1
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Xu C, Kleinschmidt H, Yang J, Leith EM, Johnson J, Tan S, Mahony S, Bai L. Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1. Mol Cell 2024; 84:2838-2855.e10. [PMID: 39019045 PMCID: PMC11334613 DOI: 10.1016/j.molcel.2024.06.022] [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: 01/09/2024] [Revised: 04/23/2024] [Accepted: 06/21/2024] [Indexed: 07/19/2024]
Abstract
Despite the unique ability of pioneer factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called chromatin immunoprecipitation with integrated synthetic oligonucleotides (ChIP-ISO) to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1, in human A549 cells. Combining ChIP-ISO with in vitro and neural network analyses, we find that (1) FOXA1 binding is strongly affected by co-binding transcription factors (TFs) AP-1 and CEBPB; (2) FOXA1 and AP-1 show binding cooperativity in vitro; (3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin; and (4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.
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Affiliation(s)
- Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianyu Yang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik M Leith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jenna Johnson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Song Tan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA; Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA.
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2
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Madden SK, Brennan A, Mason JM. A library-derived peptide inhibitor of the BZLF1 transcription factor. J Pept Sci 2024; 30:e3557. [PMID: 38041527 DOI: 10.1002/psc.3557] [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: 04/19/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
Transcription factor dysregulation is associated with many diseases, including cancer. Peptide-based molecules are increasingly recognised as important modulators of difficult intracellular protein-protein interaction targets, with peptide library screening consequently proven to be a viable strategy in developing inhibitors against a wide range of transcription factors (TFs). However, current strategies simply select the highest affinity of binding to a target TF rather than the ability to inhibit TF function. Here, we utilise our Transcription Block Survival (TBS) screening platform to enable high-throughput identification of peptides that inhibit TFs from binding to cognate DNA sites, hence inhibiting functionality. In this study, we explore whether the TBS can be expanded to derive a potent and functional peptide inhibitor of the BZLF1 transcription factor. The library-derived peptide, AcidicW, is shown to form a more stable dimer with BZLF1 than the BZLF1 homodimer, with a thermal denaturation temperature exceeding 80°C. AcidicW can also functionally inhibit the BZLF1:TRE DNA interaction with high potency and an IC50 of 612 nM.
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Affiliation(s)
- Sarah K Madden
- Department of Life Sciences, University of Bath, Bath, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Andrew Brennan
- Department of Life Sciences, University of Bath, Bath, UK
| | - Jody M Mason
- Department of Life Sciences, University of Bath, Bath, UK
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3
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Coleman DJ, Keane P, Chin PS, Ames L, Kellaway S, Blair H, Khan N, Griffin J, Holmes E, Maytum A, Potluri S, Strate L, Koscielniak K, Raghavan M, Bushweller J, Heidenreich O, Rabbitts T, Cockerill PN, Bonifer C. Pharmacological inhibition of RAS overcomes FLT3 inhibitor resistance in FLT3-ITD+ AML through AP-1 and RUNX1. iScience 2024; 27:109576. [PMID: 38638836 PMCID: PMC11024925 DOI: 10.1016/j.isci.2024.109576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/16/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
AML is characterized by mutations in genes associated with growth regulation such as internal tandem duplications (ITD) in the receptor kinase FLT3. Inhibitors targeting FLT3 (FLT3i) are being used to treat patients with FLT3-ITD+ but most relapse and become resistant. To elucidate the resistance mechanism, we compared the gene regulatory networks (GRNs) of leukemic cells from patients before and after relapse, which revealed that the GRNs of drug-responsive patients were altered by rewiring their AP-1-RUNX1 axis. Moreover, FLT3i induces the upregulation of signaling genes, and we show that multiple cytokines, including interleukin-3 (IL-3), can overcome FLT3 inhibition and send cells back into cycle. FLT3i leads to loss of AP-1 and RUNX1 chromatin binding, which is counteracted by IL-3. However, cytokine-mediated drug resistance can be overcome by a pan-RAS inhibitor. We show that cytokines instruct AML growth via the transcriptional regulators AP-1 and RUNX1 and that pan-RAS drugs bypass this barrier.
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Affiliation(s)
- Daniel J.L. Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paulynn S. Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sophie Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Helen Blair
- Wolfson Childhood Cancer Research Centre, University of Newcastle, Newcastle upon Tyne, UK
| | - Naeem Khan
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - James Griffin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Elizabeth Holmes
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Alexander Maytum
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Lara Strate
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Kinga Koscielniak
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - John Bushweller
- School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, University of Newcastle, Newcastle upon Tyne, UK
- Princess Máxima Centrum of Pediatric Oncology, Utrecht, the Netherlands
| | - Terry Rabbitts
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Peter N. Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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4
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Dong Y, Yang Y, Wang H, Feng D, Nist E, Yapundich N, Spurlock B, Craft M, Qian L, Liu J. Single-cell chromatin profiling reveals genetic programs activating proregenerative states in nonmyocyte cells. SCIENCE ADVANCES 2024; 10:eadk4694. [PMID: 38381829 PMCID: PMC10881044 DOI: 10.1126/sciadv.adk4694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Cardiac regeneration requires coordinated participation of multiple cell types whereby their communications result in transient activation of proregenerative cell states. Although the molecular characteristics and lineage origins of these activated cell states and their contribution to cardiac regeneration have been studied, the extracellular signaling and the intrinsic genetic program underlying the activation of the transient functional cell states remain largely unexplored. In this study, we delineated the chromatin landscapes of the noncardiomyocytes (nonCMs) of the regenerating heart at the single-cell level and inferred the cis-regulatory architectures and trans-acting factors that control cell type-specific gene expression programs. Moreover, further motif analysis and cell-specific genetic manipulations suggest that the macrophage-derived inflammatory signal tumor necrosis factor-α, acting via its downstream transcription factor complex activator protein-1, functions cooperatively with discrete transcription regulators to activate respective nonCM cell types critical for cardiac regeneration. Thus, our study defines the regulatory architectures and intercellular communication principles in zebrafish heart regeneration.
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Affiliation(s)
- Yanhan Dong
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Haofei Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dong Feng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elizabeth Nist
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nicholas Yapundich
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Brian Spurlock
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Madison Craft
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
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5
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Kellaway SG, Potluri S, Keane P, Blair HJ, Ames L, Worker A, Chin PS, Ptasinska A, Derevyanko PK, Adamo A, Coleman DJL, Khan N, Assi SA, Krippner-Heidenreich A, Raghavan M, Cockerill PN, Heidenreich O, Bonifer C. Leukemic stem cells activate lineage inappropriate signalling pathways to promote their growth. Nat Commun 2024; 15:1359. [PMID: 38355578 PMCID: PMC10867020 DOI: 10.1038/s41467-024-45691-4] [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: 05/02/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
Acute Myeloid Leukemia (AML) is caused by multiple mutations which dysregulate growth and differentiation of myeloid cells. Cells adopt different gene regulatory networks specific to individual mutations, maintaining a rapidly proliferating blast cell population with fatal consequences for the patient if not treated. The most common treatment option is still chemotherapy which targets such cells. However, patients harbour a population of quiescent leukemic stem cells (LSCs) which can emerge from quiescence to trigger relapse after therapy. The processes that allow such cells to re-grow remain unknown. Here, we examine the well characterised t(8;21) AML sub-type as a model to address this question. Using four primary AML samples and a novel t(8;21) patient-derived xenograft model, we show that t(8;21) LSCs aberrantly activate the VEGF and IL-5 signalling pathways. Both pathways operate within a regulatory circuit consisting of the driver oncoprotein RUNX1::ETO and an AP-1/GATA2 axis allowing LSCs to re-enter the cell cycle while preserving self-renewal capacity.
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Affiliation(s)
- Sophie G Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
- Blood Cancer and Stem Cells, Centre for Cancer Sciences, School of Medicine, University of Nottingham, Nottingham, UK.
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Helen J Blair
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Alice Worker
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paulynn S Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Assunta Adamo
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Naeem Khan
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Clinical Haematology, Queen Elizabeth Hospital, Birmingham, UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Olaf Heidenreich
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Princess Maxima Center of Pediatric Oncology, Utrecht, Netherlands
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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6
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Kalyanaraman H, Casteel DE, China SP, Zhuang S, Boss GR, Pilz RB. A plasma membrane-associated form of the androgen receptor enhances nuclear androgen signaling in osteoblasts and prostate cancer cells. Sci Signal 2024; 17:eadi7861. [PMID: 38289986 PMCID: PMC10916501 DOI: 10.1126/scisignal.adi7861] [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: 05/17/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024]
Abstract
Androgen binding to the androgen receptor (AR) in the cytoplasm induces the AR to translocate to the nucleus, where it regulates the expression of target genes. Here, we found that androgens rapidly activated a plasma membrane-associated signaling node that enhanced nuclear AR functions. In murine primary osteoblasts, dihydrotestosterone (DHT) binding to a membrane-associated form of AR stimulated plasma membrane-associated protein kinase G type 2 (PKG2), leading to the activation of multiple kinases, including ERK. Phosphorylation of AR at Ser515 by ERK increased the nuclear accumulation and binding of AR to the promoter of Ctnnb1, which encodes the transcription factor β-catenin. In male mouse osteoblasts and human prostate cancer cells, DHT induced the expression of Ctnnb1 and CTNN1B, respectively, as well as β-catenin target genes, stimulating the proliferation, survival, and differentiation of osteoblasts and the proliferation of prostate cancer cells in a PKG2-dependent fashion. Because β-catenin is a master regulator of skeletal homeostasis, these results explain the reported male-specific osteoporotic phenotype of mice lacking PKG2 in osteoblasts and imply that PKG2-dependent AR signaling is essential for maintaining bone mass in vivo. Our results suggest that widely used pharmacological PKG activators, such as sildenafil, could be beneficial for male and estrogen-deficient female patients with osteoporosis but detrimental in patients with prostate cancer.
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Affiliation(s)
- Hema Kalyanaraman
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Darren E. Casteel
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shyamsundar Pal China
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shunhui Zhuang
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gerry R. Boss
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Renate B. Pilz
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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7
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Asano K, Kikuchi K, Takehara M, Ogasawara M, Yoshioka Y, Ohnishi K, Iwata A, Shimizu S, Tanaka M. Identification of small compounds that inhibit multiple myeloma proliferation by targeting c-Maf transcriptional activity. Biochem Biophys Res Commun 2023; 684:149135. [PMID: 37879249 DOI: 10.1016/j.bbrc.2023.149135] [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: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Multiple myeloma displays the clonal B cell expansion and the overproduction of monoclonal immunoglobulins. Genetic translocations at 14q32, particularly with partners like 16q23, lead to the dysregulation of oncogene expression, including the significant enhancement of c-Maf. This aberrant expression of c-Maf has prompted research into strategies for targeting this transcription factor as a potential therapeutic avenue for multiple myeloma treatment. In this study, we introduce a screening pipeline to test small compounds for their ability to inhibit c-Maf. Using a luciferase indicator driven by the Ccl8 gene promoter, we identified two small compounds that inhibit transcriptional activity of c-Maf. These molecules impede the proliferation of c-Maf-expressing myeloma cells, and repress the expression of c-Maf target genes such as ITGB7 and CCR1. Importantly, these molecules target c-Maf-expressing multiple myeloma cells, but not c-Maf-negative myeloma cells, showing potential for tailoring therapeutic intervention. In conclusion, our screening pipeline is effective to explore leads for a novel c-Maf inhibitor for multiple myeloma therapy.
