1
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Schröder M, Renatus M, Liang X, Meili F, Zoller T, Ferrand S, Gauter F, Li X, Sigoillot F, Gleim S, Stachyra TM, Thomas JR, Begue D, Khoshouei M, Lefeuvre P, Andraos-Rey R, Chung B, Ma R, Pinch B, Hofmann A, Schirle M, Schmiedeberg N, Imbach P, Gorses D, Calkins K, Bauer-Probst B, Maschlej M, Niederst M, Maher R, Henault M, Alford J, Ahrne E, Tordella L, Hollingworth G, Thomä NH, Vulpetti A, Radimerski T, Holzer P, Carbonneau S, Thoma CR. DCAF1-based PROTACs with activity against clinically validated targets overcoming intrinsic- and acquired-degrader resistance. Nat Commun 2024; 15:275. [PMID: 38177131 PMCID: PMC10766610 DOI: 10.1038/s41467-023-44237-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Targeted protein degradation (TPD) mediates protein level through small molecule induced redirection of E3 ligases to ubiquitinate neo-substrates and mark them for proteasomal degradation. TPD has recently emerged as a key modality in drug discovery. So far only a few ligases have been utilized for TPD. Interestingly, the workhorse ligase CRBN has been observed to be downregulated in settings of resistance to immunomodulatory inhibitory drugs (IMiDs). Here we show that the essential E3 ligase receptor DCAF1 can be harnessed for TPD utilizing a selective, non-covalent DCAF1 binder. We confirm that this binder can be functionalized into an efficient DCAF1-BRD9 PROTAC. Chemical and genetic rescue experiments validate specific degradation via the CRL4DCAF1 E3 ligase. Additionally, a dasatinib-based DCAF1 PROTAC successfully degrades cytosolic and membrane-bound tyrosine kinases. A potent and selective DCAF1-BTK-PROTAC (DBt-10) degrades BTK in cells with acquired resistance to CRBN-BTK-PROTACs while the DCAF1-BRD9 PROTAC (DBr-1) provides an alternative strategy to tackle intrinsic resistance to VHL-degrader, highlighting DCAF1-PROTACS as a promising strategy to overcome ligase mediated resistance in clinical settings.
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Affiliation(s)
- Martin Schröder
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Basel, Switzerland
- Ridgeline Discovery, Basel, Switzerland
| | - Xiaoyou Liang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Fabian Meili
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Francois Gauter
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Xiaoyan Li
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Damien Begue
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Peggy Lefeuvre
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - BoYee Chung
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Renate Ma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Benika Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Andreas Hofmann
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Patricia Imbach
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Delphine Gorses
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Keith Calkins
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Matt Niederst
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rob Maher
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John Alford
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erik Ahrne
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Luca Tordella
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anna Vulpetti
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thomas Radimerski
- Novartis Institutes for BioMedical Research, Basel, Switzerland
- Ridgeline Discovery, Basel, Switzerland
| | - Philipp Holzer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Seth Carbonneau
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
- Ridgeline Discovery, Basel, Switzerland.
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2
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Gurzeler LA, Link M, Ibig Y, Schmidt I, Galuba O, Schoenbett J, Gasser-Didierlaurant C, Parker CN, Mao X, Bitsch F, Schirle M, Couttet P, Sigoillot F, Ziegelmüller J, Uldry AC, Teodorowicz W, Schmiedeberg N, Mühlemann O, Reinhardt J. Drug-induced eRF1 degradation promotes readthrough and reveals a new branch of ribosome quality control. Cell Rep 2023; 42:113159. [PMID: 37708027 DOI: 10.1016/j.celrep.2023.113159] [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: 09/16/2023] Open
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3
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Gurzeler LA, Link M, Ibig Y, Schmidt I, Galuba O, Schoenbett J, Gasser-Didierlaurant C, Parker CN, Mao X, Bitsch F, Schirle M, Couttet P, Sigoillot F, Ziegelmüller J, Uldry AC, Teodorowicz W, Schmiedeberg N, Mühlemann O, Reinhardt J. Drug-induced eRF1 degradation promotes readthrough and reveals a new branch of ribosome quality control. Cell Rep 2023; 42:113056. [PMID: 37651229 DOI: 10.1016/j.celrep.2023.113056] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/15/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Suppression of premature termination codons (PTCs) by translational readthrough is a promising strategy to treat a wide variety of severe genetic diseases caused by nonsense mutations. Here, we present two potent readthrough promoters-NVS1.1 and NVS2.1-that restore substantial levels of functional full-length CFTR and IDUA proteins in disease models for cystic fibrosis and Hurler syndrome, respectively. In contrast to other readthrough promoters that affect stop codon decoding, the NVS compounds stimulate PTC suppression by triggering rapid proteasomal degradation of the translation termination factor eRF1. Our results show that this occurs by trapping eRF1 in the terminating ribosome, causing ribosome stalls and subsequent ribosome collisions, and activating a branch of the ribosome-associated quality control network, which involves the translational stress sensor GCN1 and the catalytic activity of the E3 ubiquitin ligases RNF14 and RNF25.
