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De Paolis V, Troisi V, Bordin A, Pagano F, Caputo V, Parisi C. Unconventional p65/p52 NF-κB module regulates key tumor microenvironment-related genes in breast tumor-associated macrophages (TAMs). Life Sci 2024; 357:123059. [PMID: 39278618 DOI: 10.1016/j.lfs.2024.123059] [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: 04/19/2024] [Revised: 06/17/2024] [Accepted: 09/11/2024] [Indexed: 09/18/2024]
Abstract
The complex heterogeneity of tumor microenvironment (TME) of triple-negative breast cancer (TNBC) presents a significant obstacle to cytotoxic immune response and successful treatment, building up one of the most hostile oncological phenotypes. Among the most abundant TME components, tumor-associated macrophages (TAMs) have pivotal pro-tumoral functions, involving discordant roles for the nuclear factor kappa-B (NF-κB) transcription factors and directing to higher levels of pathway complexity. In both resting macrophages and TAMs, we recently revealed the existence of the uncharacterized NF-κB p65/p52 dimer. In the present study, we demonstrated its enhanced active nuclear localization in TAMs and validated selected immune target genes as directly regulated by dimer binding on DNA sequences. We demonstrated by ChIP-qPCR that p65/p52 enrichment on HSPG2 and CSF-1 regulatory regions is strictly dependent on macrophage polarization and tumor environment. Our data provide novel mechanisms of transcriptional regulation in TAMs, orchestrated by the varied and dynamic nature of NF-κB combinations, which needs to be considered when targeting this pathway in cancer therapies. Our results offer p65/p52, together with identified regulatory regions on genes impacting macrophage behavior and tumor biology, as novel molecular targets for TNBC, aimed at modulating TAMs functions towards anti-tumoral phenotypes and thus improving cancer treatment outcomes.
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Affiliation(s)
- Veronica De Paolis
- Institute of Biochemistry and Cell Biology, CNR-National Research Council, Via Ercole Ramarini, 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Virginia Troisi
- Institute of Biochemistry and Cell Biology, CNR-National Research Council, Via Ercole Ramarini, 32, 00015 Monterotondo Scalo, RM, Italy
| | - Antonella Bordin
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Corso della Repubblica, 79, 04100, Latina, Italy
| | - Francesca Pagano
- Institute of Biochemistry and Cell Biology, CNR-National Research Council, Via Ercole Ramarini, 32, 00015 Monterotondo Scalo, RM, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena, 324, 00161 Rome, Italy
| | - Chiara Parisi
- Institute of Biochemistry and Cell Biology, CNR-National Research Council, Via Ercole Ramarini, 32, 00015 Monterotondo Scalo, RM, Italy.
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2
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Xu Y, Baylink DJ, Xiao J, Tran L, Nguyen V, Park B, Valladares I, Lee S, Codorniz K, Tan L, Chen CS, Abdel-Azim H, Reeves ME, Mirshahidi H, Marcucci G, Cao H. Discovery of NFκB2-Coordinated Dual Regulation of Mitochondrial and Nuclear Genomes Leads to an Effective Therapy for Acute Myeloid Leukemia. Int J Mol Sci 2024; 25:8532. [PMID: 39126100 PMCID: PMC11313218 DOI: 10.3390/ijms25158532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Acute myeloid leukemia (AML) has a poor survival rate for both pediatric and adult patients due to its frequent relapse. To elucidate the bioenergetic principle underlying AML relapse, we investigated the transcriptional regulation of mitochondrial-nuclear dual genomes responsible for metabolic plasticity in treatment-resistant blasts. Both the gain and loss of function results demonstrated that NFκB2, a noncanonical transcription factor (TF) of the NFκB (nuclear factor kappa-light-chain-enhancer of activated B cells) family, can control the expression of TFAM (mitochondrial transcription factor A), which is known to be essential for metabolic biogenesis. Furthermore, genetic tracking and promoter assays revealed that NFκB2 is in the mitochondria and can bind the specific "TTGGGGGGTG" region of the regulatory D-loop domain to activate the light-strand promoter (LSP) and heavy-strand promoter 1 (HSP1), promoters of the mitochondrial genome. Based on our discovery of NFκB2's novel function of regulating mitochondrial-nuclear dual genomes, we explored a novel triplet therapy including inhibitors of NFκB2, tyrosine kinase, and mitochondrial ATP synthase that effectively eliminated primary AML blasts with mutations of the FMS-related receptor tyrosine kinase 3 (FLT3) and displayed minimum toxicity to control cells ex vivo. As such, effective treatments for AML must include strong inhibitory actions on the dual genomes mediating metabolic plasticity to improve leukemia prognosis.
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Affiliation(s)
- Yi Xu
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
| | - David J. Baylink
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Jeffrey Xiao
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Lily Tran
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Vinh Nguyen
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Brandon Park
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Ismael Valladares
- Division Regenerative Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Scott Lee
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Kevin Codorniz
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Laren Tan
- Division of Pulmonary, Critical Care, Hyperbaric and Sleep Medicine, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Chien-Shing Chen
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
| | - Hisham Abdel-Azim
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Division of Transplant and Cell Therapy, Loma Linda University Cancer Center, Loma Linda, CA 92354, USA
- Division of Hematology and Oncology, Department of Pediatrics, Loma Linda University, Loma Linda, CA 92354, USA
| | - Mark E. Reeves
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
| | - Hamid Mirshahidi
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
| | - Huynh Cao
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.-S.C.)
- Cancer Center, Loma Linda University, Loma Linda, CA 92354, USA
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3
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Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VYF, Wang Y, Ghosh G. Transient interactions modulate the affinity of NF-κB transcription factors for DNA. Proc Natl Acad Sci U S A 2024; 121:e2405555121. [PMID: 38805268 PMCID: PMC11161749 DOI: 10.1073/pnas.2405555121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/09/2024] [Indexed: 05/30/2024] Open
Abstract
The dimeric nuclear factor kappa B (NF-κB) transcription factors (TFs) regulate gene expression by binding to a variety of κB DNA elements with conserved G:C-rich flanking sequences enclosing a degenerate central region. Toward defining mechanistic principles of affinity regulated by degeneracy, we observed an unusual dependence of the affinity of RelA on the identity of the central base pair, which appears to be noncontacted in the complex crystal structures. The affinity of κB sites with A or T at the central position is ~10-fold higher than with G or C. The crystal structures of neither the complexes nor the free κB DNAs could explain the differences in affinity. Interestingly, differential dynamics of several residues were revealed in molecular dynamics simulation studies, where simulation replicates totaling 148 μs were performed on NF-κB:DNA complexes and free κB DNAs. Notably, Arg187 and Arg124 exhibited selectivity in transient interactions that orchestrated a complex interplay among several DNA-interacting residues in the central region. Binding and simulation studies with mutants supported these observations of transient interactions dictating specificity. In combination with published reports, this work provides insights into the nuanced mechanisms governing the discriminatory binding of NF-κB family TFs to κB DNA elements and sheds light on cancer pathogenesis of cRel, a close homolog of RelA.
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Affiliation(s)
- Tianjie Li
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region999077, China
| | - Shandy Shahabi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
| | - Wenfei Pan
- Faculty of Health Sciences, University of Macau, Taipa, Macau Special Administrative Region999078, China
| | - De-Bin Huang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau Special Administrative Region999078, China
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region999077, China
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
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4
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Lalle G, Lautraite R, Bouherrou K, Plaschka M, Pignata A, Voisin A, Twardowski J, Perrin-Niquet M, Stéphan P, Durget S, Tonon L, Ardin M, Degletagne C, Viari A, Belgarbi Dutron L, Davoust N, Postler TS, Zhao J, Caux C, Caramel J, Dalle S, Cassier PA, Klein U, Schmidt-Supprian M, Liblau R, Ghosh S, Grinberg-Bleyer Y. NF-κB subunits RelA and c-Rel selectively control CD4+ T cell function in multiple sclerosis and cancer. J Exp Med 2024; 221:e20231348. [PMID: 38563819 PMCID: PMC10986815 DOI: 10.1084/jem.20231348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The outcome of cancer and autoimmunity is often dictated by the effector functions of CD4+ conventional T cells (Tconv). Although activation of the NF-κB signaling pathway has long been implicated in Tconv biology, the cell-autonomous roles of the separate NF-κB transcription-factor subunits are unknown. Here, we dissected the contributions of the canonical NF-κB subunits RelA and c-Rel to Tconv function. RelA, rather than c-Rel, regulated Tconv activation and cytokine production at steady-state and was required for polarization toward the TH17 lineage in vitro. Accordingly, RelA-deficient mice were fully protected against neuroinflammation in a model of multiple sclerosis due to defective transition to a pathogenic TH17 gene-expression program. Conversely, Tconv-restricted ablation of c-Rel impaired their function in the microenvironment of transplanted tumors, resulting in enhanced cancer burden. Moreover, Tconv required c-Rel for the response to PD-1-blockade therapy. Our data reveal distinct roles for canonical NF-κB subunits in different disease contexts, paving the way for subunit-targeted immunotherapies.
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Affiliation(s)
- Guilhem Lalle
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Raphaëlle Lautraite
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Khaled Bouherrou
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Maud Plaschka
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Aurora Pignata
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), UMR INSERM 1291, CNRS 5051, Université Toulouse III, Toulouse, France
| | - Allison Voisin
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Julie Twardowski
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Marlène Perrin-Niquet
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Pierre Stéphan
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Sarah Durget
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurie Tonon
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, Gilles Thomas Bioinformatics Platform, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Maude Ardin
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, Gilles Thomas Bioinformatics Platform, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Cyril Degletagne
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Alain Viari
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, Gilles Thomas Bioinformatics Platform, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Nathalie Davoust
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure of Lyon, CNRS UMR 5239, INSERM U1293, Lyon, France
| | - Thomas S. Postler
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jingyao Zhao
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Christophe Caux
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Julie Caramel
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Stéphane Dalle
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Philippe A. Cassier
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Ulf Klein
- Division of Haematology and Immunology, Leeds Institute of Medical Research at St. James’s, University of Leeds, Leeds, UK
| | - Marc Schmidt-Supprian
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research, School of Medicine, Technical University of Munich, Munich, Germany
- German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Roland Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), UMR INSERM 1291, CNRS 5051, Université Toulouse III, Toulouse, France
| | - Sankar Ghosh
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Yenkel Grinberg-Bleyer
- Cancer Research Center of Lyon, Labex DEV2CAN, Institut Convergence Plascan, Centre Léon Bérard, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Lyon, France
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5
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Silva-Parra J, Ramírez-Martínez L, Palafox-Gómez C, Sandu C, López-Bayghen E, Vega L, Elizondo G, Loaeza-Loaeza J, Hernández-Sotelo D, Hernández-Kelly LC, Felder-Schmittbuhl MP, Ortega A. Aryl Hydrocarbon Receptor Involvement in the Sodium-Dependent Glutamate/Aspartate Transporter Regulation in Cerebellar Bergmann Glia Cells. ACS Chem Neurosci 2024; 15:1276-1285. [PMID: 38454572 PMCID: PMC10958506 DOI: 10.1021/acschemneuro.4c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
Glutamate, the major excitatory neurotransmitter in the vertebrate brain, exerts its functions through the activation of specific plasma membrane receptors and transporters. Overstimulation of glutamate receptors results in neuronal cell death through a process known as excitotoxicity. A family of sodium-dependent glutamate plasma membrane transporters is responsible for the removal of glutamate from the synaptic cleft, preventing an excitotoxic insult. Glial glutamate transporters carry out more than 90% of the brain glutamate uptake activity and are responsible for glutamate recycling through the GABA/Glutamate/Glutamine shuttle. The aryl hydrocarbon receptor is a ligand-dependent transcription factor that integrates environmental clues through its ability to heterodimerize with different transcription factors. Taking into consideration the fundamental role of glial glutamate transporters in glutamatergic synapses and that these transporters are regulated at the transcriptional, translational, and localization levels in an activity-dependent fashion, in this contribution, we explored the involvement of the aryl hydrocarbon receptor, as a model of environmental integrator, in the regulation of the glial sodium-dependent glutamate/aspartate transporter. Using the model of chick cerebellar Bergmann glia cells, we report herein that the aryl hydrocarbon receptors exert a time-dependent decrease in the transporter mRNA levels and a diminution of its uptake activity. The nuclear factor kappa light chain enhancer of the activated B cell signaling pathway is involved in this regulation. Our results favor the notion of an environmentally dependent regulation of glutamate removal in glial cells and therefore strengthen the notion of the involvement of glial cells in xenobiotic neurotoxic effects.