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Affiliation(s)
- Kenichi Asano
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan.
| | - Kenta Kikuchi
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan; Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Miki Takehara
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Manami Ogasawara
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Yuki Yoshioka
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Kie Ohnishi
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Ayaka Iwata
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Shigeomi Shimizu
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Masato Tanaka
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
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8
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Xu C, Kleinschmidt H, Yang J, Leith E, Johnson J, Tan S, Mahony S, Bai L. Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566246. [PMID: 37986839 PMCID: PMC10659273 DOI: 10.1101/2023.11.08.566246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Despite the unique ability of pioneer transcription factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called ChIP-ISO to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1. Combining ChIP-ISO with in vitro and neural network analyses, we find that 1) FOXA1 binding is strongly affected by co-binding TFs AP-1 and CEBPB, 2) FOXA1 and AP-1 show binding cooperativity in vitro, 3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin, and 4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.
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Affiliation(s)
- Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianyu Yang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik Leith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jenna Johnson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Song Tan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
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9
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Yang Y, Gomez N, Infarinato N, Adam RC, Sribour M, Baek I, Laurin M, Fuchs E. The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates. Nat Cell Biol 2023; 25:1185-1195. [PMID: 37488435 PMCID: PMC10415178 DOI: 10.1038/s41556-023-01184-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/08/2023] [Indexed: 07/26/2023]
Abstract
During development, progenitors simultaneously activate one lineage while silencing another, a feature highly regulated in adult stem cells but derailed in cancers. Equipped to bind cognate motifs in closed chromatin, pioneer factors operate at these crossroads, but how they perform fate switching remains elusive. Here we tackle this question with SOX9, a master regulator that diverts embryonic epidermal stem cells (EpdSCs) into becoming hair follicle stem cells. By engineering mice to re-activate SOX9 in adult EpdSCs, we trigger fate switching. Combining epigenetic, proteomic and functional analyses, we interrogate the ensuing chromatin and transcriptional dynamics, slowed temporally by the mature EpdSC niche microenvironment. We show that as SOX9 binds and opens key hair follicle enhancers de novo in EpdSCs, it simultaneously recruits co-factors away from epidermal enhancers, which are silenced. Unhinged from its normal regulation, sustained SOX9 subsequently activates oncogenic transcriptional regulators that chart the path to cancers typified by constitutive SOX9 expression.
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Affiliation(s)
- Yihao Yang
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Nicholas Gomez
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Allen Institute for Cell Sciences, Seattle, WA, USA
| | - Nicole Infarinato
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- PRECISIONscientia, Yardley, PA, USA
| | - Rene C Adam
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Megan Sribour
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Inwha Baek
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Kyung Hee University, Seoul, South Korea
| | - Mélanie Laurin
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
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10
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Ogden S, Ahmed I, Yang SH, Fullwood P, Francavilla C, Sharrocks AD. Oncogenic ERRB2 signals through the AP-1 transcription factor to control mesenchymal-like properties of oesophageal adenocarcinoma. NAR Cancer 2023; 5:zcad001. [PMID: 36694726 PMCID: PMC9869078 DOI: 10.1093/narcan/zcad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/08/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Oesophageal adenocarcinoma (OAC) is a deadly disease with poor survival statistics and few targeted therapies available. One of the most common molecular aberrations in OAC is amplification or activation of the gene encoding the receptor tyrosine kinase ERBB2, and ERBB2 is targeted in the clinic for this subset of patients. However, the downstream consequences of these ERBB2 activating events are not well understood. Here we used a combination of phosphoproteomics, open chromatin profiling and transcriptome analysis on cell line models and patient-derived datasets to interrogate the molecular pathways operating downstream from ERBB2. Integrated analysis of these data sets converge on a model where dysregulated ERBB2 signalling is mediated at the transcriptional level by the transcription factor AP-1. AP-1 in turn controls cell behaviour by acting on cohorts of genes that regulate cell migration and adhesion, features often associated with EMT. Our study therefore provides a valuable resource for the cancer cell signalling community and reveals novel molecular determinants underlying the dysregulated behaviour of OAC cells.
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Affiliation(s)
- Samuel Ogden
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Ibrahim Ahmed
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Shen-Hsi Yang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Paul Fullwood
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | | | - Chiara Francavilla
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
- Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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11
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Ahmed I, Yang SH, Ogden S, Zhang W, Li Y, Sharrocks AD. eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways. eLife 2023; 12:e80840. [PMID: 36803948 PMCID: PMC9998086 DOI: 10.7554/elife.80840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/20/2023] [Indexed: 02/22/2023] Open
Abstract
Cancer is driven by both genetic and epigenetic changes that impact on gene expression profiles and the resulting tumourigenic phenotype. Enhancers are transcriptional regulatory elements that are key to our understanding of how this rewiring of gene expression is achieved in cancer cells. Here, we have harnessed the power of RNA-seq data from hundreds of patients with oesophageal adenocarcinoma (OAC) or its precursor state Barrett's oesophagus coupled with open chromatin maps to identify potential enhancer RNAs and their associated enhancer regions in this cancer. We identify ~1000 OAC-specific enhancers and use these data to uncover new cellular pathways that are operational in OAC. Among these are enhancers for JUP, MYBL2, and CCNE1, and we show that their activity is required for cancer cell viability. We also demonstrate the clinical utility of our dataset for identifying disease stage and patient prognosis. Our data therefore identify an important set of regulatory elements that enhance our molecular understanding of OAC and point to potential new therapeutic directions.
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Affiliation(s)
- Ibrahim Ahmed
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Shen-Hsi Yang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Samuel Ogden
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Wei Zhang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Yaoyong Li
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | | | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
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12
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Targeting Transcription Factors ATF5, CEBPB and CEBPD with Cell-Penetrating Peptides to Treat Brain and Other Cancers. Cells 2023; 12:cells12040581. [PMID: 36831248 PMCID: PMC9954556 DOI: 10.3390/cells12040581] [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: 01/17/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Developing novel therapeutics often follows three steps: target identification, design of strategies to suppress target activity and drug development to implement the strategies. In this review, we recount the evidence identifying the basic leucine zipper transcription factors ATF5, CEBPB, and CEBPD as targets for brain and other malignancies. We describe strategies that exploit the structures of the three factors to create inhibitory dominant-negative (DN) mutant forms that selectively suppress growth and survival of cancer cells. We then discuss and compare four peptides (CP-DN-ATF5, Dpep, Bpep and ST101) in which DN sequences are joined with cell-penetrating domains to create drugs that pass through tissue barriers and into cells. The peptide drugs show both efficacy and safety in suppressing growth and in the survival of brain and other cancers in vivo, and ST101 is currently in clinical trials for solid tumors, including GBM. We further consider known mechanisms by which the peptides act and how these have been exploited in rationally designed combination therapies. We additionally discuss lacunae in our knowledge about the peptides that merit further research. Finally, we suggest both short- and long-term directions for creating new generations of drugs targeting ATF5, CEBPB, CEBPD, and other transcription factors for treating brain and other malignancies.
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13
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Adamo A, Chin P, Keane P, Assi SA, Potluri S, Kellaway SG, Coleman D, Ames L, Ptasinska A, Delwel HR, Cockerill PN, Bonifer C. Identification and interrogation of the gene regulatory network of CEBPA-double mutant acute myeloid leukemia. Leukemia 2023; 37:102-112. [PMID: 36333583 PMCID: PMC9883165 DOI: 10.1038/s41375-022-01744-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy caused by mutations in genes encoding transcriptional and epigenetic regulators together with signaling genes. It is characterized by a disturbance of differentiation and abnormal proliferation of hematopoietic progenitors. We have previously shown that each AML subtype establishes its own core gene regulatory network (GRN), consisting of transcription factors binding to their target genes and imposing a specific gene expression pattern that is required for AML maintenance. In this study, we integrate gene expression, open chromatin and ChIP data with promoter-capture Hi-C data to define a refined core GRN common to all patients with CEBPA-double mutant (CEBPAN/C) AML. These mutations disrupt the structure of a major regulator of myelopoiesis. We identify the binding sites of mutated C/EBPα proteins in primary cells, we show that C/EBPα, AP-1 factors and RUNX1 colocalize and are required for AML maintenance, and we employ single cell experiments to link important network nodes to the specific differentiation trajectory from leukemic stem to blast cells. Taken together, our study provides an important resource which predicts the specific therapeutic vulnerabilities of this AML subtype in human cells.
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Affiliation(s)
- Assunta Adamo
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Paulynn Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Sophie G Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Daniel Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - H Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK.
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14
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Brennan A, Leech JT, Kad NM, Mason JM. The effect of helix-inducing constraints and downsizing upon a transcription block survival-derived functional cJun antagonist. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101077. [PMID: 36274790 PMCID: PMC9582194 DOI: 10.1016/j.xcrp.2022.101077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Inhibition of cJun is established as a promising therapeutic approach, particularly in cancer. We recently developed the "transcription block survival" (TBS) screening platform to derive functional peptide antagonists of transcription factor activity by ablating their ability to bind to cognate DNA. Using TBS, we screened a >131,000-member peptide library to select a 63-mer peptide that bound cJun and prevented 12-O-tetradecanoylphorbol-13-acetate response element (TRE) DNA binding. Iterative truncation was next combined with a systematic exploration of side-chain cyclization to derive a minimal active sequence. The resulting dual lactamized sequence was >40% smaller and retained low nM target affinity (equilibrium binding constant [K D ] = 0.2 versus 9.7 nM), with 8 residues at the acidic region required for functional antagonism. However, even modest C-terminal truncation resulted in functional loss. The peptide functionally antagonizes cJun (half-maximal inhibitory concentration [IC50] = 13 versus 45 μM) and is considerably more stable in human serum relative to its non-lactamized counterpart and HingeW.
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Affiliation(s)
- Andrew Brennan
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - James T. Leech
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Neil M. Kad
- School of Biological Sciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M. Mason
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
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15
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Davis W, Endo M, Locke JCW. Spatially specific mechanisms and functions of the plant circadian clock. PLANT PHYSIOLOGY 2022; 190:938-951. [PMID: 35640123 PMCID: PMC9516738 DOI: 10.1093/plphys/kiac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.
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Affiliation(s)
- William Davis
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Motomu Endo
- Authors for correspondence: (M.E.); (J.C.W.L.)
