1
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Chen J, Zeng C, Jin J, Zhang P, Zhang Y, Zhang H, Li Y, Guan H. Overexpression of FHL1 suppresses papillary thyroid cancer proliferation and progression via inhibiting Wnt/β-catenin pathway. Endocrine 2024; 85:238-249. [PMID: 38191984 DOI: 10.1007/s12020-023-03675-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/25/2023] [Indexed: 01/10/2024]
Abstract
PURPOSE The four and a half LIM domain protein 1 (FHL1) has been found to act as a tumor suppressor in several cancers. However, the clinical and functional significance, as well as underlying molecular mechanisms of FHL1 in papillary thyroid cancer (PTC) are largely unknown. METHODS Bioinformatics analyses, qRT-PCR and Western blotting were used to investigate the expression of FHL1 in PTC. Cell proliferation was measured using CCK8, Edu, colony formation, and flow cytometry assays. Cell migration and invasion were examined by wound healing and Transwell assays. qRT-PCR, Western blot, immunofluorescence and Top/Fop reporter assays were performed to assess the underlying mechanisms. RESULTS FHL1 expression was significantly downregulated in PTC. FHL1 downregulation negatively correlated with stage, T classification, and N classification of the patients. The downregulation of FHL1 is associated with poor prognosis. Overexpression of FHL1 inhibited PTC cells' proliferation, invasion, migration and Wnt/β-catenin pathway activity. LiCl partially restored the inhibitory effects of FHL1 on aggressive phenotypes and Wnt/β-catenin pathway activity of PTC cells. CONCLUSION FHL1 is downregulated in PTC and its expression is associated with better clinical outcomes for patients with the disease. FHL1 acts as a tumor suppressor via, at least partially, suppressing Wnt/β-catenin pathway.
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Affiliation(s)
- Junxin Chen
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chuimian Zeng
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jiewen Jin
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Pengyuan Zhang
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yilin Zhang
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hanrong Zhang
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanbing Li
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Hongyu Guan
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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2
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Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms. Life Sci Alliance 2024; 7:e202302501. [PMID: 38803235 PMCID: PMC11109482 DOI: 10.26508/lsa.202302501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the developmental transcription factor CCAAT/enhancer-binding protein α (C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This choice between alternative start sites depends on sequence features of the CEBPA transcript, including a regulatory uORF, but the molecular basis is not fully understood. Here, we identify the factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescent reporter coupled with CRISPRi screening. Our screen uncovered a role of the ribosome rescue factor PELOTA (PELO) in promoting the expression of the longer C/EBPα isoform by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin kinase. Our work uncovers further links between ribosome recycling and translation reinitiation that regulate a key transcription factor, with implications for normal hematopoiesis and leukemogenesis.
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Affiliation(s)
- Samantha G Fernandez
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lucas Ferguson
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Nicholas T Ingolia
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
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3
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Wang W, Yuan H, Han J, Liu W. PCLassoLog: A protein complex-based, group Lasso-logistic model for cancer classification and risk protein complex discovery. Comput Struct Biotechnol J 2022; 21:365-377. [PMID: 36582441 PMCID: PMC9791601 DOI: 10.1016/j.csbj.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Risk gene identification has attracted much attention in the past two decades. Since most genes need to be translated into proteins and cooperate with other proteins to form protein complexes to carry out cellular functions, which significantly extends the functional diversity of individual proteins, revealing the molecular mechanism of cancer from a comprehensive perspective needs to shift from identifying individual risk genes toward identifying risk protein complexes. Here, we embed protein complexes into the regularized learning framework and propose a protein complex-based, group Lasso-logistic model (PCLassoLog) to discover risk protein complexes. Experiments on deep proteomic data of two cancer types show that PCLassoLog yields superior predictive performance on independent datasets. More importantly, PCLassoLog identifies risk protein complexes that not only contain individual risk proteins but also incorporate close partners that synergize with them. Furthermore, selection probabilities are calculated and two other protein complex-based models are proposed to complement PCLassoLog in identifying reliable risk protein complexes. Based on PCLassoLog, a pan-cancer analysis is performed to identify risk protein complexes in 12 cancer types. Finally, PCLassoLog is used to discover risk protein complexes associated with gene mutation. We implement all protein complex-based models as an R package PCLassoReg, which may serve as an effective tool to discover risk protein complexes in various contexts.