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Affiliation(s)
- Janisse Silva-Parra
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Leticia Ramírez-Martínez
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Cecilia Palafox-Gómez
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Cristina Sandu
- Centre
National de la Recherche Scientifique, Université
de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg 00000, France
| | - Esther López-Bayghen
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Libia Vega
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Guillermo Elizondo
- Departamento
de Biología Celular, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Jaqueline Loaeza-Loaeza
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Daniel Hernández-Sotelo
- Facultad
de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39070, Guerrero, Mexico
| | - Luisa C. Hernández-Kelly
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
| | - Marie-Paule Felder-Schmittbuhl
- Centre
National de la Recherche Scientifique, Université
de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg 00000, France
| | - Arturo Ortega
- Departamento
de Toxicología, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México 07360, Mexico
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6
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Russell ND, Jorde LB, Chow CY. Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses. G3 (BETHESDA, MD.) 2023; 13:jkad229. [PMID: 37792690 PMCID: PMC10700025 DOI: 10.1093/g3journal/jkad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 08/17/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) elicit the ER stress response, a large transcriptional response driven by 3 well-characterized transcription factors (TFs). This transcriptional response is variable across different genetic backgrounds. One mechanism in which genetic variation can lead to transcriptional variability in the ER stress response is through altered binding and activity of the 3 main TFs: XBP1, ATF6, and ATF4. This work attempts to better understand this mechanism by first creating a computational pipeline to identify potential binding sites throughout the human genome. We utilized GTEx data sets to identify cis-eQTLs that fall within predicted TF binding sites (TFBSs). We also utilized the ClinVar database to compare the number of pathogenic vs benign variants at different positions of the binding motifs. Finally, we performed a cis-eQTL analysis on human cell lines experiencing ER stress to identify cis-eQTLs that regulate the variable ER stress response. The majority of these cis-eQTLs are unique to a given condition: control or ER stress. Some of these stress-specific cis-eQTLs fall within putative binding sites of the 3 main ER stress response TFs, providing a potential mechanism by which these cis-eQTLs might be impacting gene expression under ER stress conditions through altered TF binding. This study represents the first cis-eQTL analysis on human samples experiencing ER stress and is a vital step toward identifying the genetic components responsible for the variable ER stress response.
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Affiliation(s)
- Nikki D Russell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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7
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Chen H, Xu Y, Jin J, Su XD. KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity. Sci Rep 2023; 13:16595. [PMID: 37789131 PMCID: PMC10547764 DOI: 10.1038/s41598-023-43426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/23/2023] [Indexed: 10/05/2023] Open
Abstract
It is difficult to exhaustively screen all possible DNA binding sequences for a given transcription factor (TF). Here, we developed the KaScape method, in which TFs bind to all possible DNA sequences in the same DNA pool where DNA sequences are prepared by randomized oligo synthesis and the random length can be adjusted to a length such as 4, 5, 6, or 7. After separating bound from unbound double-stranded DNAs (dsDNAs), their sequences are determined by next-generation sequencing. To demonstrate the relative binding affinities of all possible DNA sequences determined by KaScape, we developed three-dimensional KaScape viewing software based on a K-mer graph. We applied KaScape to 12 plant TF family AtWRKY proteins and found that all AtWRKY proteins bound to the core sequence GAC with similar profiles. KaScape can detect not only binding sequences consistent with the consensus W-box "TTGAC(C/T)" but also other sequences with weak affinity. KaScape provides a high-throughput, easy-to-operate, sensitive, and exhaustive method for quantitatively characterizing the relative binding strength of a TF with all possible binding sequences, allowing us to comprehensively characterize the specificity and affinity landscape of transcription factors, particularly for moderate- and low-affinity binding sites.
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Affiliation(s)
- Hong Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yongping Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Jianshi Jin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
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8
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Hussain MS, Afzal O, Gupta G, Altamimi ASA, Almalki WH, Alzarea SI, Kazmi I, Kukreti N, Gupta S, Sulakhiya K, Singh SK, Dua K. Probing the links: Long non-coding RNAs and NF-κB signalling in atherosclerosis. Pathol Res Pract 2023; 249:154773. [PMID: 37647827 DOI: 10.1016/j.prp.2023.154773] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Atherosclerosis is a chronic inflammatory disease that involves the accumulation of lipids and immune cells in the arterial wall. NF-kB signaling is a key regulator of inflammation and is known to play a critical role in atherosclerosis. Recent studies have shown that lncRNAs can regulate NF-kB and contribute to the development and progression of atherosclerosis. Preliminary findings reveal significant alterations in the expression of specific lncRNAs in atherosclerotic lesions compared to healthy arterial tissue. Experimental evidence suggests that these dysregulated lncRNAs can influence the NF-kB pathway. By unravelling the crosstalk between lncRNAs and NF-kB signaling, this review aims to enhance our understanding of the molecular mechanisms underlying atherosclerosis. Identifying novel therapeutic targets and diagnostic markers may lead to developing interventions and management strategies for this prevalent cardiovascular disease. This review summarizes the current knowledge on the role of lncRNAs in NF-kB signaling in atherosclerosis and highlights their potential as therapeutic targets for this disease.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017 Jaipur, Rajasthan, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura 302017, Jaipur, India; Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India.
| | | | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Saurabh Gupta
- Chameli Devi Institute of Pharmacy, Department of Pharmacology, Indore, Madhya Pradesh, India
| | - Kunjbihari Sulakhiya
- Neuro Pharmacology Research Laboratory (NPRL), Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia; Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
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9
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Mussbacher M, Derler M, Basílio J, Schmid JA. NF-κB in monocytes and macrophages - an inflammatory master regulator in multitalented immune cells. Front Immunol 2023; 14:1134661. [PMID: 36911661 PMCID: PMC9995663 DOI: 10.3389/fimmu.2023.1134661] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
Nuclear factor κB (NF-κB) is a dimeric transcription factor constituted by two of five protein family members. It plays an essential role in inflammation and immunity by regulating the expression of numerous chemokines, cytokines, transcription factors, and regulatory proteins. Since NF-κB is expressed in almost all human cells, it is important to understand its cell type-, tissue-, and stimulus-specific roles as well as its temporal dynamics and disease-specific context. Although NF-κB was discovered more than 35 years ago, many questions are still unanswered, and with the availability of novel technologies such as single-cell sequencing and cell fate-mapping, new fascinating questions arose. In this review, we will summarize current findings on the role of NF-κB in monocytes and macrophages. These innate immune cells show high plasticity and dynamically adjust their effector functions against invading pathogens and environmental cues. Their versatile functions can range from antimicrobial defense and antitumor immune responses to foam cell formation and wound healing. NF-κB is crucial for their activation and balances their phenotypes by finely coordinating transcriptional and epigenomic programs. Thereby, NF-κB is critically involved in inflammasome activation, cytokine release, and cell survival. Macrophage-specific NF-κB activation has far-reaching implications in the development and progression of numerous inflammatory diseases. Moreover, recent findings highlighted the temporal dynamics of myeloid NF-κB activation and underlined the complexity of this inflammatory master regulator. This review will provide an overview of the complex roles of NF-κB in macrophage signal transduction, polarization, inflammasome activation, and cell survival.
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Affiliation(s)
- Marion Mussbacher
- Department of Pharmacology and Toxicology, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
| | - Martina Derler
- Department of Pharmacology and Toxicology, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
| | - José Basílio
- Department of Vascular Biology and Thrombosis Research, Centre of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
- INESC ID–Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Johannes A. Schmid
- Department of Vascular Biology and Thrombosis Research, Centre of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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10
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Tamraz M, Al Ghossaini N, Temraz S. The Ketogenic Diet in Colorectal Cancer: A Means to an End. Int J Mol Sci 2023; 24:ijms24043683. [PMID: 36835094 PMCID: PMC9965563 DOI: 10.3390/ijms24043683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
Some diets, such as high lipid and high glucose diets, are known to increase the risk of colorectal cancer. On the other hand, little is known about diets that prevent colonic carcinogenesis. The ketogenic diet, which is characterized by high fat and very low carbohydrate content, is one such diet. The ketogenic diet decreases the amount of available glucose for tumors and shifts to the production of ketone bodies as an alternative energy source for healthy cells. Cancer cells are unable to use the ketone bodies for energy thus depriving them of the energy needed for progression and survival. Many studies reported the beneficial effects of the ketogenic diet in several types of cancers. Recently, the ketone body β-hydroxybutyrate has been found to possess anti-tumor potential in colorectal cancer. Despite its beneficial effects, the ketogenic diet also has some drawbacks, some of which are related to gastrointestinal disorders and weight loss. Thus, studies are being directed at this time towards finding alternatives to following a strict ketogenic diet and supplementing patients with the ketone bodies responsible for its beneficial effects in the hope of overcoming some potential setbacks. This article discusses the mechanism by which a ketogenic diet influences growth and proliferation of tumor cells, it sheds the light on the most recent trials regarding its use as an adjunctive measure to chemotherapy in patients with metastatic colorectal cancer, and it explains the limitations of its usage in metastatic patients and the promising role of exogenous ketone supplementation in this setting.
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Affiliation(s)
- Magie Tamraz
- Department of Nutrition and Dietetics, American University of Beirut Medical Center, Riad El Solh, Beirut 1107, Lebanon
| | - Najib Al Ghossaini
- Department of Internal Medicine, Ain Wazein Medical Village, Chouf 5841, Lebanon
| | - Sally Temraz
- Department of Internal Medicine, American University of Beirut Medical Center, Riad El Solh, Beirut 1107, Lebanon
- Correspondence: ; Tel.: +961-1-374374
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11
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Akbarpour Arsanjani A, Abuei H, Behzad-Behbahani A, Bagheri Z, Arabsolghar R, Farhadi A. Activating transcription factor 3 inhibits NF‑κB p65 signaling pathway and mediates apoptosis and cell cycle arrest in cervical cancer cells. Infect Agent Cancer 2022; 17:62. [PMID: 36522783 PMCID: PMC9753250 DOI: 10.1186/s13027-022-00475-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND As a novel tumor suppressor mediator, activating transcription factor 3 (ATF3) has recently aroused an interest in its possible therapeutic applications in various cancers. In this study, we evaluated the effect of ATF3 overexpression on the cellular level of nuclear factor kappa B (NF-κB) in human papillomavirus (HPV)-infected Ca Ski cells. Further, we examined whether ATF3 could mediate cell cycle arrest and alter the apoptosis level of Ca Ski cells. METHODS The biological behavior of Ca Ski cells was evaluated prior and subsequent to the overexpression of ATF3 by MTT assay, fluorescence microscopy, cell cycle and annexin V/PI flow cytometric analysis. The effect of ectopic ATF3 expression on the cellular level of NF-κB in HPV-positive cells was evaluated by western blotting assay. RESULTS The overexpression of ATF3 in Ca Ski cells led to significant apoptosis and cell cycle arrest in the G1 phase. Western blotting assay revealed a discernible reduction of NF-κB p65 level in cervical cancer cells. CONCLUSION ATF3 acts as a tumor suppressor factor in HPV16-infected Ca Ski cells and exerts anti-cancer effects on HPV16-related cervical cancer cells potentially by hindering cell growth and inducing cell cycle arrest through the down-regulation of NF-κB. Our results suggest that ATF3 induction or NF-κB suppression may be useful targets for HPV16-related cervical cancer prevention and treatment.
