51
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Mangé A, Coyaud E, Desmetz C, Laurent E, Béganton B, Coopman P, Raught B, Solassol J. FKBP4 connects mTORC2 and PI3K to activate the PDK1/Akt-dependent cell proliferation signaling in breast cancer. Am J Cancer Res 2019; 9:7003-7015. [PMID: 31660083 PMCID: PMC6815969 DOI: 10.7150/thno.35561] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Purpose: Among the FKBP family members, FKBP4 has been described to have a potential role in tumorigenesis, and as a putative tissue marker. We previously showed that FKBP4, an HSP90-associated co-chaperone, can elicit immune response as a tumor-specific antigen, and are overexpressed in breast cancer. Experimental design: In this study, we examined how loss of FKBP4 affect breast cancer progression and exploited protein interactomics to gain mechanistic insight into this process. Results: We found that FKBP4 expression is associated with breast cancer progression and prognosis, especially of ER-negative breast cancer. Furthermore, FKBP4 depletion specifically reduces cell growth and proliferation of triple negative breast cancer cell model and xenograft tumor model. Using specific protein interactome strategy by BirA proximity-dependent biotin identification, we demonstrated that FKBP4 is a novel PI3K-Akt-mTOR proximal interacting protein. Conclusion: Our results suggest that FKBP4 interacts with PI3K and can enhance Akt activation through PDK1 and mTORC2.
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52
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Frendo-Cumbo S, Jaldin-Fincati JR, Coyaud E, Laurent EMN, Townsend LK, Tan JMJ, Xavier RJ, Pillon NJ, Raught B, Wright DC, Brumell JH, Klip A. Deficiency of the autophagy gene ATG16L1 induces insulin resistance through KLHL9/KLHL13/CUL3-mediated IRS1 degradation. J Biol Chem 2019; 294:16172-16185. [PMID: 31515271 DOI: 10.1074/jbc.ra119.009110] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/29/2019] [Indexed: 12/23/2022] Open
Abstract
Connections between deficient autophagy and insulin resistance have emerged, however, the mechanism through which reduced autophagy impairs insulin-signaling remains unknown. We examined mouse embryonic fibroblasts lacking Atg16l1 (ATG16L1 KO mouse embryonic fibroblasts (MEFs)), an essential autophagy gene, and observed deficient insulin and insulin-like growth factor-1 signaling. ATG16L1 KO MEFs displayed reduced protein content of insulin receptor substrate-1 (IRS1), pivotal to insulin signaling, whereas IRS1myc overexpression recovered downstream insulin signaling. Endogenous IRS1 protein content and insulin signaling were restored in ATG16L1 KO mouse embryonic fibroblasts (MEF) upon proteasome inhibition. Through proximity-dependent biotin identification (BioID) and co-immunoprecipitation, we found that Kelch-like proteins KLHL9 and KLHL13, which together form an E3 ubiquitin (Ub) ligase complex with cullin 3 (CUL3), are novel IRS1 interactors. Expression of Klhl9 and Klhl13 was elevated in ATG16L1 KO MEFs and siRNA-mediated knockdown of Klhl9, Klhl13, or Cul3 recovered IRS1 expression. Moreover, Klhl13 and Cul3 knockdown increased insulin signaling. Notably, adipose tissue of high-fat fed mice displayed lower Atg16l1 mRNA expression and IRS1 protein content, and adipose tissue KLHL13 and CUL3 expression positively correlated to body mass index in humans. We propose that ATG16L1 deficiency evokes insulin resistance through induction of Klhl9 and Klhl13, which, in complex with Cul3, promote proteasomal IRS1 degradation.
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Affiliation(s)
- Scott Frendo-Cumbo
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2C1, Canada
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2C1, Canada
| | - Logan K Townsend
- Department of Human Health & Nutritional Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Joel M J Tan
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Nicolas J Pillon
- Departments of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden 171 77
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2C1, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - David C Wright
- Department of Human Health & Nutritional Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - John Hunter Brumell
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada .,Department of Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,SickKids IBD Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Amira Klip
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada .,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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53
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Dho SE, Silva-Gagliardi N, Morgese F, Coyaud E, Lamoureux E, Berry DM, Raught B, McGlade CJ. Proximity interactions of the ubiquitin ligase Mind bomb 1 reveal a role in regulation of epithelial polarity complex proteins. Sci Rep 2019; 9:12471. [PMID: 31462741 PMCID: PMC6713736 DOI: 10.1038/s41598-019-48902-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 04/29/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023] Open
Abstract
MIB1 belongs to the RING domain containing family of E3 ubiquitin ligases. In vertebrates, MIB1 plays an essential role in activation of Notch signaling during development, through the ubiquitination and endocytosis of Notch ligands. More recently, Notch independent functions for MIB1 have been described in centriole homeostasis, dendritic spine outgrowth and directional cell migration. Here we use proximity-dependent biotin identification (BioID) to define the MIB1 interactome that included 163 high confidence interactions with polypeptides linked to centrosomes and cilia, endosomal trafficking, RNA and DNA processing, the ubiquitin system, and cell adhesion. Biochemical analysis identified several proteins within these groups including CCDC14 and EPS15 that were ubiquitinated but not degraded when co-expressed with MIB1. The MIB1 interactome included the epithelial cell polarity protein, EPB41L5. MIB1 binds to and ubiquitinates EPB41L5 resulting in its degradation. Furthermore, MIB1 ubiquitinates the EPB41L5-associated polarity protein CRB1, an important determinant of the apical membrane. In polarized cells, MIB1 localized to the lateral membrane with EPB41L5 and to the tight junction with CRB1, CRB3 and ZO1. Furthermore, over expression of MIB1 resulted in altered epithelial cell morphology and apical membrane expansion. These results support a role for MIB1 in regulation of polarized epithelial cell morphology.
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Affiliation(s)
- Sascha E Dho
- Program in Cell Biology and The Arthur and Sonia Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Ave., Toronto, ON, M5G 1X8, Canada
| | - Nancy Silva-Gagliardi
- Program in Cell Biology and The Arthur and Sonia Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Ave., Toronto, ON, M5G 1X8, Canada
| | - Fabio Morgese
- Program in Cell Biology and The Arthur and Sonia Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Ave., Toronto, ON, M5G 1X8, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Emily Lamoureux
- Program in Cell Biology and The Arthur and Sonia Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Ave., Toronto, ON, M5G 1X8, Canada
| | - Donna M Berry
- Program in Cell Biology and The Arthur and Sonia Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Ave., Toronto, ON, M5G 1X8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - C Jane McGlade
- Program in Cell Biology and The Arthur and Sonia Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Ave., Toronto, ON, M5G 1X8, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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54
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Gheiratmand L, Coyaud E, Gupta GD, Laurent EMN, Hasegan M, Prosser SL, Gonçalves J, Raught B, Pelletier L. Spatial and proteomic profiling reveals centrosome-independent features of centriolar satellites. EMBO J 2019; 38:e101109. [PMID: 31304627 PMCID: PMC6627244 DOI: 10.15252/embj.2018101109] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/19/2022] Open
Abstract
Centriolar satellites are small electron-dense granules that cluster in the vicinity of centrosomes. Satellites have been implicated in multiple critical cellular functions including centriole duplication, centrosome maturation, and ciliogenesis, but their precise composition and assembly properties have remained poorly explored. Here, we perform in vivo proximity-dependent biotin identification (BioID) on 22 human satellite proteins, to identify 2,113 high-confidence interactions among 660 unique polypeptides. Mining this network, we validate six additional satellite components. Analysis of the satellite interactome, combined with subdiffraction imaging, reveals the existence of multiple unique microscopically resolvable satellite populations that display distinct protein interaction profiles. We further show that loss of satellites in PCM1-depleted cells results in a dramatic change in the satellite interaction landscape. Finally, we demonstrate that satellite composition is largely unaffected by centriole depletion or disruption of microtubules, indicating that satellite assembly is centrosome-independent. Together, our work offers the first systematic spatial and proteomic profiling of human centriolar satellites and paves the way for future studies aimed at better understanding the biogenesis and function(s) of these enigmatic structures.
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Affiliation(s)
- Ladan Gheiratmand
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Etienne Coyaud
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
| | - Gagan D Gupta
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
- Present address:
Department of Chemistry and BiologyRyerson UniversityTorontoONCanada
| | | | - Monica Hasegan
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Suzanna L Prosser
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - João Gonçalves
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Brian Raught
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoONCanada
| | - Laurence Pelletier
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
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55
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Botham AD, Coyaud E, Nirmalanandhan S, Gronda M, Hurren R, Maclean N, Germain JS, Mirali S, Laurent E, Raught B, Schimmer A. Abstract 4529: Mapping the protein interactome of mitochondrial intermembrane space proteases identifies a novel function for HTRA2. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4529] [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
Mitochondria possess unique proteases that localize to specific sub-compartments of the organelle. However, the functions of these proteases are largely ill-defined. Here, we used proximity-dependent biotinylation (BioID) to map the interactomes of seven proteases located in the intermembrane space of the mitochondria. The mitochondrial intermembrane space proteases HTRA2, OMA1, YME1L1, LACTB, IMMP1L, IMMP2L and PARL were cloned in-frame with the abortive E. coli biotin ligase BirA*, and expressed in 293 T-REx cells. Cell culture media was spiked with biotin for 24 hrs, the cells lysed, and biotinylated proteins were isolated and identified by mass spectrometry. In total, we identified 342 different proteins as high confidence interactors of the seven mitochondrial proteases. Of these, 272 are assigned a GO mitochondrial annotation, and 230 proteins interacted with only 1 or 2 proteases in our dataset. Validation efforts were focused on high temperature requirement peptidase A 2 (HTRA2). HTRA2 is a serine protease that is released into the cytoplasm during apoptosis where it binds Inhibitor of Apoptosis Proteins (IAPs). However, little is known about the function of HTRA2 in the mitochondria. HTRA2 interacted with 60 mitochondrial, 11 nuclear and 4 cytoplasmic proteins, including its known interactor XIAP, and consistent with its known localization to these cellular compartments. HTRA2 interacted with 8 out of 13 components of the MIB complex, a multiprotein assembly that is essential for proper mitochondrial cristae formation. Knockdown of HTRA2 with shRNA in 293T-REx cells disrupted cristae formation and this phenotype was rescued by expression of an shRNA-resistant HTRA2 cDNA. Compared to normal hematopoietic cells, HTRA2 mRNA expression levels are increased in a subgroup of primary AML cells. HTRA2 knockdown in OCI-AML2 leukemia cells led to a similar disruption of mitochondrial cristae. Knockdown of HTRA2 in OCI-AML2 cells led to increased levels of the MIB subunit IMMT, but not two other MIB complex subunits, SAMM50 and CHCHD3. Finally, in cell-free assays, we demonstrate that recombinant HTRA2 can degrade recombinant IMMT, but not SAMM50 or CHCHD3.Thus, we have mapped the interactomes of the proteases of the mitochondrial intermembrane space. Through this effort, we discovered that HTRA2 regulates protein levels of the MIB complex subunit IMMT and that disruption of this process affects mitochondrial cristae formation.
Citation Format: Aaron D. Botham, Etienne Coyaud, Sanjit Nirmalanandhan, Marcela Gronda, Rose Hurren, Neil Maclean, Jonathan St. Germain, Sara Mirali, Estelle Laurent, Brian Raught, Aaron Schimmer. Mapping the protein interactome of mitochondrial intermembrane space proteases identifies a novel function for HTRA2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4529.
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Affiliation(s)
- Aaron D. Botham
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Sanjit Nirmalanandhan
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Rose Hurren
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Neil Maclean
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Jonathan St. Germain
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Sara Mirali
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
| | - Aaron Schimmer
- Princess Margaret Cancer Center - University Health Network, Toronto, Ontario, Canada
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56
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Ishizawa J, Zarabi SF, Davis RE, Halgas O, Nii T, Jitkova Y, Zhao R, St-Germain J, Heese LE, Egan G, Ruvolo VR, Barghout SH, Nishida Y, Hurren R, Ma W, Gronda M, Link T, Wong K, Mabanglo M, Kojima K, Borthakur G, MacLean N, Ma JMC, Leber AB, Minden MD, Houry W, Kantarjian H, Stogniew M, Raught B, Pai EF, Schimmer AD, Andreeff M. Abstract 2720: Mitochondrial ClpP-mediated proteolysis induces selective cancer cell lethality. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2720] [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
ClpP is a mitochondrial protease and a major protein quality control mediator that primarily interacts with metabolic enzymes in mitochondria. Here, we demonstrate that activation of this protease results in prominent anti-cancer activity, and propose ClpP activation as a novel therapeutic strategy for cancer and hematologic malignancies. We used genetic and chemical tools to activate ClpP. In a genetic approach, we tested the anti-cancer effects of ClpP activation by expressing a constitutively active ClpP mutant. Indeed, induction of the active ClpP mutant induced apoptosis in vitro and inhibited tumor progression in vivo. To further explore the antineoplastic effects of ClpP activation, we then performed a chemical screen of an in-house library of on-patent and off-patent drugs and identified imipridones (ONC201 and ONC212) as potent ClpP agonists. Imipridones are first-in-class antineoplastic agents and have shown preclinical efficacy in various malignancies in vitro and in vivo and are currently being evaluated in clinical trials in a diverse spectrum of cancers. Importantly, we and others have shown that their activity is agnostic to TP53 mutational status. Of note, molecular targets of imipridones that bind the drugs and are functionally important for their cytotoxicity have never been identified. Through extensive chemical investigations, including analysis of binding mechanism of the compounds to ClpP in cell free (ITC) and cell based assays (CETSA) as well as molecular analysis of the crystal structure, we demonstrate that these molecules bind ClpP non-covalently, and activate the protease by stabilizing the ClpP 14-mer, enlarging the axial pores of the complex, and inducing structural changes in the residues surrounding and including the catalytic triad. In leukemia, lymphoma and colon cancer cells including primary acute myeloid leukemia (AML) cells, both compounds displayed potent ClpP-dependent cytotoxicity with IC50s in low micro- or nanomolar ranges. Importantly, in primary AML samples, pretreatment ClpP levels correlated with response to imipridones. In lymphoma and AML xenograft models, both genetic and chemical activation of ClpP resulted in antitumor effects, while expression of inactive D190A ClpP mutant induced resistance. Mechanistically, ClpP activation leads to increased degradation of substrates of the enzyme including respiratory chain complex subunits and mitochondrial translation system. The resultant impaired mitochondrial structure and reduction in oxygen consumption is selectively cytotoxic to malignant cells that rely highly on mitochondrial energy production for their survival, whereas normal cells are not affected. In conclusion, ClpP activation is an entirely novel therapeutic strategy for malignant tumors. Our findings also suggest a general concept of inducing TP53-independent cancer cell lethality through activation of mitochondrial proteolysis.
