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Bedir M, Outwin E, Colnaghi R, Bassett L, Abramowicz I, O'Driscoll M. A novel role for the peptidyl-prolyl cis-trans isomerase Cyclophilin A in DNA-repair following replication fork stalling via the MRE11-RAD50-NBS1 complex. EMBO Rep 2024:10.1038/s44319-024-00184-9. [PMID: 38943005 DOI: 10.1038/s44319-024-00184-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024] Open
Abstract
Cyclosporin A (CsA) induces DNA double-strand breaks in LIG4 syndrome fibroblasts, specifically upon transit through S-phase. The basis underlying this has not been described. CsA-induced genomic instability may reflect a direct role of Cyclophilin A (CYPA) in DNA repair. CYPA is a peptidyl-prolyl cis-trans isomerase (PPI). CsA inhibits the PPI activity of CYPA. Using an integrated approach involving CRISPR/Cas9-engineering, siRNA, BioID, co-immunoprecipitation, pathway-specific DNA repair investigations as well as protein expression interaction analysis, we describe novel impacts of CYPA loss and inhibition on DNA repair. We characterise a direct CYPA interaction with the NBS1 component of the MRE11-RAD50-NBS1 complex, providing evidence that CYPA influences DNA repair at the level of DNA end resection. We define a set of genetic vulnerabilities associated with CYPA loss and inhibition, identifying DNA replication fork protection as an important determinant of viability. We explore examples of how CYPA inhibition may be exploited to selectively kill cancers sharing characteristic genomic instability profiles, including MYCN-driven Neuroblastoma, Multiple Myeloma and Chronic Myelogenous Leukaemia. These findings propose a repurposing strategy for Cyclophilin inhibitors.
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Affiliation(s)
- Marisa Bedir
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Emily Outwin
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Rita Colnaghi
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Lydia Bassett
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Iga Abramowicz
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK.
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2
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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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3
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Li N, Liu T, Li H, Zhang L, Chu L, Meng Q, Qiao Q, Han W, Zhang J, Guo M, Zhao J. ILF2 promotes anchorage independence through direct regulation of PTEN. Oncol Lett 2019; 18:1689-1696. [PMID: 31423236 PMCID: PMC6614677 DOI: 10.3892/ol.2019.10510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/09/2019] [Indexed: 12/19/2022] Open
Abstract
Anoikis is a specific form of programmed cell death induced by loss of contact between cells and extracellular matrices or other cells. Only tumor cells that are resistant to anoikis can survive in the state of detachment from the primary tissue during the early stages of metastasis. The ability to resist anoikis is crucial for cancer cell metastasis. ILF2 is a proto-oncogene previously studied in glioma, NSCLC, esophageal cancer and pancreatic ductal carcinoma. The results from the present study revealed that the transcription factor interleukin enhancer-binding factor 2 (ILF2) was highly expressed in non-small cell lung cancer (NSCLC) cell lines compared with in normal cell lines. ChIP and luciferase reporter gene assays demonstrated that ILF2 inhibited the expression level of the tumor suppressor gene phosphatase and tensin homolog (PTEN) by directly binding to its upstream regulatory region. Furthermore, the results from the detection of cell adhesion and apoptosis in cell suspension culture demonstrated that this mechanism enabled NSCLC cells to reduce adherence to the matrix and to survive in this abnormal state. These results suggested that ILF2 may promote the anchorage-independence of NSCLC cells through the suppression of PTEN.