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Affiliation(s)
- Lukas-Adrian Gurzeler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marion Link
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Yvonne Ibig
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Isabel Schmidt
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Olaf Galuba
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | | | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Francis Bitsch
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Philipp Couttet
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Jana Ziegelmüller
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Wojciech Teodorowicz
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Jürgen Reinhardt
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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4
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Paul A, Annunziato S, Lu B, Sun T, Evrova O, Planas-Paz L, Orsini V, Terracciano LM, Charlat O, Loureiro ZY, Ji L, Zamponi R, Sigoillot F, Lei H, Lindeman A, Russ C, Reece-Hoyes JS, Nicholson TB, Tchorz JS, Cong F. Cell adhesion molecule KIRREL1 is a feedback regulator of Hippo signaling recruiting SAV1 to cell-cell contact sites. Nat Commun 2022; 13:930. [PMID: 35177623 PMCID: PMC8854406 DOI: 10.1038/s41467-022-28567-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 11/04/2020] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
The Hippo/YAP pathway controls cell proliferation through sensing physical and spatial organization of cells. How cell-cell contact is sensed by Hippo signaling is poorly understood. Here, we identified the cell adhesion molecule KIRREL1 as an upstream positive regulator of the mammalian Hippo pathway. KIRREL1 physically interacts with SAV1 and recruits SAV1 to cell-cell contact sites. Consistent with the hypothesis that KIRREL1-mediated cell adhesion suppresses YAP activity, knockout of KIRREL1 increases YAP activity in neighboring cells. Analyzing pan-cancer CRISPR proliferation screen data reveals KIRREL1 as the top plasma membrane protein showing strong correlation with known Hippo regulators, highlighting a critical role of KIRREL1 in regulating Hippo signaling and cell proliferation. During liver regeneration in mice, KIRREL1 is upregulated, and its genetic ablation enhances hepatic YAP activity, hepatocyte reprogramming and biliary epithelial cell proliferation. Our data suggest that KIRREL1 functions as a feedback regulator of the mammalian Hippo pathway through sensing cell-cell interaction and recruiting SAV1 to cell-cell contact sites.
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Affiliation(s)
- Atanu Paul
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Stefano Annunziato
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Bo Lu
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Tianliang Sun
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Olivera Evrova
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Lara Planas-Paz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Luigi M Terracciano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele (Milan), Italy.,IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Olga Charlat
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Zinger Yang Loureiro
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Lei Ji
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Raffaella Zamponi
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Frederic Sigoillot
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Hong Lei
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Alicia Lindeman
- 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
| | - Thomas B Nicholson
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Feng Cong
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA.
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5
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Rao P, Tullai J, Aspesi P, Mapa F, Cochran N, Sigoillot F, Roma G, Gleim S, Jacob J, Marchese J, Solomon J. Abstract 2025: Characterization of cancer cell lines made senescent by exposure to ribociclib, doxorubicin, or TGFβ1, and identification of genes required for entry into senescence and senescent cell survival. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2025] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cellular senescence is a stress-induced state of stable growth arrest characterized by high expression of cell cycle inhibitors; a dramatic change in cell morphology, including an increase in lysosomal content; and secretion of large numbers of proteins involved in immune signaling and extracellular matrix remodeling. The physiological importance of cellular senescence has been attributed to prevention of carcinogenesis, aging, development, and tissue repair, and tumor cells can undergo senescence in response to therapeutic agents. In this work, we sought to validate the senescence-inducing activity of two known inducers (doxorubicin and TGFβ1) and a CDK4/6 inhibitor (ribociclib) and to identify proteins that can kill senescent tumor cells (senolytic targets) if knocked out and to identify downstream components of the tumor cell senescence pathway. Huh7 hepatocellular carcinoma cells and SK-MEL-28 melanoma cells were induced to senescence by treatment with three different agents: ribociclib, low doses of doxorubicin, or TGFβ1. The induction of senescence was confirmed by observing growth arrest, an increase in SA-β-gal staining, dramatic cell morphology changes, loss of c-Myc protein, increased expression of p15, and increased expression of senescence-associated secretory phenotype (SASP) proteins. Induction of SASP components was measured by RNAseq and SOMAscan. All three agents induced a senescent state, with blockage at different stages of the cell cycle observed. Induction of known immune factors, including IL-8 and IL-11, were identified in senescent cells (Huh7). A whole-genome CRISPR screen identified proteins required to enter senescence and those that were incompatible with the senescent state if knocked out. Expected hits were observed (eg, TGFBR1/TGFBR2 for TGFβ1, RB for ribociclib, and TOP2A for doxorubicin) for guide DNAs (gDNAs) that blocked entry into the senescent state. No gDNA candidates for common downstream senescence pathway components were observed, suggesting that these components are essential genes or that they do not exist. gDNA-induced knockouts that were incompatible with the senescent state dropped out of the screen and represent potential senolytic targets. The screen identified BCL2L1 as the only common senolytic hit across multiple senescence-inducing reagents, confirming published reports suggesting it is a senolytic target. These data show that ribociclib, doxorubicin, and TGFβ1 induced senescence in cancer cell lines. Whole-genome CRISPR screens identified senescence pathway components for each of these agents, as well as a common senolytic target.
