1
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Yang Y, Santos DM, Pantano L, Knipe R, Abe E, Logue A, Pronzati G, Black KE, Spinney JJ, Giacona F, Bieler M, Godbout C, Nicklin P, Wyatt D, Tager AM, Seither P, Herrmann FE, Medoff BD. Screening for Inhibitors of YAP Nuclear Localization Identifies Aurora Kinase A as a Modulator of Lung Fibrosis. Am J Respir Cell Mol Biol 2022; 67:36-49. [PMID: 35377835 PMCID: PMC9798384 DOI: 10.1165/rcmb.2021-0428oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/04/2022] [Indexed: 01/01/2023] Open
Abstract
Idiopathic pulmonary fibrosis is a progressive lung disease with limited therapeutic options that is characterized by pathological fibroblast activation and aberrant lung remodeling with scar formation. YAP (Yes-associated protein) is a transcriptional coactivator that mediates mechanical and biochemical signals controlling fibroblast activation. We previously identified HMG-CoA (3-hydroxy-3-methylglutaryl coenzyme A) reductase inhibitors (statins) as YAP inhibitors based on a high-throughput small-molecule screen in primary human lung fibroblasts. Here we report that several Aurora kinase inhibitors were also identified from the top hits of this screen. MK-5108, a highly selective inhibitor for AURKA (Aurora kinase A), induced YAP phosphorylation and cytoplasmic retention and significantly reduced profibrotic gene expression in human lung fibroblasts. The inhibitory effect on YAP nuclear translocation and profibrotic gene expression is specific to inhibition of AURKA, but not Aurora kinase B or C, and is independent of the Hippo pathway kinases LATS1 and LATS2 (Large Tumor Suppressor 1 and 2). Further characterization of the effects of MK-5108 demonstrate that it inhibits YAP nuclear localization indirectly via effects on actin polymerization and TGFβ (Transforming Growth Factor β) signaling. In addition, MK-5108 treatment reduced lung collagen deposition in the bleomycin mouse model of pulmonary fibrosis. Our results reveal a novel role for AURKA in YAP-mediated profibrotic activity in fibroblasts and highlight the potential of small-molecule screens for YAP inhibitors for identification of novel agents with antifibrotic activity.
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Affiliation(s)
- Yang Yang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Daniela M Santos
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lorena Pantano
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Rachel Knipe
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Abe
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Amanda Logue
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gina Pronzati
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Katharine E Black
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jillian J Spinney
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Francesca Giacona
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | - Andrew M Tager
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Franziska E Herrmann
- Immunology and Respiratory Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Benjamin D Medoff
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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2
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Choo M, Oh S, Jo S, Jin X, Song Y, Wen H, Park S, Kang S. Highly conserved protein Rv1211 in Mycobacterium tuberculosis is a natively unfolded protein that binds to a calmodulin antagonist, trifluoperazine. Biochem Biophys Res Commun 2022; 610:182-187. [PMID: 35468422 DOI: 10.1016/j.bbrc.2022.04.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 11/02/2022]
Abstract
Rv1211 is a conserved hypothetical protein in Mycobacterium tuberculosis and is required for the growth and pathogenesis of the bacteria. The protein has been suggested as a calmodulin-like calcium-binding protein with an EF-hand motif and as a target of trifluoperazine, a calmodulin antagonist in eukaryotes that inhibits mycobacterial growth. Here, we expressed the recombinant protein of Rv1211 and performed structural and biochemical studies of Rv1211 and its interaction with Ca2+ or trifluoperazine. Surprisingly, Rv1211 exhibited an elution property typical of a natively unfolded protein. Subsequent circular dichroism experiments with temperature elevation and trifluoroethanol treatment showed that Rv1211 has unfolded structure. Additional NMR experiment confirmed the unfolded state of the protein and further showed that it does not bind to Ca2+. Still, Rv1211 did bind to trifluoperazine, as evidenced by the two-dimensional NMR spectra of 15N-labeled Rv1211. However, there were no peak shifts upon binding, showing that Rv1211 retained its unfolded state even after the trifluoperazine binding. The residues involved in the binding were clustered in the C-terminal region, as identified by the sequence assignment. Isothermal titration calorimetry showed that the Kd of trifluoperazine-Rv1211 binding is 41 μM and that the stoichiometry is 1 : 2 (Rv1211: trifluoperazine). Our results argue against the suggestion of Rv1211 as a Ca2+-binding calmodulin-like protein, and show that Rv1211 is a natively unfolded protein that binds to trifluoperazine. In addition, our results suggest the evidence of the "Fuzziness" in the Rv1211-trifluoperazine interaction that differs from the conventional binding-induced folding of natively unfolded proteins.