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Affiliation(s)
- Na Li
- Pathology Department, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Tao Liu
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Hui Li
- Pathology Department, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Lifang Zhang
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Liping Chu
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Qingge Meng
- Department of Internal Medicine, Xingtai Medical College, The Third Affiliated Hospital of Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Qinzeng Qiao
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Weikun Han
- Department of Internal Medicine, Civil Administration General Hospital of Hebei, Xingtai, Hebei 054000, P.R. China
| | - Junhui Zhang
- Pathology Department, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Minying Guo
- Pathology Department, Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
| | - Jia Zhao
- Department of Internal Medicine, The Third Affiliated Hospital of Xingtai Medical College, Xingtai, Hebei 054000, P.R. China
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Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, Bork P, Moebus S, Herms S, Fischer S, Hoffmann P, Aretz S, Steinke-Lange V. Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes. Int J Cancer 2018; 143:2800-2813. [PMID: 29987844 DOI: 10.1002/ijc.31725] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/10/2018] [Accepted: 03/26/2018] [Indexed: 12/22/2022]
Abstract
In many families with suspected Lynch syndrome (LS), no germline mutation in the causative mismatch repair (MMR) genes is detected during routine diagnostics. To identify novel causative genes for LS, the present study investigated 77 unrelated, mutation-negative patients with clinically suspected LS and a loss of MSH2 in tumor tissue. An analysis for genomic copy number variants (CNV) was performed, with subsequent next generation sequencing (NGS) of selected candidate genes in a subgroup of the cohort. Genomic DNA was genotyped using Illumina's HumanOmniExpress Bead Array. After quality control and filtering, 25 deletions and 16 duplications encompassing 73 genes were identified in 28 patients. No recurrent CNV was detected, and none of the CNVs affected the regulatory regions of MSH2. A total of 49 candidate genes from genomic regions implicated by the present CNV analysis and 30 known or assumed risk genes for colorectal cancer (CRC) were then sequenced in a subset of 38 patients using a customized NGS gene panel and Sanger sequencing. Single nucleotide variants were identified in 14 candidate genes from the CNV analysis. The most promising of these candidate genes were: (i) PRKCA, PRKDC, and MCM4, as a functional relation to MSH2 is predicted by network analysis, and (ii) CSMD1, as this is commonly mutated in CRC. Furthermore, six patients harbored POLE variants outside the exonuclease domain, suggesting that these might be implicated in hereditary CRC. Analyses in larger cohorts of suspected LS patients recruited via international collaborations are warranted to verify the present findings.
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Affiliation(s)
- Katrin Kayser
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medical Genetics Center (MGZ), Munich, Germany
| | - Deepak Vangala
- Department of Internal Medicine, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Nils Rahner
- Institute of Human Genetics, University of Düsseldorf, Düsseldorf, Germany
| | - Magnus von Knebel-Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital of Heidelberg, Heidelberg, Germany.,Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans K Schackert
- Department of Surgical Research, Technische Universität Dresden, Dresden, Germany
| | - Christoph Engel
- Institute of Medical Informatics, Statistics, and Epidemiology, University of Leipzig, Leipzig, Germany
| | | | - Juul Wijnen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tobias Doerks
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Susanne Moebus
- Centre for Urban Epidemiology, University Hospital of Duisburg-Essen, University of Duisburg-Essen, Essen, Germany
| | - Stefan Herms
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,Insitute of Medical Genetics and Pathology, University Hospital of Basel, Basel, Switzerland
| | - Sascha Fischer
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,Insitute of Medical Genetics and Pathology, University Hospital of Basel, Basel, Switzerland
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Verena Steinke-Lange
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medical Genetics Center (MGZ), Munich, Germany
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5
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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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6
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Nuclear factor 90 promotes angiogenesis by regulating HIF-1α/VEGF-A expression through the PI3K/Akt signaling pathway in human cervical cancer. Cell Death Dis 2018; 9:276. [PMID: 29449553 PMCID: PMC5833414 DOI: 10.1038/s41419-018-0334-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 01/28/2023]
Abstract
Vascular endothelial growth factor A (VEGF-A), a fundamental component of angiogenesis, provides nutrients and oxygen to solid tumors, and enhances tumor cell survival, invasion, and migration. Nuclear factor 90 (NF90), a double-stranded RNA-binding protein, is strongly expressed in several human cancers, promotes tumor growth by reducing apoptosis, and increasing cell cycle process. The mechanisms by which cervical cancer cells inducing VEGF-A expression and angiogenesis upon NF90 upregulation remain to be fully established. We demonstrated that NF90 is upregulated in human cervical cancer specimens and the expression of NF90 is paralleled with that of VEGF-A under hypoxia. The expressions of hypoxia inducible factor-1α (HIF-1α) and VEGF-A are downregulated upon NF90 knockdown, which can be rescued by ectopic expression of NF90. Suppression of NF90 decreases the tube formation and cell migration of HUVECs. Moreover, the PI3K/Akt signaling pathway participates in the regulation. Knockdown of NF90 also reduces the tumor growth and angiogenesis of cervical cancer cell line in the mouse xenograft model. Taken together, suppression of NF90 in cervical cancer cell lines can decrease VEGF-A expression, inhibit angiogenesis, and reduce tumorigenic capacity in vivo.