Citation Format: Pasupuleti Rao, Jennifer Tullai, Peter Aspesi, Felipa Mapa, Nadire Cochran, Frederic Sigoillot, Guglielmo Roma, Scott Gleim, Jaison Jacob, Jason Marchese, Jonathan Solomon. Characterization of cancer cell lines made senescent by exposure to ribociclib, doxorubicin, or TGFβ1, and identification of genes required for entry into senescence and senescent cell survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2025.
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Affiliation(s)
- Pasupuleti Rao
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Peter Aspesi
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Felipa Mapa
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Nadire Cochran
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Guglielmo Roma
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Scott Gleim
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Jaison Jacob
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Jason Marchese
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
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6
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Cho H, Shen Q, Zhang LH, Okumura M, Kawakami A, Ambrose J, Sigoillot F, Miller HR, Gleim S, Cobos-Correa A, Wang Y, Piechon P, Roma G, Eggimann F, Moore C, Aspesi P, Mapa FA, Burks H, Ross NT, Krastel P, Hild M, Maimone TJ, Fisher DE, Nomura DK, Tallarico JA, Canham SM, Jenkins JL, Forrester WC. CYP27A1-dependent anti-melanoma activity of limonoid natural products targets mitochondrial metabolism. Cell Chem Biol 2021; 28:1407-1419.e6. [PMID: 33794192 DOI: 10.1016/j.chembiol.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/24/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Three limonoid natural products with selective anti-proliferative activity against BRAF(V600E) and NRAS(Q61K)-mutation-dependent melanoma cell lines were identified. Differential transcriptome analysis revealed dependency of compound activity on expression of the mitochondrial cytochrome P450 oxidase CYP27A1, a transcriptional target of melanogenesis-associated transcription factor (MITF). We determined that CYP27A1 activity is necessary for the generation of a reactive metabolite that proceeds to inhibit cellular proliferation. A genome-wide small interfering RNA screen in combination with chemical proteomics experiments revealed gene-drug functional epistasis, suggesting that these compounds target mitochondrial biogenesis and inhibit tumor bioenergetics through a covalent mechanism. Our work suggests a strategy for melanoma-specific targeting by exploiting the expression of MITF target gene CYP27A1 and inhibiting mitochondrial oxidative phosphorylation in BRAF mutant melanomas.
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Affiliation(s)
- Hyelim Cho
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiong Shen
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lydia H Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Mikiko Okumura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Akinori Kawakami
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jessi Ambrose
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Frederic Sigoillot
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Amanda Cobos-Correa
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Ying Wang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Fabian Eggimann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Charles Moore
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Peter Aspesi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Felipa A Mapa
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Heather Burks
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Marc Hild
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - David E Fisher
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - John A Tallarico
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - William C Forrester
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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7
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Hyrina A, Jones C, Chen D, Clarkson S, Cochran N, Feucht P, Hoffman G, Lindeman A, Russ C, Sigoillot F, Tsang T, Uehara K, Xie L, Ganem D, Holdorf M. A Genome-wide CRISPR Screen Identifies ZCCHC14 as a Host Factor Required for Hepatitis B Surface Antigen Production. Cell Rep 2020; 29:2970-2978.e6. [PMID: 31801065 DOI: 10.1016/j.celrep.2019.10.113] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 03/08/2019] [Revised: 06/23/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022] Open
Abstract
A hallmark of chronic hepatitis B (CHB) virus infection is the presence of high circulating levels of non-infectious small lipid HBV surface antigen (HBsAg) vesicles. Although rare, sustained HBsAg loss is the idealized endpoint of any CHB therapy. A small molecule, RG7834, has been previously reported to inhibit HBsAg expression by targeting terminal nucleotidyltransferase proteins 4A and 4B (TENT4A and TENT4B). In this study, we describe a genome-wide CRISPR screen to identify other potential host factors required for HBsAg expression and to gain further insights into the mechanism of RG7834. We report more than 60 genes involved in regulating HBsAg and identify additional factors involved in RG7834 activity, including a zinc finger CCHC-type containing 14 (ZCCHC14) protein. We show that ZCCHC14, together with TENT4A/B, stabilizes HBsAg expression through HBV RNA tailing, providing a potential new therapeutic target to achieve functional cure in CHB patients.