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Affiliation(s)
- Wei Wang
- College of Science, Heilongjiang Institute of Technology, Harbin 150050, China
| | - Haiyan Yuan
- College of Science, Heilongjiang Institute of Technology, Harbin 150050, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China,Corresponding authors.
| | - Wei Liu
- College of Science, Heilongjiang Institute of Technology, Harbin 150050, China,Corresponding authors.
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4
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Huang Z, Yu C, Yu L, Shu H, Zhu X. The Roles of FHL3 in Cancer. Front Oncol 2022; 12:887828. [PMID: 35686099 PMCID: PMC9171237 DOI: 10.3389/fonc.2022.887828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/18/2022] [Indexed: 12/19/2022] Open
Abstract
The four and a half LIM domain protein 3, also named the LIM-protein FHL3, belongs to the LIM-only family. Based on the special structure of LIM-only proteins, FHL3 can perform significant functions in muscle proliferation and cardiovascular diseases by regulating cell growth and signal transduction. In recent years, there has been increasing evidence of a relation between FHLs and tumor biology, since FHL3 is often overexpressed or downregulated in different cancers. On the one hand, FHL3 can function as a tumor suppressor and influence the expression of downstream genes. On the other hand, FHL3 can also play a role as an oncoprotein in some cancers to promote tumor progression via phosphorylation. Thus, FHL3 is proposed to have a dual effect on cancer progression, reflecting its complex roles in cancer. This review focuses on the roles of FHL3 in cancer progression and discusses the interaction of FHL3 with other proteins and transcription factors. Finally, the clinical significance of FHL3 for the treatment of cancers is discussed.
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Affiliation(s)
- Zhenjun Huang
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Chengpeng Yu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liqing Yu
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Hongxin Shu
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Xianhua Zhu
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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5
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Hou Y, Lin J, Wang D, Zhang Y, Liang Q, Chen N, Wu J, Wu W, Liu X, Ni P. The circular RNA circ_GRHPR promotes NSCLC cell proliferation and invasion via interactions with the RNA-binding protein PCBP2. Clin Exp Pharmacol Physiol 2021; 48:1171-1181. [PMID: 33987874 PMCID: PMC8362189 DOI: 10.1111/1440-1681.13523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/05/2021] [Accepted: 05/09/2021] [Indexed: 01/22/2023]
Abstract
As the most common malignancy, lung cancer is characterised by high rates of occurrence and mortality. Although circular RNAs (circRNAs) are known to act as important regulators in cancer, their role in lung cancer remains poorly understood. In this study, circ_GRHPR expression was found to be significantly upregulated in the serum of five patients with non-small cell lung cancer (NSCLC), compared to that in healthy controls. It is expressed at high levels in NSCLC cell lines, as revealed by qRT-PCR analysis. Functionally, we demonstrated that circ_GRHPR promotes NSCLC proliferation and invasion in vitro and in vivo by cell proliferation, transwell, cell cycle, and tumour-forming assays. Mechanistically, RNA pull-down and RNA immunoprecipitation assays showed that circ_GRHPR interacts with the RNA-binding protein poly(rC)-binding protein 2 (PCBP2) and regulates its subcellular localisation by forming the circ_GRHPR/PCBP2 complex, localizing PCBP2 mainly in the cytoplasm and reducing the proportion found in the nucleus. Furthermore, we demonstrated that four-and-a-half LIM-only protein 3 (FHL3) is a tumour-stimulating factor in NSCLC that interacts with and is influenced by PCBP2. Circ_GRHPR increased FHL3 expression in the nucleus of NSCLC cells by decreasing PCBP2 expression therein and promoting the proliferation and invasion of NSCLC cells. Therefore, our study identified that circ_GRHPR promotes NSCLC proliferation and invasion, providing a possible explanation for its mechanism of action.
