1
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Li J, Moretti F, Hidvegi T, Sviben S, Fitzpatrick JAJ, Sundaramoorthi H, Pak SC, Silverman GA, Knapp B, Filipuzzi I, Alford J, Reece-Hoyes J, Nigsch F, Murphy LO, Nyfeler B, Perlmutter DH. Multiple Genes Core to ERAD, Macroautophagy and Lysosomal Degradation Pathways Participate in the Proteostasis Response in α1-Antitrypsin Deficiency. Cell Mol Gastroenterol Hepatol 2024; 17:1007-1024. [PMID: 38336172 PMCID: PMC11053228 DOI: 10.1016/j.jcmgh.2024.02.006] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND & AIMS In the classic form of α1-antitrypsin deficiency (ATD), the misfolded α1-antitrypsin Z (ATZ) variant accumulates in the endoplasmic reticulum (ER) of liver cells. A gain-of-function proteotoxic mechanism is responsible for chronic liver disease in a subgroup of homozygotes. Proteostatic response pathways, including conventional endoplasmic reticulum-associated degradation and autophagy, have been proposed as the mechanisms that allow cellular adaptation and presumably protection from the liver disease phenotype. Recent studies have concluded that a distinct lysosomal pathway called endoplasmic reticulum-to-lysosome completely supplants the role of the conventional macroautophagy pathway in degradation of ATZ. Here, we used several state-of-the-art approaches to characterize the proteostatic responses more fully in cellular systems that model ATD. METHODS We used clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing coupled to a cell selection step by fluorescence-activated cell sorter to perform screening for proteostasis genes that regulate ATZ accumulation and combined that with selective genome editing in 2 other model systems. RESULTS Endoplasmic reticulum-associated degradation genes are key early regulators and multiple autophagy genes, from classic as well as from ER-to-lysosome and other newly described ER-phagy pathways, participate in degradation of ATZ in a manner that is temporally regulated and evolves as ATZ accumulation persists. Time-dependent changes in gene expression are accompanied by specific ultrastructural changes including dilation of the ER, formation of globular inclusions, budding of autophagic vesicles, and alterations in the overall shape and component parts of mitochondria. CONCLUSIONS Macroautophagy is a critical component of the proteostasis response to cellular ATZ accumulation and it becomes more important over time as ATZ synthesis continues unabated. Multiple subtypes of macroautophagy and nonautophagic lysosomal degradative pathways are needed to respond to the high concentrations of misfolded protein that characterizes ATD and these pathways are attractive candidates for genetic variants that predispose to the hepatic phenotype.
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Affiliation(s)
- Jie Li
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | | | - Tunda Hidvegi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Sanja Sviben
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri; Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri; Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri
| | | | - Stephen C Pak
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Gary A Silverman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Britta Knapp
- Novartis Biomedical Research, Basel, Switzerland
| | | | - John Alford
- Novartis Biomedical Research, Cambridge, Massachusetts
| | | | | | - Leon O Murphy
- Novartis Biomedical Research, Cambridge, Massachusetts
| | - Beat Nyfeler
- Novartis Biomedical Research, Basel, Switzerland
| | - David H Perlmutter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri.
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2
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Cotton JL, Estrada Diez J, Sagar V, Chen J, Piquet M, Alford J, Song Y, Li X, Riester M, DiMare MT, Schumacher K, Boulay G, Sprouffske K, Fan L, Burks T, Mansur L, Wagner J, Bhang HEC, Iartchouk O, Reece-Hoyes J, Morris EJ, Hammerman PS, Ruddy DA, Korn JM, Engelman JA, Niederst MJ. Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance. Cancer Res 2023; 83:3611-3623. [PMID: 37603596 DOI: 10.1158/0008-5472.can-23-0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/11/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
For a majority of patients with non-small cell lung cancer with EGFR mutations, treatment with EGFR inhibitors (EGFRi) induces a clinical response. Despite this initial reduction in tumor size, residual disease persists that leads to disease relapse. Elucidating the preexisting biological differences between sensitive cells and surviving drug-tolerant persister cells and deciphering how drug-tolerant cells evolve in response to treatment could help identify strategies to improve the efficacy of EGFRi. In this study, we tracked the origins and clonal evolution of drug-tolerant cells at a high resolution by using an expressed barcoding system coupled with single-cell RNA sequencing. This platform enabled longitudinal profiling of gene expression and drug sensitivity in response to EGFRi across a large number of clones. Drug-tolerant cells had higher expression of key survival pathways such as YAP and EMT at baseline and could also differentially adapt their gene expression following EGFRi treatment compared with sensitive cells. In addition, drug combinations targeting common downstream components (MAPK) or orthogonal factors (chemotherapy) showed greater efficacy than EGFRi alone, which is attributable to broader targeting of the heterogeneous EGFRi-tolerance mechanisms present in tumors. Overall, this approach facilitates thorough examination of clonal evolution in response to therapy that could inform the development of improved diagnostic approaches and treatment strategies for targeting drug-tolerant cells. SIGNIFICANCE The evolution and heterogeneity of EGFR inhibitor tolerance are identified in a large number of clones at enhanced cellular and temporal resolution using an expressed barcode technology coupled with single-cell RNA sequencing.
