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Liu SS, Wan QS, Lv C, Wang JK, Jiang S, Cai D, Liu MS, Wang T, Zhang KH. Integrating trans-omics, cellular experiments and clinical validation to identify ILF2 as a diagnostic serum biomarker and therapeutic target in gastric cancer. BMC Cancer 2024; 24:465. [PMID: 38622522 PMCID: PMC11017608 DOI: 10.1186/s12885-024-12175-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/24/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) lacks serum biomarkers with clinical diagnostic value. Multi-omics analysis is an important approach to discovering cancer biomarkers. This study aimed to identify and validate serum biomarkers for GC diagnosis by cross-analysis of proteomics and transcriptomics datasets. METHODS A cross-omics analysis was performed to identify overlapping differentially expressed genes (DEGs) between our previous aptamer-based GC serum proteomics dataset and the GC tissue RNA-Seq dataset in The Cancer Genome Atlas (TCGA) database, followed by lasso regression and random forest analysis to select key overlapping DEGs as candidate biomarkers for GC. The mRNA levels and diagnostic performance of these candidate biomarkers were analyzed in the original and independent GC datasets to select valuable candidate biomarkers. The valuable candidate biomarkers were subjected to bioinformatics analysis to select those closely associated with the biological behaviors of GC as potential biomarkers. The clinical diagnostic value of the potential biomarkers was validated using serum samples, and their expression levels and functions in GC cells were validated using in vitro cell experiments. RESULTS Four candidate biomarkers (ILF2, PGM2L1, CHD7, and JCHAIN) were selected. Their mRNA levels differed significantly between tumor and normal tissues and showed different diagnostic performances for GC, with areas under the receiver operating characteristic curve (AUROCs) of 0.629-0.950 in the TCGA dataset and 0.736-0.840 in the Gene Expression Omnibus (GEO) dataset. In the bioinformatics analysis, only ILF2 (interleukin enhancer-binding factor 2) gene levels were associated with immune cell infiltration, some checkpoint gene expression, chemotherapy sensitivity, and immunotherapy response. Serum levels of ILF2 were higher in GC patients than in controls, with an AUROC of 0.944 for the diagnosis of GC, and it was also detected in the supernatants of GC cells. Knockdown of ILF2 by siRNA significantly reduced the proliferation and colony formation of GC cells. Overexpression of ILF2 significantly promotes the proliferation and colony formation of gastric cancer cells. CONCLUSIONS Trans-omics analysis of proteomics and transcriptomics is an efficient approach for discovering serum biomarkers, and ILF2 is a potential diagnostic biomarker and therapeutic target of gastric cancer.
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Affiliation(s)
- Shao-Song Liu
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China
| | - Qin-Si Wan
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China
| | - Cong Lv
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China
| | - Jin-Ke Wang
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China
| | - Song Jiang
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China
| | - Dan Cai
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China
| | - Mao-Sheng Liu
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China
| | - Ting Wang
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China
| | - Kun-He Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University; Jiangxi Institute of Gastroenterology & Hepatology, Nanchang, China, No 17, Yongwai Zheng Street, 330006, Nanchang, China.
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Azim R, Wang S, Dipu SA, Islam N, Ala Muid MR, Elahe MF. A patient-specific functional module and path identification technique from RNA-seq data. Comput Biol Med 2023; 158:106871. [PMID: 37030265 DOI: 10.1016/j.compbiomed.2023.106871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/12/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023]
Abstract
With the advancement of new technologies, a huge amount of high dimensional data is being generated which is opening new opportunities and challenges to the study of cancer and diseases. In particular, distinguishing the patient-specific key components and modules which drive tumorigenesis is necessary to analyze. A complex disease generally does not initiate from the dysregulation of a single component but it is the result of the dysfunction of a group of components and networks which differs from patient to patient. However, a patient-specific network is required to understand the disease and its molecular mechanism. We address this requirement by constructing a patient-specific network by sample-specific network theory with integrating cancer-specific differentially expressed genes and elite genes. By elucidating patient-specific networks, it can identify the regulatory modules, driver genes as well as personalized disease networks which can lead to personalized drug design. This method can provide insight into how genes are associating with each other and characterized the patient-specific disease subtypes. The results show that this method can be beneficial for the detection of patient-specific differential modules and interaction between genes. Extensive analysis using existing literature, gene enrichment and survival analysis for three cancer types STAD, PAAD and LUAD shows the effectiveness of this method over other existing methods. In addition, this method can be useful for personalized therapeutics and drug design. This methodology is implemented in the R language and is available at https://github.com/riasatazim/PatientSpecificRNANetwork.
