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Li J, Canham SM, Wu H, Henault M, Chen L, Liu G, Chen Y, Yu G, Miller HR, Hornak V, Brittain SM, Michaud GA, Tutter A, Broom W, Digan ME, McWhirter SM, Sivick KE, Pham HT, Chen CH, Tria GS, McKenna JM, Schirle M, Mao X, Nicholson TB, Wang Y, Jenkins JL, Jain RK, Tallarico JA, Patel SJ, Zheng L, Ross NT, Cho CY, Zhang X, Bai XC, Feng Y. Activation of human STING by a molecular glue-like compound. Nat Chem Biol 2024; 20:365-372. [PMID: 37828400 PMCID: PMC10907298 DOI: 10.1038/s41589-023-01434-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023]
Abstract
Stimulator of interferon genes (STING) is a dimeric transmembrane adapter protein that plays a key role in the human innate immune response to infection and has been therapeutically exploited for its antitumor activity. The activation of STING requires its high-order oligomerization, which could be induced by binding of the endogenous ligand, cGAMP, to the cytosolic ligand-binding domain. Here we report the discovery through functional screens of a class of compounds, named NVS-STGs, that activate human STING. Our cryo-EM structures show that NVS-STG2 induces the high-order oligomerization of human STING by binding to a pocket between the transmembrane domains of the neighboring STING dimers, effectively acting as a molecular glue. Our functional assays showed that NVS-STG2 could elicit potent STING-mediated immune responses in cells and antitumor activities in animal models.
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Affiliation(s)
- Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Hua Wu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lihao Chen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guoxun Liu
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Yu Chen
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Gary Yu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | - Antonin Tutter
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Wendy Broom
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Helen T Pham
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - George S Tria
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rishi K Jain
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Sejal J Patel
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lianxing Zheng
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Charles Y Cho
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Yan Feng
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
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2
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Palacino J, Swalley SE, Song C, Cheung AK, Shu L, Zhang X, Van Hoosear M, Shin Y, Chin DN, Keller CG, Beibel M, Renaud NA, Smith TM, Salcius M, Shi X, Hild M, Servais R, Jain M, Deng L, Bullock C, McLellan M, Schuierer S, Murphy L, Blommers MJJ, Blaustein C, Berenshteyn F, Lacoste A, Thomas JR, Roma G, Michaud GA, Tseng BS, Porter JA, Myer VE, Tallarico JA, Hamann LG, Curtis D, Fishman MC, Dietrich WF, Dales NA, Sivasankaran R. Corrigendum: SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol 2016; 12:304. [PMID: 26991088 DOI: 10.1038/nchembio0416-304c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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3
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Palacino J, Swalley SE, Song C, Cheung AK, Shu L, Zhang X, Van Hoosear M, Shin Y, Chin DN, Keller CG, Beibel M, Renaud NA, Smith TM, Salcius M, Shi X, Hild M, Servais R, Jain M, Deng L, Bullock C, McLellan M, Schuierer S, Murphy L, Blommers MJJ, Blaustein C, Berenshteyn F, Lacoste A, Thomas JR, Roma G, Michaud GA, Tseng BS, Porter JA, Myer VE, Tallarico JA, Hamann LG, Curtis D, Fishman MC, Dietrich WF, Dales NA, Sivasankaran R. Erratum: Corrigendum: SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol 2015; 11:741. [DOI: 10.1038/nchembio0915-741a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Palacino J, Swalley SE, Song C, Cheung AK, Shu L, Zhang X, Van Hoosear M, Shin Y, Chin DN, Keller CG, Beibel M, Renaud NA, Smith TM, Salcius M, Shi X, Hild M, Servais R, Jain M, Deng L, Bullock C, McLellan M, Schuierer S, Murphy L, Blommers MJJ, Blaustein C, Berenshteyn F, Lacoste A, Thomas JR, Roma G, Michaud GA, Tseng BS, Porter JA, Myer VE, Tallarico JA, Hamann LG, Curtis D, Fishman MC, Dietrich WF, Dales NA, Sivasankaran R. SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol 2015; 11:511-7. [PMID: 26030728 DOI: 10.1038/nchembio.1837] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/06/2015] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophy (SMA), which results from the loss of expression of the survival of motor neuron-1 (SMN1) gene, represents the most common genetic cause of pediatric mortality. A duplicate copy (SMN2) is inefficiently spliced, producing a truncated and unstable protein. We describe herein a potent, orally active, small-molecule enhancer of SMN2 splicing that elevates full-length SMN protein and extends survival in a severe SMA mouse model. We demonstrate that the molecular mechanism of action is via stabilization of the transient double-strand RNA structure formed by the SMN2 pre-mRNA and U1 small nuclear ribonucleic protein (snRNP) complex. The binding affinity of U1 snRNP to the 5' splice site is increased in a sequence-selective manner, discrete from constitutive recognition. This new mechanism demonstrates the feasibility of small molecule-mediated, sequence-selective splice modulation and the potential for leveraging this strategy in other splicing diseases.