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Affiliation(s)
- Anastasia Hyrina
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA.
| | - Christopher Jones
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Darlene Chen
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Scott Clarkson
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Nadire Cochran
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Paul Feucht
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Gregory Hoffman
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Alicia Lindeman
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Carsten Russ
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Tiffany Tsang
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Kyoko Uehara
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Lili Xie
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Don Ganem
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Meghan Holdorf
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
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8
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Ross NT, Lohmann F, Carbonneau S, Fazal A, Weihofen WA, Gleim S, Salcius M, Sigoillot F, Henault M, Carl SH, Rodríguez-Molina JB, Miller HR, Brittain SM, Murphy J, Zambrowski M, Boynton G, Wang Y, Chen A, Molind GJ, Wilbertz JH, Artus-Revel CG, Jia M, Akinjiyan FA, Turner J, Knehr J, Carbone W, Schuierer S, Reece-Hoyes JS, Xie K, Saran C, Williams ET, Roma G, Spencer M, Jenkins J, George EL, Thomas JR, Michaud G, Schirle M, Tallarico J, Passmore LA, Chao JA, Beckwith REJ. Author Correction: CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing's sarcoma. Nat Chem Biol 2020; 16:479. [PMID: 32139909 DOI: 10.1038/s41589-020-0508-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.,Vertex Pharmaceuticals, Boston, MA, USA
| | - Felix Lohmann
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Seth Carbonneau
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Aleem Fazal
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Michael Salcius
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason Murphy
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mark Zambrowski
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Aye Chen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Johannes H Wilbertz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Min Jia
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Jonathan Turner
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Kevin Xie
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Chitra Saran
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Eric T Williams
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Matt Spencer
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jeremy Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Gregory Michaud
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John Tallarico
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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9
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Hill A, Gleim S, Kiefer F, Sigoillot F, Loureiro J, Jenkins J, Morris MK. Benchmarking network algorithms for contextualizing genes of interest. PLoS Comput Biol 2019; 15:e1007403. [PMID: 31860671 PMCID: PMC6944391 DOI: 10.1371/journal.pcbi.1007403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 01/16/2019] [Revised: 01/06/2020] [Accepted: 09/11/2019] [Indexed: 12/11/2022] Open
Abstract
Computational approaches have shown promise in contextualizing genes of interest with known molecular interactions. In this work, we evaluate seventeen previously published algorithms based on characteristics of their output and their performance in three tasks: cross validation, prediction of drug targets, and behavior with random input. Our work highlights strengths and weaknesses of each algorithm and results in a recommendation of algorithms best suited for performing different tasks. In our labs, we aimed to use network algorithms to contextualize hits from functional genomics screens and gene expression studies. In order to understand how to apply these algorithms to our data, we characterized seventeen previously published algorithms based on characteristics of their output and their performance in three tasks: cross validation, prediction of drug targets, and behavior with random input.
