1
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Namoto K, Baader C, Orsini V, Landshammer A, Breuer E, Dinh KT, Ungricht R, Pikiolek M, Laurent S, Lu B, Aebi A, Schönberger K, Vangrevelinghe E, Evrova O, Sun T, Annunziato S, Lachal J, Redmond E, Wang L, Wetzel K, Capodieci P, Turner J, Schutzius G, Unterreiner V, Trunzer M, Buschmann N, Behnke D, Machauer R, Scheufler C, Parker CN, Ferro M, Grevot A, Beyerbach A, Lu WY, Forbes SJ, Wagner J, Bouwmeester T, Liu J, Sohal B, Sahambi S, Greenbaum LE, Lohmann F, Hoppe P, Cong F, Sailer AW, Ruffner H, Glatthar R, Humar B, Clavien PA, Dill MT, George E, Maibaum J, Liberali P, Tchorz JS. NIBR-LTSi is a selective LATS kinase inhibitor activating YAP signaling and expanding tissue stem cells in vitro and in vivo. Cell Stem Cell 2024; 31:554-569.e17. [PMID: 38579685 DOI: 10.1016/j.stem.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/24/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
The YAP/Hippo pathway is an organ growth and size regulation rheostat safeguarding multiple tissue stem cell compartments. LATS kinases phosphorylate and thereby inactivate YAP, thus representing a potential direct drug target for promoting tissue regeneration. Here, we report the identification and characterization of the selective small-molecule LATS kinase inhibitor NIBR-LTSi. NIBR-LTSi activates YAP signaling, shows good oral bioavailability, and expands organoids derived from several mouse and human tissues. In tissue stem cells, NIBR-LTSi promotes proliferation, maintains stemness, and blocks differentiation in vitro and in vivo. NIBR-LTSi accelerates liver regeneration following extended hepatectomy in mice. However, increased proliferation and cell dedifferentiation in multiple organs prevent prolonged systemic LATS inhibition, thus limiting potential therapeutic benefit. Together, we report a selective LATS kinase inhibitor agonizing YAP signaling and promoting tissue regeneration in vitro and in vivo, enabling future research on the regenerative potential of the YAP/Hippo pathway.
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Affiliation(s)
- Kenji Namoto
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Clara Baader
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Vanessa Orsini
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Eva Breuer
- University Hospital Zurich (USZ), Zurich, Switzerland
| | - Kieu Trinh Dinh
- German Cancer Research Center (DKFZ) Heidelberg, Research Group Experimental Hepatology, Inflammation and Cancer, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | | | | | - Bo Lu
- Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Alexandra Aebi
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | | | - Olivera Evrova
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tianliang Sun
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland; Division of Liver Diseases, Institute for Regenerative Medicine, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Julie Lachal
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Emily Redmond
- Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Louis Wang
- Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Kristie Wetzel
- Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | | | | | - Gabi Schutzius
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Markus Trunzer
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Dirk Behnke
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | | | | | - Magali Ferro
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Armelle Grevot
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Wei-Yu Lu
- University of Edinburgh, Center for Inflammation Research, Edinburgh, UK
| | - Stuart J Forbes
- University of Edinburgh, Center for Regenerative Medicine, Edinburgh, UK
| | - Jürgen Wagner
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Jun Liu
- Biomedical Research, Novartis Pharma AG, La Jolla, CA, USA
| | - Bindi Sohal
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | | | - Felix Lohmann
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Philipp Hoppe
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Feng Cong
- Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | | | - Heinz Ruffner
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Ralf Glatthar
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Bostjan Humar
- University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Michael T Dill
- German Cancer Research Center (DKFZ) Heidelberg, Research Group Experimental Hepatology, Inflammation and Cancer, Heidelberg, Germany; Department of Gastroenterology, Infectious Diseases and Intoxication, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Jürgen Maibaum
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Jan S Tchorz
- Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
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2
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Richards SM, Gubser Keller C, Kreutzer R, Greiner G, Ley S, Doelemeyer A, Dubost V, Flandre T, Kirkland S, Carbone W, Pandya R, Knehr J, Roma G, Schuierer S, Bouchez L, Seuwen K, Aebi A, Westhead D, Hintzen G, Jurisic G, Hossain I, Neri M, Manevski N, Balavenkatraman KK, Moulin P, Begrich A, Bertschi B, Huber R, Bouwmeester T, Driver VR, von Schwabedissen M, Schaefer D, Wettstein B, Wettstein R, Ruffner H. Molecular characterization of chronic cutaneous wounds reveals subregion- and wound type-specific differential gene expression. Int Wound J 2024; 21:e14447. [PMID: 38149752 PMCID: PMC10958103 DOI: 10.1111/iwj.14447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 12/28/2023] Open
Abstract
A limited understanding of the pathology underlying chronic wounds has hindered the development of effective diagnostic markers and pharmaceutical interventions. This study aimed to elucidate the molecular composition of various common chronic ulcer types to facilitate drug discovery strategies. We conducted a comprehensive analysis of leg ulcers (LUs), encompassing venous and arterial ulcers, foot ulcers (FUs), pressure ulcers (PUs), and compared them with surgical wound healing complications (WHCs). To explore the pathophysiological mechanisms and identify similarities or differences within wounds, we dissected wounds into distinct subregions, including the wound bed, border, and peri-wound areas, and compared them against intact skin. By correlating histopathology, RNA sequencing (RNA-Seq), and immunohistochemistry (IHC), we identified unique genes, pathways, and cell type abundance patterns in each wound type and subregion. These correlations aim to aid clinicians in selecting targeted treatment options and informing the design of future preclinical and clinical studies in wound healing. Notably, specific genes, such as PITX1 and UPP1, exhibited exclusive upregulation in LUs and FUs, potentially offering significant benefits to specialists in limb preservation and clinical treatment decisions. In contrast, comparisons between different wound subregions, regardless of wound type, revealed distinct expression profiles. The pleiotropic chemokine-like ligand GPR15L (C10orf99) and transmembrane serine proteases TMPRSS11A/D were significantly upregulated in wound border subregions. Interestingly, WHCs exhibited a nearly identical transcriptome to PUs, indicating clinical relevance. Histological examination revealed blood vessel occlusions with impaired angiogenesis in chronic wounds, alongside elevated expression of genes and immunoreactive markers related to blood vessel and lymphatic epithelial cells in wound bed subregions. Additionally, inflammatory and epithelial markers indicated heightened inflammatory responses in wound bed and border subregions and reduced wound bed epithelialization. In summary, chronic wounds from diverse anatomical sites share common aspects of wound pathophysiology but also exhibit distinct molecular differences. These unique molecular characteristics present promising opportunities for drug discovery and treatment, particularly for patients suffering from chronic wounds. The identified diagnostic markers hold the potential to enhance preclinical and clinical trials in the field of wound healing.
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Affiliation(s)
| | | | - Robert Kreutzer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Department of PathologyAnaPath Services GmbHLiestalSwitzerland
| | | | - Svenja Ley
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Arno Doelemeyer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Valerie Dubost
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Thierry Flandre
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Susan Kirkland
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Harvantis Pharma Consulting LtdLondonUK
| | - Walter Carbone
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Research and Development CoordinatorELI TechGroup Corso SvizzeraTorinoItaly
| | - Rishika Pandya
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Judith Knehr
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Guglielmo Roma
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Discovery Data ScienceGSK VaccinesSienaItaly
| | - Sven Schuierer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Laure Bouchez
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Therapeutics Department, Executive in ResidenceGeneral InceptionBaselSwitzerland
| | - Klaus Seuwen
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Alexandra Aebi
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - David Westhead
- Leeds Institute of Data AnalyticsUniversity of LeedsLeedsUK
| | - Gabriele Hintzen
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Translational ScienceAffimed GmbHMannheimGermany
| | - Giorgia Jurisic
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Imtiaz Hossain
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Marilisa Neri
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Nenad Manevski
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Translational PKPD and Clinical Pharmacology, Pharmaceutical Sciences, pREDF. Hoffmann‐La Roche AGBaselSwitzerland
| | | | - Pierre Moulin
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Annette Begrich
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | | | - Roland Huber
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | | | - Vickie R. Driver
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- INOVA HealthcareWound Healing and Hyperbaric CentersFalls ChurchVirginiaUSA
| | | | - Dirk Schaefer
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Barbara Wettstein
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Reto Wettstein
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Heinz Ruffner
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
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3
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Saponara E, Penno C, Orsini V, Wang ZY, Fischer A, Aebi A, Matadamas-Guzman ML, Brun V, Fischer B, Brousseau M, O'Donnell P, Turner J, Graff Meyer A, Bollepalli L, d'Ario G, Roma G, Carbone W, Annunziato S, Obrecht M, Beckmann N, Saravanan C, Osmont A, Tropberger P, Richards SM, Genoud C, Ley S, Ksiazek I, Nigsch F, Terracciano LM, Schadt HS, Bouwmeester T, Tchorz JS, Ruffner H. Loss of Hepatic Leucine-Rich Repeat-Containing G-Protein Coupled Receptors 4 and 5 Promotes Nonalcoholic Fatty Liver Disease. Am J Pathol 2023; 193:161-181. [PMID: 36410420 DOI: 10.1016/j.ajpath.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 11/19/2022]
Abstract
The roof plate-specific spondin-leucine-rich repeat-containing G-protein coupled receptor 4/5 (LGR4/5)-zinc and ring finger 3 (ZNRF3)/ring finger protein 43 (RNF43) module is a master regulator of hepatic Wnt/β-catenin signaling and metabolic zonation. However, its impact on nonalcoholic fatty liver disease (NAFLD) remains unclear. The current study investigated whether hepatic epithelial cell-specific loss of the Wnt/β-catenin modulator Lgr4/5 promoted NAFLD. The 3- and 6-month-old mice with hepatic epithelial cell-specific deletion of both receptors Lgr4/5 (Lgr4/5dLKO) were compared with control mice fed with normal diet (ND) or high-fat diet (HFD). Six-month-old HFD-fed Lgr4/5dLKO mice developed hepatic steatosis and fibrosis but the control mice did not. Serum cholesterol-high-density lipoprotein and total cholesterol levels in 3- and 6-month-old HFD-fed Lgr4/5dLKO mice were decreased compared with those in control mice. An ex vivo primary hepatocyte culture assay and a comprehensive bile acid (BA) characterization in liver, plasma, bile, and feces demonstrated that ND-fed Lgr4/5dLKO mice had impaired BA secretion, predisposing them to develop cholestatic characteristics. Lipidome and RNA-sequencing analyses demonstrated severe alterations in several lipid species and pathways controlling lipid metabolism in the livers of Lgr4/5dLKO mice. In conclusion, loss of hepatic Wnt/β-catenin activity by Lgr4/5 deletion led to loss of BA secretion, cholestatic features, altered lipid homeostasis, and deregulation of lipoprotein pathways. Both BA and intrinsic lipid alterations contributed to the onset of NAFLD.