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Affiliation(s)
- Amirhossein Akbarpour Arsanjani
- grid.412571.40000 0000 8819 4698Division of Medical Biotechnology, Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Haniyeh Abuei
- grid.412571.40000 0000 8819 4698Division of Medical Biotechnology, Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad-Behbahani
- grid.412571.40000 0000 8819 4698Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Bagheri
- grid.412571.40000 0000 8819 4698Division of Medical Biotechnology, Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Rita Arabsolghar
- grid.412571.40000 0000 8819 4698Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Farhadi
- grid.412571.40000 0000 8819 4698Division of Medical Biotechnology, Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran ,grid.412571.40000 0000 8819 4698Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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12
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Rahman SMT, Aqdas M, Martin EW, Tomassoni Ardori F, Songkiatisak P, Oh KS, Uderhardt S, Yun S, Claybourne QC, McDevitt RA, Greco V, Germain RN, Tessarollo L, Sung MH. Double knockin mice show NF-κB trajectories in immune signaling and aging. Cell Rep 2022; 41:111682. [DOI: 10.1016/j.celrep.2022.111682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/06/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
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13
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Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA. An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem 2022; 298:102349. [PMID: 35934050 PMCID: PMC9440430 DOI: 10.1016/j.jbc.2022.102349] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Many transcription factors contain intrinsically disordered transcription activation domains (TADs), which mediate interactions with coactivators to activate transcription. Historically, DNA-binding domains and TADs have been considered as modular units, but recent studies have shown that TADs can influence DNA binding. Whether these results can be generalized to more TADs is not clear. Here, we biophysically characterized the NFκB p50/RelA heterodimer including the RelA TAD and investigated the TAD's influence on NFκB-DNA interactions. In solution, we show the RelA TAD is disordered but compact, with helical tendency in two regions that interact with coactivators. We determined that the presence of the TAD increased the stoichiometry of NFκB-DNA complexes containing promoter DNA sequences with tandem κB recognition motifs by promoting the binding of NFκB dimers in excess of the number of κB sites. In addition, we measured the binding affinity of p50/RelA for DNA containing tandem κB sites and single κB sites. While the presence of the TAD enhanced the binding affinity of p50/RelA for all κB sequences tested, it also increased the affinity for nonspecific DNA sequences by over 10-fold, leading to an overall decrease in specificity for κB DNA sequences. In contrast, previous studies have generally reported that TADs decrease DNA-binding affinity and increase sequence specificity. Our results reveal a novel function of the RelA TAD in promoting binding to nonconsensus DNA, which sheds light on previous observations of extensive nonconsensus DNA binding by NFκB in vivo in response to strong inflammatory signals.
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Affiliation(s)
- Hannah E R Baughman
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Dominic Narang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Wei Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Amalia C Villagrán Suárez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Joan Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Maxwell J Bachochin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Tristan R Gunther
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Peter G Wolynes
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
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14
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Sharabi O, Greenshpan Y, Ofir N, Ottolenghi A, Levi T, Olender L, Adler-Agmon Z, Porgador A, Gazit R. High throughput screen for the improvement of inducible promoters for tumor microenvironment cues. Sci Rep 2022; 12:7169. [PMID: 35504918 PMCID: PMC9065017 DOI: 10.1038/s41598-022-11021-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/06/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer immunotherapies are highly potent and are gaining wide clinical usage. However, severe side effects require focusing effector immune cell activities on the tumor microenvironment (TME). We recently developed a chimeric antigen receptor tumor-induced vector (CARTIV), a synthetic promoter activated by TME factors. To improve CARTIV functions including background, activation levels, and synergism, we screened a library of promoters with variations in key positions. Here, we present a screening method involving turning ON/OFF stimulating TNFα and IFNγ cytokines, followed by sequential cell sorting. Sequencing of enriched promoters identified seventeen candidates, which were cloned and whose activities were then validated, leading to the identification of two CARTIVs with lower background and higher induction. We further combined a third hypoxia element with the two-factor CARTIV, demonstrating additional modular improvement. Our study presents a method of fine-tuning synthetic promoters for desired immunotherapy needs.
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Affiliation(s)
- Omri Sharabi
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yariv Greenshpan
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Noa Ofir
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tamar Levi
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Leonid Olender
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Zachor Adler-Agmon
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Angel Porgador
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Roi Gazit
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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15
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Checkpoints and Immunity in Cancers: Role of GNG12. Pharmacol Res 2022; 180:106242. [DOI: 10.1016/j.phrs.2022.106242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
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A Comprehensive View on the Quercetin Impact on Colorectal Cancer. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061873. [PMID: 35335239 PMCID: PMC8953922 DOI: 10.3390/molecules27061873] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) represents the third type of cancer in incidence and second in mortality worldwide, with the newly diagnosed case number on the rise. Among the diagnosed patients, approximately 70% have no hereditary germ-line mutations or family history of pathology, thus being termed sporadic CRC. Diet and environmental factors are to date considered solely responsible for the development of sporadic CRC; therefore; attention should be directed towards the discovery of preventative actions to combat the CRC initiation, promotion, and progression. Quercetin is a polyphenolic flavonoid plant secondary metabolite with a well-characterized antioxidant activity. It has been extensively reported as an anti-carcinogenic agent in the scientific literature, and the modulated targets of quercetin have been also characterized in the context of CRC, mainly in original research publications. In this fairly comprehensive review, we summarize the molecular targets of quercetin reported to date in in vivo and in vitro CRC models, while also giving background information about the signal transduction pathways that it up- and downregulates. Among the most relevant modulated pathways, the Wnt/β-catenin, PI3K/AKT, MAPK/Erk, JNK, or p38, p53, and NF-κB have been described. With this work, we hope to encourage further quests in the elucidation of quercetin anti-carcinogenic activity as single agent, as dietary component, or as pharmaconutrient delivered in the form of plant extracts.
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17
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Manz XD, Szulcek R, Pan X, Symersky P, Dickhoff C, Majolée J, Kremer V, Michielon E, Jordanova ES, Radonic T, Bijnsdorp IV, Piersma SR, Pham TV, Jimenez CR, Vonk Noordegraaf A, de Man FS, Boon RA, Voorberg J, Hordijk PL, Aman J, Bogaard HJ. Epigenetic Modification of the VWF Promotor Drives Platelet Aggregation on the Pulmonary Endothelium in Chronic Thromboembolic Pulmonary Hypertension. Am J Respir Crit Care Med 2022; 205:806-818. [PMID: 35081007 DOI: 10.1164/rccm.202109-2075oc] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Von Willebrand Factor (VWF) mediates platelet adhesion during thrombosis. While chronic thromboembolic pulmonary hypertension (CTEPH) is associated with increased plasma levels of VWF, the role of this protein in CTEPH has remained enigmatic. OBJECTIVE To identify the role of VWF in CTEPH. METHODS CTEPH-specific patient plasma and pulmonary endarterectomy material from CTEPH patients were used to study the relationship between inflammation, VWF expression and pulmonary thrombosis. Cell culture findings were validated in human tissue and proteomics and chromatin immunoprecipitation were used to investigate the underlying mechanism of CTEPH. MEASUREMENTS AND MAIN RESULTS VWF is increased in plasma and in the pulmonary endothelium of CTEPH patients. In vitro, the increase in VWF gene expression and the higher release of VWF protein upon endothelial activation resulted in elevated platelet adhesion to CTEPH endothelium. Proteomic analysis revealed that Nuclear Factor κB 2 (NFκB2) was significantly increased in CTEPH. We demonstrate reduced histone tri-methylation and increased histone acetylation of the VWF promotor in CTEPH endothelium, facilitating binding of NFκB2 to the VWF promotor and driving VWF transcription. Genetic interference of NFκB2 normalized the high VWF RNA expression levels and reversed the pro-thrombotic phenotype observed in CTEPH-PAEC. CONCLUSION Epigenetic regulation of the VWF promotor contributes to the creation of a local environment that favors in situ thrombosis in the pulmonary arteries. It reveals a direct molecular link between inflammatory pathways and platelet adhesion in the pulmonary vascular wall, emphasizing a possible role of in situ thrombosis in the development or progression of CTEPH.
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Affiliation(s)
- Xue D Manz
- Amsterdam UMC Locatie VUmc, 1209, Pulmonary Medicine, Amsterdam, Netherlands
| | - Robert Szulcek
- Charite Universitatsmedizin Berlin, 14903, Physiology, Berlin, Germany
| | - Xiaoke Pan
- Amsterdam UMC Locatie VUmc, 1209, Pulmonary Medicine, Amsterdam, Netherlands
| | - Petr Symersky
- Amsterdam UMC Locatie VUmc, 1209, Cardio-thoracic Surgery, Amsterdam, Netherlands
| | - Chris Dickhoff
- Amsterdam UMC Locatie VUmc, 1209, Cardio-thoracic Surgery, Amsterdam, Netherlands
| | - Jisca Majolée
- Amsterdam UMC Locatie VUmc, 1209, Physiology, Amsterdam, Netherlands
| | - Veerle Kremer
- Amsterdam UMC Locatie VUmc, 1209, Physiology, Amsterdam, Netherlands
| | - Elisabetta Michielon
- Amsterdam UMC Locatie VUmc, 1209, Molecular Cell Biology and Immunology, Amsterdam, Netherlands
| | - Ekaterina S Jordanova
- Amsterdam UMC Locatie VUmc, 1209, Center for Gynecologic Oncology Amsterdam, Amsterdam, Netherlands
| | - Teodora Radonic
- Amsterdam UMC Locatie VUmc, 1209, Pathology, Amsterdam, Netherlands
| | - Irene V Bijnsdorp
- Amsterdam UMC Locatie VUmc, 1209, Medical Oncology, Amsterdam, Netherlands
| | - Sander R Piersma
- Amsterdam UMC Locatie VUmc, 1209, Medical Oncology, Amsterdam, Netherlands
| | - Thang V Pham
- Amsterdam UMC Locatie VUmc, 1209, Medical Oncology, Amsterdam, Netherlands
| | - Connie R Jimenez
- Amsterdam UMC Locatie VUmc, 1209, Medical Oncology, Amsterdam, Netherlands
| | - Anton Vonk Noordegraaf
- Amsterdam UMC Locatie VUmc, 1209, Pulmonary Medicine, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Frances S de Man
- Amsterdam UMC Locatie VUmc, 1209, Pulmonary Medicine, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Reinier A Boon
- Amsterdam UMC Locatie VUmc, 1209, Physiology, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Jan Voorberg
- Sanquin Research, 159217, Molecular Hematology, Amsterdam, Netherlands
| | | | - Jurjan Aman
- Amsterdam UMC - Locatie VUMC, 1209, Pulmonary Diseases, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Harm Jan Bogaard
- Vrije Universiteit Amsterdam, 1190, Pulmonary Medicine, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands;
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18
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Hernández-Melchor D, Ramírez-Martínez L, Cid L, Palafox-Gómez C, López-Bayghen E, Ortega A. EAAT1-dependent slc1a3 Transcriptional Control depends on the Substrate Translocation Process. ASN Neuro 2022; 14:17590914221116574. [PMID: 35903937 PMCID: PMC9340397 DOI: 10.1177/17590914221116574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Glutamate, the major excitatory neurotransmitter in the vertebrate brain, is removed from the synaptic cleft by a family of sodium-dependent transporters expressed in neurons and glial cells. The bulk of glutamate uptake activity occurs in glial cells through the sodium-dependent glutamate/aspartate transporter (EAAT1/GLAST) and glutamate transporter 1 (EAAT2/GLT-1). EAAT1/GLAST is the predominant transporter within the cerebellum. It is highly enriched in Bergmann glial cells that span the cerebellar cortex and wrap the most abundant glutamatergic synapses in the central nervous system, the synapse formed by the parallel fibers and the Purkinje cells. In the past years, it has become evident that Bergmann glial cells are involved in glutamatergic transmission. Glutamate transporters are tightly regulated due to their essential role in tripartite synapses. Glutamate regulates EAAT1/GLAST function and gene expression in a receptor-dependent and receptor-independent manner. Through the use of the non-metabolizable EAAT1/GLAST ligand, D-Aspartate, and the well-established chick cerebellar Bergmann glia primary culture, in this contribution, we demonstrate that EAAT1/GLAST down-regulates its expression and function at the transcriptional level through the activation of a signaling pathway that includes the phosphatidyl inositol 3 kinase (PI3K), the Ca2+/diacylglycerol dependent protein kinase PKC and the nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB). These results favor the notion of an activity-dependent fine-tuning of glutamate recycling and its synaptic transactions through glial cells. Summary statement EAAT1/GLAST down-regulates its expression and function at the transcriptional level by activating a signaling pathway that includes PI3K, PKC and NF-κB, favoring the notion of an activity-dependent fine-tuning of glutamate recycling and its synaptic transactions through glial cells.