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Affiliation(s)
- Yanyan Hou
- Department of Laboratory MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jiafei Lin
- Department of Clinical Laboratory MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Danyang Wang
- Department of Laboratory MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yingwei Zhang
- Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing UniversityNanjingChina
| | - Qiuli Liang
- Department of Laboratory MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Ning Chen
- Department of Laboratory MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jiemin Wu
- Department of Laboratory MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Weiqi Wu
- Department of OncologyTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiangfan Liu
- Department of Laboratory MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Peihua Ni
- Department of Laboratory MedicineRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
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6
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Cao G, Li P, He X, Jin M, Li M, Chen S, Xu X, Sun Q, Xiong M, Chen B. FHL3 Contributes to EMT and Chemotherapy Resistance Through Up-Regulation of Slug and Activation of TGF β/Smad-Independent Pathways in Gastric Cancer. Front Oncol 2021; 11:649029. [PMID: 34150617 PMCID: PMC8213027 DOI: 10.3389/fonc.2021.649029] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/09/2021] [Indexed: 12/29/2022] Open
Abstract
Background Gastric cancer presents high risk of metastasis and chemotherapy resistance. Hence, it is important to understand the mechanisms of gastric cancer distant metastasis and chemotherapeutic resistance. Our previous study has revealed Four and a Half LIM Domains 3 (FHL3) plays as a binding partner of Glycogen Synthase Kinase 3 Beta (GSK3β), promoted tumor metastasis in pancreatic cancer. However, the role of FHL3 in gastric cancer still remains unclear. Methods TCGA database and clinical samples are used for exploring the role of FHL3 in disease progression and prognosis. Oxaliplatin (OHP) resistance cell lines were established to study the role of FHL3 in chemotherapy resistance. The experiments about cell proliferation, apoptosis, and metastasis were performed to measure the chemotherapy effects of sh-FHL3 on gastric cancer cell lines and in vivo. That FHL3 changed the EMT phenotype was verified by western blot. Finally, we explored the mechanism of FHL3-mediated EMT and chemotherapy resistance. Results mRNA and protein level of FHL3 were significantly up-regulated in gastric cancer tissues when compared with adjacent tissue. FHL3 higher expression is always accompanied with higher TNM stage and worse overall survival. FHL3 over-expressed could lead to OHP resistance. Knockdown of FHL3 slightly inhibited the cell growth, while it obviously sensitized the chemotherapy in vivo and in vitro. In addition, down-regulation of FHL3 increased the mesenchymal markers, such as Slug, Snail, Twist Family BHLH Transcription Factor 1 (Twist1), and Vimentin, while it decreased the epithelial marker E-cadherin. Cell and animal experiments also proved that down-regulation of FHL3 can decrease cancer cell metastasis. For mechanism study, FHL3 knockdown down-regulated the expression level of Mitogen-Activated Protein Kinase (MAPK)/Extracellular Regulated Protein Kinase (ERK) pathway and Transforming Growth Factor-β (TGFβ)/Phosphatidylinositol 3-Kinase (PI3K)/protein kinase B(Akt)/GSK3β-(Ring Finger Protein 146) RNF146/ubiquitin pathway. FHL3 competitively bonded the ubiquitin complex (Slug/GSK3β/RNF146) with Slug and inhibited ubiquitination of Slug. Mesenchymal phenotype cells hold higher level of Multidrug Resistance Gene1 (MDR1), and the FHL3 knockdown reverts the MDR1 in this type cell. Conclusion FHL3 high expression contributed to EMT and chemotherapy resistance via MAPK, and PI3K pathways were activated. FHL3 competitively bonded the ubiquitin complex with Slug, resulting in the up-regulation of Slug and leading to metastasis of gastric cancer.
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Affiliation(s)
- Guodong Cao
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Pengping Li
- Department of Breast Surgery, The First People's Hospital of Xiaoshan District, Hangzhou, China
| | - Xiaobo He
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mengyao Jin
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mengying Li
- Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Sihan Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xin Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiang Sun
- Jiangsu Key Laboratory of Biological Cancer, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Maoming Xiong
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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7
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Liu S, Hu Y, Wu S, He Y, Deng L. MicroRNA-663 Regulates Melanoma Progression by Inhibiting FHL3. Technol Cancer Res Treat 2020; 19:1533033820957000. [PMID: 33000682 PMCID: PMC7533922 DOI: 10.1177/1533033820957000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
microRNA-663a (miR-663a) was reported to be highly expressed in cancers. However, its roles in melanoma progression remain unclear. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted to measure miR-663a expression level in melanoma cell lines and normal cells. Cell counting kit-8 assay, wound-healing assay, and transwell invasion assay were conducted to analyze biological roles of miR-663a in melanoma. Luciferase activity reporter assay was conducted to validate the connection of miR-663a and Four and a half LIM domain (FHL) protein 3 (FHL3) in melanoma. Our results showed miR-663a expression level was significantly increased in melanoma cells compared with normal cells. Silencing miR-663a expression suppresses melanoma cell proliferation, migration, and invasion in vitro. Moreover, FHL3 was validated as a functional target of miR-663a. Knockdown of FHL3 partially rescued the inhibitory effects of miR-663a inhibitor on melanoma cell behaviors. Together, our work provided evidence that miR-663a functions as an oncogenic miRNA in melanoma.