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Affiliation(s)
- Munki Choo
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sehyun Oh
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sihyang Jo
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Xing Jin
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yonghyun Song
- Department of Biochemistry, Inha University Hospital, College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - He Wen
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Sunghyouk Park
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Sunmi Kang
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.
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3
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Cope AL, Gilchrist MA. Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach. BMC Genomics 2022; 23:408. [PMID: 35637464 PMCID: PMC9153123 DOI: 10.1186/s12864-022-08635-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/03/2022] [Indexed: 11/28/2022] Open
Abstract
Background Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression. Results Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to prevous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding. Conclusions Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08635-0).
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Affiliation(s)
- Alexander L Cope
- Genome Science and Technology, University of Tennessee, Knoxville, United States.,Current Address: Department of Genetics, Rutgers University, Piscataway, United States
| | - Michael A Gilchrist
- Genome Science and Technology, University of Tennessee, Knoxville, United States. .,National Institute for Mathematical and Biological Synthesis, Knoxville, TN, United States. .,Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, United States.
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4
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Reed F, Larsuel ST, Mayday MY, Scanlon V, Krause DS. MRTFA: A critical protein in normal and malignant hematopoiesis and beyond. J Biol Chem 2021; 296:100543. [PMID: 33722605 PMCID: PMC8079280 DOI: 10.1016/j.jbc.2021.100543] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 12/03/2022] Open
Abstract
Myocardin-related transcription factor A (MRTFA) is a coactivator of serum response factor, a transcription factor that participates in several critical cellular functions including cell growth and apoptosis. MRTFA couples transcriptional regulation to actin cytoskeleton dynamics, and the transcriptional targets of the MRTFA–serum response factor complex include genes encoding cytoskeletal proteins as well as immediate early genes. Previous work has shown that MRTFA promotes the differentiation of many cell types, including various types of muscle cells and hematopoietic cells, and MRTFA's interactions with other protein partners broaden its cellular roles. However, despite being first identified as part of the recurrent t(1;22) chromosomal translocation in acute megakaryoblastic leukemia, the mechanisms by which MRTFA functions in malignant hematopoiesis have yet to be defined. In this review, we provide an in-depth examination of the structure, regulation, and known functions of MRTFA with a focus on hematopoiesis. We conclude by identifying areas of study that merit further investigation.
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Affiliation(s)
- Fiona Reed
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shannon T Larsuel
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut, USA
| | - Madeline Y Mayday
- Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut, USA; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Vanessa Scanlon
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut, USA
| | - Diane S Krause
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut, USA; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA.
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5
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Ishibashi Y, Shoji S, Ihara D, Kubo Y, Tanaka T, Tanabe H, Hakamata T, Miyata T, Satou N, Sakagami H, Mizuguchi M, Kikuchi K, Fukuchi M, Tsuda M, Takasaki I, Tabuchi A. Expression of SOLOIST/MRTFB i4, a novel neuronal isoform of the mouse serum response factor coactivator myocardin-related transcription factor-B, negatively regulates dendritic complexity in cortical neurons. J Neurochem 2020; 159:762-777. [PMID: 32639614 DOI: 10.1111/jnc.15122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/11/2019] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
Megakaryoblastic leukemia 2 (MKL2)/myocardin-related transcription factor-B (MRTFB), a serum response factor (SRF) coactivator, is an important regulator of gene expression and neuronal morphology. Here, we show that different mouse MRTFB splice isoforms, including a novel fourth MRTFB isoform named spliced neuronal long isoform of SRF transcriptional coactivator (SOLOIST)/MRTFB isoform 4 (MRTFB i4), play distinct roles in this process. SOLOIST/MRTFB i4 has a short exon that encodes 21 amino acid residues ahead of the first RPXXXEL (RPEL) motif in MRTFB isoform 3. Quantitative PCR revealed that SOLOIST/MRTFB i4 and isoform 1 were enriched in the forebrain and neurons, and up-regulated during brain development. Conversely, isoform 3 was detected in various tissues, including both neurons and astrocytes, and was down-regulated in the developing brain. Reporter assays supported the SRF-coactivator function of SOLOIST/MRTFB i4 as well as isoform 1. Acute expression of MRTFB isoform 1, but not isoform 3 or SOLOIST/MRTFB i4, in neuronal cells within 24 hr drastically increased endogenous immediate early gene [c-fos, egr1, and activity-regulated cytoskeleton-associated protein] expression, but not endogenous actinin α1, β-actin, gelsolin, or srf gene expression measured by qPCR. Over-expression of SOLOIST/MRTFB i4 reduced the dendritic complexity of cortical neurons, whereas over-expression of isoform 1 increased this complexity. Co-expression of isoform 1 and SOLOIST/MRTFB i4 in cortical neurons revealed that isoform 1 competitively counteracted down-regulation by SOLOIST/MRTFB i4. Our findings indicate that MRTFB isoforms have unique expression patterns and differential effects on gene expression and dendritic complexity, which contribute to shaping neuronal circuits, at least in part.
