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Wan L, Jia Y, Chen N, Zheng S. Circ_0003789 Knockdown Inhibits Tumor Progression by miR-429/ ZFP36L2 Axis in Gastric Cancer. Biochem Genet 2023:10.1007/s10528-023-10535-1. [PMID: 37962691 DOI: 10.1007/s10528-023-10535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/22/2023] [Indexed: 11/15/2023]
Abstract
An increasing number of circRNAs have been found to be involved in the development of gastric cancer. However, the function of circ_0003789 in regulating gastric cancer progression is unclear. Here, we aimed to investigate the expression, function and molecular mechanism of circ_0003789 in gastric cancer pathogenesis. Circ_0003789, miR-429 and ZFP36 ring finger protein like 2 (ZFP36L2) mRNA were quantified by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation was illustrated by 5-Ethynyl-2'-deoxyuridine (Edu), cell counting kit-8 (CCK-8) and colony formation assays. Apoptosis was determined by flow cytometry. Protein level was detected by Western blotting assay. Xenograft assays were used for functional analysis of circ_0003789 in vivo. The relationship between miR-429 and circ_0003789 or ZFP36L2 was predicted by starbase3.0 online database and identified by dual luciferase reporter assay. The expression levels of circ_0003789 and ZFP36L2 were significantly upregulated in gastric cancer tissues and cells, while the expression of miR-429 was downregulated. Downregulation of circ_0003789 inhibited gastric cancer cell growth and invasion and promoted apoptosis in vitro. Circ_0003789 acted as a sponge of miR-429. Moreover, miR-429 silencing by miR-429 inhibitors attenuated the effects of circ_0003789 interference on cell growth, apoptosis and invasion. ZFP36L2 was targeted by miR-429, and the effects of miR-429 on cell growth, invasion and apoptosis were attenuated by ZFP36L2 overexpression. Circ_0003789 could enhance ZFP36L2 expression by interacting with miR-429. Silencing of circ_0003789 inhibited tumor growth in vivo. Circ_0003789 regulates tumor progression in gastric cancer through miR-429/ZFP36L2 axis. This finding implies that circ_0003789 may be a therapeutic target for gastric cancer.
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Affiliation(s)
- Lu Wan
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, 265 Yinquan Dadao, Xianning, 437000, Hubei, China
| | - Yu Jia
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, 265 Yinquan Dadao, Xianning, 437000, Hubei, China
| | - Na Chen
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, 265 Yinquan Dadao, Xianning, 437000, Hubei, China.
| | - Sen Zheng
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, 265 Yinquan Dadao, Xianning, 437000, Hubei, China.
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2
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Rynne J, Ortiz-Zapater E, Bagley DC, Zanin O, Doherty G, Kanabar V, Ward J, Jackson DJ, Parsons M, Rosenblatt J, Adcock IM, Martinez-Nunez RT. The RNA binding proteins ZFP36L1 and ZFP36L2 are dysregulated in airway epithelium in human and a murine model of asthma. Front Cell Dev Biol 2023; 11:1241008. [PMID: 37928904 PMCID: PMC10624177 DOI: 10.3389/fcell.2023.1241008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction: Asthma is the most common chronic inflammatory disease of the airways. The airway epithelium is a key driver of the disease, and numerous studies have established genome-wide differences in mRNA expression between health and asthma. However, the underlying molecular mechanisms for such differences remain poorly understood. The human TTP family is comprised of ZFP36, ZFP36L1 and ZFP36L2, and has essential roles in immune regulation by determining the stability and translation of myriad mRNAs encoding for inflammatory mediators. We investigated the expression and possible role of the tristetraprolin (TTP) family of RNA binding proteins (RBPs), poorly understood in asthma. Methods: We analysed the levels of ZFP36, ZFP36L1 and ZFP36L2 mRNA in several publicly available asthma datasets, including single cell RNA-sequencing. We also interrogated the expression of known targets of these RBPs in asthma. We assessed the lung mRNA expression and cellular localization of Zfp36l1 and Zfp36l2 in precision cut lung slices in murine asthma models. Finally, we determined the expression in airway epithelium of ZFP36L1 and ZFP36L2 in human bronchial biopsies and performed rescue experiments in primary bronchial epithelium from patients with severe asthma. Results: We found ZFP36L1 and ZFP36L2 mRNA levels significantly downregulated in the airway epithelium of patients with very severe asthma in different cohorts (5 healthy vs. 8 severe asthma; 36 moderate asthma vs. 37 severe asthma on inhaled steroids vs. 26 severe asthma on oral corticoids). Integrating several datasets allowed us to infer that mRNAs potentially targeted by these RBPs are increased in severe asthma. Zfp36l1 was downregulated in the lung of a mouse model of asthma, and immunostaining of ex vivo lung slices with a dual antibody demonstrated that Zfp36l1/l2 nuclear localization was increased in the airway epithelium of an acute asthma mouse model, which was further enhanced in a chronic model. Immunostaining of human bronchial biopsies showed that airway epithelial cell staining of ZFP36L1 was decreased in severe asthma as compared with mild, while ZFP36L2 was upregulated. Restoring the levels of ZFP36L1 and ZFP36L2 in primary bronchial epithelial cells from patients with severe asthma decreased the mRNA expression of IL6, IL8 and CSF2. Discussion: We propose that the dysregulation of ZFP36L1/L2 levels as well as their subcellular mislocalization contributes to changes in mRNA expression and cytoplasmic fate in asthma.
