, Nantong University, Nantong, China
| | - Yuyu Sun
- Affiliated Nantong Hospital 3 of Nantong University, Nantong University, Nantong, China
| | - Qinghua Wang
- Laboratory Animal Center, Medical School, Nantong University, Nantong, China
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3
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Levra Levron C, Elettrico L, Duval C, Piacenti G, Proserpio V, Donati G. Bridging tissue repair and epithelial carcinogenesis: epigenetic memory and field cancerization. Cell Death Differ 2024:10.1038/s41418-023-01254-6. [PMID: 38228801 DOI: 10.1038/s41418-023-01254-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
The epigenome coordinates spatial-temporal specific gene expression during development and in adulthood, for the maintenance of homeostasis and upon tissue repair. The upheaval of the epigenetic landscape is a key event in the onset of many pathologies including tumours, where epigenetic changes cooperate with genetic aberrations to establish the neoplastic phenotype and to drive cell plasticity during its evolution. DNA methylation, histone modifiers and readers or other chromatin components are indeed often altered in cancers, such as carcinomas that develop in epithelia. Lining the surfaces and the cavities of our body and acting as a barrier from the environment, epithelia are frequently subjected to acute or chronic tissue damages, such as mechanical injuries or inflammatory episodes. These events can activate plasticity mechanisms, with a deep impact on cells' epigenome. Despite being very effective, tissue repair mechanisms are closely associated with tumour onset. Here we review the similarities between tissue repair and carcinogenesis, with a special focus on the epigenetic mechanisms activated by cells during repair and opted by carcinoma cells in multiple epithelia. Moreover, we discuss the recent findings on inflammatory and wound memory in epithelia and describe the epigenetic modifications that characterise them. Finally, as wound memory in epithelial cells promotes carcinogenesis, we highlight how it represents an early step for the establishment of field cancerization.
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Affiliation(s)
- Chiara Levra Levron
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Luca Elettrico
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Carlotta Duval
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Gabriele Piacenti
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy.
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy.
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4
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Zhang D, Xiang KF, Xiang C, Wu Y, Wang L. Construction of novel 7 integrin-related gene signatures in thyroid cancer construction of model based on integrin genes. Medicine (Baltimore) 2023; 102:e36412. [PMID: 38115319 PMCID: PMC10727611 DOI: 10.1097/md.0000000000036412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
Advanced and metastatic THCA patients usually have a poor prognosis. Thus, this study aimed to establish a risk model to discriminate the high risk population. The expression and clinical data were obtained from TCGA database. The cluster analysis, lasso, univariate and multivariate cox analyses were used to construct risk model. K-M, ROC and DCA were applied to validate the efficiency and stability of the model. GO, KEGG, and ssGSEA analysis were performed to identify the potential mechanism of signatures. The 7-gene prognosis model was constructed, including FAM27E3, FIGN, GSTM4, BEX5, RBPMS2, PHF13, and DCSTAMP. ROC and DCA results showed our model had a better prognosis prediction performance than other risk models. The high risk score was associated with the poor prognosis of THCA patients with different clinical characteristics. The risk score was closely related to cell cycle. Further, we found that the expressions of signatures were significantly dysregulated in THCA and associated with prognosis. These gene expressions were affected by some clinical characteristics, methylation and CNV. Some signatures played a role in drug sensitivity and pathway activation. We constructed a 7-gene signature model based on the integrin-related genes, which showed a great prognostic value in THCA.
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Affiliation(s)
- Dong Zhang
- Department of General Surgery, Kong Jiang Hosptal of Yangpu District, Shanghai, China
| | - Kai-fang Xiang
- Department of Thyroid and Breast Surgery, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Cheng Xiang
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Wu
- Department of Oncology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, Wuhan, China
| | - Ling Wang
- Department of Thyroid and Breast Surgery, The First People’s Hospital of Jiangxia, Wuhan, China
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5
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Han M, Perkins MH, Novaes LS, Xu T, Chang H. Advances in transposable elements: from mechanisms to applications in mammalian genomics. Front Genet 2023; 14:1290146. [PMID: 38098473 PMCID: PMC10719622 DOI: 10.3389/fgene.2023.1290146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
It has been 70 years since Barbara McClintock discovered transposable elements (TE), and the mechanistic studies and functional applications of transposable elements have been at the forefront of life science research. As an essential part of the genome, TEs have been discovered in most species of prokaryotes and eukaryotes, and the relative proportion of the total genetic sequence they comprise gradually increases with the expansion of the genome. In humans, TEs account for about 40% of the genome and are deeply involved in gene regulation, chromosome structure maintenance, inflammatory response, and the etiology of genetic and non-genetic diseases. In-depth functional studies of TEs in mammalian cells and the human body have led to a greater understanding of these fundamental biological processes. At the same time, as a potent mutagen and efficient genome editing tool, TEs have been transformed into biological tools critical for developing new techniques. By controlling the random insertion of TEs into the genome to change the phenotype in cells and model organisms, critical proteins of many diseases have been systematically identified. Exploiting the TE's highly efficient in vitro insertion activity has driven the development of cutting-edge sequencing technologies. Recently, a new technology combining CRISPR with TEs was reported, which provides a novel targeted insertion system to both academia and industry. We suggest that interrogating biological processes that generally depend on the actions of TEs with TEs-derived genetic tools is a very efficient strategy. For example, excessive activation of TEs is an essential factor in the occurrence of cancer in humans. As potent mutagens, TEs have also been used to unravel the key regulatory elements and mechanisms of carcinogenesis. Through this review, we aim to effectively combine the traditional views of TEs with recent research progress, systematically link the mechanistic discoveries of TEs with the technological developments of TE-based tools, and provide a comprehensive approach and understanding for researchers in different fields.
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Affiliation(s)
- Mei Han
- Guangzhou National Laboratory, Guangzhou, China
| | - Matthew H. Perkins
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Leonardo Santana Novaes
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tao Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Hao Chang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Zhu EY, Schillo JL, Murray SD, Riordan JD, Dupuy AJ. Understanding cancer drug resistance with Sleeping Beauty functional genomic screens: Application to MAPK inhibition in cutaneous melanoma. iScience 2023; 26:107805. [PMID: 37860756 PMCID: PMC10582486 DOI: 10.1016/j.isci.2023.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/10/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023] Open
Abstract
Combined BRAF and MEK inhibition is an effective treatment for BRAF-mutant cutaneous melanoma. However, most patients progress on this treatment due to drug resistance. Here, we applied the Sleeping Beauty transposon system to understand how melanoma evades MAPK inhibition. We found that the specific drug resistance mechanisms differed across melanomas in our genetic screens of five cutaneous melanoma cell lines. While drivers that reactivated MAPK were highly conserved, many others were cell-line specific. One such driver, VAV1, activated a de-differentiated transcriptional program like that of hyperactive RAC1, RAC1P29S. To target this mechanism, we showed that an inhibitor of SRC, saracatinib, blunts the VAV1-induced transcriptional reprogramming. Overall, we highlighted the importance of accounting for melanoma heterogeneity in treating cutaneous melanoma with MAPK inhibitors. Moreover, we demonstrated the utility of the Sleeping Beauty transposon system in understanding cancer drug resistance.