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16
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Sanidas I, Lee H, Rumde PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ, Lawrence MS. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression. Mol Cell 2022; 82:3333-3349.e9. [PMID: 35981542 PMCID: PMC9481721 DOI: 10.1016/j.molcel.2022.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/19/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023]
Abstract
The interaction of RB with chromatin is key to understanding its molecular functions. Here, for first time, we identify the full spectrum of chromatin-bound RB. Rather than exclusively binding promoters, as is often described, RB targets three fundamentally different types of loci (promoters, enhancers, and insulators), which are largely distinguishable by the mutually exclusive presence of E2F1, c-Jun, and CTCF. While E2F/DP facilitates RB association with promoters, AP-1 recruits RB to enhancers. Although phosphorylation in CDK sites is often portrayed as releasing RB from chromatin, we show that the cell cycle redistributes RB so that it enriches at promoters in G1 and at non-promoter sites in cycling cells. RB-bound promoters include the classic E2F-targets and are similar between lineages, but RB-bound enhancers associate with different categories of genes and vary between cell types. Thus, RB has a well-preserved role controlling E2F in G1, and it targets cell-type-specific enhancers and CTCF sites when cells enter S-phase.
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Affiliation(s)
- Ioannis Sanidas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Hanjun Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Purva H Rumde
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Gaylor Boulay
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Gabriel Golczer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Marcelo Stanzione
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Soroush Hajizadeh
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Jun Zhong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Meagan B Ryan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Benjamin J Drapkin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Miguel N Rivera
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA.
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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17
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In vitro single molecule and bulk phase studies reveal the AP-1 transcription factor cFos binds to DNA without its partner cJun. J Biol Chem 2022; 298:102229. [PMID: 35787376 PMCID: PMC9364023 DOI: 10.1016/j.jbc.2022.102229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
The AP-1 transcription factor family crucially regulates progression of the cell cycle, as well as playing roles in proliferation, differentiation, and the stress response. The two best described AP-1 family members, cFos and cJun, are known to dimerize to form a functional AP-1 heterodimer that binds to a consensus response element sequence. Although cJun can also homodimerize and bind to DNA, the canonical view is that cFos cannot bind DNA without heterodimerizing with cJun. Here, we show that cFos can actually bind to DNA in the absence of cJun in vitro. Using dual color single molecule imaging of cFos alone, we directly visualize binding to and movement on DNA. Of all these DNA-bound proteins, detailed analysis suggested 30 to 46% were homodimers. Furthermore, we constructed fluorescent protein fusions of cFos and cJun for Förster resonance energy transfer experiments. These constructs indicated complete dimerization of cJun, but although cFos could dimerize, its extent was reduced. Finally, to provide orthogonal confirmation of cFos binding to DNA, we performed bulk-phase circular dichroism experiments that showed clear structural changes in DNA; these were found to be specific to the AP-1 consensus sequence. Taken together, our results clearly show cFos can interact with DNA both as monomers and dimers independently of its archetypal partner, cJun.
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18
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Brennan A, Leech JT, Kad NM, Mason JM. An Approach to Derive Functional Peptide Inhibitors of Transcription Factor Activity. JACS AU 2022; 2:996-1006. [PMID: 35557753 PMCID: PMC9088798 DOI: 10.1021/jacsau.2c00105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 06/15/2023]
Abstract
We report the development of a high-throughput, intracellular "transcription block survival" (TBS) screening platform to derive functional transcription factor antagonists. TBS is demonstrated using the oncogenic transcriptional regulator cJun, with the development of antagonists that bind cJun and prevent both dimerization and, more importantly, DNA binding remaining a primary challenge. In TBS, cognate TRE sites are introduced into the coding region of the essential gene, dihydrofolate reductase (DHFR). Introduction of cJun leads to TRE binding, preventing DHFR expression by directly blocking RNA polymerase gene transcription to abrogate cell proliferation. Peptide library screening identified a sequence that both binds cJun and antagonizes function by preventing DNA binding, as demonstrated by restored cell viability and subsequent in vitro hit validation. TBS is an entirely tag-free genotype-to-phenotype approach, selecting desirable attributes such as high solubility, target specificity, and low toxicity within a complex cellular environment. TBS facilitates rapid library screening to accelerate the identification of therapeutically valuable sequences.
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Affiliation(s)
- Andrew Brennan
- Department
of Biology & Biochemistry, University
of Bath, Bath BA2 7AY, U.K.
| | - James T. Leech
- School
of Biosciences, University of Kent, Canterbury CT2 7NH, U.K.
| | - Neil M. Kad
- School
of Biosciences, University of Kent, Canterbury CT2 7NH, U.K.
| | - Jody M. Mason
- Department
of Biology & Biochemistry, University
of Bath, Bath BA2 7AY, U.K.
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19
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Casalino L, Talotta F, Cimmino A, Verde P. The Fra-1/AP-1 Oncoprotein: From the "Undruggable" Transcription Factor to Therapeutic Targeting. Cancers (Basel) 2022; 14:cancers14061480. [PMID: 35326630 PMCID: PMC8946526 DOI: 10.3390/cancers14061480] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
The genetic and epigenetic changes affecting transcription factors, coactivators, and chromatin modifiers are key determinants of the hallmarks of cancer. The acquired dependence on oncogenic transcriptional regulators, representing a major determinant of cancer cell vulnerability, points to transcription factors as ideal therapeutic targets. However, given the unavailability of catalytic activities or binding pockets for small-molecule inhibitors, transcription factors are generally regarded as undruggable proteins. Among components of the AP-1 complex, the FOS-family transcription factor Fra-1, encoded by FOSL1, has emerged as a prominent therapeutic target. Fra-1 is overexpressed in most solid tumors, in response to the BRAF-MAPK, Wnt-beta-catenin, Hippo-YAP, IL-6-Stat3, and other major oncogenic pathways. In vitro functional analyses, validated in onco-mouse models and corroborated by prognostic correlations, show that Fra-1-containing dimers control tumor growth and disease progression. Fra-1 participates in key mechanisms of cancer cell invasion, Epithelial-to-Mesenchymal Transition, and metastatic spreading, by driving the expression of EMT-inducing transcription factors, cytokines, and microRNAs. Here we survey various strategies aimed at inhibiting tumor growth, metastatic dissemination, and drug resistance by interfering with Fra-1 expression, stability, and transcriptional activity. We summarize several tools aimed at the design and tumor-specific delivery of Fra-1/AP-1-specific drugs. Along with RNA-based therapeutics targeting the FOSL1 gene, its mRNA, or cognate regulatory circRNAs, we will examine the exploitation of blocking peptides, small molecule inhibitors, and innovative Fra-1 protein degraders. We also consider the possible caveats concerning Fra-1 inhibition in specific therapeutic contexts. Finally, we discuss a recent suicide gene therapy-based approach, aimed at selectively killing the Fra-1-overexpressing neoplastic cells.
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Affiliation(s)
- Laura Casalino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
- Correspondence: (L.C.); (P.V.)
| | | | - Amelia Cimmino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
| | - Pasquale Verde
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
- Correspondence: (L.C.); (P.V.)
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20
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Larsen SB, Cowley CJ, Sajjath SM, Barrows D, Yang Y, Carroll TS, Fuchs E. Establishment, maintenance, and recall of inflammatory memory. Cell Stem Cell 2021; 28:1758-1774.e8. [PMID: 34320411 PMCID: PMC8500942 DOI: 10.1016/j.stem.2021.07.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/21/2021] [Accepted: 07/01/2021] [Indexed: 01/12/2023]
Abstract
Known for nearly a century but through mechanisms that remain elusive, cells retain a memory of inflammation that equips them to react quickly and broadly to diverse secondary stimuli. Using murine epidermal stem cells as a model, we elucidate how cells establish, maintain, and recall inflammatory memory. Specifically, we landscape and functionally interrogate temporal, dynamic changes to chromatin accessibility, histone modifications, and transcription factor binding that occur during inflammation, post-resolution, and in memory recall following injury. We unearth an essential, unifying role for the general stress-responsive transcription factor FOS, which partners with JUN and cooperates with stimulus-specific STAT3 to establish memory; JUN then remains with other homeostatic factors on memory domains, facilitating rapid FOS re-recruitment and gene re-activation upon diverse secondary challenges. Extending our findings, we offer a comprehensive, potentially universal mechanism behind inflammatory memory and less discriminate recall phenomena with profound implications for tissue fitness in health and disease.
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Affiliation(s)
- Samantha B. Larsen
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA,New York University School of Medicine, Neuroscience Institute, New York, NY 10016, USA
| | - Christopher J. Cowley
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Sairaj M. Sajjath
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Yihao Yang
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Thomas S. Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA,Lead Contact to whom correspondence should be addressed during the review process:
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21
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Backes TM, Langfermann DS, Lesch A, Rössler OG, Laschke MW, Vinson C, Thiel G. Regulation and function of AP-1 in insulinoma cells and pancreatic β-cells. Biochem Pharmacol 2021; 193:114748. [PMID: 34461116 DOI: 10.1016/j.bcp.2021.114748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/16/2022]
Abstract
Cav1.2 L-type voltage-gated Ca2+ channels play a central role in pancreatic β-cells by integrating extracellular signals with intracellular signaling events leading to insulin secretion and altered gene transcription. Here, we investigated the intracellular signaling pathway following stimulation of Cav1.2 Ca2+ channels and addressed the function of the transcription factor activator protein-1 (AP-1) in pancreatic β-cells of transgenic mice. Stimulation of Cav1.2 Ca2+ channels activates AP-1 in insulinoma cells. Pharmacological and genetic experiments identified c-Jun N-terminal protein kinase as a signal transducer connecting Cav1.2 Ca2+ channel activation with gene transcription. Moreover, the basic region-leucine zipper proteins ATF2 and c-Jun or c-Jun-related proteins were involved in stimulus-transcription coupling. We addressed the functions of AP-1 in pancreatic β-cells analyzing a newly generated transgenic mouse model. These transgenic mice expressed A-Fos, a mutant of c-Fos that attenuates DNA binding of c-Fos dimerization partners. In insulinoma cells, A-Fos completely blocked AP-1 activation following stimulation of Cav1.2 Ca2+ channels. The analysis of transgenic A-Fos-expressing mice revealed that the animals displayed impaired glucose tolerance. Thus, we show here for the first time that AP-1 controls an important function of pancreatic β-cells in vivo, the regulation of glucose homeostasis.
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Affiliation(s)
- Tobias M Backes
- Saarland University Medical Faculty, Department of Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany
| | - Daniel S Langfermann
- Saarland University Medical Faculty, Department of Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany
| | - Andrea Lesch
- Saarland University Medical Faculty, Department of Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany
| | - Oliver G Rössler
- Saarland University Medical Faculty, Department of Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany
| | - Matthias W Laschke
- Saarland University Medical Faculty, Institute for Clinical and Experimental Surgery, D-66421 Homburg, Germany
| | | | - Gerald Thiel
- Saarland University Medical Faculty, Department of Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany.