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Affiliation(s)
- Jennifer Rynne
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Elena Ortiz-Zapater
- The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Dustin C. Bagley
- The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - Onofrio Zanin
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - George Doherty
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Varsha Kanabar
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Jon Ward
- Histochemistry Research Unit, University of Southampton, Southampton, United Kingdom
| | - David J. Jackson
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Maddy Parsons
- The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - Jody Rosenblatt
- The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - Ian M. Adcock
- National Heart and Lung Institute and Data Science Institute, Imperial College London, London, United Kingdom
| | - Rocio T. Martinez-Nunez
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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3
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Zhou Z, Fan H, Shi R, Zeng Y, Liu R, Gu H, Li Q, Sang Q, Wang L, Shi J, Chen B. A novel homozygous variant in ZFP36L2 cause female infertility due to oocyte maturation defect. Clin Genet 2023; 104:461-465. [PMID: 37211617 DOI: 10.1111/cge.14362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
Normal oocyte maturation is an important requirement for the success of human reproduction, and defects in this process will lead to female infertility and repeated IVF/ICSI failures. In order to identify genetic factors that are responsible for oocyte maturation defect, we used whole exome sequencing in the affected individual with oocyte maturation defect from a consanguineous family and identified a homozygous variant c.853_861del (p.285_287del) in ZFP36L2. ZFP36L2 is a RNA-binding protein, which regulates maternal mRNA decay and oocyte maturation. In vitro studies showed that the variant caused decreased protein levels of ZFP36L2 in oocytes due to mRNA instability and might lead to the loss of its function to degrade maternal mRNAs. Previous study showed that the pathogenic variants in ZFP36L2 were associated with early embryonic arrest. In contrast, we identified a novel ZFP36L2 variant in the affected individual with oocyte maturation defect, which further broadened the mutational and phenotypic spectrum of ZFP36L2, suggesting that ZFP36L2 might be a genetic diagnostic marker for the affected individuals with oocyte maturation defect.
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Affiliation(s)
- Zhou Zhou
- NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Shanghai, China
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Huizhen Fan
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Rong Shi
- Reproductive Center, Northwest Women's and Children's Hospital, Xi'an, Shaanxi, China
| | - Yang Zeng
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Ruyi Liu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Hao Gu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Qiaoli Li
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Qing Sang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Lei Wang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Juanzi Shi
- Reproductive Center, Northwest Women's and Children's Hospital, Xi'an, Shaanxi, China
| | - Biaobang Chen
- NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Shanghai, China
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4
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Zhang Y, Tian F, Zhao J. MiR-520d-3p suppresses the proliferation and epithelial-mesenchymal transition of cervical cancer cells by targeting ZFP36L2. Heliyon 2023; 9:e18789. [PMID: 37600385 PMCID: PMC10432607 DOI: 10.1016/j.heliyon.2023.e18789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
MiR-520d-3p has recently been reported to have anti-tumor function in several cancers, including glioma and gastric cancer. However, the biological function and its mechanism of action remain unclear in cervical cancer (CC). In this study, we observed that miR-520d-3p expression was lowly expressed in CC specimens compared with adjacent normal specimens using reverse transcription quantitative PCR. Moreover, low miR-520d-3p expression was correlated with FIGO stage and lymph node metastasis by Chi-square test. Functionally, overexpression of miR-520d-3p suppressed the proliferation and migration and invasion of two CC cell lines (HeLa and SiHa) using CCK-8 assay and wound healing assay. After target prediction, luciferase reporter assay showed that zinc finger protein 36 ring finger protein-like 2 (ZFP36L2) was a direct target of miR-520d-3p in CC cells. The expression levels of ZFP36L2 at protein and mRNA were significantly increased in CC tissues compared with adjacent tissues. The expression of ZFP36L2 was negatively correlated with miR-520d-3p in the patients with CC. Importantly, ZFP36L2 overexpression abolished the effects of miR-520d-3p on cell proliferation, migration and EMT process in CC cells. In conclusion, our findings indicate that targeting miR-520d-3p/ZFP36L2 axis might be a promising therapeutic target for CC treatment.