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Affiliation(s)
- James Palacino
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Susanne E Swalley
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Cheng Song
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Atwood K Cheung
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lei Shu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Xiaolu Zhang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Mailin Van Hoosear
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Youngah Shin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Donovan N Chin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | - Martin Beibel
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Nicole A Renaud
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Thomas M Smith
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Michael Salcius
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Xiaoying Shi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Marc Hild
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Rebecca Servais
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Monish Jain
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lin Deng
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Caroline Bullock
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Michael McLellan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Sven Schuierer
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Leo Murphy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | - Cecile Blaustein
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Frada Berenshteyn
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Arnaud Lacoste
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jason R Thomas
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Gregory A Michaud
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Brian S Tseng
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jeffery A Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Vic E Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - John A Tallarico
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lawrence G Hamann
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Daniel Curtis
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Mark C Fishman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - William F Dietrich
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Natalie A Dales
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
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Salcius M, Bauer AJ, Hao Q, Li S, Tutter A, Raphael J, Jahnke W, Rondeau JM, Bourgier E, Tallarico J, Michaud GA. SEC-TID: A Label-Free Method for Small-Molecule Target Identification. ACTA ACUST UNITED AC 2014; 19:917-27. [PMID: 24554445 DOI: 10.1177/1087057114522691] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/08/2014] [Indexed: 11/16/2022]
Abstract
Bioactive small molecules are an invaluable source of therapeutics and chemical probes for exploring biological pathways. Yet, significant hurdles in drug discovery often come from lacking a comprehensive view of the target(s) for both early tool molecules and even late-stage drugs. To address this challenge, a method is provided that allows for assessing the interactions of small molecules with thousands of targets without any need to modify the small molecule of interest or attach any component to a surface. We describe size-exclusion chromatography for target identification (SEC-TID), a method for accurately and reproducibly detecting ligand-macromolecular interactions for small molecules targeting nucleic acid and several protein classes. We report the use of SEC-TID, with a library consisting of approximately 1000 purified proteins derived from the protein databank (PDB), to identify the efficacy targets tankyrase 1 and 2 for the Wnt inhibitor XAV939. In addition, we report novel interactions for the tumor-vascular disrupting agent vadimezan/ASA404 (interacting with farnesyl pyrophosphate synthase) and the diuretic mefruside (interacting with carbonic anhydrase XIII). We believe this method can dramatically enhance our understanding of the mechanism of action and potential liabilities for small molecules in drug discovery pipelines through comprehensive profiling of candidate druggable targets.