Citation Format: Jo Ishizawa, Sarah F. Zarabi, R Eric Davis, Ondrej Halgas, Takenobu Nii, Yulia Jitkova, Ran Zhao, Jonathan St-Germain, Lauren E. Heese, Grace Egan, Vivian R. Ruvolo, Samir H. Barghout, Yuki Nishida, Rose Hurren, Wencai Ma, Marcela Gronda, Todd Link, Keith Wong, Mark Mabanglo, Kensuke Kojima, Gautam Borthakur, Neil MacLean, John Man Chun Ma, Andrew B. Leber, Mark D. Minden, Walid Houry, Hagop Kantarjian, Martin Stogniew, Brian Raught, Emil F. Pai, Aaron D. Schimmer, Michael Andreeff. Mitochondrial ClpP-mediated proteolysis induces selective cancer cell lethality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2720.
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Affiliation(s)
- Jo Ishizawa
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sarah F. Zarabi
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - R Eric Davis
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ondrej Halgas
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Takenobu Nii
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yulia Jitkova
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ran Zhao
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jonathan St-Germain
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lauren E. Heese
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Grace Egan
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Samir H. Barghout
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yuki Nishida
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rose Hurren
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wencai Ma
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marcela Gronda
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Todd Link
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Keith Wong
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark Mabanglo
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | | | - Neil MacLean
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Andrew B. Leber
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark D. Minden
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Walid Houry
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | | | - Brian Raught
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Emil F. Pai
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron D. Schimmer
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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57
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Knight JDR, Choi H, Gupta GD, Pelletier L, Raught B, Nesvizhskii AI, Gingras AC. ProHits-viz: a suite of web tools for visualizing interaction proteomics data. Nat Methods 2019; 14:645-646. [PMID: 28661499 DOI: 10.1038/nmeth.4330] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- James D R Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore
| | - Gagan D Gupta
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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58
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Ishizawa J, Zarabi SF, Davis RE, Halgas O, Nii T, Jitkova Y, Zhao R, St-Germain J, Heese LE, Egan G, Ruvolo VR, Barghout SH, Nishida Y, Hurren R, Ma W, Gronda M, Link T, Wong K, Mabanglo M, Kojima K, Borthakur G, MacLean N, Ma MCJ, Leber AB, Minden MD, Houry W, Kantarjian H, Stogniew M, Raught B, Pai EF, Schimmer AD, Andreeff M. Mitochondrial ClpP-Mediated Proteolysis Induces Selective Cancer Cell Lethality. Cancer Cell 2019; 35:721-737.e9. [PMID: 31056398 PMCID: PMC6620028 DOI: 10.1016/j.ccell.2019.03.014] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/13/2018] [Accepted: 03/29/2019] [Indexed: 12/20/2022]
Abstract
The mitochondrial caseinolytic protease P (ClpP) plays a central role in mitochondrial protein quality control by degrading misfolded proteins. Using genetic and chemical approaches, we showed that hyperactivation of the protease selectively kills cancer cells, independently of p53 status, by selective degradation of its respiratory chain protein substrates and disrupts mitochondrial structure and function, while it does not affect non-malignant cells. We identified imipridones as potent activators of ClpP. Through biochemical studies and crystallography, we show that imipridones bind ClpP non-covalently and induce proteolysis by diverse structural changes. Imipridones are presently in clinical trials. Our findings suggest a general concept of inducing cancer cell lethality through activation of mitochondrial proteolysis.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cell Survival/drug effects
- Crystallography, X-Ray
- Drug Screening Assays, Antitumor
- Endopeptidase Clp/chemistry
- Endopeptidase Clp/genetics
- Endopeptidase Clp/metabolism
- Female
- HCT116 Cells
- HEK293 Cells
- Heterocyclic Compounds, 4 or More Rings/administration & dosage
- Heterocyclic Compounds, 4 or More Rings/chemistry
- Heterocyclic Compounds, 4 or More Rings/pharmacology
- Humans
- Imidazoles
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice
- Mitochondria/metabolism
- Models, Molecular
- Point Mutation
- Protein Conformation/drug effects
- Proteolysis
- Pyridines
- Pyrimidines
- Tumor Suppressor Protein p53/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Jo Ishizawa
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Sarah F Zarabi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - R Eric Davis
- The University of Texas MD Anderson Cancer Center; Department of Lymphoma and Myeloma, Houston, TX 77030, USA
| | - Ondrej Halgas
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Takenobu Nii
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Yulia Jitkova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ran Zhao
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Lauren E Heese
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Grace Egan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Vivian R Ruvolo
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Samir H Barghout
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Yuki Nishida
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Wencai Ma
- The University of Texas MD Anderson Cancer Center, Bioinformatics and Comp Biology, Houston, TX 77030, USA
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Todd Link
- The University of Texas MD Anderson Cancer Center, Genomic Medicine, Houston, TX 77030, USA
| | - Keith Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mark Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kensuke Kojima
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; Saga University, Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Saga 849-8501, Japan
| | - Gautam Borthakur
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Man Chun John Ma
- The University of Texas MD Anderson Cancer Center; Department of Lymphoma and Myeloma, Houston, TX 77030, USA
| | - Andrew B Leber
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Hagop Kantarjian
- The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA
| | | | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Emil F Pai
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Michael Andreeff
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA.
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59
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Ceccarelli DF, Ivantsiv S, Mullin AA, Coyaud E, Manczyk N, Maisonneuve P, Kurinov I, Zhao L, Go C, Gingras AC, Raught B, Cordes S, Sicheri F. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Structure 2019; 27:1000-1012.e6. [PMID: 31056421 DOI: 10.1016/j.str.2019.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/23/2019] [Accepted: 03/27/2019] [Indexed: 12/16/2022]
Abstract
Pseudoenzymes have been identified across a diverse range of enzyme classes and fulfill important cellular functions. Examples of pseudoenzymes exist within ubiquitin conjugating and deubiquitinase (DUB) protein families. Here we characterize FAM105A/OTULINL, the only putative pseudodeubiquitinase of the ovarian tumor protease (OTU domain) family in humans. The crystal structure of FAM105A revealed that the OTU domain possesses structural deficiencies in both active site and substrate-binding infrastructure predicted to impair normal DUB function. We confirmed the absence of catalytic function against all ubiquitin linkages and an inability of FAM105A to bind ubiquitin compared with catalytically active FAM105B/OTULIN. FAM105A co-localized with KDEL markers and Lamin B1 at the endoplasmic reticulum (ER) and nuclear envelope, respectively. Accordingly, the FAM105A interactome exhibited significant enrichment in proteins localized to the ER/outer nuclear, Golgi and vesicular membranes. In light of undetectable deubiquitinase activity, we posit that FAM105A/OTULINL functions through its ability to mediate protein-protein interactions.
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Affiliation(s)
- Derek F Ceccarelli
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Sofiia Ivantsiv
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amber Anne Mullin
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Noah Manczyk
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Pierre Maisonneuve
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL 60439, USA
| | - Liang Zhao
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Chris Go
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Sabine Cordes
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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60
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Saito Y, Li L, Coyaud E, Luna A, Sander C, Raught B, Asara JM, Brown M, Muthuswamy SK. LLGL2 rescues nutrient stress by promoting leucine uptake in ER + breast cancer. Nature 2019; 569:275-279. [PMID: 30996345 DOI: 10.1038/s41586-019-1126-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/01/2019] [Indexed: 12/11/2022]
Abstract
Drosophila Lgl and its mammalian homologues, LLGL1 and LLGL2, are scaffolding proteins that regulate the establishment of apical-basal polarity in epithelial cells1,2. Whereas Lgl functions as a tumour suppressor in Drosophila1, the roles of mammalian LLGL1 and LLGL2 in cancer are unclear. The majority (about 75%) of breast cancers express oestrogen receptors (ERs)3, and patients with these tumours receive endocrine treatment4. However, the development of resistance to endocrine therapy and metastatic progression are leading causes of death for patients with ER+ disease4. Here we report that, unlike LLGL1, LLGL2 is overexpressed in ER+ breast cancer and promotes cell proliferation under nutrient stress. LLGL2 regulates cell surface levels of a leucine transporter, SLC7A5, by forming a trimeric complex with SLC7A5 and a regulator of membrane fusion, YKT6, to promote leucine uptake and cell proliferation. The oestrogen receptor targets LLGL2 expression. Resistance to endocrine treatment in breast cancer cells was associated with SLC7A5- and LLGL2-dependent adaption to nutrient stress. SLC7A5 was necessary and sufficient to confer resistance to tamoxifen treatment, identifying SLC7A5 as a potential therapeutic target for overcoming resistance to endocrine treatments in breast cancer. Thus, LLGL2 functions as a promoter of tumour growth and not as a tumour suppressor in ER+ breast cancer. Beyond breast cancer, adaptation to nutrient stress is critically important5, and our findings identify an unexpected role for LLGL2 in this process.
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Affiliation(s)
- Yasuhiro Saito
- Department of Medicine, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Lewyn Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Augustin Luna
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chris Sander
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John M Asara
- Division of Signal Transduction, Department of Medicine, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Senthil K Muthuswamy
- Department of Medicine, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. .,Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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61
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Georges A, Coyaud E, Marcon E, Greenblatt J, Raught B, Frappier L. USP7 Regulates Cytokinesis through FBXO38 and KIF20B. Sci Rep 2019; 9:2724. [PMID: 30804394 PMCID: PMC6389929 DOI: 10.1038/s41598-019-39368-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/18/2019] [Indexed: 01/13/2023] Open
Abstract
The ubiquitin specific protease 7 (USP7 or HAUSP) is known to regulate a variety of cellular processes by binding and deubiquitylating specific target proteins. To gain a more comprehensive understanding of its interactions and functions, we used affinity purification coupled to mass spectrometry to profile USP7 interactions. This revealed a novel interaction with FBXO38, a poorly characterized F-box protein. We showed that USP7 stabilizes FBXO38 dependent on its catalytic activity by protecting FBXO38 from proteasomal degradation. We used a BioID approach to profile the protein interactions (and putative functions) of FBXO38, revealing an interaction with KIF20B, a Kinesin-6 protein required for efficient cytokinesis. FBXO38 was shown to function independently from an SCF complex to stabilize KIF20B. Consequently, depletion of either FBXO38 or USP7 led to dramatic decreases in KIF20B levels and KIF20B at the midbody, which were manifested in cytokinetic defects. Furthermore, cytokinetic defects associated with USP7 silencing were rescued by restoring FBXO38 or KIF20B. The results indicate a novel mechanism of regulating cytokinesis through USP7 and FBXO38.
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Affiliation(s)
- Anna Georges
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Etienne Coyaud
- The Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre, University of Toronto, Toronto, Canada
| | - Brian Raught
- The Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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62
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Kano Y, Gebregiworgis T, Marshall CB, Radulovich N, Poon BPK, St-Germain J, Cook JD, Valencia-Sama I, Grant BMM, Herrera SG, Miao J, Raught B, Irwin MS, Lee JE, Yeh JJ, Zhang ZY, Tsao MS, Ikura M, Ohh M. Tyrosyl phosphorylation of KRAS stalls GTPase cycle via alteration of switch I and II conformation. Nat Commun 2019; 10:224. [PMID: 30644389 PMCID: PMC6333830 DOI: 10.1038/s41467-018-08115-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [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: 08/27/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
Deregulation of the RAS GTPase cycle due to mutations in the three RAS genes is commonly associated with cancer development. Protein tyrosine phosphatase SHP2 promotes RAF-to-MAPK signaling pathway and is an essential factor in RAS-driven oncogenesis. Despite the emergence of SHP2 inhibitors for the treatment of cancers harbouring mutant KRAS, the mechanism underlying SHP2 activation of KRAS signaling remains unclear. Here we report tyrosyl-phosphorylation of endogenous RAS and demonstrate that KRAS phosphorylation via Src on Tyr32 and Tyr64 alters the conformation of switch I and II regions, which stalls multiple steps of the GTPase cycle and impairs binding to effectors. In contrast, SHP2 dephosphorylates KRAS, a process that is required to maintain dynamic canonical KRAS GTPase cycle. Notably, Src- and SHP2-mediated regulation of KRAS activity extends to oncogenic KRAS and the inhibition of SHP2 disrupts the phosphorylation cycle, shifting the equilibrium of the GTPase cycle towards the stalled ‘dark state’. Deregulation of the RAS GTPase cycle due to mutations in RAS genes is commonly associated with cancer development. Here authors use NMR and mass spectrometry to shows that KRAS phosphorylation via Src alters the conformation of switch I and II regions and thereby impacts the GTPase cycle.
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Affiliation(s)
- Yoshihito Kano
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network and Department of Pathology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Betty P K Poon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Ivette Valencia-Sama
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, 5G OA4, Canada
| | - Benjamin M M Grant
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Silvia Gabriela Herrera
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jinmin Miao
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Meredith S Irwin
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, 5G OA4, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network and Department of Pathology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada. .,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.