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Affiliation(s)
- Enrica Saponara
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Carlos Penno
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Zhong-Yi Wang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Audrey Fischer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Alexandra Aebi
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Meztli L Matadamas-Guzman
- Instituto Nacional de Medicina Genómica-Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Virginie Brun
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Benoit Fischer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Margaret Brousseau
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Peter O'Donnell
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Jonathan Turner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Alexandra Graff Meyer
- Friedrich Miescher Institute for BioMedical Research, Facility for Advanced Imaging and Microscopy, Basel, Switzerland
| | - Laura Bollepalli
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Giovanni d'Ario
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Stefano Annunziato
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Michael Obrecht
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Nicolau Beckmann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Chandra Saravanan
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Arnaud Osmont
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Philipp Tropberger
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Shola M Richards
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Christel Genoud
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Svenja Ley
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Iwona Ksiazek
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Luigi M Terracciano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Istituto di Ricovero e Cura a Carattere Scientifico, Humanitas Research Hospital, Anatomia Patologica, Rozzano, Milan, Italy
| | - Heiko S Schadt
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Heinz Ruffner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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4
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Saponara E, Penno C, Orsini V, Wang ZY, Fischer A, Aebi A, Matadamas-Guzman ML, Brun V, Fischer B, Brousseau M, O'Donnell P, Turner J, Graff Meyer A, Bollepalli L, d'Ario G, Roma G, Carbone W, Annunziato S, Obrecht M, Beckmann N, Saravanan C, Osmont A, Tropberger P, Richards SM, Genoud C, Ley S, Ksiazek I, Nigsch F, Terracciano LM, Schadt HS, Bouwmeester T, Tchorz JS, Ruffner H. Loss of Hepatic Leucine-Rich Repeat-Containing G-Protein Coupled Receptors 4 and 5 Promotes Nonalcoholic Fatty Liver Disease. Am J Pathol 2023. [PMID: 36410420 DOI: 10.1016/j.ajpath.2022.10.00] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The roof plate-specific spondin-leucine-rich repeat-containing G-protein coupled receptor 4/5 (LGR4/5)-zinc and ring finger 3 (ZNRF3)/ring finger protein 43 (RNF43) module is a master regulator of hepatic Wnt/β-catenin signaling and metabolic zonation. However, its impact on nonalcoholic fatty liver disease (NAFLD) remains unclear. The current study investigated whether hepatic epithelial cell-specific loss of the Wnt/β-catenin modulator Lgr4/5 promoted NAFLD. The 3- and 6-month-old mice with hepatic epithelial cell-specific deletion of both receptors Lgr4/5 (Lgr4/5dLKO) were compared with control mice fed with normal diet (ND) or high-fat diet (HFD). Six-month-old HFD-fed Lgr4/5dLKO mice developed hepatic steatosis and fibrosis but the control mice did not. Serum cholesterol-high-density lipoprotein and total cholesterol levels in 3- and 6-month-old HFD-fed Lgr4/5dLKO mice were decreased compared with those in control mice. An ex vivo primary hepatocyte culture assay and a comprehensive bile acid (BA) characterization in liver, plasma, bile, and feces demonstrated that ND-fed Lgr4/5dLKO mice had impaired BA secretion, predisposing them to develop cholestatic characteristics. Lipidome and RNA-sequencing analyses demonstrated severe alterations in several lipid species and pathways controlling lipid metabolism in the livers of Lgr4/5dLKO mice. In conclusion, loss of hepatic Wnt/β-catenin activity by Lgr4/5 deletion led to loss of BA secretion, cholestatic features, altered lipid homeostasis, and deregulation of lipoprotein pathways. Both BA and intrinsic lipid alterations contributed to the onset of NAFLD.
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Affiliation(s)
- Enrica Saponara
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Carlos Penno
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Zhong-Yi Wang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Audrey Fischer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Alexandra Aebi
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Meztli L Matadamas-Guzman
- Instituto Nacional de Medicina Genómica-Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Virginie Brun
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Benoit Fischer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Margaret Brousseau
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Peter O'Donnell
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Jonathan Turner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Alexandra Graff Meyer
- Friedrich Miescher Institute for BioMedical Research, Facility for Advanced Imaging and Microscopy, Basel, Switzerland
| | - Laura Bollepalli
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Giovanni d'Ario
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Stefano Annunziato
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Michael Obrecht
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Nicolau Beckmann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Chandra Saravanan
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, Massachusetts
| | - Arnaud Osmont
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Philipp Tropberger
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Shola M Richards
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Christel Genoud
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Svenja Ley
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Iwona Ksiazek
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Luigi M Terracciano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Istituto di Ricovero e Cura a Carattere Scientifico, Humanitas Research Hospital, Anatomia Patologica, Rozzano, Milan, Italy
| | - Heiko S Schadt
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Heinz Ruffner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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5
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Krüttner S, Falasconi A, Valbuena S, Galimberti I, Bouwmeester T, Arber S, Caroni P. Absence of familiarity triggers hallmarks of autism in mouse model through aberrant tail-of-striatum and prelimbic cortex signaling. Neuron 2022; 110:1468-1482.e5. [DOI: 10.1016/j.neuron.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/10/2022] [Accepted: 01/28/2022] [Indexed: 12/28/2022]
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6
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Fustiñana MS, Eichlisberger T, Bouwmeester T, Bitterman Y, Lüthi A. State-dependent encoding of exploratory behaviour in the amygdala. Nature 2021; 592:267-271. [PMID: 33658711 DOI: 10.1038/s41586-021-03301-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 01/27/2021] [Indexed: 11/09/2022]
Abstract
The behaviour of an animal is determined by metabolic, emotional and social factors1,2. Depending on its state, an animal will focus on avoiding threats, foraging for food or on social interactions, and will display the appropriate behavioural repertoire3. Moreover, survival and reproduction depend on the ability of an animal to adapt to changes in the environment by prioritizing the appropriate state4. Although these states are thought to be associated with particular functional configurations of large-brain systems5,6, the underlying principles are poorly understood. Here we use deep-brain calcium imaging of mice engaged in spatial or social exploration to investigate how these processes are represented at the neuronal population level in the basolateral amygdala, which is a region of the brain that integrates emotional, social and metabolic information. We demonstrate that the basolateral amygdala encodes engagement in exploratory behaviour by means of two large, functionally anticorrelated ensembles that exhibit slow dynamics. We found that spatial and social exploration were encoded by orthogonal pairs of ensembles with stable and hierarchical allocation of neurons according to the saliency of the stimulus. These findings reveal that the basolateral amygdala acts as a low-dimensional, but context-dependent, hierarchical classifier that encodes state-dependent behavioural repertoires. This computational function may have a fundamental role in the regulation of internal states in health and disease.
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Affiliation(s)
| | | | - Tewis Bouwmeester
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Yael Bitterman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andreas Lüthi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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7
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Sun T, Pikiolek M, Orsini V, Bergling S, Holwerda S, Morelli L, Hoppe PS, Planas-Paz L, Yang Y, Ruffner H, Bouwmeester T, Lohmann F, Terracciano LM, Roma G, Cong F, Tchorz JS. AXIN2 + Pericentral Hepatocytes Have Limited Contributions to Liver Homeostasis and Regeneration. Cell Stem Cell 2019; 26:97-107.e6. [PMID: 31866224 DOI: 10.1016/j.stem.2019.10.011] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [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: 04/11/2019] [Revised: 09/05/2019] [Accepted: 10/28/2019] [Indexed: 12/22/2022]
Abstract
The existence of specialized liver stem cell populations, including AXIN2+ pericentral hepatocytes, that safeguard homeostasis and repair has been controversial. Here, using AXIN2 lineage tracing in BAC-transgenic mice, we confirm the regenerative potential of intestinal stem cells (ISCs) but find limited roles for pericentral hepatocytes in liver parenchyma homeostasis. Liver regrowth following partial hepatectomy is enabled by proliferation of hepatocytes throughout the liver, rather than by a pericentral population. Periportal hepatocyte injury triggers local repair as well as auxiliary proliferation in all liver zones. DTA-mediated ablation of AXIN2+ pericentral hepatocytes transiently disrupts this zone, which is reestablished by conversion of pericentral vein-juxtaposed glutamine synthetase (GS)- hepatocytes into GS+ hepatocytes and by compensatory proliferation of hepatocytes across liver zones. These findings show hepatocytes throughout the liver can upregulate AXIN2 and LGR5 after injury and contribute to liver regeneration on demand, without zonal dominance by a putative pericentral stem cell population.
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Affiliation(s)
- Tianliang Sun
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Monika Pikiolek
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sebastian Bergling
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sjoerd Holwerda
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Lapo Morelli
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Philipp S Hoppe
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Lara Planas-Paz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Yi Yang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Heinz Ruffner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Felix Lohmann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Feng Cong
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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8
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Rabl J, Bunker RD, Schenk AD, Cavadini S, Gill ME, Abdulrahman W, Andrés-Pons A, Luijsterburg MS, Ibrahim AFM, Branigan E, Aguirre JD, Marceau AH, Guérillon C, Bouwmeester T, Hassiepen U, Peters AHFM, Renatus M, Gelman L, Rubin SM, Mailand N, van Attikum H, Hay RT, Thomä NH. Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation. Mol Cell 2019; 75:483-497.e9. [PMID: 31253574 PMCID: PMC6695476 DOI: 10.1016/j.molcel.2019.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/30/2019] [Accepted: 05/31/2019] [Indexed: 01/03/2023]
Abstract
In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. The BRCA1-A and BRISC complexes serve in DNA double-strand break repair and immune signaling and contain the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively. The molecular basis underlying BRCA1-A and BRISC function is currently unknown. Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2α, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains. Our work explains modularity in the BRCC36 DUB family, with different adaptor subunits conferring diversified targeting and regulatory functions.
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Affiliation(s)
- Julius Rabl
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Mark E Gill
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Wassim Abdulrahman
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Amparo Andrés-Pons
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Martijn S Luijsterburg
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Adel F M Ibrahim
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Emma Branigan
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Aimee H Marceau
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Claire Guérillon
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
| | - Haico van Attikum
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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9
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Planas-Paz L, Sun T, Pikiolek M, Cochran NR, Bergling S, Orsini V, Yang Z, Sigoillot F, Jetzer J, Syed M, Neri M, Schuierer S, Morelli L, Hoppe PS, Schwarzer W, Cobos CM, Alford JL, Zhang L, Cuttat R, Waldt A, Carballido-Perrig N, Nigsch F, Kinzel B, Nicholson TB, Yang Y, Mao X, Terracciano LM, Russ C, Reece-Hoyes JS, Gubser Keller C, Sailer AW, Bouwmeester T, Greenbaum LE, Lugus JJ, Cong F, McAllister G, Hoffman GR, Roma G, Tchorz JS. YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury. Cell Stem Cell 2019; 25:39-53.e10. [PMID: 31080135 DOI: 10.1016/j.stem.2019.04.005] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 01/29/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022]
Abstract
Biliary epithelial cells (BECs) form bile ducts in the liver and are facultative liver stem cells that establish a ductular reaction (DR) to support liver regeneration following injury. Liver damage induces periportal LGR5+ putative liver stem cells that can form BEC-like organoids, suggesting that RSPO-LGR4/5-mediated WNT/β-catenin activity is important for a DR. We addressed the roles of this and other signaling pathways in a DR by performing a focused CRISPR-based loss-of-function screen in BEC-like organoids, followed by in vivo validation and single-cell RNA sequencing. We found that BECs lack and do not require LGR4/5-mediated WNT/β-catenin signaling during a DR, whereas YAP and mTORC1 signaling are required for this process. Upregulation of AXIN2 and LGR5 is required in hepatocytes to enable their regenerative capacity in response to injury. Together, these data highlight heterogeneity within the BEC pool, delineate signaling pathways involved in a DR, and clarify the identity and roles of injury-induced periportal LGR5+ cells.
