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Xiao ZX, Liang R, Olsen N, Zheng SG. Roles of IRF4 in various immune cells in systemic lupus erythematosus. Int Immunopharmacol 2024; 133:112077. [PMID: 38615379 DOI: 10.1016/j.intimp.2024.112077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Interferon regulatory factor 4 (IRF4) is a member of IRF family of transcription factors which mainly regulates the transcription of IFN. IRF4 is restrictively expressed in immune cells such as T and B cells, macrophages, as well as DC. It is essential for the development and function of these cells. Since these cells take part in the homeostasis of the immune system and dysfunction of them contributes to the initiation and progress of systemic lupus erythematosus (SLE), the roles of IRF4 in the SLE development becomes an important topic. Here we systemically discuss the biological characteristics of IRF4 in various immune cells and analyze the pathologic effects of IRF4 alteration in SLE and the potential targeting therapeutics of SLE.
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Affiliation(s)
- Ze Xiu Xiao
- Department of Immunology, the School of Cell and Gene Therapy, Songjiang Research Institute and Songjiang Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 201600, China; Department of Clinical Immunology, the Third Affiliated Hospital at the Sun Yat-sen University, Guangzhou 510630, China
| | - Rongzhen Liang
- Department of Immunology, the School of Cell and Gene Therapy, Songjiang Research Institute and Songjiang Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 201600, China
| | - Nancy Olsen
- Division of Rheumatology, Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, United States
| | - Song Guo Zheng
- Department of Immunology, the School of Cell and Gene Therapy, Songjiang Research Institute and Songjiang Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 201600, China.
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2
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Wiggins DA, Maxwell JN, Nelson DE. Exploring the role of CITED transcriptional regulators in the control of macrophage polarization. Front Immunol 2024; 15:1365718. [PMID: 38646545 PMCID: PMC11032013 DOI: 10.3389/fimmu.2024.1365718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Macrophages are tissue resident innate phagocytic cells that take on contrasting phenotypes, or polarization states, in response to the changing combination of microbial and cytokine signals at sites of infection. During the opening stages of an infection, macrophages adopt the proinflammatory, highly antimicrobial M1 state, later shifting to an anti-inflammatory, pro-tissue repair M2 state as the infection resolves. The changes in gene expression underlying these transitions are primarily governed by nuclear factor kappaB (NF-κB), Janus kinase (JAK)/signal transducer and activation of transcription (STAT), and hypoxia-inducible factor 1 (HIF1) transcription factors, the activity of which must be carefully controlled to ensure an effective yet spatially and temporally restricted inflammatory response. While much of this control is provided by pathway-specific feedback loops, recent work has shown that the transcriptional co-regulators of the CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxy-terminal domain (CITED) family serve as common controllers for these pathways. In this review, we describe how CITED proteins regulate polarization-associated gene expression changes by controlling the ability of transcription factors to form chromatin complexes with the histone acetyltransferase, CBP/p300. We will also cover how differences in the interactions between CITED1 and 2 with CBP/p300 drive their contrasting effects on pro-inflammatory gene expression.
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Affiliation(s)
| | | | - David E. Nelson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
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3
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Rundberg Nilsson AJ, Xian H, Shalapour S, Cammenga J, Karin M. IRF1 regulates self-renewal and stress responsiveness to support hematopoietic stem cell maintenance. SCIENCE ADVANCES 2023; 9:eadg5391. [PMID: 37889967 PMCID: PMC10610924 DOI: 10.1126/sciadv.adg5391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023]
Abstract
Hematopoietic stem cells (HSCs) are tightly controlled to maintain a balance between blood cell production and self-renewal. While inflammation-related signaling is a critical regulator of HSC activity, the underlying mechanisms and the precise functions of specific factors under steady-state and stress conditions remain incompletely understood. We investigated the role of interferon regulatory factor 1 (IRF1), a transcription factor that is affected by multiple inflammatory stimuli, in HSC regulation. Our findings demonstrate that the loss of IRF1 from mouse HSCs significantly impairs self-renewal, increases stress-induced proliferation, and confers resistance to apoptosis. In addition, given the frequent abnormal expression of IRF1 in leukemia, we explored the potential of IRF1 expression level as a stratification marker for human acute myeloid leukemia. We show that IRF1-based stratification identifies distinct cancer-related signatures in patient subgroups. These findings establish IRF1 as a pivotal HSC controller and provide previously unknown insights into HSC regulation, with potential implications to IRF1 functions in the context of leukemia.
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Affiliation(s)
- Alexandra J. S. Rundberg Nilsson
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Molecular Medicine and Gene Therapy, Institution for Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
- Lund Stem Cell Center, Medical Faculty, Lund University, Lund, Sweden
| | - Hongxu Xian
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shabnam Shalapour
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jörg Cammenga
- Division of Molecular Medicine and Gene Therapy, Institution for Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
- Lund Stem Cell Center, Medical Faculty, Lund University, Lund, Sweden
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
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4
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Nudelman K, Nho K, Zhang M, McDonald BC, Zhai W, Small BJ, Wegel CE, Jacobsen PB, Jim HSL, Patel SK, Graham DMA, Ahles TA, Root JC, Foroud T, Breen EC, Carroll JE, Mandelblatt JS, Saykin AJ. Genetic Variants Associated with Longitudinal Cognitive Performance in Older Breast Cancer Patients and Controls. Cancers (Basel) 2023; 15:2877. [PMID: 37296840 PMCID: PMC10252108 DOI: 10.3390/cancers15112877] [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: 03/12/2023] [Revised: 04/13/2023] [Accepted: 05/03/2023] [Indexed: 06/12/2023] Open
Abstract
Background: There have been no published genome-wide studies of the genetics of cancer- and treatment-related cognitive decline (CRCD); the purpose of this study is to identify genetic variants associated with CRCD in older female breast cancer survivors. Methods: Analyses included white non-Hispanic women with non-metastatic breast cancer aged 60+ (N = 325) and age-, racial/ethnic group-, and education-matched controls (N = 340) with pre-systemic treatment and one-year follow-up cognitive assessment. CRCD was evaluated using longitudinal domain scores on cognitive tests of attention, processing speed, and executive function (APE), and learning and memory (LM). Linear regression models of one-year cognition included an interaction term for SNP or gene SNP enrichment*cancer case/control status, controlling for demographic variables and baseline cognition. Results: Cancer patients carrying minor alleles for two SNPs, rs76859653 (chromosome 1) in the hemicentin 1 (HMCN1) gene (p = 1.624 × 10-8), and rs78786199 (chromosome 2, p = 1.925 × 10-8) in an intergenic region had lower one-year APE scores than non-carriers and controls. Gene-level analyses showed the POC5 centriolar protein gene was enriched for SNPs associated with differences in longitudinal LM performance between patients and controls. Conclusions: The SNPs associated with cognition in survivors, but not controls, were members of the cyclic nucleotide phosphodiesterase family, that play important roles in cell signaling, cancer risk, and neurodegeneration. These findings provide preliminary evidence that novel genetic loci may contribute to susceptibility to CRCD.
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Affiliation(s)
- Kelly Nudelman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Genetics Biobank, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kwangsik Nho
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Genetics Biobank, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brenna C. McDonald
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wanting Zhai
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Brent J. Small
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- School of Aging Studies, University of South Florida, Tampa, FL 33620, USA
| | - Claire E. Wegel
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Genetics Biobank, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Paul B. Jacobsen
- Division of Cancer Control and Population Studies, National Cancer Institute, Bethesda, MD 20892, USA
| | - Heather S. L. Jim
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Sunita K. Patel
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Deena M. A. Graham
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Tim A. Ahles
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James C. Root
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Genetics Biobank, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elizabeth C. Breen
- Cousins Center for Psychoneuroimmunology, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry & Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Judith E. Carroll
- Cousins Center for Psychoneuroimmunology, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry & Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Jeanne S. Mandelblatt
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Andrew J. Saykin
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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5
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Rundberg Nilsson A, Xian H, Shalapour S, Cammenga J, Karin M. IRF1 regulates self-renewal and stress-responsiveness to support hematopoietic stem cell maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525321. [PMID: 36747722 PMCID: PMC9900858 DOI: 10.1101/2023.01.24.525321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Inflammatory mediators induce emergency myelopoiesis and cycling of adult hematopoietic stem cells (HSCs) through incompletely understood mechanisms. To suppress the unwanted effects of inflammation and preserve its beneficial outcomes, the mechanisms by which inflammation affects hematopoiesis need to be fully elucidated. Rather than focusing on specific inflammatory stimuli, we here investigated the role of transcription factor Interferon (IFN) regulatory factor 1 (IRF1), which receives input from several inflammatory signaling pathways. We identify IRF1 as a master HSC regulator. IRF1 loss impairs HSC self-renewal, increases stress-induced cell cycle activation, and confers apoptosis resistance. Transcriptomic analysis revealed an aged, inflammatory signature devoid of IFN signaling with reduced megakaryocytic/erythroid priming and antigen presentation in IRF1-deficient HSCs. Finally, we conducted IRF1-based AML patient stratification to identify groups with distinct proliferative, survival and differentiation features, overlapping with our murine HSC results. Our findings position IRF1 as a pivotal regulator of HSC preservation and stress-induced responses.
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Affiliation(s)
- Alexandra Rundberg Nilsson
- Department of Pharmacology, Laboratory of Gene Regulation and
Signal Transduction, University of California San Diego (UCSD), United States
- Medical Faculty, Division of Molecular Medicine and Gene Therapy,
Institution for Laboratory Medicine, Lund University, Sweden
- Medical Faculty, Lund Stem Cell Center, Lund University,
Sweden
- Lead contact
| | - Hongxu Xian
- Department of Pharmacology, Laboratory of Gene Regulation and
Signal Transduction, University of California San Diego (UCSD), United States
| | - Shabnam Shalapour
- Department of Pharmacology, Laboratory of Gene Regulation and
Signal Transduction, University of California San Diego (UCSD), United States
- Department of Cancer Biology, The University of Texas MD Anderson
Cancer Center, United States
| | - Jörg Cammenga
- Medical Faculty, Division of Molecular Medicine and Gene Therapy,
Institution for Laboratory Medicine, Lund University, Sweden
- Medical Faculty, Lund Stem Cell Center, Lund University,
Sweden
| | - Michael Karin
- Department of Pharmacology, Laboratory of Gene Regulation and
Signal Transduction, University of California San Diego (UCSD), United States
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6
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Insights into Regulators of p53 Acetylation. Cells 2022; 11:cells11233825. [PMID: 36497084 PMCID: PMC9737083 DOI: 10.3390/cells11233825] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
The tumor suppressor p53 is a transcription factor that regulates the expression of dozens of target genes and diverse physiological processes. To precisely regulate the p53 network, p53 undergoes various post-translational modifications and alters the selectivity of target genes. Acetylation plays an essential role in cell fate determination through the activation of p53. Although the acetylation of p53 has been examined, the underlying regulatory mechanisms remain unclear and, thus, have attracted the interest of researchers. We herein discuss the role of acetylation in the p53 pathway, with a focus on p53 acetyltransferases and deacetylases. We also review recent findings on the regulators of these enzymes to understand the mode of p53 acetylation from a broader perspective.