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Zhang H, Che Y, Xuan B, Wu X, Li H. Serine hydroxymethyltransferase 2 (SHMT2) potentiates the aggressive process of oral squamous cell carcinoma by binding to interleukin enhancer-binding factor 2 (ILF2). Bioengineered 2022; 13:8785-8797. [PMID: 35333683 PMCID: PMC9161932 DOI: 10.1080/21655979.2022.2051886] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a frequent threatening head and neck malignancy. Serine hydroxymethyltransferase 2 (SHMT2) was identified to be upregulated in OSCC and its high expression was associated with poor patient prognosis. This paper set out to assess the influence of SHMT2 on OSCC progression and the potential mechanisms related to interleukin enhancer-binding factor 2 (ILF2). First of all, reverse transcription-quantitative PCR (RT-qPCR) and western blot examined the expression of SHMT2 and ILF2 in OSCC cells. Cell Counting Kit-8 (CCK-8) and colony formation assays appraised cell proliferation. Terminal-deoxynucleotidyl Transferase Mediated Nick End Labeling (TUNEL) staining was to estimate the apoptotic rate of cells. Further, wound healing and transwell assays verified the migration and invasion of cells. Western blot was adopted to detect the expression of factors related to apoptosis, migration, and epithelial–mesenchymal transition (EMT). The possible interaction of SHMT2 and ILF2 was predicted by a Molecular INTeraction (MINT) and BioGRID databases and determined using co-immunoprecipitation (IP) assay. Subsequently, ILF2 was overexpressed to investigate whether SHMT2 regulated OSCC progression by binding to ILF2. Results implied that SHMT2 possessed increased expression in OSCC cells, and OSCC cell viability, migration, invasion, EMT were inhibited and apoptosis was potentiated after its silencing. ILF2 bound to SHMT2 and ILF2 expression was downregulated after SHMT2 silencing in OSCC cells. Importantly, ILF2 overexpression abolished the suppressive role of SHMT2 interference in the progression of OSCC. Collectively, SHMT2 could promote the progression of OSCC by binding to ILF2.