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Affiliation(s)
- Eliot Y. Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jacob L. Schillo
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarina D. Murray
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jesse D. Riordan
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
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7
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Keng VW, Chiu AP, To JC, Li XX, Linden MA, Amin K, Moriarity BS, Yusa K. Transposon delivery for CRISPR-based loss-of-function screen in mice identifies NF2 as a cooperating gene involved with the canonical WNT signaling molecular class of hepatocellular carcinoma. Heliyon 2023; 9:e18774. [PMID: 37576222 PMCID: PMC10412851 DOI: 10.1016/j.heliyon.2023.e18774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023] Open
Abstract
Various molecular subclasses of hepatocellular carcinoma (HCC) exists, with many novel cooperating oncogenes and tumor suppressor genes involved in its tumorigenesis. The emerging importance of WNT signaling in HCC has been established. However, the intricate genetic mechanisms involved in this complex signaling pathway remains to be elucidated. Importantly, while some cooperating genes have been identified, there are still many unknown genes associated with catenin beta 1 (CTNNB1)-induced HCC. Mutations in both oncogenes and tumor suppressor genes are required for HCC tumorigenesis. The emergence of the CRISPR/Cas9 system has allowed researchers now to target both alleles efficiently. In this novel study, the Sleeping Beauty transposon system was used as a gene delivery system in vivo to stably integrate an expression cassette that carry pools of gRNAs and overexpress a mutant version of CTNNB1 into the hepatocyte genome. We identified 206 candidate genes that drive HCC tumorigenesis in the context of WNT signaling activation and, neurofibromin 2 (NF2) gene, a known tumor suppressor gene with clinical relevance was validated in this proof-of-principle study.
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Affiliation(s)
- Vincent W. Keng
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, China
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Amy P. Chiu
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Jeffrey C. To
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, China
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Xiao-Xiao Li
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, China
| | - Michael A. Linden
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Khalid Amin
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Branden S. Moriarity
- Masonic Cancer Center, Department of Pediatrics, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kosuke Yusa
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
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8
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Ishtiaq SM, Arshad MI, Khan JA. PPARγ signaling in hepatocarcinogenesis: Mechanistic insights for cellular reprogramming and therapeutic implications. Pharmacol Ther 2022; 240:108298. [PMID: 36243148 DOI: 10.1016/j.pharmthera.2022.108298] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/30/2022]
Abstract
Liver cancer or hepatocellular carcinoma (HCC) is leading cause of cancer-related mortalities globally. The therapeutic approaches for chronic liver diseases-associated liver cancers aimed at modulating immune check-points and peroxisome proliferator-activated receptor gamma (PPARγ) signaling pathway during multistep process of hepatocarcinogenesis that played a dispensable role in immunopathogenesis and outcomes of disease. Herein, the review highlights PPARγ-induced effects in balancing inflammatory (tumor necrosis factor alpha (TNF-α), interleukin (IL)-6, IL-1) and anti-inflammatory cytokines (IL-10, transforming growth factor beta (TGF-β), and interplay of PPARγ, hepatic stellate cells and fibrogenic niche in cell-intrinsic and -extrinsic crosstalk of hepatocarcinogenesis. PPARγ-mediated effects in pre-malignant microenvironment promote growth arrest, cell senescence and cell clearance in liver cancer pathophysiology. Furthermore, PPARγ-immune cell axis of liver microenvironment exhibits an immunomodulation strategy of resident immune cells of the liver (macrophages, natural killer cells, and dendritic cells) in concomitance with current clinical guidelines of the European Association for Study of Liver Diseases (EASL) for several liver diseases. Thus, mechanistic insights of PPARγ-associated high value targets and canonical signaling suggest PPARγ as a possible therapeutic target in reprogramming of hepatocarcinogenesis to decrease burden of liver cancers, worldwide.
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Affiliation(s)
- Syeda Momna Ishtiaq
- Institute of Physiology and Pharmacology, University of Agriculture, Faisalabad 38040, Pakistan
| | | | - Junaid Ali Khan
- Department of Pharmacology and Physiology, MNS University of Agriculture, Multan 60000, Pakistan.
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Wang L, Li B, Yi X, Xiao X, Zheng Q, Ma L. Circ_0036412 affects the proliferation and cell cycle of hepatocellular carcinoma via hedgehog signaling pathway. J Transl Med 2022; 20:154. [PMID: 35382824 PMCID: PMC8981839 DOI: 10.1186/s12967-022-03305-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 02/12/2022] [Indexed: 12/27/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC), as the most common type of liver cancer, is characterized by high recurrence and metastasis. Circular RNA (circRNA) circ_0036412 was selected for studying the underlying mechanisms of HCC. Methods Quantitative real time-polymerase chain reaction (qRT-PCR) and western blot analyzed gene and protein expression. Functional experiments evaluated HCC cell proliferation, apoptosis and cell cycle in vitro. In vivo experiments detected HCC carcinogenesis in vivo. Fluorescence in situ hybridization (FISH) assays evaluated the subcellular distribution. Luciferase reporter, Chromatin immunoprecipitation (ChIP), DNA pulldown, RNA-binding protein immunoprecipitation (RIP), and RNA pulldown assays detected the underlying mechanisms. Results Circ_0036412 is overexpressed in HCC cells and features circular structure. PRDM1 activates circ_0036412 transcription to regulate the proliferation and cell cycle of HCC cells in vitro. Circ_0036412 modulates Hedgehog pathway. GLI2 propels HCC growth in vivo. Circ_0036412 up-regulates GLI2 expression by competitively binding to miR-579-3p, thus promoting the proliferation and inhibiting cell cycle arrest of HCC cells. Circ_0036412 stabilizes GLI2 expression by recruiting ELAVL1. Circ_0036412 propels the proliferation and inhibits cell cycle arrest of HCC cells in vitro through Hedgehog pathway. Conclusions Circ_0036412 affects the proliferation and cell cycle of HCC via Hedgehog signaling pathway. It offers an insight into the targeted therapies of HCC. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03305-x.