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Affiliation(s)
- Jennifer L Cotton
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Javier Estrada Diez
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Vivek Sagar
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Julie Chen
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Michelle Piquet
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Alford
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Youngchul Song
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Xiaoyan Li
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Markus Riester
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew T DiMare
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Katja Schumacher
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Gaylor Boulay
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Kathleen Sprouffske
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Lin Fan
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Tyler Burks
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Leandra Mansur
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joel Wagner
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Hyo-Eun C Bhang
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Oleg Iartchouk
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Reece-Hoyes
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Erick J Morris
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Peter S Hammerman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - David A Ruddy
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joshua M Korn
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jeffrey A Engelman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew J Niederst
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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3
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Welte T, Goulois A, Stadler MB, Hess D, Soneson C, Neagu A, Azzi C, Wisser MJ, Seebacher J, Schmidt I, Estoppey D, Nigsch F, Reece-Hoyes J, Hoepfner D, Großhans H. Convergence of multiple RNA-silencing pathways on GW182/TNRC6. Mol Cell 2023:S1097-2765(23)00423-9. [PMID: 37369201 DOI: 10.1016/j.molcel.2023.06.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 04/02/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
The RNA-binding protein TRIM71/LIN-41 is a phylogenetically conserved developmental regulator that functions in mammalian stem cell reprogramming, brain development, and cancer. TRIM71 recognizes target mRNAs through hairpin motifs and silences them through molecular mechanisms that await identification. Here, we uncover that TRIM71 represses its targets through RNA-supported interaction with TNRC6/GW182, a core component of the miRNA-induced silencing complex (miRISC). We demonstrate that AGO2, TRIM71, and UPF1 each recruit TNRC6 to specific sets of transcripts to silence them. As cellular TNRC6 levels are limiting, competition occurs among the silencing pathways, such that the loss of AGO proteins or of AGO binding to TNRC6 enhances the activities of the other pathways. We conclude that a miRNA-like silencing activity is shared among different mRNA silencing pathways and that the use of TNRC6 as a central hub provides a means to integrate their activities.
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Affiliation(s)
- Thomas Welte
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Department of Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Alison Goulois
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Anca Neagu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Chiara Azzi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marlena J Wisser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Isabel Schmidt
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - David Estoppey
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - John Reece-Hoyes
- Department of Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Dominic Hoepfner
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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4
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Schukur L, Zimmermann T, Niewoehner O, Kerr G, Gleim S, Bauer-Probst B, Knapp B, Galli GG, Liang X, Mendiola A, Reece-Hoyes J, Rapti M, Barbosa I, Reschke M, Radimerski T, Thoma CR. Identification of the HECT E3 ligase UBR5 as a regulator of MYC degradation using a CRISPR/Cas9 screen. Sci Rep 2020; 10:20044. [PMID: 33208877 PMCID: PMC7676242 DOI: 10.1038/s41598-020-76960-z] [Citation(s) in RCA: 18] [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: 03/30/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
MYC oncoprotein is a multifunctional transcription factor that regulates the expression of a large number of genes involved in cellular growth, proliferation and metabolism. Altered MYC protein level lead to cellular transformation and tumorigenesis. MYC is deregulated in > 50% of human cancers, rendering it an attractive drug target. However, direct inhibition of this class of proteins using conventional small molecules is challenging due to their intrinsically disordered state. To discover novel posttranslational regulators of MYC protein stability and turnover, we established a genetic screen in mammalian cells by combining a fluorescent protein-based MYC abundance sensor, CRISPR/Cas9-based gene knockouts and next-generation sequencing. Our screen identifies UBR5, an E3 ligase of the HECT-type family, as a novel regulator of MYC degradation. Even in the presence of the well-described and functional MYC ligase, FBXW7, UBR5 depletion leads to accumulation of MYC in cells. We demonstrate interaction of UBR5 with MYC and reduced K48-linked ubiquitination of MYC upon loss of UBR5 in cells. Interestingly, in cancer cell lines with amplified MYC expression, depletion of UBR5 resulted in reduced cell survival, as a consequence of MYC stabilization. Finally, we show that MYC and UBR5 are co-amplified in more than 40% of cancer cells and that MYC copy number amplification correlates with enhanced transcriptional output of UBR5. This suggests that UBR5 acts as a buffer in MYC amplified settings and protects these cells from apoptosis.