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Affiliation(s)
- Hui Zhang
- Department of Stomatology, Aerospace Center Hospital, Beijing, China
| | - Yilei Che
- Department of Stomatology, Aerospace Center Hospital, Beijing, China
| | - Bin Xuan
- Department of Stomatology, Aerospace Center Hospital, Beijing, China
| | - Xiaozhen Wu
- Department of Stomatology, Aerospace Center Hospital, Beijing, China
| | - Hui Li
- Department of Stomatology, Aerospace Center Hospital, Beijing, China
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Zang B, Wang W, Wang Y, Li P, Xia T, Liu X, Chen D, Piao HL, Qi H, Ma Y. Metabolomic Characterization Reveals ILF2 and ILF3 Affected Metabolic Adaptions in Esophageal Squamous Cell Carcinoma. Front Mol Biosci 2021; 8:721990. [PMID: 34568427 PMCID: PMC8459612 DOI: 10.3389/fmolb.2021.721990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022] Open
Abstract
Esophageal cancer (EC) is a common malignant disease in eastern countries. However, a study of the metabolomic characteristics associated with other biological factors in esophageal squamous cell carcinoma (ESCC) is limited. Interleukin enhancer binding factor 2 (ILF2) and ILF3, double-stranded RNA-binding proteins, have been reported to contribute to the occurrence and development of various types of malignancy. Nevertheless, the underlying functions of ILF2 and ILF3 in ESCC metabolic reprogramming have never been reported. This study aimed to contribute to the metabolic characterization of ESCC and to investigate the metabolomic alterations associated with ILF2 and ILF3 in ESCC tissues. Here, we identified 112 differential metabolites, which were mainly enriched in phosphatidylcholine biosynthesis, fatty acid metabolism, and amino acid metabolism pathways, based on liquid chromatography–mass spectrometry and capillary electrophoresis–mass spectrometry approaches using ESCC tissues and paired para-cancer tissues from twenty-eight ESCC patients. In addition, ILF2 and ILF3 expression were significantly elevated in EC tissues compared to the histologically normal samples, and closely associated with PI3K/AKT and MAPK signaling pathways in ESCC. Moreover, in ESCC tissues with a high ILF2 expression, several short-chain acyl-carnitines (C3:0, C4:0, and C5:0) related to the BCAA metabolic pathway and long-chain acyl-carnitines (C14:0, C16:0, C16:0-OH, and C18:0) involved in the oxidation of fatty acids were obviously upregulated. Additionally, a series of intermediate metabolites involved in the glycolysis pathway, including G6P/F6P, F1,6BP, DHAP, G3P, and 2,3BPG, were remarkably downregulated in highly ILF3-expressed ESCC tissues compared with the corresponding para-cancer tissues. Overall, these findings may provide evidence for the roles of ILF2 and ILF3 during the process of ESCC metabolic alterations, and new insights into the development of early diagnosis and treatment for ESCC. Further investigation is needed to clarify the underlying mechanism of ILF2 and ILF3 on acyl-carnitines and the glycolysis pathway, respectively.
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Affiliation(s)
- Bin Zang
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Wen Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yiqian Wang
- Department of Radiotherapy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Pengfei Li
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Tian Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xiaolong Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Di Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hai-Long Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, Shenyang, China
| | - Huan Qi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yegang Ma
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
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Shiu TY, Lin HH, Shih YL, Feng AC, Huang HH, Huang TY, Hsieh CB, Chang WK, Hsieh TY. CRNDE-h transcript/miR-136-5p axis regulates interleukin enhancer binding factor 2 expression to promote hepatocellular carcinoma cell proliferation. Life Sci 2021; 284:119708. [PMID: 34153299 DOI: 10.1016/j.lfs.2021.119708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
AIMS Hepatocellular carcinoma (HCC) is a primary malignancy of the hepatocyte. Interleukin enhancer binding factor 2 (ILF2) plays a role in the development of HCC. However, the regulatory mechanisms of ILF2 expression in HCC remain unclear. In this study, we aimed to identify ILF2-targeting microRNAs (miRNAs) and to explore how they affect ILF2 expression in HCC. MAIN METHODS The tissue specimens were collected from 25 HCC patients. The underlying regulatory mechanism of ILF2 expression in HCC progression was determined using luciferase reporter assay, quantitative real-time PCR, Western blotting, and BrdU incorporation assay. KEY FINDINGS Of predicted miRNA candidates (miR-122-5p, miR-425-5p, miR-136-5p, miR-7-5p, miR-421 and miR-543), a statistically significant inverse correlation by linear correlation analysis was observed between miR-136-5p and ILF2 mRNA expressions in patients with HCC (r = -0.627, P < 0.001). Further analysis demonstrated that ILF2 was directly regulated by miR-136-5p. In addition, we showed that long noncoding RNA colorectal neoplasia differentially expressed-h (lncRNA CRNDE-h) transcript expression was significantly up-regulated in HCC, and a miR-136-5p binding site was newly found in the lncRNA CRNDE-h transcript sequence using IntaRNA tool. In terms of mechanism, highly-expressed lncRNA CRNDE-h transcript can sponge miR-136-5p, thereby preventing it from interacting with target ILF2 mRNA while promoting the proliferation of HCC cells. SIGNIFICANCE The lncRNA CRNDE-h/miR-136-5p/ILF2 axis plays a significant regulatory role in HCC progression, which may partly explain the pathogenic mechanisms of HCC and may provide promising potential targets for the diagnosis, treatment, and prognosis of HCC.