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Affiliation(s)
- Liyan Wang
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical College, No. 15 Lequn Road, Xiufeng District, Guilin, 541001, Guangxi, China
| | - Bin Li
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical College, No. 15 Lequn Road, Xiufeng District, Guilin, 541001, Guangxi, China.
| | - Xiaoyuan Yi
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical College, No. 15 Lequn Road, Xiufeng District, Guilin, 541001, Guangxi, China
| | - Xuhua Xiao
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical College, No. 15 Lequn Road, Xiufeng District, Guilin, 541001, Guangxi, China
| | - Qinghua Zheng
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical College, No. 15 Lequn Road, Xiufeng District, Guilin, 541001, Guangxi, China
| | - Lei Ma
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical College, No. 15 Lequn Road, Xiufeng District, Guilin, 541001, Guangxi, China
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10
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Yan YC, Meng GX, Ding ZN, Liu YF, Chen ZQ, Yan LJ, Yang YF, Liu H, Yang CC, Dong ZR, Hong JG, Li T. Somatic mutation and expression of BAP1 in hepatocellular carcinoma: an indicator for ferroptosis and immune checkpoint inhibitor therapies. J Cancer 2022; 13:88-101. [PMID: 34976173 PMCID: PMC8692694 DOI: 10.7150/jca.65574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/10/2021] [Indexed: 12/16/2022] Open
Abstract
BRCA1-Associated Protein 1 (BAP1) is a deubiquitylase that is found associated with multiprotein complexes that regulate key cellular pathways, and subsequent researches have revealed that BAP1 acts independently as a tumor suppressor. Somatic BAP1 mutations occur in various malignancies, but malignancies arising from mutation of tumor suppressors have unexplained tissue proclivity. Whether somatic mutation or expression alteration of BAP1 in hepatocellular carcinoma (HCC) influence carcinogenesis or immunogenicity is still unknown. In this study, we analyzed RNA expression, immune infiltration, survival and mutation data of HCC from The Cancer Genome Atlas databases. The association between BAP1 and clinicopathological features was further investigated by immunohistochemistry on tissue microarray. We found that the prognosis of patients with high BAP1 expression was significantly worse than that of patients with low BAP1 expression, and multivariate analyses revealed that BAP1 expression was an independent prognostic factor for poor prognosis. HCC with high BAP1 expression was associated with low ESTIMATE Score, recruitment of more tumor-infiltrating macrophage, and elevated levels of tumor mutation burden, microsatellite instability, neoantigen count, as well as programmed death-ligand1 in HCC. In addition, BAP1 mutated HCC showed reduced ability to promote ferroptosis and high BAP1 expression was correlated with ferroptosis. In conclusion, high BAP1 expression reflects immunosuppression and ferroptosis in HCC. BAP1 is a promising prognostic marker for survival of HCC and may act as a complementary indicator for patients to receive ferroptosis-promoting therapy or immunotherapy.
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Affiliation(s)
- Yu-Chuan Yan
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Guang-Xiao Meng
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Zi-Niu Ding
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Yan-Feng Liu
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Zhi-Qiang Chen
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Lun-Jie Yan
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Ya-Fei Yang
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Hui Liu
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Chun-Cheng Yang
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Zhao-Ru Dong
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Jian-Guo Hong
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Tao Li
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China.,Department of hepatobiliary surgery, The second Hospital of Shandong University, Jinan 250012, P.R. China
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11
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Shen J, Dai J, Zhang Y, Xie F, Yu Y, Li C, Wen T. Baseline HBV-DNA load plus AST/ALT ratio predicts prognosis of HBV-related hepatocellular carcinoma after hepatectomy: A multicentre study. J Viral Hepat 2021; 28:1587-1596. [PMID: 34464991 DOI: 10.1111/jvh.13606] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 02/05/2023]
Abstract
Hepatitis B viral (HBV) load and hepatic enzymes play a critical role in hepatocellular carcinoma (HCC) development. However, the clinical significance of these in HBV-related HCC patients after hepatectomy remains unclear. In this study, we analysed 1,940 HBV-related HCC patients who underwent hepatectomy from four hospitals in west China. Risk classification was constructed based on baseline HBV-DNA load and AST/ALT ratio. Based on the HBV-DNA load and AST/ALT ratio classification, four types with distinguishable prognoses were established. Type 1 patients had the best prognosis with 5-year overall survival (OS) of 69.8%, followed by type 2 and type 3 patients, whereas type 4 patients had the worst prognosis with 5-year OS of 42.7%. Similarly, the four types had statistically different recurrence-free survival. This classification was significantly associated with HCC recurrence (hazard ratio [HR]:1.492, p < .001) and long-term survival (HR: 1.574, p = .001). Pathologically, type 4 correlated with more advanced tumours considering tumour size and microvascular invasion than those in type 1, 2, or 3. Moreover, type 4 patients had more severe hepatic inflammation in underlying liver. Conversely, type 1 patients had an active tumour immune microenvironment as indicated by more CD8+ T cell infiltration and less PD-L1 expression. In conclusion, the classfication based on baseline HBV-DNA load and AST/ALT ratio could effectively stratify HBV-related HCC patients with distinguishable prognoses after hepatectomy.
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Affiliation(s)
- Junyi Shen
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China.,Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital of Sichuan University, Chengdu, China.,Institute of Clinical Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Junlong Dai
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yu Zhang
- Department of Hepatobiliary Surgery, Sichuan Provincial People's Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Fei Xie
- Department of Hepatobiliary and Pancreatic Surgery, The First People's Hospital of Neijiang City, Neijiang, China
| | - Yu Yu
- Department of Hepatobiliary and Pancreatic Surgery, The Second People's Hospital of Yibin, Yibin, China
| | - Chuan Li
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Tianfu Wen
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, China.,Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital of Sichuan University, Chengdu, China
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12
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Exploring liver cancer biology through functional genetic screens. Nat Rev Gastroenterol Hepatol 2021; 18:690-704. [PMID: 34163045 DOI: 10.1038/s41575-021-00465-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
As the fourth leading cause of cancer-related death in the world, liver cancer poses a major threat to human health. Although a growing number of therapies have been approved for the treatment of hepatocellular carcinoma in the past few years, most of them only provide a limited survival benefit. Therefore, an urgent need exists to identify novel targetable vulnerabilities and powerful drug combinations for the treatment of liver cancer. The advent of functional genetic screening has contributed to the advancement of liver cancer biology, uncovering many novel genes involved in tumorigenesis and cancer progression in a high-throughput manner. In addition, this unbiased screening platform also provides an efficient tool for the exploration of the mechanisms involved in therapy resistance as well as identifying potential targets for therapy. In this Review, we describe how functional screens can help to deepen our understanding of liver cancer and guide the development of new therapeutic strategies.