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Affiliation(s)
- Lina Schukur
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland. .,Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
| | - Tamara Zimmermann
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland
| | - Ole Niewoehner
- NIBR Chemical Biology and Therapeutics, Novartis, Cambridge, USA
| | - Grainne Kerr
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland
| | - Scott Gleim
- NIBR Chemical Biology and Therapeutics, Novartis, Cambridge, USA
| | - Beatrice Bauer-Probst
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland
| | - Britta Knapp
- NIBR Chemical Biology and Therapeutics, Novartis, Cambridge, USA
| | - Giorgio G Galli
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland
| | - Xiaoyou Liang
- NIBR Chemical Biology and Therapeutics, Novartis, Cambridge, USA
| | - Angelica Mendiola
- Genomics Institute of the Novartis Research Foundation, LaJolla, USA
| | - John Reece-Hoyes
- NIBR Chemical Biology and Therapeutics, Novartis, Cambridge, USA
| | - Melivoia Rapti
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland
| | - Ines Barbosa
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland
| | - Markus Reschke
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland
| | - Thomas Radimerski
- Novartis Institutes for Biomedical Research (NIBR) Oncology, Novartis, Basel, Switzerland.,Basilea Pharmaceutica, Basel, Switzerland
| | - Claudio R Thoma
- NIBR Chemical Biology and Therapeutics, Novartis, Cambridge, USA.
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5
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Kobylarz MJ, Goodwin JM, Kang ZB, Annand JW, Hevi S, O’Mahony E, McAllister G, Reece-Hoyes J, Wang Q, Alford J, Russ C, Lindeman A, Beibel M, Roma G, Carbone W, Knehr J, Loureiro J, Antczak C, Wiederschain D, Murphy LO, Menon S, Nyfeler B. An iron-dependent metabolic vulnerability underlies VPS34-dependence in RKO cancer cells. PLoS One 2020; 15:e0235551. [PMID: 32833964 PMCID: PMC7446895 DOI: 10.1371/journal.pone.0235551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 02/06/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022] Open
Abstract
VPS34 is a key regulator of endomembrane dynamics and cargo trafficking, and is essential in cultured cell lines and in mice. To better characterize the role of VPS34 in cell growth, we performed unbiased cell line profiling studies with the selective VPS34 inhibitor PIK-III and identified RKO as a VPS34-dependent cellular model. Pooled CRISPR screen in the presence of PIK-III revealed endolysosomal genes as genetic suppressors. Dissecting VPS34-dependent alterations with transcriptional profiling, we found the induction of hypoxia response and cholesterol biosynthesis as key signatures. Mechanistically, acute VPS34 inhibition enhanced lysosomal degradation of transferrin and low-density lipoprotein receptors leading to impaired iron and cholesterol uptake. Excess soluble iron, but not cholesterol, was sufficient to partially rescue the effects of VPS34 inhibition on mitochondrial respiration and cell growth, indicating that iron limitation is the primary driver of VPS34-dependency in RKO cells. Loss of RAB7A, an endolysosomal marker and top suppressor in our genetic screen, blocked transferrin receptor degradation, restored iron homeostasis and reversed the growth defect as well as metabolic alterations due to VPS34 inhibition. Altogether, our findings suggest that impaired iron mobilization via the VPS34-RAB7A axis drive VPS34-dependence in certain cancer cells.