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22
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Fosl1 is vital to heart regeneration upon apex resection in adult Xenopus tropicalis. NPJ Regen Med 2021; 6:36. [PMID: 34188056 PMCID: PMC8242016 DOI: 10.1038/s41536-021-00146-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular disease is the leading cause of death in the world due to losing regenerative capacity in the adult heart. Frogs possess remarkable capacities to regenerate multiple organs, including spinal cord, tail, and limb, but the response to heart injury and the underlying molecular mechanism remains largely unclear. Here we demonstrated that cardiomyocyte proliferation greatly contributes to heart regeneration in adult X. tropicalis upon apex resection. Using RNA-seq and qPCR, we found that the expression of Fos-like antigen 1 (Fosl1) was dramatically upregulated in early stage of heart injury. To study Fosl1 function in heart regeneration, its expression was modulated in vitro and in vivo. Overexpression of X. tropicalis Fosl1 significantly promoted the proliferation of cardiomyocyte cell line H9c2. Consistently, endogenous Fosl1 knockdown suppressed the proliferation of H9c2 cells and primary cardiomyocytes isolated from neonatal mice. Taking use of a cardiomyocyte-specific dominant-negative approach, we show that blocking Fosl1 function leads to defects in cardiomyocyte proliferation during X. tropicalis heart regeneration. We further show that knockdown of Fosl1 can suppress the capacity of heart regeneration in neonatal mice, but overexpression of Fosl1 can improve the cardiac function in adult mouse upon myocardium infarction. Co-immunoprecipitation, luciferase reporter, and ChIP analysis reveal that Fosl1 interacts with JunB and promotes the expression of Cyclin-T1 (Ccnt1) during heart regeneration. In conclusion, we demonstrated that Fosl1 plays an essential role in cardiomyocyte proliferation and heart regeneration in vertebrates, at least in part, through interaction with JunB, thereby promoting expression of cell cycle regulators including Ccnt1.
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23
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AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency. Proc Natl Acad Sci U S A 2021; 118:2104841118. [PMID: 34088849 DOI: 10.1073/pnas.2104841118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Somatic cell transcription factors are critical to maintaining cellular identity and constitute a barrier to human somatic cell reprogramming; yet a comprehensive understanding of the mechanism of action is lacking. To gain insight, we examined epigenome remodeling at the onset of human nuclear reprogramming by profiling human fibroblasts after fusion with murine embryonic stem cells (ESCs). By assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and chromatin immunoprecipitation sequencing we identified enrichment for the activator protein 1 (AP-1) transcription factor c-Jun at regions of early transient accessibility at fibroblast-specific enhancers. Expression of a dominant negative AP-1 mutant (dnAP-1) reduced accessibility and expression of fibroblast genes, overcoming the barrier to reprogramming. Remarkably, efficient reprogramming of human fibroblasts to induced pluripotent stem cells was achieved by transduction with vectors expressing SOX2, KLF4, and inducible dnAP-1, demonstrating that dnAP-1 can substitute for exogenous human OCT4. Mechanistically, we show that the AP-1 component c-Jun has two unexpected temporally distinct functions in human reprogramming: 1) to potentiate fibroblast enhancer accessibility and fibroblast-specific gene expression, and 2) to bind to and repress OCT4 as a complex with MBD3. Our findings highlight AP-1 as a previously unrecognized potent dual gatekeeper of the somatic cell state.
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24
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Fan F, Podar K. The Role of AP-1 Transcription Factors in Plasma Cell Biology and Multiple Myeloma Pathophysiology. Cancers (Basel) 2021; 13:2326. [PMID: 34066181 PMCID: PMC8151277 DOI: 10.3390/cancers13102326] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Multiple myeloma (MM) is an incurable hematologic malignancy characterized by the clonal expansion of malignant plasma cells within the bone marrow. Activator Protein-1 (AP-1) transcription factors (TFs), comprised of the JUN, FOS, ATF and MAF multigene families, are implicated in a plethora of physiologic processes and tumorigenesis including plasma cell differentiation and MM pathogenesis. Depending on the genetic background, the tumor stage, and cues of the tumor microenvironment, specific dimeric AP-1 complexes are formed. For example, AP-1 complexes containing Fra-1, Fra-2 and B-ATF play central roles in the transcriptional control of B cell development and plasma cell differentiation, while dysregulation of AP-1 family members c-Maf, c-Jun, and JunB is associated with MM cell proliferation, survival, drug resistance, bone marrow angiogenesis, and bone disease. The present review article summarizes our up-to-date knowledge on the role of AP-1 family members in plasma cell differentiation and MM pathophysiology. Moreover, it discusses novel, rationally derived approaches to therapeutically target AP-1 TFs, including protein-protein and protein-DNA binding inhibitors, epigenetic modifiers and natural products.
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Affiliation(s)
- Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1277, Wuhan 430022, China;
| | - Klaus Podar
- Department of Internal Medicine II, University Hospital Krems, Mitterweg 10, 3500 Krems an der Donau, Austria
- Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems an der Donau, Austria
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25
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Potluri S, Assi SA, Chin PS, Coleman DJL, Pickin A, Moriya S, Seki N, Heidenreich O, Cockerill PN, Bonifer C. Isoform-specific and signaling-dependent propagation of acute myeloid leukemia by Wilms tumor 1. Cell Rep 2021; 35:109010. [PMID: 33882316 DOI: 10.1016/j.celrep.2021.109010] [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: 08/07/2020] [Revised: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022] Open
Abstract
Acute myeloid leukemia (AML) is caused by recurrent mutations in members of the gene regulatory and signaling machinery that control hematopoietic progenitor cell growth and differentiation. Here, we show that the transcription factor WT1 forms a major node in the rewired mutation-specific gene regulatory networks of multiple AML subtypes. WT1 is frequently either mutated or upregulated in AML, and its expression is predictive for relapse. The WT1 protein exists as multiple isoforms. For two main AML subtypes, we demonstrate that these isoforms exhibit differential patterns of binding and support contrasting biological activities, including enhanced proliferation. We also show that WT1 responds to oncogenic signaling and is part of a signaling-responsive transcription factor hub that controls AML growth. WT1 therefore plays a central and widespread role in AML biology.
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MESH Headings
- Base Sequence
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Chromatin/chemistry
- Chromatin/metabolism
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Early Growth Response Protein 1/genetics
- Early Growth Response Protein 1/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- HEK293 Cells
- Humans
- Leukemia, Myeloid, Acute/classification
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- Signal Transduction
- Sp1 Transcription Factor/genetics
- Sp1 Transcription Factor/metabolism
- Translocation, Genetic
- WT1 Proteins/antagonists & inhibitors
- WT1 Proteins/genetics
- WT1 Proteins/metabolism
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/metabolism
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Affiliation(s)
- Sandeep Potluri
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Paulynn S Chin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Dan J L Coleman
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Anna Pickin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Shogo Moriya
- Department of Biochemistry and Genetics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Prinses Máxima Centrum for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Heidelberglaan 25, 3584CS Utrecht, the Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
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26
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Orlando KA, Douglas AK, Abudu A, Wang Y, Tessier-Cloutier B, Su W, Peters A, Sherman LS, Moore R, Nguyen V, Negri GL, Colborne S, Morin GB, Kommoss F, Lang JD, Hendricks WP, Raupach EA, Pirrotte P, Huntsman DG, Trent JM, Parker JS, Raab JR, Weissman BE. Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism. eLife 2020; 9:59073. [PMID: 33355532 PMCID: PMC7813545 DOI: 10.7554/elife.59073] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in SCCOHT cell lines +/- BRG1 reexpression. BRG1 reexpression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Gained chromatin accessibility and BRG1 recruited sites were strongly enriched for transcription-factor-binding motifs of AP-1 family members. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant-negative AP-1 cell line, we found that both AP-1 DNA-binding activity and BRG1 reexpression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that BRG1 reexpression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon by AP-1 activity.
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Affiliation(s)
- Krystal Ann Orlando
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Amber K Douglas
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Aierken Abudu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Weiping Su
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Alec Peters
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States
| | - Larry S Sherman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, United States.,Department Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, United States
| | - Rayvon Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Vinh Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Gian Luca Negri
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Shane Colborne
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada
| | - Gregg B Morin
- Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | - Jessica D Lang
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - William Pd Hendricks
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Elizabeth A Raupach
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
| | - Jeffrey M Trent
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, United States
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Jesse R Raab
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
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27
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Brennan A, Leech JT, Kad NM, Mason JM. Selective antagonism of cJun for cancer therapy. J Exp Clin Cancer Res 2020; 39:184. [PMID: 32917236 PMCID: PMC7488417 DOI: 10.1186/s13046-020-01686-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023] Open
Abstract
The activator protein-1 (AP-1) family of transcription factors modulate a diverse range of cellular signalling pathways into outputs which can be oncogenic or anti-oncogenic. The transcription of relevant genes is controlled by the cellular context, and in particular by the dimeric composition of AP-1. Here, we describe the evidence linking cJun in particular to a range of cancers. This includes correlative studies of protein levels in patient tumour samples and mechanistic understanding of the role of cJun in cancer cell models. This develops an understanding of cJun as a focal point of cancer-altered signalling which has the potential for therapeutic antagonism. Significant work has produced a range of small molecules and peptides which have been summarised here and categorised according to the binding surface they target within the cJun-DNA complex. We highlight the importance of selectively targeting a single AP-1 family member to antagonise known oncogenic function and avoid antagonism of anti-oncogenic function.
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Affiliation(s)
- Andrew Brennan
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James T Leech
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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28
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Marvaldi L, Panayotis N, Alber S, Dagan SY, Okladnikov N, Koppel I, Di Pizio A, Song DA, Tzur Y, Terenzio M, Rishal I, Gordon D, Rother F, Hartmann E, Bader M, Fainzilber M. Importin α3 regulates chronic pain pathways in peripheral sensory
neurons. Science 2020; 369:842-846. [DOI: 10.1126/science.aaz5875] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 05/26/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022]
Abstract
How is neuropathic pain regulated in peripheral sensory neurons?
Importins are key regulators of nucleocytoplasmic transport. In this study,
we found that importin α3 (also known as karyopherin subunit alpha 4) can
control pain responsiveness in peripheral sensory neurons in mice. Importin
α3 knockout or sensory neuron–specific knockdown in mice reduced
responsiveness to diverse noxious stimuli and increased tolerance to
neuropathic pain. Importin α3–bound c-Fos and importin α3–deficient neurons
were impaired in c-Fos nuclear import. Knockdown or dominant-negative
inhibition of c-Fos or c-Jun in sensory neurons reduced neuropathic pain. In
silico screens identified drugs that mimic importin α3 deficiency. These
drugs attenuated neuropathic pain and reduced c-Fos nuclear localization.
Thus, perturbing c-Fos nuclear import by importin α3 in peripheral neurons
can promote analgesia.