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13
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Chen M, Lu C, Lu H, Zhang J, Qin D, Liu S, Li X, Zhang L. Farnesoid X receptor via Notch1 directs asymmetric cell division of Sox9 + cells to prevent the development of liver cancer in a mouse model. Stem Cell Res Ther 2021; 12:232. [PMID: 33845903 PMCID: PMC8042944 DOI: 10.1186/s13287-021-02298-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/18/2021] [Indexed: 12/21/2022] Open
Abstract
Background Asymmetrical cell division (ACD) maintains the proper number of stem cells to ensure self-renewal. The rate of symmetric division increases as more cancer stem cells (CSCs) become malignant; however, the signaling pathway network involved in CSC division remains elusive. FXR (Farnesoid X receptor), a ligand-activated transcription factor, has several anti-tumor effects and has been shown to target CSCs. Here, we aimed at evaluating the role of FXR in the regulation of the cell division of CSCs. Methods The FXR target gene and downstream molecular mechanisms were confirmed by qRT-PCR, Western blot, luciferase reporter assay, EMAS, Chip, and IF analyses. Pulse-chase BrdU labeling and paired-cell experiments were used to detect the cell division of liver CSCs. Gain- and loss-of-function experiments in Huh7 cells and mouse models were performed to support findings and elucidate the function and underlying mechanisms of FXR-Notch1 in liver CSC division. Results We demonstrated that activation of Notch1 was significantly elevated in the livers of hepatocellular carcinoma (HCC) in Farnesoid X receptor-knockout (FXR-KO) mice and that FXR expression negatively correlated with Notch1 level during chronic liver injury. Activation of FXR induced the asymmetric divisions of Sox9+ liver CSCs and ameliorated liver injury. Mechanistically, FXR directs Sox9+ liver CSCs from symmetry to asymmetry via inhibition of Notch1 expression and activity. Deletion of FXR signaling or over-expression of Notch1 greatly increased Notch1 expression and activity along with ACD reduction. FXR inhibited Notch1 expression by directly binding to its promoter FXRE. FXR also positively regulated Numb expression, contributing to a feedback circuit, which decreased Notch1 activity and directed ACD. Conclusion Our findings suggest that FXR represses Notch1 expression and directs ACD of Sox9+ cells to prevent the development of liver cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02298-6.
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Affiliation(s)
- Mi Chen
- College of Veterinary Medicine/College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chenxia Lu
- The Clinical Medical College of Traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Hanwen Lu
- College of Veterinary Medicine/College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junyi Zhang
- College of Veterinary Medicine/College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dan Qin
- College of Veterinary Medicine/College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shenghui Liu
- College of Veterinary Medicine/College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaodong Li
- Hubei Provincial Hospital of TCM, Hubei Provincial Academy of TCM, Wuhan, 430061, China
| | - Lisheng Zhang
- College of Veterinary Medicine/College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China.
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14
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Ahmad A, Ishtiaq SM, Khan JA, Aslam R, Ali S, Arshad MI. COVID-19 and comorbidities of hepatic diseases in a global perspective. World J Gastroenterol 2021; 27:1296-1310. [PMID: 33833483 PMCID: PMC8015303 DOI: 10.3748/wjg.v27.i13.1296] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/17/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
The worldwide outbreak of coronavirus disease 2019 (COVID-19) has challenged the priorities of healthcare system in terms of different clinical management and infection transmission, particularly those related to hepatic-disease comorbidities. Epidemiological data evidenced that COVID-19 patients with altered liver function because of hepatitis infection and cholestasis have an adverse prognosis and experience worse health outcomes. COVID-19-associated liver injury is correlated with various liver diseases following a severe acute respiratory syndrome-coronavirus type 2 (SARS-CoV-2) infection that can progress during the treatment of COVID-19 patients with or without pre-existing liver disease. SARS-CoV-2 can induce liver injury in a number of ways including direct cytopathic effect of the virus on cholangiocytes/hepatocytes, immune-mediated damage, hypoxia, and sepsis. Indeed, immediate cytopathogenic effects of SARS-CoV-2 via its potential target, the angiotensin-converting enzyme-2 receptor, which is highly expressed in hepatocytes and cholangiocytes, renders the liver as an extra-respiratory organ with increased susceptibility to pathological outcomes. But, underlying COVID-19-linked liver disease pathogenesis with abnormal liver function tests (LFTs) is incompletely understood. Hence, we collated COVID-19-associated liver injuries with increased LFTs at the nexus of pre-existing liver diseases and COVID-19, and defining a plausible pathophysiological triad of COVID-19, hepatocellular damage, and liver disease. This review summarizes recent findings of the exacerbating role of COVID-19 in pre-existing liver disease and vice versa as well as international guidelines of clinical care, management, and treatment recommendations for COVID-19 patients with liver disease.
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Affiliation(s)
- Aqsa Ahmad
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad 38040, Punjab, Pakistan
| | - Syeda Momna Ishtiaq
- Institute of Physiology and Pharmacology, University of Agriculture Faisalabad, Faisalabad 38040, Punjab, Pakistan
| | - Junaid Ali Khan
- Institute of Physiology and Pharmacology, University of Agriculture Faisalabad, Faisalabad 38040, Punjab, Pakistan
| | - Rizwan Aslam
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad 38040, Punjab, Pakistan
| | - Sultan Ali
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad 38040, Punjab, Pakistan
| | - Muhammad Imran Arshad
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad 38040, Punjab, Pakistan
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15
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Garcia-Lezana T, Lopez-Canovas JL, Villanueva A. Signaling pathways in hepatocellular carcinoma. Adv Cancer Res 2020; 149:63-101. [PMID: 33579428 DOI: 10.1016/bs.acr.2020.10.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the recent introduction of new effective systemic agents, the survival of patients with hepatocellular carcinoma (HCC) at advanced stages remains dismal. This underscores the need for new therapies, which has spurred extensive research on the identification of the main drivers of pathway de-regulation as a source of novel therapeutic targets. Frequently altered pathways in HCC involve growth factor receptors (e.g., VEGFR, FGFR, TGFA, EGFR, IGFR) and/or its cytoplasmic intermediates (e.g., PI3K-AKT-mTOR, RAF/ERK/MAPK) as well as key pathways in cell differentiation (e.g., Wnt/β-catenin, JAK/STAT, Hippo, Hedgehog, Notch). Somatic mutations, chromosomal aberrations and epigenetic changes are common mechanisms for pathway deregulation in HCC. Aberrant pathway activation has also been explored as a biomarker to predict response to specific therapies, but currently, these strategies are not implemented when deciding systemic therapies in HCC patients. Beyond the well-established molecular cascades, there are numerous emerging signaling pathways also deregulated in HCC (e.g., tumor microenvironment, non-coding RNA, intestinal microbiota), which have opened new avenues for therapeutic exploration.