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Affiliation(s)
- Lara Planas-Paz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tianliang Sun
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Monika Pikiolek
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Nadire R Cochran
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Sebastian Bergling
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Zinger Yang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Frederic Sigoillot
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Jasna Jetzer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Maryam Syed
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Marilisa Neri
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Lapo Morelli
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Philipp S Hoppe
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Wibke Schwarzer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Carlos M Cobos
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland; Hospital Aleman, Buenos Aires, Argentina
| | - John L Alford
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Le Zhang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Rachel Cuttat
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Annick Waldt
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Bernd Kinzel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Thomas B Nicholson
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Yi Yang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | | | - Carsten Russ
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - John S Reece-Hoyes
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | | | - Andreas W Sailer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Linda E Greenbaum
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, East Hanover, NJ, USA
| | - Jesse J Lugus
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Feng Cong
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Gregory McAllister
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Gregory R Hoffman
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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10
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Bertschi NL, Voorberg-van der Wel A, Zeeman AM, Schuierer S, Nigsch F, Carbone W, Knehr J, Gupta DK, Hofman SO, van der Werff N, Nieuwenhuis I, Klooster E, Faber BW, Flannery EL, Mikolajczak SA, Chuenchob V, Shrestha B, Beibel M, Bouwmeester T, Kangwanrangsan N, Sattabongkot J, Diagana TT, Kocken CH, Roma G. Transcriptomic analysis reveals reduced transcriptional activity in the malaria parasite Plasmodium cynomolgi during progression into dormancy. eLife 2018; 7:41081. [PMID: 30589413 PMCID: PMC6344078 DOI: 10.7554/elife.41081] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/23/2018] [Indexed: 02/06/2023] Open
Abstract
Relapses of Plasmodium dormant liver hypnozoites compromise malaria eradication efforts. New radical cure drugs are urgently needed, yet the vast gap in knowledge of hypnozoite biology impedes drug discovery. We previously unraveled the transcriptome of 6 to 7 day-old P. cynomolgi liver stages, highlighting pathways associated with hypnozoite dormancy (Voorberg-van der Wel et al., 2017). We now extend these findings by transcriptome profiling of 9 to 10 day-old liver stage parasites, thus revealing for the first time the maturation of the dormant stage over time. Although progression of dormancy leads to a 10-fold decrease in transcription and expression of only 840 genes, including genes associated with housekeeping functions, we show that pathways involved in quiescence, energy metabolism and maintenance of genome integrity remain the prevalent pathways active in mature hypnozoites.
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Affiliation(s)
- Nicole L Bertschi
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | | | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Devendra K Gupta
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Sam O Hofman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Nicole van der Werff
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ivonne Nieuwenhuis
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Els Klooster
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Bart W Faber
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Erika L Flannery
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | | | - Vorada Chuenchob
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Binesh Shrestha
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Martin Beibel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Niwat Kangwanrangsan
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thierry T Diagana
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Clemens Hm Kocken
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
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11
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Voorberg-van der Wel A, Roma G, Gupta DK, Schuierer S, Nigsch F, Carbone W, Zeeman AM, Lee BH, Hofman SO, Faber BW, Knehr J, Pasini E, Kinzel B, Bifani P, Bonamy GMC, Bouwmeester T, Kocken CHM, Diagana TT. A comparative transcriptomic analysis of replicating and dormant liver stages of the relapsing malaria parasite Plasmodium cynomolgi. eLife 2017; 6:29605. [PMID: 29215331 PMCID: PMC5758109 DOI: 10.7554/elife.29605] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/05/2017] [Indexed: 01/23/2023] Open
Abstract
Plasmodium liver hypnozoites, which cause disease relapse, are widely considered to be the last barrier towards malaria eradication. The biology of this quiescent form of the parasite is poorly understood which hinders drug discovery. We report a comparative transcriptomic dataset of replicating liver schizonts and dormant hypnozoites of the relapsing parasite Plasmodium cynomolgi. Hypnozoites express only 34% of Plasmodium physiological pathways, while 91% are expressed in replicating schizonts. Few known malaria drug targets are expressed in quiescent parasites, but pathways involved in microbial dormancy, maintenance of genome integrity and ATP homeostasis were robustly expressed. Several transcripts encoding heavy metal transporters were expressed in hypnozoites and the copper chelator neocuproine was cidal to all liver stage parasites. This transcriptomic dataset is a valuable resource for the discovery of vaccines and effective treatments to combat vivax malaria.
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Affiliation(s)
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Boon Heng Lee
- Novartis Institute for Tropical Diseases, Singapore, Singapore
| | - Sam O Hofman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Bart W Faber
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Erica Pasini
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Bernd Kinzel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Pablo Bifani
- Novartis Institute for Tropical Diseases, Singapore, Singapore
| | | | | | - Clemens H M Kocken
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
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12
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Suply T, Hannedouche S, Carte N, Li J, Grosshans B, Schaefer M, Raad L, Beck V, Vidal S, Hiou-Feige A, Beluch N, Barbieri S, Wirsching J, Lageyre N, Hillger F, Debon C, Dawson J, Smith P, Lannoy V, Detheux M, Bitsch F, Falchetto R, Bouwmeester T, Porter J, Baumgarten B, Mansfield K, Carballido JM, Seuwen K, Bassilana F. A natural ligand for the orphan receptor GPR15 modulates lymphocyte recruitment to epithelia. Sci Signal 2017; 10:10/496/eaal0180. [DOI: 10.1126/scisignal.aal0180] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Surdziel E, Clay I, Nigsch F, Thiemeyer A, Allard C, Hoffman G, Reece-Hoyes JS, Phadke T, Gambert R, Keller CG, Ludwig MG, Baumgarten B, Frederiksen M, Schübeler D, Seuwen K, Bouwmeester T, Fodor BD. Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization. PLoS One 2017; 12:e0183679. [PMID: 28837623 PMCID: PMC5570424 DOI: 10.1371/journal.pone.0183679] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 01/05/2023] Open
Abstract
Macrophages are key cell types of the innate immune system regulating host defense, inflammation, tissue homeostasis and cancer. Within this functional spectrum diverse and often opposing phenotypes are displayed which are dictated by environmental clues and depend on highly plastic transcriptional programs. Among these the 'classical' (M1) and 'alternative' (M2) macrophage polarization phenotypes are the best characterized. Understanding macrophage polarization in humans may reveal novel therapeutic intervention possibilities for chronic inflammation, wound healing and cancer. Systematic loss of function screening in human primary macrophages is limited due to lack of robust gene delivery methods and limited sample availability. To overcome these hurdles we developed cell-autonomous assays using the THP-1 cell line allowing genetic screens for human macrophage phenotypes. We screened 648 chromatin and signaling regulators with a pooled shRNA library for M1 and M2 polarization modulators. Validation experiments confirmed the primary screening results and identified OGT (O-linked N-acetylglucosamine (GlcNAc) transferase) as a novel mediator of M2 polarization in human macrophages. Our approach offers a possible avenue to utilize comprehensive genetic tools to identify novel candidate genes regulating macrophage polarization in humans.
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Affiliation(s)
- Ewa Surdziel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ieuan Clay
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Anke Thiemeyer
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Cyril Allard
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Gregory Hoffman
- Novartis Institutes for Biomedical Research, Cambridge, United States of America
| | - John S. Reece-Hoyes
- Novartis Institutes for Biomedical Research, Cambridge, United States of America
| | - Tanushree Phadke
- Novartis Institutes for Biomedical Research, Cambridge, United States of America
| | - Romain Gambert
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | | | | | | | - Dirk Schübeler
- Friedrich Miescher Institute for BioMedical Research, Basel, Switzerland
| | - Klaus Seuwen
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Barna D. Fodor
- Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail:
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14
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Estoppey D, Lee CM, Janoschke M, Lee BH, Wan KF, Dong H, Mathys P, Filipuzzi I, Schuhmann T, Riedl R, Aust T, Galuba O, McAllister G, Russ C, Spiess M, Bouwmeester T, Bonamy GM, Hoepfner D. The Natural Product Cavinafungin Selectively Interferes with Zika and Dengue Virus Replication by Inhibition of the Host Signal Peptidase. Cell Rep 2017; 19:451-460. [DOI: 10.1016/j.celrep.2017.03.071] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 03/06/2017] [Accepted: 03/24/2017] [Indexed: 12/31/2022] Open
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15
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Estoppey D, Hewett JW, Guy CT, Harrington E, Thomas JR, Schirle M, Cuttat R, Waldt A, Gerrits B, Yang Z, Schuierer S, Pan X, Xie K, Carbone W, Knehr J, Lindeman A, Russ C, Frias E, Hoffman GR, Varadarajan M, Ramadan N, Reece-Hoyes JS, Wang Q, Chen X, McAllister G, Roma G, Bouwmeester T, Hoepfner D. Identification of a novel NAMPT inhibitor by CRISPR/Cas9 chemogenomic profiling in mammalian cells. Sci Rep 2017; 7:42728. [PMID: 28205648 PMCID: PMC5311948 DOI: 10.1038/srep42728] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 10/14/2016] [Accepted: 01/12/2017] [Indexed: 01/02/2023] Open
Abstract
Chemogenomic profiling is a powerful and unbiased approach to elucidate pharmacological targets and the mechanism of bioactive compounds. Until recently, genome-wide, high-resolution experiments of this nature have been limited to fungal systems due to lack of mammalian genome-wide deletion collections. With the example of a novel nicotinamide phosphoribosyltransferase (NAMPT) inhibitor, we demonstrate that the CRISPR/Cas9 system enables the generation of transient homo- and heterozygous deletion libraries and allows for the identification of efficacy targets and pathways mediating hypersensitivity and resistance relevant to the compound mechanism of action.
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Affiliation(s)
- David Estoppey
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Jeffrey W Hewett
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Chantale T Guy
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Edmund Harrington
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jason R Thomas
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rachel Cuttat
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Annick Waldt
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Bertran Gerrits
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Zinger Yang
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Xuewen Pan
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kevin Xie
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Alicia Lindeman
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Carsten Russ
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Elizabeth Frias
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gregory R Hoffman
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Malini Varadarajan
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nadire Ramadan
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - John S Reece-Hoyes
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiong Wang
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Xin Chen
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gregory McAllister
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland
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16
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Ley S, Galuba O, Salathe A, Melin N, Aebi A, Pikiolek M, Knehr J, Carbone W, Beibel M, Nigsch F, Roma G, d'Ario G, Kirkland S, Bouchez LC, Gubser Keller C, Bouwmeester T, Parker CN, Ruffner H. Screening of Intestinal Crypt Organoids: A Simple Readout for Complex Biology. SLAS Discov 2017; 22:571-582. [PMID: 28345372 DOI: 10.1177/2472555216683651] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Oral and intestinal mucositis is a debilitating side effect of radiation treatment. A mouse model of radiation-induced mucositis leads to weight loss and tissue damage, reflecting the human ailment as it responds to keratinocyte growth factor (KGF), the standard-of-care treatment. Cultured intestinal crypt organoids allowed the development of an assay monitoring the effect of treatments of intestinal epithelium to radiation-induced damage. This in vitro assay resembles the mouse model as KGF and roof plate-specific spondin-1 (RSPO1) enhanced crypt organoid recovery following radiation. Screening identified compounds that increased the survival of organoids postradiation. Testing of these compounds revealed that the organoids changed their responses over time. Unbiased transcriptome analysis was performed on crypt organoid cultures at various time points in culture to investigate this adaptive behavior. A number of genes and pathways were found to be modulated over time, providing a rationale for the altered sensitivity of the organoid cultures. This report describes an in vitro assay that reflects aspects of human disease. The assay was used to identify bioactive compounds, which served as probes to interrogate the biology of crypt organoids over prolonged culture. The pathways that are changing over time may offer potential targets for treatment of mucositis.