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Affiliation(s)
- Yuan Zhang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Fei Tian
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Jing Zhao
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, Hebei, China
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5
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Novosad VO, Maltseva DV. The RNA-Binding Proteins OAS1, ZFP36L2, and DHX58 Are Involved in the Regulation of CD44 mRNA Splicing in Colorectal Cancer Cells. Bull Exp Biol Med 2023:10.1007/s10517-023-05826-x. [PMID: 37336810 DOI: 10.1007/s10517-023-05826-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Indexed: 06/21/2023]
Abstract
Regulation of alternative splicing is carried out by RNA-binding proteins. Each alternative splicing event is controlled by several RNA-binding proteins, which in combination create the distribution of alternative splicing products in a given cell type. Transmembrane protein CD44 plays an important role at various stages of the metastatic cascade and is considered as a promising molecule for the therapy of tumor diseases and the construction of prognostic classifiers. However, the functions of specific isoforms of this protein may differ significantly. In this work, we performed a bioinformatic search of RNA-binding proteins that can determine the expression of clinically significant isoforms 3 and 4 of CD44 protein. The analysis revealed five RNA-binding proteins, three of which (OAS1, ZFP36L2, and DHX58) are shown for the first time as potential regulators of the studied process.
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Affiliation(s)
- V O Novosad
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - D V Maltseva
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia.
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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6
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Tao X, Li Y, Fan S, Wu L, Xin J, Su Y, Xian X, Huang Y, Huang R, Fang W, Liu Z. Downregulation of Linc00173 increases BCL2 mRNA stability via the miR-1275/PROCA1/ ZFP36L2 axis and induces acquired cisplatin resistance of lung adenocarcinoma. J Exp Clin Cancer Res 2023; 42:12. [PMID: 36627670 PMCID: PMC9830831 DOI: 10.1186/s13046-022-02560-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 12/04/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND LINC00173 had been reported as a cisplatin (cis-diamminedichloroplatinum, DDP) chemotherapy-resistant inducer in small-cell lung cancer (SCLC) and lung squamous cell carcinoma (LUSC). This study aimed to display reverse data for LINC00173 as a DDP chemosensitivity-inducing factor in lung adenocarcinoma (LUAD). METHODS LINC00173 was screened from the Gene Expression Omnibus database (GSE43493). The expression level of LINC00173 in LUAD tissues and cell lines was detected using in situ hybridization and quantitative reverse transcription-polymerase chain reaction. Colony formation, cell viability, half-maximal inhibitory concentration, flow cytometry, and xenograft mouse model were used to evaluate the role of LINC00173 in the chemosensitivity of LUAD to DDP. The mechanism of LINC00173 in DDP resistance by mediating miR-1275/PROCA1/ZFP36L2 axis to impair BCL2 mRNA stability was applied, and co-immunoprecipitation, chromatin immunoprecipitation, RNA antisense purification, RNA immunoprecipitation, and luciferase reporter assays were performed. RESULTS LINC00173 downregulation in patients with DDP-resistant LUAD was correlated with poor prognosis. Further, LINC00173 expression was significantly reduced in DDP-resistant LUAD cells and DDP-treated human LUAD tissues. Suppressed LINC00173 expression in LUAD cells enhanced DDP chemoresistance in vivo and in vitro, while restored LINC00173 expression in DDP-resistant LUAD cells markedly regained chemosensitivity to DDP. Mechanistically, DDP-resistant LUAD cells activated PI3K/AKT signal and further elevated the c-Myc expression. The c-Myc, as an oncogenic transcriptional factor, bound to the promoter of LINC00173 and suppressed its expression. The reduced LINC00173 expression attenuated the adsorption of oncogenic miR-1275, downregulating the expression of miR-1275 target gene PROCA1. PROCA1 played a potential tumor-suppressive role inducing cell apoptosis and DDP chemosensitivity via recruiting ZFP36L2 to bind to the 3' untranslated region of BCL2, reducing the stability of BCL2 mRNA and thus activating the apoptotic signal. CONCLUSIONS This study demonstrated a novel and critical role of LINC00173. It was transcriptionally repressed by DDP-activated PI3K/AKT/c-Myc signal in LUAD, promoting DDP-acquired chemotherapeutic resistance by regulating miR-1275 to suppress PROCA1/ZFP36L2-induced BCL2 degradation, which led to apoptotic signal reduction. These data were not consistent with the previously described role of LINC00173 in SCLC or LUSC, which suggested that LINC00173 could play fine-tuned DDP resistance roles in different pathological subtypes of lung cancer. This study demonstrated that the diminished expression of LINC00173 might serve as an indicator of DDP-acquired resistance in LUAD.