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7
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Lockyer P, Mao H, Fan Q, Li L, Yu-Lee LY, Eissa NT, Patterson C, Xie L, Pi X. LRP1-Dependent BMPER Signaling Regulates Lipopolysaccharide-Induced Vascular Inflammation. Arterioscler Thromb Vasc Biol 2017; 37:1524-1535. [PMID: 28596374 DOI: 10.1161/atvbaha.117.309521] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 05/30/2017] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Bacterial endotoxin (lipopolysaccharide)-mediated sepsis involves dysregulated systemic inflammation, which injures the lung and other organs, often fatally. Vascular endothelial cells act as both targets and mediators of lipopolysaccharide-induced inflammatory responses. Dysfunction of endothelium results in increases of proinflammatory cytokine production and permeability leakage. BMPER (bone morphogenetic protein-binding endothelial regulator), an extracellular modulator of bone morphogenetic protein signaling, has been identified as a vital component in chronic endothelial inflammatory responses and atherosclerosis. However, it is unclear whether BMPER also regulates inflammatory response in an acute setting such as sepsis. To address this question, we investigated the role of BMPER during lipopolysaccharide-induced acute lung injury. APPROACH AND RESULTS Mice missing 1 allele of BMPER (BMPER+/- mice used in the place of BMPER-/- mice that die at birth) were used for lipopolysaccharide challenge. Lipopolysaccharide-induced pulmonary inflammation and injury was reduced in BMPER+/- mice as shown by several measures, including survival rate, infiltration of inflammatory cells, edema, and production of proinflammatory cytokines. Mechanistically, we have demonstrated that BMPER is required and sufficient for the activation of nuclear factor of activated T cells c1. This BMPER-induced nuclear factor of activated T cells activation is coordinated by multiple signaling pathways, including bone morphogenetic protein-independent low-density lipoprotein receptor-related protein 1-extracellular signal-regulated kinase activation, calcineurin signaling, and low-density lipoprotein receptor-related protein 1β-mediated nuclear factor 45 nuclear export in response to BMPER treatment. CONCLUSIONS We conclude that BMPER plays a pivotal role in pulmonary inflammatory response, which provides new therapeutic options against sepsis shock. The new signaling pathway initiated by BMPER/low-density lipoprotein receptor-related protein 1 axis broadens our understanding about BMPER's role in vascular homeostasis.
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Affiliation(s)
- Pamela Lockyer
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.)
| | - Hua Mao
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.)
| | - Qiying Fan
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.)
| | - Luge Li
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.)
| | - Li-Yuan Yu-Lee
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.)
| | - N Tony Eissa
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.)
| | - Cam Patterson
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.)
| | - Liang Xie
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.)
| | - Xinchun Pi
- From the Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill (P.L.); Department of Medicine, Section of Athero & Lipo, Cardiovascular Research Institute (H.M., Q.F., L.L., L.X., X.P.), Departments of Molecular and Cellular Biology and Medicine, Section of Immunology Allergy and Rheumatology, Integrative Molecular and Biomedical Sciences (L.Y.Y.L.), and Departments of Medicine and Pathology and Immunology (N.T.E.), Baylor College of Medicine, Houston, TX; and New York-Presbyterian Hospital, New York (C.P.).
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8
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Cirilli M, Bereshchenko O, Ermakova O, Nerlov C. Insights into specificity, redundancy and new cellular functions of C/EBPa and C/EBPb transcription factors through interactome network analysis. Biochim Biophys Acta Gen Subj 2016; 1861:467-476. [PMID: 27746211 DOI: 10.1016/j.bbagen.2016.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 09/13/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND C/EBPa and C/EBPb are transcription factors with tissue specific expression regulating several important cellular processes. They work by recruiting protein complexes to a common DNA recognition motif and both are able to compensate each other's absence in many cell types, thus showing functional redundancy. They also play distinct roles in specific cellular pathways and their abnormal functioning gives raise to different human pathologies. METHODS To investigate the molecular basis of C/EBPa and C/EBPb specificity and redundancy we characterized their in vivo protein-protein interaction networks by Tandem Affinity Purification (TAP) and Mass Spectrometry (MS). To unravel the functional features of C/EBPa and C/EBPb proteomes we studied the statistical enrichment of binding partners related to Gene Ontology (GO) terms and KEGG pathways. RESULTS Our data confirmed that the C/EBPa and C/EBPb regulate biological processes like cell proliferation, apoptosis and transformation. We found that both C/EBPa and C/EBPb are involved in other cellular pathways such as RNA maturation, RNA splicing and DNA repair. Specific interactions of C/EBPa with MRE11, RUVBL1 and RUVBL2 components of DNA repair system were confirmed by co-immunoprecipitation assays. CONCLUSIONS Our comparative analysis of the C/EBPa and C/EBPb proteomes provides an insight for understanding both their redundant and specific roles in cells indicating their involvement in new pathways. Such novel predicted functions are relevant to normal cellular processes and disease phenotypes controlled by these transcription factors. GENERAL SIGNIFICANCE Functional characterization of C/EBPa and C/EBPb proteomes suggests they can regulate novel pathways and indicate potential molecular targets for therapeutic intervention.