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Affiliation(s)
- Tzu-Yue Shiu
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hsuan-Hwai Lin
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC.
| | - Yu-Lueng Shih
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - An-Chieh Feng
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hsin-Hung Huang
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Tien-Yu Huang
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chung-Bao Hsieh
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Wei-Kuo Chang
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Tsai-Yuan Hsieh
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC.
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Nourreddine S, Lavoie G, Paradis J, Ben El Kadhi K, Méant A, Aubert L, Grondin B, Gendron P, Chabot B, Bouvier M, Carreno S, Roux PP. NF45 and NF90 Regulate Mitotic Gene Expression by Competing with Staufen-Mediated mRNA Decay. Cell Rep 2021; 31:107660. [PMID: 32433969 DOI: 10.1016/j.celrep.2020.107660] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 01/16/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
In human cells, the expression of ∼1,000 genes is modulated throughout the cell cycle. Although some of these genes are controlled by specific transcriptional programs, very little is known about their post-transcriptional regulation. Here, we analyze the expression signature associated with all 687 RNA-binding proteins (RBPs) and identify 39 that significantly correlate with cell cycle mRNAs. We find that NF45 and NF90 play essential roles in mitosis, and transcriptome analysis reveals that they are necessary for the expression of a subset of mitotic mRNAs. Using proteomics, we identify protein clusters associated with the NF45-NF90 complex, including components of Staufen-mediated mRNA decay (SMD). We show that depletion of SMD components increases the binding of mitotic mRNAs to the NF45-NF90 complex and rescues cells from mitotic defects. Together, our results indicate that the NF45-NF90 complex plays essential roles in mitosis by competing with the SMD machinery for a common set of mRNAs.
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Affiliation(s)
- Sami Nourreddine
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Geneviève Lavoie
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Justine Paradis
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | | | - Antoine Méant
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Léo Aubert
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Benoit Grondin
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Michel Bouvier
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Sébastien Carreno
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada.
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Wei L, Yang C, Wang G, Li K, Zhang Y, Guan H, Sun Z, Zhong C. Interleukin Enhancer Binding Factor 2 Regulates Cell Viability and Apoptosis of Human Brain Vascular Smooth Muscle Cells. J Mol Neurosci 2020; 71:225-233. [PMID: 32748330 DOI: 10.1007/s12031-020-01638-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/16/2020] [Indexed: 12/27/2022]
Abstract
The proliferation and migration of vascular smooth muscle cells (VSMCs) are involved in the pathogenesis of intracranial aneurysm (IA) formation and rupture. Interleukin enhancer binding factor 2 (ILF2) is known as the nuclear factor of activated T cells and regulates cell growth. This study was aimed to explore the effects of ILF2 on IA progression. Human brain VSMCs (hBVSMCs) were transfected with pCDNA3.1(+), pCDNA3.1(+)-ILF2, siRNA-negative control, and siRNA-ILF2. The transfection efficiency was then evaluated by determining ILF2 expression. The cell viability and apoptosis were determined using Cell Counting Kit-8 and Annexin V-FITC cell apoptosis assay kit, respectively. Real-time quantification PCR (RT-qPCR) was applied to measure the expression levels of apoptosis-related and inflammation-related genes. Finally, western blot was used to detect the expression level of Fas cell surface death receptor 95 (CD95) and Caspase 8. Overexpression of ILF2 could significantly increase cell viability and decrease cell apoptosis (P < 0.05), while knock-down of ILF2 showed opposite trends for hBVSMCs on cell viability and apoptosis (P < 0.05). RT-qPCR results showed that ILF2 knock-down downregulated the expression levels of BCL2 apoptosis regulator (BCL2), transcriptional regulator Myc-like (c-Myc), and caspase 1 (ICE) whereas upregulated the expression levels of CD95, p21, p53, and interleukin-13 (IL-13). Additionally, the protein expression levels of CD95 and Caspase 8 were significantly decreased after ILF2 overexpression while were significantly increased after ILF2 knock-down (P < 0.05). ILF2 knock-down may inhibit cell viability and promote cell apoptosis of hBVSMCs by regulating the expression levels of apoptosis-related genes and suppressing inflammatory response.