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Affiliation(s)
- Xingyu Tao
- grid.410737.60000 0000 8653 1072Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436 China
| | - Yang Li
- grid.410737.60000 0000 8653 1072Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436 China
| | - Songqing Fan
- grid.452708.c0000 0004 1803 0208The Second Xiangya Hospital of Central South University, Changsha, 410008 China
| | - Liyang Wu
- grid.410737.60000 0000 8653 1072Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436 China
| | - Jianyang Xin
- grid.410737.60000 0000 8653 1072Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436 China
| | - Yun Su
- grid.410737.60000 0000 8653 1072Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436 China
| | - Xiaoyang Xian
- grid.410737.60000 0000 8653 1072Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436 China
| | - Yingying Huang
- grid.410737.60000 0000 8653 1072Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436 China
| | - Rongquan Huang
- grid.410737.60000 0000 8653 1072Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 511436 China
| | - Weiyi Fang
- grid.284723.80000 0000 8877 7471Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515 China ,grid.284723.80000 0000 8877 7471Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510315 China
| | - Zhen Liu
- grid.284723.80000 0000 8877 7471Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510315 China ,grid.410737.60000 0000 8653 1072Department of Pathology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436 China
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7
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Cook CP, Taylor M, Liu Y, Schmidt R, Sedgewick A, Kim E, Hailer A, North JP, Harirchian P, Wang H, Kashem SW, Shou Y, McCalmont TC, Benz SC, Choi J, Purdom E, Marson A, Ramos SBV, Cheng JB, Cho RJ. A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity. Cell Rep Med 2022; 3:100715. [PMID: 35977472 PMCID: PMC9418858 DOI: 10.1016/j.xcrm.2022.100715] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/21/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
The homeostatic mechanisms that fail to restrain chronic tissue inflammation in diseases, such as psoriasis vulgaris, remain incompletely understood. We profiled transcriptomes and epitopes of single psoriatic and normal skin-resident T cells, revealing a gradated transcriptional program of coordinately regulated inflammation-suppressive genes. This program, which is sharply suppressed in lesional skin, strikingly restricts Th17/Tc17 cytokine and other inflammatory mediators on the single-cell level. CRISPR-based deactivation of two core components of this inflammation-suppressive program, ZFP36L2 and ZFP36, replicates the interleukin-17A (IL-17A), granulocyte macrophage-colony-stimulating factor (GM-CSF), and interferon gamma (IFNγ) elevation in psoriatic memory T cells deficient in these transcripts, functionally validating their influence. Combinatoric expression analysis indicates the suppression of specific inflammatory mediators by individual program members. Finally, we find that therapeutic IL-23 blockade reduces Th17/Tc17 cell frequency in lesional skin but fails to normalize this inflammatory-suppressive program, suggesting how treated lesions may be primed for recurrence after withdrawal of treatment.
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Affiliation(s)
- Christopher P Cook
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Mark Taylor
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Yale Liu
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA; Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, ShaanXi 710004, P.R. China
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | | | - Esther Kim
- Division of Plastic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ashley Hailer
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey P North
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Paymann Harirchian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Hao Wang
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Sakeen W Kashem
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Yanhong Shou
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Timothy C McCalmont
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA; Golden State Dermatology Associates, Walnut Creek, CA, USA
| | | | - Jaehyuk Choi
- Department of Dermatology, Northwestern University, Evanston, IL, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Silvia B V Ramos
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA.
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA.
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8
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Kishigami F, Tanaka Y, Yamamoto Y, Ueno T, Kojima S, Sato K, Inoue S, Sugaya S, Ishihara S, Mano H, Kawazu M. Exploration of predictive biomarkers for postoperative recurrence of stage II/III colorectal cancer using genomic sequencing. Cancer Med 2022; 11:3457-3470. [PMID: 35343095 PMCID: PMC9487878 DOI: 10.1002/cam4.4710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/24/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022] Open
Abstract
Postoperative recurrence of colorectal cancer (CRC) eventually leads to therapeutic failure; therefore, treatment strategies based on accurate prediction of recurrence are urgently required. To identify biomarkers that can predict treatment outcomes, we compared the mutational profiles of surgically resected specimens from patients with recurrent cancer with those from patients with non‐recurrent cancer. Target sequencing, whole‐exome sequencing (WES), or whole‐genome sequencing (WGS) was performed on 89 and 58 tumors from recurrent and non‐recurrent cases, respectively. WGS revealed the driver mutations that were not detected with target sequencing or WES, including the structural variations affecting ZFP36L2. Loss of function of ZFP36L2 was frequently observed in primary tumors from recurrent cases. Furthermore, the recurrence‐free survival of patients with loss of function of ZFP36L2 was significantly shorter relative to patients with no loss of ZFP36L2 function. In summary, the study demonstrated that detailed genomic analysis could help improve precision medicine for CRC.
