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Wang CR, Gong JH, Zhao ZB, Zhu Q, Shu B, Hu JJ, Cai D, Liu XY, Dai X, Qiu C, Gong JP, Zhong GC. m 6A demethylation of FOSL1 mRNA protects hepatoma cells against necrosis under glucose deprivation. Cell Death Differ 2024; 31:1029-1043. [PMID: 38762597 PMCID: PMC11303728 DOI: 10.1038/s41418-024-01308-3] [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: 12/21/2023] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/20/2024] Open
Abstract
Stress-adaptive mechanisms enabling cancer cells to survive under glucose deprivation remain elusive. N6-methyladenosine (m6A) modification plays important roles in determining cancer cell fate and cellular stress response to nutrient deficiency. However, whether m6A modification functions in the regulation of cancer cell survival under glucose deprivation is unknown. Here, we found that glucose deprivation reduced m6A modification levels. Increasing m6A modification resulted in increased hepatoma cell necrosis under glucose deprivation, whereas decreasing m6A modification had an opposite effect. Integrated m6A-seq and RNA-seq revealed potential targets of m6A modification under glucose deprivation, including the transcription factor FOSL1; further, glucose deprivation upregulated FOSL1 by inhibiting FOSL1 mRNA decay in an m6A-YTHDF2-dependent manner through reducing m6A modification in its exon1 and 5'-UTR regions. Functionally, FOSL1 protected hepatoma cells against glucose deprivation-induced necrosis in vitro and in vivo. Mechanistically, FOSL1 transcriptionally repressed ATF3 by binding to its promoter. Meanwhile, ATF3 and MAFF interacted via their leucine zipper domains to form a heterodimer, which competed with NRF2 for binding to antioxidant response elements in the promoters of NRF2 target genes, thereby inhibiting their transcription. Consequently, FOSL1 reduced the formation of the ATF3-MAFF heterodimer, thereby enhancing NRF2 transcriptional activity and the antioxidant capacity of glucose-deprived-hepatoma cells. Thus, FOSL1 alleviated the necrosis-inducing effect of glucose deprivation-induced reactive oxygen species accumulation. Collectively, our study uncovers the protective role of m6A-FOSL1-ATF3 axis in hepatoma cell necrosis under glucose deprivation, and may provide new targets for cancer therapy.
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Affiliation(s)
- Chun-Rui Wang
- Department of Infectious Diseases, Institute for Viral Hepatitis, the Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun-Hua Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Bo Zhao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qian Zhu
- Department of Nutrition and Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Bian Shu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie-Jun Hu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dong Cai
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin-Yi Liu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Dai
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chan Qiu
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian-Ping Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guo-Chao Zhong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Smargon AA, Madrigal AA, Yee BA, Dong KD, Mueller JR, Yeo GW. Crosstalk between CRISPR-Cas9 and the human transcriptome. Nat Commun 2022; 13:1125. [PMID: 35236841 PMCID: PMC8891275 DOI: 10.1038/s41467-022-28719-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 02/09/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 in human cells and find that Cas9 reproducibly interacts with hundreds of endogenous human RNA transcripts. This association can be partially explained by a model built on gRNA secondary structure and sequence. Critically, transcriptome-wide Cas9 binding sites do not appear to correlate with published genome-wide Cas9 DNA binding or cut-site loci under gRNA co-expression. However, even under gRNA co-expression low-affinity Cas9-human RNA interactions (which we term CRISPR crosstalk) do correlate with published elevated transcriptome-wide RNA editing. Our findings do not support the hypothesis that human RNAs can broadly guide Cas9 to bind and cleave human genomic DNA, but they illustrate a cellular and RNA impact likely inherent to CRISPR-Cas systems.
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Affiliation(s)
- Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Assael A Madrigal
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kevin D Dong
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jasmine R Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA.