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Affiliation(s)
- Dinorah Hernández-Melchor
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, México
- Science, Technology and Society Program. Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, México
| | - Leticia Ramírez-Martínez
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, México
| | - Luis Cid
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, México
| | - Cecilia Palafox-Gómez
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, México
| | - Esther López-Bayghen
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, México
| | - Arturo Ortega
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, México
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Raczkowski HL, Xu LS, Wang WC, Dekoter RP. The E26 Transformation-Specific Family Transcription Factor Spi-C Is Dynamically Regulated by External Signals in B Cells. Immunohorizons 2022; 6:104-115. [PMID: 38285436 DOI: 10.4049/immunohorizons.2100111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 12/31/2021] [Indexed: 01/30/2024] Open
Abstract
Spi-C is an E26 transformation-specific transcription factor closely related to PU.1 and Spi-B. Spi-C has lineage-instructive functions important in B cell development, Ab-generating responses, and red pulp macrophage generation. This research examined the regulation of Spi-C expression in mouse B cells. To determine the mechanism of Spic regulation, we identified the Spic promoter and upstream regulatory elements. The Spic promoter had unidirectional activity that was reduced by mutation of an NF-κB binding site. Reverse transcription-quantitative PCR analysis revealed that Spic expression was reduced in B cells following treatment with cytokines BAFF + IL-4 + IL-5, anti-IgM Ab, or LPS. Cytochalasin treatment partially prevented downregulation of Spic. Unstimulated B cells upregulated Spic on culture. Spic was repressed by an upstream regulatory region interacting with the heme-binding regulator Bach2. Taken together, these data indicate that Spi-C is dynamically regulated by external signals in B cells and provide insight into the mechanism of regulation.
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Affiliation(s)
- Hannah L Raczkowski
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Division of Genetics and Development, Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada
| | - Li S Xu
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Division of Genetics and Development, Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada
| | - Wei Cen Wang
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Division of Genetics and Development, Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada
| | - Rodney P Dekoter
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Division of Genetics and Development, Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada
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20
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Huang Z, Yang M. Molecular Network of Colorectal Cancer and Current Therapeutic Options. Front Oncol 2022; 12:852927. [PMID: 35463300 PMCID: PMC9018988 DOI: 10.3389/fonc.2022.852927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC), a leading cause of cancer-related mortalities globally, results from the accumulation of multiple genetic and epigenetic alterations in the normal colonic and rectum epithelium, leading to the progression from colorectal adenomas to invasive carcinomas. Almost half of CRC patients will develop metastases in the course of the disease and most patients with metastatic CRC are incurable. Particularly, the 5-year survival rate of patients with stage 4 CRC at diagnosis is less than 10%. Although genetic understanding of these CRC tumors and paired metastases has led to major advances in elucidating early driver genes responsible for carcinogenesis and metastasis, the pathophysiological contribution of transcriptional and epigenetic aberrations in this malignancy which influence many central signaling pathways have attracted attention recently. Therefore, treatments that could affect several different molecular pathways may have pivotal implications for their efficacy. In this review, we summarize our current knowledge on the molecular network of CRC, including cellular signaling pathways, CRC microenvironment modulation, epigenetic changes, and CRC biomarkers for diagnosis and predictive/prognostic use. We also provide an overview of opportunities for the treatment and prevention strategies in this field.
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Affiliation(s)
- Zhe Huang
- The Department of 11 General Surgery, Minimally Invasive Colorectal Hernia Unit, Shengjing Hospital of China Medical University, Shenyang, China
| | - Mingli Yang
- The Department of 3Oncology, Gastrointestinal Cancer Unit, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Mingli Yang,
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21
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Meier-Soelch J, Mayr-Buro C, Juli J, Leib L, Linne U, Dreute J, Papantonis A, Schmitz ML, Kracht M. Monitoring the Levels of Cellular NF-κB Activation States. Cancers (Basel) 2021; 13:5351. [PMID: 34771516 PMCID: PMC8582385 DOI: 10.3390/cancers13215351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
The NF-κB signaling system plays an important regulatory role in the control of many biological processes. The activities of NF-κB signaling networks and the expression of their target genes are frequently elevated in pathophysiological situations including inflammation, infection, and cancer. In these conditions, the outcome of NF-κB activity can vary according to (i) differential activation states, (ii) the pattern of genomic recruitment of the NF-κB subunits, and (iii) cellular heterogeneity. Additionally, the cytosolic NF-κB activation steps leading to the liberation of DNA-binding dimers need to be distinguished from the less understood nuclear pathways that are ultimately responsible for NF-κB target gene specificity. This raises the need to more precisely determine the NF-κB activation status not only for the purpose of basic research, but also in (future) clinical applications. Here we review a compendium of different methods that have been developed to assess the NF-κB activation status in vitro and in vivo. We also discuss recent advances that allow the assessment of several NF-κB features simultaneously at the single cell level.
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Affiliation(s)
- Johanna Meier-Soelch
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Christin Mayr-Buro
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Jana Juli
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Lisa Leib
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Uwe Linne
- Mass Spectrometry Facility of the Department of Chemistry, Philipps University, 35032 Marburg, Germany;
| | - Jan Dreute
- Institute of Biochemistry, Justus Liebig University, 35392 Giessen, Germany;
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
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22
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Autoimmune Regulator Gene Polymorphisms in Egyptian Systemic Lupus Erythematosus Patients: Preliminary Results. Int J Rheumatol 2021; 2021:5546639. [PMID: 34621318 PMCID: PMC8492237 DOI: 10.1155/2021/5546639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/23/2021] [Accepted: 08/14/2021] [Indexed: 12/01/2022] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a systemic autoimmune disease. The autoimmune regulator (AIRE) is a master regulator of self-tolerance development. AIRE mutations lead to the development of autoimmune polyglandular syndrome type 1 while AIRE polymorphisms have been linked to organ-specific autoimmunity. The study is aimed at addressing the association between AIRE polymorphisms, rs2075876 (G > A) and rs760426 (A > G), and SLE susceptibility and expression in Egyptian patients. Methods Ninety-nine patients were included. One hundred and ten, and 123 control subjects were genotyped for rs2075876 and rs760426, respectively. Lupus severity was assessed using the Lupus Severity of Disease Index and Lupus Severity Index (LSI). Systemic Lupus International Collaborating Clinics (SLICC)/American College of Rheumatology (ACR) damage index was considered. Genotyping was done using StepOne Real-Time PCR. Results. AIRE rs760426 GG was more frequent in the patients under the genotype level (14.1% vs. 4.9%, p = 0.032) and recessive model (14.1% vs. 4.9%, p = 0.017, OR = 3.2 (1.2-8.7)). Musculoskeletal involvement and nephritis were associated with AIRE rs2075876 under the dominant (97.9% vs. 80.8%, p = 0.009, OR = 11 (1.3-89.2)) and recessive models (100% vs. 69.3%, p = 0.032), respectively; and both were linked to AIRE rs2075876 at the allelic level: 98.3% vs. 85%, p = 0.005, OR = 10.1 (1.3-76.6) and 82.8% vs. 68.6, p = 0.041, OR = 2.2 (1-4.7), respectively. Patients with AIRE rs2075876 A alleles had a higher damage index ( 1 ± 1.3 vs. 0.6 ± 1.1, p = 0.045) while the LSI was greater in patients with AIRE rs2075876 (8.5 ± 0.5 vs. 7.8 ± 1.3, p = 0.002) and rs760426 (8.6 ± 11 vs. 7.8 ± 1.2, p = 0.031) under the recessive models. Conclusion. AIRE rs760426 could share in SLE susceptibility while AIRE rs2075876 could influence the disease expression and burden in Egyptian patients.
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23
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Biancalana M, Natan E, Lenardo MJ, Fersht AR. NF-κB Rel subunit exchange on a physiological timescale. Protein Sci 2021; 30:1818-1832. [PMID: 34089216 PMCID: PMC8376415 DOI: 10.1002/pro.4134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/21/2022]
Abstract
The Rel proteins of the NF-κB complex comprise one of the most investigated transcription factor families, forming a variety of hetero- or homodimers. Nevertheless, very little is known about the fundamental kinetics of NF-κB complex assembly, or the inter-conversion potential of dimerised Rel subunits. Here, we examined an unexplored aspect of NF-κB dynamics, focusing on the dissociation and reassociation of the canonical p50 and p65 Rel subunits and their ability to form new hetero- or homodimers. We employed a soluble expression system to enable the facile production of NF-κB Rel subunits, and verified these proteins display canonical NF-κB nucleic acid binding properties. Using a combination of biophysical techniques, we demonstrated that, at physiological temperatures, homodimeric Rel complexes routinely exchange subunits with a half-life of less than 10 min. In contrast, we found a dramatic preference for the formation of the p50/p65 heterodimer, which demonstrated a kinetic stability of at least an order of magnitude greater than either homodimer. These results suggest that specific DNA targets of either the p50 or p65 homodimers can only be targeted when these subunits are expressed exclusively, or with the intervention of additional post-translational modifications. Together, this work implies a new model of how cells can modulate NF-κB activity by fine-tuning the relative proportions of the p50 and p65 proteins, as well as their time of expression. This work thus provides a new quantitative interpretation of Rel dimer distribution in the cell, particularly for those who are developing mathematical models of NF-κB activity.
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Affiliation(s)
- Matthew Biancalana
- Medical Research Council Laboratory of Molecular BiologyCambridge Biomedical CampusCambridgeUK
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | | | - Michael J. Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Alan R. Fersht
- Medical Research Council Laboratory of Molecular BiologyCambridge Biomedical CampusCambridgeUK
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24
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Agelopoulos M, Foutadakis S, Thanos D. The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression. Front Immunol 2021; 12:682397. [PMID: 34149720 PMCID: PMC8212036 DOI: 10.3389/fimmu.2021.682397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 01/05/2023] Open
Abstract
Regulation of gene expression in time, space and quantity is orchestrated by the functional interplay of cis-acting elements and trans-acting factors. Our current view postulates that transcription factors recognize enhancer DNA and read the transcriptional regulatory code by cooperative DNA binding to specific DNA motifs, thus instructing the recruitment of transcriptional regulatory complexes forming a plethora of higher-ordered multi-protein-DNA and protein-protein complexes. Here, we reviewed the formation of multi-dimensional chromatin assemblies implicated in gene expression with emphasis on the regulatory role of enhancer hubs as coordinators of stochastic gene expression. Enhancer hubs contain many interacting regulatory elements and represent a remarkably dynamic and heterogeneous network of multivalent interactions. A functional consequence of such complex interaction networks could be that individual enhancers function synergistically to ensure coordination, tight control and robustness in regulation of expression of spatially connected genes. In this review, we discuss fundamental paradigms of such inter- and intra- chromosomal associations both in the context of immune-related genes and beyond.