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7
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Hogg SJ, Motorna O, Kearney CJ, Derrick EB, House IG, Todorovski I, Kelly MJ, Zethoven M, Bromberg KD, Lai A, Beavis PA, Shortt J, Johnstone RW, Vervoort SJ. Distinct modulation of IFNγ-induced transcription by BET bromodomain and catalytic P300/CBP inhibition in breast cancer. Clin Epigenetics 2022; 14:96. [PMID: 35902886 PMCID: PMC9336046 DOI: 10.1186/s13148-022-01316-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022] Open
Abstract
Background Interferon gamma (IFNγ) is a pro-inflammatory cytokine that directly activates the JAK/STAT pathway. However, the temporal dynamics of chromatin remodeling and transcriptional activation initiated by IFNγ have not been systematically profiled in an unbiased manner. Herein, we integrated transcriptomic and epigenomic profiling to characterize the acute epigenetic changes induced by IFNγ stimulation in a murine breast cancer model. Results We identified de novo activation of cis-regulatory elements bound by Irf1 that were characterized by increased chromatin accessibility, differential usage of pro-inflammatory enhancers, and downstream recruitment of BET proteins and RNA polymerase II. To functionally validate this hierarchical model of IFNγ-driven transcription, we applied selective antagonists of histone acetyltransferases P300/CBP or acetyl-lysine readers of the BET family. This highlighted that histone acetylation is an antecedent event in IFNγ-driven transcription, whereby targeting of P300/CBP acetyltransferase activity but not BET inhibition could curtail the epigenetic remodeling induced by IFNγ through suppression of Irf1 transactivation. Conclusions These data highlight the ability for epigenetic therapies to reprogram pro-inflammatory gene expression, which may have therapeutic implications for anti-tumor immunity and inflammatory diseases. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01316-5.
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Affiliation(s)
- Simon J Hogg
- Gene Regulation Laboratory, Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.,Oncology Discovery, AbbVie, South San Francisco, CA, USA
| | - Olga Motorna
- Gene Regulation Laboratory, Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.,Monash Haematology, Monash Health, Clayton, Australia
| | - Conor J Kearney
- Gene Regulation Laboratory, Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Emily B Derrick
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Australia
| | - Imran G House
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Australia
| | - Izabela Todorovski
- Gene Regulation Laboratory, Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Madison J Kelly
- Gene Regulation Laboratory, Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Magnus Zethoven
- Gene Regulation Laboratory, Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | | | - Albert Lai
- Oncology Discovery, AbbVie, North Chicago, IL, USA
| | - Paul A Beavis
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Australia
| | - Jake Shortt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.,Monash Haematology, Monash Health, Clayton, Australia.,School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, 3000, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.
| | - Stephin J Vervoort
- Gene Regulation Laboratory, Peter MacCallum Cancer Center, 305 Grattan Street, Melbourne, VIC, 3000, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia. .,The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
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8
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Wang H, Xie L, Song X, Wang J, Li X, Lin Z, Su T, Liang B, Huang D. Purine-Induced IFN-γ Promotes Uric Acid Production by Upregulating Xanthine Oxidoreductase Expression. Front Immunol 2022; 13:773001. [PMID: 35154100 PMCID: PMC8829549 DOI: 10.3389/fimmu.2022.773001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/07/2022] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Limiting purine intake, inhibiting xanthine oxidoreductase (XOR) and inhibiting urate reabsorption in proximal tubule by uricosuric drugs, to reduce serum uric acid (UA) levels, are recognized treatments for gout. However, the mechanism of increased how XOR expression and activity in hyperuricemia and gout remains unclear. This study aims to explore whether exogenous purines are responsible for increased XOR expression and activity. METHODS HepG2 and Bel-7402 human hepatoma cells were stimulated with exogenous purine, or were exposed to conditioned growth medium of purine-stimulated Jurkat cells, followed by measurement of XOR expression and UA production to determine the effect of lymphocyte-secreted cytokines on XOR expression in hepatocytes. The expression of STAT1, IRF1 and CBP and their binding on the XDH promoter were detected by western blotting and ChIP-qPCR. The level of DNA methylation was determined by bisulfite sequencing PCR. Blood samples from 117 hyperuricemia patients and 119 healthy individuals were collected to analyze the correlation between purine, UA and IFN-γ concentrations. RESULTS Excess of purine was metabolized to UA in hepatocyte metabolism by XOR that was induced by IFN-γ secreted in the conditioned growth medium of Jurkat cells in response to exogenous purine, but it did not directly induce XOR expression. IFN-γ upregulated XOR expression due to the enhanced binding of STAT1 to IRF1 to further recruit CBP to the XDH promoter. Clinical data showed positive correlation of serum IFN-γ with both purine and UA, and associated risk of hyperuricemia. CONCLUSION Purine not only acts as a metabolic substrate of XOR for UA production, but it induces inflammation through IFN-γ secretion that stimulates UA production through elevation of XOR expression.
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Affiliation(s)
- Huanhuan Wang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Lingzhu Xie
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Xuhong Song
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Jing Wang
- Department of Clinical Laboratory Medicine, Mianyang Central Hospital, Mianyang, China
| | - Xinyan Li
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Zhike Lin
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Ting Su
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Bin Liang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Dongyang Huang
- Department of Cell Biology and Genetics, Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Research Center of Translational Medicine, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
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9
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Irinotecan (CPT-11) Canonical Anti-Cancer Drug Can also Modulate Antiviral and Pro-Inflammatory Responses of Primary Human Synovial Fibroblasts. Cells 2021; 10:cells10061431. [PMID: 34201243 PMCID: PMC8230279 DOI: 10.3390/cells10061431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/29/2022] Open
Abstract
Alphaviruses are a group of arboviruses that generate chronic inflammatory rheumatisms in humans. Currently, no approved vaccines or antiviral therapies are available to prevent or treat alphavirus-induced diseases. The aim of this study was to evaluate the repositioning of the anti-cancer molecule irinotecan as a potential modulator of the antiviral and inflammatory responses of primary human synovial fibroblasts (HSF), the main stromal cells of the joint synovium. HSF were exposed to O’nyong-nyong virus (ONNV) and polyinosinic-polycytidylic acid (PIC) to mimic, respectively, acute and chronic infectious settings. The cytokine IL-1β was used as a major pro-inflammatory cytokine to stimulate HSF. Quantitative RT-PCR analysis revealed that irinotecan at 15 µM was able to amplify the antiviral response (i.e., interferon-stimulated gene expression) of HSF exposed to PIC and reduce the expression of pro-inflammatory genes (CXCL8, IL-6 and COX-2) upon IL-1β treatment. These results were associated with the regulation of the expression of several genes, including those encoding for STAT1, STAT2, p53 and NF-κB. Irinotecan did not modulate these responses in both untreated cells and cells stimulated with ONNV. This suggests that this drug could be therapeutically useful for the treatment of chronic and severe (rather than acute) arthritis due to viruses.
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10
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Wang S, Somisetty VS, Bai B, Chernukhin I, Niskanen H, Kaikkonen MU, Bellet M, Carroll JS, Hurtado A. The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen. Oncogene 2020; 39:6300-6312. [PMID: 32843722 PMCID: PMC7529584 DOI: 10.1038/s41388-020-01435-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 08/05/2020] [Accepted: 08/17/2020] [Indexed: 01/13/2023]
Abstract
Tamoxifen is the most prescribed selective estrogen receptor (ER) modulator in patients with ER-positive breast cancers. Tamoxifen requires the transcription factor paired box 2 protein (PAX2) to repress the transcription of ERBB2/HER2. Now, we identified that PAX2 inhibits cell growth of ER+/HER2- tumor cells in a dose-dependent manner. Moreover, we have identified that cell growth inhibition can be achieved by expressing moderate levels of PAX2 in combination with tamoxifen treatment. Global run-on sequencing of cells overexpressing PAX2, when coupled with PAX2 ChIP-seq, identified common targets regulated by both PAX2 and tamoxifen. The data revealed that PAX2 can inhibit estrogen-induced gene transcription and this effect is enhanced by tamoxifen, suggesting that they converge on repression of the same targets. Moreover, PAX2 and tamoxifen have an additive effect and both induce coding genes and enhancer RNAs (eRNAs). PAX2-tamoxifen upregulated genes are also enriched with PAX2 eRNAs. The enrichment of eRNAs is associated with the highest expression of genes that positivity regulate apoptotic processes. In luminal tumors, the expression of a subset of these proapoptotic genes predicts good outcome and their expression are significantly reduced in tumors of patients with relapse to tamoxifen treatment. Mechanistically, PAX2 and tamoxifen coexert an antitumoral effect by maintaining high levels of transcription of tumor suppressors that promote cell death. The apoptotic effect is mediated in large part by the gene interferon regulatory factor 1. Altogether, we conclude that PAX2 contributes to better clinical outcome in tamoxifen treated ER-positive breast cancer patients by repressing estrogen signaling and inducing cell death related pathways.
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MESH Headings
- Antineoplastic Agents, Hormonal/pharmacology
- Antineoplastic Agents, Hormonal/therapeutic use
- Apoptosis/drug effects
- Apoptosis/genetics
- Breast/pathology
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Chromatin Immunoprecipitation Sequencing
- Drug Resistance, Neoplasm/genetics
- Estrogens/metabolism
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Interferon Regulatory Factor-1/genetics
- Interferon Regulatory Factor-1/metabolism
- Neoplasm Recurrence, Local/genetics
- PAX2 Transcription Factor/metabolism
- Prognosis
- Promoter Regions, Genetic/genetics
- Receptor, ErbB-2/metabolism
- Receptors, Estrogen/antagonists & inhibitors
- Receptors, Estrogen/metabolism
- Signal Transduction/drug effects
- Tamoxifen/pharmacology
- Tamoxifen/therapeutic use
- Transcriptional Activation/drug effects
- Up-Regulation
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Affiliation(s)
- Shixiong Wang
- Cell Cycle Regulations Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Blindern, P.O. 1137, 0318, Oslo, Norway
| | - Venkata S Somisetty
- Cell Cycle Regulations Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Blindern, P.O. 1137, 0318, Oslo, Norway
| | - Baoyan Bai
- Cell Cycle Regulations Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Blindern, P.O. 1137, 0318, Oslo, Norway
| | - Igor Chernukhin
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Henri Niskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland
| | - Meritxell Bellet
- Vall Hebron Institute of Oncology, Barcelona, Spain
- Vall Hebron University Hospital, Barcelona, Spain
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Antoni Hurtado
- Cancer Genomics and Proteomics Group, Department of Biomedical Sciences, University of Barcelona, Casanova, 143, 08014, Barcelona, Spain.
- August Pi i Sunyer Research Center (IDIBAPS), c/Rosselló, 149-153, 08036, Barcelona, Spain.
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11
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Li W, Edwards A, Cox MS, Raabis SM, Skarlupka JH, Steinberger AJ, Murphy B, Larsen A, Suen G. Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents. Physiol Genomics 2020; 52:333-346. [PMID: 32567508 DOI: 10.1152/physiolgenomics.00005.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Development of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity of dairy cattle. The role of early microbial colonization on GIT development in neonatal cattle and the associated molecular changes remain largely unknown, particularly for the small intestine. In this study, we performed artificial dosing of exogenous rumen fluid during the early life of the calf, starting at birth through the weaning transition at 8 wk. Six calves were included in this study. At 8 wk of age, tissue from the ileum was collected and subjected to host transcriptome and microbial metatranscriptome analysis using RNA sequencing. A total of 333 genes showed significant differential expression (DE) (fold-change ≥2; adjusted P < 0.1, mean read-count ≥10) between the treated and control calves. Gene ontology analysis indicated that these DE genes are predominantly associated with processes related to the host immune response (P < 0.0001). Association analysis between the host gene expression and the microbial genus abundance identified 57 genes as having significant correlation with the ileum microbial genera (P < 0.0001). Of these, three genes showed significant association with six microbial genera: lysozyme 2 (LYZ2), fatty acid binding protein 5 (FABP5), and fucosyltransferase (FUT1). Specifically, the profound increase in expression of LYZ2 in treated calves suggests the initiation of antibacterial activity and innate response from the host. Despite the limitation of a relatively small sample size, this study sheds light on the potential impact of early introduction of microbes on the small intestine of calves.