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63
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Kalkat M, Resetca D, Lourenco C, Chan PK, Wei Y, Shiah YJ, Vitkin N, Tong Y, Sunnerhagen M, Done SJ, Boutros PC, Raught B, Penn LZ. MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis. Mol Cell 2018; 72:836-848.e7. [PMID: 30415952 DOI: 10.1016/j.molcel.2018.09.031] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/09/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
Transforming members of the MYC family (MYC, MYCL1, and MYCN) encode transcription factors containing six highly conserved regions, termed MYC homology boxes (MBs). By conducting proteomic profiling of the MB interactomes, we demonstrate that half of the MYC interactors require one or more MBs for binding. Comprehensive phenotypic analyses reveal that two MBs, MB0 and MBII, are universally required for transformation. MBII mediates interactions with acetyltransferase-containing complexes, enabling histone acetylation, and is essential for MYC-dependent tumor initiation. By contrast, MB0 mediates interactions with transcription elongation factors via direct binding to the general transcription factor TFIIF. MB0 is dispensable for tumor initiation but is a major accelerator of tumor growth. Notably, the full transforming activity of MYC can be restored by co-expression of the non-transforming MB0 and MBII deletion proteins, indicating that these two regions confer separate molecular functions, both of which are required for oncogenic MYC activity.
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Affiliation(s)
- Manpreet Kalkat
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Diana Resetca
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Corey Lourenco
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Pak-Kei Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yong Wei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, Toronto, ON M5G 1L7, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Natasha Vitkin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yufeng Tong
- Structural Genomics Consortium, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5A 1A8, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Susan J Done
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| | - Linda Z Penn
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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64
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Tu WB, Shiah YJ, Lourenco C, Mullen PJ, Dingar D, Redel C, Tamachi A, Ba-Alawi W, Aman A, Al-Awar R, Cescon DW, Haibe-Kains B, Arrowsmith CH, Raught B, Boutros PC, Penn LZ. MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis. Cancer Cell 2018; 34:579-595.e8. [PMID: 30300580 DOI: 10.1016/j.ccell.2018.09.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 06/30/2018] [Accepted: 09/04/2018] [Indexed: 12/22/2022]
Abstract
MYC is an oncogenic driver that regulates transcriptional activation and repression. Surprisingly, mechanisms by which MYC promotes malignant transformation remain unclear. We demonstrate that MYC interacts with the G9a H3K9-methyltransferase complex to control transcriptional repression. Inhibiting G9a hinders MYC chromatin binding at MYC-repressed genes and de-represses gene expression. By identifying the MYC box II region as essential for MYC-G9a interaction, a long-standing missing link between MYC transformation and gene repression is unveiled. Across breast cancer cell lines, the anti-proliferative response to G9a pharmacological inhibition correlates with MYC sensitivity and gene signatures. Consistently, genetically depleting G9a in vivo suppresses MYC-dependent tumor growth. These findings unveil G9a as an epigenetic regulator of MYC transcriptional repression and a therapeutic vulnerability in MYC-driven cancers.
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Affiliation(s)
- William B Tu
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Yu-Jia Shiah
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Corey Lourenco
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Peter J Mullen
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada
| | | | - Cornelia Redel
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Aaliya Tamachi
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada
| | - Wail Ba-Alawi
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S1A8, Canada
| | - David W Cescon
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, ON M5G2C4, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada; Structural Genomics Consortium, Toronto, ON M5G1L7, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada; Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, Toronto, ON M5G1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada.
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65
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Sydor AM, Coyaud E, Rovelli C, Laurent E, Liu H, Raught B, Mennella V. PPP1R35 is a novel centrosomal protein that regulates centriole length in concert with the microcephaly protein RTTN. eLife 2018; 7:37846. [PMID: 30168418 PMCID: PMC6141234 DOI: 10.7554/elife.37846] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 04/26/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023] Open
Abstract
Centrosome structure, function, and number are finely regulated at the cellular level to ensure normal mammalian development. Here, we characterize PPP1R35 as a novel bona fide centrosomal protein and demonstrate that it is critical for centriole elongation. Using quantitative super-resolution microscopy mapping and live-cell imaging we show that PPP1R35 is a resident centrosomal protein located in the proximal lumen above the cartwheel, a region of the centriole that has eluded detailed characterization. Loss of PPP1R35 function results in decreased centrosome number and shortened centrioles that lack centriolar distal and microtubule wall associated proteins required for centriole elongation. We further demonstrate that PPP1R35 acts downstream of, and forms a complex with, RTTN, a microcephaly protein required for distal centriole elongation. Altogether, our study identifies a novel step in the centriole elongation pathway centered on PPP1R35 and elucidates downstream partners of the microcephaly protein RTTN.
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Affiliation(s)
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Cristina Rovelli
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Helen Liu
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Vito Mennella
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Biochemistry, University of Toronto, Ontario, Canada
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66
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Dingar D, Tu WB, Resetca D, Lourenco C, Tamachi A, De Melo J, Houlahan KE, Kalkat M, Chan PK, Boutros PC, Raught B, Penn LZ. MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability. Nat Commun 2018; 9:3502. [PMID: 30158517 PMCID: PMC6115416 DOI: 10.1038/s41467-018-05660-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
The c-MYC (MYC) oncoprotein is deregulated in over 50% of cancers, yet regulatory mechanisms controlling MYC remain unclear. To this end, we interrogated the MYC interactome using BioID mass spectrometry (MS) and identified PP1 (protein phosphatase 1) and its regulatory subunit PNUTS (protein phosphatase-1 nuclear-targeting subunit) as MYC interactors. We demonstrate that endogenous MYC and PNUTS interact across multiple cell types and that they co-occupy MYC target gene promoters. Inhibiting PP1 by RNAi or pharmacological inhibition results in MYC hyperphosphorylation at multiple serine and threonine residues, leading to a decrease in MYC protein levels due to proteasomal degradation through the canonical SCFFBXW7 pathway. MYC hyperphosphorylation can be rescued specifically with exogenous PP1, but not other phosphatases. Hyperphosphorylated MYC retained interaction with its transcriptional partner MAX, but binding to chromatin is significantly compromised. Our work demonstrates that PP1/PNUTS stabilizes chromatin-bound MYC in proliferating cells. Deregulated MYC activity is oncogenic and is deregulated in a large fraction of human cancers. Here the authors find that protein phosphatase 1 and its regulatory subunit PNUTS controls MYC stability and its interaction with chromatin.
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Affiliation(s)
- Dharmendra Dingar
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - William B Tu
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Diana Resetca
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Corey Lourenco
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Aaliya Tamachi
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Jason De Melo
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Kathleen E Houlahan
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada.,Ontario Institute for Cancer Research, Toronto, ON Canada M5G 0A3, Canada
| | - Manpreet Kalkat
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Pak-Kei Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada.,Ontario Institute for Cancer Research, Toronto, ON Canada M5G 0A3, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada.
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Truong D, Boddy KC, Canadien V, Brabant D, Fairn GD, D'Costa VM, Coyaud E, Raught B, Pérez-Sala D, Park WS, Heo WD, Grinstein S, Brumell JH. Salmonella
exploits host Rho GTPase signalling pathways through the phosphatase activity of SopB. Cell Microbiol 2018; 20:e12938. [DOI: 10.1111/cmi.12938] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/11/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Dorothy Truong
- Cell Biology Program; Hospital for Sick Children; Toronto ON Canada
- Department of Molecular Genetics; University of Toronto; Toronto ON Canada
| | - Kirsten C. Boddy
- Cell Biology Program; Hospital for Sick Children; Toronto ON Canada
- Institute of Medical Science; University of Toronto; Toronto ON Canada
| | | | - Danielle Brabant
- Cell Biology Program; Hospital for Sick Children; Toronto ON Canada
| | - Gregory D. Fairn
- Institute of Medical Science; University of Toronto; Toronto ON Canada
- Keenan Research Centre for Biomedical Science; St. Michael's Hospital; Toronto ON Canada
| | | | - Etienne Coyaud
- Princess Margaret Cancer Centre; University Health Network; Toronto Ontario Canada
| | - Brian Raught
- Princess Margaret Cancer Centre; University Health Network; Toronto Ontario Canada
- Department of Medical Biophysics; University of Toronto; Toronto Ontario Canada
| | - Dolores Pérez-Sala
- Department of Structural and Chemical Biology; Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas; Madrid Spain
| | - Wei Sun Park
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Won Do Heo
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- Center for Cognition and Sociality; Institute of Basic Science (IBS); Daejeon Republic of Korea
| | - Sergio Grinstein
- Cell Biology Program; Hospital for Sick Children; Toronto ON Canada
- Institute of Medical Science; University of Toronto; Toronto ON Canada
- Keenan Research Centre for Biomedical Science; St. Michael's Hospital; Toronto ON Canada
- Department of Biochemistry; University of Toronto; Toronto ON Canada
| | - John H. Brumell
- Cell Biology Program; Hospital for Sick Children; Toronto ON Canada
- Department of Molecular Genetics; University of Toronto; Toronto ON Canada
- Institute of Medical Science; University of Toronto; Toronto ON Canada
- Sickkids IBD Centre; Hospital for Sick Children; Toronto ON Canada
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68
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Li L, Guturi KKN, Gautreau B, Patel PS, Saad A, Morii M, Mateo F, Palomero L, Barbour H, Gomez A, Ng D, Kotlyar M, Pastrello C, Jackson HW, Khokha R, Jurisica I, Affar EB, Raught B, Sanchez O, Alaoui-Jamali M, Pujana MA, Hakem A, Hakem R. Ubiquitin ligase RNF8 suppresses Notch signaling to regulate mammary development and tumorigenesis. J Clin Invest 2018; 128:4525-4542. [PMID: 30222135 DOI: 10.1172/jci120401] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 07/26/2018] [Indexed: 12/27/2022] Open
Abstract
The E3 ubiquitin ligase RNF8 plays critical roles in maintaining genomic stability by promoting the repair of DNA double-strand breaks (DSBs) through ubiquitin signaling. Abnormal activation of Notch signaling and defective repair of DSBs promote breast cancer risk. Here, we found that low expression of the full-length RNF8 correlated with poor prognosis for breast cancer patients. Our data revealed that in addition to its role in the repair of DSBs, RNF8 regulated Notch1 signaling and cell-fate determination of mammary luminal progenitors. Mechanistically, RNF8 acted as a negative regulator of Notch signaling by ubiquitylating the active NOTCH1 protein (N1ICD), leading to its degradation. Consistent with abnormal activation of Notch signaling and impaired repair of DSBs in Rnf8-mutant mammary epithelial cells, we observed increased risk of mammary tumorigenesis in mouse models for RNF8 deficiency. Notably, deficiency of RNF8 sensitized breast cancer cells to combination of pharmacological inhibitors of Notch signaling and poly(ADP-ribose) polymerase (PARP), suggesting implications for treatment of breast cancer associated with impaired RNF8 expression or function.
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Affiliation(s)
- Li Li
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kiran Kumar Naidu Guturi
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Brandon Gautreau
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Amine Saad
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Departments of Medicine and Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Mayako Morii
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Francesca Mateo
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Luis Palomero
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Haithem Barbour
- Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Antonio Gomez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Deborah Ng
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Chiara Pastrello
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Hartland W Jackson
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Rama Khokha
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - El Bachir Affar
- Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Otto Sanchez
- University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - Moulay Alaoui-Jamali
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Departments of Medicine and Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Miguel A Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Anne Hakem
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Razq Hakem
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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69
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Coyaud E, Ranadheera C, Cheng D, Gonçalves J, Dyakov BJA, Laurent EMN, St-Germain J, Pelletier L, Gingras AC, Brumell JH, Kim PK, Safronetz D, Raught B. Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus. Mol Cell Proteomics 2018; 17:2242-2255. [PMID: 30037810 DOI: 10.1074/mcp.tir118.000800] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [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: 04/26/2018] [Revised: 07/06/2018] [Indexed: 11/06/2022] Open
Abstract
Zika virus (ZIKV) is a membrane enveloped Flavivirus with a positive strand RNA genome, transmitted by Aedes mosquitoes. The geographical range of ZIKV has dramatically expanded in recent decades resulting in increasing numbers of infected individuals, and the spike in ZIKV infections has been linked to significant increases in both Guillain-Barré syndrome and microcephaly. Although a large number of host proteins have been physically and/or functionally linked to other Flaviviruses, very little is known about the virus-host protein interactions established by ZIKV. Here we map host cell protein interaction profiles for each of the ten polypeptides encoded in the ZIKV genome, generating a protein topology network comprising 3033 interactions among 1224 unique human polypeptides. The interactome is enriched in proteins with roles in polypeptide processing and quality control, vesicle trafficking, RNA processing and lipid metabolism. >60% of the network components have been previously implicated in other types of viral infections; the remaining interactors comprise hundreds of new putative ZIKV functional partners. Mining this rich data set, we highlight several examples of how ZIKV may usurp or disrupt the function of host cell organelles, and uncover an important role for peroxisomes in ZIKV infection.
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Affiliation(s)
- Etienne Coyaud
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Charlene Ranadheera
- §Public Health Agency of Canada, Zoonotic Diseases and Special Pathogens Program, Winnipeg, Manitoba, Canada
| | - Derrick Cheng
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‖Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - João Gonçalves
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Boris J A Dyakov
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Estelle M N Laurent
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laurence Pelletier
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,§§Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,¶¶Sick Kids IBD Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter K Kim
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‖Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David Safronetz
- §Public Health Agency of Canada, Zoonotic Diseases and Special Pathogens Program, Winnipeg, Manitoba, Canada
| | - Brian Raught
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; .,‖‖Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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70
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Zhai A, Qiu L, Coyaud É, Pan Q, Blencowe BJ, Raught B, Privé GG. The crystal structure of RTFDC1 reveals a RING-like pseudoheterodimer responsible for pre-mRNA splicing regulation. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318098483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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71
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Tsofack SP, Botham A, Li Z, Wei EN, Croucher D, Jitkova I, MacLean N, Schimmer AD, Raught B, Trudel S. Abstract 5489: Characterization of mitochondrial STAT3 (mitostat3) function and the mitoStat3 interactome as a therapeutic strategy for multiple myeloma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5489] [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
The oncogenic transcription factor STAT3 is an appealing therapeutic target in cancer including multiple myeloma (MM) where its inhibition has the potential to downregulate aberrant signaling from various upstream molecules. STAT3 has been studied extensively as a transcription factor however, much less is known about its non-classical functions in the mitochondria and in turn, the role of mitochondrial STAT3 (mitoStat3) in cancer biology. Data suggests that mitoStat3 is critical for mediating Ras-induced oncogenic transformation. As activating mutations of the MAPK pathway are reported in over 50% of myeloma patients, we sought to characterize the function of mitoStat3 in MM.