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Affiliation(s)
- Fumishi Kishigami
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Surgical Oncology, The University of Tokyo, Tokyo, Japan
| | - Yosuke Tanaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Yamamoto
- Department of Surgical Oncology, The University of Tokyo, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuhito Sato
- Department of Surgical Oncology, The University of Tokyo, Tokyo, Japan
| | - Satoshi Inoue
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Saori Sugaya
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
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Su W, Liao M, Tan H, Chen Y, Zhao R, Jin W, Zhu S, Zhang Y, He L, Liu B. Identification of autophagic target RAB13 with small-molecule inhibitor in low-grade glioma via integrated multi-omics approaches coupled with virtual screening of traditional Chinese medicine databases. Cell Prolif 2021; 54:e13135. [PMID: 34632655 PMCID: PMC8666277 DOI: 10.1111/cpr.13135] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/08/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
Objectives Autophagy, a highly conserved lysosomal degradation process in eukaryotic cells, has been widely reported closely related to the progression of many types of human cancers, including LGG; however, the intricate relationship between autophagy and LGG remains to be clarified. Materials and methods Multi‐omics methods were used to integrate omics data to determine potential autophagy regulators in LGG. The expression of ZFP36L2 and RAB13 in SW1088 cells was experimentally manipulated using cDNAs and small interfering RNAs (siRNA). RT‐qPCR detects RNAi gene knockout and cDNA overexpression efficiency. The expression levels of proteins in SW1088 cells were evaluated using Western blot analysis and immunofluorescence analysis. Homology modelling and molecular docking were used to identify compounds from Multi‐Traditional Chinese Medicine (TCM) Databases. The apoptosis ratios were determined by flow cytometry analysis of Annexin‐V/PI double staining. We detect the number of autophagosomes by GFP‐MRFP‐LC3 plasmid transfection to verify the process of autophagy flow. Results We integrated various omics data from LGG, including EXP, MET and CNA data, with the SNF method and the LASSO algorithm, and identified ZFP36L2 and RAB13 as positive regulators of autophagy, which are closely related to the core autophagy regulators. Both transcription level and protein expression level of the four autophagy regulators, including ULK1, FIP200, ATG16L1 and ATG2B, and LC3 puncta were increased by ZFP36L2 and RAB13 overexpression. In addition, RAB13 participates in autophagy through ATG2B, FIP200, ULK1, ATG16L1 and Beclin‐1. Finally, we screened multi‐TCM databases and identified gallic acid as a novel potential RAB13 inhibitor, which was confirmed to negatively regulate autophagy as well as to induce cell death in SW1088 cells. Conclusion Our study identified the key autophagic regulators ZFP36L2 and Rab13 in LGG progression, and demonstrated that gallic acid is a small molecular inhibitor of RAB13, which negatively regulates autophagy and provides a possible small molecular medicine for the subsequent treatment of LGG.
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Affiliation(s)
- Wei Su
- Department of Neurology and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Minru Liao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Huidan Tan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yanmei Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Rongyan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Wenke Jin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shiou Zhu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yiwen Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Li He
- Department of Neurology and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, China
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Che Mat MF, Mohamad Hanif EA, Abdul Murad NA, Ibrahim K, Harun R, Jamal R. Silencing of ZFP36L2 increases sensitivity to temozolomide through G2/M cell cycle arrest and BAX mediated apoptosis in GBM cells. Mol Biol Rep 2021; 48:1493-1503. [PMID: 33590411 DOI: 10.1007/s11033-021-06144-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Despite the advancements in primary brain tumour diagnoses and treatments, the mortality rate remains high, particularly in glioblastoma (GBM). Chemoresistance, predominantly in recurrent cases, results in decreased mean survival of patients with GBM. We aimed to determine the chemosensitisation and oncogenic characteristics of zinc finger protein 36-like 2 (ZFP36L2) in LN18 GBM cells via RNA interference (RNAi) delivery. We conducted a meta-analysis of microarray datasets and RNAi screening using pooled small interference RNA (siRNA) to identify the druggable genes responsive to GBM chemosensitivity. Temozolomide-resistant LN18 cells were used to evaluate the effects of gene silencing on chemosensitisation to the sub-lethal dose (1/10 of the median inhibitory concentration [IC50]) of temozolomide. ZFP36L2 protein expression was detected by western blotting. Cell viability, proliferation, cell cycle and apoptosis assays were carried out using commercial kits. A human apoptosis array kit was used to determine the apoptosis pathway underlying chemosensitisation by siRNA against ZFP36L2 (siZFP36L2). Statistical analyses were performed using one-way analysis of variance; p > 0.05 was considered significant. The meta-analysis and RNAi screening identified ZFP36L2 as a potential marker of GBM. ZFP36L2 knockdown significantly induced apoptosis (p < 0.05). Moreover, ZFP36L2 inhibition led to increased cell cycle arrest and decreased cell proliferation. Downstream analysis showed that the sub-lethal dose of temozolomide and siZFP26L2 caused major upregulation of BCL2-associated X, apoptosis regulator (BAX). ZFP36L2 has oncogenic and chemosensitive characteristics and may play an important role in gliomagenesis through cell proliferation, cell cycle arrest and apoptosis. This suggests that RNAi combined with chemotherapy treatment such as temozolomide may be a potential GBM therapeutic intervention in the future.
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Affiliation(s)
- Mohd Firdaus Che Mat
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Ezanee Azlina Mohamad Hanif
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Nor Azian Abdul Murad
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Kamariah Ibrahim
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Roslan Harun
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia.
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Medical Centre, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia.