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Affiliation(s)
- Teresa Garcia-Lezana
- Division of Liver Diseases, Liver Cancer Program, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Juan Luis Lopez-Canovas
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), University of Córdoba, Córdoba, Spain
| | - Augusto Villanueva
- Division of Liver Diseases, Liver Cancer Program, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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16
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Weber J, Braun CJ, Saur D, Rad R. In vivo functional screening for systems-level integrative cancer genomics. Nat Rev Cancer 2020; 20:573-593. [PMID: 32636489 DOI: 10.1038/s41568-020-0275-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Herein, we review functional screening strategies in mice using genetic perturbation and chemical mutagenesis. We outline the spectrum of genetic tools that exist, such as transposons, CRISPR and RNAi and describe discoveries emerging from their use. Genome-wide or targeted screens are being used to uncover genomic and regulatory landscapes in oncogenesis, metastasis or drug resistance. Versatile screening systems support experimentation in diverse genetic and spatio-temporal settings to integrate molecular, cellular or environmental context-dependencies. We also review the combination of in vivo screening and barcoding strategies to study genetic interactions and quantitative cancer dynamics during tumour evolution. These scalable functional genomics approaches are transforming our ability to interrogate complex biological systems.
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Affiliation(s)
- Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany.
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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17
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Ili C, Buchegger K, Demond H, Castillo-Fernandez J, Kelsey G, Zanella L, Abanto M, Riquelme I, López J, Viscarra T, García P, Bellolio E, Saavedra D, Brebi P. Landscape of Genome-Wide DNA Methylation of Colorectal Cancer Metastasis. Cancers (Basel) 2020; 12:E2710. [PMID: 32971738 PMCID: PMC7564781 DOI: 10.3390/cancers12092710] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer is a heterogeneous disease caused by both genetic and epigenetics factors. Analysing DNA methylation changes occurring during colorectal cancer progression and metastasis formation is crucial for the identification of novel epigenetic markers of patient prognosis. Genome-wide methylation sequencing of paired samples of colon (normal adjacent, primary tumour and lymph node metastasis) showed global hypomethylation and CpG island (CGI) hypermethylation of primary tumours compared to normal. In metastasis we observed high global and non-CGI regions methylation, but lower CGI methylation, compared to primary tumours. Gene ontology analysis showed shared biological processes between hypermethylated CGIs in metastasis and primary tumours. After complementary analysis with The Cancer Genome Atlas (TCGA) cohort, FIGN, HTRA3, BDNF, HCN4 and STAC2 genes were found associated with poor survival. We mapped the methylation landscape of colon normal tissues, primary tumours and lymph node metastasis, being capable of identified methylation changes throughout the genome. Furthermore, we found five genes with potential for methylation biomarkers of poor prognosis in colorectal cancer patients.
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Affiliation(s)
- Carmen Ili
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
| | - Kurt Buchegger
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
- Departamento Ciencias Básicas, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile
| | - Hannah Demond
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; (J.C.-F.); (G.K.)
| | - Juan Castillo-Fernandez
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; (J.C.-F.); (G.K.)
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; (J.C.-F.); (G.K.)
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 1TN, UK
| | - Louise Zanella
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
| | - Michel Abanto
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile;
| | - Ismael Riquelme
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco 4810101, Chile;
| | - Jaime López
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
| | - Tamara Viscarra
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
| | - Patricia García
- Department of Pathology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330034, Chile;
| | - Enrique Bellolio
- Departamento Anatomía Patológica, Facultad de Medicina, Universidad de La Frontera, Temuco 4781180, Chile;
- Departamento de Medicina Interna, Hospital Hernán Henríquez Aravena, Temuco 4781151, Chile;
| | - David Saavedra
- Departamento de Medicina Interna, Hospital Hernán Henríquez Aravena, Temuco 4781151, Chile;
- Clínica Alemana de Temuco, Temuco 4810297, Chile
| | - Priscilla Brebi
- Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4810296, Chile; (C.I.); (K.B.); (H.D.); (L.Z.); (J.L.); (T.V.)
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18
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Baliou S, Kyriakopoulos AM, Spandidos DA, Zoumpourlis V. Role of taurine, its haloamines and its lncRNA TUG1 in both inflammation and cancer progression. On the road to therapeutics? (Review). Int J Oncol 2020; 57:631-664. [PMID: 32705269 PMCID: PMC7384849 DOI: 10.3892/ijo.2020.5100] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
For one century, taurine is considered as an end product of sulfur metabolism. In this review, we discuss the beneficial effect of taurine, its haloamines and taurine upregulated gene 1 (TUG1) long non‑coding RNA (lncRNA) in both cancer and inflammation. We outline how taurine or its haloamines (N‑Bromotaurine or N‑Chlorotaurine) can induce robust and efficient responses against inflammatory diseases, providing insight into their molecular mechanisms. We also provide information about the use of taurine as a therapeutic approach to cancer. Taurine can be combined with other chemotherapeutic drugs, not only mediating durable responses in various malignancies, but also circumventing the limitations met from chemotherapeutic drugs, thus improving the therapeutic outcome. Interestingly, the lncRNA TUG1 is regarded as a promising therapeutic approach, which can overcome acquired resistance of cancer cells to selected strategies. In this regard, we can translate basic knowledge about taurine and its TUG1 lncRNA into potential therapeutic options directed against specific oncogenic signaling targets, thereby bridging the gap between bench and bedside.
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Affiliation(s)
| | | | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion 71003, Greece
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19
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Chen TC, Tallo-Parra M, Cao QM, Kadener S, Böttcher R, Pérez-Vilaró G, Boonchuen P, Somboonwiwat K, Díez J, Sarnow P. Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells. PLoS Pathog 2020; 16:e1008346. [PMID: 32764824 PMCID: PMC7437927 DOI: 10.1371/journal.ppat.1008346] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 08/19/2020] [Accepted: 06/28/2020] [Indexed: 12/14/2022] Open
Abstract
Viruses subvert macromolecular pathways in infected host cells to aid in viral gene amplification or to counteract innate immune responses. Roles for host-encoded, noncoding RNAs, including microRNAs, have been found to provide pro- and anti-viral functions. Recently, circular RNAs (circRNAs), that are generated by a nuclear back-splicing mechanism of pre-mRNAs, have been implicated to have roles in DNA virus-infected cells. This study examines the circular RNA landscape in uninfected and hepatitis C virus (HCV)-infected liver cells. Results showed that the abundances of distinct classes of circRNAs were up-regulated or down-regulated in infected cells. Identified circRNAs displayed pro-viral effects. One particular up-regulated circRNA, circPSD3, displayed a very pronounced effect on viral RNA abundances in both hepatitis C virus- and Dengue virus-infected cells. Though circPSD3 has been shown to bind factor eIF4A3 that modulates the cellular nonsense-mediated decay (NMD) pathway, circPSD3 regulates RNA amplification in a pro-viral manner at a post-translational step, while eIF4A3 exhibits the anti-viral property of the NMD pathway. Findings from the global analyses of the circular RNA landscape argue that pro-, and likely, anti-viral functions are executed by circRNAs that modulate viral gene expression as well as host pathways. Because of their long half-lives, circRNAs likely play hitherto unknown, important roles in viral pathogenesis.