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Affiliation(s)
- Michael Salcius
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Andras J Bauer
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Qin Hao
- Analytical Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Shu Li
- Analytical Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Antonin Tutter
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jacob Raphael
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Wolfgang Jahnke
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jean-Michel Rondeau
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Emmanuelle Bourgier
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - John Tallarico
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Gregory A Michaud
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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6
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Nyfeler B, Hoepfner D, Palestrant D, Kirby CA, Whitehead L, Yu R, Deng G, Caughlan RE, Woods AL, Jones AK, Barnes SW, Walker JR, Gaulis S, Hauy E, Brachmann SM, Krastel P, Studer C, Riedl R, Estoppey D, Aust T, Movva NR, Wang Z, Salcius M, Michaud GA, McAllister G, Murphy LO, Tallarico JA, Wilson CJ, Dean CR. Identification of elongation factor G as the conserved cellular target of argyrin B. PLoS One 2012; 7:e42657. [PMID: 22970117 PMCID: PMC3438169 DOI: 10.1371/journal.pone.0042657] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 07/10/2012] [Indexed: 11/19/2022] Open
Abstract
Argyrins, produced by myxobacteria and actinomycetes, are cyclic octapeptides with antibacterial and antitumor activity. Here, we identify elongation factor G (EF-G) as the cellular target of argyrin B in bacteria, via resistant mutant selection and whole genome sequencing, biophysical binding studies and crystallography. Argyrin B binds a novel allosteric pocket in EF-G, distinct from the known EF-G inhibitor antibiotic fusidic acid, revealing a new mode of protein synthesis inhibition. In eukaryotic cells, argyrin B was found to target mitochondrial elongation factor G1 (EF-G1), the closest homologue of bacterial EF-G. By blocking mitochondrial translation, argyrin B depletes electron transport components and inhibits the growth of yeast and tumor cells. Further supporting direct inhibition of EF-G1, expression of an argyrin B-binding deficient EF-G1 L693Q variant partially rescued argyrin B-sensitivity in tumor cells. In summary, we show that argyrin B is an antibacterial and cytotoxic agent that inhibits the evolutionarily conserved target EF-G, blocking protein synthesis in bacteria and mitochondrial translation in yeast and mammalian cells.
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Affiliation(s)
- Beat Nyfeler
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Dominic Hoepfner
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Deborah Palestrant
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Christina A. Kirby
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Lewis Whitehead
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachussetts, United States of America
| | - Robert Yu
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Gejing Deng
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Ruth E. Caughlan
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Angela L. Woods
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Adriana K. Jones
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - S. Whitney Barnes
- Novartis Institute for Functional Genomics, Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - John R. Walker
- Novartis Institute for Functional Genomics, Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Swann Gaulis
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ervan Hauy
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Saskia M. Brachmann
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Philipp Krastel
- Center for Proteomic Chemistry, Natural Products Unit, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Christian Studer
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ralph Riedl
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - David Estoppey
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thomas Aust
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - N. Rao Movva
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Zuncai Wang
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Michael Salcius
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Gregory A. Michaud
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Gregory McAllister
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Leon O. Murphy
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - John A. Tallarico
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Christopher J. Wilson
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachussetts, United States of America
| | - Charles R. Dean
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
- * E-mail:
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Wang Z, Michaud GA, Cheng Z, Zhang Y, Hinds TR, Fan E, Cong F, Xu W. Recognition of the iso-ADP-ribose moiety in poly(ADP-ribose) by WWE domains suggests a general mechanism for poly(ADP-ribosyl)ation-dependent ubiquitination. Genes Dev 2012; 26:235-40. [PMID: 22267412 PMCID: PMC3278890 DOI: 10.1101/gad.182618.111] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 12/19/2011] [Indexed: 01/24/2023]
Abstract
Protein poly(ADP-ribosyl)ation and ubiquitination are two key post-translational modifications regulating many biological processes. Through crystallographic and biochemical analysis, we show that the RNF146 WWE domain recognizes poly(ADP-ribose) (PAR) by interacting with iso-ADP-ribose (iso-ADPR), the smallest internal PAR structural unit containing the characteristic ribose-ribose glycosidic bond formed during poly(ADP-ribosyl)ation. The key iso-ADPR-binding residues we identified are highly conserved among WWE domains. Binding assays further demonstrate that PAR binding is a common function for the WWE domain family. Since many WWE domain-containing proteins are known E3 ubiquitin ligases, our results suggest that protein poly(ADP-ribosyl)ation may be a general mechanism to target proteins for ubiquitination.