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Affiliation(s)
- Svenja Ley
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Olaf Galuba
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Adrian Salathe
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Nicolas Melin
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Alexandra Aebi
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Monika Pikiolek
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Judith Knehr
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Walter Carbone
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Martin Beibel
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Florian Nigsch
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Guglielmo Roma
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Giovanni d'Ario
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Susan Kirkland
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Laure C Bouchez
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Caroline Gubser Keller
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Tewis Bouwmeester
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Christian N Parker
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
| | - Heinz Ruffner
- 1 Novartis Institutes for BioMedical Research (NIBR), Developmental and Molecular Pathways (DMP), Basel, Switzerland
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17
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Planas-Paz L, Orsini V, Boulter L, Calabrese D, Pikiolek M, Nigsch F, Xie Y, Roma G, Donovan A, Marti P, Beckmann N, Dill MT, Carbone W, Bergling S, Isken A, Mueller M, Kinzel B, Yang Y, Mao X, Nicholson TB, Zamponi R, Capodieci P, Valdez R, Rivera D, Loew A, Ukomadu C, Terracciano LM, Bouwmeester T, Cong F, Heim MH, Forbes SJ, Ruffner H, Tchorz JS. Corrigendum: The RSPO-LGR4/5-ZNRF3/RNF43 module controls liver zonation and size. Nat Cell Biol 2016; 18:1260. [PMID: 27784900 DOI: 10.1038/ncb3428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Kiessling MK, Schuierer S, Stertz S, Beibel M, Bergling S, Knehr J, Carbone W, de Vallière C, Tchinda J, Bouwmeester T, Seuwen K, Rogler G, Roma G. Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening. BMC Genomics 2016; 17:723. [PMID: 27613601 PMCID: PMC5016932 DOI: 10.1186/s12864-016-3042-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Genome-wide CRISPR-Cas9 dropout screens can identify genes whose knockout affects cell viability. Recent CRISPR screens detected thousands of essential genes required for cellular survival and key cellular processes; however discovering novel lineage-specific genetic dependencies from the many hits still remains a challenge. RESULTS To assess whether CRISPR-Cas9 dropout screens can help identify cancer dependencies, we screened two human cancer cell lines carrying known and distinct oncogenic mutations using a genome-wide sgRNA library. We found that the gRNA targeting the driver mutation EGFR was one of the highest-ranking candidates in the EGFR-mutant HCC-827 lung adenocarcinoma cell line. Likewise, sgRNAs for NRAS and MAP2K1 (MEK1), a downstream kinase of mutant NRAS, were identified among the top hits in the NRAS-mutant neuroblastoma cell line CHP-212. Depletion of these genes targeted by the sgRNAs strongly correlated with the sensitivity to specific kinase inhibitors of the EGFR or RAS pathway in cell viability assays. In addition, we describe other dependencies such as TBK1 in HCC-827 cells and TRIB2 in CHP-212 cells which merit further investigation. CONCLUSIONS We show that genome-wide CRISPR dropout screens are suitable for the identification of oncogenic drivers and other essential genes.
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Affiliation(s)
- Michael K. Kiessling
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Sven Schuierer
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sebastian Bergling
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Cheryl de Vallière
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Joelle Tchinda
- Department of Oncology, Children University Hospital Zürich, Zürich, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Klaus Seuwen
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
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19
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Riccardi S, Bergling S, Sigoillot F, Beibel M, Werner A, Leighton-Davies J, Knehr J, Bouwmeester T, Parker CN, Roma G, Kinzel B. MiR-210 promotes sensory hair cell formation in the organ of corti. BMC Genomics 2016; 17:309. [PMID: 27121005 PMCID: PMC4848794 DOI: 10.1186/s12864-016-2620-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 04/14/2016] [Indexed: 12/20/2022] Open
Abstract
Background Hearing loss is the most common sensory defect afflicting several hundred million people worldwide. In most cases, regardless of the original cause, hearing loss is related to the degeneration and death of hair cells and their associated spiral ganglion neurons. Despite this knowledge, relatively few studies have reported regeneration of the auditory system. Significant gaps remain in our understanding of the molecular mechanisms underpinning auditory function, including the factors required for sensory cell regeneration. Recently, the identification of transcriptional activators and repressors of hair cell fate has been augmented by the discovery of microRNAs (miRNAs) associated with hearing loss. As miRNAs are central players of differentiation and cell fate, identification of miRNAs and their gene targets may reveal new pathways for hair cell regeneration, thereby providing new avenues for the treatment of hearing loss. Results In order to identify new genetic elements enabling regeneration of inner ear sensory hair cells, next-generation miRNA sequencing (miRSeq) was used to identify the most prominent miRNAs expressed in the mouse embryonic inner ear cell line UB/OC-1 during differentiation towards a hair cell like phenotype. Based on these miRSeq results eight most differentially expressed miRNAs were selected for further characterization. In UB/OC-1, miR-210 silencing in vitro resulted in hair cell marker expression, whereas ectopic expression of miR-210 resulted in new hair cell formation in cochlear explants. Using a lineage tracing mouse model, transdifferentiation of supporting epithelial cells was identified as the likely mechanism for this new hair cell formation. Potential miR-210 targets were predicted in silico and validated experimentally using a miR-trap approach. Conclusion MiRSeq followed by ex vivo validation revealed miR-210 as a novel factor driving transdifferentiation of supporting epithelial cells to sensory hair cells suggesting that miR-210 might be a potential new factor for hearing loss therapy. In addition, identification of inner ear pathways regulated by miR-210 identified potential new drug targets for the treatment of hearing loss. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2620-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabrina Riccardi
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Sebastian Bergling
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Frederic Sigoillot
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Cambridge, USA
| | - Martin Beibel
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Annick Werner
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Juliet Leighton-Davies
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Judith Knehr
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Tewis Bouwmeester
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Christian N Parker
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Bernd Kinzel
- Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland.
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20
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Bidinosti M, Botta P, Krüttner S, Proenca CC, Stoehr N, Bernhard M, Fruh I, Mueller M, Bonenfant D, Voshol H, Carbone W, Neal SJ, McTighe SM, Roma G, Dolmetsch RE, Porter JA, Caroni P, Bouwmeester T, Lüthi A, Galimberti I. CLK2 inhibition ameliorates autistic features associated with SHANK3 deficiency. Science 2016; 351:1199-203. [PMID: 26847545 DOI: 10.1126/science.aad5487] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/22/2016] [Indexed: 12/17/2022]
Abstract
SH3 and multiple ankyrin repeat domains 3 (SHANK3) haploinsufficiency is causative for the neurological features of Phelan-McDermid syndrome (PMDS), including a high risk of autism spectrum disorder (ASD). We used unbiased, quantitative proteomics to identify changes in the phosphoproteome of Shank3-deficient neurons. Down-regulation of protein kinase B (PKB/Akt)-mammalian target of rapamycin complex 1 (mTORC1) signaling resulted from enhanced phosphorylation and activation of serine/threonine protein phosphatase 2A (PP2A) regulatory subunit, B56β, due to increased steady-state levels of its kinase, Cdc2-like kinase 2 (CLK2). Pharmacological and genetic activation of Akt or inhibition of CLK2 relieved synaptic deficits in Shank3-deficient and PMDS patient-derived neurons. CLK2 inhibition also restored normal sociability in a Shank3-deficient mouse model. Our study thereby provides a novel mechanistic and potentially therapeutic understanding of deregulated signaling downstream of Shank3 deficiency.
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Affiliation(s)
- Michael Bidinosti
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Paolo Botta
- Friedrich Miescher Institute, Basel, Switzerland
| | | | - Catia C Proenca
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Natacha Stoehr
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Mario Bernhard
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Isabelle Fruh
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Matthias Mueller
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Debora Bonenfant
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Hans Voshol
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Walter Carbone
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sarah J Neal
- Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, USA
| | | | - Guglielmo Roma
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Jeffrey A Porter
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Pico Caroni
- Friedrich Miescher Institute, Basel, Switzerland
| | - Tewis Bouwmeester
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Ivan Galimberti
- Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland.
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21
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Agarinis C, Orsini V, Megel P, Abraham Y, Yang H, Mickanin C, Myer V, Bouwmeester T, Tchorz JS, Parker CN. Activation of Yap-Directed Transcription by Knockdown of Conserved Cellular Functions. ACTA ACUST UNITED AC 2015; 21:269-76. [PMID: 26637552 DOI: 10.1177/1087057115617906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 07/14/2015] [Accepted: 10/26/2015] [Indexed: 10/22/2022]
Abstract
The Yap-Hippo pathway has a significant role in regulating cell proliferation and growth, thus controlling organ size and regeneration. The Hippo pathway regulates two highly conserved, transcription coactivators, YAP and TAZ. The upstream regulators of the Yap-Hippo pathway have not been fully characterized. The aim of this study was to use a siRNA screen, in a liver biliary cell line, to identify regulators of the Yap-Hippo pathway that allow activation of the YAP transcription coactivator at high cell density. Activation of the YAP transcription coactivator was monitored using a high-content, image-based assay that measured the intracellular localization of native YAP protein. Active siRNAs were identified and further validated by quantification of CYR61 mRNA levels (a known YAP target gene). The effect of compounds targeting the putative gene targets identified as hits was also used for further validation. A number of validated hits reveal basic aspects of Yap-Hippo biology, such as components of the nuclear pore, by which YAP cytoplasmic-nuclear shuttling occurs, or how proteasomal degradation regulates intracellular YAP concentrations, which then alter YAP localization and transcription. Such results highlight how targeting conserved cellular functions can lead to validated activity in phenotypic assays.
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Affiliation(s)
- C Agarinis
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - V Orsini
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - P Megel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Y Abraham
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - H Yang
- Novartis Institutes for Biomedical Research, Novartis, Cambridge, MA, USA
| | - C Mickanin
- Novartis Institutes for Biomedical Research, Novartis, Cambridge, MA, USA
| | - V Myer
- Novartis Institutes for Biomedical Research, Novartis, Cambridge, MA, USA
| | - T Bouwmeester
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - J S Tchorz
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - C N Parker
- Novartis Institutes for Biomedical Research, Basel, Switzerland
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22
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Marti P, Stein C, Blumer T, Abraham Y, Dill MT, Pikiolek M, Orsini V, Jurisic G, Megel P, Makowska Z, Agarinis C, Tornillo L, Bouwmeester T, Ruffner H, Bauer A, Parker CN, Schmelzle T, Terracciano LM, Heim MH, Tchorz JS. YAP promotes proliferation, chemoresistance, and angiogenesis in human cholangiocarcinoma through TEAD transcription factors. Hepatology 2015; 62:1497-510. [PMID: 26173433 DOI: 10.1002/hep.27992] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 07/13/2015] [Indexed: 12/13/2022]
Abstract
UNLABELLED The Yes-associated protein (YAP)/Hippo pathway has been implicated in tissue development, regeneration, and tumorigenesis. However, its role in cholangiocarcinoma (CC) is not established. We show that YAP activation is a common feature in CC patient biopsies and human CC cell lines. Using microarray expression profiling of CC cells with overexpressed or down-regulated YAP, we show that YAP regulates genes involved in proliferation, apoptosis, and angiogenesis. YAP activity promotes CC growth in vitro and in vivo by functionally interacting with TEAD transcription factors (TEADs). YAP activity together with TEADs prevents apoptosis induced by cytotoxic drugs, whereas YAP knockdown sensitizes CC cells to drug-induced apoptosis. We further show that the proangiogenic microfibrillar-associated protein 5 (MFAP5) is a direct transcriptional target of YAP/TEAD in CC cells and that secreted MFAP5 promotes tube formation of human microvascular endothelial cells. High YAP activity in human CC xenografts and clinical samples correlates with increased MFAP5 expression and CD31(+) vasculature. CONCLUSIONS These findings establish YAP as a key regulator of proliferation and antiapoptotic mechanisms in CC and provide first evidence that YAP promotes angiogenesis by regulating the expression of secreted proangiogenic proteins.