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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3
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Kooti A, Abuei H, Farhadi A, Behzad-Behbahani A, Zarrabi M. Activating transcription factor 3 mediates apoptotic functions through a p53-independent pathway in human papillomavirus 18 infected HeLa cells. Virus Genes 2022; 58:88-97. [DOI: 10.1007/s11262-022-01887-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022]
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4
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Chen Y, Lee K, Liang Y, Qin S, Zhu Y, Liu J, Yao S. A Cholesterol Homeostasis-Related Gene Signature Predicts Prognosis of Endometrial Cancer and Correlates With Immune Infiltration. Front Genet 2021; 12:763537. [PMID: 34790227 PMCID: PMC8591263 DOI: 10.3389/fgene.2021.763537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Endometrial cancer (EC) is one of the most common gynecological malignancies in women. Cholesterol metabolism has been confirmed to be closely related to tumor proliferation, invasion and metastasis. However, the correlation between cholesterol homeostasis-related genes and prognosis of EC remains unclear. Methods: EC patients from the Cancer Genome Atlas (TCGA) database were randomly divided into training cohort and test cohort. Transcriptome analysis, univariate survival analysis and LASSO Cox regression analysis were adopted to construct a cholesterol homeostasis-related gene signature from the training cohort. Subsequently, Kaplan-Meier (KM) plot, receiver operating characteristic (ROC) curve and principal component analysis (PCA) were utilized to verify the predictive performance of the gene signature in two cohorts. Additionally, enrichment analysis and immune infiltration analysis were performed on differentially expressed genes (DEGs) between two risk groups. Results: Seven cholesterol homeostasis-related genes were selected to establish a gene signature. KM plot, ROC curve and PCA in two cohorts demonstrated that the gene signature was an efficient independent prognostic indicator. The enrichment analysis and immune infiltration analysis indicated that the high-risk group generally had lower immune infiltrating cells and immune function. Conclusion: We constructed and validated a cholesterol homeostasis-related gene signature to predict the prognosis of EC, which correlated to immune infiltration and expected to help the diagnosis and precision treatment of EC.
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Affiliation(s)
- Yili Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaping Lee
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanchun Liang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shuhang Qin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuan Zhu
- Department of Obstetrics and Gynecology, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Junxiu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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5
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Branca JJV, Carrino D, Gulisano M, Ghelardini C, Di Cesare Mannelli L, Pacini A. Oxaliplatin-Induced Neuropathy: Genetic and Epigenetic Profile to Better Understand How to Ameliorate This Side Effect. Front Mol Biosci 2021; 8:643824. [PMID: 34026827 PMCID: PMC8138476 DOI: 10.3389/fmolb.2021.643824] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
In the most recent decades, oxaliplatin has been used as a chemotherapeutic agent for colorectal cancer and other malignancies as well. Oxaliplatin interferes with tumor growth predominantly exerting its action in DNA synthesis inhibition by the formation of DNA-platinum adducts that, in turn, leads to cancer cell death. On the other hand, unfortunately, this interaction leads to a plethora of systemic side effects, including those affecting the peripheral and central nervous system. Oxaliplatin therapy has been associated with acute and chronic neuropathic pain that induces physicians to reduce the dose of medication or discontinue treatment. Recently, the capability of oxaliplatin to alter the genetic and epigenetic profiles of the nervous cells has been documented, and the understanding of gene expression and transcriptional changes may help to find new putative treatments for neuropathy. The present article is aimed to review the effects of oxaliplatin on genetic and epigenetic mechanisms to better understand how to ameliorate neuropathic pain in order to enhance the anti-cancer potential and improve patients’ quality of life.
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Affiliation(s)
- Jacopo Junio Valerio Branca
- Histology and Anatomy Section, Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Donatello Carrino
- Histology and Anatomy Section, Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Massimo Gulisano
- Histology and Anatomy Section, Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Carla Ghelardini
- Pharmacology and Toxicology Section, Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Firenze, Firenze, Italy
| | - Lorenzo Di Cesare Mannelli
- Pharmacology and Toxicology Section, Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Firenze, Firenze, Italy
| | - Alessandra Pacini
- Histology and Anatomy Section, Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
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6
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Borgoni S, Sofyalı E, Soleimani M, Wilhelm H, Müller-Decker K, Will R, Noronha A, Beumers L, Verschure PJ, Yarden Y, Magnani L, van Kampen AH, Moerland PD, Wiemann S. Time-Resolved Profiling Reveals ATF3 as a Novel Mediator of Endocrine Resistance in Breast Cancer. Cancers (Basel) 2020; 12:E2918. [PMID: 33050633 PMCID: PMC7650760 DOI: 10.3390/cancers12102918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/29/2020] [Accepted: 10/07/2020] [Indexed: 01/05/2023] Open
Abstract
Breast cancer is one of the leading causes of death for women worldwide. Patients whose tumors express Estrogen Receptor α account for around 70% of cases and are mostly treated with targeted endocrine therapy. However, depending on the degree of severity of the disease at diagnosis, 10 to 40% of these tumors eventually relapse due to resistance development. Even though recent novel approaches as the combination with CDK4/6 inhibitors increased the overall survival of relapsing patients, this remains relatively short and there is a urgent need to find alternative targetable pathways. In this study we profiled the early phases of the resistance development process to uncover drivers of this phenomenon. Time-resolved analysis revealed that ATF3, a member of the ATF/CREB family of transcription factors, acts as a novel regulator of the response to therapy via rewiring of central signaling processes towards the adaptation to endocrine treatment. ATF3 was found to be essential in controlling crucial processes such as proliferation, cell cycle, and apoptosis during the early response to treatment through the regulation of MAPK/AKT signaling pathways. Its essential role was confirmed in vivo in a mouse model, and elevated expression of ATF3 was verified in patient datasets, adding clinical relevance to our findings. This study proposes ATF3 as a novel mediator of endocrine resistance development in breast cancer and elucidates its role in the regulation of downstream pathways activities.