We first confirmed the presence of STAT3 in the mitochondria of myeloma cell lines, AMO1 and XG6 by Western blot analysis. We next used CRISPR/CAS9 to knockdown STAT3 in XG6 and AMO1 cells, which resulted in inhibition of cell proliferation (XG6 and AMO1), apoptosis (XG6) and reduced oxygen consumption rate as measured by extracellular flux analysis (Seahorse assay). To better define the role of mitoStat3 and to identify indirect strategies to interfere with STAT3 activity, we employed a proximity-dependent Biotin Identification (BioID) method to discover mitoStat3 interacting proteins. BioID is a unique method to screen for physiologically relevant protein interactions that occur in living cells. First, wild-type STAT3 was fused to a mitochondrial localization Signal (MLS-Stat3), cloned into pcDNA5 FRT/TO [MCS]-BirAR118G-FLAG plasmid and transfected into HEK293 TRE-x Flp-In cells. BioID identified 225 high confidence mitoStat3-interacting partners in MLS-Stat3 transfected cells. The most abundant proteins in the mitoStat3 interactome included those with roles in mitochondrial translation and mitochondrial electron transport. Futhermore, mitoStat3 was found to interact with the translocase of inner membrane protein Tim44, which together with Tim23 complex facilitates translocation of proteins into the mitochondrial matrix. Genetic knockdown of Tim23 in XG6 cells resulted in decreased mitoStat3 suggesting that this complex may be involved in the import of STAT3 into the mitochondria. Additional mitoStat3 interacting proteins identified by BioID are currently being validated and will be presented.
Taken together, results support the further exploration of the role of mitoStat3 in myeloma cells. Further, identification of mitoStat3 interacting proteins including Tim44 and others may inform alternative strategies to therapeutically target oncogenic STAT3.
Citation Format: Serges P. Tsofack, Aaron Botham, Zhihua Li, Ellen Nong Wei, Danielle Croucher, Ioulia Jitkova, Neil MacLean, Aaron D. Schimmer, Brian Raught, Suzanne Trudel. Characterization of mitochondrial STAT3 (mitostat3) function and the mitoStat3 interactome as a therapeutic strategy for multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5489.
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Affiliation(s)
- Serges P. Tsofack
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron Botham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhihua Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ellen Nong Wei
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Danielle Croucher
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ioulia Jitkova
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron D. Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Suzanne Trudel
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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Melo JD, Kim SS, Lourenco C, Resetca D, Sunnerhagen M, Raught B, Penn LZ. Abstract 5423: Lysine-52 stabilizes the MYC oncoprotein through a SCFFBXW7-independent mechanism. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5423] [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
The oncogenic transcription factor c-MYC (MYC) is deregulated, and often overexpressed, in more than 50% of cancers. MYC deregulation is associated with poor prognosis and aggressive disease, suggesting that the development of therapeutic inhibitors targeting MYC would dramatically impact patient care and outcome. MYC is a highly regulated transcription factor, with a protein and mRNA half-life of approximately 30 min. The most extensively studied pathway regulating MYC protein stability involves ubiquitylation and proteasomal degradation mediated by the E3-ligase, SCFFBXW7. Here we provide evidence for a SCFFBXW7-independent regulatory mechanism centered on Lysine 52 (K52) within MYC Box I (MBI) of the MYC protein. This residue has been shown to be post-translationally modified by both ubiquitylation and SUMOylation, hinting at the interplay of post-translational modifications at this site, and the importance of this residue. We demonstrate that mutation of K52 to arginine (R) renders the MYC protein more labile. Mechanistically, we show that the degradation pathway regulated by K52 is independent of the Cullin-Ring-Ligase (CRL) family of E3-ligases, which includes not only the canonical SCFFBXW7, but also a number of other known MYC-targeting E3-ligases, such as SCFSKP2, SCFβTCRP, SCFFBXO28 and DCXTRUSS. To characterize this degradation pathway further we will utilize unbiased and targeted experiments to elucidate the proteins involved. Taken together, our data identifies a novel regulatory pathway centred on K52 that may be exploited for the development of anti-MYC therapeutics.
Citation Format: Jason De Melo, Sam S. Kim, Corey Lourenco, Diana Resetca, Maria Sunnerhagen, Brian Raught, Linda Z. Penn. Lysine-52 stabilizes the MYC oncoprotein through a SCFFBXW7-independent mechanism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5423.
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Affiliation(s)
- Jason De Melo
- 1University Health Network, Toronto, Ontario, Canada
| | - Sam S. Kim
- 1University Health Network, Toronto, Ontario, Canada
| | | | | | | | - Brian Raught
- 1University Health Network, Toronto, Ontario, Canada
| | - Linda Z. Penn
- 1University Health Network, Toronto, Ontario, Canada
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Milos S, Siddaway R, Pajovic S, Campos E, Raught B, Hawkins C. Abstract 1477: The interactomes of H3.1 and H3.3 reveal novel interactions, and associations with histone chaperones. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1477] [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
Pediatric high grade gliomas are incurable brain tumors with very high mortality rates. Recent genomic studies have uncovered unique driver mutations involving histone genes encoding either H3.1 or H3.3. Histone H3 interacts with diverse variety of cellular machinery which regulates chromatin structure and function, transcription, and DNA replication. Previous efforts using IP-mass spectroscopy have revealed a great deal about H3.1 and H3.3 biology and the different interaction networks between them, including the chaperones that transport histones around the cell and incorporate them into chromatin. For example HIRA specifically deposits H3.3 into active chromatin, while CAF-1 has been shown to deposit H3.1 during DNA replication. However, these studies typically use high salt extraction, which disrupts all but the most stable protein-protein interactions. In order to more fully characterise the interactome of histone H3.1 and H3.3 in an unbiased fashion and provide insight into their potentially different roles in pediatric brain tumors, we employed proximity dependent biotinylation (BioID). We generated Flp-In HEK293 cells expressing FLAG-BirA*, alone or fused to H3.1 or H3.3, under the control of a doxycycline-inducible promoter. BirA* is a highly promiscuous biotin ligase that biotinylates proteins within a 20 nm radius. Cells were induced with doxycycline and biotin for 24 hours. SDS-based lysis and streptavidin pulldowns followed by mass-spectrometry analysis were used to identify proteins interacting with FLAG-BirA*-H3.1/H3.3 but not FLAG-BirA* alone. We validated our results by affinity purification followed by western blotting, and proximity ligation assays. FLAG-BirA*-H3 displays normal cellular localisation and is incorporated into DNA in nucleosomes of the same stability as endogenous H3-containing nucleosomes. Furthermore, chromatin stability is not changed in the presence of FLAG-BirA*-H3, showing that FLAG-BirA* fusion does not affect normal histone functions. Comparison with mass spectroscopy data indentified many previously described interactors, as well as 465 interactors not previously identified by affinity purification-mass spectroscopy, suggesting novel histone functions. The interactomes of H3.1 and H3.3 were strikingly similar, however key difference were identified. As expected, the histone chaperones NASP and ASF1 were similarly enriched in both H3 proteins, while HIRA was enriched with H3.3 vs. H3.1. Surprisingly, however, CAF-1 was not enriched in H3.1 vs. H3.3 suggesting CAF-1 may also serve as a chaperone for H3.3. Our results suggest BioID is a useful tool for unbiased interactome characterization, including proteins such as histones that require harsh extraction methods. Identification and understanding of histone H3.1 and H3.3 interactors will further aid in uncovering what role histone mutations may play in cancer initiation.
Citation Format: Scott Milos, Robert Siddaway, Sanja Pajovic, Eric Campos, Brian Raught, Cynthia Hawkins. The interactomes of H3.1 and H3.3 reveal novel interactions, and associations with histone chaperones [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1477.
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Affiliation(s)
- Scott Milos
- 1The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Sanja Pajovic
- 1The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eric Campos
- 1The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brian Raught
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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74
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Odeh HM, Coyaud E, Raught B, Matunis MJ. The SUMO-specific isopeptidase SENP2 is targeted to intracellular membranes via a predicted N-terminal amphipathic α-helix. Mol Biol Cell 2018; 29:1878-1890. [PMID: 29874116 PMCID: PMC6085828 DOI: 10.1091/mbc.e17-07-0445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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] [Indexed: 11/11/2022] Open
Abstract
Sumoylation regulates a wide range of essential cellular functions, many of which are associated with activities in the nucleus. Although there is also emerging evidence for the involvement of the small ubiquitin-related modifier (SUMO) at intracellular membranes, the mechanisms by which sumoylation is regulated at membranes is largely unexplored. In this study, we report that the SUMO-specific isopeptidase, SENP2, uniquely associates with intracellular membranes. Using in vivo analyses and in vitro binding assays, we show that SENP2 is targeted to intracellular membranes via a predicted N-terminal amphipathic α-helix that promotes direct membrane binding. Furthermore, we demonstrate that SENP2 binding to intracellular membranes is regulated by interactions with the nuclear import receptor karyopherin-α. Consistent with membrane association, biotin identification (BioID) revealed interactions between SENP2 and endoplasmic reticulum, Golgi, and inner nuclear membrane-associated proteins. Collectively, our findings indicate that SENP2 binds to intracellular membranes where it interacts with membrane-associated proteins and has the potential to regulate their sumoylation and membrane-associated functions.
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Affiliation(s)
- Hana M Odeh
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C4, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
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75
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Chen J, Castelvecchi GD, Li-Villarreal N, Raught B, Krezel AM, McNeill H, Solnica-Krezel L. Atypical Cadherin Dachsous1b Interacts with Ttc28 and Aurora B to Control Microtubule Dynamics in Embryonic Cleavages. Dev Cell 2018; 45:376-391.e5. [PMID: 29738714 PMCID: PMC5983389 DOI: 10.1016/j.devcel.2018.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 08/21/2017] [Revised: 02/22/2018] [Accepted: 04/09/2018] [Indexed: 01/15/2023]
Abstract
Atypical cadherin Dachsous (Dchs) is a conserved regulator of planar cell polarity, morphogenesis, and tissue growth during animal development. Dchs functions in part by regulating microtubules by unknown molecular mechanisms. Here we show that maternal zygotic (MZ) dchs1b zebrafish mutants exhibit cleavage furrow progression defects and impaired midzone microtubule assembly associated with decreased microtubule turnover. Mechanistically, Dchs1b interacts via a conserved motif in its intracellular domain with the tetratricopeptide motifs of Ttc28 and regulates its subcellular distribution. Excess Ttc28 impairs cleavages and decreases microtubule turnover, while ttc28 inactivation increases turnover. Moreover, ttc28 deficiency in dchs1b mutants suppresses the microtubule dynamics and midzone microtubule assembly defects. Dchs1b also binds to Aurora B, a known regulator of cleavages and microtubules. Embryonic cleavages in MZdchs1b mutants exhibit increased, and in MZttc28 mutants decreased, sensitivity to Aurora B inhibition. Thus, Dchs1b regulates microtubule dynamics and embryonic cleavages by interacting with Ttc28 and Aurora B.
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Affiliation(s)
- Jiakun Chen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gina D Castelvecchi
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nanbing Li-Villarreal
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Andrzej M Krezel
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Helen McNeill
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Genetics, University of Toronto, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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76
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Liu Y, Gupta GD, Barnabas DD, Agircan FG, Mehmood S, Wu D, Coyaud E, Johnson CM, McLaughlin SH, Andreeva A, Freund SMV, Robinson CV, Cheung SWT, Raught B, Pelletier L, van Breugel M. Direct binding of CEP85 to STIL ensures robust PLK4 activation and efficient centriole assembly. Nat Commun 2018; 9:1731. [PMID: 29712910 PMCID: PMC5928214 DOI: 10.1038/s41467-018-04122-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 10/16/2017] [Accepted: 04/05/2018] [Indexed: 02/08/2023] Open
Abstract
Centrosomes are required for faithful chromosome segregation during mitosis. They are composed of a centriole pair that recruits and organizes the microtubule-nucleating pericentriolar material. Centriole duplication is tightly controlled in vivo and aberrations in this process are associated with several human diseases, including cancer and microcephaly. Although factors essential for centriole assembly, such as STIL and PLK4, have been identified, the underlying molecular mechanisms that drive this process are incompletely understood. Combining protein proximity mapping with high-resolution structural methods, we identify CEP85 as a centriole duplication factor that directly interacts with STIL through a highly conserved interaction interface involving a previously uncharacterised domain of STIL. Structure-guided mutational analyses in vivo demonstrate that this interaction is essential for efficient centriolar targeting of STIL, PLK4 activation and faithful daughter centriole assembly. Taken together, our results illuminate a molecular mechanism underpinning the spatiotemporal regulation of the early stages of centriole duplication.
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Affiliation(s)
- Yi Liu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gagan D Gupta
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Deepak D Barnabas
- Medical Research Council - Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Fikret G Agircan
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Christopher M Johnson
- Medical Research Council - Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Stephen H McLaughlin
- Medical Research Council - Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Antonina Andreeva
- Medical Research Council - Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Stefan M V Freund
- Medical Research Council - Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Sally W T Cheung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Mark van Breugel
- Medical Research Council - Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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77
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Baczyk D, Audette MC, Coyaud E, Raught B, Kingdom JC. Spatiotemporal distribution of small ubiquitin-like modifiers during human placental development and in response to oxidative and inflammatory stress. J Physiol 2018; 596:1587-1600. [PMID: 29468681 PMCID: PMC5924830 DOI: 10.1113/jp275288] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 02/05/2018] [Indexed: 12/28/2022] Open
Abstract
Key points The post‐translational modification of target proteins by SUMOylation occurs in response to stressful stimuli in a variety of organ systems. Small ubiquitin‐like modifier (SUMO) isoforms 1–4 have recently been identified in the human placenta, and are upregulated in the major obstetrical complication of pre‐eclampsia. This is the first study to characterize the spatiotemporal distribution of SUMO isoforms and their targets during placental development across gestation and in response to stress induced by pre‐eclampsia and chorioamnionitis. Keratins were identified as major targets of placental SUMOylation. The interaction with SUMOs and cytoskeletal filaments provides evidence for SUMOylation possibly contributing to underlying dysfunctional trophoblast turnover, which is a hallmark feature of pre‐eclampsia. Further understanding the role of individual SUMO isoforms and SUMOylation underlying placental dysfunction may provide a target for a novel therapeutic candidate as an approach for treating pre‐eclampsia complicated with placental pathology.