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Affiliation(s)
- Abby Hill
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Scott Gleim
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Florian Kiefer
- Novartis Informatics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Frederic Sigoillot
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Joseph Loureiro
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jeremy Jenkins
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Melody K. Morris
- Respiratory Disease Area Department, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
- * E-mail:
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10
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Ross NT, Lohmann F, Carbonneau S, Fazal A, Weihofen WA, Gleim S, Salcius M, Sigoillot F, Henault M, Carl SH, Rodríguez-Molina JB, Miller HR, Brittain SM, Murphy J, Zambrowski M, Boynton G, Wang Y, Chen A, Molind GJ, Wilbertz JH, Artus-Revel CG, Jia M, Akinjiyan FA, Turner J, Knehr J, Carbone W, Schuierer S, Reece-Hoyes JS, Xie K, Saran C, Williams ET, Roma G, Spencer M, Jenkins J, George EL, Thomas JR, Michaud G, Schirle M, Tallarico J, Passmore LA, Chao JA, Beckwith REJ. CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing's sarcoma. Nat Chem Biol 2019; 16:50-59. [PMID: 31819276 DOI: 10.1038/s41589-019-0424-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/01/2019] [Indexed: 02/07/2023]
Abstract
The post-genomic era has seen many advances in our understanding of cancer pathways, yet resistance and tumor heterogeneity necessitate multiple approaches to target even monogenic tumors. Here, we combine phenotypic screening with chemical genetics to identify pre-messenger RNA endonuclease cleavage and polyadenylation specificity factor 3 (CPSF3) as the target of JTE-607, a small molecule with previously unknown target. We show that CPSF3 represents a synthetic lethal node in a subset of acute myeloid leukemia (AML) and Ewing's sarcoma cancer cell lines. Inhibition of CPSF3 by JTE-607 alters expression of known downstream effectors in AML and Ewing's sarcoma lines, upregulates apoptosis and causes tumor-selective stasis in mouse xenografts. Mechanistically, it prevents the release of newly synthesized pre-mRNAs, resulting in read-through transcription and the formation of DNA-RNA hybrid R-loop structures. This study implicates pre-mRNA processing, and specifically CPSF3, as a druggable target providing an avenue to therapeutic intervention in cancer.
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Affiliation(s)
- Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.,Vertex Pharmaceuticals, Boston, MA, USA
| | - Felix Lohmann
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Seth Carbonneau
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Aleem Fazal
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Michael Salcius
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason Murphy
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mark Zambrowski
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Aye Chen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Johannes H Wilbertz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Min Jia
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Jonathan Turner
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Kevin Xie
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Chitra Saran
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Eric T Williams
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Matt Spencer
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jeremy Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Gregory Michaud
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John Tallarico
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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11
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Zeng H, Castillo-Cabrera J, Manser M, Lu B, Yang Z, Strande V, Begue D, Zamponi R, Qiu S, Sigoillot F, Wang Q, Lindeman A, Reece-Hoyes JS, Russ C, Bonenfant D, Jiang X, Wang Y, Cong F. Genome-wide CRISPR screening reveals genetic modifiers of mutant EGFR dependence in human NSCLC. eLife 2019; 8:50223. [PMID: 31741433 PMCID: PMC6927754 DOI: 10.7554/elife.50223] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 07/16/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022] Open
Abstract
EGFR-mutant NSCLCs frequently respond to EGFR tyrosine kinase inhibitors (TKIs). However, the responses are not durable, and the magnitude of tumor regression is variable, suggesting the existence of genetic modifiers of EGFR dependency. Here, we applied a genome-wide CRISPR-Cas9 screening to identify genetic determinants of EGFR TKI sensitivity and uncovered putative candidates. We show that knockout of RIC8A, essential for G-alpha protein activation, enhanced EGFR TKI-induced cell death. Mechanistically, we demonstrate that RIC8A is a positive regulator of YAP signaling, activation of which rescued the EGFR TKI sensitizing phenotype resulting from RIC8A knockout. We also show that knockout of ARIH2, or other components in the Cullin-5 E3 complex, conferred resistance to EGFR inhibition, in part by promoting nascent protein synthesis through METAP2. Together, these data uncover a spectrum of previously unidentified regulators of EGFR TKI sensitivity in EGFR-mutant human NSCLC, providing insights into the heterogeneity of EGFR TKI treatment responses. Cancer is caused by cells growing and dividing uncontrollably as a result of mutations in certain genes. Many human lung cancers have a mutation in the gene that makes the protein EGFR. In healthy cells, EGFR allows a cell to respond to chemical signals that encourage healthy growth. In cancer, the altered EGFR is always on, which allows the cell to rapidly grow without any control, resulting in cancer. One approach to treating these cancers is with drugs that block the activity of mutant EGFR. Although these drugs have been very successful, they do not always succeed in completely treating the cancer. This is because over time the cancer cells can become resistant to the drug and start forming new tumors. One way that this can happen is if random mutations lead to changes in other proteins that make the drug less effective or stop it from accessing the EGFR proteins. However, it is unclear how other proteins in cancer cells affect the response to these EGFR inhibiting drugs. Now, Zeng et al. have used gene editing to systematically remove every protein from human lung cancer cells grown in the laboratory to see how this affects resistance to EGFR inhibitor treatment. This revealed that a number of different proteins could change how cancer cells responded to the drug. For instance, cells lacking the protein RIC8A were more sensitive to EGFR inhibitors and less likely to develop resistance. This is because loss of RIC8A turns down a key cell survival pathway in cancer cells. Whereas, cancer cells lacking the ARIH2 protein were able to produce more proteins that are needed for cancer cell growth, which resulted in them having increased resistance to EGFR inhibitors. The proteins identified in this study could be used to develop new drugs that improve the effectiveness of EGFR inhibitors. Understanding how cancer cells respond to EGFR inhibitor treatment could help determine how likely a patient is to develop resistance to these drugs.