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Affiliation(s)
- Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Emre Sofyalı
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Maryam Soleimani
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.H.C.v.K.); (P.D.M.)
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Heike Wilhelm
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
| | - Karin Müller-Decker
- Tumor Models Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Rainer Will
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Ashish Noronha
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel; (A.N.); (Y.Y.)
| | - Lukas Beumers
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Pernette J. Verschure
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel; (A.N.); (Y.Y.)
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, W12 0NN London, UK;
| | - Antoine H.C. van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.H.C.v.K.); (P.D.M.)
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.H.C.v.K.); (P.D.M.)
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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7
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Gallic Acid Inhibits Lipid Accumulation via AMPK Pathway and Suppresses Apoptosis and Macrophage-Mediated Inflammation in Hepatocytes. Nutrients 2020; 12:nu12051479. [PMID: 32443660 PMCID: PMC7285059 DOI: 10.3390/nu12051479] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease, sometimes ranges from simple steatosis to nonalcoholic steatohepatitis (NASH). Various hits including excessive hepatic steatosis, oxidative stress, apoptosis, and inflammation, contribute to NASH development. Gallic acid (GA), a natural polyphenol, was reported to exert a protective effect on hepatic steatosis in animal models, but the precise molecular mechanisms remain unclear. Here, we examined the effect of GA on hepatic lipid accumulation, apoptosis, and inflammatory response caused by hepatocyte–macrophage crosstalk. We demonstrated that GA attenuated palmitic acid (PA)-induced fat accumulation via the activation of AMP-activated protein kinase (AMPK) in HepG2 cells. GA also ameliorated cell viability and suppressed apoptosis-related gene expression and caspase 3/7 activity induced by PA and H2O2. In a co-culture of lipid-laden Hepa 1-6 hepatocytes and RAW 264 macrophages, GA reduced inflammatory mediator expression and induced antioxidant enzyme expression. These results indicate that GA suppresses hepatic lipid accumulation, apoptosis, and inflammation caused by the interaction between hepatocytes and macrophages. The potential effects of GA observed in our study could be effective in preventing NASH and its complications.
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8
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Asakawa Y, Okabe A, Fukuyo M, Li W, Ikeda E, Mano Y, Funata S, Namba H, Fujii T, Kita K, Matsusaka K, Kaneda A. Epstein-Barr virus-positive gastric cancer involves enhancer activation through activating transcription factor 3. Cancer Sci 2020; 111:1818-1828. [PMID: 32119176 PMCID: PMC7226279 DOI: 10.1111/cas.14370] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/26/2022] Open
Abstract
Epstein‐Barr virus (EBV) is associated with particular forms of gastric cancer (GC). We previously showed that EBV infection into gastric epithelial cells induced aberrant DNA hypermethylation in promoter regions and silencing of tumor suppressor genes. We here undertook integrated analyses of transcriptome and epigenome alteration during EBV infection in gastric cells, to investigate activation of enhancer regions and related transcription factors (TFs) that could contribute to tumorigenesis. Formaldehyde‐assisted isolation of regulatory elements (FAIRE) sequencing (‐seq) data revealed 19 992 open chromatin regions in putative H3K4me1+ H3K4me3− enhancers in EBV‐infected MKN7 cells (MKN7_EB), with 10 260 regions showing increase of H3K27ac. Motif analysis showed candidate TFs, eg activating transcription factor 3 (ATF3), to possibly bind to these activated enhancers. ATF3 was considerably upregulated in MKN7_EB due to EBV factors including EBV‐determined nuclear antigen 1 (EBNA1), EBV‐encoded RNA 1, and latent membrane protein 2A. Expression of mutant EBNA1 decreased copy number of the EBV genome, resulting in relative downregulation of ATF3 expression. Epstein‐Barr virus was also infected into normal gastric epithelial cells, GES1, confirming upregulation of ATF3. Chromatin immunoprecipitation‐seq analysis on ATF3 binding sites and RNA‐seq analysis on ATF3 knocked‐down MKN7_EB revealed 96 genes targeted by ATF3‐activating enhancers, which are related with cancer hallmarks, eg evading growth suppressors. These 96 ATF3 target genes were significantly upregulated in MKN7_EB compared with MKN7 and significantly downregulated when ATF3 was knocked down in EBV‐positive GC cells SNU719 and NCC24. Knockdown of ATF3 in EBV‐infected MKN7, SNU719, and NCC24 cells all led to significant decrease of cellular growth through an increase of apoptotic cells. These indicate that enhancer activation though ATF3 might contribute to tumorigenesis of EBV‐positive GC.