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Affiliation(s)
| | | | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
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25
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Stormberg T, Filliaux S, Baughman HER, Komives EA, Lyubchenko YL. Transcription factor NF-κB unravels nucleosomes. Biochim Biophys Acta Gen Subj 2021; 1865:129934. [PMID: 34029641 DOI: 10.1016/j.bbagen.2021.129934] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022]
Abstract
NF-κB is a transcription factor responsible for activating hundreds of genes in mammalian organisms. To accomplish its function, NF-κB must interact with DNA occupied by nucleosomes, but how this interaction occurs is unclear. Here we used Atomic Force Microscopy to characterize complexes of NF-κB with nucleosomes assembled on different DNA templates. The assembly of NF-κB-nucleosome complexes leads to a substantial decrease of DNA wrapping efficiency from 149 ± 2 bp (SEM) for the control nucleosome sample to 135 ± 3 bp for complexes of nucleosomes with NF-κB. Mapping of the nucleosomes did not reveal displacement of under-wrapped nucleosomes from their original position, suggesting that unravelling involves dissociation of one or both flanks of the nucleosomes. Binding of NF-κB to the core was identified by nucleosome core volume measurements. We discovered two binding modes of NF-κB associated with nucleosome unravelling - NF-κB bound to the nucleosome core and to the DNA flanks. From these findings we propose two models explaining the interaction of NF-κB with the nucleosome complex. The partial unravelling of nucleosomes by NF-κB makes the DNA segment at the edge of the nucleosome core accessible, facilitating the transcription process. We speculate that NF-κB can function as a pioneer factor, enhancing its ability to facilitate rapid transcriptional response to cell stress.
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Affiliation(s)
- Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Shaun Filliaux
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Hannah E R Baughman
- Department of Chemistry and Biochemistry, UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0378, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0378, USA.
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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26
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Regulation of Transcription Factor NF-κB in Its Natural Habitat: The Nucleus. Cells 2021; 10:cells10040753. [PMID: 33805563 PMCID: PMC8066257 DOI: 10.3390/cells10040753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 01/11/2023] Open
Abstract
Activation of the transcription factor NF-κB elicits an individually tailored transcriptional response in order to meet the particular requirements of specific cell types, tissues, or organs. Control of the induction kinetics, amplitude, and termination of gene expression involves multiple layers of NF-κB regulation in the nucleus. Here we discuss some recent advances in our understanding of the mutual relations between NF-κB and chromatin regulators also in the context of different levels of genome organization. Changes in the 3D folding of the genome, as they occur during senescence or in cancer cells, can causally contribute to sustained increases in NF-κB activity. We also highlight the participation of NF-κB in the formation of hierarchically organized super enhancers, which enable the coordinated expression of co-regulated sets of NF-κB target genes. The identification of mechanisms allowing the specific regulation of NF-κB target gene clusters could potentially enable targeted therapeutic interventions, allowing selective interference with subsets of the NF-κB response without a complete inactivation of this key signaling system.
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27
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Ozawa T, Kaneko S, Szulzewsky F, Qiao Z, Takadera M, Narita Y, Kondo T, Holland EC, Hamamoto R, Ichimura K. C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation. Acta Neuropathol Commun 2021; 9:36. [PMID: 33685520 PMCID: PMC7941712 DOI: 10.1186/s40478-021-01135-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 12/13/2022] Open
Abstract
Recurrent C11orf95-RELA fusions (RELAFUS) are the hallmark of supratentorial ependymomas. The presence of RELA as the fusion partner indicates a close association of aberrant NF-κB activity with tumorigenesis. However, the oncogenic role of the C11orf95 has not been determined. Here, we performed ChIP-seq analyses to explore genomic regions bound by RELAFUS and H3K27ac proteins in human 293T and mouse ependymoma cells. We then utilized published RNA-Seq data from human and mouse RELAFUS tumors and identified target genes that were directly regulated by RELAFUS in these tumors. Subsequent transcription factor motif analyses of RELAFUS target genes detected a unique GC-rich motif recognized by the C11orf95 moiety, that is present in approximately half of RELAFUS target genes. Luciferase assays confirmed that a promoter carrying this motif is sufficient to drive RELAFUS-dependent gene expression. Further, the RELAFUS target genes were found to be overlapped with Rela target genes primarily via non-canonical NF-κB binding sites. Using a series of truncation and substitution mutants of RELAFUS, we also show that the activation domain in the RELAFUS moiety is necessary for the regulation of gene expression of these RELAFUS target genes. Lastly, we performed an anti-cancer drug screening with mouse ependymoma cells and identified potential anti-ependymoma drugs that are related to the oncogenic mechanism of RELAFUS. These findings suggested that RELAFUS might induce ependymoma formation through oncogenic pathways orchestrated by both C11orf95 and RELA target genes. Thus, our study unveils a complex gene function of RELAFUS as an oncogenic transcription factor in RELAFUS positive ependymomas.
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28
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Käppel S, Eggeling R, Rümpler F, Groth M, Melzer R, Theißen G. DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq. PLANT MOLECULAR BIOLOGY 2021; 105:543-557. [PMID: 33486697 PMCID: PMC7892521 DOI: 10.1007/s11103-020-01108-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/11/2020] [Indexed: 05/13/2023]
Abstract
We studied the DNA-binding profile of the MADS-domain transcription factor SEPALLATA3 and mutant variants by SELEX-seq. DNA-binding characteristics of SEPALLATA3 mutant proteins lead us to propose a novel DNA-binding mode. MIKC-type MADS-domain proteins, which function as essential transcription factors in plant development, bind as dimers to a 10-base-pair AT-rich motif termed CArG-box. However, this consensus motif cannot fully explain how the abundant family members in flowering plants can bind different target genes in specific ways. The aim of this study was to better understand the DNA-binding specificity of MADS-domain transcription factors. Also, we wanted to understand the role of a highly conserved arginine residue for binding specificity of the MADS-domain transcription factor family. Here, we studied the DNA-binding profile of the floral homeotic MADS-domain protein SEPALLATA3 by performing SELEX followed by high-throughput sequencing (SELEX-seq). We found a diverse set of bound sequences and could estimate the in vitro binding affinities of SEPALLATA3 to a huge number of different sequences. We found evidence for the preference of AT-rich motifs as flanking sequences. Whereas different CArG-boxes can act as SEPALLATA3 binding sites, our findings suggest that the preferred flanking motifs are almost always the same and thus mostly independent of the identity of the central CArG-box motif. Analysis of SEPALLATA3 proteins with a single amino acid substitution at position 3 of the DNA-binding MADS-domain further revealed that the conserved arginine residue, which has been shown to be involved in a shape readout mechanism, is especially important for the recognition of nucleotides at positions 3 and 8 of the CArG-box motif. This leads us to propose a novel DNA-binding mode for SEPALLATA3, which is different from that of other MADS-domain proteins known.
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Affiliation(s)
- Sandra Käppel
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Ralf Eggeling
- Department of Computer Science, University of Helsinki, Pietari Kalmin katu 5, 00014, Helsinki, Finland
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany
- Institute for Biomedical Informatics, University of Tübingen, Tübingen, Germany
| | - Florian Rümpler
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Core Facility DNA Sequencing, Beutenbergstraße 11, 07745, Jena, Germany
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany.
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29
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Rasi Bonab F, Baghbanzadeh A, Ghaseminia M, Bolandi N, Mokhtarzadeh A, Amini M, Dadashzadeh K, Hajiasgharzadeh K, Baradaran B, Bannazadeh Baghi H. Molecular pathways in the development of HPV-induced cervical cancer. EXCLI JOURNAL 2021; 20:320-337. [PMID: 33746665 PMCID: PMC7975633 DOI: 10.17179/excli2021-3365] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022]
Abstract
Recently, human papillomavirus (HPV) has gained considerable attention in cervical cancer research studies. It is one of the most important sexually transmitted diseases that can affect 160 to 289 out of 10000 persons every year. Due to the infectious nature of this virus, HPV can be considered a serious threat. The knowledge of viral structure, especially for viral oncoproteins like E6, E7, and their role in causing cancer is very important. This virus has different paths (PI3K/Akt, Wnt/β-catenin, ERK/MAPK, and JAK/STAT) that are involved in the transmission of signaling paths through active molecules like MEK (pMEK), ERK (pERK), and Akt (pAkt). It's eventually through these paths that cancer is developed. Precise knowledge of these paths and their signals give us the prognosis to adopt appropriate goals for prevention and control of these series of cancer.
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Affiliation(s)
- Farnaz Rasi Bonab
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Laboratory Sciences, Marand Branch, Islamic Azad University, Marand, Iran
| | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Moslem Ghaseminia
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nadia Bolandi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kianoosh Dadashzadeh
- Department of Laboratory Sciences, Marand Branch, Islamic Azad University, Marand, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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30
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High-Throughput Analysis of the Cell and DNA Site-Specific Binding of Native NF-κB Dimers Using Nuclear Extract Protein-Binding Microarrays (NextPBMs). Methods Mol Biol 2021; 2366:43-66. [PMID: 34236632 DOI: 10.1007/978-1-0716-1669-7_4] [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: 01/04/2023]
Abstract
Nuclear factor-kappa B (NF-κB) transcription factors coordinate gene expression in response to a broad array of cellular signals. In vertebrates, there are five NF-κB proteins (c-Rel, RelA/p65, RelB, p50, and p52) that can form various dimeric combinations exhibiting both common and dimer-specific DNA-binding specificity. In this chapter, we describe the use of the nuclear extract protein-binding microarray (nextPBM), a high-throughput method to characterize the DNA binding of transcription factors present in cell nuclear extracts. NextPBMs allow for sensitive analysis of the DNA binding of NF-κB dimers and their interactions with cell-specific cofactors.
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31
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Connor MG, Camarasa TMN, Patey E, Rasid O, Barrio L, Weight CM, Miller DP, Heyderman RS, Lamont RJ, Enninga J, Hamon MA. The histone demethylase KDM6B fine-tunes the host response to Streptococcus pneumoniae. Nat Microbiol 2020; 6:257-269. [PMID: 33349663 DOI: 10.1038/s41564-020-00805-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 09/28/2020] [Indexed: 01/08/2023]
Abstract
Streptococcus pneumoniae is a natural colonizer of the human respiratory tract and an opportunistic pathogen. Although epithelial cells are among the first to encounter pneumococci, the cellular processes and contribution of epithelial cells to the host response are poorly understood. Here, we show that a S. pneumoniae serotype 6B ST90 strain, which does not cause disease in a murine infection model, induces a unique NF-κB signature response distinct from an invasive-disease-causing isolate of serotype 4 (TIGR4). This signature is characterized by activation of p65 and requires a histone demethylase KDM6B. We show, molecularly, that the interaction of the 6B strain with epithelial cells leads to chromatin remodelling within the IL-11 promoter in a KDM6B-dependent manner, where KDM6B specifically demethylates histone H3 lysine 27 dimethyl. Remodelling of the IL-11 locus facilitates p65 access to three NF-κB sites that are otherwise inaccessible when stimulated by IL-1β or TIGR4. Finally, we demonstrate through chemical inhibition of KDM6B with GSK-J4 inhibitor and through exogenous addition of IL-11 that the host responses to the 6B ST90 and TIGR4 strains can be interchanged both in vitro and in a murine model of infection in vivo. Our studies therefore reveal how a chromatin modifier governs cellular responses during infection.
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Affiliation(s)
| | - Tiphaine M N Camarasa
- G5 Chromatin and Infection, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Emma Patey
- G5 Chromatin and Infection, Institut Pasteur, Paris, France.,University of Glasgow, Scotland, UK
| | - Orhan Rasid
- G5 Chromatin and Infection, Institut Pasteur, Paris, France
| | - Laura Barrio
- Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur, Paris, France.,UMR CNRS, Paris, France
| | - Caroline M Weight
- Division of Infection and Immunity, University College London, London, UK
| | - Daniel P Miller
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, UK
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA
| | - Jost Enninga
- Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur, Paris, France.,UMR CNRS, Paris, France
| | - Melanie A Hamon
- G5 Chromatin and Infection, Institut Pasteur, Paris, France.