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Affiliation(s)
- Tzu-Chun Chen
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Marc Tallo-Parra
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Qian M. Cao
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sebastian Kadener
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - René Böttcher
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gemma Pérez-Vilaró
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Pakpoom Boonchuen
- Department of Biochemistry, Chulalongkorn University, Bangkog, Thailand
| | | | - Juana Díez
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Peter Sarnow
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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20
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Zhou B, Wang J, Gao J, Xie J, Chen Y. Fidgetin as a potential prognostic biomarker for hepatocellular carcinoma. Int J Med Sci 2020; 17:2888-2894. [PMID: 33162817 PMCID: PMC7645349 DOI: 10.7150/ijms.49913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/27/2020] [Indexed: 12/04/2022] Open
Abstract
Background: Fidgetin (FIGN), a conserved ATP-dependent enzyme, is regarded as a hepatocellular carcinoma (HCC) risk gene, but the prognostic implication of FIGN in HCC remains obscure. In this study, we investigate the expression of FIGN in HCC and to evaluate its prognostic value. Methods: A total of 216 patients with HCC who experienced hepatectomy were recruited in this study. The expression of FIGN in HCC samples was evaluated by quantitative real-time PCR, immunohistochemistry and immunoblotting analysis. And Cox regression model was used to evaluate the prognostic value of all covariates. Results: Of the 216 HCC patients, 67 (31.0%) had tumors with high FIGN expression and 149 (69.0%) had tumors with low FIGN expression. FIGN expression was positively correlated with TNM stage (P = 0.039), tumor with incomplete capsule (P = 0.036), microvascular invasion (P = 0.023), and portal vein tumor thrombus (P = 0.003). High expression of FIGN indicated shorter overall survival (OS) (hazard ratio: 4.569, P = 0.036) and disease-free survival (DFS) (hazard ratio: 6.487, P = 0.001). Conclusion: Our results indicate that high Fidgetin expression is associated with tumor progression and suggest a worse prognosis in HCC. Fidgetin might serve as a potential target for therapy.
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Affiliation(s)
- Bin Zhou
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Jisheng Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Jing Gao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Junqing Xie
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Yiming Chen
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
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Qu H, Gao X, Wang ZY, Yi JJ. Comparative study on hepatoprotection of pine nut (Pinus koraiensis Sieb. et Zucc.) polysaccharide against different types of chemical-induced liver injury models in vivo. Int J Biol Macromol 2019; 155:1050-1059. [PMID: 31712149 DOI: 10.1016/j.ijbiomac.2019.11.069] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 12/15/2022]
Abstract
A novel polysaccharide (PNP80b-2) was obtained from Pinus koraiensis pine nut, which has been proved to possess good hepatoprotective effects in vitro. This study comprehensively investigated its hepatoprotective activities against different types of chemical-induced liver injury in vivo. Carbon tetrachloride, alcohol and acetaminophen were used as hepatic toxicants to establish chemical pollutant-induced liver injury (CILI) model, alcohol induced-liver injury (AILI) model and drug-induced liver injury (DILI) model, respectively. The results showed that PNP80b-2 prevented elevation of biomarkers for liver injury in each model, including alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and total bilirubin (TBIL). The expression of cytochrome P450 in damaged hepatocytes was also downregulated. Additionally, PNP80b-2 enhanced hepatic antioxidant capacity through upregulating the expression of NRF2 and HO-1, thereby increasing superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and catalase (CAT) activities and decreasing malondialdehyde (MDA) levels. The uncontrolled production of inflammatory factors including tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6) and cyclooxygenase-2 (COX-2) in CILI, AILI and DILI models was also suppressed by PNP80b-2. By contrast, PNP80b-2 exerted the strongest hepatoprotection against AILI model, through improving hepatic antioxidant capacity via NRF2/ARE pathway and regulating inflammation response. Thus, PNP80b-2 is a promising functional food to prevent AILI.
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Affiliation(s)
- Hang Qu
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, PR China
| | - Xin Gao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, PR China
| | - Zhen-Yu Wang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001, PR China.
| | - Juan-Juan Yi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, PR China.
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22
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Liu Y, Kim HG, Dong E, Dong C, Huang M, Liu Y, Liangpunsakul S, Dong XC. Sesn3 deficiency promotes carcinogen-induced hepatocellular carcinoma via regulation of the hedgehog pathway. Biochim Biophys Acta Mol Basis Dis 2019; 1865:2685-2693. [PMID: 31351129 DOI: 10.1016/j.bbadis.2019.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/15/2019] [Accepted: 07/23/2019] [Indexed: 01/01/2023]
Abstract
Sestrin 3 (Sesn3) belongs to a small protein family that has been implicated in multiple biological processes including anti-oxidative stress, anti-aging, cell signaling, and metabolic homeostasis. However, the role of Sesn3 in hepatocellular carcinoma (HCC) remains unclear. Here we generated a Sesn3 knockout mouse model and induced HCC development by a combination of a single dose of diethylnitrosamine and chronic feeding of a choline deficient-high fat diet. After 6 months of the dietary treatment, Sesn3 knockout mice developed more severe HCC with higher levels of alpha-fetoprotein, arginase 1, and cytokeratin 19, but also higher metastatic rates than wild-type mice. Histological analysis revealed elevated extracellular matrix and cancer stem cell markers including Acta2, Cd44, and Cd133. Signaling analysis showed activated IL6-Stat3 and Akt pathways. Biochemical and microscopic analyses uncovered a novel inhibitory regulation of Gli2, a downstream transcription factor of the hedgehog signaling, by Sesn3. Two of the Gli2-regulated genes - Pdgfrb and Cd44 were upregulated in the Sesn3-deficient liver tissue. In conclusion, our data suggest that Sesn3 plays a critical tumor suppressor role in the liver partly through the inhibition of the hedgehog signaling.