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Affiliation(s)
- Letizia Marvaldi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nicolas Panayotis
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Stefanie Alber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shachar Y. Dagan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nataliya Okladnikov
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Indrek Koppel
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Agostina Di Pizio
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Didi-Andreas Song
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yarden Tzur
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marco Terenzio
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
- Molecular Neuroscience Unit, Okinawa Institute of Science and Technology, Kunigami-gun, Okinawa 904-0412, Japan
| | - Ida Rishal
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dalia Gordon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Franziska Rother
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Center for Structural and Cellular Biology in Medicine, Institute of Biology, University of Lübeck, 23538 Lübeck, Germany
| | - Enno Hartmann
- Center for Structural and Cellular Biology in Medicine, Institute of Biology, University of Lübeck, 23538 Lübeck, Germany
| | - Michael Bader
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- Center for Structural and Cellular Biology in Medicine, Institute of Biology, University of Lübeck, 23538 Lübeck, Germany
- Charité – Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Mike Fainzilber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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29
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Tigani W, Rossi MP, Artimagnella O, Santo M, Rauti R, Sorbo T, Ulloa Severino FP, Provenzano G, Allegra M, Caleo M, Ballerini L, Bozzi Y, Mallamaci A. Foxg1 Upregulation Enhances Neocortical Activity. Cereb Cortex 2020; 30:5147-5165. [PMID: 32383447 DOI: 10.1093/cercor/bhaa107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
Foxg1 is an ancient transcription factor gene orchestrating a number of neurodevelopmental processes taking place in the rostral brain. In this study, we investigated its impact on neocortical activity. We found that mice overexpressing Foxg1 in neocortical pyramidal cells displayed an electroencephalography (EEG) with increased spike frequency and were more prone to kainic acid (KA)-induced seizures. Consistently, primary cultures of neocortical neurons gain-of-function for Foxg1 were hyperactive and hypersynchronized. That reflected an unbalanced expression of key genes encoding for ion channels, gamma aminobutyric acid and glutamate receptors, and was likely exacerbated by a pronounced interneuron depletion. We also detected a transient Foxg1 upregulation ignited in turn by neuronal activity and mediated by immediate early genes. Based on this, we propose that even small changes of Foxg1 levels may result in a profound impact on pyramidal cell activity, an issue relevant to neuronal physiology and neurological aberrancies associated to FOXG1 copy number variations.
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Affiliation(s)
- Wendalina Tigani
- Laboratory of Cerebral Cortex Development, Neuroscience Area, SISSA, Trieste 34136, Italy
| | - Moira Pinzan Rossi
- Laboratory of Cerebral Cortex Development, Neuroscience Area, SISSA, Trieste 34136, Italy.,AgenTus Therapeutics, Inc., Cambridge CB4 OWG, United Kingdom
| | - Osvaldo Artimagnella
- Laboratory of Cerebral Cortex Development, Neuroscience Area, SISSA, Trieste 34136, Italy
| | - Manuela Santo
- Laboratory of Cerebral Cortex Development, Neuroscience Area, SISSA, Trieste 34136, Italy
| | - Rossana Rauti
- Laboratory of Neurons and Nanomaterials, Neuroscience Area, SISSA, Trieste 34136, Italy.,Dept. Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Teresa Sorbo
- Laboratory of Neurons and Nanomaterials, Neuroscience Area, SISSA, Trieste 34136, Italy
| | - Francesco Paolo Ulloa Severino
- Laboratory of Bionanotechnologies, Neuroscience Area, SISSA, Trieste 34136, Italy.,Cell Biology Dept, Duke University Medical Center, Duke University, Durham NC-27710, USA
| | - Giovanni Provenzano
- Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Manuela Allegra
- Neuroscience Institute, Neurophysiology Section, National Research Council (CNR), Pisa 56124, Italy.,Laboratory G5 Circuits Neuronaux, Institut Pasteur, Paris 75015, France
| | - Matteo Caleo
- Neuroscience Institute, Neurophysiology Section, National Research Council (CNR), Pisa 56124, Italy.,Department of Biomedical Sciences, University of Padua, Padua 35121, Italy
| | - Laura Ballerini
- Laboratory of Neurons and Nanomaterials, Neuroscience Area, SISSA, Trieste 34136, Italy
| | - Yuri Bozzi
- Neuroscience Institute, Neurophysiology Section, National Research Council (CNR), Pisa 56124, Italy.,Center for Mind/Brain Sciences, University of Trento, Trento 38068, Italy
| | - Antonello Mallamaci
- Laboratory of Cerebral Cortex Development, Neuroscience Area, SISSA, Trieste 34136, Italy
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30
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Beisaw A, Kuenne C, Guenther S, Dallmann J, Wu CC, Bentsen M, Looso M, Stainier DYR. AP-1 Contributes to Chromatin Accessibility to Promote Sarcomere Disassembly and Cardiomyocyte Protrusion During Zebrafish Heart Regeneration. Circ Res 2020; 126:1760-1778. [PMID: 32312172 DOI: 10.1161/circresaha.119.316167] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
RATIONALE The adult human heart is an organ with low regenerative potential. Heart failure following acute myocardial infarction is a leading cause of death due to the inability of cardiomyocytes to proliferate and replenish lost cardiac muscle. While the zebrafish has emerged as a powerful model to study endogenous cardiac regeneration, the molecular mechanisms by which cardiomyocytes respond to damage by disassembling sarcomeres, proliferating, and repopulating the injured area remain unclear. Furthermore, we are far from understanding the regulation of the chromatin landscape and epigenetic barriers that must be overcome for cardiac regeneration to occur. OBJECTIVE To identify transcription factor regulators of the chromatin landscape, which promote cardiomyocyte regeneration in zebrafish, and investigate their function. METHODS AND RESULTS Using the Assay for Transposase-Accessible Chromatin coupled to high-throughput sequencing (ATAC-Seq), we first find that the regenerating cardiomyocyte chromatin accessibility landscape undergoes extensive changes following cryoinjury, and that activator protein-1 (AP-1) binding sites are the most highly enriched motifs in regions that gain accessibility during cardiac regeneration. Furthermore, using bioinformatic and gene expression analyses, we find that the AP-1 response in regenerating adult zebrafish cardiomyocytes is largely different from the response in adult mammalian cardiomyocytes. Using a cardiomyocyte-specific dominant negative approach, we show that blocking AP-1 function leads to defects in cardiomyocyte proliferation as well as decreased chromatin accessibility at the fbxl22 and ilk loci, which regulate sarcomere disassembly and cardiomyocyte protrusion into the injured area, respectively. We further show that overexpression of the AP-1 family members Junb and Fosl1 can promote changes in mammalian cardiomyocyte behavior in vitro. CONCLUSIONS AP-1 transcription factors play an essential role in the cardiomyocyte response to injury by regulating chromatin accessibility changes, thereby allowing the activation of gene expression programs that promote cardiomyocyte dedifferentiation, proliferation, and protrusion into the injured area.
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Affiliation(s)
- Arica Beisaw
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Guenther
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Julia Dallmann
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Chi-Chung Wu
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Y R Stainier
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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31
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Differential Signaling Mediated by ApoE2, ApoE3, and ApoE4 in Human Neurons Parallels Alzheimer's Disease Risk. J Neurosci 2019; 39:7408-7427. [PMID: 31331998 DOI: 10.1523/jneurosci.2994-18.2019] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/25/2022] Open
Abstract
In blood, apolipoprotein E (ApoE) is a component of circulating lipoproteins and mediates the clearance of these lipoproteins from blood by binding to ApoE receptors. Humans express three genetic ApoE variants, ApoE2, ApoE3, and ApoE4, which exhibit distinct ApoE receptor-binding properties and differentially affect Alzheimer's disease (AD), such that ApoE2 protects against, and ApoE4 predisposes to AD. In brain, ApoE-containing lipoproteins are secreted by activated astrocytes and microglia, but their functions and role in AD pathogenesis are largely unknown. Ample evidence suggests that ApoE4 induces microglial dysregulation and impedes Aβ clearance in AD, but the direct neuronal effects of ApoE variants are poorly studied. Extending previous studies, we here demonstrate that the three ApoE variants differentially activate multiple neuronal signaling pathways and regulate synaptogenesis. Specifically, using human neurons (male embryonic stem cell-derived) cultured in the absence of glia to exclude indirect glial mechanisms, we show that ApoE broadly stimulates signal transduction cascades. Among others, such stimulation enhances APP synthesis and synapse formation with an ApoE4>ApoE3>ApoE2 potency rank order, paralleling the relative risk for AD conferred by these ApoE variants. Unlike the previously described induction of APP transcription, however, ApoE-induced synaptogenesis involves CREB activation rather than cFos activation. We thus propose that in brain, ApoE acts as a glia-secreted signal that activates neuronal signaling pathways. The parallel potency rank order of ApoE4>ApoE3>ApoE2 in AD risk and neuronal signaling suggests that ApoE4 may in an apparent paradox promote AD pathogenesis by causing a chronic increase in signaling, possibly via enhancing APP expression.SIGNIFICANCE STATEMENT Humans express three genetic variants of apolipoprotein E (ApoE), ApoE2, ApoE3, and ApoE4. ApoE4 constitutes the most important genetic risk factor for Alzheimer's disease (AD), whereas ApoE2 protects against AD. Significant evidence suggests that ApoE4 impairs microglial function and impedes astrocytic Aβ clearance in brain, but the direct neuronal effects of ApoE are poorly understood, and the differences between ApoE variants in these effects are unclear. Here, we report that ApoE acts on neurons as a glia-secreted signaling molecule that, among others, enhances synapse formation. In activating neuronal signaling, the three ApoE variants exhibit a differential potency of ApoE4>ApoE3>ApoE2, which mirrors their relative effects on AD risk, suggesting that differential signaling by ApoE variants may contribute to AD pathogenesis.
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32
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Pang M, Rodríguez-Gonzalez M, Hernandez M, Recinos CC, Seldeen KL, Troen BR. AP-1 and Mitf interact with NFATc1 to stimulate cathepsin K promoter activity in osteoclast precursors. J Cell Biochem 2019; 120:12382-12392. [PMID: 30816596 DOI: 10.1002/jcb.28504] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 11/08/2022]
Abstract
Cathepsin K (CTSK) is a secreted protease that plays an essential role in osteoclastic bone resorption and osteoporotic bone loss. We have previously shown that activator protein 1 (AP-1) stimulates CTSK promoter activity and that proximal nuclear factor of activated T cells cytoplasmic 1 (NFATc1)-binding sites play a major role in the stimulation of CTSK gene expression by receptor activator of NFκB ligand (RANKL). In the present study, we have extended these observations and further dissected the effects of transcription factors involved in the regulation of CTSK gene expression. Our aim was to investigate the cooperative interplay among transcription factors AP-1, microphthalmia-associated transcription factor (Mitf), and NFATc1, and the consequent regulatory effects on CTSK transcription. Experiments were carried out in RAW 264.7 cells, which can be readily differentiated to osteoclasts upon RANKL stimulation. Our data show that AP-1, Mitf, and NFATc1 are capable of independently stimulating CTSK promoter activity. A combination of any two factors further enhances CTSK promoter activity, with the combination of AP-1 (c-fos/c-jun) and NFATc1 inducing the largest increase. We further identify a synergistic effect when all three factors cooperate intimately at the proximal promoter region, yielding maximal transcriptional upregulation of the CTSK promoter. RANKL induces temporal localization of AP-1 and NFATc1 to the CTSK promoter. These results suggest that the interaction of multiple transcription factors mediate a maximal response to RANKL-induced CTSK gene expression.