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Affiliation(s)
- Yuta Asakawa
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Genome Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Wenzhe Li
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Eriko Ikeda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yasunobu Mano
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Sayaka Funata
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroe Namba
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahiro Fujii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,School of Medicine, Chiba University, Chiba, Japan
| | - Kazuko Kita
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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9
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Ku HC, Cheng CF. Master Regulator Activating Transcription Factor 3 (ATF3) in Metabolic Homeostasis and Cancer. Front Endocrinol (Lausanne) 2020; 11:556. [PMID: 32922364 PMCID: PMC7457002 DOI: 10.3389/fendo.2020.00556] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
Activating transcription factor 3 (ATF3) is a stress-induced transcription factor that plays vital roles in modulating metabolism, immunity, and oncogenesis. ATF3 acts as a hub of the cellular adaptive-response network. Multiple extracellular signals, such as endoplasmic reticulum (ER) stress, cytokines, chemokines, and LPS, are connected to ATF3 induction. The function of ATF3 as a regulator of metabolism and immunity has recently sparked intense attention. In this review, we describe how ATF3 can act as both a transcriptional activator and a repressor. We then focus on the role of ATF3 and ATF3-regulated signals in modulating metabolism, immunity, and oncogenesis. The roles of ATF3 in glucose metabolism and adipose tissue regulation are also explored. Next, we summarize how ATF3 regulates immunity and maintains normal host defense. In addition, we elaborate on the roles of ATF3 as a regulator of prostate, breast, colon, lung, and liver cancers. Further understanding of how ATF3 regulates signaling pathways involved in glucose metabolism, adipocyte metabolism, immuno-responsiveness, and oncogenesis in various cancers, including prostate, breast, colon, lung, and liver cancers, is then provided. Finally, we demonstrate that ATF3 acts as a master regulator of metabolic homeostasis and, therefore, may be an appealing target for the treatment of metabolic dyshomeostasis, immune disorders, and various cancers.
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Affiliation(s)
- Hui-Chen Ku
- Department of Pediatrics, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taipei, Taiwan
| | - Ching-Feng Cheng
- Department of Pediatrics, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Department of Pediatrics, Tzu Chi University, Hualien, Taiwan
- *Correspondence: Ching-Feng Cheng
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10
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Kaplan N, Wang J, Wray B, Patel P, Yang W, Peng H, Lavker RM. Single-Cell RNA Transcriptome Helps Define the Limbal/Corneal Epithelial Stem/Early Transit Amplifying Cells and How Autophagy Affects This Population. Invest Ophthalmol Vis Sci 2019; 60:3570-3583. [PMID: 31419300 PMCID: PMC6701873 DOI: 10.1167/iovs.19-27656] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose Single-cell RNA-sequencing (scRNA-seq) was used to interrogate the relatively rare stem (SC) and early transit amplifying (TA) cell populations in limbal/corneal epithelia from wild-type and autophagy-compromised mice. Methods We conducted scRNA-seq on ocular anterior segmental tissue from wild-type and beclin 1–deficient (beclin1+/−) mice, using a 10X Gemomics pipeline. Cell populations were distinguished by t-distributed stochastic neighbor embedding. Seurat analysis was conducted to compare gene expression profiles between these two groups of mice. Differential protein expression patterns were validated by immunofluorescence staining and immunoblotting. Results Unbiased clustering detected 10 distinct populations: three clusters of mesenchymal and seven clusters of epithelial cells, based on their unique molecular signatures. A discrete group of mesenchymal cells expressed genes associated with corneal stromal SCs. We identified three limbal/corneal epithelial cell subpopulations designated as stem/early TA, mature TA, and differentiated corneal epithelial cells. Thioredoxin-interacting protein and PDZ-binding kinase (PBK) were identified as novel regulators of stem/early TA cell quiescence. PBK arrested corneal epithelial cells in G2/M phase of the cell cycle. Beclin1+/− mice displayed a decrease in proliferation-associated (Ki67, Lrig1) and stress-response (H2ax) genes. The most increased gene in beclin1+/− mice was transcription factor ATF3, which negatively regulates limbal epithelial cell proliferation. Conclusions Establishment of a comprehensive atlas of genes expressed by stromal and epithelial cells from limbus and cornea forms the foundation for unraveling regulatory networks among these distinct tissues. Similarly, scRNA-seq profiling of the anterior segmental epithelia from wild-type and autophagy-deficient mice provides new insights into how autophagy influences proliferation in these tissues.
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Affiliation(s)
- Nihal Kaplan
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Junyi Wang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States.,Department of Ophthalmology, Ophthalmology and Visual Science Key Lab of PLA, Chinese PLA General Hospital, Beijing, China
| | - Brian Wray
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Priyam Patel
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Wending Yang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Han Peng
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Robert M Lavker
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
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