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Affiliation(s)
- Marek J. Kobylarz
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Jonathan M. Goodwin
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Zhao B. Kang
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - John W. Annand
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Sarah Hevi
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Ellen O’Mahony
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Gregory McAllister
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - John Reece-Hoyes
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Qiong Wang
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - John Alford
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Carsten Russ
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Alicia Lindeman
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Joseph Loureiro
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Christophe Antczak
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Dmitri Wiederschain
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Leon O. Murphy
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Suchithra Menon
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
- * E-mail: (SM); (BN)
| | - Beat Nyfeler
- Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail: (SM); (BN)
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6
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Alimov I, Menon S, Cochran N, Maher R, Wang Q, Alford J, Concannon JB, Yang Z, Harrington E, Llamas L, Lindeman A, Hoffman G, Schuhmann T, Russ C, Reece-Hoyes J, Canham SM, Cai X. Bile acid analogues are activators of pyrin inflammasome. J Biol Chem 2019; 294:3359-3366. [PMID: 30647128 DOI: 10.1074/jbc.ra118.005103] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/21/2018] [Indexed: 01/02/2023] Open
Abstract
Bile acids are critical metabolites in the gastrointestinal tract and contribute to maintaining intestinal immune homeostasis through cross-talk with the gut microbiota. The conversion of bile acids by the gut microbiome is now recognized as a factor affecting both host metabolism and immune responses, but its physiological roles remain unclear. We conducted a screen for microbiome metabolites that would function as inflammasome activators and herein report the identification of 12-oxo-lithocholic acid (BAA485), a potential microbiome-derived bile acid metabolite. We demonstrate that the more potent analogue 11-oxo-12S-hydroxylithocholic acid methyl ester (BAA473) can induce secretion of interleukin-18 (IL-18) through activation of the inflammasome in both myeloid and intestinal epithelial cells. Using a genome-wide CRISPR screen with compound induced pyroptosis in THP-1 cells, we identified that inflammasome activation by BAA473 is pyrin-dependent (MEFV). To our knowledge, the bile acid analogues BAA485 and BAA473 are the first small molecule activators of the pyrin inflammasome. We surmise that pyrin inflammasome activation through microbiota-modified bile acid metabolites such as BAA473 and BAA485 plays a role in gut microbiota regulated intestinal immune response. The discovery of these two bioactive compounds may help to further unveil the importance of pyrin in gut homeostasis and autoimmune diseases.
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Affiliation(s)
- Irina Alimov
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Suchithra Menon
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Nadire Cochran
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Rob Maher
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Qiong Wang
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - John Alford
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - John B Concannon
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Zinger Yang
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Edmund Harrington
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Luis Llamas
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Alicia Lindeman
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Gregory Hoffman
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Tim Schuhmann
- the Novartis Institute for Biomedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Carsten Russ
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - John Reece-Hoyes
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Stephen M Canham
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Xinming Cai
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
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7
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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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8
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Ji L, Lu B, Wang Z, Yang Z, Reece-Hoyes J, Russ C, Xu W, Cong F. Identification of ICAT as an APC Inhibitor, Revealing Wnt-Dependent Inhibition of APC-Axin Interaction. Mol Cell 2018; 72:37-47.e4. [DOI: 10.1016/j.molcel.2018.07.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/18/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022]
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9
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Ihry RJ, Worringer KA, Salick MR, Frias E, Ho D, Theriault K, Kommineni S, Chen J, Sondey M, Ye C, Randhawa R, Kulkarni T, Yang Z, McAllister G, Russ C, Reece-Hoyes J, Forrester W, Hoffman GR, Dolmetsch R, Kaykas A. p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med 2018; 24:939-946. [PMID: 29892062 DOI: 10.1038/s41591-018-0050-6] [Citation(s) in RCA: 609] [Impact Index Per Article: 101.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/28/2018] [Indexed: 12/13/2022]
Abstract
CRISPR/Cas9 has revolutionized our ability to engineer genomes and conduct genome-wide screens in human cells1-3. Whereas some cell types are amenable to genome engineering, genomes of human pluripotent stem cells (hPSCs) have been difficult to engineer, with reduced efficiencies relative to tumour cell lines or mouse embryonic stem cells3-13. Here, using hPSC lines with stable integration of Cas9 or transient delivery of Cas9-ribonucleoproteins (RNPs), we achieved an average insertion or deletion (indel) efficiency greater than 80%. This high efficiency of indel generation revealed that double-strand breaks (DSBs) induced by Cas9 are toxic and kill most hPSCs. In previous studies, the toxicity of Cas9 in hPSCs was less apparent because of low transfection efficiency and subsequently low DSB induction3. The toxic response to DSBs was P53/TP53-dependent, such that the efficiency of precise genome engineering in hPSCs with a wild-type P53 gene was severely reduced. Our results indicate that Cas9 toxicity creates an obstacle to the high-throughput use of CRISPR/Cas9 for genome engineering and screening in hPSCs. Moreover, as hPSCs can acquire P53 mutations14, cell replacement therapies using CRISPR/Cas9-enginereed hPSCs should proceed with caution, and such engineered hPSCs should be monitored for P53 function.