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Affiliation(s)
- Zhizhi Wang
- Department of Biological Structure
- Biomolecular Structure and Design Program, University of Washington, Seattle, Washington 98195, USA
| | - Gregory A. Michaud
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | | | - Yue Zhang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | | | - Erkang Fan
- Department of Biological Structure
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Feng Cong
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
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Zhang Y, Liu S, Mickanin C, Feng Y, Charlat O, Michaud GA, Schirle M, Shi X, Hild M, Bauer A, Myer VE, Finan PM, Porter JA, Huang SMA, Cong F. RNF146 is a poly(ADP-ribose)-directed E3 ligase that regulates axin degradation and Wnt signalling. Nat Cell Biol 2011; 13:623-9. [PMID: 21478859 DOI: 10.1038/ncb2222] [Citation(s) in RCA: 301] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 02/04/2011] [Indexed: 12/13/2022]
Abstract
The Wnt/β-catenin signalling pathway plays essential roles in embryonic development and adult tissue homeostasis, and deregulation of this pathway has been linked to cancer. Axin is a concentration-limiting component of the β-catenin destruction complex, and its stability is regulated by tankyrase. However, the molecular mechanism by which tankyrase-dependent poly(ADP-ribosyl)ation (PARsylation) is coupled to ubiquitylation and degradation of axin remains undefined. Here, we identify RNF146, a RING-domain E3 ubiquitin ligase, as a positive regulator of Wnt signalling. RNF146 promotes Wnt signalling by mediating tankyrase-dependent degradation of axin. Mechanistically, RNF146 directly interacts with poly(ADP-ribose) through its WWE domain, and promotes degradation of PARsylated proteins. Using proteomics approaches, we have identified BLZF1 and CASC3 as further substrates targeted by tankyrase and RNF146 for degradation. Thus, identification of RNF146 as a PARsylation-directed E3 ligase establishes a molecular paradigm that links tankyrase-dependent PARsylation to ubiquitylation. RNF146-dependent protein degradation may emerge as a major mechanism by which tankyrase exerts its function.
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Affiliation(s)
- Yue Zhang
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
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9
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Michaud GA, Salcius M, Zhou F, Papov VV, Merkel J, Murtha M, Predki P, Schweitzer B. Applications of protein arrays for small molecule drug discovery and characterization. Biotechnol Genet Eng Rev 2008; 22:197-211. [PMID: 18476332 DOI: 10.1080/02648725.2006.10648071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Gregory A Michaud
- Invitrogen, Protein Array Center, 688 East Main Street, Branford, CT 06405, USA.
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10
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Meng L, Michaud GA, Merkel JS, Zhou F, Huang J, Mattoon DR, Schweitzer B. Protein kinase substrate identification on functional protein arrays. BMC Biotechnol 2008; 8:22. [PMID: 18307815 PMCID: PMC2270825 DOI: 10.1186/1472-6750-8-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2007] [Accepted: 02/28/2008] [Indexed: 02/08/2023] Open
Abstract
Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an important new tool that enables multiplex analysis of protein phosphorylation, and thus can be utilized to identify novel kinase substrates. Integrating this technology with a systems biology approach to cell signalling will help uncover new layers in our understanding of this essential class of enzymes.
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Affiliation(s)
- Lihao Meng
- Invitrogen Corp,, Protein Array Center, 688 East Main Street, Branford, CT 06405, USA.
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11
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Boyle SN, Michaud GA, Schweitzer B, Predki PF, Koleske AJ. A Critical Role for Cortactin Phosphorylation by Abl-Family Kinases in PDGF-Induced Dorsal-Wave Formation. Curr Biol 2007; 17:445-51. [PMID: 17306540 DOI: 10.1016/j.cub.2007.01.057] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 01/11/2007] [Accepted: 01/17/2007] [Indexed: 11/26/2022]
Abstract
Proper regulation of cell morphogenesis and migration by adhesion and growth-factor receptors requires Abl-family tyrosine kinases [1-3]. Several substrates of Abl-family kinase have been identified, but they are unlikely to mediate all of the downstream actions of these kinases on cytoskeletal structure. We used a human protein microarray to identify the actin-regulatory protein cortactin as a novel substrate of the Abl and Abl-related gene (Arg) nonreceptor tyrosine kinases. Cortactin stimulates cell motility [4-6], and its upregulation in several cancers correlates with poor prognosis [7]. Even though cortactin can be tyrosine phosphorylated by Src-family kinases in vitro [8], we show that Abl and Arg are more adept at binding and phosphorylating cortactin. Importantly, we demonstrate that platelet-derived growth-factor (PDGF)-induced cortactin phosphorylation on three tyrosine residues requires Abl or Arg. Cortactin triggers F-actin-dependent dorsal waves in fibroblasts after PDGF treatment and thus results in actin reorganization and lamellipodial protrusion [9]. We provide evidence that Abl/Arg-mediated phosphorylation of cortactin is required for this PDGF-induced dorsal-wave response. Our results reveal that Abl-family kinases target cortactin as an effector of cytoskeletal rearrangements in response to PDGF.