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Affiliation(s)
- Wenli Li
- The Cell Wall Utilization and Biology Laboratory, US Dairy Forage Research Center, US Department of Agriculture Agricultural Research Service, Madison, Wisconsin
| | - Andrea Edwards
- Department of Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Madison S Cox
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sarah M Raabis
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Joseph H Skarlupka
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin
| | | | - Brianna Murphy
- Department of Nutritional Science, University of Wisconsin-Madison, Madison, Wisconsin
| | - Anna Larsen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin
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12
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Valverde-Estrella L, López-Serrat M, Sánchez-Sànchez G, Vico T, Lloberas J, Celada A. Induction of Samhd1 by interferon gamma and lipopolysaccharide in murine macrophages requires IRF1. Eur J Immunol 2020; 50:1321-1334. [PMID: 32270872 DOI: 10.1002/eji.201948491] [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: 11/27/2019] [Revised: 03/02/2020] [Accepted: 04/06/2020] [Indexed: 12/11/2022]
Abstract
SAMHD1 is an enzyme with phosphohydrolase activity. Mutations in SAMHD1 have been linked to the development of Aicardi-Goutières syndrome in humans. This enzyme also has the capacity to restrict HIV virus replication in macrophages. Here, we report that Samhd1 is highly expressed in murine macrophages and is regulated by proinflammatory (IFN-γ and LPS) but not by anti-inflammatory (IL-4 or IL-10) activators. The induction of Samhd1 follows the pattern of an intermediate gene that requires protein synthesis. In transient transfection experiments using the Samhd1 promoter, we found that a fragment of 27 bps of this gene, falling between -937 and -910 bps relative to the transcription start site, is required for IFN-γ-dependent activation. Using EMSAs, we determined that IFN-γ treatment led to the elimination of a protein complex. Chromatin immunoprecipitation assays and siRNA experiments revealed that IRF1 is required for IFN-γ- or LPS-induced Samhd1 expression. Therefore, our results indicate that Samhd1 is stimulated by proinflammatory agents IFN-γ and LPS. Moreover, they reveal that these two agents, via IRF1, eliminate a protein complex that may be related to a repressor, thereby, triggering Samhd1 expression.
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Affiliation(s)
- Lorena Valverde-Estrella
- Macrophage Biology Group, Department of Cellular Biology, Physiology and Immunology, Universitat de Barcelona, Barcelona, Spain
| | - Martí López-Serrat
- Macrophage Biology Group, Department of Cellular Biology, Physiology and Immunology, Universitat de Barcelona, Barcelona, Spain
| | - Guillem Sánchez-Sànchez
- Macrophage Biology Group, Department of Cellular Biology, Physiology and Immunology, Universitat de Barcelona, Barcelona, Spain
| | - Tania Vico
- Macrophage Biology Group, Department of Cellular Biology, Physiology and Immunology, Universitat de Barcelona, Barcelona, Spain
| | - Jorge Lloberas
- Macrophage Biology Group, Department of Cellular Biology, Physiology and Immunology, Universitat de Barcelona, Barcelona, Spain
| | - Antonio Celada
- Macrophage Biology Group, Department of Cellular Biology, Physiology and Immunology, Universitat de Barcelona, Barcelona, Spain
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13
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Li Y, Liu Y, Huang Y, Yang K, Xiao T, Xiong J, Wang K, Liu C, He T, Yu Y, Han W, Wang Y, Bi X, Zhang J, Huang Y, Zhang B, Zhao J. IRF-1 promotes renal fibrosis by downregulation of Klotho. FASEB J 2020; 34:4415-4429. [PMID: 31965641 DOI: 10.1096/fj.201902446r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/29/2019] [Accepted: 01/13/2020] [Indexed: 01/06/2023]
Abstract
Although the key role of renal fibrosis in the progression of chronic kidney disease (CKD) is well known, the causes of renal fibrosis are not fully clarified. In this study, interferon regulatory factor 1 (IRF-1), a mammalian transcription factor, was highly expressed in fibrotic kidney of CKD patients. Concordantly, the expression level of IRF-1 was significantly elevated in the kidney of unilateral ureteral obstruction (UUO) and Adriamycin nephropathy (ADR) mice. In tubular epithelial cells, overexpression of IRF-1 could induce profibrotic markers expression, which accompanied by dramatic downregulation of Klotho, an important inhibitor of renal fibrosis. Luciferase reporter analysis and ChIP assay revealed that IRF-1 repressed Klotho expression by downregulation of C/EBP-β, which regulates Klotho gene transcription via directly binding to its promoter. Further investigation showed that tumor necrosis factor-alpha may be an important inducement for the increase of IRF-1 in tubular epithelial cells after UUO and genetic deletion of IRF-1 attenuated renal fibrosis in UUO mice. Hence, these findings demonstrate that IRF-1 contributes to the pathogenesis of renal fibrosis by downregulation of Klotho, and suppresses IRF-1 may be a potential therapeutic target for CKD.
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Affiliation(s)
- Yan Li
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yong Liu
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yinghui Huang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Ke Yang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Tangli Xiao
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jiachuan Xiong
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Kailong Wang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Chi Liu
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Ting He
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yanlin Yu
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Wenhao Han
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yue Wang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xianjin Bi
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jingbo Zhang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yunjian Huang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Bo Zhang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jinghong Zhao
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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14
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Otálora-Otálora BA, Florez M, López-Kleine L, Canas Arboleda A, Grajales Urrego DM, Rojas A. Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases. Front Genet 2019; 10:1260. [PMID: 31867044 PMCID: PMC6908522 DOI: 10.3389/fgene.2019.01260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/14/2019] [Indexed: 12/09/2022] Open
Abstract
Background: Epidemiological and clinical evidence points cancer comorbidity with pulmonary chronic disease. The acquisition of some hallmarks of cancer by cells affected with lung pathologies as a cell adaptive mechanism to a shear stress, suggests that could be associated with the establishment of tumoral processes. Objective: To propose a bioinformatic pipeline for the identification of all deregulated genes and the transcriptional regulators (TFs) that are coexpressed during lung cancer establishment, and therefore could be important for the acquisition of the hallmarks of cancer. Methods: Ten microarray datasets (six of lung cancer, four of lung diseases) comparing normal and diseases-related lung tissue were selected to identify hub differentiated expressed genes (DEGs) in common between lung pathologies and lung cancer, along with transcriptional regulators through the utilization of specialized libraries from R language. DAVID bioinformatics tool for gene enrichment analyses was used to identify genes with experimental evidence associated to tumoral processes and signaling pathways. Coexpression networks of DEGs and TFs in lung cancer establishment were created with Coexnet library, and a survival analysis of the main hub genes was made. Results: Two hundred ten DEGs were identified in common between lung cancer and other lung diseases related to the acquisition of tumoral characteristics, which are coexpressed in a lung cancer network with TFs, suggesting that could be related to the establishment of the tumoral pathology in lung. The comparison of the coexpression networks of lung cancer and other lung diseases allowed the identification of common connectivity patterns (CCPs) with DEGs and TFs correlated to important tumoral processes and signaling pathways, that haven´t been studied to experimentally validate their role in the early stages of lung cancer. Some of the TFs identified showed a correlation between its expression levels and the survival of lung cancer patients. Conclusion: Our findings indicate that lung diseases share genes with lung cancer which are coexpressed in lung cancer, and might be able to explain the epidemiological observations that point to direct and inverse comorbid associations between some chronic lung diseases and lung cancer and represent a complex transcriptomic scenario.
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Affiliation(s)
| | - Mauro Florez
- Departamento de Estadística, Grupo de Investigación en Bioinformática y Biología de sistemas – GiBBS, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Liliana López-Kleine
- Departamento de Estadística, Grupo de Investigación en Bioinformática y Biología de sistemas – GiBBS, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Adriana Rojas
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
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15
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Hayek S, Pietrancosta N, Hovhannisyan AA, Alves de Sousa R, Bekaddour N, Ermellino L, Tramontano E, Arnould S, Sardet C, Dairou J, Diaz O, Lotteau V, Nisole S, Melikyan G, Herbeuval JP, Vidalain PO. Cerpegin-derived furo[3,4-c]pyridine-3,4(1H,5H)-diones enhance cellular response to interferons by de novo pyrimidine biosynthesis inhibition. Eur J Med Chem 2019; 186:111855. [PMID: 31740051 DOI: 10.1016/j.ejmech.2019.111855] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022]
Abstract
There is an increasing interest in the field of cancer therapy for small compounds targeting pyrimidine biosynthesis, and in particular dihydroorotate dehydrogenase (DHODH), the fourth enzyme of this metabolic pathway. Three available DHODH structures, featuring three different known inhibitors, were used as templates to screen in silico an original chemical library from Erevan University. This process led to the identification of P1788, a compound chemically related to the alkaloid cerpegin, as a new class of pyrimidine biosynthesis inhibitors. In line with previous reports, we investigated the effect of P1788 on the cellular innate immune response. Here we show that pyrimidine depletion by P1788 amplifies cellular response to both type-I and type II interferons, but also induces DNA damage as assessed by γH2AX staining. Moreover, the addition of inhibitors of the DNA damage response led to the suppression of the P1788 stimulatory effects on the interferon pathway. This demonstrates that components of the DNA damage response are bridging the inhibition of pyrimidine biosynthesis by P1788 to the interferon signaling pathway. Altogether, these results provide new insights on the mode of action of novel pyrimidine biosynthesis inhibitors and their development for cancer therapies.
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Affiliation(s)
- Simon Hayek
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Nicolas Pietrancosta
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | | | - Rodolphe Alves de Sousa
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Nassima Bekaddour
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Laura Ermellino
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France; Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Stéphanie Arnould
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Julien Dairou
- Chimie Bio-inorganique des Dérivés Soufrés et Pharmacochimie (CBDSP), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Olivier Diaz
- Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, Lyon, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, Lyon, France
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier, CNRS UMR9004, Université de Montpellier, Montpellier, France
| | - Gagik Melikyan
- Department of Organic Chemistry, Yerevan State University, Yerevan, Armenia.
| | - Jean-Philippe Herbeuval
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Pierre-Olivier Vidalain
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France.