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Affiliation(s)
- Yunjian Liu
- Department of Hepatobiliary Surgery, the Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi Province 332000, China; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hyeong Geug Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Chuanpeng Dong
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Menghao Huang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Suthat Liangpunsakul
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Xiaocheng Charlie Dong
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
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23
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Feddersen CR, Wadsworth LS, Zhu EY, Vaughn HR, Voigt AP, Riordan JD, Dupuy AJ. A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells. BMC Genomics 2019; 20:497. [PMID: 31208320 PMCID: PMC6580595 DOI: 10.1186/s12864-019-5888-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/06/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gain-of-function screens are less common, although some reports have utilized arrayed viral expression libraries or the CRISPR activation system. However, a variety of technical and logistical challenges make these approaches difficult for many labs to execute. In addition, genome-wide shRNA or CRISPR libraries typically contain of hundreds of thousands of individual engineered elements, and the associated complexity creates issues with replication and reproducibility for these methods. RESULTS Here we describe a simple, reproducible approach using the SB transposon system to perform phenotypic cell-based genetic screens. This approach employs only three plasmids to perform unbiased, whole-genome transposon mutagenesis. We also describe a ligation-mediated PCR method that can be used in conjunction with the included software tools to map raw sequence data, identify candidate genes associated with phenotypes of interest, and predict the impact of recurrent transposon insertions on candidate gene function. Finally, we demonstrate the high reproducibility of our approach by having three individuals perform independent replicates of a mutagenesis screen to identify drivers of vemurafenib resistance in cultured melanoma cells. CONCLUSIONS Collectively, our work establishes a facile, adaptable method that can be performed by labs of any size to perform robust, genome-wide screens to identify genes that influence phenotypes of interest.
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Affiliation(s)
- Charlotte R. Feddersen
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Lexy S. Wadsworth
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Eliot Y. Zhu
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Hayley R. Vaughn
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Andrew P. Voigt
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Jesse D. Riordan
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Adam J. Dupuy
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52246 USA
- Department of Anatomy & Cell Biology, Cancer Biology Graduate Program, University of Iowa, MERF, 375 Newton Road, Iowa City, IA 3202 USA
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24
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Kieckhaefer JE, Maina F, Wells R, Wangensteen KJ. Liver Cancer Gene Discovery Using Gene Targeting, Sleeping Beauty, and CRISPR/Cas9. Semin Liver Dis 2019; 39:261-274. [PMID: 30912094 PMCID: PMC7485130 DOI: 10.1055/s-0039-1678725] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a devastating and prevalent cancer with limited treatment options. Technological advances have enabled genetic screens to be employed in HCC model systems to characterize genes regulating tumor initiation and growth. Relative to traditional methods for studying cancer biology, such as candidate gene approaches or expression analysis, genetic screens have several advantages: they are unbiased, with no a priori selection; can directly annotate gene function; and can uncover gene-gene interactions. In HCC, three main types of screens have been conducted and are reviewed here: (1) transposon-based mutagenesis screens, (2) knockdown screens using RNA interference (RNAi) or the CRISPR/Cas9 system, and (3) overexpression screens using CRISPR activation (CRISPRa) or cDNAs. These methods will be valuable in future genetic screens to delineate the mechanisms underlying drug resistance and to identify new treatments for HCC.
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Affiliation(s)
- Julia E. Kieckhaefer
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania, Philadelphia, PA, USA
| | - Flavio Maina
- Aix Marseille University, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Marseille, France
| | - Rebecca Wells
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania, Philadelphia, PA, USA
- Pathology and Laboratory Medicine and Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kirk J. Wangensteen
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania, Philadelphia, PA, USA
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25
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UPF1 inhibits the hepatocellular carcinoma progression by targeting long non-coding RNA UCA1. Sci Rep 2019; 9:6652. [PMID: 31040354 PMCID: PMC6491801 DOI: 10.1038/s41598-019-43148-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the major causes of cancer-related death worldwide. However, the molecular mechanism underlying HCC carcinogenesis remains to be further elucidated. Up-frameshift protein 1 (UPF1) is a RNA/DNA-dependent ATPase and ATP-dependent RNA helicase. Here, we explored the expression and function of UPF1 in HCC. In this study, we demonstrated that UPF1 expression was significantly reduced in hepatocellular carcinoma (HCC) tissues compared with the adjacent normal tissues. And further functional assays revealed that knockdown of UPF1 promoted HCC cells growth and invasion. Furthermore, we found that UPF1 could bind to long non-coding RNA urothelial cancer associated 1 (UCA1) and was negatively correlated with UCA1. UCA1 expression also affected HCC growth and invasion. Knockdown of UCA1 ameliorated the effect of UPF1 knock down on HCC growth and invasion. Knockdown of UPF1 enhances glycolysis in HCC. Taken together, our results provided new insights for finding novel therapeutic targets for hepatocellular carcinoma progression.
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26
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Guimaraes-Young A, Feddersen CR, Dupuy AJ. Sleeping Beauty Mouse Models of Cancer: Microenvironmental Influences on Cancer Genetics. Front Oncol 2019; 9:611. [PMID: 31338332 PMCID: PMC6629774 DOI: 10.3389/fonc.2019.00611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
The Sleeping Beauty (SB) transposon insertional mutagenesis system offers a streamlined approach to identify genetic drivers of cancer. With a relatively random insertion profile, SB is uniquely positioned for conducting unbiased forward genetic screens. Indeed, SB mouse models of cancer have revealed insights into the genetics of tumorigenesis. In this review, we highlight experiments that have exploited the SB system to interrogate the genetics of cancer in distinct biological contexts. We also propose experimental designs that could further our understanding of the relationship between tumor microenvironment and tumor progression.
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Affiliation(s)
- Amy Guimaraes-Young
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Charlotte R Feddersen
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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27
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Lin C, Yuan G, Hu Z, Zeng Y, Qiu X, Yu H, He S. Bioinformatics analysis of the interactions among lncRNA, miRNA and mRNA expression, genetic mutations and epigenetic modifications in hepatocellular carcinoma. Mol Med Rep 2018; 19:1356-1364. [PMID: 30535497 DOI: 10.3892/mmr.2018.9728] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/21/2018] [Indexed: 11/05/2022] Open
Abstract
The present study aimed to investigate the regulatory networks involving long noncoding RNA (lncRNA), microRNA (miRNA), mRNA, genetic mutations and epigenetic modifications in hepatocellular carcinoma (HCC) by analyzing datasets from The Cancer Genome Atlas (TCGA) database. TCGA was mined, and miRNAs, lncRNAs and mRNAs that were differentially expressed in HCC were identified using R software. A gene regulatory network was constructed using Cytoscape software. Representative genes were selected for functional enrichment analysis using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. The associations among various proteins and protein networks were identified using the online software Search Tool for the Retrieval of Interacting Genes/Proteins. The cBioPortal database was used to analyze the association between genetic mutations and epigenetic modification, and the development of HCC. A total of 35 mRNAs were predicted to be targeted by 77 lncRNAs and 16 miRNAs, establishing a lncRNA‑miRNA‑mRNA regulatory network for HCC. Multivariable Cox regression analysis suggested that long intergenic non‑protein coding RNA 200, miRNA‑137, PDZ binding kinase and DNA polymerase θ were independent prognostic factors. In a regulatory network centered on miRNA‑424, six mRNA target genes were associated with HCC survival rates. Protein‑protein interaction analysis suggested that cell division cycle 25A (CDC25A) interacted with centrosomal protein 55 (CEP55), claspin, E2F transcription factor 7 and cyclin E1 (CCNE1. Mutations in CEP55 affected overall survival and disease‑free survival in HCC, whereas, mutations in CDC25A affected overall survival, and mutations in E2F7 affected disease‑free survival. Decreased methylation levels of CEP55, CDC25A and CCNE1 were associated with vascular invasion. The survival rate of patients with hypermethylation of CCNE1 and CEP55 was significantly associated with the rate of methylation of these loci. The present study provides an integrated bioinformatics analysis of gene expression, genetic mutations and epigenetic modifications that may be associated with the development of HCC.