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11
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Makita S, Takatori H, Iwata A, Tanaka S, Furuta S, Ikeda K, Suto A, Suzuki K, Ramos SBV, Nakajima H. RNA-Binding Protein ZFP36L2 Downregulates Helios Expression and Suppresses the Function of Regulatory T Cells. Front Immunol 2020; 11:1291. [PMID: 32655569 PMCID: PMC7324482 DOI: 10.3389/fimmu.2020.01291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
The zinc finger protein 36-like 2, ZFP36L2, is a member of a small family of RNA-binding proteins composed by ZFP36 (also known as tristetraprolin, TTP), ZFP36L1 and ZFP36L2 in humans, with corresponding murine orthologs. These proteins bind to adenine uridine-rich element (ARE) in the 3′untranslated region of target messenger RNA and stimulate target degradation. ZFP36 functions as an anti-inflammatory modulator in murine models of inflammatory diseases by down-regulating the production of inflammatory cytokines such as tumor necrosis factor-α. However, how ZFP36L1 and ZFP36L2 alter the function of CD4+ T cells is not completely understood. We addressed this issue by searching for the target genes of ZFP36L2 by comprehensive transcriptome analysis. We observed that ZFP36L2 is highly expressed in naïve CD4+ T cells; however, when CD4+ T cells are stimulated through their T cell receptors, ZFP36L2 expression is rapidly reduced in both humans and mice. Among CD4+ T cell populations, the expression levels of ZFP36L2 in regulatory T cells (Tregs) were significantly lower than those in naïve or effector CD4+ T cells. RNA-sequence analysis revealed that the forced expression of ZFP36L2 decreased Ikzf2 (encoding Helios) expression in Foxp3+ Tregs and inhibited the ability of induced Tregs (iTregs). ZFP36L2 directly bound to and destabilized the 3′untranslated region of Ikzf2 mRNA, which contains AU-rich elements. These results indicate that ZFP36L2 reduces the expression of Ikzf2 and suppresses iTreg function, raising the interesting possibility that the inhibition of ZFP36L2 in iTregs could be a therapeutic strategy for autoimmune diseases.
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Affiliation(s)
- Sohei Makita
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Takatori
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Rheumatology, Hamamatsu Medical Center, Shizuoka, Japan
| | - Arifumi Iwata
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shigeru Tanaka
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shunsuke Furuta
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kei Ikeda
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akira Suto
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kotaro Suzuki
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Silvia B V Ramos
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
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12
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Liu J, Lu W, Liu S, Wang Y, Li S, Xu Y, Xing H, Tang K, Tian Z, Rao Q, Wang M, Wang J. ZFP36L2, a novel AML1 target gene, induces AML cells apoptosis and inhibits cell proliferation. Leuk Res 2018. [PMID: 29518627 DOI: 10.1016/j.leukres.2018.02.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The t(8;21)(q22;q22) translocation generated the fusion protein AML1-ETO. AML1-ETO recruits histone deacetylase (HDAC) complex via its ETO part to repress AML1-mediated transactivation. Our previous study demonstrated that HDAC inhibitor phenylbutyrate (PB) could induce AML1-ETO positive leukemia cell line Kasumi-1 cells to undergo differentiation and apoptosis accompanied by significant changes in gene expression profile. ZFP36L2 was one of the up-regulated genes in Kasumi-1 cells induced by PB treatment. In this study, ZFP36L2 was found to express at a lower level in acute myeloid leukemia (AML) patients with t(8;21) compared to AML patients without t(8;21). In order to investigate the correlation between the expression of ZFP36L2 and AML1 or AML1-ETO, the putative AML1 binding sites in the enhancer/promoter region of ZFP36L2 gene were predicted through the bioinformatics analysis. And the biological function of ZFP36L2 in leukemic cells was further investigated. The results demonstrated that AML1 could transactivate ZFP36L2 significantly by binding on specific site of the ZFP36L2 promoter sequence. And overexpression of ZFP36L2 in leukemia cells could inhibit the cell proliferation, promote cell-cycle arrest in G0/G1 phase and induce the cell apoptosis. In conclusion, ZFP36L2 could be transactivated by AML1, which subsequently induced cell-cycle arrest and apoptosis of leukemia cells.