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Affiliation(s)
- Manhui Pang
- Division of Geriatrics and Palliative Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System Research Service, Buffalo, New York
| | - Maria Rodríguez-Gonzalez
- Division of Geriatrics and Palliative Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System Research Service, Buffalo, New York
| | - Mireya Hernandez
- Division of Geriatrics and Palliative Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System Research Service, Buffalo, New York
| | - Claudia Carolina Recinos
- Division of Geriatrics and Palliative Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System Research Service, Buffalo, New York
| | - Kenneth Ladd Seldeen
- Division of Geriatrics and Palliative Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System Research Service, Buffalo, New York
| | - Bruce Robert Troen
- Division of Geriatrics and Palliative Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System Research Service, Buffalo, New York
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33
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Brechun KE, Arndt KM, Woolley GA. Selection of Protein-Protein Interactions of Desired Affinities with a Bandpass Circuit. J Mol Biol 2019; 431:391-400. [PMID: 30448232 DOI: 10.1016/j.jmb.2018.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022]
Abstract
We have developed a genetic circuit in Escherichia coli that can be used to select for protein-protein interactions of different strengths by changing antibiotic concentrations in the media. The genetic circuit links protein-protein interaction strength to β-lactamase activity while simultaneously imposing tuneable positive and negative selection pressure for β-lactamase activity. Cells only survive if they express interacting proteins with affinities that fall within set high- and low-pass thresholds; i.e. the circuit therefore acts as a bandpass filter for protein-protein interactions. We show that the circuit can be used to recover protein-protein interactions of desired affinity from a mixed population with a range of affinities. The circuit can also be used to select for inhibitors of protein-protein interactions of defined strength.
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Affiliation(s)
- Katherine E Brechun
- Department of Chemistry, University of Toronto, Toronto, Canada; Molecular Biotechnology, University of Potsdam, Potsdam, Germany
| | - Katja M Arndt
- Molecular Biotechnology, University of Potsdam, Potsdam, Germany.
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Canada.
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34
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Assi SA, Imperato MR, Coleman DJL, Pickin A, Potluri S, Ptasinska A, Chin PS, Blair H, Cauchy P, James SR, Zacarias-Cabeza J, Gilding LN, Beggs A, Clokie S, Loke JC, Jenkin P, Uddin A, Delwel R, Richards SJ, Raghavan M, Griffiths MJ, Heidenreich O, Cockerill PN, Bonifer C. Subtype-specific regulatory network rewiring in acute myeloid leukemia. Nat Genet 2019; 51:151-162. [PMID: 30420649 PMCID: PMC6330064 DOI: 10.1038/s41588-018-0270-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by a variety of alterations in transcription factors, epigenetic regulators and signaling molecules. To determine how different mutant regulators establish AML subtype-specific transcriptional networks, we performed a comprehensive global analysis of cis-regulatory element activity and interaction, transcription factor occupancy and gene expression patterns in purified leukemic blast cells. Here, we focused on specific subgroups of subjects carrying mutations in genes encoding transcription factors (RUNX1, CEBPα), signaling molecules (FTL3-ITD, RAS) and the nuclear protein NPM1). Integrated analysis of these data demonstrates that each mutant regulator establishes a specific transcriptional and signaling network unrelated to that seen in normal cells, sustaining the expression of unique sets of genes required for AML growth and maintenance.
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Affiliation(s)
- Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anna Pickin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paulynn Suyin Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Helen Blair
- Northern Institute for Cancer Research, University of Newcastle, Newcastle, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sally R James
- Section of Experimental Haematology, Leeds Institute for Molecular Medicine, University of Leeds, Leeds, UK
| | | | - L Niall Gilding
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Andrew Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sam Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Justin C Loke
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Phil Jenkin
- CMT Laboratory NHS Blood & Transplant, Edgbaston, Birmingham, UK
| | - Ash Uddin
- CMT Laboratory NHS Blood & Transplant, Edgbaston, Birmingham, UK
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stephen J Richards
- Haematological Malignancy Diagnostic Service, St. James's University Hospital, Leeds, UK
| | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Clinical Haematology, Queen Elizabeth Hospital, Birmingham, UK
| | - Michael J Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Olaf Heidenreich
- Northern Institute for Cancer Research, University of Newcastle, Newcastle, UK
- Princess Maxima Centrum for Pediatric Oncology, Utrecht, The Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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35
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Martinez-Soria N, McKenzie L, Draper J, Ptasinska A, Issa H, Potluri S, Blair HJ, Pickin A, Isa A, Chin PS, Tirtakusuma R, Coleman D, Nakjang S, Assi S, Forster V, Reza M, Law E, Berry P, Mueller D, Osborne C, Elder A, Bomken SN, Pal D, Allan JM, Veal GJ, Cockerill PN, Wichmann C, Vormoor J, Lacaud G, Bonifer C, Heidenreich O. The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation. Cancer Cell 2018; 34:626-642.e8. [PMID: 30300583 PMCID: PMC6179967 DOI: 10.1016/j.ccell.2018.08.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/20/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Oncogenic transcription factors such as the leukemic fusion protein RUNX1/ETO, which drives t(8;21) acute myeloid leukemia (AML), constitute cancer-specific but highly challenging therapeutic targets. We used epigenomic profiling data for an RNAi screen to interrogate the transcriptional network maintaining t(8;21) AML. This strategy identified Cyclin D2 (CCND2) as a crucial transmitter of RUNX1/ETO-driven leukemic propagation. RUNX1/ETO cooperates with AP-1 to drive CCND2 expression. Knockdown or pharmacological inhibition of CCND2 by an approved drug significantly impairs leukemic expansion of patient-derived AML cells and engraftment in immunodeficient murine hosts. Our data demonstrate that RUNX1/ETO maintains leukemia by promoting cell cycle progression and identifies G1 CCND-CDK complexes as promising therapeutic targets for treatment of RUNX1/ETO-driven AML.
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Affiliation(s)
- Natalia Martinez-Soria
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Lynsey McKenzie
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Julia Draper
- Cancer Research UK Manchester Institute, Manchester M20 4GJ, UK
| | - Anetta Ptasinska
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Hasan Issa
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Sandeep Potluri
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Helen J Blair
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Anna Pickin
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Asmida Isa
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Paulynn Suyin Chin
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ricky Tirtakusuma
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Daniel Coleman
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Salam Assi
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Victoria Forster
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Mojgan Reza
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Ed Law
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Philip Berry
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorothee Mueller
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Cameron Osborne
- Department of Medical & Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Alex Elder
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Simon N Bomken
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Deepali Pal
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - James M Allan
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gareth J Veal
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Peter N Cockerill
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich 80539, Germany
| | - Josef Vormoor
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Princess Maxima Center for Pediatric Oncology, Utrecht 3584CS, the Netherlands
| | - Georges Lacaud
- Cancer Research UK Manchester Institute, Manchester M20 4GJ, UK
| | - Constanze Bonifer
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Princess Maxima Center for Pediatric Oncology, Utrecht 3584CS, the Netherlands.
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36
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Schleussner N, Merkel O, Costanza M, Liang HC, Hummel F, Romagnani C, Durek P, Anagnostopoulos I, Hummel M, Jöhrens K, Niedobitek A, Griffin PR, Piva R, Sczakiel HL, Woessmann W, Damm-Welk C, Hinze C, Stoiber D, Gillissen B, Turner SD, Kaergel E, von Hoff L, Grau M, Lenz G, Dörken B, Scheidereit C, Kenner L, Janz M, Mathas S. The AP-1-BATF and -BATF3 module is essential for growth, survival and TH17/ILC3 skewing of anaplastic large cell lymphoma. Leukemia 2018; 32:1994-2007. [PMID: 29588546 PMCID: PMC6127090 DOI: 10.1038/s41375-018-0045-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 12/20/2017] [Accepted: 01/08/2018] [Indexed: 01/26/2023]
Abstract
Transcription factor AP-1 is constitutively activated and IRF4 drives growth and survival in ALK+ and ALK- anaplastic large cell lymphoma (ALCL). Here we demonstrate high-level BATF and BATF3 expression in ALCL. Both BATFs bind classical AP-1 motifs and interact with in ALCL deregulated AP-1 factors. Together with IRF4, they co-occupy AP-1-IRF composite elements, differentiating ALCL from non-ALCL. Gene-specific inactivation of BATFs, or global AP-1 inhibition results in ALCL growth retardation and/or cell death in vitro and in vivo. Furthermore, the AP-1-BATF module establishes TH17/group 3 innate lymphoid cells (ILC3)-associated gene expression in ALCL cells, including marker genes such as AHR, IL17F, IL22, IL26, IL23R and RORγt. Elevated IL-17A and IL-17F levels were detected in a subset of children and adolescents with ALK+ ALCL. Furthermore, a comprehensive analysis of primary lymphoma data confirms TH17-, and in particular ILC3-skewing in ALCL compared with PTCL. Finally, pharmacological inhibition of RORC as single treatment leads to cell death in ALCL cell lines and, in combination with the ALK inhibitor crizotinib, enforces death induction in ALK+ ALCL. Our data highlight the crucial role of AP-1/BATFs in ALCL and lead to the concept that some ALCL might originate from ILC3.
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Affiliation(s)
- Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Olaf Merkel
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Mariantonia Costanza
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Huan-Chang Liang
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Franziska Hummel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Chiara Romagnani
- German Rheumatism Research Centre, German Rheumatism Research Centre (DRFZ), A Leibniz Institute, 10117, Berlin, Germany
- Medical Department I, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Pawel Durek
- German Rheumatism Research Centre, German Rheumatism Research Centre (DRFZ), A Leibniz Institute, 10117, Berlin, Germany
| | | | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Korinna Jöhrens
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Antonia Niedobitek
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | | | - Roberto Piva
- Department of Molecular Biotechnology and Health Sciences, Center for Experimental Research and Medical Studies, University of Torino, Torino, Italy
| | - Henrike L Sczakiel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Wilhelm Woessmann
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
- NHL-BFM Study Centre and Department of Paediatric Haematology and Oncology, Justus-Liebig-University, Giessen, Germany
| | - Christine Damm-Welk
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
- NHL-BFM Study Centre and Department of Paediatric Haematology and Oncology, Justus-Liebig-University, Giessen, Germany
| | - Christian Hinze
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
- Department of Nephrology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Dagmar Stoiber
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria
| | - Bernd Gillissen
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Suzanne D Turner
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK
| | - Eva Kaergel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Linda von Hoff
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Michael Grau
- Department of Medicine A, Albert-Schweitzer-Campus 1, University Hospital Münster, 48149, Münster, Germany
- Cluster of Excellence EXC 1003, Cells in Motion, 48149, Münster, Germany
| | - Georg Lenz
- Department of Medicine A, Albert-Schweitzer-Campus 1, University Hospital Münster, 48149, Münster, Germany
- Cluster of Excellence EXC 1003, Cells in Motion, 48149, Münster, Germany
| | - Bernd Dörken
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | | | - Lukas Kenner
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria.
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK.
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria.