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Affiliation(s)
- Maurizio Cirilli
- Institute of Cell Biology and Neurobiology (IBCN), CNR, via Ramarini 32, 00015 Monterotondo, Italy
| | - Oxana Bereshchenko
- Mouse Biology Unit, European Molecular Biology Laboratory, via Ramarini 32, 00015 Monterotondo, Italy; Department of Medicine, University of Perugia, Perugia 06132, Italy
| | - Olga Ermakova
- Mouse Biology Unit, European Molecular Biology Laboratory, via Ramarini 32, 00015 Monterotondo, Italy.
| | - Claus Nerlov
- Mouse Biology Unit, European Molecular Biology Laboratory, via Ramarini 32, 00015 Monterotondo, Italy; MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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9
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Zhang Y, Huang L, Fu H, Smith OK, Lin CM, Utani K, Rao M, Reinhold WC, Redon CE, Ryan M, Kim R, You Y, Hanna H, Boisclair Y, Long Q, Aladjem MI. A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells. Nat Commun 2016; 7:11748. [PMID: 27272143 PMCID: PMC4899857 DOI: 10.1038/ncomms11748] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/26/2016] [Indexed: 12/28/2022] Open
Abstract
Mammalian chromosome replication starts from distinct sites; however, the principles governing initiation site selection are unclear because proteins essential for DNA replication do not exhibit sequence-specific DNA binding. Here we identify a replication-initiation determinant (RepID) protein that binds a subset of replication-initiation sites. A large fraction of RepID-binding sites share a common G-rich motif and exhibit elevated replication initiation. RepID is required for initiation of DNA replication from RepID-bound replication origins, including the origin at the human beta-globin (HBB) locus. At HBB, RepID is involved in an interaction between the replication origin (Rep-P) and the locus control region. RepID-depleted murine embryonic fibroblasts exhibit abnormal replication fork progression and fewer replication-initiation events. These observations are consistent with a model, suggesting that RepID facilitates replication initiation at a distinct group of human replication origins. Origins of mammalian DNA replication are poorly characterised because they lack an Identifiable consensus sequence. Here the authors identify RepID, a protein that binds to a subset of G-rich replication origins and facilitates initiation from those origins.
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Affiliation(s)
- Ya Zhang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Liang Huang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Owen K Smith
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chii Mei Lin
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Koichi Utani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mishal Rao
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael Ryan
- In Silico Solutions, Fairfax, Virginia 22033, USA
| | - RyangGuk Kim
- In Silico Solutions, Fairfax, Virginia 22033, USA
| | - Yang You
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Harlington Hanna
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yves Boisclair
- Department of Animal Science, Cornell University, Ithaca, New York 14853-4801, USA
| | - Qiaoming Long
- Department of Animal Science, Cornell University, Ithaca, New York 14853-4801, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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10
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Murphy J, Hall WW, Ratner L, Sheehy N. Novel interactions between the HTLV antisense proteins HBZ and APH-2 and the NFAR protein family: Implications for the HTLV lifecycles. Virology 2016; 494:129-42. [PMID: 27110706 DOI: 10.1016/j.virol.2016.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/17/2023]
Abstract
The human T-cell leukaemia virus type 1 and type 2 (HTLV-1/HTLV-2) antisense proteins HBZ and APH-2 play key roles in the HTLV lifecycles and persistence in the host. Nuclear Factors Associated with double-stranded RNA (NFAR) proteins NF90/110 function in the lifecycles of several viruses and participate in host innate immunity against infection and oncogenesis. Using GST pulldown and co-immunoprecipitation assays we demonstrate specific novel interactions between HBZ/APH-2 and NF90/110 and characterised the protein domains involved. Moreover we show that NF90/110 significantly enhance Tax mediated LTR activation, an effect that was abolished by HBZ but enhanced by APH-2. Additionally we found that HBZ and APH-2 modulate the promoter activity of survivin and are capable of antagonising NF110-mediated survivin activation. Thus interactions between HTLV antisense proteins and the NFAR protein family have an overall positive impact on HTLV infection. Hence NFARs may represent potential therapeutic targets in HTLV infected cells.