Abstract SUMOylation is a dynamic, reversible post‐translational modification that regulates cellular protein stability and localization. SUMOylation occurs in response to various stressors, including hypoxia and inflammation, features common in the obstetrical condition of pre‐eclampsia. SUMO isoforms 1–4 have recently been identified in the human placenta, but less is known about their role in response to pre‐eclamptic stress. We hypothesized that SUMOylation components have a unique spatiotemporal distribution during placental development and that their subcellular localization can be further modulated by extra‐cellular stressors. Placental SUMO expression was examined across gestation. First‐trimester human placental explants and JAR cells were subjected to hypoxia or TNF‐α cytokine, and subcellular translocation of SUMOs was monitored. SUMOylation target proteins were elucidated using mass spectrometry and proximity ligation assay. Placental SUMO‐1 and SUMO‐4 were restricted to villous cytotrophoblast cells in first trimester and syncytium by term, while SUMO‐2/3 staining was evenly distributed throughout the trophoblast across gestation. In placental villous explants, oxidative stress induced hyperSUMOylation of SUMO‐1 and SUMO‐4 in the syncytial cytoplasm, whereas SUMO‐2/3 nuclear expression increased. Oxidative stress also upregulated cytoplasmic SUMO‐1 and SUMO‐4 protein expression (P < 0.05), similar to pre‐eclamptic placentas. Keratins were identified as major targets of placental SUMOylation. Oxidative stress increased the cytokeratin‐7 to SUMO‐1 and SUMO‐4 interactions, while inflammatory stress increased its interaction with SUMO‐2/3. Overall, SUMOs display a unique spatiotemporal distribution in normal human placental development. Our data indicate SUMOylation in pre‐eclampsia, which may impair the stability of cytoskeleton filaments and thus promote trophoblast shedding into the maternal circulation in this condition. The post‐translational modification of target proteins by SUMOylation occurs in response to stressful stimuli in a variety of organ systems. Small ubiquitin‐like modifier (SUMO) isoforms 1–4 have recently been identified in the human placenta, and are upregulated in the major obstetrical complication of pre‐eclampsia. This is the first study to characterize the spatiotemporal distribution of SUMO isoforms and their targets during placental development across gestation and in response to stress induced by pre‐eclampsia and chorioamnionitis. Keratins were identified as major targets of placental SUMOylation. The interaction with SUMOs and cytoskeletal filaments provides evidence for SUMOylation possibly contributing to underlying dysfunctional trophoblast turnover, which is a hallmark feature of pre‐eclampsia. Further understanding the role of individual SUMO isoforms and SUMOylation underlying placental dysfunction may provide a target for a novel therapeutic candidate as an approach for treating pre‐eclampsia complicated with placental pathology.
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Affiliation(s)
- Dora Baczyk
- Program in Development and Fetal Health, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5T3H7, Canada
| | - Melanie C Audette
- Program in Development and Fetal Health, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5T3H7, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G1L7, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G1L7, Canada
| | - John C Kingdom
- Program in Development and Fetal Health, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5T3H7, Canada.,Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Maternal-Fetal Medicine Division, Department of Obstetrics and Gynecology, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
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78
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Hesketh GG, Youn JY, Samavarchi-Tehrani P, Raught B, Gingras AC. Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry. Methods Mol Biol 2018; 1550:115-136. [PMID: 28188527 DOI: 10.1007/978-1-4939-6747-6_10] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Complete understanding of cellular function requires knowledge of the composition and dynamics of protein interaction networks, the importance of which spans all molecular cell biology fields. Mass spectrometry-based proteomics approaches are instrumental in this process, with affinity purification coupled to mass spectrometry (AP-MS) now widely used for defining interaction landscapes. Traditional AP-MS methods are well suited to providing information regarding the temporal aspects of soluble protein-protein interactions, but the requirement to maintain protein-protein interactions during cell lysis and AP means that both weak-affinity interactions and spatial information is lost. A more recently developed method called BioID employs the expression of bait proteins fused to a nonspecific biotin ligase, BirA*, that induces in vivo biotinylation of proximal proteins. Coupling this method to biotin affinity enrichment and mass spectrometry negates many of the solubility and interaction strength issues inherent in traditional AP-MS methods, and provides unparalleled spatial context for protein interactions. Here we describe the parallel implementation of both BioID and FLAG AP-MS allowing simultaneous exploration of both spatial and temporal aspects of protein interaction networks.
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Affiliation(s)
- Geoffrey G Hesketh
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ji-Young Youn
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | | | - Brian Raught
- Princess Margaret Cancer Centre, Princess Margaret Research Institute, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Canada. .,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave., Rm 992A (9th floor), Toronto, ON, Canada, M5G 1X5.
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79
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Silva J, Aivio S, Knobel PA, Bailey LJ, Casali A, Vinaixa M, Garcia-Cao I, Coyaud É, Jourdain AA, Pérez-Ferreros P, Rojas AM, Antolin-Fontes A, Samino-Gené S, Raught B, González-Reyes A, Ribas de Pouplana L, Doherty AJ, Yanes O, Stracker TH. EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nat Cell Biol 2018; 20:162-174. [PMID: 29335528 DOI: 10.1038/s41556-017-0016-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/27/2017] [Indexed: 02/08/2023]
Abstract
Mitochondria are subcellular organelles that are critical for meeting the bioenergetic and biosynthetic needs of the cell. Mitochondrial function relies on genes and RNA species encoded both in the nucleus and mitochondria, and on their coordinated translation, import and respiratory complex assembly. Here, we characterize EXD2 (exonuclease 3'-5' domain-containing 2), a nuclear-encoded gene, and show that it is targeted to the mitochondria and prevents the aberrant association of messenger RNAs with the mitochondrial ribosome. Loss of EXD2 results in defective mitochondrial translation, impaired respiration, reduced ATP production, increased reactive oxygen species and widespread metabolic abnormalities. Depletion of the Drosophila melanogaster EXD2 orthologue (CG6744) causes developmental delays and premature female germline stem cell attrition, reduced fecundity and a dramatic extension of lifespan that is reversed with an antioxidant diet. Our results define a conserved role for EXD2 in mitochondrial translation that influences development and ageing.
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Affiliation(s)
- Joana Silva
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Suvi Aivio
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department for Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Laura J Bailey
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Andreu Casali
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maria Vinaixa
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Isabel Garcia-Cao
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexis A Jourdain
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pablo Pérez-Ferreros
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,EMBL Australia, University of New South Wales, Lowy Cancer Research Center, Single Molecule Science Node, Sydney and Arc Center of Excellence in Advance Molecular Imaging, Sydney, New South Wales, Australia
| | - Ana M Rojas
- Computational Biology and Bioinformatics Group, Institute of Biomedicine of Seville (IBIS/CSIC/US/JA), Campus Hospital Universitario Virgen del Rocio, Seville, Spain
| | - Albert Antolin-Fontes
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sara Samino-Gené
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Acaimo González-Reyes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Seville, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Oscar Yanes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
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80
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Sandí MJ, Marshall CB, Balan M, Coyaud É, Zhou M, Monson DM, Ishiyama N, Chandrakumar AA, La Rose J, Couzens AL, Gingras AC, Raught B, Xu W, Ikura M, Morrison DK, Rottapel R. MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity. Sci Signal 2017; 10:10/503/eaan3286. [PMID: 29089450 DOI: 10.1126/scisignal.aan3286] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The PAR-1-MARK pathway controls cell polarity through the phosphorylation of microtubule-associated proteins. Rho-Rac guanine nucleotide exchange factor 2 (ARHGEF2), which activates Ras homolog family member A (RHOA), is anchored to the microtubule network and sequestered in an inhibited state through binding to dynein light chain Tctex-1 type 1 (DYNLT1). We showed in mammalian cells that liver kinase B1 (LKB1) activated the microtubule affinity-regulating kinase 3 (MARK3), which in turn phosphorylated ARHGEF2 at Ser151 This modification disrupted the interaction between ARHGEF2 and DYNLT1 by generating a 14-3-3 binding site in ARHGEF2, thus causing ARHGEF2 to dissociate from microtubules. Phosphorylation of ARHGEF2 by MARK3 stimulated RHOA activation and the formation of stress fibers and focal adhesions, and was required for organized cellular architecture in three-dimensional culture. Protein phosphatase 2A (PP2A) dephosphorylated Ser151 in ARHGEF2 to restore the inhibited state. Thus, we have identified a regulatory switch controlled by MARK3 that couples microtubules to the actin cytoskeleton to establish epithelial cell polarity through ARHGEF2.
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Affiliation(s)
- María-José Sandí
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Marc Balan
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Ming Zhou
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Daniel M Monson
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Arun A Chandrakumar
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - José La Rose
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Amber L Couzens
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Deborah K Morrison
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Robert Rottapel
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada. .,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Division of Rheumatology, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
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81
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Kim BR, Coyaud E, Laurent EMN, St-Germain J, Van de Laar E, Tsao MS, Raught B, Moghal N. Identification of the SOX2 Interactome by BioID Reveals EP300 as a Mediator of SOX2-dependent Squamous Differentiation and Lung Squamous Cell Carcinoma Growth. Mol Cell Proteomics 2017; 16:1864-1888. [PMID: 28794006 PMCID: PMC5629269 DOI: 10.1074/mcp.m116.064451] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 05/05/2017] [Indexed: 11/06/2022] Open
Abstract
Lung cancer is the leading cause of cancer mortality worldwide, with squamous cell carcinoma (SQCC) being the second most common form. SQCCs are thought to originate in bronchial basal cells through an injury response to smoking, which results in this stem cell population committing to hyperplastic squamous rather than mucinous and ciliated fates. Copy number gains in SOX2 in the region of 3q26-28 occur in 94% of SQCCs, and appear to act both early and late in disease progression by stabilizing the initial squamous injury response in stem cells and promoting growth of invasive carcinoma. Thus, anti-SOX2 targeting strategies could help treat early and/or advanced disease. Because SOX2 itself is not readily druggable, we sought to characterize SOX2 binding partners, with the hope of identifying new strategies to indirectly interfere with SOX2 activity. We now report the first use of proximity-dependent biotin labeling (BioID) to characterize the SOX2 interactome in vivo We identified 82 high confidence SOX2-interacting partners. An interaction with the coactivator EP300 was subsequently validated in both basal cells and SQCCs, and we demonstrate that EP300 is necessary for SOX2 activity in basal cells, including for induction of the squamous fate. We also report that EP300 copy number gains are common in SQCCs and that growth of lung cancer cell lines with 3q gains, including SQCC cells, is dependent on EP300. Finally, we show that EP300 inhibitors can be combined with other targeted therapeutics to achieve more effective growth suppression. Our work supports the use of BioID to identify interacting protein partners of nondruggable oncoproteins such as SOX2, as an effective strategy to discover biologically relevant, druggable targets.
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Affiliation(s)
- Bo Ram Kim
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- §Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Etienne Coyaud
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Estelle M N Laurent
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Jonathan St-Germain
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Emily Van de Laar
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Ming-Sound Tsao
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- ¶Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Brian Raught
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- §Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Nadeem Moghal
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada;
- §Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
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82
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Swayampakula M, McDonald PC, Vallejo M, Coyaud E, Chafe SC, Westerback A, Venkateswaran G, Shankar J, Gao G, Laurent EMN, Lou Y, Bennewith KL, Supuran CT, Nabi IR, Raught B, Dedhar S. The interactome of metabolic enzyme carbonic anhydrase IX reveals novel roles in tumor cell migration and invadopodia/MMP14-mediated invasion. Oncogene 2017; 36:6244-6261. [PMID: 28692057 PMCID: PMC5684442 DOI: 10.1038/onc.2017.219] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [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: 03/17/2017] [Revised: 05/05/2017] [Accepted: 05/30/2017] [Indexed: 12/15/2022]
Abstract
Carbonic anhydrase IX (CAIX) is a hypoxia inducible factor 1-induced, cell surface pH regulating enzyme with an established role in tumor progression and clinical outcome. However, the molecular basis of CAIX-mediated tumor progression remains unclear. Here, we have utilized proximity dependent biotinylation (BioID) to map the CAIX ‘interactome’ in breast cancer cells in order to identify physiologically relevant CAIX-associating proteins with potential roles in tumor progression. High confidence proteins identified include metabolic transporters, β1 integrins, integrin-associated protein CD98hc and matrix metalloprotease 14 (MMP14). Biochemical studies validate the association of CAIX with α2β1 integrin, CD98hc and MMP14, and immunofluorescence microscopy demonstrates colocalization of CAIX with α2β1 integrin and MMP14 in F-actin/cofilin-positive lamellipodia/pseudopodia, and with MMP14 to cortactin/Tks5-positive invadopodia. Modulation of CAIX expression and activity results in significant changes in cell migration, collagen degradation and invasion. Mechanistically, we demonstrate that CAIX associates with MMP14 through potential phosphorylation residues within its intracellular domain, and that CAIX enhances MMP14-mediated collagen degradation by directly contributing hydrogen ions required for MMP14 catalytic activity. These findings establish hypoxia-induced CAIX as a novel metabolic component of cellular migration and invasion structures, and provide new mechanistic insights into its role in tumor cell biology.