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Affiliation(s)
- Patricia Marti
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Claudia Stein
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Tanja Blumer
- Division of Gastroenterology and Hepatology, University Hospital Basel, Basel, Switzerland
| | - Yann Abraham
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Michael T Dill
- Division of Gastroenterology and Hepatology, University Hospital Basel, Basel, Switzerland
| | - Monika Pikiolek
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Giorgia Jurisic
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Philippe Megel
- Novartis Institutes for Biomedical Research, Oncology, Novartis Pharma AG, Basel, Switzerland
| | - Zuzanna Makowska
- Division of Gastroenterology and Hepatology, University Hospital Basel, Basel, Switzerland
| | - Claudia Agarinis
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Luigi Tornillo
- Institute for Pathology, University Hospital Basel, Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Heinz Ruffner
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Andreas Bauer
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Christian N Parker
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
| | - Tobias Schmelzle
- Novartis Institutes for Biomedical Research, Oncology, Novartis Pharma AG, Basel, Switzerland
| | | | - Markus H Heim
- Division of Gastroenterology and Hepatology, University Hospital Basel, Basel, Switzerland
| | - Jan S Tchorz
- Novartis Institutes for Biomedical Research, Developmental and Molecular Pathways, Novartis Pharma AG, Basel, Switzerland
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Bizet AA, Becker-Heck A, Ryan R, Weber K, Filhol E, Krug P, Halbritter J, Delous M, Lasbennes MC, Linghu B, Oakeley EJ, Zarhrate M, Nitschké P, Garfa-Traore M, Serluca F, Yang F, Bouwmeester T, Pinson L, Cassuto E, Dubot P, Elshakhs NAS, Sahel JA, Salomon R, Drummond IA, Gubler MC, Antignac C, Chibout S, Szustakowski JD, Hildebrandt F, Lorentzen E, Sailer AW, Benmerah A, Saint-Mezard P, Saunier S. Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization. Nat Commun 2015; 6:8666. [PMID: 26487268 PMCID: PMC4617596 DOI: 10.1038/ncomms9666] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [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: 02/27/2015] [Accepted: 09/17/2015] [Indexed: 01/20/2023] Open
Abstract
Ciliopathies are a large group of clinically and genetically heterogeneous disorders caused by defects in primary cilia. Here we identified mutations in TRAF3IP1 (TNF Receptor-Associated Factor Interacting Protein 1) in eight patients from five families with nephronophthisis (NPH) and retinal degeneration, two of the most common manifestations of ciliopathies. TRAF3IP1 encodes IFT54, a subunit of the IFT-B complex required for ciliogenesis. The identified mutations result in mild ciliary defects in patients but also reveal an unexpected role of IFT54 as a negative regulator of microtubule stability via MAP4 (microtubule-associated protein 4). Microtubule defects are associated with altered epithelialization/polarity in renal cells and with pronephric cysts and microphthalmia in zebrafish embryos. Our findings highlight the regulation of cytoplasmic microtubule dynamics as a role of the IFT54 protein beyond the cilium, contributing to the development of NPH-related ciliopathies.
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Affiliation(s)
- Albane A. Bizet
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Anita Becker-Heck
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Rebecca Ryan
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Kristina Weber
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Emilie Filhol
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Pauline Krug
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Jan Halbritter
- Division of Nephrology, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Nephrology, Department of Internal Medicine, University Clinic Leipzig, 04103 Leipzig, Germany
| | - Marion Delous
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | | | - Bolan Linghu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Edward J. Oakeley
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Mohammed Zarhrate
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
- Inserm UMR-1163, Genomic Core Facility, 75015 Paris, France
| | - Patrick Nitschké
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Bioinformatics Core Facility, 75015 Paris, France
| | - Meriem Garfa-Traore
- Cell Imaging Platform, INSERM US24 Structure Fédérative de recherche Necker, Paris Descartes Sorbonne Paris Cité University, 75015 Paris, France
| | - Fabrizio Serluca
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Fan Yang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Tewis Bouwmeester
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Lucile Pinson
- Department of Medical Genetic, Arnaud de Villeneuve University Health Center, 34090 Montpellier, France
| | - Elisabeth Cassuto
- Nephrology department, L'Archet II Hospital, Nice University Health Center, 06202 Nice, France
| | - Philippe Dubot
- Hemodialysis-Nephrology Department, William Morey Hospital, 71321 Chalon-sur-Saône, France
| | - Neveen A. Soliman Elshakhs
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Cairo University, Egyptian Group for Orphan Renal Diseases, 11956 Cairo, Egypt
| | - José A. Sahel
- INSERM U968, CNRS UMR 7210; Sorbonne Universités, Université Pierre et Marie Curie, UMR S968, Institut de la vision, 75012 Paris, France
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM, Direction de l'Hospitalisation et de l'Organisation des Soins, Centre d'Investigation Clinique 1423, 75012 Paris, France
| | - Rémi Salomon
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
- Assistance Publique—Hôpitaux de Paris, Pediatric Nephrologic department, Necker-Enfants Malades Hospital, 75015 Paris, France
| | - Iain A. Drummond
- Nephrology Division, Massachusetts General Hospital, Charlestown, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Marie-Claire Gubler
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Corinne Antignac
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Genetics, Necker-Enfants Malades Hospital, 75015 Paris, France
| | - Salahdine Chibout
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | | | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Andreas W. Sailer
- Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Alexandre Benmerah
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | | | - Sophie Saunier
- Inserm UMR-1163, Laboratory of Hereditary Kidney Diseases, 75015 Paris, France
- Paris Descartes Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
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Stein C, Bardet AF, Roma G, Bergling S, Clay I, Ruchti A, Agarinis C, Schmelzle T, Bouwmeester T, Schübeler D, Bauer A. YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers. PLoS Genet 2015; 11:e1005465. [PMID: 26295846 PMCID: PMC4546604 DOI: 10.1371/journal.pgen.1005465] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [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: 04/10/2015] [Accepted: 07/23/2015] [Indexed: 12/30/2022] Open
Abstract
YAP1 is a major effector of the Hippo pathway and a well-established oncogene. Elevated YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is observed in several types of human cancers. Here we investigated its genomic binding landscape in YAP1-activated cancer cells, as well as in non-transformed cells. We demonstrate that TEAD transcription factors mediate YAP1 chromatin-binding genome-wide, further explaining their dominant role as primary mediators of YAP1-transcriptional activity. Moreover, we show that YAP1 largely exerts its transcriptional control via distal enhancers that are marked by H3K27 acetylation and that YAP1 is necessary for this chromatin mark at bound enhancers and the activity of the associated genes. This work establishes YAP1-mediated transcriptional regulation at distal enhancers and provides an expanded set of target genes resulting in a fundamental source to study YAP1 function in a normal and cancer setting. The YAP1/Hippo signaling pathway is a key regulator of organ size and tissue homeostasis, and its dysregulation is linked to cancer development. Elevated activity of YAP1, a transcriptional coactivator and well-established oncogene has been reported to occur in human cancers. Comprehensive identification of YAP1 regulated genes and its mode of action will be of high importance to uncover YAP1 biology that could be exploited for a therapeutic intervention. To this end, we performed genome-wide analyses to identify YAP1 occupied sites in cancer cell lines representing different YAP1/Hippo pathway tumor etiologies and in non-transformed fibroblasts. Our data demonstrate that YAP1 activity is mediated predominantly via TEAD transcription factors supporting the importance of TEADs as main mediators of YAP1-coactivator activity. We further show that YAP1 and TEAD1 exert their transcriptional control via binding to enhancers, leading to characteristic chromatin changes and distal activation of genes. By linking enhancers to genes, we provide a list of novel YAP1 target genes in an oncogenic setting that we show can readily be exploited in tumor classification and provides a foundation for further investigations.
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Affiliation(s)
- Claudia Stein
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Anaïs Flore Bardet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sebastian Bergling
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Ieuan Clay
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Alexandra Ruchti
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Claudia Agarinis
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tobias Schmelzle
- Oncology, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Faculty of Sciences, Basel, Switzerland
- * E-mail: (DS); (AB)
| | - Andreas Bauer
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
- * E-mail: (DS); (AB)
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25
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Becker-Heck A, Bizet A, Ryan R, Krug P, Filhol E, Linghu B, Oakeley E, Serluca F, Legendre F, Dörner N, Lasbennes MC, Duca J, Yang F, Damask A, Klickstein L, Labow M, Schebesta M, Bouwmeester T, Valette H, Pinson L, Goubaux B, Dubot P, Salomon R, Antignac C, Gubler M, Jeanpierre C, Chibout S, Bole-Feysot C, Nitschké P, Benmerah A, Szustakowski JD, Sailer AW, Saunier S, Saint-Mezard P. Identification of human mutations in TRAF3IP1 in patients with nephronophthisis and retinal degeneration. Cilia 2015. [PMCID: PMC4519160 DOI: 10.1186/2046-2530-4-s1-p52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Kaufmann M, Schuffenhauer A, Fruh I, Klein J, Thiemeyer A, Rigo P, Gomez-Mancilla B, Heidinger-Millot V, Bouwmeester T, Schopfer U, Mueller M, Fodor BD, Cobos-Correa A. High-Throughput Screening Using iPSC-Derived Neuronal Progenitors to Identify Compounds Counteracting Epigenetic Gene Silencing in Fragile X Syndrome. ACTA ACUST UNITED AC 2015; 20:1101-11. [PMID: 26024946 DOI: 10.1177/1087057115588287] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [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: 01/27/2015] [Accepted: 04/15/2015] [Indexed: 12/21/2022]
Abstract
Fragile X syndrome (FXS) is the most common form of inherited mental retardation, and it is caused in most of cases by epigenetic silencing of the Fmr1 gene. Today, no specific therapy exists for FXS, and current treatments are only directed to improve behavioral symptoms. Neuronal progenitors derived from FXS patient induced pluripotent stem cells (iPSCs) represent a unique model to study the disease and develop assays for large-scale drug discovery screens since they conserve the Fmr1 gene silenced within the disease context. We have established a high-content imaging assay to run a large-scale phenotypic screen aimed to identify compounds that reactivate the silenced Fmr1 gene. A set of 50,000 compounds was tested, including modulators of several epigenetic targets. We describe an integrated drug discovery model comprising iPSC generation, culture scale-up, and quality control and screening with a very sensitive high-content imaging assay assisted by single-cell image analysis and multiparametric data analysis based on machine learning algorithms. The screening identified several compounds that induced a weak expression of fragile X mental retardation protein (FMRP) and thus sets the basis for further large-scale screens to find candidate drugs or targets tackling the underlying mechanism of FXS with potential for therapeutic intervention.
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Affiliation(s)
- Markus Kaufmann
- Center of Proteomic Chemistry, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Ansgar Schuffenhauer
- Center of Proteomic Chemistry, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Isabelle Fruh
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Jessica Klein
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Anke Thiemeyer
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Pierre Rigo
- Center of Proteomic Chemistry, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Baltazar Gomez-Mancilla
- Translational Medicine, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Valerie Heidinger-Millot
- Center of Proteomic Chemistry, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Tewis Bouwmeester
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Ulrich Schopfer
- Center of Proteomic Chemistry, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Matthias Mueller
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Barna D Fodor
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
| | - Amanda Cobos-Correa
- Center of Proteomic Chemistry, Novartis Institutes for Biomedical Research, Novartis Campus, Basel, Switzerland
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27
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Krumova P, Reyniers L, Meyer M, Lobbestael E, Stauffer D, Gerrits B, Muller L, Hoving S, Kaupmann K, Voshol J, Fabbro D, Bauer A, Rovelli G, Taymans JM, Bouwmeester T, Baekelandt V. Chemical genetic approach identifies microtubule affinity-regulating kinase 1 as a leucine-rich repeat kinase 2 substrate. FASEB J 2015; 29:2980-92. [PMID: 25854701 DOI: 10.1096/fj.14-262329] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 08/18/2014] [Accepted: 03/09/2015] [Indexed: 12/25/2022]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of autosomal-dominant forms of Parkinson's disease. LRRK2 is a modular, multidomain protein containing 2 enzymatic domains, including a kinase domain, as well as several protein-protein interaction domains, pointing to a role in cellular signaling. Although enormous efforts have been made, the exact pathophysiologic mechanisms of LRRK2 are still not completely known. In this study, we used a chemical genetics approach to identify LRRK2 substrates from mouse brain. This approach allows the identification of substrates of 1 particular kinase in a complex cellular environment. Several of the identified peptides are involved in the regulation of microtubule (MT) dynamics, including microtubule-associating protein (MAP)/microtubule affinity-regulating kinase 1 (MARK1). MARK1 is a serine/threonine kinase known to phosphorylate MT-binding proteins such as Tau, MAP2, and MAP4 at KXGS motifs leading to MT destabilization. In vitro kinase assays and metabolic-labeling experiments in living cells confirmed MARK1 as an LRRK2 substrate. Moreover, we also showed that LRRK2 and MARK1 are interacting in eukaryotic cells. Our findings contribute to the identification of physiologic LRRK2 substrates and point to a potential mechanism explaining the reported effects of LRRK2 on neurite morphology.