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32
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Antonangeli F, Natalini A, Garassino MC, Sica A, Santoni A, Di Rosa F. Regulation of PD-L1 Expression by NF-κB in Cancer. Front Immunol 2020; 11:584626. [PMID: 33324403 PMCID: PMC7724774 DOI: 10.3389/fimmu.2020.584626] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/25/2020] [Indexed: 12/31/2022] Open
Abstract
Immune checkpoints are inhibitory receptor/ligand pairs regulating immunity that are exploited as key targets of anti-cancer therapy. Although the PD-1/PD-L1 pair is one of the most studied immune checkpoints, several aspects of its biology remain to be clarified. It has been established that PD-1 is an inhibitory receptor up-regulated by activated T, B, and NK lymphocytes and that its ligand PD-L1 mediates a negative feedback of lymphocyte activation, contributing to the restoration of the steady state condition after acute immune responses. This loop might become detrimental in the presence of either a chronic infection or a growing tumor. PD-L1 expression in tumors is currently used as a biomarker to orient therapeutic decisions; nevertheless, our knowledge about the regulation of PD-L1 expression is limited. The present review discusses how NF-κB, a master transcription factor of inflammation and immunity, is emerging as a key positive regulator of PD-L1 expression in cancer. NF-κB directly induces PD-L1 gene transcription by binding to its promoter, and it can also regulate PD-L1 post-transcriptionally through indirect pathways. These processes, which under conditions of cellular stress and acute inflammation drive tissue homeostasis and promote tissue healing, are largely dysregulated in tumors. Up-regulation of PD-L1 in cancer cells is controlled via NF-κB downstream of several signals, including oncogene- and stress-induced pathways, inflammatory cytokines, and chemotherapeutic drugs. Notably, a shared signaling pathway in epithelial cancers induces both PD-L1 expression and epithelial–mesenchymal transition, suggesting that PD-L1 is part of the tissue remodeling program. Furthermore, PD-L1 expression by tumor infiltrating myeloid cells can contribute to the immune suppressive features of the tumor environment. A better understanding of the interplay between NF-κB signaling and PD-L1 expression is highly relevant to cancer biology and therapy.
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Affiliation(s)
- Fabrizio Antonangeli
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Rome, Italy
| | - Ambra Natalini
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Rome, Italy
| | - Marina Chiara Garassino
- Medical Oncology Department, Istituto Nazionale dei Tumori, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
| | - Antonio Sica
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, A. Avogadro, Novara, Italy.,Humanitas Clinical and Research Center, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
| | - Angela Santoni
- Department of Molecular Medicine, Laboratory Affiliated to Istituto Pasteur Italia, Sapienza University of Rome, Rome, Italy
| | - Francesca Di Rosa
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Rome, Italy
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33
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Proteoglycan from Bacillus sp. BS11 Inhibits the Inflammatory Response by Suppressing the MAPK and NF-κB Pathways in Lipopolysaccharide-Induced RAW264.7 Macrophages. Mar Drugs 2020; 18:md18120585. [PMID: 33255264 PMCID: PMC7761495 DOI: 10.3390/md18120585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
Inflammation is involved in the pathogenesis of many debilitating diseases. Proteoglycan isolated from marine Bacillus sp. BS11 (EPS11) was shown to have anticancer activity, but its anti-inflammatory potential remains elusive. In the present study, the anti-inflammatory effects and mechanism of EPS11 were evaluated using a lipopolysaccharide (LPS)-induced RAW264.7 macrophage model. Biochemical characterization showed that the total sugar content and protein content of EPS11 were 49.5% and 30.2% respectively. EPS11 was composed of mannose, glucosamine, galactosamine, glucose, galactose, rhamnose, and glucuronic acid. Its molecular weight was determined to be 3.06 × 105 Da. The protein determination of EPS11 was also performed. EPS11 displayed a strong anti-inflammatory effect on LPS-stimulated RAW264.7 macrophages in vitro, which significantly suppressed inflammatory cytokines and mediators (such as NO, TNF-α, IL-6 and IL-1β, and COX-2). Western blot analysis indicated that EPS11 could downregulate the expression of many key proteins in mitogen-activated protein kinases (MAPKs) and transcription factor nuclear factor-κB (NF-κB) signaling pathways. In particular, EPS11 almost completely inhibited the expression of NF-κB P65, which indicated that EPS11 acted primarily on the NF-κB pathways. These findings offer new insights into the molecular mechanism underlying the anti-inflammatory effect of EPS11.
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34
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Leslie J, Macia MG, Luli S, Worrell JC, Reilly WJ, Paish HL, Knox A, Barksby BS, Gee LM, Zaki MYW, Collins AL, Burgoyne RA, Cameron R, Bragg C, Xu X, Chung GW, Brown CDA, Blanchard AD, Nanthakumar CB, Karsdal M, Robinson SM, Manas DM, Sen G, French J, White SA, Murphy S, Trost M, Zakrzewski JL, Klein U, Schwabe RF, Mederacke I, Nixon C, Bird T, Teuwen LA, Schoonjans L, Carmeliet P, Mann J, Fisher AJ, Sheerin NS, Borthwick LA, Mann DA, Oakley F. c-Rel orchestrates energy-dependent epithelial and macrophage reprogramming in fibrosis. Nat Metab 2020; 2:1350-1367. [PMID: 33168981 PMCID: PMC7116435 DOI: 10.1038/s42255-020-00306-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
Fibrosis is a common pathological feature of chronic disease. Deletion of the NF-κB subunit c-Rel limits fibrosis in multiple organs, although the mechanistic nature of this protection is unresolved. Using cell-specific gene-targeting manipulations in mice undergoing liver damage, we elucidate a critical role for c-Rel in controlling metabolic changes required for inflammatory and fibrogenic activities of hepatocytes and macrophages and identify Pfkfb3 as the key downstream metabolic mediator of this response. Independent deletions of Rel in hepatocytes or macrophages suppressed liver fibrosis induced by carbon tetrachloride, while combined deletion had an additive anti-fibrogenic effect. In transforming growth factor-β1-induced hepatocytes, c-Rel regulates expression of a pro-fibrogenic secretome comprising inflammatory molecules and connective tissue growth factor, the latter promoting collagen secretion from HMs. Macrophages lacking c-Rel fail to polarize to M1 or M2 states, explaining reduced fibrosis in RelΔLysM mice. Pharmacological inhibition of c-Rel attenuated multi-organ fibrosis in both murine and human fibrosis. In conclusion, activation of c-Rel/Pfkfb3 in damaged tissue instigates a paracrine signalling network among epithelial, myeloid and mesenchymal cells to stimulate fibrogenesis. Targeting the c-Rel-Pfkfb3 axis has potential for therapeutic applications in fibrotic disease.
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Affiliation(s)
- Jack Leslie
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Marina García Macia
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Saimir Luli
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Julie C Worrell
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - William J Reilly
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hannah L Paish
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Amber Knox
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ben S Barksby
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lucy M Gee
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Marco Y W Zaki
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biochemistry Department, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Amy L Collins
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Burgoyne
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rainie Cameron
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charlotte Bragg
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Xin Xu
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Git W Chung
- Newcells Biotech, The Biosphere, Newcastle Helix, Newcastle upon Tyne, UK
| | - Colin D A Brown
- Newcells Biotech, The Biosphere, Newcastle Helix, Newcastle upon Tyne, UK
| | - Andrew D Blanchard
- Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, UK
| | - Carmel B Nanthakumar
- Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, UK
| | - Morten Karsdal
- Nordic Bioscience A/S, Biomarkers & Research, Herlev, Denmark
| | - Stuart M Robinson
- Department of Hepatobiliary Surgery, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Derek M Manas
- Department of Hepatobiliary Surgery, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gourab Sen
- Department of Hepatobiliary Surgery, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jeremy French
- Department of Hepatobiliary Surgery, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Steven A White
- Department of Hepatobiliary Surgery, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sandra Murphy
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthias Trost
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Johannes L Zakrzewski
- Center for Discovery and Innovation and John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Ulf Klein
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | | | - Ingmar Mederacke
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, UK
| | - Tom Bird
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK
- MRC Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Laure-Anne Teuwen
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Jelena Mann
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Fibrofind, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew J Fisher
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Institute of Transplantation, The Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Neil S Sheerin
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lee A Borthwick
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Fibrofind, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Derek A Mann
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Fibrofind, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
- Fibrofind, Medical School, Newcastle University, Newcastle upon Tyne, UK.
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35
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Moser BA, Steinhardt RC, Escalante-Buendia Y, Boltz DA, Barker KM, Cassaidy BJ, Rosenberger MG, Yoo S, McGonnigal BG, Esser-Kahn AP. Increased vaccine tolerability and protection via NF-κB modulation. SCIENCE ADVANCES 2020; 6:eaaz8700. [PMID: 32917696 PMCID: PMC11206472 DOI: 10.1126/sciadv.aaz8700] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/24/2020] [Indexed: 05/20/2023]
Abstract
Improving adjuvant responses is a promising pathway to develop vaccines against some pathogens (e.g., HIV or dengue). One challenge in adjuvant development is modulating the inflammatory response, which can cause excess side effects, while maintaining immune activation and protection. No approved adjuvants yet have the capability to independently modulate inflammation and protection. Here, we demonstrate a method to limit inflammation while retaining and often increasing the protective responses. To accomplish this goal, we combined a partial selective nuclear factor kappa B (NF-kB) inhibitor with several current adjuvants. The resulting vaccines reduce systemic inflammation and boost protective responses. In an influenza challenge model, we demonstrate that this approach enhances protection. This method was tested across a broad range of adjuvants and antigens. We anticipate these studies will lead to an alternative approach to vaccine formulation design that may prove broadly applicable to a wide range of adjuvants and vaccines.
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Affiliation(s)
- B A Moser
- Pritzker School for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
| | - R C Steinhardt
- Pritzker School for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
| | - Y Escalante-Buendia
- Pritzker School for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
| | - D A Boltz
- Division of Microbiology and Molecular Biology, IIT Research Institute, Illinois Institute of Technology, 10W. 35th Street, Chicago, IL 60616, USA
| | - K M Barker
- Division of Microbiology and Molecular Biology, IIT Research Institute, Illinois Institute of Technology, 10W. 35th Street, Chicago, IL 60616, USA
| | - B J Cassaidy
- Pritzker School for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
| | - M G Rosenberger
- Pritzker School for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
| | - S Yoo
- Department of Chemistry, Chemical Engineering & Materials Science, Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - B G McGonnigal
- Department of Chemistry, Chemical Engineering & Materials Science, Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - A P Esser-Kahn
- Pritzker School for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA.
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Bourges C, Groff AF, Burren OS, Gerhardinger C, Mattioli K, Hutchinson A, Hu T, Anand T, Epping MW, Wallace C, Smith KG, Rinn JL, Lee JC. Resolving mechanisms of immune-mediated disease in primary CD4 T cells. EMBO Mol Med 2020; 12:e12112. [PMID: 32239644 PMCID: PMC7207160 DOI: 10.15252/emmm.202012112] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Deriving mechanisms of immune-mediated disease from GWAS data remains a formidable challenge, with attempts to identify causal variants being frequently hampered by strong linkage disequilibrium. To determine whether causal variants could be identified from their functional effects, we adapted a massively parallel reporter assay for use in primary CD4 T cells, the cell type whose regulatory DNA is most enriched for immune-mediated disease SNPs. This enabled the effects of candidate SNPs to be examined in a relevant cellular context and generated testable hypotheses into disease mechanisms. To illustrate the power of this approach, we investigated a locus that has been linked to six immune-mediated diseases but cannot be fine-mapped. By studying the lead expression-modulating SNP, we uncovered an NF-κB-driven regulatory circuit which constrains T-cell activation through the dynamic formation of a super-enhancer that upregulates TNFAIP3 (A20), a key NF-κB inhibitor. In activated T cells, this feedback circuit is disrupted-and super-enhancer formation prevented-by the risk variant at the lead SNP, leading to unrestrained T-cell activation via a molecular mechanism that appears to broadly predispose to human autoimmunity.