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16
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Caetano MS, Younes AI, Barsoumian HB, Quigley M, Menon H, Gao C, Spires T, Reilly TP, Cadena AP, Cushman TR, Schoenhals JE, Li A, Nguyen QN, Cortez MA, Welsh JW. Triple Therapy with MerTK and PD1 Inhibition Plus Radiotherapy Promotes Abscopal Antitumor Immune Responses. Clin Cancer Res 2019; 25:7576-7584. [PMID: 31540976 DOI: 10.1158/1078-0432.ccr-19-0795] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/10/2019] [Accepted: 09/17/2019] [Indexed: 01/07/2023]
Abstract
PURPOSE Radiotherapy (RT) traditionally has been used for local tumor control in the treatment of cancer. The recent discovery that radiotherapy can have anticancer effects on the immune system has led to recognition of its ability to sensitize the tumor microenvironment to immunotherapy. However, radiation can also prompt adverse immunosuppressive effects that block aspects of systemic response at other tumor sites. Our hypothesis was that inhibition of the MER proto-oncogene tyrosine kinase (MerTK) in combination with anti-programmed cell death-1 (α-PD1) checkpoint blockade will enhance immune-mediated responses to radiotherapy. EXPERIMENTAL DESIGN We tested the efficacy of this triple therapy (Radiation + α-PD1 + α-MerTK mAbs) in 129Sv/Ev mice with bilateral lung adenocarcinoma xenografts. Primary tumors were treated with stereotactic radiotherapy (36 Gy in 3 12-Gy fractions), and tumors were monitored for response. RESULTS The triple therapy significantly delayed abscopal tumor growth, improved survival rates, and reduced numbers of lung metastases. We further found that the triple therapy increased the activated CD8+ and NK cells populations measured by granzyme B expression with upregulation of CD8+CD103+ tissue-resident memory cells (TRM) within the abscopal tumor microenvironment relative to radiation only. CONCLUSIONS The addition of α-PD1 + α-MerTK mAbs to radiotherapy could alter the cell death to be more immunogenic and generate adaptive immune response via increasing the retention of TRM cells in the tumor islets of the abscopal tumors which was proven to play a major role in survival of non-small cell lung cancer patients.
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Affiliation(s)
- Mauricio S Caetano
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ahmed I Younes
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Michael Quigley
- Bristol-Myers Squibb (BMS), Redwood City, California and Princeton, New Jersey
| | - Hari Menon
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chan Gao
- Bristol-Myers Squibb (BMS), Redwood City, California and Princeton, New Jersey
| | - Thomas Spires
- Bristol-Myers Squibb (BMS), Redwood City, California and Princeton, New Jersey
| | - Timothy P Reilly
- Bristol-Myers Squibb (BMS), Redwood City, California and Princeton, New Jersey
| | - Alexandra P Cadena
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Taylor R Cushman
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas.,University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Jonathan E Schoenhals
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas.,University of Texas Southwestern Medical School, Dallas, Texas
| | - Ailin Li
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Radiation Oncology, First Hospital of China Medical University, China
| | - Quynh-Nhu Nguyen
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria Angelica Cortez
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James W Welsh
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas.
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17
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Storchi L, Remoli AL, Marsili G, Acchioni C, Acchioni M, Battistini A, Sgarbanti M, Marrone A. A model of the three-dimensional structure of human interferon responsive factor 1 and its modifications upon phosphorylation or phosphorylation-mimicking mutations. J Biomol Struct Dyn 2019; 37:4632-4643. [PMID: 30569833 DOI: 10.1080/07391102.2018.1557558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Interferon responsive factor 1 (IRF-1) is a pleiotropic transcription factor, possessing non-redundant biological activities that depend on its interaction with different protein partners and multiple post-translational modifications including phosphorylation. In particular, a 5'-SXXXSXS-3' motif of the protein represents the target of the IκB-related kinases, TANK-binding kinase (TBK)-1 and inhibitor of nuclear factor kappa-B kinase (IKK)-ε. Here, a 3D model of human IRF-1 was determined by using multi-template comparative modeling and molecular dynamics approaches. Models obtained through either phosphorylation or aspartate mutation of residues 215, 219 and 221 were also calculated and compared to the wild type. Calculations indicated that each of these modifications mainly induces a rigidification of the protein structure and only slightly changes in electrostatics and hydrophobicity of IRF-1 surface, resulting in the impairment of the capacity of IRF-1 containing as partate mutations (S221D and S215D/S219D/S221D) to synergize with tumour necrosis factor (TNF)-α stimulation in inducing interferon (IFN) promoter-mediated reporter gene activation. Therefore, these changes are qualitatively correlated to the amount of negative charge located on the 215-221 segments of IRF-1 by phosphorylation or aspartate mutation. Hypotheses on the structural mechanism that governs the phosphorylation-related damping of IRF-1 activity were also drawn. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loriano Storchi
- Department of Pharmacy, Università "G d'Annunzio" di Chieti-Pescara , Chieti , Italy.,Molecular Discovery Limited , Pinner, Middlesex, London , United Kingdom
| | - Anna Lisa Remoli
- Department of Infectious Diseases, Istituto Superiore di Sanità , Rome , Italy
| | - Giulia Marsili
- Department of Infectious Diseases, Istituto Superiore di Sanità , Rome , Italy
| | - Chiara Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità , Rome , Italy
| | - Marta Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità , Rome , Italy
| | - Angela Battistini
- Department of Infectious Diseases, Istituto Superiore di Sanità , Rome , Italy
| | - Marco Sgarbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità , Rome , Italy
| | - Alessandro Marrone
- Department of Pharmacy, Università "G d'Annunzio" di Chieti-Pescara , Chieti , Italy
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18
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Benitez-Guijarro M, Lopez-Ruiz C, Tarnauskaitė Ž, Murina O, Mian Mohammad M, Williams TC, Fluteau A, Sanchez L, Vilar-Astasio R, Garcia-Canadas M, Cano D, Kempen MJH, Sanchez-Pozo A, Heras SR, Jackson AP, Reijns MA, Garcia-Perez JL. RNase H2, mutated in Aicardi-Goutières syndrome, promotes LINE-1 retrotransposition. EMBO J 2018; 37:e98506. [PMID: 29959219 PMCID: PMC6068448 DOI: 10.15252/embj.201798506] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 12/03/2022] Open
Abstract
Long INterspersed Element class 1 (LINE-1) elements are a type of abundant retrotransposons active in mammalian genomes. An average human genome contains ~100 retrotransposition-competent LINE-1s, whose activity is influenced by the combined action of cellular repressors and activators. TREX1, SAMHD1 and ADAR1 are known LINE-1 repressors and when mutated cause the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). Mutations in RNase H2 are the most common cause of AGS, and its activity was proposed to similarly control LINE-1 retrotransposition. It has therefore been suggested that increased LINE-1 activity may be the cause of aberrant innate immune activation in AGS Here, we establish that, contrary to expectations, RNase H2 is required for efficient LINE-1 retrotransposition. As RNase H1 overexpression partially rescues the defect in RNase H2 null cells, we propose a model in which RNase H2 degrades the LINE-1 RNA after reverse transcription, allowing retrotransposition to be completed. This also explains how LINE-1 elements can retrotranspose efficiently without their own RNase H activity. Our findings appear to be at odds with LINE-1-derived nucleic acids driving autoinflammation in AGS.
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Affiliation(s)
- Maria Benitez-Guijarro
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Cesar Lopez-Ruiz
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Olga Murina
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Mahwish Mian Mohammad
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Thomas C Williams
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Laura Sanchez
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Raquel Vilar-Astasio
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Marta Garcia-Canadas
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - David Cano
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Marie-Jeanne Hc Kempen
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Antonio Sanchez-Pozo
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Sara R Heras
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Martin Am Reijns
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Jose L Garcia-Perez
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
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19
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Amber S, Zahid S. Data integration for functional annotation of regulatory single nucleotide polymorphisms associated with Alzheimer's disease susceptibility. Gene 2018; 672:115-125. [PMID: 29883757 DOI: 10.1016/j.gene.2018.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Alzheimer's disease (AD), the most common form of dementia affects 24.3 million people worldwide. More than twenty genetic loci have been associated with AD and a significant number of genetic variants were mapped within these loci. A large proportion of genome wide significant variants lie outside the coding region. However, the plausible function of these variants is still unexplored. OBJECTIVE The present study aimed to unravel the regulatory role of proxy single nucleotide polymorphisms (SNPs), to determine their risk of developing AD. METHODS The RegulomeDB was employed to predict the regulatory role of proxy SNPs. Protein association network and functional enrichment analysis was performed using String10.5 and gene ontology, respectively. RESULTS A total of 451 SNPs were examined through SNAP web portal (r2 ≤ 0.80) which returned 2186 proxy SNPs in linkage disequilibrium (LD) with genome wide significant SNPs for AD. Out of 2186 SNPs analyzed in RegulomeDB, 151 had the scores < 3 that indicates the high degree of their potential regulatory function. Further analysis revealed that out of these 151 SNPs, 37 were genome wide significant for AD, 17 were significantly associated with diseases other than AD, 89 were proxy SNPs (not genome wide significant) for various diseases including AD while 8 SNPs were novel proxy SNPs for AD. CONCLUSION These findings support the notion that the non-coding variants can be strongly associated with disease risk. Further validation through genome wide association studies will be helpful for the elucidation of their regulatory potential.
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Affiliation(s)
- Sanila Amber
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Zahid
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
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20
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Lu R, Mucaki EJ, Rogan PK. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs. Nucleic Acids Res 2017; 45:e27. [PMID: 27899659 PMCID: PMC5389469 DOI: 10.1093/nar/gkw1036] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023] Open
Abstract
Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes.
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Affiliation(s)
- Ruipeng Lu
- Department of Computer Science, Western University, London, Ontario, N6A 5B7, Canada
| | - Eliseos J Mucaki
- Department of Biochemistry, Western University, London, Ontario, N6A 5C1, Canada
| | - Peter K Rogan
- Department of Computer Science, Western University, London, Ontario, N6A 5B7, Canada.,Department of Biochemistry, Western University, London, Ontario, N6A 5C1, Canada.,Department of Oncology, Western University, London, Ontario, N6A 4L6, Canada.,Cytognomix Inc., London, Ontario, N5X 3X5, Canada
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21
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Azarbarzin S, Feizi MAH, Safaralizadeh R, Kazemzadeh M, Fateh A. The Value of MiR-383, an Intronic MiRNA, as a Diagnostic and Prognostic Biomarker in Intestinal-Type Gastric Cancer. Biochem Genet 2017; 55:244-252. [PMID: 28243881 DOI: 10.1007/s10528-017-9793-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 02/16/2017] [Indexed: 12/13/2022]
Abstract
MicroRNAs, a class of gene expression regulatory non-coding RNAs, participate in the pathogenic mechanisms of gastric cancer which is one of the life-treating cancers. Due to its aberrant expression in some types of human cancer, miR-383 has the value of being investigated in relation to cancer treatment and diagnosis. MiR-383 is placed in intron of SGCZ, a protein-coding gene, which is subject to dysregulation in various diseases. The purpose of the current study was to investigate the contribution of miR-383 to intestinal-type gastric adenocarcinoma tumorigenesis. The expression level of miR-383 was investigated by qRT-PCR in pairs of tumorous and adjacent tumor-free tissues of 40 patients with gastric cancer during endoscopy. Also, the susceptibility of miR-383 as a tumor marker and the relationship between its aberrant expression and clinicopathological features were determined. qRT-PCR data showed that miR-383 was dysregulated during gastric tumorigenesis. MiR-383 was dramatically downregulated up to sevenfold in intestinal-type gastric adenocarcinoma compared with adjacent tumor-free tissues (P < 0.001). Misregulation of miR-383 did not reveal a significant correlation with clinical characteristics. The ROC area of 80% with 76% sensitivity and 84% specificity was determined by P < 0.001. The current study demonstrated downregulation of miR-383 in intestinal-type gastric adenocarcinoma. Downregulation of miR-383 might be used as a potential tumor marker for the diagnosis of gastric cancer or could be a potential target for gene therapy.