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Affiliation(s)
- Jane Murphy
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William W Hall
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lee Ratner
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Noreen Sheehy
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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11
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Abstract
Oncogenic transcription factors are commonly activated in acute leukemias and subvert normal gene expression networks to reprogram hematopoietic progenitors into preleukemic stem cells, as exemplified by LIM-only 2 (LMO2) in T-cell acute lymphoblastic leukemia (T-ALL). Whether or not these oncoproteins interfere with other DNA-dependent processes is largely unexplored. Here, we show that LMO2 is recruited to DNA replication origins by interaction with three essential replication enzymes: DNA polymerase delta (POLD1), DNA primase (PRIM1), and minichromosome 6 (MCM6). Furthermore, tethering LMO2 to synthetic DNA sequences is sufficient to transform these sequences into origins of replication. We next addressed the importance of LMO2 in erythroid and thymocyte development, two lineages in which cell cycle and differentiation are tightly coordinated. Lowering LMO2 levels in erythroid progenitors delays G1-S progression and arrests erythropoietin-dependent cell growth while favoring terminal differentiation. Conversely, ectopic expression in thymocytes induces DNA replication and drives these cells into cell cycle, causing differentiation blockade. Our results define a novel role for LMO2 in directly promoting DNA synthesis and G1-S progression.
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12
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hnRNP K in PU.1-containing complexes recruited at the CD11b promoter: a distinct role in modulating granulocytic and monocytic differentiation of AML-derived cells. Biochem J 2014; 463:115-22. [PMID: 25005557 DOI: 10.1042/bj20140358] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PU.1 is essential for the differentiation of haemopoietic precursors and is strongly implicated in leukaemogenesis, yet the protein interactions that regulate its activity in different myeloid lineages are still largely unknown. In the present study, by combining fluorescent EMSA (electrophoretic mobility-shift assay) with MS, we reveal the presence of hnRNP K (heterogeneous nuclear ribonucleoprotein K) in molecular complexes that PU.1 forms on the CD11b promoter during the agonist-induced maturation of AML (acute myeloid leukaemia)-derived cells along both the granulocytic and the monocytic lineages. Although hnRNP K and PU.1 act synergistically during granulocytic differentiation, hnRNP K seems to have a negative effect on PU.1 activity during monocytic maturation. Since hnRNP K acts as a docking platform, integrating signal transduction pathways to nucleic acid-directed processes, it may assist PU.1 in activating or repressing transcription by recruiting lineage-specific components of the transcription machinery. It is therefore possible that hnRNP K plays a key role in the mechanisms underlying the specific targeting of protein-protein interactions identified as mediators of transcriptional activation or repression and may be responsible for the block of haemopoietic differentiation.
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13
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Castella S, Bernard R, Corno M, Fradin A, Larcher JC. Ilf3 and NF90 functions in RNA biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:243-56. [PMID: 25327818 DOI: 10.1002/wrna.1270] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/09/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Abstract
Double-stranded RNA-binding proteins (DRBPs) are known to regulate many processes of RNA metabolism due, among others, to the presence of double-stranded RNA (dsRNA)-binding motifs (dsRBMs). Among these DRBPs, Interleukin enhancer-binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by mutually exclusive and alternative splicings of the Ilf3 gene. They share common N-terminal and central sequences but display specific C-terminal regions. They present a large heterogeneity generated by several post-transcriptional and post-translational modifications involved in their subcellular localization and biological functions. While Ilf3 and NF90 were first identified as activators of gene expression, they are also implicated in cellular processes unrelated to RNA metabolism such as regulation of the cell cycle or of enzymatic activites. The implication of Ilf3 and NF90 in RNA biology will be discussed with a focus on eukaryote transcription and translation regulation, on viral replication and translation as well as on noncoding RNA field.