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Affiliation(s)
- Jia Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Wenting Lu
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Shuang Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Ying Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Saisai Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yingxi Xu
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Haiyan Xing
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Kejing Tang
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Zheng Tian
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Qing Rao
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Min Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
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13
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Dumdie JN, Cho K, Ramaiah M, Skarbrevik D, Mora-Castilla S, Stumpo DJ, Lykke-Andersen J, Laurent LC, Blackshear PJ, Wilkinson MF, Cook-Andersen H. Chromatin Modification and Global Transcriptional Silencing in the Oocyte Mediated by the mRNA Decay Activator ZFP36L2. Dev Cell 2018; 44:392-402.e7. [PMID: 29408237 DOI: 10.1016/j.devcel.2018.01.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 06/21/2017] [Accepted: 01/05/2018] [Indexed: 12/19/2022]
Abstract
Global transcriptional silencing is a highly conserved mechanism central to the oocyte-to-embryo transition. We report the unexpected discovery that global transcriptional silencing in oocytes depends on an mRNA decay activator. Oocyte-specific loss of ZFP36L2 an RNA-binding protein that promotes AU-rich element-dependent mRNA decay prevents global transcriptional silencing and causes oocyte maturation and fertilization defects, as well as complete female infertility in the mouse. Single-cell RNA sequencing revealed that ZFP36L2 downregulates mRNAs encoding transcription and chromatin modification regulators, including a large group of mRNAs for histone demethylases targeting H3K4 and H3K9, which we show are bound and degraded by ZFP36L2. Oocytes lacking Zfp36l2 fail to accumulate histone methylation at H3K4 and H3K9, marks associated with the transcriptionally silent, developmentally competent oocyte state. Our results uncover a ZFP36L2-dependent mRNA decay mechanism that acts as a developmental switch during oocyte growth, triggering wide-spread shifts in chromatin modification and global transcription.
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Affiliation(s)
- Jennifer N Dumdie
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kyucheol Cho
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Skarbrevik
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sergio Mora-Castilla
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Deborah J Stumpo
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Louise C Laurent
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA; Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, NC 27703, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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14
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Ball CB, Solem AC, Meganck RM, Laederach A, Ramos SBV. Impact of RNA structure on ZFP36L2 interaction with luteinizing hormone receptor mRNA. RNA 2017; 23:1209-1223. [PMID: 28455422 PMCID: PMC5513066 DOI: 10.1261/rna.060467.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/16/2017] [Indexed: 06/07/2023]
Abstract
ZFP36L2 (L2) destabilizes AU-rich element (ARE)-containing transcripts and has been implicated in female fertility. We have shown that only one of three putative AREs within the 3' UTR of murine luteinizing hormone receptor mRNA, ARE2197 (UAUUUAU), is capable of interacting with L2. To assess whether structural elements of ARE2197 could explain this unique binding ability, we performed whole-transcript SHAPE-MaP (selective 2' hydroxyl acylation by primer extension-mutational profiling) of the full-length mLHR mRNA. The data revealed that the functional ARE2197 is located in a hairpin loop structure and most nucleotides are highly reactive. In contrast, each of the nonbinding AREs, 2301 and 2444, contains only a pentamer AUUUA; and in ARE2301 much of the ARE sequence is poorly accessible. Because the functional mARE was also found to be conserved in humans at the sequence level (ARE 2223), we decided to investigate whether binding and structure are also preserved. Similar to mouse, only one ARE in hLHR mRNA is capable of binding to L2; and it is also located in a hairpin structure, based on our SHAPE-MaP data. To investigate the role of secondary structure in the binding, we mutated specific nucleotides in both functional AREs. Mutations in the flexible stem region proximal to the loop that enforce strong base-pairing, drastically reduced L2 binding affinity; this confirms that the structural context is critical for L2 recognition of hARE2223. Collectively, our results suggest that a combination of minimal ARE sequence, placement of the ARE in a hairpin loop, and stem flexibility mediate high-affinity L2 binding to hLHR mRNA.
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Affiliation(s)
- Christopher B Ball
- Biochemistry and Biophysics Department, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Amanda C Solem
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Rita M Meganck
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Alain Laederach
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Bioinformatics and Computational Biology Program, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Silvia B V Ramos
- Biochemistry and Biophysics Department, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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15
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Abstract
To identify novel cancer-related genes targeted by copy number alterations, we performed genomic profiling of T-cell acute lymphoblastic leukemia (T-ALL) cell lines. In 3/8, we identified a shared deletion at chromosomal position 2p16.3-p21. Within the minimally deleted region, we recognized several candidate tumor suppressor (TS) genes, including FBXO11 and FOXN2. An additional deletion at chromosome 14q23.2-q32.11 included FOXN3, highlighting this class of FOX genes as potential TS. Quantitative expression analyses of FBXO11, FOXN2, and FOXN3 confirmed reduced transcript levels in the identified cell lines. Moreover, reduced expression of these genes was also observed in about 7% of T-ALL patients, showing their clinical relevance in this malignancy. Bioinformatic analyses revealed concurrent reduction of FOXN2 and/or FOXN3 together with homeobox gene ZHX1. Consistently, experiments demonstrated that both FOXN2 and FOXN3 directly activated transcription of ZHX1. Taken together, we identified novel TS genes forming a regulatory network in T-cell development and leukemogenesis.