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Affiliation(s)
- Shirin Azarbarzin
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mina Kazemzadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Alavieh Fateh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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22
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HIV-1 Tat Recruits HDM2 E3 Ligase To Target IRF-1 for Ubiquitination and Proteasomal Degradation. mBio 2016; 7:mBio.01528-16. [PMID: 27795392 PMCID: PMC5082900 DOI: 10.1128/mbio.01528-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In addition to its ability to regulate HIV-1 promoter activation, the viral transactivator Tat also functions as a determinant of pathogenesis and disease progression by directly and indirectly modulating the host anti-HIV response, largely through the capacity of Tat to interact with and modulate the activities of multiple host proteins. We previously demonstrated that Tat modulated both viral and host transcriptional machinery by interacting with the cellular transcription factor interferon regulatory factor 1 (IRF-1). In the present study, we investigated the mechanistic basis and functional significance of Tat−IRF-1 interaction and demonstrate that Tat dramatically decreased IRF-1 protein stability. To accomplish this, Tat exploited the cellular HDM2 (human double minute 2 protein) ubiquitin ligase to accelerate IRF-1 proteasome-mediated degradation, resulting in a quenching of IRF-1 transcriptional activity during HIV-1 infection. These data identify IRF-1 as a new target of Tat-induced modulation of the cellular protein machinery and reveal a new strategy developed by HIV-1 to evade host immune responses. Current therapies have dramatically reduced morbidity and mortality associated with HIV infection and have converted infection from a fatal pathology to a chronic disease that is manageable via antiretroviral therapy. Nevertheless, HIV-1 infection remains a challenge, and the identification of useful cellular targets for therapeutic intervention remains a major goal. The cellular transcription factor IRF-1 impacts various physiological functions, including the immune response to viral infection. In this study, we have identified a unique mechanism by which HIV-1 evades IRF-1-mediated host immune responses and show that the viral protein Tat accelerates IRF-1 proteasome-mediated degradation and inactivates IRF-1 function. Restoration of IRF-1 functionality may thus be regarded as a potential strategy to reinstate both a direct antiviral response and a more broadly acting immune regulatory circuit.
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23
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Li Z, An L, Li H, Wang S, Zhou Y, Yuan F, Li L. Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network. Sci Rep 2016; 6:25515. [PMID: 27149165 PMCID: PMC4857740 DOI: 10.1038/srep25515] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/18/2016] [Indexed: 02/08/2023] Open
Abstract
Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1, and CDH2, and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate, and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer.
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Affiliation(s)
- Zhandong Li
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Lifeng An
- Department of Otorhinolaryngology and Head &Neck, China-Japan Union Hospital attached to Jilin University, Changchun, China
| | - Hao Li
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - ShaoPeng Wang
- School of Life Sciences, Shanghai University, Shanghai, China
| | - You Zhou
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences &Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Yuan
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences &Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Li
- Department of Otorhinolaryngology and Head &Neck, China-Japan Union Hospital attached to Jilin University, Changchun, China
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Li Z, Chen B, Feng M, Ouyang H, Zheng M, Ye Q, Nie Q, Zhang X. MicroRNA-23b Promotes Avian Leukosis Virus Subgroup J (ALV-J) Replication by Targeting IRF1. Sci Rep 2015; 5:10294. [PMID: 25980475 PMCID: PMC4434839 DOI: 10.1038/srep10294] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/08/2015] [Indexed: 12/31/2022] Open
Abstract
Avian leukosis virus subgroup J (ALV-J) can cause several different leukemia-like proliferative diseases in the hemopoietic system of chickens. Here, we investigated the transcriptome profiles and miRNA expression profiles of ALV-J-infected and uninfected chicken spleens to identify the genes and miRNAs related to ALV-J invasion. In total, 252 genes and 167 miRNAs were differentially expressed in ALV-J-infected spleens compared to control uninfected spleens. miR-23b expression was up-regulated in ALV-J-infected spleens compared with the control spleens, and transcriptome analysis revealed that the expression of interferon regulatory factor 1 (IRF1) was down-regulated in ALV-J-infected spleens compared to uninfected spleens. A dual-luciferase reporter assay showed that IRF1 was a direct target of miR-23b. miR-23b overexpression significantly (P = 0.0022) decreased IRF1 mRNA levels and repressed IRF1-3′-UTR reporter activity. In vitro experiments revealed that miR-23b overexpression strengthened ALV-J replication, whereas miR-23b loss of function inhibited ALV-J replication. IRF1 overexpression inhibited ALV-J replication, and IRF1 knockdown enhanced ALV-J replication. Moreover, IRF1 overexpression significantly (P = 0.0014) increased IFN-β expression. In conclusion, these results suggested that miR-23b may play an important role in ALV-J replication by targeting IRF1.
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Affiliation(s)
- Zhenhui Li
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Biao Chen
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Min Feng
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Hongjia Ouyang
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Ming Zheng
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Qiao Ye
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Qinghua Nie
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Xiquan Zhang
- 1] Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China [2] Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
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25
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Zhang Z, Shi L, Song L, Ephrem E, Petri M, Sullivan KE. Interferon regulatory factor 1 marks activated genes and can induce target gene expression in systemic lupus erythematosus. Arthritis Rheumatol 2015; 67:785-96. [PMID: 25418955 DOI: 10.1002/art.38964] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 11/13/2014] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Interferon regulatory factor 1 (IRF-1) mediates both induction of interferons (IFNs) and responses to type I IFNs. It has been implicated as a critical mediator of inflammation in murine lupus models. In a previous study of chromatin modifications in monocytes from patients with systemic lupus erythematosus (SLE), IRF-1 was implicated as being associated with increased histone acetylation in this disease. The present study was undertaken to directly investigate IRF-1 binding sites on chromatin. METHODS Cells from 9 female SLE patients and 7 female controls were examined. Monocytes were purified from peripheral blood and subjected to library preparation using a validated antibody to IRF-1. IRF-1 binding sites on chromatin were identified by chromatin immunoprecipitation followed by sequencing. The effect of IRF-1 on target gene expression was confirmed using an overexpression system in cell lines, and coimmunoprecipitation was used to identify protein interactions. RESULTS IRF-1 binding around transcribed regions was increased in SLE patient monocytes, but histone modifications at potential IRF-1 binding sites without detectable IRF-1 binding were increased as well. Overexpression of IRF-1 was sufficient to drive transcription of target genes. IRF-1 overexpression was also able to alter histone modifications at a focus set of target genes, and treatment with an IRF-1 inhibitor reduced both expression and histone modifications at target genes. IRF-1 was found to interact with a select set of histone-modifying enzymes and other transcription factors. CONCLUSION IRF-1 is an important signaling protein in the interferon pathway. It not only activates gene expression as a transcription factor, but may perpetuate disease by leading to a dysregulated epigenome.
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Affiliation(s)
- Zhe Zhang
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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26
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Reed SM, Quelle DE. p53 Acetylation: Regulation and Consequences. Cancers (Basel) 2014; 7:30-69. [PMID: 25545885 PMCID: PMC4381250 DOI: 10.3390/cancers7010030] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 12/12/2014] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications of p53 are critical in modulating its tumor suppressive functions. Ubiquitylation, for example, plays a major role in dictating p53 stability, subcellular localization and transcriptional vs. non-transcriptional activities. Less is known about p53 acetylation. It has been shown to govern p53 transcriptional activity, selection of growth inhibitory vs. apoptotic gene targets, and biological outcomes in response to diverse cellular insults. Yet recent in vivo evidence from mouse models questions the importance of p53 acetylation (at least at certain sites) as well as canonical p53 functions (cell cycle arrest, senescence and apoptosis) to tumor suppression. This review discusses the cumulative findings regarding p53 acetylation, with a focus on the acetyltransferases that modify p53 and the mechanisms regulating their activity. We also evaluate what is known regarding the influence of other post-translational modifications of p53 on its acetylation, and conclude with the current outlook on how p53 acetylation affects tumor suppression. Due to redundancies in p53 control and growing understanding that individual modifications largely fine-tune p53 activity rather than switch it on or off, many questions still remain about the physiological importance of p53 acetylation to its role in preventing cancer.
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Affiliation(s)
- Sara M Reed
- Department of Pharmacology, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
| | - Dawn E Quelle
- Department of Pharmacology, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
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27
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AbuSara N, Razavi S, Derwish L, Komatsu Y, Licursi M, Hirasawa K. Restoration of IRF1-dependent anticancer effects by MEK inhibition in human cancer cells. Cancer Lett 2014; 357:575-81. [PMID: 25497010 DOI: 10.1016/j.canlet.2014.12.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/02/2014] [Accepted: 12/05/2014] [Indexed: 02/09/2023]
Abstract
Interferon regulatory factor (IRF1) is a potent antiviral, antitumor and immune regulatory protein. Recently, we found that activated Ras/MEK inhibits antiviral response by downregulating IRF1 expression and renders cancer cells susceptible to oncolytic viruses. In this study, we sought to determine whether IRF1 downregulation underlies oncogenesis induced by Ras/MEK activation in human cancer cells. Treatment of the MEK inhibitor U0126 promoted IRF1 expression in 7 of 11 cancer cell lines we tested. IRF1 promotion was also observed in human cancer cell lines treated with different MEK inhibitors or with RNAi oligonucleotides against extracellular signal-regulated kinases (ERKs). Restoration of the expression of antitumor genes, p27 and p53 upregulated modulator of apoptosis (PUMA), by MEK inhibition was less in IRF1 shRNA knockdown cancer cells than in vector control cancer cells, suggesting that Ras/MEK targets IRF1 for the downregulation of the antitumor genes. Moreover, apoptosis induction by U0126 was significantly reduced in IRF1 shRNA knockdown cells than vector control cells. This study demonstrates that IRF1 expression is suppressed by activated Ras/MEK in human cancer cells and that IRF1 plays essential roles in apoptosis induced by Ras/MEK inhibition.
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Affiliation(s)
- Nader AbuSara
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Seyd Razavi
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Leena Derwish
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Yumiko Komatsu
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Maria Licursi
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Kensuke Hirasawa
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
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28
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McGarvey PB, Suzek BE, Baraniuk JN, Rao S, Conkright B, Lababidi S, Sutherland A, Forshee R, Madhavan S. In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases. BMC Immunol 2014; 15:61. [PMID: 25486901 PMCID: PMC4266212 DOI: 10.1186/s12865-014-0061-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/01/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Near universal administration of vaccines mandates intense pharmacovigilance for vaccine safety and a stringently low tolerance for adverse events. Reports of autoimmune diseases (AID) following vaccination have been challenging to evaluate given the high rates of vaccination, background incidence of autoimmunity, and low incidence and variable times for onset of AID after vaccinations. In order to identify biologically plausible pathways to adverse autoimmune events of vaccine-related AID, we used a systems biology approach to create a matrix of innate and adaptive immune mechanisms active in specific diseases, responses to vaccine antigens, adjuvants, preservatives and stabilizers, for the most common vaccine-associated AID found in the Vaccine Adverse Event Reporting System. RESULTS This report focuses on Guillain-Barre Syndrome (GBS), Rheumatoid Arthritis (RA), Systemic Lupus Erythematosus (SLE), and Idiopathic (or immune) Thrombocytopenic Purpura (ITP). Multiple curated databases and automated text mining of PubMed literature identified 667 genes associated with RA, 448 with SLE, 49 with ITP and 73 with GBS. While all data sources provided valuable and unique gene associations, text mining using natural language processing (NLP) algorithms provided the most information but required curation to remove incorrect associations. Six genes were associated with all four AIDs. Thirty-three pathways were shared by the four AIDs. Classification of genes into twelve immune system related categories identified more "Th17 T-cell subtype" genes in RA than the other AIDs, and more "Chemokine plus Receptors" genes associated with RA than SLE. Gene networks were visualized and clustered into interconnected modules with specific gene clusters for each AID, including one in RA with ten C-X-C motif chemokines. The intersection of genes associated with GBS, GBS peptide auto-antigens, influenza A infection, and influenza vaccination created a subnetwork of genes that inferred a possible role for the MAPK signaling pathway in influenza vaccine related GBS. CONCLUSIONS Results showing unique and common gene sets, pathways, immune system categories and functional clusters of genes in four autoimmune diseases suggest it is possible to develop molecular classifications of autoimmune and inflammatory events. Combining this information with cellular and other disease responses should greatly aid in the assessment of potential immune-mediated adverse events following vaccination.