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Affiliation(s)
- Liang Wei
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Cheng Yang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Guangxue Wang
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Keqin Li
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Yanfei Zhang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Hongxin Guan
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Zhiyang Sun
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
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Jin J, Wang W, Ai S, Liu W, Song Y, Luo Z, Zhang Q, Wu K, Liu Y, Wu J. Enterovirus 71 Represses Interleukin Enhancer-Binding Factor 2 Production and Nucleus Translocation to Antagonize ILF2 Antiviral Effects. Viruses 2019; 12:v12010022. [PMID: 31878072 PMCID: PMC7019514 DOI: 10.3390/v12010022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/09/2019] [Accepted: 12/17/2019] [Indexed: 12/23/2022] Open
Abstract
Enterovirus 71 (EV71) infection causes hand-foot-mouth disease (HFMD), meningoencephalitis, neonatal sepsis, and even fatal encephalitis in children, thereby presenting a serious risk to public health. It is important to determine the mechanisms underlying the regulation of EV71 infection. In this study, we initially show that the interleukin enhancer-binding factor 2 (ILF2) reduces EV71 50% tissue culture infective dose (TCID50) and attenuates EV71 plaque-formation unit (PFU), thereby repressing EV71 infection. Microarray data analyses show that ILF2 mRNA is reduced upon EV71 infection. Cellular studies indicate that EV71 infection represses ILF2 mRNA expression and protein production in human leukemic monocytes (THP-1) -differentiated macrophages and human rhabdomyosarcoma (RD) cells. In addition, EV71 nonstructural protein 2B interacts with ILF2 in human embryonic kidney (HEK293T) cells. Interestingly, in the presence of EV71 2B, ILF2 is translocated from the nucleus to the cytoplasm, and it colocalizes with 2B in the cytoplasm. Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein.
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Affiliation(s)
- Jing Jin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.J.); (S.A.); (W.L.); (Y.S.); (Q.Z.); (K.W.); (Y.L.)
| | - Wenbiao Wang
- Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China; (W.W.); (Z.L.)
| | - Sha Ai
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.J.); (S.A.); (W.L.); (Y.S.); (Q.Z.); (K.W.); (Y.L.)
| | - Weiyong Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.J.); (S.A.); (W.L.); (Y.S.); (Q.Z.); (K.W.); (Y.L.)
| | - Yu Song
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.J.); (S.A.); (W.L.); (Y.S.); (Q.Z.); (K.W.); (Y.L.)
| | - Zhen Luo
- Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China; (W.W.); (Z.L.)
| | - Qi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.J.); (S.A.); (W.L.); (Y.S.); (Q.Z.); (K.W.); (Y.L.)
| | - Kailang Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.J.); (S.A.); (W.L.); (Y.S.); (Q.Z.); (K.W.); (Y.L.)
| | - Yingle Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.J.); (S.A.); (W.L.); (Y.S.); (Q.Z.); (K.W.); (Y.L.)
- Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China; (W.W.); (Z.L.)
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.J.); (S.A.); (W.L.); (Y.S.); (Q.Z.); (K.W.); (Y.L.)
- Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China; (W.W.); (Z.L.)