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Affiliation(s)
- Stefan Nagel
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Claudia Pommerenke
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Corinna Meyer
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Maren Kaufmann
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Roderick A F MacLeod
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Hans G Drexler
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
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Cargnin F, Nechiporuk T, Müllendorff K, Stumpo DJ, Blackshear PJ, Ballas N, Mandel G. An RNA binding protein promotes axonal integrity in peripheral neurons by destabilizing REST. J Neurosci 2014; 34:16650-61. [PMID: 25505318 DOI: 10.1523/JNEUROSCI.1650-14.2014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The RE1 Silencing Transcription Factor (REST) acts as a governor of the mature neuronal phenotype by repressing a large consortium of neuronal genes in non-neuronal cells. In the developing nervous system, REST is present in progenitors and downregulated at terminal differentiation to promote acquisition of mature neuronal phenotypes. Paradoxically, REST is still detected in some regions of the adult nervous system, but how REST levels are regulated, and whether REST can still repress neuronal genes, is not known. Here, we report that homeostatic levels of REST are maintained in mature peripheral neurons by a constitutive post-transcriptional mechanism. Specifically, using a three-hybrid genetic screen, we identify the RNA binding protein, ZFP36L2, associated previously only with female fertility and hematopoiesis, and show that it regulates REST mRNA stability. Dorsal root ganglia in Zfp36l2 knock-out mice, or wild-type ganglia expressing ZFP36L2 shRNA, show higher steady-state levels of Rest mRNA and protein, and extend thin and disintegrating axons. This phenotype is due, at least in part, to abnormally elevated REST levels in the ganglia because the axonal phenotype is attenuated by acute knockdown of REST in Zfp36l2 KO DRG explants. The higher REST levels result in lower levels of target genes, indicating that REST can still fine-tune gene expression through repression. Thus, REST levels are titrated in mature peripheral neurons, in part through a ZFP36L2-mediated post-transcriptional mechanism, with consequences for axonal integrity.
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Lin NY, Lin TY, Yang WH, Wang SC, Wang KT, Su YL, Jiang YW, Chang GD, Chang CJ. Differential expression and functional analysis of the tristetraprolin family during early differentiation of 3T3-L1 preadipocytes. Int J Biol Sci 2012; 8:761-77. [PMID: 22701344 PMCID: PMC3371571 DOI: 10.7150/ijbs.4036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 05/15/2012] [Indexed: 01/09/2023] Open
Abstract
The tristetraprolin (TTP) family comprises zinc finger-containing AU-rich element (ARE)-binding proteins consisting of three major members: TTP, ZFP36L1, and ZFP36L2. The present study generated specific antibodies against each TTP member to evaluate its expression during differentiation of 3T3-L1 preadipocytes. In contrast to the inducible expression of TTP, results indicated constitutive expression of ZFP36L1 and ZFP36L2 in 3T3-L1 preadipocytes and their phosphorylation in response to differentiation signals. Physical RNA pull-down and functional luciferase assays revealed that ZFP36L1 and ZFP36L2 bound to the 3' untranslated region (UTR) of MAPK phosphatase-1 (MKP-1) mRNA and downregulated Mkp-1 3'UTR-mediated luciferase activity. Mkp-1 is an immediate early gene for which the mRNA is transiently expressed in response to differentiation signals. The half-life of Mkp-1 mRNA was longer at 30 min of induction than at 1 h and 2 h of induction. Knockdown of TTP or ZFP36L2 increased the Mkp-1 mRNA half-life at 1 h of induction. Knockdown of ZFP36L1, but not ZFP36L2, increased Mkp-1 mRNA basal levels via mRNA stabilization and downregulated ERK activation. Differentiation induced phosphorylation of ZFP36L1 through ERK and AKT signals. Phosphorylated ZFP36L1 then interacted with 14-3-3, which might decrease its mRNA destabilizing activity. Inhibition of adipogenesis also occurred in ZFP36L1 and TTP knockdown cells. The findings indicate that the differential expression of TTP family members regulates immediate early gene expression and modulates adipogenesis.
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Affiliation(s)
- Nien-Yi Lin
- 1. Institute of Biological Chemistry, Academia Sinica, 128, Academia Road Sec 2, Nankang, Taipei 115, Taiwan
| | - Tzi-Yang Lin
- 2. Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, 1 Roosevelt Road Sec 4, Taipei 106, Taiwan
| | - Wen-Hsuan Yang
- 2. Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, 1 Roosevelt Road Sec 4, Taipei 106, Taiwan
| | - Shun-Chang Wang
- 1. Institute of Biological Chemistry, Academia Sinica, 128, Academia Road Sec 2, Nankang, Taipei 115, Taiwan
| | - Kuan-Ting Wang
- 2. Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, 1 Roosevelt Road Sec 4, Taipei 106, Taiwan
| | - Yu-Lun Su
- 2. Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, 1 Roosevelt Road Sec 4, Taipei 106, Taiwan
| | - Yu-Wun Jiang
- 2. Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, 1 Roosevelt Road Sec 4, Taipei 106, Taiwan
| | - Geen-Dong Chang
- 2. Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, 1 Roosevelt Road Sec 4, Taipei 106, Taiwan
| | - Ching-Jin Chang
- 1. Institute of Biological Chemistry, Academia Sinica, 128, Academia Road Sec 2, Nankang, Taipei 115, Taiwan
- 2. Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, 1 Roosevelt Road Sec 4, Taipei 106, Taiwan
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