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Affiliation(s)
- Peter B McGarvey
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, 2115 Wisconsin Ave NW, Suite 110, Washington, DC, 20007, USA. .,Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC, 20007, USA.
| | - Baris E Suzek
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, 2115 Wisconsin Ave NW, Suite 110, Washington, DC, 20007, USA. .,Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC, 20007, USA. .,Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey.
| | - James N Baraniuk
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University Medical Center, 3800 Reservoir Road, NW, Washington, DC, 20007, USA.
| | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, 2115 Wisconsin Ave NW, Suite 110, Washington, DC, 20007, USA.
| | - Brian Conkright
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, 2115 Wisconsin Ave NW, Suite 110, Washington, DC, 20007, USA.
| | - Samir Lababidi
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
| | - Andrea Sutherland
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA. .,Department of International Health, Johns Hopkins School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA.
| | - Richard Forshee
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, 2115 Wisconsin Ave NW, Suite 110, Washington, DC, 20007, USA.
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Knaack SA, Siahpirani AF, Roy S. A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components. Cancer Inform 2014; 13:69-84. [PMID: 25374456 PMCID: PMC4213198 DOI: 10.4137/cin.s14058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/19/2022] Open
Abstract
Many human diseases including cancer are the result of perturbations to transcriptional regulatory networks that control context-specific expression of genes. A comparative approach across multiple cancer types is a powerful approach to illuminate the common and specific network features of this family of diseases. Recent efforts from The Cancer Genome Atlas (TCGA) have generated large collections of functional genomic data sets for multiple types of cancers. An emerging challenge is to devise computational approaches that systematically compare these genomic data sets across different cancer types that identify common and cancer-specific network components. We present a module- and network-based characterization of transcriptional patterns in six different cancers being studied in TCGA: breast, colon, rectal, kidney, ovarian, and endometrial. Our approach uses a recently developed regulatory network reconstruction algorithm, modular regulatory network learning with per gene information (MERLIN), within a stability selection framework to predict regulators for individual genes and gene modules. Our module-based analysis identifies a common theme of immune system processes in each cancer study, with modules statistically enriched for immune response processes as well as targets of key immune response regulators from the interferon regulatory factor (IRF) and signal transducer and activator of transcription (STAT) families. Comparison of the inferred regulatory networks from each cancer type identified a core regulatory network that included genes involved in chromatin remodeling, cell cycle, and immune response. Regulatory network hubs included genes with known roles in specific cancer types as well as genes with potentially novel roles in different cancer types. Overall, our integrated module and network analysis recapitulated known themes in cancer biology and additionally revealed novel regulatory hubs that suggest a complex interplay of immune response, cell cycle, and chromatin remodeling across multiple cancers.
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Affiliation(s)
- Sara A Knaack
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, USA
| | - Alireza Fotuhi Siahpirani
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, USA. ; Department of Computer Sciences, University of Wisconsin, Madison, WI, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, USA. ; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
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O'Hara A, Simpson J, Morin P, Loveridge CJ, Williams AC, Novo SM, Stark LA. p300-mediated acetylation of COMMD1 regulates its stability, and the ubiquitylation and nucleolar translocation of the RelA NF-κB subunit. J Cell Sci 2014; 127:3659-65. [PMID: 25074812 PMCID: PMC4150058 DOI: 10.1242/jcs.149328] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 06/20/2014] [Indexed: 12/02/2022] Open
Abstract
Nucleolar sequestration of the RelA subunit of nuclear factor (NF)-κB is an important mechanism for regulating NF-κB transcriptional activity. Ubiquitylation, facilitated by COMMD1 (also known as MURR1), acts as a crucial nucleolar-targeting signal for RelA, but how this ubiquitylation is regulated, and how it differs from cytokine-mediated ubiquitylation, which causes proteasomal degradation of RelA, is poorly understood. Here, we report a new role for p300 (also known as EP300) in controlling stimulus-specific ubiquitylation of RelA, through modulation of COMMD1. We show that p300 is required for stress-mediated ubiquitylation and nucleolar translocation of RelA, but that this effect is indirect. We also demonstrate that COMMD1 is acetylated by p300 and that acetylation protects COMMD1 from XIAP-mediated proteosomal degradation. Furthermore, we demonstrate that COMMD1 acetylation is enhanced by aspirin-mediated stress, and that this acetylation is absolutely required for the protein to bind RelA under these conditions. In contrast, tumour necrosis factor (TNF) has no effect on COMMD1 acetylation. Finally, we demonstrate these findings have relevance in a whole tissue setting. These data offer a new paradigm for the regulation of NF-κB transcriptional activity, and the multiple other pathways controlled by COMMD1.
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Affiliation(s)
- Andrew O'Hara
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - James Simpson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Pierre Morin
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Carolyn J Loveridge
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ann C Williams
- Colorectal Tumour Biology Group, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Sonia M Novo
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Lesley A Stark
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
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Arockiaraj J, Sathyamoorthi A, Kumaresan V, Palanisamy R, Chaurasia MK, Bhatt P, Gnanam AJ, Pasupuleti M, Arasu A. A murrel interferon regulatory factor-1: molecular characterization, gene expression and cell protection activity. Mol Biol Rep 2014; 41:5299-309. [PMID: 24859976 DOI: 10.1007/s11033-014-3401-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/06/2014] [Indexed: 01/27/2023]
Abstract
In this study, we have reported a first murrel interferon regulatory factor-1 (designated as Murrel IRF-1) which is identified from a constructed cDNA library of striped murrel Channa striatus. The identified sequence was obtained by internal sequencing method from the library. The Murrel IRF-1 varies in size of the polypeptide from the earlier reported fish IRF-1. It contains a DNA binding domain along with a tryptophan pentad repeats, a nuclear localization signal and a transactivation domain. The homologous analysis showed that the Murrel IRF-1 had a significant sequence similarity with other known fish IRF-1 groups. The phylogenetic analysis exhibited that the Murrel IRF-1 clustered together with IRF-1 members, but the other members including IRF-2, 3, 4, 5, 6, 7, 8, 9 and 10 were clustered individually. The secondary structure of Murrel IRF-1 contains 27% α-helices (85 aa residues), 5.7% β-sheets (19 aa residues) and 67.19% random coils (210 aa residues). Furthermore, we predicted a tertiary structure of Murrel IRF-1 using I-Tasser program and analyzed the structure on PyMol surface view. The RNA structure of the Murrel IRF-1 along with its minimum free energy (-284.43 kcal/mol) was also predicted. The highest gene expression was observed in spleen and its expression was inducted with pathogenic microbes which cause epizootic ulcerative syndrome in murrels such as fungus, Aphanomyces invadans and bacteria, Aeromonas hydrophila, and poly I:C, a viral RNA analog. The results of cell protection assay suggested that the Murrel IRF-1 regulates the early defense response in C. striatus. Moreover, it showed Murrel IRF-1 as a potential candidate which can be developed as a therapeutic agent to control microbial infections in striped murrel. Overall, these results indicate the immune importance of IRF-1, however, the interferon signaling mechanism in murrels upon infection is yet to be studied at proteomic level.
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Affiliation(s)
- Jesu Arockiaraj
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, Chennai, 603 203, Tamil Nadu, India,
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Qiu W, Zhou J, Zhu G, Zhao D, He F, Zhang J, Lu Y, Yu T, Liu L, Wang Y. Sublytic C5b-9 triggers glomerular mesangial cell apoptosis via XAF1 gene activation mediated by p300-dependent IRF-1 acetylation. Cell Death Dis 2014; 5:e1176. [PMID: 24743731 PMCID: PMC4001307 DOI: 10.1038/cddis.2014.153] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/06/2014] [Accepted: 03/10/2014] [Indexed: 11/10/2022]
Abstract
The apoptosis of glomerular mesangial cells (GMCs) in rat Thy-1 nephritis (Thy-1N), a model of human mesangioproliferative glomerulonephritis (MsPGN), is accompanied by sublytic C5b-9 deposition. However, the mechanism by which sublytic C5b-9 induces GMC apoptosis is unclear. In the present studies, the effect of X-linked inhibitor of apoptosis-associated factor 1 (XAF1) expression on GMC apoptosis and the role of p300 and interferon regulatory factor-1 (IRF-1) in mediating XAF1 gene activation were determined, both in the GMCs induced by sublytic C5b-9 (in vitro) and in the renal tissues of rats with Thy-1N (in vivo). The in vitro studies demonstrated that IRF-1-enhanced XAF1 gene activation and its regulation by p300-mediated IRF-1 acetylation were involved in GMC apoptosis induced by sublytic C5b-9. The element of IRF-1 binding to XAF1 promoter and two acetylated sites of IRF-1 protein were also revealed. In vivo, silence of p300, IRF-1 or XAF1 genes in the renal tissues diminished GMC apoptosis and secondary GMC proliferation as well as urinary protein secretion in Thy-1N rats. Together, these data implicate that sublytic C5b-9 induces the expression of both p300 and IRF-1, as well as p300-dependent IRF-1 acetylation that may contribute to XAF1 gene activation and subsequent GMC apoptosis in Thy-1N rats.
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Affiliation(s)
- W Qiu
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - J Zhou
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - G Zhu
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - D Zhao
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - F He
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - J Zhang
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Y Lu
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - T Yu
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - L Liu
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Y Wang
- Department of Microbiology and Immunology, Nanjing Medical University, Nanjing, People's Republic of China
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In vivo radiation response of proneural glioma characterized by protective p53 transcriptional program and proneural-mesenchymal shift. Proc Natl Acad Sci U S A 2014; 111:5248-53. [PMID: 24706837 DOI: 10.1073/pnas.1321014111] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma is the most common adult primary brain tumor and has a dismal median survival. Radiation is a mainstay of treatment and significantly improves survival, yet recurrence is nearly inevitable. Better understanding the radiation response of glioblastoma will help improve strategies to treat this devastating disease. Here, we present a comprehensive study of the in vivo radiation response of glioma cells in a mouse model of proneural glioblastoma. These tumors are a heterogeneous mix of cell types with differing radiation sensitivities. To explicitly study the gene expression changes comprising the radiation response of the Olig2(+) tumor bulk cells, we used translating ribosome affinity purification (TRAP) from Olig2-TRAP transgenic mice. Comparing both ribosome-associated and total pools of mRNA isolated from Olig2(+) cells indicated that the in vivo gene expression response to radiation occurs primarily at the total transcript level. Genes related to apoptosis and cell growth were significantly altered. p53 and E2F were implicated as major regulators of the radiation response, with p53 activity needed for the largest gene expression changes after radiation. Additionally, radiation induced a marked shift away from a proneural expression pattern toward a mesenchymal one. This shift occurs in Olig2(+) cells within hours and in multiple genetic backgrounds. Targets for Stat3 and CEBPB, which have been suggested to be master regulators of a mesenchymal shift, were also up-regulated by radiation. These data provide a systematic description of the events following radiation and may be of use in identifying biological processes that promote glioma radioresistance.