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Affiliation(s)
- Hao Zeng
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Johnny Castillo-Cabrera
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Mika Manser
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Bo Lu
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Zinger Yang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Vaik Strande
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Damien Begue
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Raffaella Zamponi
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Shumei Qiu
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Frederic Sigoillot
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Qiong Wang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Alicia Lindeman
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - John S Reece-Hoyes
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Carsten Russ
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Debora Bonenfant
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Xiaomo Jiang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Youzhen Wang
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Feng Cong
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
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12
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Ji L, Lu B, Zamponi R, Charlat O, Aversa R, Yang Z, Sigoillot F, Zhu X, Hu T, Reece-Hoyes JS, Russ C, Michaud G, Tchorz JS, Jiang X, Cong F. USP7 inhibits Wnt/β-catenin signaling through promoting stabilization of Axin. Nat Commun 2019; 10:4184. [PMID: 31519875 PMCID: PMC6744515 DOI: 10.1038/s41467-019-12143-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [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: 01/28/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
Axin is a key scaffolding protein responsible for the formation of the β-catenin destruction complex. Stability of Axin protein is regulated by the ubiquitin-proteasome system, and modulation of cellular concentration of Axin protein has a profound effect on Wnt/β-catenin signaling. Although E3s promoting Axin ubiquitination have been identified, the deubiquitinase responsible for Axin deubiquitination and stabilization remains unknown. Here, we identify USP7 as a potent negative regulator of Wnt/β-catenin signaling through CRISPR screens. Genetic ablation or pharmacological inhibition of USP7 robustly increases Wnt/β-catenin signaling in multiple cellular systems. USP7 directly interacts with Axin through its TRAF domain, and promotes deubiquitination and stabilization of Axin. Inhibition of USP7 regulates osteoblast differentiation and adipocyte differentiation through increasing Wnt/β-catenin signaling. Our study reveals a critical mechanism that prevents excessive degradation of Axin and identifies USP7 as a target for sensitizing cells to Wnt/β-catenin signaling. Axin is a scaffolding protein known for its role in Wnt signalling that can be marked with a variety of post-translational modifications. Here, Cong et al. demonstrate that USP7 de-ubiquinates Axin and that canonical Wnt signaling output can be increased with USP7 inhibitors.
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Affiliation(s)
- Lei Ji
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Bo Lu
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Raffaella Zamponi
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA.,Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emila, Italy
| | - Olga Charlat
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Robert Aversa
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - 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
| | - Xiaoping Zhu
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Tiancen Hu
- 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
| | - Carsten Russ
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Gregory Michaud
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Jan S Tchorz
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Xiaomo Jiang
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Feng Cong
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA.
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13
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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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14
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Nolin E, Gans S, Llamas L, Bandyopadhyay S, Brittain SM, Bernasconi-Elias P, Carter KP, Loureiro JJ, Thomas JR, Schirle M, Yang Y, Guo N, Roma G, Schuierer S, Beibel M, Lindeman A, Sigoillot F, Chen A, Xie KX, Ho S, Reece-Hoyes J, Weihofen WA, Tyskiewicz K, Hoepfner D, McDonald RI, Guthrie N, Dogra A, Guo H, Shao J, Ding J, Canham SM, Boynton G, George EL, Kang ZB, Antczak C, Porter JA, Wallace O, Tallarico JA, Palmer AE, Jenkins JL, Jain RK, Bushell SM, Fryer CJ. Discovery of a ZIP7 inhibitor from a Notch pathway screen. Nat Chem Biol 2019; 15:179-188. [PMID: 30643281 DOI: 10.1038/s41589-018-0200-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 11/14/2018] [Indexed: 12/15/2022]
Abstract
The identification of activating mutations in NOTCH1 in 50% of T cell acute lymphoblastic leukemia has generated interest in elucidating how these mutations contribute to oncogenic transformation and in targeting the pathway. A phenotypic screen identified compounds that interfere with trafficking of Notch and induce apoptosis via an endoplasmic reticulum (ER) stress mechanism. Target identification approaches revealed a role for SLC39A7 (ZIP7), a zinc transport family member, in governing Notch trafficking and signaling. Generation and sequencing of a compound-resistant cell line identified a V430E mutation in ZIP7 that confers transferable resistance to the compound NVS-ZP7-4. NVS-ZP7-4 altered zinc in the ER, and an analog of the compound photoaffinity labeled ZIP7 in cells, suggesting a direct interaction between the compound and ZIP7. NVS-ZP7-4 is the first reported chemical tool to probe the impact of modulating ER zinc levels and investigate ZIP7 as a novel druggable node in the Notch pathway.