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Affiliation(s)
- Scott N Boyle
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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12
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Abstract
Small molecules, such as metabolites and hormones, interact with proteins to regulate numerous biological pathways, which are often aberrant in disease. Small molecule drugs have been successfully exploited to specifically perturb such processes and thereby, decrease and even eliminate disease progression. Although there are compelling reasons to fully characterize interactions of small molecules with all proteins from an organism for which an intended drug regimen is planned, currently available technologies are not yet up to this task. High-content functional protein microarrays, containing hundreds to thousands of proteins, are new tools that show great potential for meeting this need. In this chapter, we review examples and methods for profiling small molecules on high-content functional protein arrays and discuss considerations for troubleshooting.
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13
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Jin F, Hazbun T, Michaud GA, Salcius M, Predki PF, Fields S, Huang J. A pooling-deconvolution strategy for biological network elucidation. Nat Methods 2006; 3:183-9. [PMID: 16489335 PMCID: PMC2803036 DOI: 10.1038/nmeth859] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 01/23/2006] [Indexed: 12/21/2022]
Abstract
The generation of large-scale data sets is a fundamental requirement of systems biology. But despite recent advances, generation of such high-coverage data remains a major challenge. We developed a pooling-deconvolution strategy that can dramatically decrease the effort required. This strategy, pooling with imaginary tags followed by deconvolution (PI-deconvolution), allows the screening of 2(n) probe proteins (baits) in 2 x n pools, with n replicates for each bait. Deconvolution of baits with their binding partners (preys) can be achieved by reading the prey's profile from the 2 x n experiments. We validated this strategy for protein-protein interaction mapping using both proteome microarrays and a yeast two-hybrid array, demonstrating that PI-deconvolution can be used to identify interactions accurately with fewer experiments and better coverage. We also show that PI-deconvolution can be used to identify protein-small molecule interactions inferred from profiling the yeast deletion collection. PI-deconvolution should be applicable to a wide range of library-against-library approaches and can also be used to optimize array designs.
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Affiliation(s)
- Fulai Jin
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Tony Hazbun
- Howard Hughes Medical Institute, Departments of Genome Sciences and Medicine, University of Washington, Box 357730, Seattle, WA 98195, USA
| | - Gregory A. Michaud
- Protein Microarray Center, Invitrogen Life Technologies, 688 East Main Street, Branford, CT 06405, USA
| | - Michael Salcius
- Protein Microarray Center, Invitrogen Life Technologies, 688 East Main Street, Branford, CT 06405, USA
| | - Paul F. Predki
- Protein Microarray Center, Invitrogen Life Technologies, 688 East Main Street, Branford, CT 06405, USA
| | - Stanley Fields
- Howard Hughes Medical Institute, Departments of Genome Sciences and Medicine, University of Washington, Box 357730, Seattle, WA 98195, USA
| | - Jing Huang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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14
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Hesselberth JR, Miller JP, Golob A, Stajich JE, Michaud GA, Fields S. Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. Genome Biol 2006; 7:R30. [PMID: 16606443 PMCID: PMC1557994 DOI: 10.1186/gb-2006-7-4-r30] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Revised: 02/10/2006] [Accepted: 03/09/2006] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The WW domain is found in a large number of eukaryotic proteins implicated in a variety of cellular processes. WW domains bind proline-rich protein and peptide ligands, but the protein interaction partners of many WW domain-containing proteins in Saccharomyces cerevisiae are largely unknown. RESULTS We used protein microarray technology to generate a protein interaction map for 12 of the 13 WW domains present in proteins of the yeast S. cerevisiae. We observed 587 interactions between these 12 domains and 207 proteins, most of which have not previously been described. We analyzed the representation of functional annotations within the network, identifying enrichments for proteins with peroxisomal localization, as well as for proteins involved in protein turnover and cofactor biosynthesis. We compared orthologs of the interacting proteins to identify conserved motifs known to mediate WW domain interactions, and found substantial evidence for the structural conservation of such binding motifs throughout the yeast lineages. The comparative approach also revealed that several of the WW domain-containing proteins themselves have evolutionarily conserved WW domain binding sites, suggesting a functional role for inter- or intramolecular association between proteins that harbor WW domains. On the basis of these results, we propose a model for the tuning of interactions between WW domains and their protein interaction partners. CONCLUSION Protein microarrays provide an appealing alternative to existing techniques for the construction of protein interaction networks. Here we built a network composed of WW domain-protein interactions that illuminates novel features of WW domain-containing proteins and their protein interaction partners.