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Affiliation(s)
- Christophe Bourges
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Abigail F Groff
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Oliver S Burren
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kaia Mattioli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Anna Hutchinson
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, UK
| | - Theodore Hu
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Tanmay Anand
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Madeline W Epping
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Chris Wallace
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kenneth Gc Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - James C Lee
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
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37
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Upregulation of CASP9 through NF-κB and Its Target MiR-1276 Contributed to TNFα-promoted Apoptosis of Cancer Cells Induced by Doxorubicin. Int J Mol Sci 2020; 21:ijms21072290. [PMID: 32225068 PMCID: PMC7177739 DOI: 10.3390/ijms21072290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/17/2020] [Accepted: 03/23/2020] [Indexed: 12/18/2022] Open
Abstract
Under some conditions, nuclear factor-κB (NF-κB) has a pro-apoptotic role, but the mechanisms underlying this function remain unclear. This study demonstrated that NF-κB directly binds to CASP9 and miR1276 in tumor necrosis factor α (TNFα)-treated HeLa and HepG2 cells. NF-κB upregulated CASP9 expression, whereas downregulated miR1276 expression in the TNFα-treated cells. The miR1276 repressed CASP9 expression in both cells. As a result, a typical NF-κB-mediated coherent feed-forward loop was formed in the TNFα-treated cells. It was proposed that the NF-κB-mediated loop may contribute to cell apoptosis under certain conditions. This opinion was supported by the following evidence: TNFα promoted the apoptosis of HeLa and HepG2 cells induced by doxorubicin (DOX). CASP9 was significantly upregulated and activated by TNFα in the DOX-induced cells. Moreover, a known inhibitor of CASP9 activation significantly repressed the TNFα promotion of apoptosis induced by DOX. These findings indicate that CASP9 is a new mediator of the NF-κB pro-apoptotic pathway, at least in such conditions. This study therefore provides new insights into the pro-apoptotic role of NF-κB. The results also shed new light on the molecular mechanism underlying TNFα-promotion of cancer cells apoptosis induced by some anticancer drugs such as DOX.
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38
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Mendez JM, Keestra-Gounder AM. NF-κB-dependent Luciferase Activation and Quantification of Gene Expression in Salmonella Infected Tissue Culture Cells. J Vis Exp 2020. [PMID: 31984953 DOI: 10.3791/60567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The dimeric transcription factor NF-κB regulates many cellular response pathways, including inflammatory pathways by inducing the expression of various cytokines and chemokines. NF-κB is constitutively expressed and is sequestered in the cytosol by the inhibitory protein nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha (IκBα). Activation of NF-κB requires the degradation of IκBα, which then exposes a nuclear localization signal on NF-κB and promotes its trafficking to the nucleus. Once in the nucleus, NF-κB binds to the promotor region of NF-κB target genes such as interleukin 6 (IL-6) and IL-23, to promote their expression. The activation of NF-κB occurs independently of transcription or translation. Therefore, the activation state of NF-κB must be measured either by quantifying NF-κB specifically in the nucleus, or by quantifying expression of NF-κB target genes. In this protocol, cells stably transfected with an NF-κB::luciferase reporter construct are assayed for NF-κB activation using in vitro tissue culture techniques. These cells are infected with Salmonella Typhimurium to activate NF-κB, which traffics to the nucleus and binds to κB sites in the promoter region of luciferase, inducing its expression. Cells are lysed and analyzed with the luciferase assay system. The amount of luciferase produced by the cells correlates with the intensity of the luminescence signal, which is detected by a plate reader. The luminescence signal generated by this procedure provides a quick and highly sensitive method by which to assess NF-κB activation under a range of conditions. This protocol also utilizes quantitative reverse transcription PCR (RT-qPCR) to detect relative mRNA levels that are indicative of gene expression.
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Affiliation(s)
- Jonathan M Mendez
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus
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39
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Sun Y, Li Z, Lau C, Lu J. Antibody free ELISA-like assay for the detection of transcription factors based on double-stranded DNA thermostability. Analyst 2020; 145:3339-3344. [DOI: 10.1039/c9an02631b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Transcription factors (TFs) play critical roles in gene expression regulation and disease development. Herein we report a chemiluminescence assay for the detection of transcription factor based on double-stranded DNA thermostability.
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Affiliation(s)
- Yue Sun
- School of Pharmacy
- Fudan University
- Shanghai 201203
- P.R. China
| | - Zhiyan Li
- School of Pharmacy
- Fudan University
- Shanghai 201203
- P.R. China
| | - Choiwan Lau
- School of Pharmacy
- Fudan University
- Shanghai 201203
- P.R. China
| | - Jianzhong Lu
- School of Pharmacy
- Fudan University
- Shanghai 201203
- P.R. China
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40
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Soleimani A, Rahmani F, Ferns GA, Ryzhikov M, Avan A, Hassanian SM. Role of the NF-κB signaling pathway in the pathogenesis of colorectal cancer. Gene 2019; 726:144132. [PMID: 31669643 DOI: 10.1016/j.gene.2019.144132] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 09/12/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
The NF-κB signaling pathway is a key regulator of CRC cell proliferation, apoptosis, angiogenesis, inflammation, metastasis, and drug resistance. Over-activation of the NF-κB pathway is a feature of colorectal cancer (CRC). While new combinatorial treatments have improved overall patient outcome; quality of life, cost of care, and patient survival rate have seen little improvement. Suppression of the NF-κB signaling pathway using biological or specific pharmacological inhibitors is a potential therapeutic approach in the treatment of colon cancer. This review summarizes the regulatory role of NF-κB signaling pathway in the pathogenesis of CRC for a better understanding and hence a better management of the disease.
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Affiliation(s)
- Atena Soleimani
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzad Rahmani
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Mikhail Ryzhikov
- Division of Pulmonary and Critical Care Medicine, Washington University, School of Medicine, Saint Louis, MO, USA
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Mulero MC, Wang VYF, Huxford T, Ghosh G. Genome reading by the NF-κB transcription factors. Nucleic Acids Res 2019; 47:9967-9989. [PMID: 31501881 PMCID: PMC6821244 DOI: 10.1093/nar/gkz739] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/05/2019] [Accepted: 08/21/2019] [Indexed: 12/25/2022] Open
Abstract
The NF-κB family of dimeric transcription factors regulates transcription by selectively binding to DNA response elements present within promoters or enhancers of target genes. The DNA response elements, collectively known as κB sites or κB DNA, share the consensus 5'-GGGRNNNYCC-3' (where R, Y and N are purine, pyrimidine and any nucleotide base, respectively). In addition, several DNA sequences that deviate significantly from the consensus have been shown to accommodate binding by NF-κB dimers. X-ray crystal structures of NF-κB in complex with diverse κB DNA have helped elucidate the chemical principles that underlie target selection in vitro. However, NF-κB dimers encounter additional impediments to selective DNA binding in vivo. Work carried out during the past decades has identified some of the barriers to sequence selective DNA target binding within the context of chromatin and suggests possible mechanisms by which NF-κB might overcome these obstacles. In this review, we first highlight structural features of NF-κB:DNA complexes and how distinctive features of NF-κB proteins and DNA sequences contribute to specific complex formation. We then discuss how native NF-κB dimers identify DNA binding targets in the nucleus with support from additional factors and how post-translational modifications enable NF-κB to selectively bind κB sites in vivo.
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Affiliation(s)
- Maria Carmen Mulero
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Yang JH, Chen WT, Lee MC, Fang WH, Hsu YJ, Chin-Lin, Chen HC, Chang HL, Chen CF, Tu MY, Kuo CW, Lin YH, Hsiao PJ, Su SL. Investigation of the variants at the binding site of inflammatory transcription factor NF-κB in patients with end-stage renal disease. BMC Nephrol 2019; 20:300. [PMID: 31382928 PMCID: PMC6683452 DOI: 10.1186/s12882-019-1471-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background A chronic inflammatory state is a prominent feature in patients with end-stage renal disease (ESRD). Nuclear factor-kappa B (NF-κB) is a transcription factor that regulates the expression of genes involved in inflammation. Some genetic studies have demonstrated that the NF-κB genetic mutation could cause kidney injury and kidney disease progression. However, the association of a gene polymorphism in the transcription factor binding site of NF-κB with kidney disease is not clear. Methods We used the Taiwan Biobank database, the University of California, Santa Cruz, reference genome, and a chromatin immunoprecipitation sequencing database to find single nucleotide polymorphisms (SNPs) at potential binding sites of NF-κB. In addition, we performed a case–control study and genotyped 847 patients with ESRD and 846 healthy controls at Tri-Service General Hospital from 2015 to 2016. Furthermore, we used the ChIP assay to identify the binding activity of different genotypes and used Luciferase reporter assay to examine the function of the rs9395890 polymorphism. Result The results of biometric screening in the databases revealed 15 SNPs with the potential binding site of NF-κB. Genotype distributions of rs9395890 were significantly different in ESRD cases and healthy controls (P = 0.049). The ChIP assay revealed an approximately 1.49-fold enrichment of NF-κB of the variant type TT when compared to that of the wild-type GG in rs9395890 (P = 0.027; TT = 3.20 ± 0.16, GT = 2.81 ± 0.20, GG = 1.71 ± 0.18). The luciferase reporter assay showed that the NF-κB binding site activity in T allele was slightly higher than that in G allele, though it is not significant. Conclusions Our findings indicate that rs9395890 is associated with susceptibility to ESRD in Taiwan population. Electronic supplementary material The online version of this article (10.1186/s12882-019-1471-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jia-Hwa Yang
- School of Public Health and Graduate institute of Life Sciences, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 114, Taiwan, Republic of China.,Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan, Republic of China
| | - Wei-Teing Chen
- Division of Chest Medicine, Department of Medicine, Cheng Hsin General Hospital, Taipei, Taiwan, Republic of China.,Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Meng-Chang Lee
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Wen-Hui Fang
- Department of Family and Community Medicine, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - Yu-Juei Hsu
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - Chin-Lin
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hsiang-Cheng Chen
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hsueh-Lu Chang
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chien-Fu Chen
- Department of Orthopedics, Taichung Armed Forces General Hospital, Taichung, Taiwan, Republic of China
| | - Min-Yu Tu
- Department of Orthopedics, Kaohsiung Armed Forces General Hospital, Gangshan Branch, Kaohsiung, Taiwan, Republic of China
| | - Chien-Wei Kuo
- Division of Nephrology Dialysis, Shih-Kang Clinic, New Taipei City, Taiwan, Republic of China
| | - Yuan-Hau Lin
- Division of Nephrology Dialysis, Yuan-Lin Clinic, Taipei, Taiwan, Republic of China
| | - Po-Jen Hsiao
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan, Republic of China. .,Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan City, Taiwan, Republic of China. .,Big Data Research Center, Fu-Jen Catholic University, Taipei, Taiwan, Republic of China. .,Department of Life Sciences, National Central University, Taoyuan City, Taiwan, Republic of China.
| | - Sui-Lung Su
- School of Public Health and Graduate institute of Life Sciences, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 114, Taiwan, Republic of China. .,School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China.