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Affiliation(s)
- Robert J Ihry
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Kathleen A Worringer
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Max R Salick
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Elizabeth Frias
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Daniel Ho
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Kraig Theriault
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sravya Kommineni
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Julie Chen
- Department of Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Ranjit Randhawa
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Tripti Kulkarni
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Zinger Yang
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Gregory McAllister
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Carsten Russ
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - John Reece-Hoyes
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - William Forrester
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Gregory R Hoffman
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ricardo Dolmetsch
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ajamete Kaykas
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
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10
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Wang Z, Plasschaert LW, Aryal S, Renaud NA, Yang Z, Choo-Wing R, Pessotti AD, Kirkpatrick ND, Cochran NR, Carbone W, Maher R, Lindeman A, Russ C, Reece-Hoyes J, McAllister G, Hoffman GR, Roma G, Jaffe AB. TRRAP is a central regulator of human multiciliated cell formation. J Cell Biol 2018; 217:1941-1955. [PMID: 29588376 PMCID: PMC5987713 DOI: 10.1083/jcb.201706106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 06/17/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/24/2022] Open
Abstract
Multiciliated cells (MCCs) function to promote directional fluid flow across epithelial tissues. Wang et al. show that TRRAP, a component of multiple histone acetyltransferase complexes, is required for airway MCC formation and regulates a network of genes involved in MCC differentiation and function. The multiciliated cell (MCC) is an evolutionarily conserved cell type, which in vertebrates functions to promote directional fluid flow across epithelial tissues. In the conducting airway, MCCs are generated by basal stem/progenitor cells and act in concert with secretory cells to perform mucociliary clearance to expel pathogens from the lung. Studies in multiple systems, including Xenopus laevis epidermis, murine trachea, and zebrafish kidney, have uncovered a transcriptional network that regulates multiple steps of multiciliogenesis, ultimately leading to an MCC with hundreds of motile cilia extended from their apical surface, which beat in a coordinated fashion. Here, we used a pool-based short hairpin RNA screening approach and identified TRRAP, an essential component of multiple histone acetyltransferase complexes, as a central regulator of MCC formation. Using a combination of immunofluorescence, signaling pathway modulation, and genomic approaches, we show that (a) TRRAP acts downstream of the Notch2-mediated basal progenitor cell fate decision and upstream of Multicilin to control MCC differentiation; and (b) TRRAP binds to the promoters and regulates the expression of a network of genes involved in MCC differentiation and function, including several genes associated with human ciliopathies.
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Affiliation(s)
- Zhao Wang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Lindsey W Plasschaert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Shivani Aryal
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Nicole A Renaud
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Zinger Yang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Rayman Choo-Wing
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Angelica D Pessotti
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Nadire R Cochran
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Rob Maher
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Alicia Lindeman
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Carsten Russ
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - John Reece-Hoyes
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Gregory McAllister
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Gregory R Hoffman
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Aron B Jaffe
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
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11
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Michlits G, Hubmann M, Wu SH, Vainorius G, Budusan E, Zhuk S, Burkard TR, Novatchkova M, Aichinger M, Lu Y, Reece-Hoyes J, Nitsch R, Schramek D, Hoepfner D, Elling U. CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens. Nat Methods 2017; 14:1191-1197. [PMID: 29039415 DOI: 10.1038/nmeth.4466] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [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: 04/05/2017] [Accepted: 09/11/2017] [Indexed: 12/12/2022]
Abstract
Pooled CRISPR screens are a powerful tool for assessments of gene function. However, conventional analysis is based exclusively on the relative abundance of integrated single guide RNAs (sgRNAs) between populations, which does not discern distinct phenotypes and editing outcomes generated by identical sgRNAs. Here we present CRISPR-UMI, a single-cell lineage-tracing methodology for pooled screening to account for cell heterogeneity. We generated complex sgRNA libraries with unique molecular identifiers (UMIs) that allowed for screening of clonally expanded, individually tagged cells. A proof-of-principle CRISPR-UMI negative-selection screen provided increased sensitivity and robustness compared with conventional analysis by accounting for underlying cellular and editing-outcome heterogeneity and detection of outlier clones. Furthermore, a CRISPR-UMI positive-selection screen uncovered new roadblocks in reprogramming mouse embryonic fibroblasts as pluripotent stem cells, distinguishing reprogramming frequency and speed (i.e., effect size and probability). CRISPR-UMI boosts the predictive power, sensitivity, and information content of pooled CRISPR screens.