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Affiliation(s)
- Saijun Liu
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yunfeng Hu
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shi Wu
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yong He
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Liehua Deng
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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8
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Brandes N, Linial N, Linial M. PWAS: proteome-wide association study-linking genes and phenotypes by functional variation in proteins. Genome Biol 2020; 21:173. [PMID: 32665031 PMCID: PMC7386203 DOI: 10.1186/s13059-020-02089-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 07/01/2020] [Indexed: 12/16/2022] Open
Abstract
We introduce Proteome-Wide Association Study (PWAS), a new method for detecting gene-phenotype associations mediated by protein function alterations. PWAS aggregates the signal of all variants jointly affecting a protein-coding gene and assesses their overall impact on the protein's function using machine learning and probabilistic models. Subsequently, it tests whether the gene exhibits functional variability between individuals that correlates with the phenotype of interest. PWAS can capture complex modes of heritability, including recessive inheritance. A comparison with GWAS and other existing methods proves its capacity to recover causal protein-coding genes and highlight new associations. PWAS is available as a command-line tool.
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Affiliation(s)
- Nadav Brandes
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Nathan Linial
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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9
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FHL3 promotes pancreatic cancer invasion and metastasis through preventing the ubiquitination degradation of EMT associated transcription factors. Aging (Albany NY) 2020; 12:53-69. [PMID: 31935687 PMCID: PMC6977653 DOI: 10.18632/aging.102564] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/20/2019] [Indexed: 12/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is intractable due to its strong invasiveness and metastatic ability. Epithelial-mesenchymal transition (EMT) is the pivotal driver of tumor invasion and metastasis. The four-and-a-half LIM domain (FHL) family is involved in regulating transforming growth factor (TGF)-β and Ras signaling, which might control the EMT process. In this study, we found that higher expression of four-and-a-half LIM domains 3 (FHL3) predicted poor prognosis in PDAC. The decreasing of FHL3 changed the EMT phenotype by blocking the TGFβ/Atk/GSK3β/ubiquitin pathways. Interestingly, the GSK3β inhibitor could abrogate the role of FHL3 in the regulation of snail1 and twist1 expression, which implied that GSK3β plays a pivotal role in the FHL3-mediated EMT process. Furthermore, we found that FHL3 can directly bind to GSK3β, which weakened the interaction between GSK3β and snail1/twist1. We also found that the LIM-3 domain of FHL3 was required for the binding of FHL3 to GSK3β. Collectively, our study implied that FHL3, as a binding partner of GSK3β, promoted tumor metastasis in PDAC through inhibiting the ubiquitin-degradation of snail1 and twist1.
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10
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Li G, Wang D, Ma W, An K, Liu Z, Wang X, Yang C, Du F, Han X, Chang S, Yu H, Zhang Z, Zhao Z, Zhang Y, Wang J, Sun Y. Transcriptomic and epigenetic analysis of breast cancer stem cells. Epigenomics 2018; 10:765-783. [PMID: 29480027 DOI: 10.2217/epi-2018-0008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
AIM Cancer stem cells (CSCs) drive triple-negative breast cancer recurrence via their properties of self-renewal, invasiveness and radio/chemotherapy resistance. This study examined how CSCs might sustain these properties. MATERIALS & METHODS Transcriptomes, DNA methylomes and histone modifications were compared between CSCs and non CSCs. RESULTS Transcriptome analysis revealed several pathways that were activated in CSCs, whereas cell cycle regulation pathways were inhibited. Cell development and signaling genes were differentially methylated, with histone methylation analysis suggesting distinct H3K4me2 and H3K27me3 enrichment profiles. An integrated analysis revealed several tumor suppressor genes downregulated in CSCs. CONCLUSION Differential activation of various signaling pathways and genes contributes to the tumor-promoting properties of CSCs. Therapeutic targets identified in the analysis may contribute to improving treatment options for patients.