- University of Veterinary Medicine, Vienna, Austria.
- CBmed, Center for Biomarker Research in Medicine, 8010, Graz, Austria.
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, 13125, Berlin, Germany
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany.
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, 13125, Berlin, Germany.
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37
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Hoffmann HM, Gong P, Tamrazian A, Mellon PL. Transcriptional interaction between cFOS and the homeodomain-binding transcription factor VAX1 on the GnRH promoter controls Gnrh1 expression levels in a GnRH neuron maturation specific manner. Mol Cell Endocrinol 2018; 461:143-154. [PMID: 28890143 PMCID: PMC5756504 DOI: 10.1016/j.mce.2017.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/23/2017] [Accepted: 09/05/2017] [Indexed: 12/18/2022]
Abstract
Gonadotropin-releasing hormone (GnRH) is required for pubertal onset and reproduction, thus the control of GnRH transcription is tightly regulated during development and adulthood. GnRH neuron development depends on transcription factors of the homeodomain family. For example, Ventral anterior homeobox 1 (Vax1) is necessary to maintain GnRH expression after embryonic day 13 in the mouse. To further our understanding of the mechanisms by which VAX1 regulates GnRH gene expression, we asked whether VAX1 interacts with other transcription factors to modify GnRH expression levels. Using the GnRH cell lines, GN11 and GT1-7, we found that activation of PKC enhances expression of the immediate early gene cFos in both GN11, and GT1-7, and represses expression of Vax1 in GT1-7. Further, VAX1 interacts with cFOS while bound to the GnRH promoter. In immature GN11 cells, VAX1 and cFOS enhance GnRH expression, whereas VAX1 and cFOS have a repressive role in the mature GT1-7 cells.
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Affiliation(s)
- Hanne M Hoffmann
- Department of Reproductive Medicine, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Ping Gong
- Department of Reproductive Medicine, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Anika Tamrazian
- Department of Reproductive Medicine, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Pamela L Mellon
- Department of Reproductive Medicine, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Boga S, Bouzada D, García Peña D, Vázquez López M, Vázquez ME. Sequence-Specific DNA Recognition with Designed Peptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700988] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Boga
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Diego García Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Inorgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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Ghouili F, Martin LJ. Cooperative regulation of Gja1 expression by members of the AP-1 family cJun and cFos in TM3 Leydig and TM4 Sertoli cells. Gene 2017; 635:24-32. [DOI: 10.1016/j.gene.2017.09.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/28/2017] [Accepted: 09/08/2017] [Indexed: 12/26/2022]
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Baxter D, Ullman CG, Frigotto L, Mason JM. Exploiting Overlapping Advantages of In Vitro and In Cellulo Selection Systems to Isolate a Novel High-Affinity cJun Antagonist. ACS Chem Biol 2017; 12:2579-2588. [PMID: 28880076 DOI: 10.1021/acschembio.7b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have combined two peptide library-screening systems, exploiting the benefits offered by both to select novel antagonistic agents of cJun. CIS display is an in vitro cell-free system that allows very large libraries (≤1014) to be interrogated. However, affinity-based screening conditions can poorly reflect those relevant to therapeutic application, particularly for difficult intracellular targets, and can lead to false positives. In contrast, an in cellulo screening system such as the Protein-fragment Complementation Assay (PCA) selects peptides with high target affinity while additionally profiling for target specificity, protease resistance, solubility, and lack of toxicity in a more relevant context. A disadvantage is the necessity to transform cells, limiting library sizes that can be screened to ≤106. However, by combining both cell-free and cell-based systems, we isolated a peptide (CPW) from a ∼1010 member library, which forms a highly stable interaction with cJun (Tm = 63 °C, Kd = 750 nM, ΔG = -8.2 kcal/mol) using the oncogenic transcriptional regulator Activator Protein-1 (AP-1) as our exemplar target. In contrast, CIS display alone selected a peptide with low affinity for cJun (Tm = 34 °C, Kd = 25 μM, ΔG = -6.2 kcal/mol), highlighting the benefit of CIS → PCA. Furthermore, increased library size with CIS → PCA vs PCA alone allows the freedom to introduce noncanonical options, such as interfacial aromatics, and solvent exposed options that may allow the molecule to explore alternative structures and interact with greater affinity and efficacy with the target. CIS → PCA therefore offers significant potential as a peptide-library screening platform by synergistically combining the relative attributes of both assays to generate therapeutically interesting compounds that may otherwise not be identified.
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Affiliation(s)
- Daniel Baxter
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Christopher G. Ullman
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Laura Frigotto
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jody M. Mason
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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41
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Baxter D, Perry SR, Hill TA, Kok WM, Zaccai NR, Brady RL, Fairlie DP, Mason JM. Downsizing Proto-oncogene cFos to Short Helix-Constrained Peptides That Bind Jun. ACS Chem Biol 2017. [PMID: 28636317 DOI: 10.1021/acschembio.7b00303] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components. Structural integrity in the presence and absence of Jun was assessed by circular dichroism spectroscopy, while the thermodynamics of binding to cFos was measured by isothermal titration calorimetry. A 25-residue constrained peptide, one-third shorter yet 25% more helical than the structurally characterized 37-residue Fos-derived peptide, retained 80% of the binding free energy as a result of preorganization in a Jun-binding helix conformation, with the entropy gain (TΔS = +3.2 kcal/mol) compensating for the enthalpy loss. Attaching a cell-penetrating peptide (TAT48-57) and a nuclear localization signal (SV40) promoted cell uptake, localization to the nucleus, and inhibition of the proliferation of two breast cancer cell lines.
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Affiliation(s)
- Daniel Baxter
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K
| | - Samuel R. Perry
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - W. Mei Kok
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nathan R. Zaccai
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - R. Leo Brady
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - David P. Fairlie
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jody M. Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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Britton E, Rogerson C, Mehta S, Li Y, Li X, Fitzgerald RC, Ang YS, Sharrocks AD. Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma. PLoS Genet 2017; 13:e1006879. [PMID: 28859074 PMCID: PMC5578490 DOI: 10.1371/journal.pgen.1006879] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/20/2017] [Indexed: 01/04/2023] Open
Abstract
Oesophageal adenocarcinoma (OAC) is one of the ten most prevalent forms of cancer and is showing a rapid increase in incidence and yet exhibits poor survival rates. Compared to many other common cancers, the molecular changes that occur in this disease are relatively poorly understood. However, genes encoding chromatin remodeling enzymes are frequently mutated in OAC. This is consistent with the emerging concept that cancer cells exhibit reprogramming of their chromatin environment which leads to subsequent changes in their transcriptional profile. Here, we have used ATAC-seq to interrogate the chromatin changes that occur in OAC using both cell lines and patient-derived material. We demonstrate that there are substantial changes in the regulatory chromatin environment in the cancer cells and using this data we have uncovered an important role for ETS and AP1 transcription factors in driving the changes in gene expression found in OAC cells.
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Affiliation(s)
- Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Shaveta Mehta
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Christie Hospital, Manchester, United Kingdom
| | - Yaoyong Li
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Xiaodun Li
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | | | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Yeng S. Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- GI Science Centre, Salford Royal NHS FT, University of Manchester, Stott Lane, Salford, United Kingdom
| | - Andrew D. Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- GI Science Centre, Salford Royal NHS FT, University of Manchester, Stott Lane, Salford, United Kingdom
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EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas. PLoS One 2017; 12:e0181902. [PMID: 28732076 PMCID: PMC5521836 DOI: 10.1371/journal.pone.0181902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/10/2017] [Indexed: 01/23/2023] Open
Abstract
Long non-coding RNAs are being increasingly recognised as important molecules involved in regulating a diverse array of biological functions. For example, many long non-coding RNAs have been associated with tumourigenesis and in this context their molecular functions often involves impacting on chromatin and transcriptional control processes. One important cellular control system that is often deregulated in cancer cells is the ERK MAP kinase pathway. Here we have investigated whether ERK pathway signaling in response to EGF stimulation, leads to changes in the production of long non-coding RNAs. We identify several different classes of EGF pathway-regulated lncRNAs. We focus on one of the inducible lincRNAs, EGF inducible long intergenic non-coding RNA 1 (EINCR1). EINCR1 is predominantly nuclear and shows delayed activation kinetics compared to other immediate-early EGF-inducible genes. In humans it is expressed in a tissue-specific manner and is mainly confined to the heart but it exhibits little evolutionary conservation. Importantly, in several cancers EINCR1 shows elevated expression levels which correlate with poor survival in lung adenocarcinoma patients. In the context of lung adenocarcinomas, EINCR1 expression is anti-correlated with the expression of several protein coding EGF-regulated genes. A potential functional connection is demonstrated as EINCR1 overexpression is shown to reduce the expression of EGF-regulated protein coding genes including FOS and FOSB.
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Paakinaho V, Presman DM, Ball DA, Johnson TA, Schiltz RL, Levitt P, Mazza D, Morisaki T, Karpova TS, Hager GL. Single-molecule analysis of steroid receptor and cofactor action in living cells. Nat Commun 2017. [PMID: 28635963 PMCID: PMC5482060 DOI: 10.1038/ncomms15896] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Population-based assays have been employed extensively to investigate the interactions of transcription factors (TFs) with chromatin and are often interpreted in terms of static and sequential binding. However, fluorescence microscopy techniques reveal a more dynamic binding behaviour of TFs in live cells. Here we analyse the strengths and limitations of in vivo single-molecule tracking and performed a comprehensive analysis on the intranuclear dwell times of four steroid receptors and a number of known cofactors. While the absolute residence times estimates can depend on imaging acquisition parameters due to sampling bias, our results indicate that only a small proportion of factors are specifically bound to chromatin at any given time. Interestingly, the glucocorticoid receptor and its cofactors affect each other’s dwell times in an asymmetric manner. Overall, our data indicate transient rather than stable TF-cofactors chromatin interactions at response elements at the single-molecule level. Transcription factors (TFs) are thought to regulate gene expression by stably binding to target DNA elements. Here, the authors use single-molecule tracking to analyse the dynamic behaviour of steroid receptors TFs and show that most specific interactions with chromatin are transient and dynamic.
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Affiliation(s)
- Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Peter Levitt
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Davide Mazza
- Istituto Scientifico Ospedale San Raffaele, Centro di Imaging Sperimentale e Università Vita-Salute San Raffaele, 20132 Milano, Italy
| | - Tatsuya Morisaki
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
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Huang YWA, Zhou B, Wernig M, Südhof TC. ApoE2, ApoE3, and ApoE4 Differentially Stimulate APP Transcription and Aβ Secretion. Cell 2017; 168:427-441.e21. [PMID: 28111074 DOI: 10.1016/j.cell.2016.12.044] [Citation(s) in RCA: 356] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/27/2016] [Accepted: 12/22/2016] [Indexed: 12/14/2022]
Abstract
Human apolipoprotein E (ApoE) apolipoprotein is primarily expressed in three isoforms (ApoE2, ApoE3, and ApoE4) that differ only by two residues. ApoE4 constitutes the most important genetic risk factor for Alzheimer's disease (AD), ApoE3 is neutral, and ApoE2 is protective. How ApoE isoforms influence AD pathogenesis, however, remains unclear. Using ES-cell-derived human neurons, we show that ApoE secreted by glia stimulates neuronal Aβ production with an ApoE4 > ApoE3 > ApoE2 potency rank order. We demonstrate that ApoE binding to ApoE receptors activates dual leucine-zipper kinase (DLK), a MAP-kinase kinase kinase that then activates MKK7 and ERK1/2 MAP kinases. Activated ERK1/2 induces cFos phosphorylation, stimulating the transcription factor AP-1, which in turn enhances transcription of amyloid-β precursor protein (APP) and thereby increases amyloid-β levels. This molecular mechanism also regulates APP transcription in mice in vivo. Our data describe a novel signal transduction pathway in neurons whereby ApoE activates a non-canonical MAP kinase cascade that enhances APP transcription and amyloid-β synthesis.