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34
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Gupta M, Rath PC. Interferon regulatory factor-1 (IRF-1) interacts with regulated in development and DNA damage response 2 (REDD2) in the cytoplasm of mouse bone marrow cells. Int J Biol Macromol 2014; 65:41-50. [PMID: 24412152 DOI: 10.1016/j.ijbiomac.2014.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 12/12/2013] [Accepted: 01/02/2014] [Indexed: 01/07/2023]
Abstract
IRF-1 is a critical hematopoietic transcription factor, which regulates cell growth, development of immune cells, immune response, tumor suppression, apoptosis and autophagy in mammalian cells. Protein-protein interactions of IRF-1 in mouse bone marrow cells (BMCs) by GST-IRF-1 pull-down followed by mass spectrometry, coimmunoprecipitation, immunoblotting and colocalization show that regulated in development and DNA damage response 2 (REDD2) is an IRF-1-interacting protein. REDD2 is a highly conserved mammalian regulatory protein of the TSC2/mTOR pathway. It is structurally similar to REDD1 but has a distinct loop region. Cellular IRF-1 and REDD2 complex is present in the cytoplasm of BMCs as distinct speckles in punctate pattern. In vitro interaction of recombinant IRF-1 and REDD2 shows their physical interaction. Taken together, our results suggest that IRF-1 physically interacts with REDD2 in the large cytoplasmic protein complex, which may function as cellular signaling proteins for 'cross-talk' of mTOR and cytokine pathways during regulation of cell growth/proliferation, apoptosis and autophagy of mammalian bone marrow cells during health and disease.
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Affiliation(s)
- Manish Gupta
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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35
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IκB kinase ε targets interferon regulatory factor 1 in activated T lymphocytes. Mol Cell Biol 2014; 34:1054-65. [PMID: 24396068 DOI: 10.1128/mcb.01161-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IκB kinase ε (IKK-ε) has an essential role as a regulator of innate immunity, functioning downstream of pattern recognition receptors to modulate NF-κB and interferon (IFN) signaling. In the present study, we investigated IKK-ε activation following T cell receptor (TCR)/CD28 stimulation of primary CD4(+) T cells and its role in the stimulation of a type I IFN response. IKK-ε was activated following TCR/CD28 stimulation of primary CD4(+) T cells; however, in T cells treated with poly(I·C), TCR/CD28 costimulation blocked induction of IFN-β transcription. We demonstrated that IKK-ε phosphorylated the transcription factor IFN regulatory factor 1 (IRF-1) at amino acid (aa) 215/219/221 in primary CD4(+) T cells and blocked its transcriptional activity. At the mechanistic level, IRF-1 phosphorylation impaired the physical interaction between IRF-1 and the NF-κB RelA subunit and interfered with PCAF-mediated acetylation of NF-κB RelA. These results demonstrate that TCR/CD28 stimulation of primary T cells stimulates IKK-ε activation, which in turn contributes to suppression of IFN-β production.
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Lucas-Hourani M, Dauzonne D, Jorda P, Cousin G, Lupan A, Helynck O, Caignard G, Janvier G, André-Leroux G, Khiar S, Escriou N, Desprès P, Jacob Y, Munier-Lehmann H, Tangy F, Vidalain PO. Inhibition of pyrimidine biosynthesis pathway suppresses viral growth through innate immunity. PLoS Pathog 2013; 9:e1003678. [PMID: 24098125 PMCID: PMC3789760 DOI: 10.1371/journal.ppat.1003678] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 08/16/2013] [Indexed: 12/19/2022] Open
Abstract
Searching for stimulators of the innate antiviral response is an appealing approach to develop novel therapeutics against viral infections. Here, we established a cell-based reporter assay to identify compounds stimulating expression of interferon-inducible antiviral genes. DD264 was selected out of 41,353 compounds for both its immuno-stimulatory and antiviral properties. While searching for its mode of action, we identified DD264 as an inhibitor of pyrimidine biosynthesis pathway. This metabolic pathway was recently identified as a prime target of broad-spectrum antiviral molecules, but our data unraveled a yet unsuspected link with innate immunity. Indeed, we showed that DD264 or brequinar, a well-known inhibitor of pyrimidine biosynthesis pathway, both enhanced the expression of antiviral genes in human cells. Furthermore, antiviral activity of DD264 or brequinar was found strictly dependent on cellular gene transcription, nuclear export machinery, and required IRF1 transcription factor. In conclusion, the antiviral property of pyrimidine biosynthesis inhibitors is not a direct consequence of pyrimidine deprivation on the virus machinery, but rather involves the induction of cellular immune response. Our therapeutic arsenal to treat viral diseases is extremely limited, and there is a critical need for molecules that could be used against multiple viruses. Among possible strategies, there is a growing interest for molecules stimulating cellular defense mechanisms. We recently developed a functional assay to identify stimulators of antiviral genes, and selected compound DD264 from a chemical library using this approach. While searching for its mode of action, we identified this molecule as an inhibitor of pyrimidine biosynthesis, a metabolic pathway that fuels the cell with pyrimidine nucleobases for both DNA and RNA synthesis. Interestingly, it was recently shown that inhibitors of this metabolic pathway prevent the replication of RNA viruses. Here, we established a functional link between pyrimidine biosynthesis pathway and the induction of antiviral genes, and demonstrated that pyrimidine biosynthesis inhibitors like DD264 or brequinar critically rely on cellular immune response to inhibit virus growth. Thus, pyrimidine deprivation is not directly responsible for the antiviral activity of pyrimidine biosynthesis inhibitors, which rather involves the induction of a metabolic stress and subsequent triggering of cellular defense mechanisms.
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Affiliation(s)
- Marianne Lucas-Hourani
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Daniel Dauzonne
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR176, Paris, France
| | - Pierre Jorda
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR176, Paris, France
| | - Gaëlle Cousin
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR176, Paris, France
| | - Alexandru Lupan
- Institut Pasteur, Unité de Chimie et Biocatalyse, Paris, France
- CNRS, UMR3523, Paris, France
| | - Olivier Helynck
- Institut Pasteur, Unité de Chimie et Biocatalyse, Paris, France
- CNRS, UMR3523, Paris, France
| | - Grégory Caignard
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Geneviève Janvier
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Biochimie Structurale, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Samira Khiar
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Nicolas Escriou
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Philippe Desprès
- Institut Pasteur, Unité Interactions moléculaires Flavivirus-Hôtes, Paris, France
| | - Yves Jacob
- CNRS, UMR3569, Paris, France
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- Dana-Farber Cancer Institute, Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Boston, Massachusetts, United States of America
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Paris, France
- CNRS, UMR3523, Paris, France
- * E-mail: (HML); (FT); (POV)
| | - Frédéric Tangy
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
- * E-mail: (HML); (FT); (POV)
| | - Pierre-Olivier Vidalain
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
- * E-mail: (HML); (FT); (POV)
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Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 2013; 14:509. [PMID: 23889801 PMCID: PMC3750612 DOI: 10.1186/1471-2164-14-509] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. CONCLUSIONS We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
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Affiliation(s)
- Walter C Dunlap
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Damir Baranasic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Janko Diminic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ranko Gacesa
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Madeleine JH van Oppen
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Paul F Long
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
- Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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Stiehler C, Bünger C, Overall RW, Royer L, Schroeder M, Foss M, Besenbacher F, Kruhøffer M, Kassem M, Günther KP, Stiehler M. Whole-Genome Expression Analysis of Human Mesenchymal Stromal Cells Exposed to Ultrasmooth Tantalum vs. Titanium Oxide Surfaces. Cell Mol Bioeng 2012. [DOI: 10.1007/s12195-012-0255-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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39
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van Golen RF, van Gulik TM, Heger M. The sterile immune response during hepatic ischemia/reperfusion. Cytokine Growth Factor Rev 2012; 23:69-84. [PMID: 22609105 DOI: 10.1016/j.cytogfr.2012.04.006] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 04/16/2012] [Indexed: 12/14/2022]
Abstract
Hepatic ischemia and reperfusion elicits an immune response that lacks a microbial constituent yet poses a potentially lethal threat to the host. In this sterile setting, the immune system is alarmed by endogenous danger signals that are release by stressed and dying liver cells. The detection of these immunogenic messengers by sentinel leukocyte populations constitutes the proximal trigger for a self-perpetuating cycle of inflammation, in which consecutive waves of cytokines and chemokines orchestrate the influx of various leukocyte subsets that ultimately confer tissue destruction. This review focuses on the temporal organization of sterile hepatic inflammation, using surgery-induced trauma as a template disease state.
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Affiliation(s)
- Rowan F van Golen
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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40
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Qi H, Zhu H, Lou M, Fan Y, Liu H, Shen J, Li Z, Lv X, Shan J, Zhu L, Chin YE, Shao J. Interferon regulatory factor 1 transactivates expression of human DNA polymerase η in response to carcinogen N-methyl-N'-nitro-N-nitrosoguanidine. J Biol Chem 2012; 287:12622-33. [PMID: 22367195 DOI: 10.1074/jbc.m111.313429] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
DNA polymerase η (Polη) implements translesion DNA synthesis but has low fidelity in replication. We have previously shown that Polη plays an important role in the genesis of nontargeted mutations at undamaged DNA sites in cells exposed to the carcinogen N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Here, we report that MNNG-induced Polη expression in an interferon regulatory factor 1 (IRF1)-dependent manner in human cells. Mutagenesis analysis showed that four critical residues (Arg-82, Cys-83, Asn-86, and Ser-87) located in the IRF family conserved DNA binding domain-helix α3 were involved in DNA binding and POLH transactivation by IRF1. Furthermore, Polη up-regulation induced by IRF1 was responsible for the increase of mutation frequency in a SupF shuttle plasmid replicated in the MNNG-exposed cells. Interestingly, IRF1 was acetylated by the histone acetyltransferase CBP in these cells. Lys → Arg substitution revealed that Lys-78 of helix α3 was the major acetylation site, and the IRF1-K78R mutation partially inhibited DNA binding and its transcriptional activity. Thus, we propose that IRF1 activation is responsible for MNNG-induced Polη up-regulation, which contributes to mutagenesis and ultimately carcinogenesis in cells.
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Affiliation(s)
- Hongyan Qi
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou 310058, China
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41
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Interferon regulatory factor 1 mediates acetylation and release of high mobility group box 1 from hepatocytes during murine liver ischemia-reperfusion injury. Shock 2011; 35:293-301. [PMID: 20856174 DOI: 10.1097/shk.0b013e3181f6aab0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Damage-associated molecular patterns (DAMPs) initiate inflammatory pathways that are common to both sterile and infectious processes. The DAMP, high-mobility group box 1 (HMGB1), and the transcription factor, interferon regulatory factor 1 (IRF-1), have been independently associated as key players in ischemia-reperfusion (I/R) injury. Our study demonstrates that IRF-1 contributes to hepatocellular release of HMGB1 and further that IRF-1 is a necessary component of HMGB1 release in response to hypoxia or after liver I/R. We also link the nuclear upregulation of IRF-1 to the presence of functional Toll-like receptor 4 (TLR4), a pattern recognition receptor also important in sterile and infectious processes. Using IRF-1 chimeric mice, we show that IRF-1 upregulation in hepatic parenchymal cells, and not in the bone marrow-derived immune cells, is responsible for HMGB1 release during ischemic liver injury. Finally, our study also demonstrates a role for IRF-1 in modulating the acetylation status and subsequent release of HMGB1 through histone acetyltransferases. We found that serum HMGB1 is acetylated after liver I/R and that this process was dependent on IRF-1. Additionally, liver I/R induced a direct association of IRF-1 and the nuclear histone acetyltransferase enzyme p300. Together, these findings suggest that I/R-induced release of acetylated HMGB1 is a process that is dependent on TLR4-mediated upregulation of IRF-1.