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Affiliation(s)
- Sandrine Castella
- Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, Sorbonne Universités, UPMC Univ Paris 06, Paris, France; Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, CNRS, UMR 7622, Paris, France
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14
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Abstract
Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation. Recent efforts indicate that the human genome likely contains hundreds of thousands of enhancers, with a typical gene embedded in a milieu of tens of enhancers. Proliferation of cis-regulatory DNAs is accompanied by increased complexity and functional diversification of transcriptional machineries recognizing distal enhancers and core promoters and by the high-order spatial organization of genetic elements. We review progress in unraveling one of the outstanding mysteries of modern biology: the dynamic communication of remote enhancers with target promoters in the specification of cellular identity.
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15
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Smith OK, Aladjem MI. Chromatin structure and replication origins: determinants of chromosome replication and nuclear organization. J Mol Biol 2014; 426:3330-41. [PMID: 24905010 DOI: 10.1016/j.jmb.2014.05.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/22/2014] [Accepted: 05/24/2014] [Indexed: 12/29/2022]
Abstract
The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review, we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome's three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication.
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Affiliation(s)
- Owen K Smith
- DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Mirit I Aladjem
- DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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16
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Regulation of Gγ-globin gene by ATF2 and its associated proteins through the cAMP-response element. PLoS One 2013; 8:e78253. [PMID: 24223142 PMCID: PMC3819381 DOI: 10.1371/journal.pone.0078253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/10/2013] [Indexed: 01/12/2023] Open
Abstract
The upstream Gγ-globin cAMP-response element (G-CRE) plays an important role in regulating Gγ-globin expression through binding of ATF2 and its DNA-binding partners defined in this study. ATF2 knockdown resulted in a significant reduction of γ-globin expression accompanied by decreased ATF2 binding to the G-CRE. By contrast, stable ATF2 expression in K562 cells increased γ-globin transcription which was reduced by ATF2 knockdown. Moreover, a similar effect of ATF2 on γ-globin expression was observed in primary erythroid progenitors. To understand the role of ATF2 in γ-globin expression, chromatographically purified G-CRE/ATF2-interacting proteins were subjected to mass spectrometry analysis; major binding partners included CREB1, cJun, Brg1, and histone deacetylases among others. Immunoprecipitation assays demonstrated interaction of these proteins with ATF2 and in vivo GCRE binding in CD34+ cells undergoing erythroid differentiation which was correlated with γ-globin expression during development. These results suggest synergism between developmental stage-specific recruitments of the ATF2 protein complex and expression of γ-globin during erythropoiesis. Microarray studies in K562 cells support ATF2 plays diverse roles in hematopoiesis and chromatin remodeling.
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17
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Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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18
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Yu Y, Pan X, Ding Y, Liu X, Tang H, Shen C, Shen H, Yang P. An iTRAQ based quantitative proteomic strategy to explore novel secreted proteins in metastatic hepatocellular carcinoma cell lines. Analyst 2013; 138:4505-11. [PMID: 23752568 DOI: 10.1039/c3an00517h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Secretomics is receiving more and more considerable attention due to the key roles of secreted proteins in cancer. Most of the potential biomarkers for clinical diagnosis and treatment of cancer are secreted proteins. However, the low concentration of secreted proteins and contaminants released from dead cells are a great challenge to secretomic profiling studies. Although some bioinformatics tools such as SecretomeP and SignalP can help to annotate or predict secreted proteins, they also cause false positive or negative rates of identification especially for nonclassical secreted proteins. Therefore, an iTRAQ based quantitative proteomics strategy was set up in this work and applied in the secretomics study of metastatic HCC cell lines. A total of 94 proteins were identified as secreted and 31 of them were newly found in our data. Compared with the known secreted proteins participating in inter-cellular signalling, most of the newly identified secreted proteins were metabolic enzymes, such as PKM2 and EHHADH, whose functions focused on the synthesis/metabolism of glucose, fatty acids and amino acids. Exploring their secretion would help to further study their bio-functions in conditioned media and the effects on the interactions of cancer cells and the microenvironment. Differences between the secretomes of the two metastatic HCC cell lines were also explored in the same experiment. This strategy showed its superiority in accurately identifying secreted proteins as well as monitoring their variation under different biological conditions.