- Correspondence: ; Tel.: +86-27-68754979
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Lian S, Li L, Zhou Y, Liu Z, Wang L. The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers. PeerJ 2019; 7:e7696. [PMID: 31576243 PMCID: PMC6753928 DOI: 10.7717/peerj.7696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND RNA-binding proteins (RBPs) play important roles in cellular homeostasis by regulating the expression of thousands of transcripts, which have been reported to be involved in human tumorigenesis. Despite previous reports of the dysregulation of RBPs in cancers, the degree of dysregulation of RBPs in cancers and the intrinsic relevance between dysregulated RBPs and clinical TNM information remains unknown. Furthermore, the co-expressed networks of dysregulated RBPs with transcriptional factors and lncRNAs also require further investigation. RESULTS Here, we firstly analyzed the deviations of expression levels of 1,542 RBPs from 20 cancer types and found that (1) RBPs are dysregulated in almost all 20 cancer types, especially in BLCA, COAD, READ, STAD, LUAD, LUSC and GBM with proportion of deviation larger than 300% compared with non-RBPs in normal tissues. (2) Up- and down-regulated RBPs also show opposed patterns of differential expression in cancers and normal tissues. In addition, down-regulated RBPs show a greater degree of dysregulated expression than up-regulated RBPs do. Secondly, we analyzed the intrinsic relevance between dysregulated RBPs and clinical TNM information and found that (3) Clinical TNM information for two cancer types-CHOL and KICH-is shown to be closely related to patterns of differentially expressed RBPs (DE RBPs) by co-expression cluster analysis. Thirdly, we identified ten key RBPs (seven down-regulated and three up-regulated) in CHOL and seven key RBPs (five down-regulated and two up-regulated) in KICH by analyzing co-expression correlation networks. Fourthly, we constructed the co-expression networks of key RBPs between 1,570 TFs and 4,147 lncRNAs for CHOL and KICH, respectively. CONCLUSIONS These results may provide an insight into the understanding of the functions of RBPs in human carcinogenesis. Furthermore, key RBPs and the co-expressed networks offer useful information for potential prognostic biomarkers and therapeutic targets for patients with cancers at the N and M stages in two cancer types CHOL and KICH.
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Affiliation(s)
- Shuaibin Lian
- College of Physics and Electronic Engineering, XinYang Normal University, Xinyang, HeNan, China
| | - Liansheng Li
- College of Life Sciences, XinYang Normal University, Xinyang, HeNan, China
| | - Yongjie Zhou
- College of Physics and Electronic Engineering, XinYang Normal University, Xinyang, HeNan, China
| | - Zixiao Liu
- College of Physics and Electronic Engineering, XinYang Normal University, Xinyang, HeNan, China
| | - Lei Wang
- College of Life Sciences, XinYang Normal University, Xinyang, HeNan, China
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10
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Jin Z, Xu L, Zhang L, Zhao M, Li D, Ye L, Ma Y, Ren S, Yu H, Wang D, Liang C, Chen B. Interleukin enhancer binding factor 2 is a prognostic biomarker for breast cancer that also predicts neoadjuvant chemotherapy responses. Am J Transl Res 2018; 10:1677-1689. [PMID: 30018709 PMCID: PMC6038075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
Interleukin enhancer binding factor 2 (ILF2) participates in several aspects of DNA and RNA metabolism and regulates gene expression at multiple levels; however, its role in breast cancer remains undefined. The variant statuses of ILF2 in human breast cancer were evaluated using the COSMIC database. Altered ILF2 expression in normal breast tissue relative to cancer tissue and in breast cancer patients with different clinicopathological characteristics, molecular subtypes, clinical outcomes and chemotherapy responses were examined using the Oncomine, GOBO, Kaplan-Meier plotter and GEO datasets. To explore possible biological networks connected to ILF2 in breast cancer, we performed ingenuity pathway analysis on ILF2-related differentially expressed genes. We found that many breast cancers had increased ILF2 copy number variations and increased ILF2 expression. We also observed that elevated ILF2 expression was correlated with aggressive features, such as high histological grade, BRCA1 mutations, and the triple-negative/basal-like subtype, which resulted in shorter survival in these cases. Moreover, ILF2 expression predicted responses to anthracycline/taxane-based treatment. Ingenuity pathway analysis revealed that ILF2-related biological functions included promoting cell survival, viability, and proliferation, as well as cell cycle progression and DNA repair. Certain well-known oncogenes (MYC and HGF), cytokines (CSF2, IFNG and IL5) and microRNAs (miR-21, miR-155-5p and let-7) may participate in the ILF2 expression network in breast cancer. In summary, ILF2 is involved in the development and progression of breast cancer and may be a predictive biomarker for better responses to anthracycline/taxane-based treatments.