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42
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Huggins P, Zhong S, Shiff I, Beckerman R, Laptenko O, Prives C, Schulz MH, Simon I, Bar-Joseph Z. DECOD: fast and accurate discriminative DNA motif finding. ACTA ACUST UNITED AC 2011; 27:2361-7. [PMID: 21752801 DOI: 10.1093/bioinformatics/btr412] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Motif discovery is now routinely used in high-throughput studies including large-scale sequencing and proteomics. These datasets present new challenges. The first is speed. Many motif discovery methods do not scale well to large datasets. Another issue is identifying discriminative rather than generative motifs. Such discriminative motifs are important for identifying co-factors and for explaining changes in behavior between different conditions. RESULTS To address these issues we developed a method for DECOnvolved Discriminative motif discovery (DECOD). DECOD uses a k-mer count table and so its running time is independent of the size of the input set. By deconvolving the k-mers DECOD considers context information without using the sequences directly. DECOD outperforms previous methods both in speed and in accuracy when using simulated and real biological benchmark data. We performed new binding experiments for p53 mutants and used DECOD to identify p53 co-factors, suggesting new mechanisms for p53 activation. AVAILABILITY The source code and binaries for DECOD are available at http://www.sb.cs.cmu.edu/DECOD CONTACT: zivbj@cs.cmu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peter Huggins
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Narayan V, Halada P, Hernychová L, Chong YP, Žáková J, Hupp TR, Vojtesek B, Ball KL. A multiprotein binding interface in an intrinsically disordered region of the tumor suppressor protein interferon regulatory factor-1. J Biol Chem 2011; 286:14291-303. [PMID: 21245151 DOI: 10.1074/jbc.m110.204602] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The interferon-regulated transcription factor and tumor suppressor protein IRF-1 is predicted to be largely disordered outside of the DNA-binding domain. One of the advantages of intrinsically disordered protein domains is thought to be their ability to take part in multiple, specific but low affinity protein interactions; however, relatively few IRF-1-interacting proteins have been described. The recent identification of a functional binding interface for the E3-ubiquitin ligase CHIP within the major disordered domain of IRF-1 led us to ask whether this region might be employed more widely by regulators of IRF-1 function. Here we describe the use of peptide aptamer-based affinity chromatography coupled with mass spectrometry to define a multiprotein binding interface on IRF-1 (Mf2 domain; amino acids 106-140) and to identify Mf2-binding proteins from A375 cells. Based on their function as known transcriptional regulators, a selection of the Mf2 domain-binding proteins (NPM1, TRIM28, and YB-1) have been validated using in vitro and cell-based assays. Interestingly, although NPM1, TRIM28, and YB-1 all bind to the Mf2 domain, they have differing amino acid specificities, demonstrating the degree of combinatorial diversity and specificity available through linear interaction motifs.
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Affiliation(s)
- Vikram Narayan
- CRUK Interferon and Cell Signalling Group, Cell Signalling Unit, Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom
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Histone acetyltransferases as regulators of nonhistone proteins: the role of interferon regulatory factor acetylation on gene transcription. J Biomed Biotechnol 2010; 2011:640610. [PMID: 21234331 PMCID: PMC3018675 DOI: 10.1155/2011/640610] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 12/05/2010] [Indexed: 11/17/2022] Open
Abstract
When studying transcription factors, it is necessary to investigate posttranslational modifications. Histone acetyltransferases (HATs) are typical of the modification enzymes involved in chromatin regulation. HATs acetylate the transcription factors (nonhistone proteins) as well as histones. Interferon regulatory factors (IRFs) are transcription factors that bind to the interferon regulatory element (IRF-E) and are involved in regulating cell growth, differentiation, and the immune and hematopoietic systems. During the process of binding to a specific DNA element, IRFs also bind to coactivators such as HATs and become modified. This review looks at how IRFs associate with HATs, p300, and PCAF, and thereby contribute to transcriptional activation.
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45
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Möller A, Pion E, Narayan V, Ball KL. Intracellular activation of interferon regulatory factor-1 by nanobodies to the multifunctional (Mf1) domain. J Biol Chem 2010; 285:38348-61. [PMID: 20817723 DOI: 10.1074/jbc.m110.149476] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IRF-1 is a tumor suppressor protein that activates gene expression from a range of promoters in response to stimuli spanning viral infection to DNA damage. Studies on the post-translational regulation of IRF-1 have been hampered by a lack of suitable biochemical tools capable of targeting the endogenous protein. In this study, phage display technology was used to develop a monoclonal nanobody targeting the C-terminal Mf1 domain (residues 301-325) of IRF-1. Intracellular expression of the nanobody demonstrated that the transcriptional activity of IRF-1 is constrained by the Mf1 domain as nanobody binding gave an increase in expression from IRF-1-responsive promoters of up to 8-fold. Furthermore, Mf1-directed nanobodies have revealed an unexpected function for this domain in limiting the rate at which the IRF-1 protein is degraded. Thus, the increase in IRF-1 transcriptional activity observed on nanobody binding is accompanied by a significant reduction in the half-life of the protein. In support of the data obtained using nanobodies, a single point mutation (P325A) involving the C-terminal residue of IRF-1 has been identified, which results in greater transcriptional activity and a significant increase in the rate of degradation. The results presented here support a role for the Mf1 domain in limiting both IRF-1-dependent transcription and the rate of IRF-1 turnover. In addition, the data highlight a route for activation of downstream genes in the IRF-1 tumor suppressor pathway using biologics.
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Affiliation(s)
- Angeli Möller
- Cell Signalling Unit, University of Edinburgh Cancer Research UK Centre, Crewe Road South, Edinburgh EH4 2XR, Scotland, United Kingdom
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47
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Abstract
The p53 tumour suppressor is modified through mutation or changes in expression in most cancers, leading to the altered regulation of hundreds of genes that are directly influenced by this sequence-specific transcription factor. Central to the p53 master regulatory network are the target response element (RE) sequences. The extent of p53 transactivation and transcriptional repression is influenced by many factors, including p53 levels, cofactors and the specific RE sequences, all of which contribute to the role that p53 has in the aetiology of cancer. This Review describes the identification and functionality of REs and highlights the inclusion of non-canonical REs that expand the universe of genes and regulation mechanisms in the p53 tumour suppressor network.
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Affiliation(s)
- Daniel Menendez
- Laboratory of Molecular Genetics, National Institute of Environmental Health Science, Research Triangle Park, North Carolina 27709, USA
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48
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Narayan V, Eckert M, Zylicz A, Zylicz M, Ball KL. Cooperative regulation of the interferon regulatory factor-1 tumor suppressor protein by core components of the molecular chaperone machinery. J Biol Chem 2009; 284:25889-99. [PMID: 19502235 DOI: 10.1074/jbc.m109.019505] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our understanding of the post-translational processes involved in regulating the interferon regulatory factor-1 (IRF-1) tumor suppressor protein is limited. The introduction of mutations within the C-terminal Mf1 domain (amino acids 301-325) impacts on IRF-1-mediated gene repression and growth suppression as well as the rate of IRF-1 degradation. However, nothing is known about the proteins that interact with this region to modulate IRF-1 function. A biochemical screen for Mf1-interacting proteins has identified an LXXLL motif that is required for binding of Hsp70 family members and cooperation with Hsp90 to regulate IRF-1 turnover and activity. These conclusions are supported by the finding that Hsp90 inhibitors suppress IRF-1-dependent transcription shortly after treatment, although at later time points inhibition of Hsp90 leads to an Hsp70-dependent depletion of nuclear IRF-1. Conversely, the half-life of IRF-1 is increased by Hsp90 in an ATPase-dependent manner leading to the accumulation of nuclear but not cytoplasmic IRF-1. This study begins to elucidate the role of the Mf1 domain of IRF-1 in orchestrating the recruitment of regulatory factors that can impact on both its turnover and transcriptional activity.
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Affiliation(s)
- Vikram Narayan
- Cancer Research UK Interferon and Cell Signalling Group, Cell Signalling Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, Scotland, United Kingdom
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49
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Pion E, Narayan V, Eckert M, Ball KL. Role of the IRF-1 enhancer domain in signalling polyubiquitination and degradation. Cell Signal 2009; 21:1479-87. [PMID: 19450680 DOI: 10.1016/j.cellsig.2009.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 05/11/2009] [Indexed: 01/09/2023]
Abstract
The interferon regulated transcription factor IRF-1 is a tumour suppressor protein that is activated in response to viral infection and cell signalling activated by double stranded DNA lesions. IRF-1 has a short half-life (t(0.5) 20-40 min) allowing rapid changes in steady state levels by modulating its rate of degradation and/or synthesis. However, little is known about the pathway(s) leading to IRF-1 protein degradation or what determines the rate of degradation in cells. Here we establish a role for discrete motifs in the enhancer domain of IRF-1 in directing polyubiquitination and degradation. By studying the structure of the enhancer domain as related to its role in the turnover of IRF-1 we have demonstrated that this region is not subject to modification by ubiquitin but rather that it contains both an ubiquitination signal and a distinct degradation signal. Removal of the C-terminal 70 amino acids from IRF-1 inhibits both its degradation and polyubiquitination, whereas removal of the C-terminal 25 amino acids inhibits degradation of the protein but does not prevent its ubiquitination. Furthermore, consistent with the C-terminus being involved in targeting or recognition by an E3-ligase or associated protein(s) the enhancer domain can act in trans to inhibit IRF-1 ubiquitination by endogenous E3-ligase activity. The identification of structural determinants that signals IRF-1 polyubiquitination and which can be uncoupled from IRF-1 degradation lends support to the idea that the degradation of selective substrates can be regulated at multiple steps in the ubiquitin-proteasome system.
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Affiliation(s)
- Emmanuelle Pion
- CRUK Interferon and Cell Signalling Group, Cell Signalling Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH42XR, UK
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50
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Koeppel M, van Heeringen SJ, Smeenk L, Navis AC, Janssen-Megens EM, Lohrum M. The novel p53 target gene IRF2BP2 participates in cell survival during the p53 stress response. Nucleic Acids Res 2008; 37:322-35. [PMID: 19042971 PMCID: PMC2632907 DOI: 10.1093/nar/gkn940] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The tumor suppressor p53 contributes to the cellular fate after genotoxic insults, mainly through the regulation of target genes, thereby allowing e.g. repair mechanisms resulting in cell survival or inducing apoptosis. Unresolved so far is the issue, which exact mechanisms lead to one or the other cellular outcome. Here, we describe the interferon regulatory factor-2-binding protein-2 (IRF2BP2) as a new direct target gene of p53, influencing the p53-mediated cellular decision. We show that upregulation of IRF2BP2 after treatment with actinomycin D (Act.D) is dependent on functional p53 in different cell lines. This occurs in parallel with the down-regulation of the interacting partner of IRF2BP2, the interferon regulatory factor-2 (IRF2), which is known to positively influence cell growth. Analyzing the molecular functions of IRF2BP2, it appears to be able to impede on the p53-mediated transactivation of the p21- and the Bax-gene. We show here that overexpressed IRF2BP2 has an impact on the cellular stress response after Act.D treatment and that it diminishes the induction of apoptosis after doxorubicin treatment. Furthermore, the knockdown of IRF2BP2 leads to an upregulation of p21 and faster induction of apoptosis after doxorubicin as well as Act.D treatment.
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Affiliation(s)
- Max Koeppel
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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