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Affiliation(s)
- Yanyan Yu
- Department of Chemistry and Institutes of Biomedical Sciences of Shanghai Medical School, Fudan University, 138 Yi Xueyuan Road, Shanghai, 200032, PR China
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19
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Pourfarzad F, Aghajanirefah A, de Boer E, Ten Have S, Bryn van Dijk T, Kheradmandkia S, Stadhouders R, Thongjuea S, Soler E, Gillemans N, von Lindern M, Demmers J, Philipsen S, Grosveld F. Locus-specific proteomics by TChP: targeted chromatin purification. Cell Rep 2013; 4:589-600. [PMID: 23911284 DOI: 10.1016/j.celrep.2013.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/01/2013] [Accepted: 07/07/2013] [Indexed: 12/20/2022] Open
Abstract
Here, we show that transcription factors bound to regulatory sequences can be identified by purifying these unique sequences directly from mammalian cells in vivo. Using targeted chromatin purification (TChP), a double-pull-down strategy with a tetracycline-sensitive "hook" bound to a specific promoter, we identify transcription factors bound to the repressed γ-globin gene-associated regulatory regions. After validation of the binding, we show that, in human primary erythroid cells, knockdown of a number of these transcription factors induces γ-globin gene expression. Reactivation of γ-globin gene expression ameliorates the symptoms of β-thalassemia and sickle cell disease, and these factors provide potential targets for the development of therapeutics for treating these patients.
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Affiliation(s)
- Farzin Pourfarzad
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, the Netherlands; Center for Biomedical Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, the Netherlands
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20
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Shamanna RA, Hoque M, Pe'ery T, Mathews MB. Induction of p53, p21 and apoptosis by silencing the NF90/NF45 complex in human papilloma virus-transformed cervical carcinoma cells. Oncogene 2012. [PMID: 23208500 PMCID: PMC4032571 DOI: 10.1038/onc.2012.533] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The heterodimeric nuclear factor 90/nuclear factor 45 complex (NF90/NF45) binds nucleic acids and is a multifunctional regulator of gene expression. Here we report that depletion of NF90/NF45 restores the expression of the p53 and p21 proteins in cervical carcinoma cells infected with high-risk human papillomaviruses (HPV). Knockdown of either NF90 or NF45 by RNA interference led to greatly elevated levels of p53 and p21 proteins in HPV-derived HeLa and SiHa cells, but not in other cancerous or normal cell lines. In HeLa cells, p21 mRNA increased concomitantly but the level of p53 mRNA was unaffected. RNA interference directed against p53 prevented the induction of both proteins. These results indicated that the up-regulation of p21 is due to p53-dependent transcription, whereas p53 is regulated post-transcriptionally. Proteasome-mediated turnover of p53 is accelerated by the HPV E6 and cellular E6AP proteins. We therefore examined the hypothesis that this pathway is regulated by NF90/NF45. Indeed, depletion of NF90 attenuated the expression of E6 RNA and inhibited transcription from the HPV early promoter, revealing a new role for NF90/NF45 in HPV gene expression. The transcription inhibition was largely independent of the reduction of P-TEFb levels caused by NF90 depletion. Consistent with p53 derepression, NF90/NF45-depleted HeLa cells displayed elevated PARP cleavage and susceptibility to camptothecin-induced apoptosis. We conclude that high-risk strains of HPV utilize the cellular NF90/NF45 complex for viral E6 expression in infected cervical carcinoma cell lines. Interference with NF90/NF45 function could assist in controlling cervical carcinoma.
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Affiliation(s)
- R A Shamanna
- 1] Department of Biochemistry and Molecular Biology, New Jersey Medical School, UMDNJ, Newark, NJ, USA [2] Graduate School of Biomedical Sciences, UMDNJ, Newark, NJ, USA
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21
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Dellino GI, Cittaro D, Piccioni R, Luzi L, Banfi S, Segalla S, Cesaroni M, Mendoza-Maldonado R, Giacca M, Pelicci PG. Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing. Genome Res 2012. [PMID: 23187890 PMCID: PMC3530669 DOI: 10.1101/gr.142331.112] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G1 and the probability of firing during S.
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Affiliation(s)
- Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy.