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Affiliation(s)
- Petranka Krumova
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Lauran Reyniers
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Marc Meyer
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Evy Lobbestael
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Daniela Stauffer
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Bertran Gerrits
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Lionel Muller
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Sjouke Hoving
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Klemens Kaupmann
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Johannes Voshol
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Doriano Fabbro
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Andreas Bauer
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Giorgio Rovelli
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Jean-Marc Taymans
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Tewis Bouwmeester
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Veerle Baekelandt
- *Novartis Institutes for Biomedical Research, Basel, Switzerland; and Department of Neurosciences, Research Group for Neurobiology and Gene Therapy, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
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28
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Cai X, Xu Y, Cheung AK, Tomlinson RC, Alcázar-Román A, Murphy L, Billich A, Zhang B, Feng Y, Klumpp M, Rondeau JM, Fazal AN, Wilson CJ, Myer V, Joberty G, Bouwmeester T, Labow MA, Finan PM, Porter JA, Ploegh HL, Baird D, De Camilli P, Tallarico JA, Huang Q. PIKfyve, a class III PI kinase, is the target of the small molecular IL-12/IL-23 inhibitor apilimod and a player in Toll-like receptor signaling. ACTA ACUST UNITED AC 2014; 20:912-21. [PMID: 23890009 DOI: 10.1016/j.chembiol.2013.05.010] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/16/2013] [Accepted: 05/29/2013] [Indexed: 12/15/2022]
Abstract
Toll-like receptor (TLR) signaling is a key component of innate immunity. Aberrant TLR activation leads to immune disorders via dysregulation of cytokine production, such as IL-12/IL-23. Herein, we identify and characterize PIKfyve, a lipid kinase, as a critical player in TLR signaling using apilimod as an affinity tool. Apilimod is a potent small molecular inhibitor of IL-12/IL-23 with an unknown target and has been evaluated in clinical trials for patients with Crohn's disease or rheumatoid arthritis. Using a chemical genetic approach, we show that it binds to PIKfyve and blocks its phosphotransferase activity, leading to selective inhibition of IL-12/IL-23p40. Pharmacological or genetic inactivation of PIKfyve is necessary and sufficient for suppression of IL-12/IL-23p40 expression. Thus, we have uncovered a phosphoinositide-mediated regulatory mechanism that controls TLR signaling.
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Affiliation(s)
- Xinming Cai
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
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29
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Kinzel B, Pikiolek M, Orsini V, Sprunger J, Isken A, Zietzling S, Desplanches M, Dubost V, Breustedt D, Valdez R, Liu D, Theil D, Müller M, Dietrich B, Bouwmeester T, Ruffner H, Tchorz JS. Functional roles of Lgr4 and Lgr5 in embryonic gut, kidney and skin development in mice. Dev Biol 2014; 390:181-90. [PMID: 24680895 DOI: 10.1016/j.ydbio.2014.03.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 03/03/2014] [Accepted: 03/18/2014] [Indexed: 10/25/2022]
Abstract
Lgr4 and Lgr5 are known markers of adult and embryonic tissue stem cells in various organs. However, whether Lgr4 and Lgr5 are important for embryonic development remains unclear. To study their functions during intestinal crypt, skin and kidney development we now generated mice lacking either Lgr4 (Lgr4KO), Lgr5 (Lgr5KO) or both receptors (Lgr4/5dKO). E16.5 Lgr4KO mice displayed complete loss of Lgr5+/Olfm4+intestinal stem cells, compromised Wnt signaling and impaired proliferation and differentiation of gut epithelium. Similarly, E16.5 Lgr4KO mice showed reduced basal cell proliferation and hair follicle numbers in the developing skin, as well as dilated kidney tubules and ectatic Bowman׳s spaces. Although Lgr4KO and Lgr5KO mice both died perinatally, Lgr5 deletion did not compromise embryonic development of gut, kidney or skin. Concomitant deletion of Lgr4 and Lgr5 did not prevent perinatal lethality, in contrast to a previous report that suggested rescue of Lgr5 KO perinatal lethality by a hypomorphic Lgr4 mutant. While the double deletion did not further promote the phenotypes observed in Lgr4KO intestines, impaired kidney cell proliferation, reduced epidermal thickness, loss of Lgr5+follicular epithelium and impaired hair follicle development were only observed in Lgr4/5dKO mice. This supports complementary functions of both receptors. Our findings clearly establish the importance of Lgr4 and Lgr5 during embryonic gut, skin and kidney development, with a dominant role of Lgr4.
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Affiliation(s)
- Bernd Kinzel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Monika Pikiolek
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Joëlle Sprunger
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Andrea Isken
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Svenja Zietzling
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Magali Desplanches
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Valerie Dubost
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Daniel Breustedt
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Reginald Valdez
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Dong Liu
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Diethilde Theil
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Matthias Müller
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Bill Dietrich
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Heinz Ruffner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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30
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Ruffner H, Jaffe A, Wiellette E, Mueller M, Parker C, Bouwmeester T. The use of stem cells in discovery and toxicology. Toxicol Lett 2013. [DOI: 10.1016/j.toxlet.2013.06.032] [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: 10/26/2022]
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31
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Proenca CC, Stoehr N, Bernhard M, Seger S, Genoud C, Roscic A, Paganetti P, Liu S, Murphy LO, Kuhn R, Bouwmeester T, Galimberti I. Atg4b-dependent autophagic flux alleviates Huntington's disease progression. PLoS One 2013; 8:e68357. [PMID: 23861892 PMCID: PMC3704647 DOI: 10.1371/journal.pone.0068357] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/29/2013] [Indexed: 01/24/2023] Open
Abstract
The accumulation of aggregated mutant huntingtin (mHtt) inclusion bodies is involved in Huntigton’s disease (HD) progression. Medium sized-spiny neurons (MSNs) in the corpus striatum are highly vulnerable to mHtt aggregate accumulation and degeneration, but the mechanisms and pathways involved remain elusive. Here we have developed a new model to study MSNs degeneration in the context of HD. We produced organotypic cortico-striatal slice cultures (CStS) from HD transgenic mice mimicking specific features of HD progression. We then show that induction of autophagy using catalytic inhibitors of mTOR prevents MSNs degeneration in HD CStS. Furthermore, disrupting autophagic flux by overexpressing Atg4b in neurons and slice cultures, accelerated mHtt aggregation and neuronal death, suggesting that Atg4b-dependent autophagic flux influences HD progression. Under these circumstances induction of autophagy using catalytic inhibitors of mTOR was inefficient and did not affect mHtt aggregate accumulation and toxicity, indicating that mTOR inhibition alleviates HD progression by inducing Atg4b-dependent autophagic flux. These results establish modulators of Atg4b-dependent autophagic flux as new potential targets in the treatment of HD.
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Affiliation(s)
- Catia C. Proenca
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Natacha Stoehr
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Mario Bernhard
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | | | | | | | - Shanming Liu
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Leon O. Murphy
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Tewis Bouwmeester
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ivan Galimberti
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail:
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32
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Brauchle M, Yao Z, Arora R, Thigale S, Clay I, Inverardi B, Fletcher J, Taslimi P, Acker MG, Gerrits B, Voshol J, Bauer A, Schübeler D, Bouwmeester T, Ruffner H. Protein complex interactor analysis and differential activity of KDM3 subfamily members towards H3K9 methylation. PLoS One 2013; 8:e60549. [PMID: 23593242 PMCID: PMC3623819 DOI: 10.1371/journal.pone.0060549] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [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: 10/23/2012] [Accepted: 02/26/2013] [Indexed: 11/19/2022] Open
Abstract
Histone modifications play an important role in chromatin organization and gene regulation, and their interpretation is referred to as epigenetic control. The methylation levels of several lysine residues in histone tails are tightly controlled, and JmjC domain-containing proteins are one class of broadly expressed enzymes catalyzing methyl group removal. However, several JmjC proteins remain uncharacterized, gaps persist in understanding substrate recognition, and the integration of JmjC proteins into signaling pathways is just emerging. The KDM3 subfamily is an evolutionarily conserved group of histone demethylase proteins, thought to share lysine substrate specificity. Here we use a systematic approach to compare KDM3 subfamily members. We show that full-length KDM3A and KDM3B are H3K9me1/2 histone demethylases whereas we fail to observe histone demethylase activity for JMJD1C using immunocytochemical and biochemical approaches. Structure-function analyses revealed the importance of a single amino acid in KDM3A implicated in the catalytic activity towards H3K9me1/2 that is not conserved in JMJD1C. Moreover, we use quantitative proteomic analyses to identify subsets of the interactomes of the 3 proteins. Specific interactor candidates were identified for each of the three KDM3 subfamily members. Importantly, we find that SCAI, a known transcriptional repressor, interacts specifically with KDM3B. Taken together, we identify substantial differences in the biology of KDM3 histone demethylases, namely enzymatic activity and protein-protein interactions. Such comparative approaches pave the way to a better understanding of histone demethylase specificity and protein function at a systems level and are instrumental in identifying the more subtle differences between closely related proteins.
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Affiliation(s)
- Michael Brauchle
- Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail: (MB); (HR)
| | - Zhiping Yao
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Rishi Arora
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Sachin Thigale
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Ieuan Clay
- Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Bruno Inverardi
- Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Joy Fletcher
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Paul Taslimi
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Michael G. Acker
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Bertran Gerrits
- Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Johannes Voshol
- Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Andreas Bauer
- Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Tewis Bouwmeester
- Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Heinz Ruffner
- Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail: (MB); (HR)
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33
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Ruffner H, Sprunger J, Charlat O, Leighton-Davies J, Grosshans B, Salathe A, Zietzling S, Beck V, Therier M, Isken A, Xie Y, Zhang Y, Hao H, Shi X, Liu D, Song Q, Clay I, Hintzen G, Tchorz J, Bouchez LC, Michaud G, Finan P, Myer VE, Bouwmeester T, Porter J, Hild M, Bassilana F, Parker CN, Cong F. R-Spondin potentiates Wnt/β-catenin signaling through orphan receptors LGR4 and LGR5. PLoS One 2012; 7:e40976. [PMID: 22815884 PMCID: PMC3397969 DOI: 10.1371/journal.pone.0040976] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 06/18/2012] [Indexed: 01/10/2023] Open
Abstract
The Wnt/β-catenin signaling pathbway controls many important biological processes. R-Spondin (RSPO) proteins are a family of secreted molecules that strongly potentiate Wnt/β-catenin signaling, however, the molecular mechanism of RSPO action is not yet fully understood. We performed an unbiased siRNA screen to identify molecules specifically required for RSPO, but not Wnt, induced β-catenin signaling. From this screen, we identified LGR4, then an orphan G protein-coupled receptor (GPCR), as the cognate receptor of RSPO. Depletion of LGR4 completely abolished RSPO-induced β-catenin signaling. The loss of LGR4 could be compensated by overexpression of LGR5, suggesting that LGR4 and LGR5 are functional homologs. We further demonstrated that RSPO binds to the extracellular domain of LGR4 and LGR5, and that overexpression of LGR4 strongly sensitizes cells to RSPO-activated β-catenin signaling. Supporting the physiological significance of RSPO-LGR4 interaction, Lgr4−/− crypt cultures failed to grow in RSPO-containing intestinal crypt culture medium. No coupling between LGR4 and heterotrimeric G proteins could be detected in RSPO-treated cells, suggesting that LGR4 mediates RSPO signaling through a novel mechanism. Identification of LGR4 and its relative LGR5, an adult stem cell marker, as the receptors of RSPO will facilitate the further characterization of these receptor/ligand pairs in regenerative medicine applications.