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Affiliation(s)
- Jay R Hesselberth
- Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA
| | - John P Miller
- Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA
- Current address: Buck Institute, Redwood Boulevard, Novato, CA 94945, USA
| | - Anna Golob
- Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA
| | - Jason E Stajich
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | | | - Stanley Fields
- Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA
- Department of Medicine, and Howard Hughes Medical Institute, University of Washington, Box 357730, Seattle, WA 98195, USA
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15
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Michaud GA, Samuels ML, Schweitzer B. Functional protein arrays to facilitate drug discovery and development. IDrugs 2006; 9:266-72. [PMID: 16596480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Protein microarrays are miniaturized formats for studying proteins. This technology is empowering investigators with the ability to profile numerous types of interactions to progress basic science research and to advance drug discovery and development. Protein microarrays are poised to make significant contributions to our understanding of biology and disease because: (i) both covalent and non-covalent interactions can be reconstituted on solid-state supports; and (ii) a wealth of knowledge can be generated rapidly from such simple experiments. This feature focuses on applications of protein microarrays that have tremendous potential for addressing bottlenecks in disease-focused discovery efforts.
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Affiliation(s)
- Gregory A Michaud
- Invitrogen Corp, Research and Development, Protein Array Center, Branford, CT 06405, USA.
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16
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Abstract
The increased use of antibodies as therapeutics, as well as the growing demand for large numbers of antibodies for high-throughput protein analyses, has been accompanied by a need for more specific antibodies. An array containing every protein for the relevant organism represents the ideal format for an assay to test antibody specificity since it allows the simultaneous screening of thousands of proteins in relatively normalized quantities. Indeed, the use of a yeast proleome array to profile the specificity of several antibodies directed against yeast proteins has recently been described. In this chapter, we present a detailed description of the methods used to probe protein arrays with antibodies as well as the technical issues to consider when carrying out such experiments.
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Affiliation(s)
- Rhonda Bangham
- Research and Development, Protometrix Inc., Branford, CT, USA
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17
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Merkel JS, Michaud GA, Salcius M, Schweitzer B, Predki PF. Functional protein microarrays: just how functional are they? Curr Opin Biotechnol 2005; 16:447-52. [PMID: 16006113 DOI: 10.1016/j.copbio.2005.06.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 05/10/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
Arrays of immobilized proteins have been developed for the discovery and characterization of protein functions ranging from molecular recognition to enzymatic activity. The success of these applications is highly dependent upon the maintenance of protein structure and function while in an immobilized state - a largely untested hypothesis. However, the immobilization of functional proteins is not without precedent. Active enzymes have been successfully immobilized for industrial applications for several decades. Furthermore, a survey of recent protein microarray literature reveals that an even wider range of proteins can maintain 'proper' function while immobilized. These reports help to validate the functionality of so-called functional protein microarrays.
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Affiliation(s)
- Janie S Merkel
- Invitrogen Corporation, Protein Microarray Center, 688 East Main Street, Branford, Connecticut 06405, USA
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18
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Michaud GA, Salcius M, Zhou F, Bangham R, Bonin J, Guo H, Snyder M, Predki PF, Schweitzer BI. Analyzing antibody specificity with whole proteome microarrays. Nat Biotechnol 2003; 21:1509-12. [PMID: 14608365 DOI: 10.1038/nbt910] [Citation(s) in RCA: 227] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Accepted: 08/28/2003] [Indexed: 11/09/2022]
Abstract
Although approximately 10,000 antibodies are available from commercial sources, antibody reagents are still unavailable for most proteins. Furthermore, new applications such as antibody arrays and monoclonal antibody therapeutics have increased the demand for more specific antibodies to reduce cross-reactivity and side effects. An array containing every protein for the relevant organism represents the ideal format for an assay to test antibody specificity, because it allows the simultaneous screening of thousands of proteins for possible cross-reactivity. As an initial test of this approach, we screened 11 polyclonal and monoclonal antibodies to approximately 5,000 different yeast proteins deposited on a glass slide and found that, in addition to recognizing their cognate proteins, the antibodies cross-reacted with other yeast proteins to varying degrees. Some of the interactions of the antibodies with noncognate proteins could be deduced by alignment of the primary amino acid sequences of the antigens and cross-reactive proteins; however, these interactions could not be predicted a priori. Our findings show that proteome array technology has potential to improve antibody design and selection for applications in both medicine and research.