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22
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McConnell KH, Dixon M, Calvi BR. The histone acetyltransferases CBP and Chameau integrate developmental and DNA replication programs in Drosophila ovarian follicle cells. Development 2012; 139:3880-90. [PMID: 22951641 DOI: 10.1242/dev.083576] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DNA replication origin activity changes during development. Chromatin modifications are known to influence the genomic location of origins and the time during S phase that they initiate replication in different cells. However, how chromatin regulates origins in concert with cell differentiation remains poorly understood. Here, we use developmental gene amplification in Drosophila ovarian follicle cells as a model to investigate how chromatin modifiers regulate origins in a developmental context. We find that the histone acetyltransferase (HAT) Chameau (Chm) binds to amplicon origins and is partially required for their function. Depletion of Chm had relatively mild effects on origins during gene amplification and genomic replication compared with previous knockdown of its ortholog HBO1 in human cells, which has severe effects on origin function. We show that another HAT, CBP (Nejire), also binds amplicon origins and is partially required for amplification. Knockdown of Chm and CBP together had a more severe effect on nucleosome acetylation and amplicon origin activity than knockdown of either HAT alone, suggesting that these HATs collaborate in origin regulation. In addition to their local function at the origin, we show that Chm and CBP also globally regulate the developmental transition of follicle cells into the amplification stages of oogenesis. Our results reveal a complexity of origin epigenetic regulation by multiple HATs during development and suggest that chromatin modifiers are a nexus that integrates differentiation and DNA replication programs.
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The chromatin backdrop of DNA replication: lessons from genetics and genome-scale analyses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:794-801. [PMID: 22342530 DOI: 10.1016/j.bbagrm.2012.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/27/2012] [Accepted: 01/31/2012] [Indexed: 01/04/2023]
Abstract
The entire cellular genome must replicate during each cell cycle, but it is yet unclear how replication proceeds along with chromatin condensation and remodeling while ensuring the fidelity of the replicated genome. Mapping replication initiation sites can provide clues for the coordination of DNA replication and transcription on a whole-genome scale. Here we discuss recent insights obtained from genome-scale analyses of replication initiation sites and transcription in mammalian cells and ask how transcription and chromatin modifications affect the frequency of replication initiation events. We also discuss DNA sequences, such as insulators and replicators, which modulate replication and transcription of target genes, and use genome-wide maps of replication initiation sites to evaluate possible commonalities between replicators and chromatin insulators. This article is part of a Special Issue entitled: Chromatin in time and space.
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Interaction of HTLV-1 Tax with minichromosome maintenance proteins accelerates the replication timing program. Blood 2011; 119:151-60. [PMID: 22058115 DOI: 10.1182/blood-2011-05-356790] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Tax oncoprotein encoded by the human T-cell leukemia virus type 1 plays a pivotal role in viral persistence and pathogenesis. Human T-cell leukemia virus type 1-infected cells proliferate faster than normal lymphocytes, expand through mitotic division, and accumulate genomic lesions. Here, we show that Tax associates with the minichromosome maintenance MCM2-7 helicase complex and localizes to origins of replication. Tax modulates the spatiotemporal program of origin activation and fires supplementary origins at the onset of S phase. Thereby, Tax increases the DNA replication rate, accelerates S phase progression, but also generates a replicative stress characterized by the presence of genomic lesions. Mechanistically, Tax favors p300 recruitment and histone hyperacetylation at late replication domains, advancing their replication timing in early S phase.
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The NF90/NF45 complex participates in DNA break repair via nonhomologous end joining. Mol Cell Biol 2011; 31:4832-43. [PMID: 21969602 DOI: 10.1128/mcb.05849-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nuclear factor 90 (NF90), an RNA-binding protein implicated in the regulation of gene expression, exists as a heterodimeric complex with NF45. We previously reported that depletion of the NF90/NF45 complex results in a multinucleated phenotype. Time-lapse microscopy revealed that binucleated cells arise by incomplete abscission of progeny cells followed by fusion. Multinucleate cells arose through aberrant division of binucleated cells and displayed abnormal metaphase plates and anaphase chromatin bridges suggestive of DNA repair defects. NF90 and NF45 are known to interact with the DNA-dependent protein kinase (DNA-PK), which is involved in telomere maintenance and DNA repair by nonhomologous end joining (NHEJ). We hypothesized that NF90 modulates the activity of DNA-PK. In an in vitro NHEJ assay system, DNA end joining was reduced by NF90/NF45 immunodepletion or by RNA digestion to an extent similar to that for catalytic subunit DNA-PKcs immunodepletion. In vivo, NF90/NF45-depleted cells displayed increased γ-histone 2A.X foci, indicative of an accumulation of double-strand DNA breaks (DSBs), and increased sensitivity to ionizing radiation consistent with decreased DSB repair. Further, NF90/NF45 knockdown reduced end-joining activity in vivo. These results identify the NF90/NF45 complex as a regulator of DNA damage repair mediated by DNA-PK and suggest that structured RNA may modulate this process.
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