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Affiliation(s)
- Chengjie Lin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Guandou Yuan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhigao Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yonglian Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiaoqiang Qiu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hongping Yu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Songqing He
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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28
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Zhang C, Wang P, Li Y, Huang C, Ni W, Chen Y, Shi J, Chen G, Hu X, Ye M, Duan S, Wang K. Role of MicroRNAs in the Development of Hepatocellular Carcinoma in Nonalcoholic Fatty Liver Disease. Anat Rec (Hoboken) 2018; 302:193-200. [PMID: 30312023 DOI: 10.1002/ar.23954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 02/24/2018] [Accepted: 03/09/2018] [Indexed: 12/19/2022]
Abstract
Hepatocellular carcinoma (HCC) is a prevalent liver malignancy that can be developed from nonalcoholic fatty liver disease (NAFLD). Numerous pathophysiological alterations, including insulin resistance, specific cytokine release, oxidative stress, and mitochondrial damage, are involved in the transition of NAFLD to cirrhosis and HCC. MicroRNAs, as post-transcriptional modulators, play a critical role in the pathogenesis of NAFLD-related HCC by regulating lipid metabolism, glucose homeostasis, cell proliferation, apoptosis, migration, and differentiation. This review summarizes the current progress of microRNAs in the risk and prognosis of NAFLD-related HCC. Anat Rec, 302:193-200, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Cheng Zhang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Ping Wang
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yongqiang Li
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Changxin Huang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Wei Ni
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yidan Chen
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Junping Shi
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Gongying Chen
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xiangrong Hu
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Meng Ye
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Shiwei Duan
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Kaifeng Wang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
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29
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Molecular profiling of nonalcoholic fatty liver disease-associated hepatocellular carcinoma using SB transposon mutagenesis. Proc Natl Acad Sci U S A 2018; 115:E10417-E10426. [PMID: 30327349 PMCID: PMC6217425 DOI: 10.1073/pnas.1808968115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the fastest rising cause of hepatocellular carcinoma (HCC) in Western countries; however, the molecular mechanisms driving NAFLD-HCC remain elusive. Using Sleeping Beauty transposon mutagenesis in two mouse models of NAFLD-HCC, we identified hundreds of NAFLD-HCC candidate cancer genes that were enriched in pathways often associated with NAFLD and HCC. We also showed that Sav1, which functions in the Hippo signaling pathway and was the most frequently mutated gene identified by SB in both screens, prevents progression of steatohepatitis and subsequent HCC development in coordination with PI3K signaling via suppression of Yap, a downstream effector of the Hippo pathway. Our forward genetic screens have thus identified pathways and genes driving the development of NAFLD-HCC. Nonalcoholic fatty liver disease (NAFLD) is the fastest rising cause of hepatocellular carcinoma (HCC) in Western countries; however, the molecular mechanisms that cause NAFLD-HCC remain elusive. To identify molecular drivers of NAFLD-HCC, we performed Sleeping Beauty (SB) transposon mutagenesis screens in liver-specific Pten knockout and in high-fat diet-fed mice, which are murine models of NAFLD-HCC. SB mutagenesis accelerated liver tumor formation in both models and identified 588 and 376 candidate cancer genes (CCGs), respectively; 257 CCGs were common to both screens and were enriched in signaling pathways known to be important for human HCC. Comparison of these CCGs with those identified in a previous SB screen of hepatitis B virus-induced HCC identified a core set of 141 CCGs that were mutated in all screens. Forty-one CCGs appeared specific for NAFLD-HCC, including Sav1, a component of the Hippo signaling pathway and the most frequently mutated gene identified in both NAFLD-HCC screens. Liver-specific deletion of Sav1 was found to promote hepatic lipid accumulation, apoptosis, and fibrogenesis, leading to the acceleration of hepatocarcinogenesis in liver-specific Pten mutant mice. Sav1/Pten double-mutant livers also showed a striking up-regulation of markers of liver progenitor cells (LPCs), along with synergistic activation of Yap, which is a major downstream effector of Hippo signaling. Lastly, Yap activation, in combination with Pten inactivation, was found to accelerate cell growth and sphere formation of LPCs in vitro and induce their malignant transformation in allografts. Our forward genetic screens in mice have thus identified pathways and genes driving the development of NAFLD-HCC.
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30
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O'Donnell KA. Advances in functional genetic screening with transposons and CRISPR/Cas9 to illuminate cancer biology. Curr Opin Genet Dev 2018; 49:85-94. [PMID: 29587177 PMCID: PMC6312197 DOI: 10.1016/j.gde.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/18/2022]
Abstract
Large-scale genome sequencing studies have identified a wealth of mutations in human tumors and have dramatically advanced the field of cancer genetics. However, the functional consequences of an altered gene in tumor progression cannot always be inferred from mutation status alone. This underscores the critical need for complementary methods to assign functional significance to mutated genes in cancer. Transposons are mobile genetic elements that serve as powerful tools for insertional mutagenesis. Over the last decade, investigators have employed mouse models with ondemand transposon-mediated mutagenesis to perform unbiased genetic screens to identify clinically relevant genes that participate in the pathogenesis of human cancer. Two distinct DNA transposon mutagenesis systems, Sleeping Beauty (SB) and PiggyBac (PB), have been applied extensively in vivo and more recently, in ex vivo settings. These studies have informed our understanding of the genes and pathways that drive cancer initiation, progression, and metastasis. This review highlights the latest progress on cancer gene identification for specific cancer subtypes, as well as new technological advances and incorporation of the CRISPR/Cas9 toolbox into transposon-mediated functional genetic studies.
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Affiliation(s)
- Kathryn A O'Donnell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States.
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