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Affiliation(s)
- Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Maria Hubmann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Szu-Hsien Wu
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Gintautas Vainorius
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Elena Budusan
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Sergei Zhuk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Martin Aichinger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Yiqing Lu
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John Reece-Hoyes
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Roberto Nitsch
- Discovery Sciences RAD, AstraZeneca R&D, Gothenburg, Sweden
| | - Daniel Schramek
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
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12
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Wang H, Lu B, Castillo J, Zhang Y, Yang Z, McAllister G, Lindeman A, Reece-Hoyes J, Tallarico J, Russ C, Hoffman G, Xu W, Schirle M, Cong F. Tankyrase Inhibitor Sensitizes Lung Cancer Cells to Endothelial Growth Factor Receptor (EGFR) Inhibition via Stabilizing Angiomotins and Inhibiting YAP Signaling. J Biol Chem 2016; 291:15256-66. [PMID: 27231341 DOI: 10.1074/jbc.m116.722967] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [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: 02/19/2016] [Indexed: 11/06/2022] Open
Abstract
YAP signaling pathway plays critical roles in tissue homeostasis, and aberrant activation of YAP signaling has been implicated in cancers. To identify tractable targets of YAP pathway, we have performed a pathway-based pooled CRISPR screen and identified tankyrase and its associated E3 ligase RNF146 as positive regulators of YAP signaling. Genetic ablation or pharmacological inhibition of tankyrase prominently suppresses YAP activity and YAP target gene expression. Using a proteomic approach, we have identified angiomotin family proteins, which are known negative regulators of YAP signaling, as novel tankyrase substrates. Inhibition of tankyrase or depletion of RNF146 stabilizes angiomotins. Angiomotins physically interact with tankyrase through a highly conserved motif at their N terminus, and mutation of this motif leads to their stabilization. Tankyrase inhibitor-induced stabilization of angiomotins reduces YAP nuclear translocation and decreases downstream YAP signaling. We have further shown that knock-out of YAP sensitizes non-small cell lung cancer to EGFR inhibitor Erlotinib. Tankyrase inhibitor, but not porcupine inhibitor, which blocks Wnt secretion, enhances growth inhibitory activity of Erlotinib. This activity is mediated by YAP inhibition and not Wnt/β-catenin inhibition. Our data suggest that tankyrase inhibition could serve as a novel strategy to suppress YAP signaling for combinatorial targeted therapy.
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Affiliation(s)
- Hui Wang
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Bo Lu
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Johnny Castillo
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Yue Zhang
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Zinger Yang
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Gregory McAllister
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Alicia Lindeman
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - John Reece-Hoyes
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - John Tallarico
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Carsten Russ
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Greg Hoffman
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Wenqing Xu
- Department of Biological Structure, University of Washington, Seattle, Washington 98195
| | - Markus Schirle
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Feng Cong
- From the Department of Developmental and Molecular Pathways, Novartis Institute of Biomedical Research, Cambridge, Massachusetts 02139 and
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13
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Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, Lee D, Rosenberg J, Svrzikapa N, Blanc A, Carnec A, Carvunis AR, Pulak R, Shingles J, Reece-Hoyes J, Hunt-Newbury R, Viveiros R, Mohler WA, Tasan M, Roth FP, Le Peuch C, Hope IA, Johnsen R, Moerman DG, Barabási AL, Baillie D, Vidal M. Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat Biotechnol 2007; 25:663-8. [PMID: 17486083 DOI: 10.1038/nbt1305] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 04/13/2007] [Indexed: 12/13/2022]
Abstract
Differential regulation of gene expression is essential for cell fate specification in metazoans. Characterizing the transcriptional activity of gene promoters, in time and in space, is therefore a critical step toward understanding complex biological systems. Here we present an in vivo spatiotemporal analysis for approximately 900 predicted C. elegans promoters (approximately 5% of the predicted protein-coding genes), each driving the expression of green fluorescent protein (GFP). Using a flow-cytometer adapted for nematode profiling, we generated 'chronograms', two-dimensional representations of fluorescence intensity along the body axis and throughout development from early larvae to adults. Automated comparison and clustering of the obtained in vivo expression patterns show that genes coexpressed in space and time tend to belong to common functional categories. Moreover, integration of this data set with C. elegans protein-protein interactome data sets enables prediction of anatomical and temporal interaction territories between protein partners.
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Affiliation(s)
- Denis Dupuy
- Center for Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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