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Affiliation(s)
- M Swayampakula
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - P C McDonald
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - M Vallejo
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - E Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - S C Chafe
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - A Westerback
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - G Venkateswaran
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - J Shankar
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - G Gao
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - E M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Y Lou
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - K L Bennewith
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - C T Supuran
- Laboratorio di Chimica Bioinorganica, Universita degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - I R Nabi
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - B Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - S Dedhar
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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83
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Doiron K, Goyon V, Coyaud E, Rajapakse S, Raught B, McBride HM. The dynamic interacting landscape of MAPL reveals essential functions for SUMOylation in innate immunity. Sci Rep 2017; 7:107. [PMID: 28273895 PMCID: PMC5427825 DOI: 10.1038/s41598-017-00151-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 03/10/2016] [Accepted: 02/13/2017] [Indexed: 01/05/2023] Open
Abstract
Activation of the innate immune response triggered by dsRNA viruses occurs through the assembly of the Mitochondrial Anti-Viral Signaling (MAVS) complex. Upon recognition of viral dsRNA, the cytosolic receptor RIG-I is activated and recruited to MAVS to activate the immune signaling response. We here demonstrate a strict requirement for a mitochondrial anchored protein ligase, MAPL (also called MUL1) in the signaling events that drive the transcriptional activation of antiviral genes downstream of Sendai virus infection, both in vivo and in vitro. A biotin environment scan of MAPL interacting polypeptides identified a series of proteins specific to Sendai virus infection; including RIG-I, IFIT1, IFIT2, HERC5 and others. Upon infection, RIG-I is SUMOylated in a MAPL-dependent manner, a conjugation step that is required for its activation. Consistent with this, MAPL was not required for signaling downstream of a constitutively activated form of RIG-I. These data highlight a critical role for MAPL and mitochondrial SUMOylation in the early steps of antiviral signaling.
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Affiliation(s)
- Karine Doiron
- Montreal Neurological Institute, McGill University, 3801 University Ave, Montreal, Quebec, H3A 2B4, Canada
| | - Vanessa Goyon
- Montreal Neurological Institute, McGill University, 3801 University Ave, Montreal, Quebec, H3A 2B4, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College St., Toronto, ON M5G 1L7, Canada
| | - Sanjeeva Rajapakse
- Montreal Neurological Institute, McGill University, 3801 University Ave, Montreal, Quebec, H3A 2B4, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College St., Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Heidi M McBride
- Montreal Neurological Institute, McGill University, 3801 University Ave, Montreal, Quebec, H3A 2B4, Canada.
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84
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Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C. A global genetic interaction network maps a wiring diagram of cellular function. Science 2017; 353:353/6306/aaf1420. [PMID: 27708008 DOI: 10.1126/science.aaf1420] [Citation(s) in RCA: 741] [Impact Index Per Article: 105.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell.
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Affiliation(s)
- Michael Costanzo
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. Simons Center for Data Analysis, Simons Foundation, 160 Fifth Avenue, New York, NY 10010, USA
| | - Elizabeth N Koch
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Anastasia Baryshnikova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Guihong Tan
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Matej Usaj
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Julia Hanchard
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Susan D Lee
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Erin B Styles
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Maximilian Billmann
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Jolanda van Leeuwen
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Nydia van Dyk
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto ON, Canada
| | - Elena Kuzmin
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Justin Nelson
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. Program in Biomedical Informatics and Computational Biology, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Jeff S Piotrowski
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan
| | - Tharan Srikumar
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto ON, Canada
| | - Sondra Bahr
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Yiqun Chen
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Christoph F Kurat
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Sheena C Li
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan
| | - Zhijian Li
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Mojca Mattiazzi Usaj
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan 277-8561
| | - Natasha Pascoe
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Bryan-Joseph San Luis
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Sara Sharifpoor
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Emira Shuteriqi
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Scott W Simpkins
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. Program in Biomedical Informatics and Computational Biology, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Jamie Snider
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Harsha Garadi Suresh
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Yizhao Tan
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Hongwei Zhu
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Noel Malod-Dognin
- Computer Science Deptartment, University College London, London WC1E 6BT, UK
| | - Vuk Janjic
- Department of Computing, Imperial College London, UK
| | - Natasa Przulj
- Computer Science Deptartment, University College London, London WC1E 6BT, UK. School of Computing (RAF), Union University, Belgrade, Serbia
| | - Olga G Troyanskaya
- Simons Center for Data Analysis, Simons Foundation, 160 Fifth Avenue, New York, NY 10010, USA. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Igor Stagljar
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Tian Xia
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, China, 430074
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan 277-8561
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto ON, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto ON, Canada
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany. Department of Genetics, School of Medicine and Stanford Genome Technology Center Stanford University, Palo Alto, CA 94304, USA
| | - Claire L Moore
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Adam P Rosebrock
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Amy A Caudy
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. Program in Biomedical Informatics and Computational Biology, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA.
| | - Brenda Andrews
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1.
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan.
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85
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Hua R, Cheng D, Coyaud É, Freeman S, Di Pietro E, Wang Y, Vissa A, Yip CM, Fairn GD, Braverman N, Brumell JH, Trimble WS, Raught B, Kim PK. VAPs and ACBD5 tether peroxisomes to the ER for peroxisome maintenance and lipid homeostasis. J Cell Biol 2017; 216:367-377. [PMID: 28108526 PMCID: PMC5294787 DOI: 10.1083/jcb.201608128] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/14/2016] [Accepted: 01/04/2017] [Indexed: 12/15/2022] Open
Abstract
Peroxisomes and the ER exchange lipids for various metabolic and anabolic reactions. In this study, Hua et al. show that the interaction between the ER-resident VAPs with the peroxisomal protein ACBD5 tethers peroxisomes to the ER. This tether is required for the exchange of lipids, including cholesterol, between the two organelles. Lipid exchange between the endoplasmic reticulum (ER) and peroxisomes is necessary for the synthesis and catabolism of lipids, the trafficking of cholesterol, and peroxisome biogenesis in mammalian cells. However, how lipids are exchanged between these two organelles is not understood. In this study, we report that the ER-resident VAMP-associated proteins A and B (VAPA and VAPB) interact with the peroxisomal membrane protein acyl-CoA binding domain containing 5 (ACBD5) and that this interaction is required to tether the two organelles together, thereby facilitating the lipid exchange between them. Depletion of either ACBD5 or VAP expression results in increased peroxisome mobility, suggesting that VAP–ACBD5 complex acts as the primary ER–peroxisome tether. We also demonstrate that tethering of peroxisomes to the ER is necessary for peroxisome growth, the synthesis of plasmalogen phospholipids, and the maintenance of cellular cholesterol levels. Collectively, our data highlight the importance of VAP–ACBD5–mediated contact between the ER and peroxisomes for organelle maintenance and lipid homeostasis.
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Affiliation(s)
- Rong Hua
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Derrick Cheng
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G1L7, Canada
| | - Spencer Freeman
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada
| | - Erminia Di Pietro
- Department of Pediatrics and Human Genetics, Research Institute of the McGill University Health Center and McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Yuqing Wang
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Adriano Vissa
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Nancy Braverman
- Department of Pediatrics and Human Genetics, Research Institute of the McGill University Health Center and McGill University, Montreal, Quebec H4A 3J1, Canada
| | - John H Brumell
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,SickKids Inflammatory Bowel Disease Centre, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario M5S1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G1L7, Canada
| | - William S Trimble
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Brian Raught
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G1L7, Canada
| | - Peter K Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada .,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
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86
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Wheaton K, Sarkari F, Stanly Johns B, Davarinejad H, Egorova O, Kaustov L, Raught B, Saridakis V, Sheng Y. UbE2E1/UBCH6 Is a Critical in Vivo E2 for the PRC1-catalyzed Ubiquitination of H2A at Lys-119. J Biol Chem 2017; 292:2893-2902. [PMID: 28073915 DOI: 10.1074/jbc.m116.749564] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 07/20/2016] [Revised: 01/09/2017] [Indexed: 11/06/2022] Open
Abstract
UbE2E1/UbcH6 is an E2 ubiquitin-conjugating enzyme that is regulated by USP7. We identified UbE2E1 as a novel component of Polycomb repressive complex 1 (PRC1), the E3 ligase complex responsible for histone H2A ubiquitination and gene silencing. We demonstrate that UbE2E1 is critical for the monoubiquitination of H2A at residue Lys-119 (uH2AK119) through its association with the PRC1 complex. UbE2E1 interacts with PRC1 subunits including Ring1A and Ring1B. Overexpression of UbE2E1 results in increased levels of uH2AK119, whereas overexpression of catalytically inactive UbE2E1_C131A or UbE2E1 knockdown results in decreased levels of uH2AK119. The down-regulation of H2A ubiquitination by loss of function of UbE2E1 is correlated with alleviated p16INK4a promoter repression and induced growth inhibition in HCT116 cells. These results are specific to UbE2E1 as knockdown of UbE2D E2s does not show any effect on uH2AK119. We extended the UbE2E1 regulation of uH2AK119 to USP7 and showed that USP7 is also a key regulator for monoubiquitination at H2A Lys-119 as both knockdown and deletion of USP7 results in decreased levels of uH2AK119. This study reveals that UbE2E1 is an in vivo E2 for the PRC1 ligase complex and thus plays an important role in the regulation of H2A Lys-119 monoubiquitination.
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Affiliation(s)
- Keith Wheaton
- From the Department of Biology, York University, Toronto, Ontario M3J1P3 and
| | - Feroz Sarkari
- From the Department of Biology, York University, Toronto, Ontario M3J1P3 and
| | - Beena Stanly Johns
- From the Department of Biology, York University, Toronto, Ontario M3J1P3 and
| | - Hossein Davarinejad
- From the Department of Biology, York University, Toronto, Ontario M3J1P3 and
| | - Olga Egorova
- From the Department of Biology, York University, Toronto, Ontario M3J1P3 and
| | - Lilia Kaustov
- the Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Brian Raught
- the Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Vivian Saridakis
- From the Department of Biology, York University, Toronto, Ontario M3J1P3 and
| | - Yi Sheng
- From the Department of Biology, York University, Toronto, Ontario M3J1P3 and
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87
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Liyanage SU, Coyaud E, Laurent EMN, Hurren R, Maclean N, Wood SR, Kazak L, Shamas-Din A, Holt I, Raught B, Schimmer A. Characterizing the mitochondrial DNA polymerase gamma interactome by BioID identifies Ruvbl2 localizes to the mitochondria. Mitochondrion 2016; 32:31-35. [PMID: 27845271 DOI: 10.1016/j.mito.2016.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 08/23/2016] [Revised: 10/13/2016] [Accepted: 11/02/2016] [Indexed: 10/20/2022]
Abstract
Human mitochondrial DNA (mtDNA) is replicated by the mitochondrial DNA polymerase gamma (POLG). Using proximity dependent biotin labelling (BioID), we characterized the POLG interactome and identified new interaction partners involved in mtDNA maintenance, transcription, translation and protein quality control. We also identified interaction with the nuclear AAA+ ATPase Ruvbl2, suggesting mitochondrial localization for this protein. Ruvbl2 was detected in mitochondria-enriched fractions in leukemic cells. Additionally, transgenic overexpression of Ruvbl2 from an alternative translation initiation site resulted in mitochondrial co-localization. Overall, POLG interactome mapping identifies novel proteins which support mitochondrial biogenesis and a potential novel mitochondrial isoform of Ruvbl2.
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Affiliation(s)
- Sanduni U Liyanage
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, ON, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Neil Maclean
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Stuart R Wood
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Lawrence Kazak
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Aisha Shamas-Din
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ian Holt
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aaron Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, ON, Canada.
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88
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Guturi KKN, Bohgaki M, Bohgaki T, Srikumar T, Ng D, Kumareswaran R, El Ghamrasni S, Jeon J, Patel P, Eldin MS, Bristow R, Cheung P, Stewart GS, Raught B, Hakem A, Hakem R. RNF168 and USP10 regulate topoisomerase IIα function via opposing effects on its ubiquitylation. Nat Commun 2016; 7:12638. [PMID: 27558965 PMCID: PMC5007378 DOI: 10.1038/ncomms12638] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 10/04/2015] [Accepted: 07/19/2016] [Indexed: 12/21/2022] Open
Abstract
Topoisomerase IIα (TOP2α) is essential for chromosomal condensation and segregation, as well as genomic integrity. Here we report that RNF168, an E3 ligase mutated in the human RIDDLE syndrome, interacts with TOP2α and mediates its ubiquitylation. RNF168 deficiency impairs decatenation activity of TOP2α and promotes mitotic abnormalities and defective chromosomal segregation. Our data also indicate that RNF168 deficiency, including in human breast cancer cell lines, confers resistance to the anti-cancer drug and TOP2 inhibitor etoposide. We also identify USP10 as a deubiquitylase that negatively regulates TOP2α ubiquitylation and restrains its chromatin association. These findings provide a mechanistic link between the RNF168/USP10 axis and TOP2α ubiquitylation and function, and suggest a role for RNF168 in the response to anti-cancer chemotherapeutics that target TOP2.
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Affiliation(s)
- Kiran Kumar Naidu Guturi
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Miyuki Bohgaki
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Toshiyuki Bohgaki
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Tharan Srikumar
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Deborah Ng
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Ramya Kumareswaran
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Samah El Ghamrasni
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Justin Jeon
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Parasvi Patel
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Mohamed Saad Eldin
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Rob Bristow
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Peter Cheung
- Department of Biology, York University, Toronto, Ontario, Canada M3J 1P3
| | - Grant S Stewart
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Brian Raught
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Anne Hakem
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Razqallah Hakem
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
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89
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Resetca D, Dingar D, Kalkat M, Raught B, Penn LZ. Abstract 2010: Charactering the interactomes of the Myc family of oncogenes. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2010] [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
The Myc family of transcription factors, c-Myc, N-Myc and L-Myc, are known to be deregulated in a large variety of cancers. Mechanisms responsible for the deregulation of the activity of Myc family members in cancer are not well understood. A number of protein-protein interactions and post-translational modifications have been suggested to promote the oncogenic activity of Myc. Traditional biochemical approaches have not been successful at mapping the interactors of Myc family members due to their tight association with chromatin and the labile nature of Myc proteins. Mapping the protein-protein interactions that support the aberrant activity of Myc family of oncoproteins in cancer cells is of high interest, particularly in a more natural context in xenograft models in vivo.