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Affiliation(s)
- Yu-Wen Alvin Huang
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University Medical School, Stanford, CA 94305, USA
| | - Bo Zhou
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University Medical School, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University Medical School, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University Medical School, Stanford, CA 94305, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University Medical School, Stanford, CA 94305, USA.
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46
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Obier N, Cauchy P, Assi SA, Gilmour J, Lie-A-Ling M, Lichtinger M, Hoogenkamp M, Noailles L, Cockerill PN, Lacaud G, Kouskoff V, Bonifer C. Cooperative binding of AP-1 and TEAD4 modulates the balance between vascular smooth muscle and hemogenic cell fate. Development 2016; 143:4324-4340. [PMID: 27802171 PMCID: PMC5201045 DOI: 10.1242/dev.139857] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/10/2016] [Indexed: 12/22/2022]
Abstract
The transmission of extracellular signals into the nucleus involves inducible transcription factors, but how different signalling pathways act in a cell type-specific fashion is poorly understood. Here, we studied the regulatory role of the AP-1 transcription factor family in blood development using embryonic stem cell differentiation coupled with genome-wide transcription factor binding and gene expression analyses. AP-1 factors respond to MAP kinase signalling and comprise dimers of FOS, ATF and JUN proteins. To examine genes regulated by AP-1 and to examine how it interacts with other inducible transcription factors, we abrogated its global DNA-binding activity using a dominant-negative FOS peptide. We show that FOS and JUN bind to and activate a specific set of vascular genes and that AP-1 inhibition shifts the balance between smooth muscle and hematopoietic differentiation towards blood. Furthermore, AP-1 is required for de novo binding of TEAD4, a transcription factor connected to Hippo signalling. Our bottom-up approach demonstrates that AP-1- and TEAD4-associated cis-regulatory elements form hubs for multiple signalling-responsive transcription factors and define the cistrome that regulates vascular and hematopoietic development by extrinsic signals.
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Affiliation(s)
- Nadine Obier
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Pierre Cauchy
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Jane Gilmour
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Michael Lie-A-Ling
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Monika Lichtinger
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Maarten Hoogenkamp
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Laura Noailles
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Peter N Cockerill
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Georges Lacaud
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Valerie Kouskoff
- CRUK Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Constanze Bonifer
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
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47
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Optogenetic Inhibitor of the Transcription Factor CREB. ACTA ACUST UNITED AC 2016; 22:1531-1539. [PMID: 26590638 DOI: 10.1016/j.chembiol.2015.09.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/11/2015] [Accepted: 09/24/2015] [Indexed: 01/28/2023]
Abstract
Current approaches for optogenetic control of transcription do not mimic the activity of endogenous transcription factors, which act at numerous sites in the genome in a complex interplay with other factors. Optogenetic control of dominant negative versions of endogenous transcription factors provides a mechanism for mimicking the natural regulation of gene expression. Here we describe opto-DN-CREB, a blue-light-controlled inhibitor of the transcription factor CREB created by fusing the dominant negative inhibitor A-CREB to photoactive yellow protein (PYP). A light-driven conformational change in PYP prevents coiled-coil formation between A-CREB and CREB, thereby activating CREB. Optogenetic control of CREB function was characterized in vitro, in HEK293T cells, and in neurons where blue light enabled control of expression of the CREB targets NR4A2 and c-Fos. Dominant negative inhibitors exist for numerous transcription factors; linking these to optogenetic domains offers a general approach for spatiotemporal control of native transcriptional events.
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Stratton MS, Lin CY, Anand P, Tatman PD, Ferguson BS, Wickers ST, Ambardekar AV, Sucharov CC, Bradner JE, Haldar SM, McKinsey TA. Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers Is Suppressed by a MicroRNA. Cell Rep 2016; 16:1366-1378. [PMID: 27425608 PMCID: PMC4972677 DOI: 10.1016/j.celrep.2016.06.074] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 05/04/2016] [Accepted: 06/16/2016] [Indexed: 12/20/2022] Open
Abstract
BRD4 governs pathological cardiac gene expression by binding acetylated chromatin, resulting in enhanced RNA polymerase II (Pol II) phosphorylation and transcription elongation. Here, we describe a signal-dependent mechanism for the regulation of BRD4 in cardiomyocytes. BRD4 expression is suppressed by microRNA-9 (miR-9), which targets the 3' UTR of the Brd4 transcript. In response to stress stimuli, miR-9 is downregulated, leading to derepression of BRD4 and enrichment of BRD4 at long-range super-enhancers (SEs) associated with pathological cardiac genes. A miR-9 mimic represses stimulus-dependent targeting of BRD4 to SEs and blunts Pol II phosphorylation at proximal transcription start sites, without affecting BRD4 binding to SEs that control constitutively expressed cardiac genes. These findings suggest that dynamic enrichment of BRD4 at SEs genome-wide serves a crucial role in the control of stress-induced cardiac gene expression and define a miR-dependent signaling mechanism for the regulation of chromatin state and Pol II phosphorylation.
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Affiliation(s)
- Matthew S Stratton
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Priti Anand
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Philip D Tatman
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Medical Scientist Training Program, University of Colorado Denver, Aurora, CO 80045, USA
| | - Bradley S Ferguson
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Sean T Wickers
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Amrut V Ambardekar
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Carmen C Sucharov
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Saptarsi M Haldar
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Division of Cardiology, Department of Medicine and Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Timothy A McKinsey
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Medical Scientist Training Program, University of Colorado Denver, Aurora, CO 80045, USA.
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Abstract
UNLABELLED Brain-derived neurotrophic factor (BDNF), a member of the neurotrophin family, regulates both survival and differentiation of several neuronal populations in the nervous system during development, as well as synaptic plasticity in the adult brain. BDNF exerts its biological functions through its receptor TrkB. Although the regulation of BDNF transcription by neuronal activity has been widely studied, little is known about TrkB signaling-dependent expression of BDNF. Using rat primary cortical neuron cultures, we show that the BDNF gene is a subject to an extensive autoregulatory loop, where TrkB signaling upregulates the expression of all major BDNF transcripts, mainly through activating MAPK pathways. Investigating the mechanisms behind this autoregulation, we found that AP-1 transcription factors, comprising Jun and Fos family members, participate in the induction of BDNF exon I, III, and VI transcripts. AP-1 transcription factors directly upregulate the expression of exon I transcripts by binding two novel AP-1 cis-elements in promoter I. Moreover, our results show that the effect of AP-1 proteins on the activity of rat BDNF promoters III and VI is indirect, because AP-1 proteins were not detected to bind the respective promoter regions by chromatin immunoprecipitation (ChIP). Collectively, we describe an extensive positive feedback system in BDNF regulation, adding a new layer to the elaborate control of BDNF gene expression. SIGNIFICANCE STATEMENT Here, we show for the first time that in rat primary cortical neurons the expression of all major BDNF transcripts (exon I, II, III, IV, VI, and IXa transcripts) is upregulated in response to TrkB signaling, and that AP-1 transcription factors participate in the induction of exon I, III, and VI transcripts. Moreover, we have described two novel functional AP-1 cis-elements in BDNF promoter I, responsible for the activation of the promoter in response to TrkB signaling. Our results indicate the existence of a positive feedback loop for obtaining sufficient BDNF levels necessary for various TrkB signaling-dependent physiological outcomes in neurons.
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50
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Juilland M, Gonzalez M, Erdmann T, Banz Y, Jevnikar Z, Hailfinger S, Tzankov A, Grau M, Lenz G, Novak U, Thome M. CARMA1- and MyD88-dependent activation of Jun/ATF-type AP-1 complexes is a hallmark of ABC diffuse large B-cell lymphomas. Blood 2016; 127:1780-9. [PMID: 26747248 PMCID: PMC4863344 DOI: 10.1182/blood-2015-07-655647] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/01/2016] [Indexed: 12/22/2022] Open
Abstract
A hallmark of the diffuse large B-cell lymphoma (DLBCL) of the activated B-cell (ABC) type, a molecular subtype characterized by adverse outcome, is constitutive activation of the transcription factor nuclear factor-κB (NF-κB), which controls expression of genes promoting cellular survival and proliferation. Much less, however, is known about the role of the transcription factor activator protein-1 (AP-1) in ABC DLBCL. Here, we show that AP-1, like NF-κB, was controlled by constitutive activation of the B-cell receptor signaling component caspase recruitment domain-containing membrane-associated guanylate kinase 1 (CARMA1) and/or the Toll-like receptor signaling component myeloid differentiation primary response gene 88 (MyD88) in ABC DLBCL cell lines. In contrast to germinal center (GC) B-cell (GCB) DLBCL, ABC DLBCL cell lines expressed high levels of the AP-1 family members c-Jun, JunB, and JunD, which formed heterodimeric complexes with the AP-1 family members activating transcription factor (ATF) 2, ATF3, and ATF7. Inhibition of these complexes by a dominant-negative approach led to impaired growth of a majority of ABC DLBCL cell lines. Individual silencing of c-Jun, ATF2, or ATF3 decreased cellular survival and revealed c-Jun/ATF2-dependent control of ATF3 expression. As a consequence, ATF3 expression was much higher in ABC vs GCB DLBCL cell lines. Samples derived from DLBCL patients showed a clear trend toward high and nuclear ATF3 expression in nodal DLBCL of the non-GC or ABC subtype. These findings identify the activation of AP-1 complexes of the Jun/ATF-type as an important element controlling the growth of ABC DLBCL.
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Affiliation(s)
- Mélanie Juilland
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | | | - Tabea Erdmann
- Translational Oncology, Department of Medicine A, University Hospital Münster, Münster, Germany; Cluster of Excellence EXC 1003, Cells in Motion, Münster, Germany
| | - Yara Banz
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Zala Jevnikar
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Stephan Hailfinger
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Alexandar Tzankov
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Michael Grau
- Department of Physics, Philipps-University Marburg, Marburg, Germany; and
| | - Georg Lenz
- Translational Oncology, Department of Medicine A, University Hospital Münster, Münster, Germany; Cluster of Excellence EXC 1003, Cells in Motion, Münster, Germany
| | - Urban Novak
- Department of Medical Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Margot Thome
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
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