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Affiliation(s)
- Yuta Ishibashi
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Shizuku Shoji
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Daisuke Ihara
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan.,Laboratory of Molecular Neurobiology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yukimi Kubo
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Takuro Tanaka
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroki Tanabe
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Tomoyuki Hakamata
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Tomoaki Miyata
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Natsumi Satou
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroyuki Sakagami
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Mineyuki Mizuguchi
- Laboratory of Structural Biology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Keietsu Kikuchi
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Mamoru Fukuchi
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan.,Present affiliation: Laboratory of Molecular Neuroscience, Faculty of Pharmacy, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Masaaki Tsuda
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Ichiro Takasaki
- Department of Pharmacology, Graduate School of Science and Engineering, Graduate School of Innovative Life Sciences, University of Toyama, Toyama, Japan
| | - Akiko Tabuchi
- Laboratory of Molecular Neurobiology, Graduate School of Medicine & Pharmaceutical Sciences, University of Toyama, Toyama, Japan.,Laboratory of Molecular Neurobiology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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6
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Kikuchi K, Ihara D, Fukuchi M, Tanabe H, Ishibashi Y, Tsujii J, Tsuda M, Kaneda M, Sakagami H, Okuno H, Bito H, Yamazaki Y, Ishikawa M, Tabuchi A. Involvement of SRF coactivator MKL2 in BDNF-mediated activation of the synaptic activity-responsive element in the Arc gene. J Neurochem 2018; 148:204-218. [PMID: 30244496 DOI: 10.1111/jnc.14596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022]
Abstract
The expression of immediate early genes (IEGs) is thought to be an essential molecular basis of neuronal plasticity for higher brain function. Many IEGs contain serum response element in their transcriptional regulatory regions and their expression is controlled by serum response factor (SRF). SRF is known to play a role in concert with transcriptional cofactors. However, little is known about how SRF cofactors regulate IEG expression during the process of neuronal plasticity. We hypothesized that one of the SRF-regulated neuronal IEGs, activity-regulated cytoskeleton-associated protein (Arc; also termed Arg3.1), is regulated by an SRF coactivator, megakaryoblastic leukemia (MKL). To test this hypothesis, we initially investigated which binding site of the transcription factor or SRF cofactor contributes to brain-derived neurotrophic factor (BDNF)-induced Arc gene transcription in cultured cortical neurons using transfection and reporter assays. We found that BDNF caused robust induction of Arc gene transcription through a cAMP response element, binding site of myocyte enhancer factor 2, and binding site of SRF in an Arc enhancer, the synaptic activity-responsive element (SARE). Regardless of the requirement for the SRF-binding site, the binding site of a ternary complex factor, another SRF cofactor, did not affect BDNF-mediated Arc gene transcription. In contrast, chromatin immunoprecipitation revealed occupation of MKL at the SARE. Furthermore, knockdown of MKL2, but not MKL1, significantly decreased BDNF-mediated activation of the SARE. Taken together, these findings suggest a novel mechanism by which MKL2 controls the Arc SARE in response to BDNF stimulation.