A new mass spectrometry-based technique, BioID-MS, which relies on proximity-based biotin labeling, has recently emerged as a key advance for the characterization of hard-to-detect protein-protein interactions in living cells. Herein, we are reporting a new application of the BioID-MS technique for the characterization of c-Myc interactors in human cell line in vivo, in mouse tumor xenografts. Using the in vivo BioID assay, we were able to identify more than 30 known and validated c-Myc interactors, some of which include the components of the STAGA complex and SWI/SNF chromatin remodelling complex. We were further able to identify more than 100 novel high-confidence c-Myc interactors, which include components of the DNA repair and replication machinery, general transcription and elongation factors, and the co-regulator of transcription-like DNA helicase protein chromodomain 8 (CHD8). Using ENCODE ChIP-seq datasets we were able to map some of the high-confidence interactors to coincident binding sites with c-Myc throughout the genome. This provided further credibility that the newly identified putative interactors could co-occupy sites on chromatin with c-Myc and could be functionally important for activity. Furthermore, we validated the Myc-CHD8 interaction using a number of approaches, including yeast two hybrid and proximity-based ligation assays.
These findings suggest that the BioID-MS technique can be used to extend the mapping of the Myc interactome and contribute to a greater understanding of Myc regulation by protein-protein interactions. Furthermore, we are currently in the process of employing this technique to map the interactomes of two other Myc family members, N-Myc and L-Myc. We are interested in identifying common interactors of the Myc family members that contribute to their oncogenic activity, validate them, and explore whether these interactors could be potential therapeutic targets in cancers with deregulated Myc activity.
Citation Format: Diana Resetca, Dharmesh Dingar, Manpreet Kalkat, Brian Raught, Linda Z. Penn. Charactering the interactomes of the Myc family of oncogenes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2010.
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Affiliation(s)
| | - Dharmesh Dingar
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Brian Raught
- 3Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Linda Z. Penn
- 3Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
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90
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Stojanova A, Tu WB, Ponzielli R, Kotlyar M, Chan PK, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ. MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation. Cell Cycle 2016; 15:1693-705. [PMID: 27267444 PMCID: PMC4957596 DOI: 10.1080/15384101.2016.1146836] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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] [Indexed: 12/20/2022] Open
Abstract
MYC is a key driver of cellular transformation and is deregulated in most human cancers. Studies of MYC and its interactors have provided mechanistic insight into its role as a regulator of gene transcription. MYC has been previously linked to chromatin regulation through its interaction with INI1 (SMARCB1/hSNF5/BAF47), a core member of the SWI/SNF chromatin remodeling complex. INI1 is a potent tumor suppressor that is inactivated in several types of cancers, most prominently as the hallmark alteration in pediatric malignant rhabdoid tumors. However, the molecular and functional interaction of MYC and INI1 remains unclear. Here, we characterize the MYC-INI1 interaction in mammalian cells, mapping their minimal binding domains to functionally significant regions of MYC (leucine zipper) and INI1 (repeat motifs), and demonstrating that the interaction does not interfere with MYC-MAX interaction. Protein-protein interaction network analysis expands the MYC-INI1 interaction to the SWI/SNF complex and a larger network of chromatin regulatory complexes. Genome-wide analysis reveals that the DNA-binding regions and target genes of INI1 significantly overlap with those of MYC. In an INI1-deficient rhabdoid tumor system, we observe that with re-expression of INI1, MYC and INI1 bind to common target genes and have opposing effects on gene expression. Functionally, INI1 re-expression suppresses cell proliferation and MYC-potentiated transformation. Our findings thus establish the antagonistic roles of the INI1 and MYC transcriptional regulators in mediating cellular and oncogenic functions.
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Affiliation(s)
- Angelina Stojanova
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - William B Tu
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Romina Ponzielli
- b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Max Kotlyar
- b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Pak-Kei Chan
- b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Paul C Boutros
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada.,c Informatics and Biocomputing Program, Ontario Institute for Cancer Research , Toronto , Ontario , Canada
| | - Fereshteh Khosravi
- b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Igor Jurisica
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada.,d Department of Computer Science , University of Toronto , Toronto , Ontario , Canada
| | - Brian Raught
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Linda Z Penn
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
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91
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Lundberg SM, Tu WB, Raught B, Penn LZ, Hoffman MM, Lee SI. ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. Genome Biol 2016; 17:82. [PMID: 27139377 PMCID: PMC4852466 DOI: 10.1186/s13059-016-0925-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 01/14/2016] [Accepted: 03/15/2016] [Indexed: 01/12/2023] Open
Abstract
A cell's epigenome arises from interactions among regulatory factors-transcription factors and histone modifications-co-localized at particular genomic regions. We developed a novel statistical method, ChromNet, to infer a network of these interactions, the chromatin network, by inferring conditional-dependence relationships among a large number of ChIP-seq data sets. We applied ChromNet to all available 1451 ChIP-seq data sets from the ENCODE Project, and showed that ChromNet revealed previously known physical interactions better than alternative approaches. We experimentally validated one of the previously unreported interactions, MYC-HCFC1. An interactive visualization tool is available at http://chromnet.cs.washington.edu.
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Affiliation(s)
- Scott M Lundberg
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - William B Tu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Linda Z Penn
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Michael M Hoffman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Su-In Lee
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA. .,Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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92
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Liu G, Knight JDR, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC. Data Independent Acquisition analysis in ProHits 4.0. J Proteomics 2016; 149:64-68. [PMID: 27132685 DOI: 10.1016/j.jprot.2016.04.042] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [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: 12/15/2015] [Revised: 03/18/2016] [Accepted: 04/27/2016] [Indexed: 11/30/2022]
Abstract
Affinity purification coupled with mass spectrometry (AP-MS) is a powerful technique for the identification and quantification of physical interactions. AP-MS requires careful experimental design, appropriate control selection and quantitative workflows to successfully identify bona fide interactors amongst a large background of contaminants. We previously introduced ProHits, a Laboratory Information Management System for interaction proteomics, which tracks all samples in a mass spectrometry facility, initiates database searches and provides visualization tools for spectral counting-based AP-MS approaches. More recently, we implemented Significance Analysis of INTeractome (SAINT) within ProHits to provide scoring of interactions based on spectral counts. Here, we provide an update to ProHits to support Data Independent Acquisition (DIA) with identification software (DIA-Umpire and MSPLIT-DIA), quantification tools (through DIA-Umpire, or externally via targeted extraction), and assessment of quantitative enrichment (through mapDIA) and scoring of interactions (through SAINT-intensity). With additional improvements, notably support of the iProphet pipeline, facilitated deposition into ProteomeXchange repositories and enhanced export and viewing functions, ProHits 4.0 offers a comprehensive suite of tools to facilitate affinity proteomics studies. SIGNIFICANCE It remains challenging to score, annotate and analyze proteomics data in a transparent manner. ProHits was previously introduced as a LIMS to enable storing, tracking and analysis of standard AP-MS data. In this revised version, we expand ProHits to include integration with a number of identification and quantification tools based on Data-Independent Acquisition (DIA). ProHits 4.0 also facilitates data deposition into public repositories, and the transfer of data to new visualization tools.
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Affiliation(s)
- Guomin Liu
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - James D R Knight
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jian Ping Zhang
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Chih-Chiang Tsou
- Department of Pathology, University of Michigan, Ann Arbor, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Jian Wang
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
| | - Jean-Philippe Lambert
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Brett Larsen
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Brian Raught
- Princess Margaret Cancer Institute, Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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93
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Heir P, Srikumar T, Bikopoulos G, Bunda S, Poon BP, Lee JE, Raught B, Ohh M. Oxygen-dependent Regulation of Erythropoietin Receptor Turnover and Signaling. J Biol Chem 2016; 291:7357-72. [PMID: 26846855 DOI: 10.1074/jbc.m115.694562] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 09/28/2015] [Indexed: 01/29/2023] Open
Abstract
von Hippel-Lindau (VHL) disease is a rare familial cancer predisposition syndrome caused by a loss or mutation in a single gene,VHL, but it exhibits a wide phenotypic variability that can be categorized into distinct subtypes. The phenotypic variability has been largely argued to be attributable to the extent of deregulation of the α subunit of hypoxia-inducible factor α, a well established target of VHL E3 ubiquitin ligase, ECV (Elongins/Cul2/VHL). Here, we show that erythropoietin receptor (EPOR) is hydroxylated on proline 419 and 426 via prolyl hydroxylase 3. EPOR hydroxylation is required for binding to the β domain of VHL and polyubiquitylation via ECV, leading to increased EPOR turnover. In addition, several type-specific VHL disease-causing mutants, including those that have retained proper binding and regulation of hypoxia-inducible factor α, showed a severe defect in binding prolyl hydroxylated EPOR peptides. These results identify EPOR as the secondbona fidehydroxylation-dependent substrate of VHL that potentially influences oxygen homeostasis and contributes to the complex genotype-phenotype correlation in VHL disease.
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Affiliation(s)
- Pardeep Heir
- From the Departments of Laboratory Medicine and Pathobiology and
| | - Tharan Srikumar
- the Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | | | - Severa Bunda
- From the Departments of Laboratory Medicine and Pathobiology and
| | - Betty P Poon
- From the Departments of Laboratory Medicine and Pathobiology and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8 and
| | - Jeffrey E Lee
- From the Departments of Laboratory Medicine and Pathobiology and
| | - Brian Raught
- the Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Michael Ohh
- From the Departments of Laboratory Medicine and Pathobiology and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8 and
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94
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Bunda S, Burrell K, Heir P, Zeng L, Alamsahebpour A, Kano Y, Raught B, Zhang ZY, Zadeh G, Ohh M. Inhibition of SHP2-mediated dephosphorylation of Ras suppresses oncogenesis. Nat Commun 2015; 6:8859. [PMID: 26617336 PMCID: PMC4674766 DOI: 10.1038/ncomms9859] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/12/2015] [Indexed: 11/22/2022] Open
Abstract
Ras is phosphorylated on a conserved tyrosine at position 32 within the switch I region via Src kinase. This phosphorylation inhibits the binding of effector Raf while promoting the engagement of GTPase-activating protein (GAP) and GTP hydrolysis. Here we identify SHP2 as the ubiquitously expressed tyrosine phosphatase that preferentially binds to and dephosphorylates Ras to increase its association with Raf and activate downstream proliferative Ras/ERK/MAPK signalling. In comparison to normal astrocytes, SHP2 activity is elevated in astrocytes isolated from glioblastoma multiforme (GBM)-prone H-Ras(12V) knock-in mice as well as in glioma cell lines and patient-derived GBM specimens exhibiting hyperactive Ras. Pharmacologic inhibition of SHP2 activity attenuates cell proliferation, soft-agar colony formation and orthotopic GBM growth in NOD/SCID mice and decelerates the progression of low-grade astrocytoma to GBM in a spontaneous transgenic glioma mouse model. These results identify SHP2 as a direct activator of Ras and a potential therapeutic target for cancers driven by a previously ‘undruggable' oncogenic or hyperactive Ras. Aberrant Ras signalling resulting in downstream Mek/Erk pathway activation is found in many cancers. Here, the authors show that the phosphatase SHP2 dephosphorylates Ras resulting in increased Ras activity, and that increased SHP2 activity is found in glioblastomas.
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Affiliation(s)
- Severa Bunda
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada
| | - Kelly Burrell
- Brain Tumour Research Centre, Hospital for Sick Children, University Health Network, Toronto Medical Discovery Tower, 101 College Street, East Tower, Toronto, M5G1L7 Ontario, Canada
| | - Pardeep Heir
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada
| | - Lifan Zeng
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Amir Alamsahebpour
- Brain Tumour Research Centre, Hospital for Sick Children, University Health Network, Toronto Medical Discovery Tower, 101 College Street, East Tower, Toronto, M5G1L7 Ontario, Canada
| | - Yoshihito Kano
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, Toronto Medical Discovery Tower, 9-701A, 101 College Street, Toronto, M5G1L7 Ontario, Canada
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Gelareh Zadeh
- Brain Tumour Research Centre, Hospital for Sick Children, University Health Network, Toronto Medical Discovery Tower, 101 College Street, East Tower, Toronto, M5G1L7 Ontario, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada
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95
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Tu WB, Stojanova A, Ponzielli R, Kotlyar M, Chan PK, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ. Abstract A36: Interaction of the MYC oncoprotein with the tumor suppressive SWI/SNF complex member INI1. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.myc15-a36] [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
The MYC oncogene is a key driver of cellular transformation that is deregulated in more than half of all human cancers. The transcriptional regulatory function of MYC and the wide spectrum of biological processes it mediates are critically tied to its chromatin interactors and epigenetic context. MYC is linked to chromatin remodeling through its interaction with INI1 (SMARCB1/hSNF5/BAF47), a core member of the SWI/SNF complex and a potent tumour suppressor. Recent sequencing efforts in many cancer types also identified frequent mutations in other members of this complex. However, the mechanistic understanding of the SWI/SNF complex in contributing to oncogenesis and its functional and molecular interaction with MYC remain unclear. Herein, we provide a comprehensive characterization of the MYC-INI1 interaction. We demonstrate their direct interaction and extensively delineate their minimal regions of interaction, corresponding to functionally important regions of MYC (leucine zipper) and INI1 (Repeats I and II). Genome-wide analysis reveals that INI1 and other SWI/SNF complex members share significant portions of MYC DNA-binding regions and target genes. Network analysis demonstrates MYC interaction with the SWI/SNF complex and an extended network of shared interactors belonging to additional chromatin regulatory complexes. Collectively, our findings provide significant insight into the interaction of MYC and INI1 at the level of protein-protein and protein-chromatin interactions.
Citation Format: William B. Tu, Angelina Stojanova, Romina Ponzielli, Max Kotlyar, Pak-Kei Chan, Paul C. Boutros, Fereshteh Khosravi, Igor Jurisica, Brian Raught, Linda Z. Penn. Interaction of the MYC oncoprotein with the tumor suppressive SWI/SNF complex member INI1. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr A36.