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Affiliation(s)
- Erin Nolin
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sara Gans
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Luis Llamas
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | | | - Kyle P Carter
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | | | - Jason R Thomas
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Yi Yang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ning Guo
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alicia Lindeman
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Amy Chen
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Kevin X Xie
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Samuel Ho
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | | | | | | | | | - Abhishek Dogra
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Haibing Guo
- Novartis Institutes for Biomedical Research, Shanghai, China
| | - Jian Shao
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jian Ding
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Geoff Boynton
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Zhao B Kang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Owen Wallace
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Amy E Palmer
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | | | - Rishi K Jain
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Simon M Bushell
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | - Christy J Fryer
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
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15
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Kedves AT, Gleim S, Liang X, Bonal DM, Sigoillot F, Harbinski F, Sanghavi S, Benander C, George E, Gokhale PC, Nguyen QD, Kirschmeier PT, Distel RJ, Jenkins J, Goldberg MS, Forrester WC. Recurrent ubiquitin B silencing in gynecological cancers establishes dependence on ubiquitin C. J Clin Invest 2017; 127:4554-4568. [PMID: 29130934 DOI: 10.1172/jci92914] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 01/17/2017] [Accepted: 10/09/2017] [Indexed: 02/06/2023] Open
Abstract
Transcriptional repression of ubiquitin B (UBB) is a cancer-subtype-specific alteration that occurs in a substantial population of patients with cancers of the female reproductive tract. UBB is 1 of 2 genes encoding for ubiquitin as a polyprotein consisting of multiple copies of ubiquitin monomers. Silencing of UBB reduces cellular UBB levels and results in an exquisite dependence on ubiquitin C (UBC), the second polyubiquitin gene. UBB is repressed in approximately 30% of high-grade serous ovarian cancer (HGSOC) patients and is a recurrent lesion in uterine carcinosarcoma and endometrial carcinoma. We identified ovarian tumor cell lines that retain UBB in a repressed state, used these cell lines to establish orthotopic ovarian tumors, and found that inducible expression of a UBC-targeting shRNA led to tumor regression, and substantial long-term survival benefit. Thus, we describe a recurrent cancer-specific lesion at the level of ubiquitin production. Moreover, these observations reveal the prognostic value of UBB repression and establish UBC as a promising therapeutic target for ovarian cancer patients with recurrent UBB silencing.
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Affiliation(s)
- Alexia T Kedves
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Scott Gleim
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Xiaoyou Liang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Dennis M Bonal
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Frederic Sigoillot
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Fred Harbinski
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Sneha Sanghavi
- Neurosciences, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Christina Benander
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Elizabeth George
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | | | | | | | - Jeremy Jenkins
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | - William C Forrester
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
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16
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Riba A, Emmenlauer M, Chen A, Sigoillot F, Cong F, Dehio C, Jenkins J, Zavolan M. Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results. Cell Syst 2017; 4:182-193.e4. [PMID: 28215525 DOI: 10.1016/j.cels.2017.01.011] [Citation(s) in RCA: 12] [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: 09/27/2016] [Revised: 12/09/2016] [Accepted: 01/13/2017] [Indexed: 12/31/2022]
Abstract
RNAi is broadly used to map gene regulatory networks, but the identification of genes that are responsible for the observed phenotypes is challenging, as small interfering RNAs (siRNAs) simultaneously downregulate the intended on targets and many partially complementary off targets. Additionally, the scarcity of publicly available control datasets hinders the development and comparative evaluation of computational methods for analyzing the data. Here, we introduce PheLiM (https://github.com/andreariba/PheLiM), a method that uses predictions of siRNA on- and off-target downregulation to infer gene-specific contributions to phenotypes. To assess the performance of PheLiM, we carried out siRNA- and CRISPR/Cas9-based genome-wide screening of two well-characterized pathways, bone morphogenetic protein (BMP) and nuclear factor κB (NF-κB), and we reanalyzed publicly available siRNA screens. We demonstrate that PheLiM has the overall highest accuracy and most reproducible results compared to other available methods. PheLiM can accommodate various methods for predicting siRNA off targets and is broadly applicable to the identification of genes underlying complex phenotypes.