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Affiliation(s)
- Guochao Li
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Dong Wang
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wencui Ma
- Heze Third People's Hospital, Shandong 274031, PR China
| | - Ke An
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zongzhi Liu
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xinyu Wang
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
| | - Caiyun Yang
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fengxia Du
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiao Han
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shuang Chang
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hui Yu
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zilong Zhang
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zitong Zhao
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yan Zhang
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
| | - Junyun Wang
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yingli Sun
- Key Laboratory of Genomic & Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
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11
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Zhang Y, Li W, Zhu M, Li Y, Xu Z, Zuo B. FHL3 differentially regulates the expression of MyHC isoforms through interactions with MyoD and pCREB. Cell Signal 2015; 28:60-73. [PMID: 26499038 DOI: 10.1016/j.cellsig.2015.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 10/09/2015] [Accepted: 10/19/2015] [Indexed: 12/24/2022]
Abstract
In skeletal muscle, muscle fiber types are defined by four adult myosin heavy chain (MyHC) isoforms. Four and a half LIM domain protein 3 (FHL3) regulates myoblasts differentiation and gene expression by acting as a transcriptional co-activator or co-repressor. However, how FHL3 regulates MyHC expression is currently not clear. In this study, we found that FHL3 down-regulated the expression of MyHC 1/slow and up-regulated the expression of MyHC 2a and MyHC 2b, whereas no significant effect was found on MyHC 2x expression. MyoD and phosphorylated cAMP response element binding protein (pCREB) played important roles in the regulation of MyHC 1/slow and MyHC 2a expression by FHL3, respectively. FHL3 could interact with MyoD, CREB and pCREB in vivo. pCREB had stronger interaction with the cyclic AMP-responsive elements (CRE) of the MyHC 2a promoter compared with CREB, and FHL3 significantly affected the binding capacity of pCREB to CRE. We established a model in which FHL3 promotes the expression of MyHC 2a through CREB-mediated transcription and inhibits the expression of MyHC 1/slow by inhibiting MyoD transcription activity during myogenesis. Our data support the notion that FHL3 plays important roles in the regulation of muscle fiber type composition.
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Affiliation(s)
- Yunxia Zhang
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Wentao Li
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Mingfei Zhu
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yuan Li
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.
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Han W, Xia Q, Yin B, Peng XZ. Ribotrap analysis of proteins associated with FHL3 3'untranslated region in glioma cells. ACTA ACUST UNITED AC 2014; 29:78-84. [PMID: 24998228 DOI: 10.1016/s1001-9294(14)60032-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To screen the proteins associated with four-and-a-half LIM domains 3 (FHL3) 3' untranslated region (3'UTR) in glioma cells. METHODS Western blot was adopted to detect the regulatory effect of poly(C)-binding protein 2 (PCBP2) on FHL3. Biotin pull-down and sliver staining were employed to screen and verify the candidate binding proteins of FHL3 3'UTR. Then liquid chromatography-tandem mass spectrometry (LC-MS/MS) and molecule annotation system were used to identify and analyze the candidate binding proteins. Immuno- precipitation was conducted to study the interaction between PCBP2 and polypyrimidine tract-binding protein 1 (PTBP1), a binding protein identified by LC-MS/MS. RESULTS PCBP2 could bind to FHL3 mRNA 3'UTR-A and inhibited the expression of FHL3 in T98G glioms cells. 22 candidate binding proteins were identified. Among them, there were 11 RNA binding proteins, including PCBP2. PTBP1 associated with FHL3 mRNA 3'UTR and interacted with PCBP2 protein. CONCLUSIONS PCBP2 and PTBP1 can both associate with FHL3 mRNA 3'UTR through forming a protein complex.
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Affiliation(s)
- Wei Han
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Qing Xia
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | | | - Xiao-Zhong Peng
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
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Cai X, Wang J, Huang X, Fu W, Xia W, Zou M, Wang Y, Wang J, Xu D. Identification and characterization of MT-1X as a novel FHL3-binding partner. PLoS One 2014; 9:e93723. [PMID: 24690879 PMCID: PMC3972135 DOI: 10.1371/journal.pone.0093723] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/06/2014] [Indexed: 11/20/2022] Open
Abstract
Four and a half LIM domain protein 3 (FHL3) is a member of the FHL protein family that plays roles in the regulation of cell survival, cell adhesion and signal transduction. However, the mechanism of action for FHL3 is not yet clear. The aim of present study was to identify novel binding partner of FHL3 and to explore the underlying mechanism. With the use of yeast two-hybrid screening system, FHL3 was used as the bait to screen human fetal hepatic cDNA library for interacting proteins. Methionine-1X was identified as a novel FHL3 binding partner. The interaction between FHL3 and the full length MT-1X was further confirmed by yeast two-hybrid assay, co-immunoprecipitation and GST pull-down assays. Furthermore,the result demonstrated that MT-1X knockdown promoted the FHL3-induced inhibitory effect on HepG2 cells by regulating FHL3-mediated Smad signaling and involving in the modulation the expression of G2/M phase-related proteins through interaction with FHL3. These findings suggest that functional interactions between FHL3 and MT-1X may provide some clues to the mechanisms of FHL3-regulated cell proliferation.