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Affiliation(s)
- Keietsu Kikuchi
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Daisuke Ihara
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Mamoru Fukuchi
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroki Tanabe
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yuta Ishibashi
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Junya Tsujii
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Masaaki Tsuda
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Marisa Kaneda
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroyuki Sakagami
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Hiroyuki Okuno
- Department of Biochemistry and Molecular Biology, Graduate School of Medical and Dental Sciences, Kagoshima University, Sakuragaoka, Kagoshima, Japan
| | - Haruhiko Bito
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuya Yamazaki
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Mitsuru Ishikawa
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Akiko Tabuchi
- Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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7
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Abtew E, Domb AJ, Basu A. Synthesis of glycopeptides from glucosaminic acid. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/pola.28666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ester Abtew
- Institute of Drug Research; School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem; Jerusalem 91120 Israel
| | - Abraham J. Domb
- Institute of Drug Research; School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem; Jerusalem 91120 Israel
| | - Arijit Basu
- Institute of Drug Research; School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem; Jerusalem 91120 Israel
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8
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Kubiniok P, Lavoie H, Therrien M, Thibault P. Time-resolved Phosphoproteome Analysis of Paradoxical RAF Activation Reveals Novel Targets of ERK. Mol Cell Proteomics 2017; 16:663-679. [PMID: 28188228 DOI: 10.1074/mcp.m116.065128] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/31/2016] [Indexed: 12/19/2022] Open
Abstract
Small molecules targeting aberrant RAF activity, like vemurafenib (PLX4032), are highly effective against cancers harboring the V600E BRAF mutation and are now approved for clinical use against metastatic melanoma. However, in tissues showing elevated RAS activity and in RAS mutant tumors, these inhibitors stimulate RAF dimerization, resulting in inhibitor resistance and downstream "paradoxical" ERK activation. To understand the global signaling response of cancer cells to RAF inhibitors, we profiled the temporal changes of the phosphoproteome of two colon cancer cell lines (Colo205 and HCT116) that respond differently to vemurafenib. Comprehensive data mining and filtering identified a total of 37,910 phosphorylation sites, 660 of which were dynamically modulated upon treatment with vemurafenib. We established that 83% of these dynamic phosphorylation sites were modulated in accordance with the phospho-ERK profile of the two cell lines. Accordingly, kinase substrate prediction algorithms linked most of these dynamic sites to direct ERK1/2-mediated phosphorylation, supporting a low off-target rate for vemurafenib. Functional classification of target proteins indicated the enrichment of known (nuclear pore, transcription factors, and RAS-RTK signaling) and novel (Rho GTPases signaling and actin cytoskeleton) ERK-controlled functions. Our phosphoproteomic data combined with experimental validation established novel dynamic connections between ERK signaling and the transcriptional regulators TEAD3 (Hippo pathway), MKL1, and MKL2 (Rho serum-response elements pathway). We also confirm that an ERK-docking site found in MKL1 is directly antagonized by overlapping actin binding, defining a novel mechanism of actin-modulated phosphorylation. Altogether, time-resolved phosphoproteomics further documented vemurafenib selectivity and identified novel ERK downstream substrates.
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Affiliation(s)
- Peter Kubiniok
- From the ‡Institute for Research in Immunology and Cancer and.,Departments of §Chemistry
| | - Hugo Lavoie
- From the ‡Institute for Research in Immunology and Cancer and
| | - Marc Therrien
- From the ‡Institute for Research in Immunology and Cancer and .,‖Pathology and Cell Biology, and
| | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer and .,Departments of §Chemistry.,‡‡Biochemistry, Université de Montréal, C.P. 6128, Succursale Centreville, Montréal, Québec H3C 3J7, Canada
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9
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Abstract
A new class of polymers that resemble a peptidic backbone with pendant sugar side chains.
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Affiliation(s)
- Ester Abtew
- Institute of Drug Research
- School of Pharmacy-Faculty of Medicine
- The Hebrew University of Jerusalem
- Jerusalem
- 91120 Israel
| | - Abraham J. Domb
- Institute of Drug Research
- School of Pharmacy-Faculty of Medicine
- The Hebrew University of Jerusalem
- Jerusalem
- 91120 Israel
| | - Arijit Basu
- Institute of Drug Research
- School of Pharmacy-Faculty of Medicine
- The Hebrew University of Jerusalem
- Jerusalem
- 91120 Israel
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