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Mitkin NA, Korneev K, Gorbacheva AM, Kuprash DV. Relative Efficiency of Transcription Factor Binding to Allelic Variants of Regulatory Regions of Human Genes in Immunoprecipitation and Real-Time PCR. Mol Biol 2019. [DOI: 10.1134/s0026893319030117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Gamboa-Cedeño AM, Castillo M, Xiao W, Waldmann TA, Ranuncolo SM. Alternative and canonical NF-kB pathways DNA-binding hierarchies networks define Hodgkin lymphoma and Non-Hodgkin diffuse large B Cell lymphoma respectively. J Cancer Res Clin Oncol 2019; 145:1437-1448. [PMID: 30941572 PMCID: PMC8317045 DOI: 10.1007/s00432-019-02909-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/25/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE Despite considerable evidence that supports the NF-kB role in the immune system and lymphomagenesis, it is unclear whether specific NF-kB dimers control a particular set of genes that account for their biological functions. Our previous work showed that Hodgkin Lymphoma (HL) is unique, among germinal center (GC)-derived lymphomas, with respect to its dependency on Rel-B to survive. In contrast, diffuse large B-Cell lymphoma (DLBCL) including both Activated B-Cell-Like and Germinal Center B-Cell-Like, requires cREL and Rel-A to survive and it is not affected by Rel-B depletion. These findings highlighted the activity of specific NF-kB subunits in different GC-derived lymphomas. METHODS Sequenced chromatin immunoprecipitated DNA fragments (ChIP-Seq) analysis revealed an extensive NF-kB DNA-binding network in DLBCL and HL. The ChIP-Seq data was merged with microarray analysis following the Rel-A, Rel-B or cRel knockdown to determine effectively regulated genes. RESULTS Downstream target analysis showed enrichment for cell cycle control, among other signatures. Rel-B and cRel controlled different genes within the same signature in HL and DLBCL, respectively. BCL2 was exclusively controlled by Rel-B in HL. Both mRNA and protein levels decreased following Rel-B depletion meanwhile there was no change upon cRel knock-down. BCL2 exogenous expression partially rescued the death induced by decreased Rel-B in HL cells. CONCLUSION The Rel-B hierarchical network defined HL and the cRel hierarchical network characterized DLBCL. Each Rel member performs specific functions in distinct GC-derived lymphomas. This result should be considered for the development of targeted therapies that are aimed to selectively inhibit individual NF-kB dimers.
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Affiliation(s)
- Angélica María Gamboa-Cedeño
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET-Instituto Universitario del Hospital Italiano-Hospital Italiano de Buenos Aires, Potosí 4240 C.P., C1183AEG, Buenos Aires, Argentina
| | - Mariángeles Castillo
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET-Instituto Universitario del Hospital Italiano-Hospital Italiano de Buenos Aires, Potosí 4240 C.P., C1183AEG, Buenos Aires, Argentina
| | - Wenming Xiao
- Center for Information Technology, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Thomas A Waldmann
- Lymphoid Malignancies Branch, Center for Cancer Research (CCR), NCI-NIH, Bethesda, MD, USA
| | - Stella Maris Ranuncolo
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET-Instituto Universitario del Hospital Italiano-Hospital Italiano de Buenos Aires, Potosí 4240 C.P., C1183AEG, Buenos Aires, Argentina.
- Departamento de Histología y Biología Celular, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.
- National Council of Scientific and Technological Research (CONICET), Buenos Aires, Argentina.
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I-BET151 suppresses osteoclast formation and inflammatory cytokines secretion by targetting BRD4 in multiple myeloma. Biosci Rep 2019; 39:BSR20181245. [PMID: 30455393 PMCID: PMC6522735 DOI: 10.1042/bsr20181245] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/24/2018] [Accepted: 11/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background: Multiple myeloma (MM) is an incurable hematologic cancer, accompanied by excessive osteoclast formation and inflammatory cytokine secretion. The mechanisms by which bromodomain and extra-terminal domain (BET) protein inhibitor I-BET151 regulates osteoclast differentiation and inflammatory cytokine secretion in MM are largely unknown. Methods: The isolated peripheral blood mononuclear cells from normal or patients with MM were treated with receptor activator of NF-κB ligand (RANKL) and M-CSF to induce osteoclast differentiation. RAW 264.7 cells were treated with RANKL. I-BET151 was applied to investigate the effects of BRD4 inhibition on osteoclast formation and inflammatory cytokine secretion. Osteoclast formation was determined by tartrate-resistant acid phosphatase (TRACP) staining. The expression of osteoclast-specific genes TRACP, matrix metalloproteinase-9 (MMP-9), cathepsin K (Ctsk), and c-Src was tested using quantitative real-time PCR. And the level of inflammatory cytokines TNF-α, IL-1β, and IL-6 was assessed by ELISA. Tumor necrosis factor receptor-associated factor 6 (TRAF6), BRD4, nuclear and cytoplasm p65, IκB-α, nuclear factor of activated T cells cytoplasmic (NFATc1), and osteoprotegerin (OPG) expression were measured by Western blotting. RNAi technology was applied to knock down BET family member BRD4. Results: I-BET151 dose-dependently suppressed osteoclast formation, inhibited the levels of osteoclast-specific genes TRACP, MMP-9, Ctsk, and c-Src and inflammatory cytokines TNF-α, IL-1β, and IL-6 secretion in peripheral blood mononuclear cells and RAW 264.7. I-BET151 inhibited the protein levels of BRD4 and NFATc1, increased OPG expression, and suppressed IκB-α degradation and p65 nuclear translocation. Further, the effects of I-BET151 on osteoclast formation, osteoclast-specific genes expression, inflammatory cytokine secretion, and NF-κB inhibition were promoted by BRD4 knockdown. Conclusion: I-BET151 inhibits osteoclast formation and inflammatory cytokine secretion by targetting BRD4-mediated RANKL-NF-κB signal pathway and BRD4 inhibition might be beneficial for MM treatment.
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Abstract
For nearly a century adaptive landscapes have provided overviews of the evolutionary process and yet they remain metaphors. We redefine adaptive landscapes in terms of biological processes rather than descriptive phenomenology. We focus on the underlying mechanisms that generate emergent properties such as epistasis, dominance, trade-offs and adaptive peaks. We illustrate the utility of landscapes in predicting the course of adaptation and the distribution of fitness effects. We abandon aged arguments concerning landscape ruggedness in favor of empirically determining landscape architecture. In so doing, we transform the landscape metaphor into a scientific framework within which causal hypotheses can be tested.
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Affiliation(s)
- Xiao Yi
- BioTechnology Institute, University of Minnesota, St. Paul, MN
| | - Antony M Dean
- BioTechnology Institute, University of Minnesota, St. Paul, MN
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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47
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Brignall R, Moody AT, Mathew S, Gaudet S. Considering Abundance, Affinity, and Binding Site Availability in the NF-κB Target Selection Puzzle. Front Immunol 2019; 10:609. [PMID: 30984185 PMCID: PMC6450194 DOI: 10.3389/fimmu.2019.00609] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/07/2019] [Indexed: 12/21/2022] Open
Abstract
The NF-κB transcription regulation system governs a diverse set of responses to various cytokine stimuli. With tools from in vitro biochemical characterizations, to omics-based whole genome investigations, great strides have been made in understanding how NF-κB transcription factors control the expression of specific sets of genes. Nonetheless, these efforts have also revealed a very large number of potential binding sites for NF-κB in the human genome, and a puzzle emerges when trying to explain how NF-κB selects from these many binding sites to direct cell-type- and stimulus-specific gene expression patterns. In this review, we surmise that target gene transcription can broadly be thought of as a function of the nuclear abundance of the various NF-κB dimers, the affinity of NF-κB dimers for the regulatory sequence and the availability of this regulatory site. We use this framework to place quantitative information that has been gathered about the NF-κB transcription regulation system into context and thus consider questions it answers, and questions it raises. We end with a brief discussion of some of the future prospects that new approaches could bring to our understanding of how NF-κB transcription factors orchestrate diverse responses in different biological contexts.
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Affiliation(s)
- Ruth Brignall
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| | - Amy T Moody
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States.,Laboratory for Systems Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, United States.,Department of Microbiology, Tufts University School of Medicine, Boston, MA, United States
| | - Shibin Mathew
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| | - Suzanne Gaudet
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
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Fouani L, Kovacevic Z, Richardson DR. Targeting Oncogenic Nuclear Factor Kappa B Signaling with Redox-Active Agents for Cancer Treatment. Antioxid Redox Signal 2019; 30:1096-1123. [PMID: 29161883 DOI: 10.1089/ars.2017.7387] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SIGNIFICANCE Nuclear factor kappa B (NF-κB) signaling is essential under physiologically relevant conditions. However, aberrant activation of this pathway plays a pertinent role in tumorigenesis and contributes to resistance. Recent Advances: The importance of the NF-κB pathway means that its targeting must be specific to avoid side effects. For many currently used therapeutics and those under development, the ability to generate reactive oxygen species (ROS) is a promising strategy. CRITICAL ISSUES As cancer cells exhibit greater ROS levels than their normal counterparts, they are more sensitive to additional ROS, which may be a potential therapeutic niche. It is known that ROS are involved in (i) the activation of NF-κB signaling, when in sublethal amounts; and (ii) high levels induce cytotoxicity resulting in apoptosis. Indeed, ROS-induced cytotoxicity is valuable for its capabilities in killing cancer cells, but establishing the potency of ROS for effective inhibition of NF-κB signaling is necessary. Indeed, some cancer treatments, currently used, activate NF-κB and may stimulate oncogenesis and confer resistance. FUTURE DIRECTIONS Thus, combinatorial approaches using ROS-generating agents alongside conventional therapeutics may prove an effective tactic to reduce NF-κB activity to kill cancer cells. One strategy is the use of thiosemicarbazones, which form redox-active metal complexes that generate high ROS levels to deliver potent antitumor activity. These agents also upregulate the metastasis suppressor, N-myc downstream regulated gene 1 (NDRG1), which functions as an NF-κB signaling inhibitor. It is proposed that targeting NF-κB signaling may proffer a new therapeutic niche to improve the efficacy of anticancer regimens.
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Affiliation(s)
- Leyla Fouani
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, University of Sydney, Sydney, Australia
| | - Zaklina Kovacevic
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, University of Sydney, Sydney, Australia
| | - Des R Richardson
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, University of Sydney, Sydney, Australia
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Cadet J, Wagner JR, Angelov D. Biphotonic Ionization of DNA: From Model Studies to Cell. Photochem Photobiol 2018; 95:59-72. [PMID: 30380156 DOI: 10.1111/php.13042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
Oxidation reactions triggered by low-intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high-intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one-electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8-oxo-7,8-dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra- and interstrand cross-links together with DNA-protein cross-links. Information is provided on the utilization of high-intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid-protein interactions and nucleic acid reactivity through DNA-protein cross-links and DNA footprinting experiments.
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Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule LBMC, CNRS-UMR 5239, Université de Lyon, École Normale Supérieure de Lyon, Lyon, France
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50
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Kalita CA, Brown CD, Freiman A, Isherwood J, Wen X, Pique-Regi R, Luca F. High-throughput characterization of genetic effects on DNA-protein binding and gene transcription. Genome Res 2018; 28:1701-1708. [PMID: 30254052 PMCID: PMC6211638 DOI: 10.1101/gr.237354.118] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/20/2018] [Indexed: 12/29/2022]
Abstract
Many variants associated with complex traits are in noncoding regions and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, Biallelic Targeted STARR-seq (BiT-STARR-seq), that identifies allele-specific expression (ASE) while accounting for PCR duplicates through unique molecular identifiers. We tested 75,501 oligos (43,500 SNPs) and identified 2720 SNPs with significant ASE (FDR < 10%). To validate disruption of binding as one of the mechanisms underlying ASE, we developed a new high-throughput allele-specific binding assay for NFKB1. We identified 2684 SNPs with allele-specific binding (ASB) (FDR < 10%); 256 of these SNPs also had ASE (OR = 1.97, P-value = 0.0006). Of variants associated with complex traits, 1531 resulted in ASE, and 1662 showed ASB. For example, we characterized that the Crohn's disease risk variant for rs3810936 increases NFKB1 binding and results in altered gene expression.
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Affiliation(s)
- Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48202, USA
| | - Christopher D Brown
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew Freiman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48202, USA
| | - Jenna Isherwood
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48202, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48202, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48202, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48202, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48202, USA
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