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Affiliation(s)
- William B. Tu
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Angelina Stojanova
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Romina Ponzielli
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Max Kotlyar
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Pak-Kei Chan
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | | | - Fereshteh Khosravi
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Igor Jurisica
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Brian Raught
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Linda Z. Penn
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
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96
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Kalkat M, Chan PK, Wasylishen AR, Srikumar T, Kim SS, Ponzielli R, Bazett-Jones DP, Raught B, Penn LZ. Abstract A08: Identification of c-MYC SUMOylation by mass spectrometry. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.myc15-a08] [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
The c-MYC transcription factor is a master regulator of many cellular processes and deregulation of this oncogene has been linked to more than 50% of all cancers. In normal cells, MYC is tightly controlled at a number of steps, including at the transcriptional, translational and post-translational levels. Altered regulation at any of these steps can result in deregulated, oncogenic MYC. One well-studied canonical pathway that is known to regulate MYC activity and stability at the post-translational level is the GSK3 pathway. The GSK3-FBXW7 axis regulates MYC via phosphorylation at T58, followed by ubiquitylation of MYC by the E3 ubiquitin ligase complex SCF-FBXW7 and subsequent proteasomal degradation. Accordingly, substituting threonine 58 with alanine (T58A) confers increased stability and transformative potential. Thus, characterizing the post-translational modifications (PTMs) of MYC can lead to a better understanding of the regulatory mechanisms controlling this potent oncogene. SUMOylation is a post-translational modification that utilizes a series of E1, E2 and E3 proteins for conjugation of a small ubiquitin-like modifier (SUMO) moiety to its target protein. Growing evidence indicates that SUMOylation has many important roles in the cell, such as response to cellular stressors and transcriptional regulation. Moreover, recent reports have unveiled a potential role for SUMOylation in MYC-driven tumourigenesis. Here, using immunoprecipitation combined with mass spectrometry, we identified a MYC SUMOylation site (K326). Abrogation of signaling through this residue by substitution with arginine (K326R) has no obvious effects on MYC half-life, intracellular localization, transcriptional targets, nor on the biological effects of MYC overexpression in three different cell systems assessed for soft agar colony formation, proliferation, and apoptosis. While we have definitively demonstrated that MYC SUMOylation can occur on K326, future work will be needed to elucidate the mechanisms and biological significance of MYC regulation by SUMOylation.
Citation Format: Manpreet Kalkat, Pak-Kei Chan, Amanda R. Wasylishen, Tharan Srikumar, Sam S. Kim, Romina Ponzielli, David P. Bazett-Jones, Brian Raught, Linda Z. Penn. Identification of c-MYC SUMOylation by mass spectrometry. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr A08.
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Affiliation(s)
| | - Pak-Kei Chan
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | | | | | - Sam S. Kim
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | | | | | - Brian Raught
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | - Linda Z. Penn
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
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Lourenco C, Wasylishen A, Chan-Seng-Yue M, Bros C, Dingar D, Tu W, Kalkat M, Chan PK, Mullen P, Raught B, Boutros P, Penn L. Abstract A10: The myc post-translational landscape: How novel gain-of-function mutants are revealing new stability and functional regulatory systems. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.myc15-a10] [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
The c-MYC (MYC) oncogene plays an important role in tumorigenesis and is implicated in >50% of all human cancers. Deregulation of MYC can occur through abnormally high expression levels, but also through oncogenic lesions in upstream signaling cascades. The study of these signaling pathways have provided an alternative approach for the development of MYC-targeted therapeutics. For example, the study of post-translational modifications (PTMs) of MYC, such as P-T58 and the T58A gain-of-function mutant, identified FBXW7 as a tumor suppressor and the deubiquitinating enzyme USP28 as a therapeutic target.
We considered that MYC is highly modified post-translationally and that unknown mechanistic pathways may be modifying residues, in addition to T58, in order to control MYC stability and/or function. These undiscovered pathways may therefore provide additional opportunities for the development of MYC-targeted therapeutics. These considerations led to recent work in the Penn lab that uncovered clusters of negatively regulating residues of MYC function. These residues include S71/S81, a cluster of residues referred to as MYC-4 (T343, S344, S347 and S348) and a cluster of 6 lysine residues (6K) at the C-terminal end of MYC (K298, K317, K323, K326, K341 and K355). These negatively regulating residues were characterized using alanine (S71/S81 and 340 cluster) and arginine (C-terminal lysines) substitution mutants in our established transformation assays. The S71/S81A and MYC-4A mutants scored with having gain-of-function activity in comparison to wild-type MYC in multiple transformation assays including growth in soft agar and the disruption of regular acini formation using a normal, immortalized MCF10A cell line. In addition, these mutants were shown to regulate additional genes compared to wild-type MYC using genome-wide mRNA expression analysis of MCF10A acini, suggesting that these MYC proteins have gained additional transcriptional targets. Additionally, substitution of the C-terminal lysine residues with arginine (6KR) also revealed gain-of-function activity. 6KR expressing MCF10A and SH-EP cells had increased anchorage-independent growth compared to cells expressing wild-type MYC and was also more potent in promoting xenograft tumor growth of Rat1A and SH-EP cells. Interestingly, all three mutants do not have extended half-lives as seen with T58A, suggesting that functional activity and not stability is contributing to these transformative phenotypes.
The above mutants reveal that each of S71/S81, MYC-4 and C-terminal 6K residues are critically important for the negative regulation of MYC-induced transformation. To further explore these regions of MYC, we used mass spectrometry to identify post-translational modifications that occurred on MYC in growing cells. These data confirm phosphorylation events on S71/81 as well as at MYC-4A. Strikingly, three modifications were directly observed on three of the six lysine residues; acetylation of lysine 323, ubiquitylation of lysine 355 and SUMOylation of lysine 326. The importance of these modifications and the roles that these modifications have in regulating MYC activity are currently under investigation using our established transformation assays. I now aim to understand the contribution of single or multiple modifications within the indicated clusters and how these modifications modulate MYC activity.
Citation Format: Corey Lourenco, Amanda Wasylishen, Michelle Chan-Seng-Yue, Christina Bros, Dharmendra Dingar, William Tu, Manpreet Kalkat, Pak-Kei Chan, Peter Mullen, Brian Raught, Paul Boutros, Linda Penn. The myc post-translational landscape: How novel gain-of-function mutants are revealing new stability and functional regulatory systems. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr A10.
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Affiliation(s)
| | | | | | | | | | - William Tu
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | | | - Pak-Kei Chan
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | - Peter Mullen
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | - Brian Raught
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | - Paul Boutros
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Linda Penn
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
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Dingar D, Kalkat M, Chan PK, Bailey SD, Srikumar T, Tu WB, Coyaud E, Ponzielli R, Kolyar M, Jurisica I, Huang A, Lupien M, Raught B, Penn LZ. Abstract B04: In vivo BioID identifies novel Myc interacting partners. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.myc15-b04] [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
Myc oncoprotein is a major driver of cancer initiation and progression, and thus targeting its activity would mark a key therapeutic advance. In a genetic preclinical mouse model, systemic Myc inhibition using the dominant-negative Myc mutant, termed Omomyc, showed that Ras-driven lung cancer could be eradicated without any harmful long-term effects to the animal. However, developing an anti-cancer agent that directly binds and inhibits Myc has not been possible, to date. Therefore, new strategies are required to inhibit Myc in cancer. Understanding the Myc interactome may unravel novel approaches to target Myc in cancer. The BioID proximity-based biotin labeling technique was recently developed for the characterization of protein-protein interaction networks. In BioID, the protein of interest is expressed as a fusion partner biotin ligase (BirA*), which activates biotin. The active biotin reacts with lysine residues on nearby polypeptides. Following a stringent cell lysis and streptavidin-sepharose pulldown, biotinylated proteins can be identified using MS. To date, this method has been applied to a number of different polypeptides expressed in cultured cells. Here we report the adaptation of BioID to the identification of protein-protein interactions surrounding the Myc oncoprotein in human cells grown both under standard culture conditions and in mice as tumor xenografts. Notably, in vivo BioID yielded >100 high confidence Myc interacting proteins, including >30 known binding partners such as MAX (Myc-associated factor X), TRRAP (transformation/transcription domain-associated protein), the enhancer of polycomb homologs 1 and 2 (EPC1, EPC2), lysine acetyltransferase 5 (KAT5). Putative novel Myc interactors include components of the STAGA/KAT5 and SWI/SNF chromatin remodelling complexes (see Penn lab abstract Tu et al), DNA repair and replication factors, general transcription and elongation factors, and transcriptional co-regulators such as the DNA helicase chromodomain 8 (CHD8). Providing additional confidence in these findings, ENCODE ChIP-seq datasets highlight significant coincident binding throughout the genome for the Myc interactors identified here, and we validate the previously unreported CHD8 (an ATP-dependent helicase)-Myc interaction using both a yeast two hybrid analysis and the proximity-based ligation assay (PLA). Additionally, we also validate Myc-BRD4 and Myc-TRIM24 interaction by PLA. In sum, here we identify bona fide interacting partners of Myc in vivo by use of BioID. Our study shows for the first time Myc interactome in vivo, understanding these interactors will shed more light on Myc oncogenesis, which can be used to therapeutically target Myc in cancer.
Citation Format: Dharmendra Dingar, Manpreet Kalkat, Pak-Kei Chan, Swneke D. Bailey, Tharan Srikumar, William B. Tu, Etienne Coyaud, Romina Ponzielli, Max Kolyar, Igor Jurisica, Annie Huang, Mathieu Lupien, Brian Raught, Linda Z. Penn. In vivo BioID identifies novel Myc interacting partners. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr B04.
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Affiliation(s)
| | | | - Pak-Kei Chan
- 1Princess Margaret Cancer Centre/UHN, Toronto, ON, Canada,
| | | | | | - William B. Tu
- 1Princess Margaret Cancer Centre/UHN, Toronto, ON, Canada,
| | - Etienne Coyaud
- 1Princess Margaret Cancer Centre/UHN, Toronto, ON, Canada,
| | | | - Max Kolyar
- 1Princess Margaret Cancer Centre/UHN, Toronto, ON, Canada,
| | - Igor Jurisica
- 1Princess Margaret Cancer Centre/UHN, Toronto, ON, Canada,
| | - Annie Huang
- 2The Hospital for Sick Children, Toronto, ON, Canada
| | - Mathieu Lupien
- 1Princess Margaret Cancer Centre/UHN, Toronto, ON, Canada,
| | - Brian Raught
- 1Princess Margaret Cancer Centre/UHN, Toronto, ON, Canada,
| | - Linda Z. Penn
- 1Princess Margaret Cancer Centre/UHN, Toronto, ON, Canada,
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Yeh C, Coyaud É, Bashkurov M, van der Lelij P, Cheung SWT, Peters JM, Raught B, Pelletier L. The Deubiquitinase USP37 Regulates Chromosome Cohesion and Mitotic Progression. Curr Biol 2015; 25:2290-9. [PMID: 26299517 DOI: 10.1016/j.cub.2015.07.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 01/05/2015] [Revised: 06/08/2015] [Accepted: 07/09/2015] [Indexed: 12/31/2022]
Abstract
A bipolar mitotic spindle facilitates the equal segregation of chromosomes to two daughter cells. To achieve bipolar attachment of microtubules to kinetochores of sister chromatids, chromatids must remain paired after replication. This cohesion is mediated by the conserved cohesin complex comprised of SMC1, SMC3, SCC1, and either SA1 or SA2 in humans. Because defects in spindle assembly or sister chromatid cohesion can lead to aneuploidy in daughter cells, proper regulation of these processes is essential for fidelity in chromosome segregation. In an RNAi screen for regulators of spindle assembly, we identify the deubiquitinase USP37 as a regulator of mitotic progression, centrosome integrity, and chromosome alignment. USP37 associates with cohesin and contributes to sister chromatid resolution. Cohesion defects are rescued by expression of an RNAi-resistant USP37, but not the catalytically impaired USP37(C350A) mutant. Further, USP37 associates with WAPL, a negative regulator of cohesion necessary for cohesin release in prophase, in a manner dependent on USP37's second and third ubiquitin-interacting motifs. Depletion of USP37 reduces the stability of chromatin-associated WAPL and increases the fraction of WAPL that is more heavily ubiquitylated in mitosis. Consistently, overexpression of USP37(C350A) results in increased modification of WAPL, and addition of purified USP37(WT), but not USP37(C350A), to WAPL immunoprecipitates results in a reduction of ubiquitylated products. Taken together, our results ascribe a novel function for USP37 in mitotic progression and further suggest that USP37 positively regulates the stability of chromatin-associated WAPL to facilitate sister chromatid resolution.
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Affiliation(s)
- Christina Yeh
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Mikhail Bashkurov
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Petra van der Lelij
- Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Sally W T Cheung
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Jan Michael Peters
- Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Srikumar T, Lewicki MC, Raught B. Raw data for the identification of SUMOylated proteins in S. cerevisiae subjected to two types of osmotic shock, using affinity purification coupled with mass spectrometry. Data Brief 2015. [PMID: 26217701 PMCID: PMC4459562 DOI: 10.1016/j.dib.2014.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The small ubiquitin-related modifier (SUMO) “stress response” (SSR) is a poorly understood evolutionarily conserved phenomenon in which steady-state SUMO conjugate levels are dramatically increased in response to environmental stresses. Here we describe the data acquired using affinity-purification coupled with mass spectrometry to identify proteins that are SUMOylated in response to two different types of osmotic stress, 1 M sorbitol and 1 M KCl. The mass spectrometry dataset described here has been uploaded to the MassIVE repository with ID: MSV000078739, and consists of 32 raw MS files acquired in data-dependent mode on a Thermo Q-Exactive instrument. iProphet-processed MS/MS search results and associated SAINT scores are also included as a reference. These data are discussed and interpreted in “The S. cerevisiae SUMO stress response is a conjugation–deconjugation cycle that targets the transcription machinery”, by Lewicki et al. in the Journal of Proteomics, 2014 [1].
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Affiliation(s)
- Tharan Srikumar
- Princess Margaret Cancer Centre, University Health Network, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Megan C. Lewicki
- Princess Margaret Cancer Centre, University Health Network, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Corresponding author at: 101 College St., MaRS TMDT East 9-804, Toronto, ON, Canada M5G 1L7. Tel.: +1 416 581 7478.
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