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Affiliation(s)
- Heinz Ruffner
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
- * E-mail: (HR); (FC)
| | - Joëlle Sprunger
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Olga Charlat
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Juliet Leighton-Davies
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Bianka Grosshans
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Adrian Salathe
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Svenja Zietzling
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Valérie Beck
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Maxime Therier
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Andrea Isken
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Yang Xie
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Yue Zhang
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Huaixiang Hao
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Xiaoying Shi
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Dong Liu
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Qinhui Song
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Ieuan Clay
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Gabriele Hintzen
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Jan Tchorz
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Laure C. Bouchez
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Gregory Michaud
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Peter Finan
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Vic E. Myer
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Tewis Bouwmeester
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Jeff Porter
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Marc Hild
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Fred Bassilana
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Christian N. Parker
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland
| | - Feng Cong
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
- * E-mail: (HR); (FC)
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34
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Bonavia A, Franti M, Pusateri Keaney E, Kuhen K, Seepersaud M, Radetich B, Shao J, Honda A, Dewhurst J, Balabanis K, Monroe J, Wolff K, Osborne C, Lanieri L, Hoffmaster K, Amin J, Markovits J, Broome M, Skuba E, Cornella-Taracido I, Joberty G, Bouwmeester T, Hamann L, Tallarico JA, Tommasi R, Compton T, Bushell SM. Identification of broad-spectrum antiviral compounds and assessment of the druggability of their target for efficacy against respiratory syncytial virus (RSV). Proc Natl Acad Sci U S A 2011; 108:6739-44. [PMID: 21502533 PMCID: PMC3084118 DOI: 10.1073/pnas.1017142108] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The search for novel therapeutic interventions for viral disease is a challenging pursuit, hallmarked by the paucity of antiviral agents currently prescribed. Targeting of viral proteins has the inextricable challenge of rise of resistance. Safe and effective vaccines are not possible for many viral pathogens. New approaches are required to address the unmet medical need in this area. We undertook a cell-based high-throughput screen to identify leads for development of drugs to treat respiratory syncytial virus (RSV), a serious pediatric pathogen. We identified compounds that are potent (nanomolar) inhibitors of RSV in vitro in HEp-2 cells and in primary human bronchial epithelial cells and were shown to act postentry. Interestingly, two scaffolds exhibited broad-spectrum activity among multiple RNA viruses. Using the chemical matter as a probe, we identified the targets and identified a common cellular pathway: the de novo pyrimidine biosynthesis pathway. Both targets were validated in vitro and showed no significant cell cytotoxicity except for activity against proliferative B- and T-type lymphoid cells. Corollary to this finding was to understand the consequences of inhibition of the target to the host. An in vivo assessment for antiviral efficacy failed to demonstrate reduced viral load, but revealed microscopic changes and a trend toward reduced pyrimidine pools and findings in histopathology. We present here a discovery program that includes screen, target identification, validation, and druggability that can be broadly applied to identify and interrogate other host factors for antiviral effect starting from chemical matter of unknown target/mechanism of action.
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Affiliation(s)
- Aurelio Bonavia
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Michael Franti
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Erin Pusateri Keaney
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Kelli Kuhen
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Mohindra Seepersaud
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Branko Radetich
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Jian Shao
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Ayako Honda
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Janetta Dewhurst
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Kara Balabanis
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - James Monroe
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Karen Wolff
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Colin Osborne
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Leanne Lanieri
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Keith Hoffmaster
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Jakal Amin
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Judit Markovits
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Michelle Broome
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Elizabeth Skuba
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Ivan Cornella-Taracido
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Gerard Joberty
- Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tewis Bouwmeester
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Lawrence Hamann
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - John A. Tallarico
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Ruben Tommasi
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Teresa Compton
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
| | - Simon M. Bushell
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139; and
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35
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Leupin O, Piters E, Halleux C, Hu S, Kramer I, Morvan F, Bouwmeester T, Schirle M, Bueno-Lozano M, Fuentes FJR, Itin PH, Boudin E, de Freitas F, Jennes K, Brannetti B, Charara N, Ebersbach H, Geisse S, Lu CX, Bauer A, Van Hul W, Kneissel M. Bone overgrowth-associated mutations in the LRP4 gene impair sclerostin facilitator function. J Biol Chem 2011; 286:19489-500. [PMID: 21471202 DOI: 10.1074/jbc.m110.190330] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Humans lacking sclerostin display progressive bone overgrowth due to increased bone formation. Although it is well established that sclerostin is an osteocyte-secreted bone formation inhibitor, the underlying molecular mechanisms are not fully elucidated. We identified in tandem affinity purification proteomics screens LRP4 (low density lipoprotein-related protein 4) as a sclerostin interaction partner. Biochemical assays with recombinant proteins confirmed that sclerostin LRP4 interaction is direct. Interestingly, in vitro overexpression and RNAi-mediated knockdown experiments revealed that LRP4 specifically facilitates the previously described inhibitory action of sclerostin on Wnt1/β-catenin signaling. We found the extracellular β-propeller structured domain of LRP4 to be required for this sclerostin facilitator activity. Immunohistochemistry demonstrated that LRP4 protein is present in human and rodent osteoblasts and osteocytes, both presumed target cells of sclerostin action. Silencing of LRP4 by lentivirus-mediated shRNA delivery blocked sclerostin inhibitory action on in vitro bone mineralization. Notably, we identified two mutations in LRP4 (R1170W and W1186S) in patients suffering from bone overgrowth. We found that these mutations impair LRP4 interaction with sclerostin and its concomitant sclerostin facilitator effect. Together these data indicate that the interaction of sclerostin with LRP4 is required to mediate the inhibitory function of sclerostin on bone formation, thus identifying a novel role for LRP4 in bone.
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Affiliation(s)
- Olivier Leupin
- Musculoskeletal Disease Area, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
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36
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Jagani Z, Mora-Blanco EL, Sansam CG, McKenna ES, Wilson B, Chen D, Klekota J, Tamayo P, Nguyen PTL, Tolstorukov M, Park PJ, Cho YJ, Hsiao K, Buonamici S, Pomeroy SL, Mesirov JP, Ruffner H, Bouwmeester T, Luchansky SJ, Murtie J, Kelleher JF, Warmuth M, Sellers WR, Roberts CWM, Dorsch M. Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat Med 2010; 16:1429-33. [PMID: 21076395 DOI: 10.1038/nm.2251] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 09/30/2010] [Indexed: 01/18/2023]
Abstract
Aberrant activation of the Hedgehog (Hh) pathway can drive tumorigenesis. To investigate the mechanism by which glioma-associated oncogene family zinc finger-1 (GLI1), a crucial effector of Hh signaling, regulates Hh pathway activation, we searched for GLI1-interacting proteins. We report that the chromatin remodeling protein SNF5 (encoded by SMARCB1, hereafter called SNF5), which is inactivated in human malignant rhabdoid tumors (MRTs), interacts with GLI1. We show that Snf5 localizes to Gli1-regulated promoters and that loss of Snf5 leads to activation of the Hh-Gli pathway. Conversely, re-expression of SNF5 in MRT cells represses GLI1. Consistent with this, we show the presence of a Hh-Gli-activated gene expression profile in primary MRTs and show that GLI1 drives the growth of SNF5-deficient MRT cells in vitro and in vivo. Therefore, our studies reveal that SNF5 is a key mediator of Hh signaling and that aberrant activation of GLI1 is a previously undescribed targetable mechanism contributing to the growth of MRT cells.
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Affiliation(s)
- Zainab Jagani
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
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37
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Korthäuer U, Bouwmeester T, Weber L. We want to unleash more synergy and creativity. Chimia (Aarau) 2010; 64:758-762. [PMID: 21138167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
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38
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Gaither LA, Borawski J, Anderson LJ, Balabanis KA, Devay P, Joberty G, Rau C, Schirle M, Bouwmeester T, Mickanin C, Zhao S, Vickers C, Lee L, Deng G, Baryza J, Fujimoto RA, Lin K, Compton T, Wiedmann B. Multiple cyclophilins involved in different cellular pathways mediate HCV replication. Virology 2009; 397:43-55. [PMID: 19932913 DOI: 10.1016/j.virol.2009.10.043] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 08/25/2009] [Accepted: 10/28/2009] [Indexed: 02/08/2023]
Abstract
Three cyclophilin inhibitors (DEBIO-025, SCY635, and NIM811) are currently in clinical trials for hepatitis C therapy. The mechanism of action of these, however, is not completely understood. There are at least 16 cyclophilins expressed in human cells which are involved in a diverse set of cellular processes. Large-scale siRNA experiments, chemoproteomic assays with cyclophilin binding compounds, and mRNA profiling of HCV replicon containing cells were used to identify the cyclophilins that are instrumental to HCV replication. The previously reported cyclophilin A was confirmed and additional cyclophilin containing pathways were identified. Together, the experiments provide strong evidence that NIM811 reduces viral replication by inhibition of multiple cyclophilins and pathways with protein trafficking as the most strongly and persistently affected pathway.
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Affiliation(s)
- L Alex Gaither
- Novartis Institutes of Biomedical Research, Cambridge, MA 02139, USA
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39
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Marwick JA, Wallis G, Meja K, Kuster B, Bouwmeester T, Chakravarty P, Fletcher D, Whittaker PA, Barnes PJ, Ito K, Adcock IM, Kirkham PA. Oxidative stress modulates theophylline effects on steroid responsiveness. Biochem Biophys Res Commun 2008; 377:797-802. [PMID: 18951874 DOI: 10.1016/j.bbrc.2008.10.065] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 10/10/2008] [Indexed: 01/04/2023]
Abstract
Oxidative stress is a central factor in many chronic inflammatory diseases such as severe asthma and chronic obstructive pulmonary disease (COPD). Oxidative stress reduces the anti-inflammatory corticosteroid action and may therefore contribute to the relative corticosteroid insensitivity seen in these diseases. Low concentrations of theophylline can restore the anti-inflammatory action of corticosteroids in oxidant exposed cells, however the mechanism remains unknown. Here, we demonstrate that a low concentration of theophylline restores corticosteroid repression of pro-inflammatory mediator release and histone acetylation in oxidant exposed cells. Global gene expression analysis shows that theophylline regulates distinct pathways in naïve and oxidant exposed cells and reverses oxidant mediated modulated of pathways. Furthermore, quantitative chemoproteomics revealed that theophylline has few high affinity targets in naive cells but an elevated affinity in oxidant stressed cells. In conclusion, oxidative stress alters theophylline binding profile and gene expression which may result in restoration of corticosteroid function.
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Affiliation(s)
- John A Marwick
- National Heart & Lung Institute, Airways Disease Section, Imperial College London, Guy-Scadding Building, Dovehouse Steet, London SW3 6LY, UK.
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40
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Snow AJ, Puri P, Acker-Palmer A, Bouwmeester T, Vijayaraghavan S, Kline D. Phosphorylation-dependent interaction of tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein (YWHA) with PADI6 following oocyte maturation in mice. Biol Reprod 2008; 79:337-47. [PMID: 18463355 DOI: 10.1095/biolreprod.108.069328] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Proteins in the tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein family (YWHA; also known as 14-3-3) are involved in the regulation of many intracellular processes. We have examined the interaction of YWHA with peptidylarginine deiminase type VI (PADI6), an abundant protein in mammalian oocytes, eggs, and early embryos. Peptidylarginine deiminases catalyze the posttranslational modification of peptidylarginine to citrulline. PADI6 is associated with oocyte cytoplasmic sheets, and PADI6-deficient mice are infertile because of disruption of development beyond the two-cell stage. We found that PADI6 undergoes a dramatic developmental change in phosphorylation during oocyte maturation. This change in phosphorylation is linked to an interaction of PADI6 with YWHA in the mature egg. Recombinant glutathione S-transferase YWHA pull-down experiments and transgenic tandem affinity purification with liquid chromatography-mass spectrometry demonstrate a binding interaction between YWHA and PADI6 in mature eggs. YWHA proteins modulate or complement intracellular events involving phosphorylation-dependent switching or protein modification. These results indicate that phosphorylation and/or YWHA binding may serve as a means of intracellular PADI6 regulation.
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Affiliation(s)
- Alan J Snow
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242, USA
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41
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Abstract
Systematic genome-wide and pathway-specific protein-protein interaction screens have generated a putative, organizing framework of the spatial interconnectivity of a large number of human proteins, including numerous therapeutically relevant disease-associated proteins. The intrinsic value for drug discovery is that these physical protein-protein interaction networks may contribute to a mechanistic understanding of the pathophysiology of disease and can aid in the identification and prioritization of tractable targets and generate hypotheses on how to best drug non-tractable, disease-associated targets. Here, we review the 'therapeutic potential' of the 1st generation sub-genome-scale human interaction networks and disease-associated protein networks generated by yeast two-hybrid screens and affinity purification-mass spectrometry approaches.