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19
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Abstract
Improvements in technology that allow miniaturization and high-throughput analyses of thousand of genes and gene products have changed the focus and scope of research and development in both academia and industry. It is now possible to study entire proteomes with the goals of elucidating protein expression, subcellular localization, biochemical activities, and their regulation. Alterations in different cell types and conditions and in normal and disease states can be revealed. This wealth of information not only has facilitated our basic understanding of many biological processes but also has enormous potential for drug discovery and development.
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Affiliation(s)
- Gregory A Michaud
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
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20
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Abstract
Olsalazine (OLZ), a relatively new form of 5-aminosalicylic acid (5-ASA), is being used for the treatment of colitis. A major side effect of olsalazine is diarrhea, reported in 12-25% of patients. One suggested mechanism for this side effect is enhanced ileal water and electrolyte secretion. We propose that OLZ may also inhibit ileal bile acid (BA) transport, resulting in choleretic diarrhea. This would result in excess BAs reaching the colon, with consequent BA-induced secretory diarrhea. Therefore, we studied the effect of OLZ on rat ileal absorption of taurocholate. BA uptake was determined in rat ileal segments, everted sacs, brush border membrane vesicles (BBMV), and Xenopus laevis oocytes. Segments and everted sacs were treated with 5 mM OLZ for 30 min prior to and throughout 10-min taurocholate (Tc) uptake. Terminal ileal BBMV were used to study the effect of OLZ on sodium-dependent bile acid uptake independent of cellular metabolism. Direct effects on the bile acid carrier were examined using Xenopus laevis oocytes expressing the cloned apical rat ileal BA transporter. In ileal segments 5 mM OLZ inhibited 10-min Tc uptake by 69.4 +/- 8.8% (P < 0.01) (N = 10 animals). Increasing concentrations of OLZ resulted in a dose-dependent inhibition of Tc uptake. Ten-minute Tc uptake with 0.5, 1.0, 2.0, 2.5, and 5 mM OLZ was inhibited by 13.5, 39.6, 49.7, and 70.5%, respectively. In BBMV, OLZ inhibited 45-sec Tc uptake in a dose-dependent manner but did not effect Na-dependent L-alanine uptake.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- A Chawla
- Department of Pediatrics, North Shore University Hospital-Cornell University Medical College, Manhasset, NY, USA
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21
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Abstract
Sodium-dependent bile acid uptake is developmentally regulated in the rat ileum. Transport activity is abruptly expressed on postnatal d 17, although the mechanisms controlling this expression are poorly understood. Changes in bile salt metabolism and hepatic transport result in a marked increase in bile flow before postnatal d 17, and thus this study examined the effects of bile salt feeding on the development of ileal bile acid transport. Twelve-d-old rat pups were gavage-fed saline, taurocholate, or mannitol on a daily basis for 3 d. Sodium-dependent bile acid transport was studied by rapid filtration using ileal brush-border membrane vesicles prepared from the various experimental groups. Taurocholate feeding resulted in precocious development of sodium-dependent bile acid transport and induction of sucrase activity. Mannitol feeding, used as a control for the effects of diarrhea-induced stress, resulted in similar sucrase activity, yet sodium-dependent bile acid transport was induced to only half the level observed in taurocholate-fed animals (3.2 +/- 1.6 versus 6.9 +/- 2.0 pmol/mg protein/45 s, p < 0.001). Serum corticosterone levels were similar in the mannitol- and taurocholate-fed animals (3.8 +/- 1.3 versus 4.6 +/- 1.8 micrograms/dL). Both feedings lead to histologic maturation of the ileum, with a more pronounced effect in the taurocholate-fed pups. Bile salt feeding induces precocious expression of ileal bile acid transport, apparently by both diarrhea-induced stress and a bile salt-specific effect.
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Affiliation(s)
- B L Shneider
- Department of Pediatrics, Yale University, New Haven, Connecticut 06510
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