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Affiliation(s)
- Andrea Riba
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Mario Emmenlauer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Amy Chen
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Frederic Sigoillot
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Feng Cong
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Christoph Dehio
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Jeremy Jenkins
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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17
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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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18
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Yilmazel B, Hu Y, Sigoillot F, Smith JA, Shamu CE, Perrimon N, Mohr SE. Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis. BMC Bioinformatics 2014; 15:192. [PMID: 24934636 PMCID: PMC4073188 DOI: 10.1186/1471-2105-15-192] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/10/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND RNA interference (RNAi) is an effective and important tool used to study gene function. For large-scale screens, RNAi is used to systematically down-regulate genes of interest and analyze their roles in a biological process. However, RNAi is associated with off-target effects (OTEs), including microRNA (miRNA)-like OTEs. The contribution of reagent-specific OTEs to RNAi screen data sets can be significant. In addition, the post-screen validation process is time and labor intensive. Thus, the availability of robust approaches to identify candidate off-targeted transcripts would be beneficial. RESULTS Significant efforts have been made to eliminate false positive results attributable to sequence-specific OTEs associated with RNAi. These approaches have included improved algorithms for RNAi reagent design, incorporation of chemical modifications into siRNAs, and the use of various bioinformatics strategies to identify possible OTEs in screen results. Genome-wide Enrichment of Seed Sequence matches (GESS) was developed to identify potential off-targeted transcripts in large-scale screen data by seed-region analysis. Here, we introduce a user-friendly web application that provides researchers a relatively quick and easy way to perform GESS analysis on data from human or mouse cell-based screens using short interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), as well as for Drosophila screens using shRNAs. Online GESS relies on up-to-date transcript sequence annotations for human and mouse genes extracted from NCBI Reference Sequence (RefSeq) and Drosophila genes from FlyBase. The tool also accommodates analysis with user-provided reference sequence files. CONCLUSION Online GESS provides a straightforward user interface for genome-wide seed region analysis for human, mouse and Drosophila RNAi screen data. With the tool, users can either use a built-in database or provide a database of transcripts for analysis. This makes it possible to analyze RNAi data from any organism for which the user can provide transcript sequences.
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Affiliation(s)
| | | | | | | | | | | | - Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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19
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King R, Zeng X, Sigoillot F, Gaur S, Choi S, Cuny G. Phenotypic screening in complex cellular extracts to identify novel antimitotic targets and compounds. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.464.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Xing Zeng
- Cell BiologyHarvard Medical SchoolBostonMA
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20
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Zeng X, Sigoillot F, Gaur S, Choi S, Pfaff KL, Oh DC, Hathaway N, Dimova N, Cuny GD, King RW. Pharmacologic inhibition of the anaphase-promoting complex induces a spindle checkpoint-dependent mitotic arrest in the absence of spindle damage. Cancer Cell 2010; 18:382-95. [PMID: 20951947 PMCID: PMC2957475 DOI: 10.1016/j.ccr.2010.08.010] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 07/01/2010] [Accepted: 08/10/2010] [Indexed: 12/13/2022]
Abstract
Microtubule inhibitors are important cancer drugs that induce mitotic arrest by activating the spindle assembly checkpoint (SAC), which, in turn, inhibits the ubiquitin ligase activity of the anaphase-promoting complex (APC). Here, we report a small molecule, tosyl-L-arginine methyl ester (TAME), which binds to the APC and prevents its activation by Cdc20 and Cdh1. A prodrug of TAME arrests cells in metaphase without perturbing the spindle, but nonetheless the arrest is dependent on the SAC. Metaphase arrest induced by a proteasome inhibitor is also SAC dependent, suggesting that APC-dependent proteolysis is required to inactivate the SAC. We propose that mutual antagonism between the APC and the SAC yields a positive feedback loop that amplifies the ability of TAME to induce mitotic arrest.
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Affiliation(s)
- Xing Zeng
- Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, MA
| | - Frederic Sigoillot
- Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, MA
| | - Shantanu Gaur
- Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, MA
| | - Sungwoon Choi
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School, 65 Landsdowne St, Cambridge, MA
| | - Kathleen L. Pfaff
- Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, MA
| | - Dong-Chan Oh
- Department of Biological Chemistry and Molecular Pharmacology, 240 Longwood Ave, Harvard Medical School, Boston, MA
- Natural Products Research Institute, College of Pharmacy, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Nathaniel Hathaway
- Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, MA
| | - Nevena Dimova
- Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, MA
| | - Gregory D. Cuny
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School, 65 Landsdowne St, Cambridge, MA
| | - Randall W. King
- Department of Cell Biology, 240 Longwood Ave, Harvard Medical School, Boston, MA
- Correspondence:
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