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Affiliation(s)
- Heinz Ruffner
- Cellzome AG, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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42
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Bantscheff M, Eberhard D, Abraham Y, Bastuck S, Boesche M, Hobson S, Mathieson T, Perrin J, Raida M, Rau C, Reader V, Sweetman G, Bauer A, Bouwmeester T, Hopf C, Kruse U, Neubauer G, Ramsden N, Rick J, Kuster B, Drewes G. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol 2007; 25:1035-44. [PMID: 17721511 DOI: 10.1038/nbt1328] [Citation(s) in RCA: 815] [Impact Index Per Article: 47.9] [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: 04/05/2007] [Accepted: 07/16/2007] [Indexed: 11/08/2022]
Abstract
We describe a chemical proteomics approach to profile the interaction of small molecules with hundreds of endogenously expressed protein kinases and purine-binding proteins. This subproteome is captured by immobilized nonselective kinase inhibitors (kinobeads), and the bound proteins are quantified in parallel by mass spectrometry using isobaric tags for relative and absolute quantification (iTRAQ). By measuring the competition with the affinity matrix, we assess the binding of drugs to their targets in cell lysates and in cells. By mapping drug-induced changes in the phosphorylation state of the captured proteome, we also analyze signaling pathways downstream of target kinases. Quantitative profiling of the drugs imatinib (Gleevec), dasatinib (Sprycel) and bosutinib in K562 cells confirms known targets including ABL and SRC family kinases and identifies the receptor tyrosine kinase DDR1 and the oxidoreductase NQO2 as novel targets of imatinib. The data suggest that our approach is a valuable tool for drug discovery.
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43
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Fernández-Montalván A, Bouwmeester T, Joberty G, Mader R, Mahnke M, Pierrat B, Schlaeppi JM, Worpenberg S, Gerhartz B. Biochemical characterization of USP7 reveals post-translational modification sites and structural requirements for substrate processing and subcellular localization. FEBS J 2007; 274:4256-70. [PMID: 17651432 DOI: 10.1111/j.1742-4658.2007.05952.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ubiquitin specific protease 7 (USP7) belongs to the family of deubiquitinating enzymes. Among other functions, USP7 is involved in the regulation of stress response pathways, epigenetic silencing and the progress of infections by DNA viruses. USP7 is a 130-kDa protein with a cysteine peptidase core, N- and C-terminal domains required for protein-protein interactions. In the present study, recombinant USP7 full length, along with several variants corresponding to domain deletions, were expressed in different hosts in order to analyze post-translational modifications, oligomerization state, enzymatic properties and subcellular localization patterns of the enzyme. USP7 is phosphorylated at S18 and S963, and ubiquitinated at K869 in mammalian cells. In in vitro activity assays, N- and C-terminal truncations affected the catalytic efficiency of the enzyme different. Both the protease core alone and in combination with the N-terminal domain are over 100-fold less active than the full length enzyme, whereas a construct including the C-terminal region displays a rather small decrease in catalytic efficiency. Limited proteolysis experiments revealed that USP7 variants containing the C-terminal domain interact more tightly with ubiquitin. Besides playing an important role in substrate recognition and processing, this region might be involved in enzyme dimerization. USP7 constructs lacking the N-terminal domain failed to localize in the cell nucleus, but no nuclear localization signal could be mapped within the enzyme's first 70 amino acids. Instead, the tumor necrosis factor receptor associated factor-like region (amino acids 70-205) was sufficient to achieve the nuclear localization of the enzyme, suggesting that interaction partners might be required for USP7 nuclear import.
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44
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Angrand PO, Segura I, Völkel P, Ghidelli S, Terry R, Brajenovic M, Vintersten K, Klein R, Superti-Furga G, Drewes G, Kuster B, Bouwmeester T, Acker-Palmer A. Transgenic Mouse Proteomics Identifies New 14-3-3-associated Proteins Involved in Cytoskeletal Rearrangements and Cell Signaling. Mol Cell Proteomics 2006; 5:2211-27. [PMID: 16959763 DOI: 10.1074/mcp.m600147-mcp200] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Identification of protein-protein interactions is crucial for unraveling cellular processes and biochemical mechanisms of signal transduction. Here we describe, for the first time, the application of the tandem affinity purification (TAP) and LC-MS method to the characterization of protein complexes from transgenic mice. The TAP strategy developed in transgenic mice allows the emplacement of complexes in their physiological environment in contact with proteins that might only be specifically expressed in certain tissues while simultaneously ensuring the right stoichiometry of the TAP protein versus their binding partners and represents a novelty in proteomics approaches used so far. Mouse lines expressing TAP-tagged 14-3-3zeta protein were generated, and protein interactions were determined. 14-3-3 proteins are general regulators of cell signaling and represent up to 1% of the total brain protein. This study allowed the identification of almost 40 novel 14-3-3zeta-binding proteins. Biochemical and functional characterization of some of these interactions revealed new mechanisms of action of 14-3-3zeta in several signaling pathways, such as glutamate receptor signaling via binding to homer homolog 3 (Homer 3) and in cytoskeletal rearrangements and spine morphogenesis by binding and regulating the activity of the signaling complex formed by G protein-coupled receptor kinase-interactor 1 (GIT1) and p21-activated kinase-interacting exchange factor beta (betaPIX).
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Affiliation(s)
- Pierre-Olivier Angrand
- Cellzome AG and the European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
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45
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Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006; 440:631-6. [PMID: 16429126 DOI: 10.1038/nature04532] [Citation(s) in RCA: 1826] [Impact Index Per Article: 101.4] [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: 10/17/2005] [Accepted: 12/15/2005] [Indexed: 11/08/2022]
Abstract
Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.
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46
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Gagneur J, Krause R, Bouwmeester T, Casari G. Modular decomposition of protein-protein interaction networks. Genome Biol 2004; 5:R57. [PMID: 15287979 PMCID: PMC507882 DOI: 10.1186/gb-2004-5-8-r57] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [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: 04/23/2004] [Revised: 05/19/2004] [Accepted: 06/07/2004] [Indexed: 11/16/2022] Open
Abstract
We introduce an algorithmic method, termed modular decomposition, that defines the organization of protein-interaction networks as a hierarchy of nested modules. Modular decomposition derives the logical rules of how to combine proteins into the actual functional complexes by identifying groups of proteins acting as a single unit (sub-complexes) and those that can be alternatively exchanged in a set of similar complexes. The method is applied to experimental data on the pro-inflammatory tumor necrosis factor-alpha (TNF-alpha)/NFkappaB transcription factor pathway.
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Affiliation(s)
- Julien Gagneur
- Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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47
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Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K, Cruciat C, Eberhard D, Gagneur J, Ghidelli S, Hopf C, Huhse B, Mangano R, Michon AM, Schirle M, Schlegl J, Schwab M, Stein MA, Bauer A, Casari G, Drewes G, Gavin AC, Jackson DB, Joberty G, Neubauer G, Rick J, Kuster B, Superti-Furga G. A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 2004; 6:97-105. [PMID: 14743216 DOI: 10.1038/ncb1086] [Citation(s) in RCA: 777] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2003] [Accepted: 12/22/2003] [Indexed: 11/08/2022]
Abstract
Signal transduction pathways are modular composites of functionally interdependent sets of proteins that act in a coordinated fashion to transform environmental information into a phenotypic response. The pro-inflammatory cytokine tumour necrosis factor (TNF)-alpha triggers a signalling cascade, converging on the activation of the transcription factor NF-kappa B, which forms the basis for numerous physiological and pathological processes. Here we report the mapping of a protein interaction network around 32 known and candidate TNF-alpha/NF-kappa B pathway components by using an integrated approach comprising tandem affinity purification, liquid-chromatography tandem mass spectrometry, network analysis and directed functional perturbation studies using RNA interference. We identified 221 molecular associations and 80 previously unknown interactors, including 10 new functional modulators of the pathway. This systems approach provides significant insight into the logic of the TNF-alpha/NF-kappa B pathway and is generally applicable to other pathways relevant to human disease.
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48
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Brajenovic M, Joberty G, Küster B, Bouwmeester T, Drewes G. Comprehensive proteomic analysis of human Par protein complexes reveals an interconnected protein network. J Biol Chem 2003; 279:12804-11. [PMID: 14676191 DOI: 10.1074/jbc.m312171200] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The polarization of eukaryotic cells is controlled by the concerted activities of asymmetrically localized proteins. The PAR proteins, first identified in Caenorhabditis elegans, are common regulators of cell polarity conserved from nematode and flies to man. However, little is known about the molecular mechanisms by which these proteins and protein complexes establish cell polarity in mammals. We have mapped multiprotein complexes formed around the putative human Par orthologs MARK4 (microtubule-associated protein/microtubule affinity-regulating kinase 4) (Par-1), Par-3, LKB1 (Par-4), 14-3-3zeta and eta (Par-5), Par-6a, -b, -c, and PKClambda (PKC3). We employed a proteomic approach comprising tandem affinity purification (TAP) of protein complexes from cultured cells and protein sequencing by tandem mass spectrometry. From these data we constructed a highly interconnected protein network consisting of three core complex "modules" formed around MARK4 (Par-1), Par-3.Par-6, and LKB1 (Par-4). The network confirms most previously reported interactions. In addition we identified more than 50 novel interactors, some of which, like the 14-3-3 phospho-protein scaffolds, occur in more than one distinct complex. We demonstrate that the complex formation between LKB1.Par-4, PAPK, and Mo25 results in the translocation of LKB1 from the nucleus to the cytoplasm and to tight junctions and show that the LKB1 complex may activate MARKs, which are known to introduce 14-3-3 binding sites into several substrates. Our findings suggest co-regulation and/or signaling events between the distinct Par complexes and provide a basis for further elucidation of the molecular mechanisms that govern cell polarity.
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49
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Abstract
The availability of complete, annotated genome sequences for a variety of eukaryotic organisms has paved the way for a paradigm shift in biomedical research from the 'one gene-one hypothesis' approach to more global, systematic strategies that analyse genes or proteins on a genome- and proteome-wide scale. One daunting task in the post-genome era is to determine how the complement of expressed cellular proteins - the proteome - is organised into functional, higher-order networks, by mapping all constitutive and dynamic protein-protein interactions. Traditionally, reductionist approaches have typically focused on a few, selected gene products and their interactions in a particular physiological context. In contrast, more holistic strategies aim at understanding complex biological systems, for example global protein-protein interaction networks on a cellular or organismal level. Several large-scale proteomics technologies have been developed to generate comprehensive, cellular protein-protein interaction maps.
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Affiliation(s)
- Gerard Drewes
- Cellzome AG, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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50
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Abstract
Gastrulation in vertebrates is a highly dynamic process driven by convergent extension movements of internal mesodermal cells, under the regulatory activity of the Spemann-Mangold or gastrula organizer. In a large-scale screen for genes expressed in the organizer, we have isolated a novel gene, termed Xmc, an acronym for Xenopus marginal coil. Xmc encodes a protein containing two widely spaced evolutionarily non-conserved coiled coils. Xmc protein is found in vesicular aggregates in the cytoplasm and associated with the inner plasma membrane. We show that Xmc is expressed in a dynamic fashion around the blastoporal circumference, in mesodermal cells undergoing morphogenetic movements, in a pattern similar to FGF target genes. Likewise, Xmc expression can be induced by ectopic XeFGF signaling and the early mesodermal expression is dependent on FGF receptor-mediated signaling. Morpholino-mediated translational 'knock-down' of Xmc results in embryos that display a reduced elongation of the antero-posterior axis and in a pronounced inhibition of morphogenetic movements in embryos and dorsal marginal zone explants. Xmc loss-of-function does not interfere with mesoderm induction or maintenance per se. Our results suggest that Xmc is a novel FGF target gene that is required for morphogenetic movements during gastrulation in Xenopus.
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Affiliation(s)
- Giovanni Frazzetto
- Developmental Biology Programme, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany.
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