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Affiliation(s)
- Xin Cai
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - JinFeng Wang
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - Xin Huang
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - Wenliang Fu
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - Wenrong Xia
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - Minji Zou
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - YuanYuan Wang
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - Jiaxi Wang
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
| | - Donggang Xu
- Laboratory of Genome Engineering, Beijing Institute of Basic Medical Sciences, Beijing, PR China
- * E-mail:
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The histone deacetylase SIRT6 suppresses the expression of the RNA-binding protein PCBP2 in glioma. Biochem Biophys Res Commun 2014; 446:364-9. [DOI: 10.1016/j.bbrc.2014.02.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 02/25/2014] [Indexed: 02/06/2023]
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The four and a half LIM family members are novel interactants of the human T-cell leukemia virus type 1 Tax oncoprotein. J Virol 2013; 87:7435-44. [PMID: 23616667 DOI: 10.1128/jvi.00070-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia (ATL). The viral regulatory protein Tax1 plays a pivotal role in T-cell transformation and ATL development. Previous studies in our laboratory, using the yeast 2-hybrid approach to screen a T-cell library for Tax1-interacting partners, identified the cellular Four and a Half Lim domain protein 3 (FHL3) as a possible Tax1-interacting candidate. FHL3 is a member of the FHL family of proteins, which function as transcriptional coactivators and cytoskeleton regulators and have a role in cancer progression and development. The aim of this study was to investigate the physical and functional interaction between Tax1 and members of the FHL family of proteins. We show that Tax1 and FHL3 interact both in vitro and in vivo. Furthermore, both FHL1 and -2 also interact with Tax1. We have demonstrated that FHL3 enhances Tax1-mediated activation of the viral long terminal repeat (LTR) without affecting basal activity and that FHL1 to -3 regulate NF-κB activation by Tax1 in a cell-specific manner. In addition, we have found that the interaction between Tax1 and FHL1 to -3 affects the localization of these proteins, leading to their redistribution in cells. Tax1 also affected FHL3 cytoskeleton function by increasing FHL3-mediated cell spreading. Overall, our results suggest that the interaction between Tax1 and the FHL family alters both the transactivating activity and the subcellular localization of Tax1 and provide new insights into molecular mechanisms that underlie the oncogenic nature of this HTLV-1 protein.
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Han W, Xin Z, Zhao Z, Bao W, Lin X, Yin B, Zhao J, Yuan J, Qiang B, Peng X. RNA-binding protein PCBP2 modulates glioma growth by regulating FHL3. J Clin Invest 2013; 123:2103-18. [PMID: 23585479 DOI: 10.1172/jci61820] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/07/2013] [Indexed: 02/01/2023] Open
Abstract
PCBP2 is a member of the poly(C)-binding protein (PCBP) family, which plays an important role in posttranscriptional and translational regulation by interacting with single-stranded poly(C) motifs in target mRNAs. Several PCBP family members have been reported to be involved in human malignancies. Here, we show that PCBP2 is upregulated in human glioma tissues and cell lines. Knockdown of PCBP2 inhibited glioma growth in vitro and in vivo through inhibition of cell-cycle progression and induction of caspase-3-mediated apoptosis. Thirty-five mRNAs were identified as putative PCBP2 targets/interactors using RIP-ChIP protein-RNA interaction arrays in a human glioma cell line, T98G. Four-and-a-half LIM domain 3 (FHL3) mRNA was downregulated in human gliomas and was identified as a PCBP2 target. Knockdown of PCBP2 enhanced the expression of FHL3 by stabilizing its mRNA. Overexpression of FHL3 attenuated cell growth and induced apoptosis. This study establishes a link between PCBP2 and FHL3 proteins and identifies a new pathway for regulating glioma progression.
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Affiliation(s)
- Wei Han
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Lin J, Qin X, Zhu Z, Mu J, Zhu L, Wu K, Jiao H, Xu X, Ye Q. FHL family members suppress vascular endothelial growth factor expression through blockade of dimerization of HIF1α and HIF1β. IUBMB Life 2012; 64:921-30. [DOI: 10.1002/iub.1089] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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