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Affiliation(s)
- Zining Jin
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Lu Xu
- Department of Medical Oncology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Lei Zhang
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Min Zhao
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Dongbao Li
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Lijun Ye
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Ying Ma
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Siyu Ren
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Hailan Yu
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Danyu Wang
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Chunyan Liang
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
| | - Bo Chen
- Department of Breast Surgery, The First Hospital of China Medical UniversityShenyang 110001, Liaoning Province, China
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11
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Jin J, Li A, Wang W, Wu J. Interleukin-enhanced binding factor 2 interacts with NLRP3 to inhibit the NLRP3 inflammasome activation. Biochem Biophys Res Commun 2018; 500:398-404. [DOI: 10.1016/j.bbrc.2018.04.087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/11/2018] [Indexed: 01/19/2023]
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12
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Shi C, Yang Y, Yu J, Meng F, Zhang T, Gao Y. The long noncoding RNA LINC00473, a target of microRNA 34a, promotes tumorigenesis by inhibiting ILF2 degradation in cervical cancer. Am J Cancer Res 2017; 7:2157-2168. [PMID: 29218240 PMCID: PMC5714745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023] Open
Abstract
Cervical cancer is one of the most common gynecological malignancies in women worldwide. The long non-coding RNA (lncRNA) LINC00473 is increased in some human cancer tissues and it plays important roles in tumorigenesis. However, neither the expression pattern nor the biological functions of LINC00473 have been elucidated in cervical cancer so far. In the present study, gain- and loss-of-function assays showed that LINC00473 promoted cell proliferation and inhibited cell apoptosis in cervical cancer cells in vitro. Moreover, we found that LINC00473 enhanced the growth of cervical cancer cells in vivo. Mechanistic investigation showed that LINC00473 directly interacted with ILF2 and suppressed its degradation. Finally, we demonstrated that miR-34a reduced the stability of LINC00473. These findings may have important implications for developing novel therapeutic strategies for cervical cancer.
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Affiliation(s)
- Can Shi
- Department of Obstetrics and Gynecology, Huai'an First People's Hospital, Nanjing Medical UniversityHuai'an 223300, Jiangsu, P. R. China
| | - Yijun Yang
- Department of Obstetrics and Gynecology, Huai'an First People's Hospital, Nanjing Medical UniversityHuai'an 223300, Jiangsu, P. R. China
| | - Juanpeng Yu
- Department of Obstetrics and Gynecology, Huai'an First People's Hospital, Nanjing Medical UniversityHuai'an 223300, Jiangsu, P. R. China
| | - Fei Meng
- Department of Obstetrics and Gynecology, Huai'an First People's Hospital, Nanjing Medical UniversityHuai'an 223300, Jiangsu, P. R. China
| | - Ting Zhang
- Department of Obstetrics and Gynecology, Huai'an First People's Hospital, Nanjing Medical UniversityHuai'an 223300, Jiangsu, P. R. China
| | - Yingchun Gao
- Department of Obstetrics and Gynecology, Huai'an First People's Hospital, Nanjing Medical UniversityHuai'an 223300, Jiangsu, P. R. China
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